Structure of entinostat Form B, C21H20N4O3, derived using laboratory powder diffraction data and density functional techniques

Kaduk, J.A.; Rai, S.K.

doi:10.1107/S2056989025007406

research communications

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ISSN: 2056-9890

Volume 81| Part 9| September 2025| Pages 865-869

https://doi.org/10.1107/S2056989025007406

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Structure of entinostat Form B, C₂₁H₂₀N₄O₃, derived using laboratory powder diffraction data and density functional techniques

James A. Kaduk ^a ^* and Sunil Kumar Rai ^b

^aDepartment of Chemistry, North Central College, 131 S. Loomis, St., Naperville IL, 60540 , USA, and ^bDepartment of Chemistry, Faculty of Science, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
^*Correspondence e-mail: [email protected]

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 24 July 2025; accepted 18 August 2025; online 21 August 2025)

The crystal structure of entinostat Form B, C₂₁H₂₀N₄O₃, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. Entinostat crystallizes in space group Pna2₁ and the crystal structure consists of interlocking layers of entinostat molecules parallel to the bc plane. A strong N—H⋯N hydrogen bond links the molecules into zigzag chains propagating along the b-axis direction. The graph set for this pattern is C¹₁(8). Two N—H⋯O hydrogen bonds link the molecules along the c-axis direction. The graph sets for this pattern are C¹₁(4) and C¹₁(7).

Keywords: powder diffraction; entinostat; Rietveld refinement; density functional theory.

CCDC references: 2481225; 2481224

1. Chemical context

Entinostat, C₂₁H₂₀N₄O₃ (also known as SNDX-275 and MS-275), is undergoing clinic trials for treatment of various cancers. The rights to entinostat are owned by Syndax Pharmaceuticals. The systematic name (CAS Registry No. 209783-80-2) is pyridin-3-ylmethyl N-({4-[(2-aminophenyl)carbamoyl]phenyl}methyl)carbamate.

International Patent Application WO2010/022988 A1 (Schneider et al., 2010 ; Bayer Schering Pharma) discloses crystalline Forms A, B, and C of entinostat and processes for their preparation. The material characterized here appears to be Form B (Fig. 1). Crystalline Forms D and E are disclosed in International Patent Application 2017/081278 A1 (Stefinovic & Reece, 2017 ; Sandoz AG). Stable amorphous entinostat is claimed in International Patent Application WO2017/216761 (Peddireddy et al., 2017 ; Dr. Reddys Laboratories). Cocrystals of entinostat with maleic acid (Form A) and succinic acid (Forms A, B, and C) are claimed in US Patent Application US2024/023948 A1 (Bonnaud & Prentice, 2024 ; Macfarlan Smith Ltd.). This work was carried out as part of a project aimed at preparing cocrystals of active pharmaceutical ingredients using mechanochemical techniques.

Figure 1
Comparison of the laboratory pattern of entinostat (measured using Mo K_α radiation; black) to that of Form B reported by Schneider et al. (2010

; red). The patent pattern (measured using Cu K_α radiation) was digitized using UN-SCAN-IT (Silk Scientific, 2013

) and converted to the Mo K_α wavelength of 0.7093187 Å using JADE Pro (MDI, 2025

). Image generated using JADE Pro (MDI, 2025

2. Structural commentary

The root-mean-square Cartesian displacement between the Rietveld-refined and VASP-optimized structures is 0.068 Å (Fig. 2). The agreement is within the normal range for correct structures (van de Streek & Neumann, 2014 ). The asymmetric unit of the structure is illustrated in Fig. 3. The remaining discussion will emphasize the VASP-optimized structure.

Figure 2
Comparison of the refined structure of the entinostat molecule (red) to the VASP-optimized structure (blue). The comparison was generated using the Mercury calculate/molecule overlay tool; the r.m.s. difference is 0.068 Å. Image generated using Mercury (Macrae et al., 2020

Figure 3
The asymmetric unit of entinostat Form B, with the atom numbering. The atoms are represented by 50% probability spheroids. Image generated using Mercury (Macrae et al., 2020

All of the bond distances, bond angles, and torsion angles fall within the normal ranges indicated by a Mercury Mogul geometry check (Macrae et al., 2020 ). Quantum chemical geometry optimization of the isolated entinostat molecule (DFT/B3LYP/6-31G*/water) using Spartan 24 (Wavefunction, 2023 ) indicated that the observed conformation is only 3.8 kcal mol⁻¹ higher in energy than a local minimum, even though the r.m.s. displacement is 0.498 Å. The global minimum-energy conformation is much more compact (folded on itself to yield parallel phenyl rings), indicating that intermolecular interactions are important in determining the solid-state conformation. The false minimum structures contained different conformations of the molecule in roughly the same positions and orientation.

3. Supramolecular features

The extended structure (Fig. 4) consists of interlocking layers of entinostat molecules lying parallel to the bc plane. Hydrogen bonds (discussed below) link the molecules along the b- and c-axis directions. The mean planes of the aminophenyl, phenyl, and pyridine rings correspond approximately to the (17,–5,–2), (13,–7,–3), and (26,–3,4) Miller planes, respectively. The Mercury aromatics analyser indicates strong interactions (centroid–centroid distance = 5.07 Å) between the two types of phenyl rings, moderate interactions with distances of 5.63 and 5.77 Å, as well as weaker interactions.

Figure 4
The crystal structure of entinostat Form B, viewed down the c-axis. Image generated using DIAMOND (Brandenburg & Putz, 2023

Analysis of the contributions to the total crystal energy of the structure using the Forcite module of Materials Studio (Dassault Systèmes, 2023 ) indicates that bond, angle, and torsion distortion terms contribute about equally to the intramolecular energy. The intermolecular energy is dominated by electrostatic attractions, which in this force field based analysis also include hydrogen bonds. The hydrogen bonds are better discussed using the results of the DFT calculation.

A strong N—H⋯N hydrogen bond links the molecules into zigzag chains along the b-axis direction (Table 1). The graph set (Etter, 1990 ; Bernstein et al., 1995 ; Motherwell et al., 2000 ) for this pattern is C₁¹(8). Two N—H⋯O hydrogen bonds link the molecules along the c-axis direction. The graph sets for this pattern are C₁¹(4) and C₁¹(7). The energies of the N—H⋯O hydrogen bonds were calculated using the correlation of Wheatley & Kaduk (2019 ). Several inter- and intramolecular C—H⋯O hydrogen bonds, as well as one C—H⋯N hydrogen bond, contribute to the lattice energy.

Table 1
Hydrogen-bond geometry (Å, °) for entinostat Form B

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H35⋯N7ⁱ	1.05	1.86	2.906	174
N5—H36⋯O2ⁱⁱ	1.03	1.91	2.923	168
N6—H45⋯O2ⁱⁱ	1.02	2.03	3.034	166
C9—H29⋯O3ⁱⁱⁱ	1.10	2.39	3.482	170
C25—H43⋯O3ⁱ	1.09	2.33	3.281	144
C26—H46⋯O1^iv	1.09	2.34	3.199	135
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (ii) ; (iii) ; (iv) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

The volume enclosed by the Hirshfeld surface of entinostat (Fig. 5, Hirshfeld, 1977 , Spackman et al., 2021 ) is 448.9 Å³ or 98.1% of 1/4 of the unit-cell volume. The packing density is thus fairly typical. The only significant close contacts (red in Fig. 5) involve the hydrogen bonds. The volume per non-hydrogen atom is smaller than normal, at 16.3 Å³.

Figure 5
The Hirshfeld surface of entinostat Form B. Intermolecular contacts longer than the sums of the van der Waals radii are colored blue, and contacts shorter than the sums of the radii are colored red. Contacts equal to the sums of radii are white. Image generated using CrystalExplorer (Spackman et al., 2021

The Bravais–Friedel–Donnay–Harker (Bravais, 1866 ; Friedel, 1907 ; Donnay & Harker, 1937 ) algorithm suggests that we might expect platy morphology for entinostat, with {200} as the principal faces. A second order spherical harmonic model was included in the refinement. The texture index was 1.002 (1), indicating that preferred orientation was not significant in the rotated capillary specimen.

4. Database survey

A reduced cell search in the Cambridge Structural Database (CSD, version 2025.1.0 May 2025; Groom et al., 2016 ) yielded 33 hits, but no structures for entinostat or its derivatives. A connectivity search of the entinostat molecule in the CSD yielded no hits. A search of the pattern against the Powder Diffraction File (Kabekkodu et al., 2024 ) yielded no hits, and a name search on `entinostat' also yielded no hits.

5. Synthesis and crystallization

The sample characterized here was obtained from a commercial source, was gently ground in a mortar and pestle and sieved to < 325 mesh.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The pattern was indexed using DICVOL14 (Louër & Boultif, 2014 ) on a primitive orthorhombic unit cell with a = 38.2913, b = 9.4545, c = 5.0779 Å, V = 1838.31 Å³, and Z = 4.

Table 2
Experimental details

	Rietveld
Crystal data
Chemical formula	C₂₁H₂₀N₄O₃
M_r	376.42
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	300
a, b, c (Å)	38.236 (5), 9.4459 (7), 5.0673 (4)
V (Å³)	1830.2 (2)
Z	4
Radiation type	Mo Kα_1,2, λ = 0.70932, 0.71361 Å
Specimen shape, size (mm)	Cylinder, 12 × 0.7

Data collection
Diffractometer	PANalytical Empyrean
Specimen mounting	Glass capillary
Data collection mode	Transmission
Scan method	Step
2θ values (°)	2θ_min = 1.002 2θ_max = 49.991 2θ_step = 0.008

Refinement
R factors and goodness of fit	R_p = 0.029, R_wp = 0.036, R_exp = 0.029, R(F²) = 0.11709, χ² = 1.636
No. of parameters	107
No. of restraints	72
H-atom treatment	Only H-atom displacement parameters refined
(Δ/σ)_max	0.368
Computer programs: FOX (Favre-Nicolin & Černý, 2002) and GSAS-II (Toby & Von Dreele, 2013).

The space group was ambiguous. Space groups Pna2₁, Pca2₁, Pba2, and P2₁2₁2₁ yielded similar profile fits, so the structure was solved in all of them using Monte Carlo-simulated annealing techniques as implemented in FOX (Favre-Nicolin & Černý, 2002 ) and/or EXPO2014 (Altomare et al., 2013 ). The entinostat molecule was downloaded from PubChem (Kim et al., 2023 ) as Conformer3D_COMPOUND_CID_4261.sdf. It was converted to a *.mol2 file using Mercury (Macrae et al., 2020), and to a Fenske-Hall Z-matrix using OpenBabel (O'Boyle et al., 2011 ). The structures were optimized using VASP (Kresse & Furthmüller, 1996 ). Since space group Pna2₁ yielded the lowest energy, it was adopted for the final refinements and discussion.

Several false minima were encountered during structure solution. There were three signs that these were not the correct structure, even though R_wp was as low as 0.0466: (1) the agreement of the Rietveld-refined and DFT-optimized structure was poor (root-mean-square Cartesian displacement ∼0.9 Å – outside the normal range for correct structures); (2) the DFT optimization was very slow to converge (> 600 cycles of geometry optimization); (3) the displacement coefficients were much larger than expected (> 0.2 Å²). To overcome these false minima, additional cycles (183) of parallel tempering in FOX were carried out to yield the structure described here.

Rietveld refinement was carried out with GSAS-II (Toby & Von Dreele, 2013 ). Only the 1.5–40.0° portion of the pattern was included in the refinements (d_min = 1.037 Å). All non-H bond distances and angles were subjected to restraints, based on a Mercury/Mogul geometry check (Sykes et al., 2011 ; Bruno et al., 2004 ). The Mogul average and standard deviation for each quantity were used as the restraint parameters. The three aromatic rings were restrained to be planar. The restraints contributed 3.2% to the overall χ². The hydrogen atoms were included in calculated positions, which were recalculated during the refinement using Materials Studio (Dassault Systèmes, 2023). The U_iso of the heavy atoms were grouped by chemical similarity. The U_iso for the H atoms were fixed at 1.3× the U_iso of the heavy atoms to which they are attached. The peak profiles were described using the generalized microstrain model (Stephens, 1999 ). The background was modeled using a four-term shifted Chebyshev polynomial, with a peak at 11.61° to model the scattering from the glass capillary. The final refinement of 107 variables using 4608 observations and 72 restraints yielded the residuals R_wp = 0.0697 and GOF = 1.28. The largest peak (0.19 Å from N7) and hole (1.46 Å from C10) in the difference-Fourier map are 0.61 (12) and −0.53 (12) e Å⁻³, respectively. The final Rietveld plot is shown in Fig. 6. The largest features in the normalized error plot are in the intensities of some of the peaks.

Figure 6
The Rietveld plot for entinostat Form B. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot, and the red line is the background curve. The blue tick marks indicate the peak positions.

The crystal structure of entinostat was optimized (fixed experimental unit cell) with density functional techniques using VASP (Kresse & Furthmüller, 1996) through the MedeA graphical interface (Materials Design, 2024 ). The calculation was carried out on 32 cores of a 144-core (768 Gb memory) HPE Superdome Flex 280 Linux server at North Central College. The calculation used the GGA-PBE functional, a plane wave cutoff energy of 400.0 eV, and a k-point spacing of 0.5 Å⁻¹ leading to a 1 × 2 × 3 mesh, and took ∼4.2 h. Single-point density functional calculations (fixed experimental cell) and population analysis were carried out using CRYSTAL23 (Erba et al., 2023 ). The basis sets for the H, C, N and O atoms in the calculation were those of Gatti et al. (1994 ). The calculations were run on a 3.5 GHz PC using 8 k-points and the B3LYP functional, and took ∼2.4 h.

Supporting information

CCDC references: 2481225; 2481224

Crystal structure: contains datablocks Rietveld, VASP. DOI: https://doi.org/10.1107/S2056989025007406/hb8151sup1.cif

Supporting information file. DOI: https://doi.org/10.1107/S2056989025007406/hb8151Rietveldsup2.cml

checkCIF report

Computing details top

Pyridin-3-ylmethyl N-({4-[(2-aminophenyl)carbamoyl]phenyl}methyl)carbamate (Rietveld) top

Crystal data top

C₂₁H₂₀N₄O₃	V = 1830.2 (2) Å³
M_r = 376.42	Z = 4
Orthorhombic, Pna2₁	D_x = 1.366 Mg m⁻³
a = 38.236 (5) Å	Mo Kα_1,2 radiation, λ = 0.70932, 0.71361 Å
b = 9.4459 (7) Å	T = 300 K
c = 5.0673 (4) Å	cylinder, 12 × 0.7 mm

Data collection top

PANalytical Empyrean diffractometer	Data collection mode: transmission
Radiation source: sealed X-ray tube	Scan method: step
Zr filter monochromator	2θ_min = 1.002°, 2θ_max = 49.991°, 2θ_step = 0.008°
Specimen mounting: glass capillary

Refinement top

Least-squares matrix: full	72 restraints
R_p = 0.029	23 constraints
R_wp = 0.036	Only H-atom displacement parameters refined
R_exp = 0.029	Weighting scheme based on measured s.u.'s
R(F²) = 0.11709	(Δ/σ)_max = 0.368
5864 data points	Background function: Background function: "chebyschev-1" function with 4 terms: 871.1(20), -360.1(18), 11.3(15), -45.5(16), Background peak parameters: pos, int, sig, gam: 11.611(13), 6.24(5)e5, 7.58(9)e4, 0.100,
Profile function: Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L: peak variance(Gauss) = Utan(Th)²+Vtan(Th)+W: peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L U, V, W in (centideg)², X & Y in centideg 25.531, 9.905, 0.000, 1.091, 3.951, 0.034,	Preferred orientation correction: Simple spherical harmonic correction Order = 2 Coefficients: 0:0:C(2,0) = 0.103(29); 0:0:C(2,2) = -0.018(21)
107 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.7170 (5)	0.3108 (13)	1.26983	0.055 (8)*
O2	0.5094 (5)	0.313 (3)	0.331 (4)	0.029 (9)*
O3	0.7017 (6)	0.5418 (13)	1.292 (8)	0.055 (8)*
N4	0.6773 (5)	0.393 (2)	0.994 (5)	0.055 (8)*
N5	0.4935 (5)	0.278 (3)	0.760 (5)	0.029 (9)*
N6	0.4756 (7)	0.052 (3)	1.089 (7)	0.055 (10)*
N7	0.8163 (6)	0.5927 (17)	1.337 (8)	0.033 (9)*
C8	0.6206 (3)	0.4434 (17)	0.780 (5)	0.027 (8)*
C9	0.6556 (6)	0.500 (2)	0.869 (8)	0.055 (8)*
C10	0.5512 (3)	0.3708 (19)	0.659 (5)	0.027 (8)*
C11	0.6038 (4)	0.502 (3)	0.563 (5)	0.027 (8)*
C12	0.6023 (5)	0.347 (4)	0.933 (6)	0.027 (8)*
C13	0.5696 (3)	0.467 (2)	0.504 (5)	0.027 (8)*
C14	0.5681 (5)	0.311 (3)	0.875 (6)	0.027 (8)*
C15	0.5163 (4)	0.318 (3)	0.568 (4)	0.029 (9)*
C16	0.4613 (4)	0.207 (2)	0.725 (6)	0.055 (10)*
C17	0.4533 (7)	0.091 (3)	0.889 (8)	0.055 (10)*
C18	0.4383 (9)	0.246 (4)	0.523 (9)	0.055 (10)*
C19	0.6981 (5)	0.4247 (11)	1.198 (5)	0.055 (8)*
C20	0.7430 (4)	0.335 (2)	1.474 (4)	0.055 (8)*
C21	0.4222 (8)	0.017 (3)	0.844 (9)	0.055 (10)*
C22	0.7750 (5)	0.4006 (19)	1.352 (8)	0.033 (9)*
C23	0.4077 (7)	0.169 (4)	0.483 (8)	0.055 (10)*
C24	0.3997 (8)	0.056 (4)	0.643 (8)	0.055 (10)*
C25	0.7929 (8)	0.335 (3)	1.149 (7)	0.033 (9)*
C26	0.7880 (8)	0.529 (2)	1.439 (7)	0.033 (9)*
C27	0.8221 (8)	0.398 (3)	1.040 (9)	0.033 (9)*
C28	0.8329 (6)	0.526 (2)	1.140 (7)	0.033 (9)*
H29	0.67008	0.54448	0.69050	0.0713*
H30	0.65046	0.58991	1.01441	0.0713*
H31	0.62060	0.54691	0.39817	0.0356*
H32	0.61567	0.29902	1.10662	0.0356*
H33	0.55888	0.51030	0.32747	0.0356*
H34	0.55238	0.26635	1.04151	0.0356*
H35	0.67159	0.28737	0.92867	0.0713*
H36	0.50674	0.20423	0.89818	0.0372*
H37	0.45017	0.32241	0.38325	0.0721*
H38	0.74850	0.23110	1.55041	0.0713*
H39	0.73009	0.39869	1.62195	0.0713*
H40	0.41682	−0.08211	0.94296	0.0721*
H41	0.39034	0.23483	0.36479	0.0721*
H42	0.37377	0.02234	0.63785	0.0721*
H43	0.78356	0.22806	1.07112	0.0432*
H44	0.47309	−0.06399	1.12476	0.0721*
H45	0.46876	0.11006	1.27176	0.0721*
H46	0.77066	0.58946	1.57984	0.0432*
H47	0.83386	0.33515	0.89816	0.0432*
H48	0.85627	0.56225	1.10069	0.0432*

Geometric parameters (Å, º) top

O1—C19	1.345 (3)	C19—O3	1.213 (2)
O1—C20	1.453 (3)	C19—N4	1.337 (3)
O2—C15	1.229 (3)	C20—O1	1.453 (3)
O3—C19	1.213 (2)	C20—C22	1.503 (3)
N4—C9	1.454 (2)	C20—H38	1.076 (19)
N4—C19	1.337 (3)	C20—H39	1.08 (2)
N4—H35	1.08 (2)	C21—C17	1.399 (3)
N5—C15	1.361 (4)	C21—C24	1.383 (2)
N5—C16	1.416 (3)	C21—H40	1.081 (19)
N5—H36	1.11 (3)	C22—C20	1.503 (3)
N6—C17	1.376 (4)	C22—C25	1.382 (3)
N6—H44	1.11 (2)	C22—C26	1.382 (3)
N6—H45	1.11 (4)	C23—C18	1.387 (2)
N7—C26	1.342 (3)	C23—C24	1.376 (3)
N7—C28	1.340 (3)	C23—H41	1.09 (3)
C8—C9	1.511 (3)	C24—C21	1.383 (2)
C8—C11	1.386 (2)	C24—C23	1.376 (3)
C8—C12	1.386 (2)	C24—H42	1.042 (19)
C9—N4	1.454 (2)	C25—C22	1.382 (3)
C9—C8	1.511 (3)	C25—C27	1.382 (2)
C9—H29	1.14 (4)	C25—H43	1.140 (15)
C9—H30	1.14 (4)	C26—N7	1.342 (3)
C10—C13	1.389 (2)	C26—C22	1.382 (3)
C10—C14	1.390 (2)	C26—H46	1.13 (3)
C10—C15	1.498 (3)	C27—C25	1.382 (2)
C11—C8	1.386 (2)	C27—C28	1.373 (3)
C11—C13	1.384 (2)	C27—H47	1.04 (3)
C11—H31	1.14 (2)	C28—N7	1.340 (3)
C12—C8	1.386 (2)	C28—C27	1.373 (3)
C12—C14	1.385 (2)	C28—H48	0.977 (17)
C12—H32	1.110 (17)	H29—C9	1.14 (4)
C13—C10	1.389 (2)	H30—C9	1.14 (4)
C13—C11	1.384 (2)	H31—C11	1.14 (2)
C13—H33	1.065 (18)	H32—C12	1.110 (17)
C14—C10	1.390 (2)	H33—C13	1.065 (18)
C14—C12	1.385 (2)	H34—C14	1.12 (2)
C14—H34	1.12 (2)	H35—N4	1.08 (2)
C15—O2	1.229 (3)	H36—N5	1.11 (3)
C15—N5	1.361 (4)	H37—C18	1.11 (3)
C15—C10	1.498 (3)	H38—C20	1.076 (19)
C16—N5	1.416 (3)	H39—C20	1.08 (2)
C16—C17	1.4050 (16)	H40—C21	1.081 (19)
C16—C18	1.395 (2)	H41—C23	1.09 (3)
C17—N6	1.376 (4)	H42—C24	1.042 (19)
C17—C16	1.4050 (16)	H43—C25	1.140 (15)
C17—C21	1.399 (3)	H44—N6	1.11 (2)
C18—C16	1.395 (2)	H45—N6	1.11 (4)
C18—C23	1.387 (2)	H46—C26	1.13 (3)
C18—H37	1.11 (3)	H47—C27	1.04 (3)
C19—O1	1.345 (3)	H48—C28	0.977 (17)

C19—O1—C20	115.7 (3)	C17—C16—C18	120.10 (11)
C9—N4—C19	121.6 (3)	N6—C17—C16	120.91 (14)
C9—N4—H35	113.2 (7)	N6—C17—C21	120.61 (15)
C19—N4—H35	124.4 (12)	C16—C17—C21	118.48 (10)
C15—N5—C16	126.8 (3)	C16—C18—C23	119.96 (16)
C15—N5—H36	109.5 (16)	C16—C18—H37	112.5 (17)
C16—N5—H36	100.2 (10)	C23—C18—H37	126.2 (18)
C17—N6—H44	109 (4)	O1—C19—O3	124.2 (2)
C17—N6—H45	109 (3)	O1—C19—N4	110.5 (2)
H44—N6—H45	109 (3)	O3—C19—N4	125.00 (19)
C26—N7—C28	117.34 (18)	O1—C20—C22	109.4 (3)
C9—C8—C11	120.4 (3)	O1—C20—H38	104.3 (11)
C9—C8—C12	120.7 (3)	C22—C20—H38	111.5 (18)
C11—C8—C12	118.22 (13)	O1—C20—H39	105.5 (9)
N4—C9—C8	113.0 (3)	C22—C20—H39	115.3 (14)
N4—C9—H29	109 (3)	H38—C20—H39	110.2 (17)
C8—C9—H29	108.9 (15)	C17—C21—C24	120.91 (13)
N4—C9—H30	109.5 (15)	C17—C21—H40	121 (2)
C8—C9—H30	108 (3)	C24—C21—H40	117 (3)
H29—C9—H30	108.9 (14)	C20—C22—C25	121.4 (2)
C13—C10—C14	118.34 (12)	C20—C22—C26	121.5 (2)
C13—C10—C15	119.6 (3)	C25—C22—C26	117.08 (14)
C14—C10—C15	121.4 (3)	C18—C23—C24	120.38 (13)
C8—C11—C13	121.06 (13)	C18—C23—H41	108 (2)
C8—C11—H31	118.0 (13)	C24—C23—H41	129 (3)
C13—C11—H31	117.6 (12)	C21—C24—C23	120.16 (12)
C8—C12—C14	120.99 (13)	C21—C24—H42	122 (3)
C8—C12—H32	118.7 (11)	C23—C24—H42	116 (3)
C14—C12—H32	120.3 (11)	C22—C25—C27	120.07 (15)
C10—C13—C11	120.70 (12)	C22—C25—H43	120.0 (11)
C10—C13—H33	122.3 (9)	C27—C25—H43	119.8 (13)
C11—C13—H33	116.9 (9)	N7—C26—C22	123.98 (18)
C10—C14—C12	120.69 (12)	N7—C26—H46	119.3 (15)
C10—C14—H34	119.9 (13)	C22—C26—H46	115.8 (14)
C12—C14—H34	115.9 (18)	C25—C27—C28	118.54 (16)
O2—C15—N5	123.4 (3)	C25—C27—H47	112.3 (15)
O2—C15—C10	120.3 (2)	C28—C27—H47	129.0 (15)
N5—C15—C10	116.3 (2)	N7—C28—C27	123.0 (2)
N5—C16—C17	118.9 (2)	N7—C28—H48	115 (2)
N5—C16—C18	121.0 (2)	C27—C28—H48	121 (2)

(VASP) top

Crystal data top

C21H20N4O₃	b = 9.44590 Å
M_r = 376.42	c = 5.06730 Å
Orthorhombic, Pna2₁	V = 1830.17 Å³
a = 38.23600 Å	Z = 4

Data collection top

DFT optimization	k = →
h = →	l = →

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	B_iso*/B_eq
O1	0.71602	0.30908	1.29383
O2	0.50809	0.30967	0.33129
O3	0.70419	0.54791	1.27319
N4	0.67730	0.38675	0.99681
N5	0.49333	0.28080	0.76790
N6	0.47635	0.04721	1.08292
N7	0.81620	0.59379	1.32902
C8	0.62069	0.44093	0.78248
C9	0.65707	0.49049	0.85136
C10	0.55157	0.36158	0.65553
C11	0.60342	0.50113	0.56549
C12	0.60305	0.33908	0.93232
C13	0.56950	0.46114	0.50143
C14	0.56879	0.30057	0.87182
C15	0.51586	0.31652	0.57107
C16	0.46077	0.21116	0.73033
C17	0.45309	0.09247	0.89166
C18	0.43725	0.25439	0.53534
C19	0.69932	0.42603	1.19110
C20	0.74344	0.33754	1.48371
C21	0.42225	0.01638	0.83831
C22	0.77550	0.39878	1.35610
C23	0.40654	0.17878	0.48894
C24	0.39948	0.05794	0.63863
C25	0.79359	0.32785	1.15597
C26	0.78808	0.53075	1.43545
C27	0.82290	0.39187	1.04445
C28	0.83313	0.52485	1.13556
H29	0.67074	0.52182	0.66856
H30	0.65555	0.58672	0.97420
H31	0.61678	0.57992	0.44388
H32	0.61618	0.29023	1.10028
H33	0.55649	0.50636	0.33008
H34	0.55578	0.22174	0.99486
H35	0.67774	0.28113	0.93441
H36	0.50169	0.29696	0.95825
H37	0.44352	0.34670	0.41575
H38	0.74910	0.23349	1.57088
H39	0.73357	0.40837	1.63868
H40	0.41672	−0.07745	0.95741
H41	0.38877	0.21199	0.33265
H42	0.37603	−0.00446	0.59901
H43	0.78509	0.22433	1.08477
H44	0.46617	−0.02342	1.21369
H45	0.48953	0.12451	1.18386
H46	0.77497	0.58984	1.59210
H47	0.83767	0.33956	0.88829
H48	0.85582	0.57876	1.05182

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H35···N7ⁱ	1.05	1.86	2.906	174
N5—H36···O2ⁱⁱ	1.03	1.91	2.923	168
N6—H45···O2ⁱⁱ	1.02	2.03	3.034	166
C9—H29···O3ⁱⁱⁱ	1.10	2.39	3.482	170
C25—H43···O3ⁱ	1.09	2.33	3.281	144
C26—H46···O1^iv	1.09	2.34	3.199	135

Symmetry codes: (i) −x+3/2, y−1/2, z−1/2; (ii) x, y, z+1; (iii) x, y, z−1; (iv) −x+3/2, y+1/2, z+1/2.

Acknowledgements

SKR thanks the University of Lucknow for providing research infrastructure.

Funding information

Funding for this research was provided by: SERB-ANRF New Delhi India (grant No. SUB/2022/002726).

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