The title compound, IFB-Lactam-1 (systematic name: 2,15-dihydroxy-7-methyl-6-azabicyclo[11.3.0]hexadec-3-en-5-one), C16H27NO3, is a newly characterized natural anti-Gloeosporium kaki Hori compound. It was isolated from the EtOAc extract of the fermentation broth of an endophytic fungus Trichoderma sp. from cabbage. It is a 13-membered macrocyclic lactam which shares a two-atom edge with a cyclopentanol ring.
Supporting information
CCDC reference: 629405
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.009 Å
- R factor = 0.074
- wR factor = 0.239
- Data-to-parameter ratio = 10.0
checkCIF/PLATON results
No syntax errors found
Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low ....... 0.96
Alert level C
STRVA01_ALERT_4_C Flack test results are meaningless.
From the CIF: _refine_ls_abs_structure_Flack 0.000
From the CIF: _refine_ls_abs_structure_Flack_su 10.000
PLAT032_ALERT_4_C Std. Uncertainty in Flack Parameter too High ... 10.00
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ?
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ?
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for N1
PLAT320_ALERT_2_C Check Hybridisation of C10 in Main Residue . ?
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 9
PLAT361_ALERT_2_C Long C(sp3)-C(sp3) Bond C5 - C9 ... 1.65 Ang.
PLAT361_ALERT_2_C Long C(sp3)-C(sp3) Bond C13 - C14 ... 1.65 Ang.
PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C1 - C2 ... 1.54 Ang.
PLAT414_ALERT_2_C Short Intra D-H..H-X H1A .. H3 .. 1.90 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor N1 - H1A ... ?
PLAT850_ALERT_2_C Check Flack Parameter Exact Value 0.00 and su .. 10.00
Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 25.49
From the CIF: _reflns_number_total 1859
Count of symmetry unique reflns 1942
Completeness (_total/calc) 95.73%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 0
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C15 = . R
0 ALERT level A = In general: serious problem
1 ALERT level B = Potentially serious problem
13 ALERT level C = Check and explain
6 ALERT level G = General alerts; check
7 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
8 ALERT type 2 Indicator that the structure model may be wrong or deficient
2 ALERT type 3 Indicator that the structure quality may be low
3 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
Data collection: SMART (Siemens, 1996); cell refinement: SMART; data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1997); software used to prepare material for publication: SHELXTL.
2,15-dihydroxy-7-methyl-6-azabicyclo[11.3.0]hexadec-3-en-5-one
top
Crystal data top
C16H27NO3 | F(000) = 620 |
Mr = 281.39 | Dx = 1.034 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1688 reflections |
a = 7.4001 (9) Å | θ = 3.8–26.5° |
b = 12.9986 (13) Å | µ = 0.07 mm−1 |
c = 18.860 (2) Å | T = 298 K |
V = 1814.1 (4) Å3 | Prism, colourless |
Z = 4 | 0.27 × 0.23 × 0.20 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1859 independent reflections |
Radiation source: fine-focus sealed tube | 1583 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
φ and ω scans | θmax = 25.5°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −8→8 |
Tmin = 0.961, Tmax = 0.988 | k = −8→14 |
9063 measured reflections | l = −22→22 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.074 | H-atom parameters constrained |
wR(F2) = 0.239 | w = 1/[σ2(Fo2) + (0.1522P)2 + 1.1271P] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max < 0.001 |
1859 reflections | Δρmax = 0.38 e Å−3 |
185 parameters | Δρmin = −0.37 e Å−3 |
2 restraints | Absolute structure: Flack (1983) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0 (10) |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor
wR and goodness of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The threshold expression of F2 >
σ(F2) is used only for calculating R-factors(gt) etc.
and is not relevant to the choice of reflections for refinement.
R-factors based on F2 are statistically about twice as large
as those based on F, and R- factors based on ALL data will be
even larger. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | −0.2937 (8) | 0.5788 (5) | 0.2053 (3) | 0.0480 (14) | |
C2 | −0.3015 (8) | 0.5144 (5) | 0.1367 (3) | 0.0457 (13) | |
H2 | −0.3544 | 0.4495 | 0.1361 | 0.055* | |
C3 | −0.2289 (7) | 0.5556 (4) | 0.0777 (3) | 0.0405 (12) | |
H3 | −0.1943 | 0.6244 | 0.0769 | 0.049* | |
C4 | −0.2032 (7) | 0.4865 (5) | 0.0103 (3) | 0.0434 (13) | |
H4 | −0.2520 | 0.5237 | −0.0307 | 0.052* | |
C5 | 0.0022 (7) | 0.4691 (4) | −0.0022 (2) | 0.0395 (13) | |
H5 | 0.0494 | 0.4323 | 0.0392 | 0.047* | |
C6 | 0.0404 (8) | 0.3974 (5) | −0.0716 (3) | 0.0493 (15) | |
H6A | 0.0306 | 0.3246 | −0.0612 | 0.059* | |
H6B | −0.0374 | 0.4150 | −0.1112 | 0.059* | |
C7 | 0.2395 (9) | 0.4317 (5) | −0.0838 (3) | 0.0637 (19) | |
H7 | 0.2732 | 0.4182 | −0.1332 | 0.076* | |
C8 | 0.2529 (10) | 0.5525 (5) | −0.0687 (3) | 0.0650 (19) | |
H8A | 0.2248 | 0.5909 | −0.1114 | 0.078* | |
H8B | 0.3744 | 0.5703 | −0.0538 | 0.078* | |
C9 | 0.1110 (7) | 0.5801 (4) | −0.0072 (3) | 0.0437 (13) | |
H9 | 0.0282 | 0.6337 | −0.0240 | 0.052* | |
C10 | 0.2096 (8) | 0.6181 (5) | 0.0608 (3) | 0.0456 (14) | |
H10A | 0.1871 | 0.5657 | 0.0964 | 0.055* | |
H10B | 0.3375 | 0.6142 | 0.0500 | 0.055* | |
C11 | 0.1844 (8) | 0.7169 (5) | 0.0973 (3) | 0.0473 (14) | |
H11A | 0.0567 | 0.7215 | 0.1086 | 0.057* | |
H11B | 0.2081 | 0.7699 | 0.0624 | 0.057* | |
C12 | 0.2863 (8) | 0.7492 (6) | 0.1647 (3) | 0.0608 (17) | |
H12A | 0.3111 | 0.8224 | 0.1628 | 0.073* | |
H12B | 0.4011 | 0.7133 | 0.1667 | 0.073* | |
C13 | 0.1775 (9) | 0.7252 (6) | 0.2322 (3) | 0.0620 (18) | |
H13A | 0.2586 | 0.7228 | 0.2725 | 0.074* | |
H13B | 0.1213 | 0.6581 | 0.2274 | 0.074* | |
C14 | 0.0199 (9) | 0.8127 (6) | 0.2464 (4) | 0.0605 (18) | |
H14A | 0.0537 | 0.8575 | 0.2854 | 0.073* | |
H14B | 0.0005 | 0.8542 | 0.2044 | 0.073* | |
C15 | −0.1557 (8) | 0.7491 (7) | 0.2654 (3) | 0.0595 (18) | |
H15 | −0.1314 | 0.7036 | 0.3057 | 0.071* | |
C16 | −0.3078 (11) | 0.8329 (8) | 0.2869 (4) | 0.084 (3) | |
H16A | −0.3258 | 0.8798 | 0.2482 | 0.126* | |
H16B | −0.2686 | 0.8703 | 0.3280 | 0.126* | |
H16C | −0.4194 | 0.7983 | 0.2973 | 0.126* | |
N1 | −0.2081 (6) | 0.6848 (3) | 0.2001 (2) | 0.0378 (10) | |
H1A | −0.1880 | 0.7100 | 0.1587 | 0.045* | |
O2 | −0.3540 (8) | 0.5386 (5) | 0.2597 (2) | 0.0773 (16) | |
O3 | −0.2908 (6) | 0.3723 (3) | 0.0111 (2) | 0.0546 (11) | |
H3A | −0.3897 | 0.3736 | −0.0084 | 0.082* | |
O4 | 0.3517 (6) | 0.3623 (4) | −0.0346 (3) | 0.0678 (14) | |
H4A | 0.3112 | 0.3036 | −0.0356 | 0.102* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.033 (3) | 0.057 (3) | 0.053 (3) | 0.003 (3) | 0.004 (3) | 0.005 (3) |
C2 | 0.030 (3) | 0.052 (3) | 0.055 (3) | −0.005 (3) | 0.004 (2) | 0.002 (3) |
C3 | 0.027 (2) | 0.039 (3) | 0.056 (3) | −0.002 (2) | 0.000 (2) | 0.004 (2) |
C4 | 0.028 (2) | 0.058 (3) | 0.044 (3) | 0.000 (3) | −0.005 (2) | 0.004 (2) |
C5 | 0.031 (3) | 0.054 (3) | 0.033 (2) | 0.005 (2) | −0.004 (2) | 0.001 (2) |
C6 | 0.043 (3) | 0.063 (4) | 0.041 (3) | −0.004 (3) | −0.006 (2) | −0.006 (3) |
C7 | 0.047 (4) | 0.097 (5) | 0.048 (3) | −0.006 (4) | 0.011 (3) | −0.009 (3) |
C8 | 0.057 (4) | 0.089 (5) | 0.049 (3) | −0.009 (4) | 0.014 (3) | 0.012 (3) |
C9 | 0.034 (3) | 0.058 (3) | 0.040 (3) | 0.001 (3) | −0.003 (2) | 0.014 (3) |
C10 | 0.028 (2) | 0.061 (4) | 0.047 (3) | −0.006 (3) | −0.002 (2) | 0.008 (3) |
C11 | 0.034 (3) | 0.059 (4) | 0.049 (3) | −0.005 (3) | −0.001 (2) | 0.001 (3) |
C12 | 0.029 (3) | 0.089 (5) | 0.064 (4) | −0.006 (4) | −0.004 (3) | −0.014 (3) |
C13 | 0.043 (3) | 0.089 (5) | 0.054 (3) | −0.004 (3) | −0.011 (3) | 0.003 (3) |
C14 | 0.047 (4) | 0.083 (5) | 0.051 (3) | −0.011 (4) | −0.002 (3) | −0.011 (3) |
C15 | 0.048 (3) | 0.092 (5) | 0.039 (3) | −0.004 (4) | 0.003 (2) | −0.010 (3) |
C16 | 0.055 (4) | 0.123 (7) | 0.074 (5) | 0.001 (5) | 0.014 (4) | −0.031 (5) |
N1 | 0.033 (2) | 0.053 (3) | 0.0272 (17) | −0.008 (2) | 0.0028 (18) | 0.0022 (18) |
O2 | 0.078 (4) | 0.097 (4) | 0.057 (2) | −0.021 (3) | 0.025 (2) | 0.004 (3) |
O3 | 0.0314 (19) | 0.058 (2) | 0.074 (3) | −0.005 (2) | −0.011 (2) | −0.006 (2) |
O4 | 0.032 (2) | 0.075 (3) | 0.096 (3) | −0.006 (2) | −0.004 (2) | −0.008 (3) |
Geometric parameters (Å, º) top
C1—O2 | 1.234 (7) | C10—C11 | 1.469 (8) |
C1—N1 | 1.519 (8) | C10—H10A | 0.9700 |
C1—C2 | 1.543 (8) | C10—H10B | 0.9700 |
C2—C3 | 1.347 (7) | C11—C12 | 1.537 (8) |
C2—H2 | 0.9300 | C11—H11A | 0.9700 |
C3—C4 | 1.567 (8) | C11—H11B | 0.9700 |
C3—H3 | 0.9300 | C12—C13 | 1.537 (9) |
C4—C5 | 1.555 (7) | C12—H12A | 0.9700 |
C4—O3 | 1.620 (7) | C12—H12B | 0.9700 |
C4—H4 | 0.9800 | C13—C14 | 1.651 (11) |
C5—C6 | 1.632 (7) | C13—H13A | 0.9700 |
C5—C9 | 1.655 (7) | C13—H13B | 0.9700 |
C5—H5 | 0.9800 | C14—C15 | 1.581 (10) |
C6—C7 | 1.556 (9) | C14—H14A | 0.9700 |
C6—H6A | 0.9700 | C14—H14B | 0.9700 |
C6—H6B | 0.9700 | C15—N1 | 1.538 (7) |
C7—O4 | 1.538 (9) | C15—C16 | 1.618 (11) |
C7—C8 | 1.599 (8) | C15—H15 | 0.9800 |
C7—H7 | 0.9800 | C16—H16A | 0.9600 |
C8—C9 | 1.605 (8) | C16—H16B | 0.9600 |
C8—H8A | 0.9700 | C16—H16C | 0.9600 |
C8—H8B | 0.9700 | N1—H1A | 0.8600 |
C9—C10 | 1.557 (7) | O3—H3A | 0.8200 |
C9—H9 | 0.9800 | O4—H4A | 0.8200 |
| | | |
O2—C1—N1 | 126.1 (5) | C11—C10—H10A | 105.5 |
O2—C1—C2 | 116.9 (5) | C9—C10—H10A | 105.5 |
N1—C1—C2 | 117.0 (4) | C11—C10—H10B | 105.5 |
C3—C2—C1 | 117.5 (5) | C9—C10—H10B | 105.5 |
C3—C2—H2 | 121.2 | H10A—C10—H10B | 106.1 |
C1—C2—H2 | 121.2 | C10—C11—C12 | 124.3 (5) |
C2—C3—C4 | 119.4 (5) | C10—C11—H11A | 106.2 |
C2—C3—H3 | 120.3 | C12—C11—H11A | 106.2 |
C4—C3—H3 | 120.3 | C10—C11—H11B | 106.2 |
C5—C4—C3 | 108.9 (4) | C12—C11—H11B | 106.2 |
C5—C4—O3 | 105.0 (4) | H11A—C11—H11B | 106.4 |
C3—C4—O3 | 117.9 (4) | C11—C12—C13 | 111.8 (5) |
C5—C4—H4 | 108.2 | C11—C12—H12A | 109.3 |
C3—C4—H4 | 108.2 | C13—C12—H12A | 109.3 |
O3—C4—H4 | 108.2 | C11—C12—H12B | 109.3 |
C4—C5—C6 | 112.0 (4) | C13—C12—H12B | 109.3 |
C4—C5—C9 | 110.9 (4) | H12A—C12—H12B | 107.9 |
C6—C5—C9 | 111.6 (4) | C12—C13—C14 | 111.4 (6) |
C4—C5—H5 | 107.4 | C12—C13—H13A | 109.3 |
C6—C5—H5 | 107.4 | C14—C13—H13A | 109.3 |
C9—C5—H5 | 107.4 | C12—C13—H13B | 109.3 |
C7—C6—C5 | 96.8 (4) | C14—C13—H13B | 109.3 |
C7—C6—H6A | 112.4 | H13A—C13—H13B | 108.0 |
C5—C6—H6A | 112.4 | C15—C14—C13 | 104.9 (6) |
C7—C6—H6B | 112.4 | C15—C14—H14A | 110.8 |
C5—C6—H6B | 112.4 | C13—C14—H14A | 110.8 |
H6A—C6—H6B | 110.0 | C15—C14—H14B | 110.8 |
O4—C7—C6 | 104.7 (5) | C13—C14—H14B | 110.8 |
O4—C7—C8 | 115.8 (5) | H14A—C14—H14B | 108.8 |
C6—C7—C8 | 108.3 (5) | N1—C15—C14 | 108.1 (5) |
O4—C7—H7 | 109.3 | N1—C15—C16 | 113.0 (5) |
C6—C7—H7 | 109.3 | C14—C15—C16 | 106.1 (6) |
C8—C7—H7 | 109.3 | N1—C15—H15 | 109.9 |
C7—C8—C9 | 107.9 (5) | C14—C15—H15 | 109.9 |
C7—C8—H8A | 110.1 | C16—C15—H15 | 109.9 |
C9—C8—H8A | 110.1 | C15—C16—H16A | 109.5 |
C7—C8—H8B | 110.1 | C15—C16—H16B | 109.5 |
C9—C8—H8B | 110.1 | H16A—C16—H16B | 109.5 |
H8A—C8—H8B | 108.4 | C15—C16—H16C | 109.5 |
C10—C9—C8 | 111.1 (5) | H16A—C16—H16C | 109.5 |
C10—C9—C5 | 117.2 (4) | H16B—C16—H16C | 109.5 |
C8—C9—C5 | 99.5 (4) | C1—N1—C15 | 123.1 (4) |
C10—C9—H9 | 109.5 | C1—N1—H1A | 118.5 |
C8—C9—H9 | 109.5 | C15—N1—H1A | 118.5 |
C5—C9—H9 | 109.5 | C4—O3—H3A | 109.5 |
C11—C10—C9 | 127.2 (5) | C7—O4—H4A | 109.5 |
| | | |
O2—C1—C2—C3 | −177.1 (6) | C4—C5—C9—C10 | 98.6 (5) |
N1—C1—C2—C3 | 1.4 (7) | C6—C5—C9—C10 | −135.9 (5) |
C1—C2—C3—C4 | 169.5 (5) | C4—C5—C9—C8 | −141.7 (4) |
C2—C3—C4—C5 | −111.2 (6) | C6—C5—C9—C8 | −16.1 (5) |
C2—C3—C4—O3 | 8.3 (7) | C8—C9—C10—C11 | 122.5 (6) |
C3—C4—C5—C6 | 179.9 (4) | C5—C9—C10—C11 | −124.1 (6) |
O3—C4—C5—C6 | 52.7 (5) | C9—C10—C11—C12 | 179.8 (5) |
C3—C4—C5—C9 | −54.8 (5) | C10—C11—C12—C13 | −95.0 (7) |
O3—C4—C5—C9 | 178.0 (4) | C11—C12—C13—C14 | −79.4 (7) |
C4—C5—C6—C7 | 159.3 (5) | C12—C13—C14—C15 | 134.5 (5) |
C9—C5—C6—C7 | 34.4 (5) | C13—C14—C15—N1 | −63.7 (6) |
C5—C6—C7—O4 | 84.8 (5) | C13—C14—C15—C16 | 174.8 (5) |
C5—C6—C7—C8 | −39.2 (6) | O2—C1—N1—C15 | 10.9 (9) |
O4—C7—C8—C9 | −84.3 (6) | C2—C1—N1—C15 | −167.4 (5) |
C6—C7—C8—C9 | 32.9 (7) | C14—C15—N1—C1 | 146.2 (5) |
C7—C8—C9—C10 | 115.1 (5) | C16—C15—N1—C1 | −96.7 (7) |
C7—C8—C9—C5 | −9.0 (6) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···O4i | 0.82 | 1.98 | 2.785 (6) | 167 |
O4—H4A···O3ii | 0.82 | 2.45 | 3.257 (7) | 167 |
Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+1/2, −z. |