# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  9 18:37:17 2020
#   Inital geometry file: a 168 line input string
#   Ligand name: methyl (2R,3R)-2,3-dihydroxy-3-[(1aS,11S,11aR,14Z,18R)-3,7,8,18-tetrahydroxy-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]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](O)[C@@](C)(O)[C@@]12O[C@@]13[C@H](O)C#C\C=C/C#C[C@@H]2Nc4c3cc(O)c5C(=O)c6ccc(O)c(O)c6C(=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
 D77  D77  'methyl (2R,3R)-2,3-dihydroxy-3-[(1aS,11S,11aR,14Z,18R)-3,7,8,18-tetrahydroxy-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]butanoate'  ligand  62  41  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D77
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
 D77  CAA  C  CH3   0  -0.463   7.9217   0.3262   1.2392
 D77  OAV  O  O2    0  -0.546   6.4941   0.3995   1.3373
 D77  CAX  C  C     0   0.518   5.8660  -0.6174   1.8800
 D77  OAC  O  O     0  -0.253   6.4025  -1.5956   2.3397
 D77  CBK  C  CH1   0  -0.067   4.3555  -0.4305   1.9011
 D77  OAJ  O  OH1   0  -0.649   3.8057  -1.2734   2.8746
 D77  CBM  C  CT    0   0.154   3.7186  -0.7954   0.5230
 D77  CAB  C  CH3   0  -0.785   4.4361  -0.1825  -0.6737
 D77  OAK  O  OH1   0  -0.655   3.8630  -2.1847   0.3591
 D77  CBO  C  CT    0   0.161   2.1891  -0.4451   0.5750
 D77  OAW  O  O2    0  -0.452   1.7143   0.0859   1.7884
 D77  CBN  C  CT    0   0.127   1.5629   0.8926   0.6313
 D77  CBB  C  CR6   0   0.060   0.1092   1.0325   0.2493
 D77  CAT  C  CR16  0  -0.319  -0.4786   2.2541   0.0592
 D77  CAZ  C  CR6   0   0.337  -1.8620   2.3922  -0.1472
 D77  OAG  O  OH1   0  -0.698  -2.3183   3.6273  -0.3255
 D77  CBH  C  CR66  0  -0.055  -2.6749   1.2639  -0.1237
 D77  CBD  C  CR6   0   0.371  -4.1139   1.4291  -0.3142
 D77  OAD  O  O     0  -0.421  -4.6080   2.5503  -0.4713
 D77  CBF  C  CR66  0   0.113  -4.9610   0.2388  -0.3142
 D77  CAS  C  CR16  0  -0.339  -6.3266   0.3676  -0.4825
 D77  CAR  C  CR16  0  -0.277  -7.1401  -0.7582  -0.4885
 D77  CAY  C  CR6   0   0.263  -6.5995  -2.0197  -0.3303
 D77  OAF  O  OH1   0  -0.660  -7.3154  -3.1476  -0.3341
 D77  CBA  C  CR6   0   0.309  -5.2047  -2.1728  -0.1577
 D77  OAH  O  OH1   0  -0.658  -4.7563  -3.4135  -0.0236
 D77  CBG  C  CR66  0  -0.294  -4.3871  -1.0378  -0.1475
 D77  CBE  C  CR6   0   0.345  -2.9425  -1.1976   0.0438
 D77  OAE  O  O     0  -0.167  -2.4758  -2.3391   0.1974
 D77  CBI  C  CR66  0  -0.251  -2.0891  -0.0198   0.0528
 D77  CBC  C  CR6   0   0.376  -0.6994  -0.1421   0.2107
 D77  NAU  N  NH1   0  -0.712  -0.0681  -1.3387   0.3235
 D77  CBL  C  CH1   0  -0.067   1.2848  -1.4590  -0.1468
 D77  CAO  C  CSP   0  -0.075   1.3989  -1.0956  -1.5705
 D77  CAM  C  CSP   0  -0.077   1.4763  -0.5081  -2.6224
 D77  CAQ  C  C1    0  -0.387   1.6731   0.3628  -3.7242
 D77  CAP  C  C1    0  -0.269   2.0571   1.6416  -3.5227
 D77  CAL  C  CSP   0   0.193   2.2737   2.1155  -2.2055
 D77  CAN  C  CSP   0  -0.112   2.3962   2.3243  -1.0229
 D77  CBJ  C  CH1   0  -0.089   2.4474   2.1201   0.4356
 D77  OAI  O  OH1   0  -0.692   2.0229   3.1830   1.2357
 D77  H1   H  HCH3  0   0.281   8.2281  -0.4989   0.5977
 D77  H2   H  HCH3  0   0.269   8.2365   1.2662   0.7984
 D77  H3   H  HCH3  0   0.255   8.3765   0.2122   2.2217
 D77  H4   H  HCH1  0   0.316   4.1598   0.6151   2.1562
 D77  H5   H  HOH1  0   0.469   4.5104  -1.8275   3.2354
 D77  H6   H  HCH3  0   0.338   5.4187  -0.6393  -0.7930
 D77  H7   H  HCH3  0   0.257   3.8786  -0.3686  -1.5871
 D77  H8   H  HCH3  0   0.245   4.5827   0.8910  -0.5923
 D77  H9   H  HOH1  0   0.474   3.5921  -2.6179   1.1798
 D77  H10  H  HCR6  0   0.293   0.0995   3.1643   0.0906
 D77  H11  H  HOH1  0   0.463  -3.2989   3.5585  -0.4234
 D77  H12  H  HCR6  0   0.269  -6.7704   1.3441  -0.6139
 D77  H13  H  HCR6  0   0.268  -8.2098  -0.6474  -0.6222
 D77  H14  H  HOH1  0   0.467  -8.2526  -2.9539  -0.4521
 D77  H15  H  HOH1  0   0.471  -3.7773  -3.3504   0.0762
 D77  H16  H  HNH1  0   0.400  -0.6527  -2.1570   0.2286
 D77  H17  H  HCH1  0   0.334   1.5944  -2.4854   0.0325
 D77  H18  H  H     0   0.298   1.5158  -0.0007  -4.7315
 D77  H20  H  H     0   0.255   2.2085   2.3026  -4.3663
 D77  H22  H  HCH1  0   0.282   3.4787   1.8598   0.6946
 D77  H23  H  HOH1  0   0.460   2.6562   3.9037   1.1466

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
 D77  CAQ  CAM  single    1.418  0.020  1.418
 D77  CAQ  CAP  double    1.350  0.020  1.350
 D77  OAK  CBM  single    1.406  0.020  1.406
 D77  CAM  CAO  triple    1.207  0.020  1.207
 D77  CAB  CBM  single    1.524  0.020  1.524
 D77  CAP  CAL  single    1.417  0.020  1.417
 D77  CAO  CBL  single    1.474  0.020  1.474
 D77  OAV  CAA  single    1.433  0.020  1.433
 D77  OAV  CAX  single    1.313  0.020  1.313
 D77  CBM  CBK  single    1.561  0.020  1.561
 D77  CBM  CBO  single    1.570  0.020  1.570
 D77  CBL  CBO  single    1.538  0.020  1.538
 D77  CBL  NAU  single    1.437  0.020  1.437
 D77  CAL  CAN  triple    1.207  0.020  1.207
 D77  OAJ  CBK  single    1.400  0.020  1.400
 D77  CAX  CBK  single    1.522  0.020  1.522
 D77  CAX  OAC  double    1.207  0.020  1.207
 D77  CBO  OAW  single    1.407  0.020  1.407
 D77  CBO  CBN  single    1.478  0.020  1.478
 D77  OAH  CBA  single    1.326  0.020  1.326
 D77  NAU  CBC  single    1.358  0.020  1.358
 D77  OAE  CBE  double    1.243  0.020  1.243
 D77  CAN  CBJ  single    1.474  0.020  1.474
 D77  OAF  CAY  single    1.336  0.020  1.336
 D77  CBA  CAY  aromatic  1.414  0.020  1.414
 D77  CBA  CBG  aromatic  1.399  0.020  1.399
 D77  CBE  CBG  single    1.466  0.020  1.466
 D77  CBE  CBI  single    1.454  0.020  1.454
 D77  OAW  CBN  single    1.419  0.020  1.419
 D77  CBC  CBI  single    1.404  0.020  1.404
 D77  CBC  CBB  aromatic  1.427  0.020  1.427
 D77  CBJ  CBN  single    1.526  0.020  1.526
 D77  CBJ  OAI  single    1.396  0.020  1.396
 D77  CBN  CBB  single    1.510  0.020  1.510
 D77  CAY  CAR  aromatic  1.382  0.020  1.382
 D77  CBG  CBF  aromatic  1.410  0.020  1.410
 D77  CBI  CBH  aromatic  1.422  0.020  1.422
 D77  CBB  CAT  aromatic  1.369  0.020  1.369
 D77  CAR  CAS  aromatic  1.389  0.020  1.389
 D77  CBF  CAS  aromatic  1.382  0.020  1.382
 D77  CBF  CBD  single    1.461  0.020  1.461
 D77  CBH  CBD  single    1.461  0.020  1.461
 D77  CBH  CAZ  aromatic  1.391  0.020  1.391
 D77  CAT  CAZ  aromatic  1.405  0.020  1.405
 D77  CBD  OAD  double    1.235  0.020  1.235
 D77  CAZ  OAG  single    1.329  0.020  1.329
 D77  CAA  H1   single    0.970  0.020  1.090
 D77  CAA  H2   single    0.970  0.020  1.090
 D77  CAA  H3   single    0.970  0.020  1.090
 D77  CBK  H4   single    0.970  0.020  1.090
 D77  OAJ  H5   single    0.850  0.020  0.980
 D77  CAB  H6   single    0.970  0.020  1.090
 D77  CAB  H7   single    0.970  0.020  1.090
 D77  CAB  H8   single    0.970  0.020  1.090
 D77  OAK  H9   single    0.850  0.020  0.980
 D77  CAT  H10  single    0.930  0.020  1.080
 D77  OAG  H11  single    0.850  0.020  0.980
 D77  CAS  H12  single    0.930  0.020  1.080
 D77  CAR  H13  single    0.930  0.020  1.080
 D77  OAF  H14  single    0.850  0.020  0.980
 D77  OAH  H15  single    0.850  0.020  0.980
 D77  NAU  H16  single    0.890  0.020  1.040
 D77  CBL  H17  single    0.970  0.020  1.090
 D77  CAQ  H18  single    0.930  0.020  1.080
 D77  CAP  H20  single    0.930  0.020  1.080
 D77  CBJ  H22  single    0.970  0.020  1.090
 D77  OAI  H23  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
 D77  H3   CAA  H2   109.65  3.000
 D77  H3   CAA  H1   109.55  3.000
 D77  H2   CAA  H1   109.60  3.000
 D77  H3   CAA  OAV  111.08  3.000
 D77  H2   CAA  OAV  105.82  3.000
 D77  H1   CAA  OAV  111.06  3.000
 D77  CAX  OAV  CAA  117.74  3.000
 D77  CBK  CAX  OAC  122.38  3.000
 D77  OAC  CAX  OAV  124.94  3.000
 D77  CBK  CAX  OAV  112.67  3.000
 D77  H4   CBK  CBM  110.87  3.000
 D77  H4   CBK  OAJ  110.06  3.000
 D77  CBM  CBK  OAJ  108.23  3.000
 D77  H4   CBK  CAX  107.35  3.000
 D77  OAJ  CBK  CAX  108.99  3.000
 D77  CBM  CBK  CAX  111.34  3.000
 D77  H5   OAJ  CBK  108.57  3.000
 D77  CBO  CBM  OAK  108.93  3.000
 D77  CBO  CBM  CAB  113.26  3.000
 D77  OAK  CBM  CAB  104.92  3.000
 D77  CBO  CBM  CBK  108.42  3.000
 D77  CAB  CBM  CBK  114.01  3.000
 D77  OAK  CBM  CBK  106.97  3.000
 D77  H8   CAB  H7   107.56  3.000
 D77  H8   CAB  H6   107.49  3.000
 D77  H7   CAB  H6   107.38  3.000
 D77  H8   CAB  CBM  113.71  3.000
 D77  H7   CAB  CBM  110.47  3.000
 D77  H6   CAB  CBM  109.98  3.000
 D77  H9   OAK  CBM  108.35  3.000
 D77  CBL  CBO  CBN  111.43  3.000
 D77  CBN  CBO  OAW   58.85  3.000
 D77  CBL  CBO  OAW  117.06  3.000
 D77  CBN  CBO  CBM  128.02  3.000
 D77  OAW  CBO  CBM  116.20  3.000
 D77  CBL  CBO  CBM  114.21  3.000
 D77  CBN  OAW  CBO   63.08  3.000
 D77  CBJ  CBN  CBB  116.83  3.000
 D77  CBB  CBN  OAW  111.21  3.000
 D77  CBJ  CBN  OAW  120.02  3.000
 D77  CBB  CBN  CBO  118.83  3.000
 D77  CBJ  CBN  CBO  118.53  3.000
 D77  OAW  CBN  CBO   58.08  3.000
 D77  CBC  CBB  CAT  119.19  3.000
 D77  CAT  CBB  CBN  122.09  3.000
 D77  CBC  CBB  CBN  118.45  3.000
 D77  H10  CAT  CAZ  116.67  3.000
 D77  H10  CAT  CBB  121.26  3.000
 D77  CAZ  CAT  CBB  122.05  3.000
 D77  CBH  CAZ  OAG  123.75  3.000
 D77  OAG  CAZ  CAT  116.68  3.000
 D77  CBH  CAZ  CAT  119.55  3.000
 D77  H11  OAG  CAZ  106.83  3.000
 D77  CBI  CBH  CBD  121.60  3.000
 D77  CBD  CBH  CAZ  118.81  3.000
 D77  CBI  CBH  CAZ  119.58  3.000
 D77  CBF  CBD  OAD  120.51  3.000
 D77  OAD  CBD  CBH  120.87  3.000
 D77  CBF  CBD  CBH  118.62  3.000
 D77  CBG  CBF  CAS  120.08  3.000
 D77  CAS  CBF  CBD  119.80  3.000
 D77  CBG  CBF  CBD  120.12  3.000
 D77  H12  CAS  CAR  119.43  3.000
 D77  H12  CAS  CBF  120.33  3.000
 D77  CAR  CAS  CBF  120.25  3.000
 D77  H13  CAR  CAY  119.59  3.000
 D77  H13  CAR  CAS  119.72  3.000
 D77  CAY  CAR  CAS  120.69  3.000
 D77  CBA  CAY  OAF  115.95  3.000
 D77  CBA  CAY  CAR  119.93  3.000
 D77  OAF  CAY  CAR  124.12  3.000
 D77  H14  OAF  CAY  110.58  3.000
 D77  CBG  CBA  OAH  124.11  3.000
 D77  CBG  CBA  CAY  119.32  3.000
 D77  OAH  CBA  CAY  116.57  3.000
 D77  H15  OAH  CBA  106.62  3.000
 D77  CBE  CBG  CBA  119.24  3.000
 D77  CBE  CBG  CBF  121.02  3.000
 D77  CBA  CBG  CBF  119.74  3.000
 D77  CBI  CBE  OAE  121.51  3.000
 D77  CBI  CBE  CBG  119.39  3.000
 D77  OAE  CBE  CBG  119.10  3.000
 D77  CBC  CBI  CBE  120.72  3.000
 D77  CBC  CBI  CBH  120.03  3.000
 D77  CBE  CBI  CBH  119.25  3.000
 D77  NAU  CBC  CBI  123.12  3.000
 D77  CBI  CBC  CBB  119.49  3.000
 D77  NAU  CBC  CBB  117.38  3.000
 D77  H16  NAU  CBL  116.50  3.000
 D77  H16  NAU  CBC  115.92  3.000
 D77  CBL  NAU  CBC  118.96  3.000
 D77  H17  CBL  CAO  111.72  3.000
 D77  H17  CBL  NAU  107.04  3.000
 D77  CAO  CBL  NAU  111.61  3.000
 D77  H17  CBL  CBO  112.18  3.000
 D77  NAU  CBL  CBO  110.16  3.000
 D77  CAO  CBL  CBO  104.20  3.000
 D77  CAM  CAO  CBL  180.00  3.000
 D77  CAQ  CAM  CAO  180.00  3.000
 D77  H18  CAQ  CAP  119.89  3.000
 D77  H18  CAQ  CAM  119.77  3.000
 D77  CAP  CAQ  CAM  120.34  3.000
 D77  H20  CAP  CAL  119.94  3.000
 D77  H20  CAP  CAQ  120.12  3.000
 D77  CAL  CAP  CAQ  119.94  3.000
 D77  CAN  CAL  CAP  180.00  3.000
 D77  CBJ  CAN  CAL  180.00  3.000
 D77  H22  CBJ  OAI  109.38  3.000
 D77  H22  CBJ  CAN  107.45  3.000
 D77  OAI  CBJ  CAN  116.81  3.000
 D77  H22  CBJ  CBN  108.94  3.000
 D77  OAI  CBJ  CBN  111.26  3.000
 D77  CAN  CBJ  CBN  102.61  3.000
 D77  H23  OAI  CBJ  108.45  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
 D77  CONST_01  CBH  CBI  CBC  CBB     0.00   0.0  0
 D77  CONST_02  CBH  CAZ  CAT  CBB     0.00   0.0  0
 D77  CONST_03  CBI  CBC  CBB  CAT     0.00   0.0  0
 D77  CONST_04  CBI  CBH  CAZ  CAT     0.00   0.0  0
 D77  CONST_05  CBC  CBI  CBH  CAZ     0.00   0.0  0
 D77  CONST_06  CBC  CBB  CAT  CAZ     0.00   0.0  0
 D77  CONST_07  CAY  CBA  CBG  CBF     0.00   0.0  0
 D77  CONST_08  CAY  CAR  CAS  CBF     0.00   0.0  0
 D77  CONST_09  CBA  CAY  CAR  CAS     0.00   0.0  0
 D77  CONST_10  CBA  CBG  CBF  CAS     0.00   0.0  0
 D77  CONST_11  CBG  CBA  CAY  CAR     0.00   0.0  0
 D77  CONST_12  CBG  CBF  CAS  CAR     0.00   0.0  0
 D77  CONST_13  OAG  CAZ  CAT  CBB   180.00   0.0  0
 D77  CONST_14  CBI  CBH  CAZ  OAG   180.00   0.0  0
 D77  CONST_15  CBD  CBH  CAZ  OAG     0.00   0.0  0
 D77  CONST_16  OAH  CBA  CBG  CBF   180.00   0.0  0
 D77  CONST_17  OAF  CAY  CAR  CAS   180.00   0.0  0
 D77  CONST_18  OAH  CBA  CAY  CAR   180.00   0.0  0
 D77  CONST_19  CBG  CBA  CAY  OAF   180.00   0.0  0
 D77  CONST_20  CBE  CBG  CBA  OAH     0.00   0.0  0
 D77  CONST_21  H10  CAT  CBB  CBN     0.00   0.0  0
 D77  CONST_22  H12  CAS  CBF  CBD     0.00   0.0  0
 D77  CONST_23  H13  CAR  CAS  CBF   180.00   0.0  0
 D77  Var_01    CBB  CBN  OAW  CBO   111.57  30.0  3
 D77  Var_02    CBC  CBB  CBN  OAW   -47.09  30.0  2
 D77  Var_03    NAU  CBC  CBB  CBN    -9.68  30.0  1
 D77  Var_04    CAZ  CAT  CBB  CBN  -172.66  30.0  1
 D77  Var_05    CBL  NAU  CBC  CBB   -29.15  30.0  1
 D77  Var_06    CBE  CBI  CBC  CBB  -178.43  30.0  1
 D77  Var_07    CBK  CAX  OAV  CAA  -178.87  30.0  3
 D77  Var_08    H1   CAA  OAV  CAX    62.91  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
 D77  chir_01  CBK  CBM  OAJ  CAX  negativ
 D77  chir_02  CBM  CAB  CBK  CBO  negativ
 D77  chir_05  CBL  CAO  CBO  NAU  negativ
 D77  chir_06  CBJ  OAI  CAN  CBN  positiv
 D77  chir_07  CBO  CBL  OAW  CBN  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
 D77  plan-1  CAZ  0.020
 D77  plan-1  CBH  0.020
 D77  plan-1  CBD  0.020
 D77  plan-1  OAD  0.020
 D77  plan-1  CBF  0.020
 D77  plan-1  CAS  0.020
 D77  plan-1  CAR  0.020
 D77  plan-1  CAY  0.020
 D77  plan-1  OAF  0.020
 D77  plan-1  CBA  0.020
 D77  plan-1  OAH  0.020
 D77  plan-1  CBG  0.020
 D77  plan-1  CBE  0.020
 D77  plan-1  OAE  0.020
 D77  plan-1  CBI  0.020
 D77  plan-1  CBC  0.020
 D77  plan-1  H12  0.020
 D77  plan-1  H13  0.020
 D77  plan-2  OAV  0.020
 D77  plan-2  CAX  0.020
 D77  plan-2  OAC  0.020
 D77  plan-2  CBK  0.020

