# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 01:54:47 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: methyl (2E)-3-[(1aS,11S,11aS,14Z,18R)-3,18-dihydroxy-4,9-dioxo-4,9,10,11-tetrahydro-11aH-11,1a-hept[3]ene[1,5]diynonaphtho[2,3-h]oxireno[c]quinolin-11a-yl]but-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)\C=C(/C)[C@@]12O[C@@]13[C@H](O)C#C\C=C/C#C[C@@H]2Nc4c3cc(O)c5C(=O)c6ccccc6C(=O)c45
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 9VG  9VG  'methyl (2E)-3-[(1aS,11S,11aS,14Z,18R)-3,18-dihydroxy-4,9-dioxo-4,9,10,11-tetrahydro-11aH-11,1a-hept[3]ene[1,5]diynonaphtho[2,3-h]oxireno[c]quinolin-11a-yl]but-2-enoate'  ligand  56  37  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9VG
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 9VG  CAA  C  CH3   0  -0.423   -8.4697   7.1200   -2.6296
 9VG  OAU  O  O2    0  -0.460   -8.9884   6.2485   -3.6327
 9VG  CAW  C  C     0   0.590  -10.0594   6.6564   -4.3051
 9VG  OAC  O  O     0  -0.446  -10.6043   7.7149   -4.0990
 9VG  CAN  C  C1    0  -0.406  -10.4306   5.6406   -5.3092
 9VG  CAX  C  C     0   0.107  -11.4807   5.6958   -6.1362
 9VG  CAB  C  CH3   0  -0.734  -12.5253   6.7656   -6.1986
 9VG  CBJ  C  CT    0   0.199  -11.7518   4.5725   -7.0974
 9VG  OAV  O  O2    0  -0.445  -12.1736   4.9956   -8.3705
 9VG  CBK  C  CT    0   0.189  -10.9680   4.2422   -8.2964
 9VG  CAZ  C  CR6   0   0.154  -11.1355   2.8722   -8.8923
 9VG  CAS  C  CR16  0  -0.413  -10.2842   2.3975   -9.8526
 9VG  CAY  C  CR6   0   0.393  -10.5127   1.1758  -10.5067
 9VG  OAF  O  OH1   0  -0.620   -9.6133   0.8072  -11.4125
 9VG  CBF  C  CR66  0  -0.247  -11.6568   0.4413  -10.2060
 9VG  CBB  C  CR6   0   0.394  -11.8888  -0.8091  -10.9206
 9VG  OAD  O  O     0  -0.457  -11.0967  -1.2127  -11.7737
 9VG  CBD  C  CR66  0  -0.005  -13.0904  -1.5934  -10.5997
 9VG  CAQ  C  CR16  0  -0.270  -13.3433  -2.7808  -11.2822
 9VG  CAO  C  CR16  0  -0.234  -14.4715  -3.5241  -10.9826
 9VG  CAP  C  CR16  0  -0.229  -15.3523  -3.0860   -9.9998
 9VG  CAR  C  CR16  0  -0.275  -15.1053  -1.9070   -9.3174
 9VG  CBE  C  CR66  0  -0.012  -13.9725  -1.1524   -9.6113
 9VG  CBC  C  CR6   0   0.359  -13.7346   0.1096   -8.8693
 9VG  OAE  O  O     0  -0.427  -14.5415   0.4522   -8.0125
 9VG  CBG  C  CR66  0  -0.130  -12.5482   0.9021   -9.1977
 9VG  CBA  C  CR6   0   0.297  -12.2773   2.0992   -8.5185
 9VG  NAT  N  NH1   0  -0.671  -13.0591   2.5682   -7.5063
 9VG  CBI  C  CH1   0  -0.305  -12.4487   3.3591   -6.4728
 9VG  CAK  C  CSP   0   0.116  -11.3539   2.6409   -5.7954
 9VG  CAI  C  CSP   0   0.092  -10.2926   2.1502   -5.4955
 9VG  CAM  C  C1    0  -0.410   -8.9517   1.7396   -5.2816
 9VG  CAL  C  C1    0  -0.407   -7.9505   2.2860   -6.0041
 9VG  CAH  C  CSP   0   0.130   -8.2424   3.2738   -6.9778
 9VG  CAJ  C  CSP   0   0.025   -8.6986   4.0858   -7.7462
 9VG  CBH  C  CH1   0  -0.161   -9.6349   4.9586   -8.4775
 9VG  OAG  O  OH1   0  -0.644   -9.3539   5.1719   -9.8287
 9VG  H1   H  HCH3  0   0.253   -7.5849   6.6279   -2.2373
 9VG  H2   H  HCH3  0   0.240   -8.1906   8.0876   -3.0460
 9VG  H3   H  HCH3  0   0.240   -9.1873   7.2700   -1.8231
 9VG  H4   H  H     0   0.281   -9.7638   4.7934   -5.3660
 9VG  H5   H  HCH3  0   0.272  -12.5331   7.3900   -5.3146
 9VG  H6   H  HCH3  0   0.267  -12.3575   7.4067   -7.0665
 9VG  H7   H  HCH3  0   0.256  -13.5154   6.3238   -6.3229
 9VG  H8   H  HCR6  0   0.290   -9.4155   2.9615  -10.1583
 9VG  H9   H  HOH1  0   0.484   -9.9140  -0.0502  -11.7940
 9VG  H10  H  HCR6  0   0.274  -12.6584  -3.1232  -12.0457
 9VG  H11  H  HCR6  0   0.277  -14.6667  -4.4463  -11.5127
 9VG  H12  H  HCR6  0   0.277  -16.2343  -3.6667   -9.7650
 9VG  H13  H  HCR6  0   0.273  -15.7952  -1.5710   -8.5560
 9VG  H14  H  HNH1  0   0.420  -13.8165   1.9627   -7.2208
 9VG  H15  H  HCH1  0   0.326  -13.2314   3.6609   -5.7754
 9VG  H16  H  H     0   0.296   -8.7329   0.9902   -4.5318
 9VG  H18  H  H     0   0.299   -6.9272   1.9752   -5.8388
 9VG  H20  H  HCH1  0   0.287   -9.6907   5.9144   -7.9425
 9VG  H21  H  HOH1  0   0.474   -8.5686   5.7265   -9.8944

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 9VG  OAD  CBB  double    1.232  0.020  1.232
 9VG  OAF  CAY  single    1.329  0.020  1.329
 9VG  CAQ  CAO  aromatic  1.384  0.020  1.384
 9VG  CAQ  CBD  aromatic  1.393  0.020  1.393
 9VG  CBB  CBD  single    1.470  0.020  1.470
 9VG  CBB  CBF  single    1.459  0.020  1.459
 9VG  CAY  CBF  aromatic  1.392  0.020  1.392
 9VG  CAY  CAS  aromatic  1.404  0.020  1.404
 9VG  CAO  CAP  aromatic  1.391  0.020  1.391
 9VG  CBD  CBE  aromatic  1.396  0.020  1.396
 9VG  CBF  CBG  aromatic  1.423  0.020  1.423
 9VG  CAS  CAZ  aromatic  1.368  0.020  1.368
 9VG  OAG  CBH  single    1.397  0.020  1.397
 9VG  CAP  CAR  aromatic  1.384  0.020  1.384
 9VG  CBE  CAR  aromatic  1.392  0.020  1.392
 9VG  CBE  CBC  single    1.483  0.020  1.483
 9VG  CBG  CBC  single    1.464  0.020  1.464
 9VG  CBG  CBA  aromatic  1.403  0.020  1.403
 9VG  CAZ  CBA  aromatic  1.429  0.020  1.429
 9VG  CAZ  CBK  single    1.503  0.020  1.503
 9VG  CBC  OAE  double    1.226  0.020  1.226
 9VG  CBA  NAT  single    1.362  0.020  1.362
 9VG  CBH  CBK  single    1.524  0.020  1.524
 9VG  CBH  CAJ  single    1.474  0.020  1.474
 9VG  OAV  CBK  single    1.424  0.020  1.424
 9VG  OAV  CBJ  single    1.406  0.020  1.406
 9VG  CBK  CBJ  single    1.470  0.020  1.470
 9VG  CAJ  CAH  triple    1.208  0.020  1.208
 9VG  NAT  CBI  single    1.438  0.020  1.438
 9VG  CBJ  CBI  single    1.532  0.020  1.532
 9VG  CBJ  CAX  single    1.503  0.020  1.503
 9VG  CAH  CAL  single    1.417  0.020  1.417
 9VG  CBI  CAK  single    1.474  0.020  1.474
 9VG  CAB  CAX  single    1.497  0.020  1.497
 9VG  CAX  CAN  double    1.338  0.020  1.338
 9VG  CAK  CAI  triple    1.207  0.020  1.207
 9VG  CAL  CAM  double    1.350  0.020  1.350
 9VG  CAI  CAM  single    1.419  0.020  1.419
 9VG  CAN  CAW  single    1.476  0.020  1.476
 9VG  CAW  OAC  double    1.208  0.020  1.208
 9VG  CAW  OAU  single    1.329  0.020  1.329
 9VG  OAU  CAA  single    1.426  0.020  1.426
 9VG  CAA  H1   single    0.970  0.020  1.090
 9VG  CAA  H2   single    0.970  0.020  1.090
 9VG  CAA  H3   single    0.970  0.020  1.090
 9VG  CAN  H4   single    0.930  0.020  1.080
 9VG  CAB  H5   single    0.970  0.020  1.090
 9VG  CAB  H6   single    0.970  0.020  1.090
 9VG  CAB  H7   single    0.970  0.020  1.090
 9VG  CAS  H8   single    0.930  0.020  1.080
 9VG  OAF  H9   single    0.850  0.020  0.980
 9VG  CAQ  H10  single    0.930  0.020  1.080
 9VG  CAO  H11  single    0.930  0.020  1.080
 9VG  CAP  H12  single    0.930  0.020  1.080
 9VG  CAR  H13  single    0.930  0.020  1.080
 9VG  NAT  H14  single    0.890  0.020  1.040
 9VG  CBI  H15  single    0.970  0.020  1.090
 9VG  CAM  H16  single    0.930  0.020  1.080
 9VG  CAL  H18  single    0.930  0.020  1.080
 9VG  CBH  H20  single    0.970  0.020  1.090
 9VG  OAG  H21  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 9VG  H3   CAA  H2   109.22  3.000
 9VG  H3   CAA  H1   109.37  3.000
 9VG  H2   CAA  H1   109.37  3.000
 9VG  H3   CAA  OAU  111.42  3.000
 9VG  H2   CAA  OAU  111.52  3.000
 9VG  H1   CAA  OAU  105.87  3.000
 9VG  CAW  OAU  CAA  117.48  3.000
 9VG  CAN  CAW  OAC  127.28  3.000
 9VG  OAC  CAW  OAU  123.10  3.000
 9VG  CAN  CAW  OAU  109.62  3.000
 9VG  H4   CAN  CAX  118.99  3.000
 9VG  H4   CAN  CAW  114.87  3.000
 9VG  CAX  CAN  CAW  126.14  3.000
 9VG  CBJ  CAX  CAB  112.44  3.000
 9VG  CAB  CAX  CAN  127.10  3.000
 9VG  CBJ  CAX  CAN  120.40  3.000
 9VG  H7   CAB  H6   106.65  3.000
 9VG  H7   CAB  H5   108.66  3.000
 9VG  H6   CAB  H5   108.15  3.000
 9VG  H7   CAB  CAX  110.41  3.000
 9VG  H6   CAB  CAX  110.22  3.000
 9VG  H5   CAB  CAX  112.54  3.000
 9VG  CBI  CBJ  CBK  113.39  3.000
 9VG  CBI  CBJ  OAV  118.09  3.000
 9VG  CBK  CBJ  OAV   59.28  3.000
 9VG  CBI  CBJ  CAX  114.40  3.000
 9VG  CBK  CBJ  CAX  126.40  3.000
 9VG  OAV  CBJ  CAX  114.09  3.000
 9VG  CBK  OAV  CBJ   62.59  3.000
 9VG  CBH  CBK  CAZ  118.60  3.000
 9VG  CBH  CBK  OAV  119.06  3.000
 9VG  CAZ  CBK  OAV  111.55  3.000
 9VG  OAV  CBK  CBJ   58.13  3.000
 9VG  CBH  CBK  CBJ  117.23  3.000
 9VG  CAZ  CBK  CBJ  117.95  3.000
 9VG  CBA  CAZ  CAS  119.55  3.000
 9VG  CBA  CAZ  CBK  118.58  3.000
 9VG  CAS  CAZ  CBK  121.67  3.000
 9VG  H8   CAS  CAY  116.96  3.000
 9VG  H8   CAS  CAZ  121.20  3.000
 9VG  CAY  CAS  CAZ  121.83  3.000
 9VG  CBF  CAY  OAF  123.85  3.000
 9VG  CBF  CAY  CAS  119.47  3.000
 9VG  OAF  CAY  CAS  116.66  3.000
 9VG  H9   OAF  CAY  107.38  3.000
 9VG  CBG  CBF  CBB  121.68  3.000
 9VG  CBG  CBF  CAY  119.80  3.000
 9VG  CBB  CBF  CAY  118.49  3.000
 9VG  CBD  CBB  OAD  120.12  3.000
 9VG  CBD  CBB  CBF  118.71  3.000
 9VG  OAD  CBB  CBF  121.18  3.000
 9VG  CBE  CBD  CAQ  120.10  3.000
 9VG  CBE  CBD  CBB  120.15  3.000
 9VG  CAQ  CBD  CBB  119.75  3.000
 9VG  H10  CAQ  CAO  119.95  3.000
 9VG  H10  CAQ  CBD  120.07  3.000
 9VG  CAO  CAQ  CBD  119.98  3.000
 9VG  H11  CAO  CAP  120.05  3.000
 9VG  H11  CAO  CAQ  119.93  3.000
 9VG  CAP  CAO  CAQ  120.02  3.000
 9VG  H12  CAP  CAR  119.71  3.000
 9VG  H12  CAP  CAO  120.05  3.000
 9VG  CAR  CAP  CAO  120.24  3.000
 9VG  H13  CAR  CBE  119.96  3.000
 9VG  H13  CAR  CAP  119.87  3.000
 9VG  CBE  CAR  CAP  120.17  3.000
 9VG  CBC  CBE  CAR  119.08  3.000
 9VG  CBC  CBE  CBD  121.44  3.000
 9VG  CAR  CBE  CBD  119.48  3.000
 9VG  CBG  CBC  OAE  122.61  3.000
 9VG  OAE  CBC  CBE  118.81  3.000
 9VG  CBG  CBC  CBE  118.58  3.000
 9VG  CBA  CBG  CBC  120.65  3.000
 9VG  CBA  CBG  CBF  119.91  3.000
 9VG  CBC  CBG  CBF  119.43  3.000
 9VG  NAT  CBA  CBG  122.87  3.000
 9VG  NAT  CBA  CAZ  117.83  3.000
 9VG  CBG  CBA  CAZ  119.30  3.000
 9VG  H14  NAT  CBI  116.40  3.000
 9VG  H14  NAT  CBA  115.70  3.000
 9VG  CBI  NAT  CBA  118.68  3.000
 9VG  H15  CBI  CAK  111.96  3.000
 9VG  H15  CBI  NAT  107.89  3.000
 9VG  CAK  CBI  NAT  112.19  3.000
 9VG  H15  CBI  CBJ  111.58  3.000
 9VG  CAK  CBI  CBJ  103.61  3.000
 9VG  NAT  CBI  CBJ  109.61  3.000
 9VG  CAI  CAK  CBI  180.00  3.000
 9VG  CAM  CAI  CAK  180.00  3.000
 9VG  H16  CAM  CAL  120.06  3.000
 9VG  H16  CAM  CAI  119.73  3.000
 9VG  CAL  CAM  CAI  120.21  3.000
 9VG  H18  CAL  CAH  119.99  3.000
 9VG  H18  CAL  CAM  120.21  3.000
 9VG  CAH  CAL  CAM  119.80  3.000
 9VG  CAJ  CAH  CAL  180.00  3.000
 9VG  CBH  CAJ  CAH  180.00  3.000
 9VG  H20  CBH  OAG  110.42  3.000
 9VG  H20  CBH  CAJ  107.84  3.000
 9VG  OAG  CBH  CAJ  116.27  3.000
 9VG  H20  CBH  CBK  107.89  3.000
 9VG  CAJ  CBH  CBK  102.61  3.000
 9VG  OAG  CBH  CBK  111.27  3.000
 9VG  H21  OAG  CBH  108.54  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 9VG  CONST_01  CBF  CAY  CAS  CAZ     0.00   0.0  0
 9VG  CONST_02  CBF  CBG  CBA  CAZ     0.00   0.0  0
 9VG  CONST_03  CBG  CBF  CAY  CAS     0.00   0.0  0
 9VG  CONST_04  CBG  CBA  CAZ  CAS     0.00   0.0  0
 9VG  CONST_05  CBA  CBG  CBF  CAY     0.00   0.0  0
 9VG  CONST_06  CBA  CAZ  CAS  CAY     0.00   0.0  0
 9VG  CONST_07  CAP  CAO  CAQ  CBD     0.00   0.0  0
 9VG  CONST_08  CAP  CAR  CBE  CBD     0.00   0.0  0
 9VG  CONST_09  CAR  CAP  CAO  CAQ     0.00   0.0  0
 9VG  CONST_10  CAR  CBE  CBD  CAQ     0.00   0.0  0
 9VG  CONST_11  CBE  CBD  CAQ  CAO     0.00   0.0  0
 9VG  CONST_12  CBE  CAR  CAP  CAO     0.00   0.0  0
 9VG  CONST_13  OAF  CAY  CAS  CAZ   180.00   0.0  0
 9VG  CONST_14  CBB  CBF  CAY  OAF     0.00   0.0  0
 9VG  CONST_15  CBG  CBF  CAY  OAF   180.00   0.0  0
 9VG  CONST_16  H8   CAS  CAZ  CBK     0.00   0.0  0
 9VG  CONST_17  H10  CAQ  CBD  CBB     0.00   0.0  0
 9VG  CONST_18  H11  CAO  CAQ  CBD   180.00   0.0  0
 9VG  CONST_19  H13  CAR  CBE  CBD   180.00   0.0  0
 9VG  CONST_20  H12  CAP  CAO  CAQ   180.00   0.0  0
 9VG  Var_01    CAZ  CBK  OAV  CBJ   110.35  30.0  3
 9VG  Var_02    CAS  CAZ  CBK  OAV   127.43  30.0  2
 9VG  Var_03    CAY  CAS  CAZ  CBK  -173.55  30.0  1
 9VG  Var_04    CBG  CBA  CAZ  CBK   171.31  30.0  1
 9VG  Var_05    CBI  NAT  CBA  CAZ   -29.84  30.0  1
 9VG  Var_06    CBB  CBF  CAY  CAS   178.58  30.0  1
 9VG  Var_07    CBD  CBB  CBF  CAY   179.56  30.0  2
 9VG  Var_08    CAQ  CBD  CBB  CBF   179.08  30.0  2
 9VG  Var_09    CBE  CBC  CBG  CBF    -0.39  30.0  2
 9VG  Var_10    CAO  CAQ  CBD  CBB   179.89  30.0  1
 9VG  Var_11    CAR  CBE  CBD  CBB  -179.91  30.0  1
 9VG  Var_12    CBG  CBC  CBE  CBD     0.34  30.0  2
 9VG  Var_13    OAV  CBJ  CAX  CAN  -139.75  30.0  2
 9VG  Var_14    CBJ  CAX  CAN  CAW  -178.97   0.0  2
 9VG  Var_15    H5   CAB  CAX  CBJ   160.73  30.0  3
 9VG  Var_16    CAN  CAW  OAU  CAA   178.95  30.0  1
 9VG  Var_17    CAX  CAN  CAW  OAU   177.80  30.0  1
 9VG  Var_18    H1   CAA  OAU  CAW  -177.57  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 9VG  chir_03  CBI  NAT  CBJ  CAK  positiv
 9VG  chir_04  CBH  OAG  CBK  CAJ  negativ
 9VG  chir_05  CBJ  CBK  CBI  CAX  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 9VG  plan-1  CBF  0.020
 9VG  plan-1  CBB  0.020
 9VG  plan-1  OAD  0.020
 9VG  plan-1  CBD  0.020
 9VG  plan-2  CBE  0.020
 9VG  plan-2  CBC  0.020
 9VG  plan-2  OAE  0.020
 9VG  plan-2  CBG  0.020
 9VG  plan-3  CAW  0.020
 9VG  plan-3  CAN  0.020
 9VG  plan-3  CAX  0.020
 9VG  plan-3  CAB  0.020
 9VG  plan-3  CBJ  0.020
 9VG  plan-3  H4   0.020
 9VG  plan-4  OAU  0.020
 9VG  plan-4  CAW  0.020
 9VG  plan-4  OAC  0.020
 9VG  plan-4  CAN  0.020

