# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:15:36 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (8R)-5-(4-amino-3-bromophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)N1N=C(c2ccc(N)c(Br)c2)c3cc4OCOc4cc3C[C@H]1C
#
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
 GYB  GYB  (8R)-5-(4-amino-3-bromophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide  ligand  46  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYB
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
 GYB  CAH  C   CH3   0  -0.507   1.0231   4.1625   2.8096
 GYB  NAI  N   NH1   0  -0.670   0.9643   3.1223   1.8133
 GYB  CAJ  C   C     0   0.737   1.8623   3.0649   0.8103
 GYB  OAS  O   O     0  -0.544   2.8191   3.8293   0.7346
 GYB  NAK  N   NT    0  -0.411   1.6830   2.0439  -0.1048
 GYB  NAL  N   N     0  -0.291   0.4444   1.4042  -0.0522
 GYB  CAB  C   CH1   0  -0.052   2.3132   2.1976  -1.4216
 GYB  CAA  C   CH3   0  -0.671   1.6644   3.2914  -2.2610
 GYB  CAC  C   CH2   0  -0.581   2.2953   0.8637  -2.1666
 GYB  CAD  C   CR6   0   0.143   2.6224  -0.2955  -1.2749
 GYB  CAE  C   CR16  0  -0.418   3.8154  -1.0101  -1.4348
 GYB  CAF  C   CR56  0   0.321   4.0400  -2.0659  -0.5859
 GYB  OAG  O   O     0  -0.481   5.1117  -2.8845  -0.5263
 GYB  CAR  C   CH2   0   0.068   4.7828  -3.9078   0.4077
 GYB  OAQ  O   O     0  -0.486   3.6155  -3.4799   1.0951
 GYB  CAP  C   CR56  0   0.299   3.1275  -2.4280   0.3931
 GYB  CAO  C   CR16  0  -0.358   1.9478  -1.7552   0.5636
 GYB  CAN  C   CR6   0  -0.015   1.7057  -0.6659  -0.2918
 GYB  CAM  C   C     0   0.211   0.4681   0.1229  -0.1237
 GYB  CAU  C   CR6   0   0.007  -0.8179  -0.5835  -0.0217
 GYB  CAV  C   CR16  0  -0.260  -1.9112   0.0144   0.6056
 GYB  CAY  C   CR6   0  -0.169  -3.1236  -0.6377   0.6893
 GYB  BR1  BR  BR    0  -0.043  -4.5492   0.2163   1.5936
 GYB  CAX  C   CR6   0   0.374  -3.3221  -1.9161   0.1340
 GYB  NBA  N   NH2   0  -0.849  -4.4916  -2.6006   0.2371
 GYB  CAW  C   CR16  0  -0.321  -2.2146  -2.4952  -0.5069
 GYB  CAT  C   CR16  0  -0.286  -0.9982  -1.8526  -0.5764
 GYB  H1   H   HCH3  0   0.245   0.2246   3.9908   3.5262
 GYB  H2   H   HCH3  0   0.234   1.9693   4.1465   3.3499
 GYB  H3   H   HCH3  0   0.228   0.8916   5.1600   2.3849
 GYB  H4   H   HNH1  0   0.404   0.1316   2.5619   1.7487
 GYB  H6   H   HCH1  0   0.262   3.3530   2.4588  -1.2248
 GYB  H7   H   HCH3  0   0.242   1.7244   4.2607  -1.7677
 GYB  H8   H   HCH3  0   0.234   2.1693   3.3788  -3.2241
 GYB  H9   H   HCH3  0   0.227   0.6145   3.0640  -2.4530
 GYB  H10  H   HCH2  0   0.255   1.3141   0.7118  -2.6269
 GYB  H11  H   HCH2  0   0.278   3.0103   0.9259  -2.9880
 GYB  H12  H   HCR6  0   0.272   4.5313  -0.7341  -2.1981
 GYB  H13  H   HCH2  0   0.237   4.5813  -4.8423  -0.1258
 GYB  H14  H   HCR6  0   0.279   1.2404  -2.0382   1.3318
 GYB  H16  H   HCR6  0   0.275  -1.7991   0.9989   1.0396
 GYB  H17  H   HNH2  0   0.395  -5.3497  -2.0940   0.3786
 GYB  H18  H   HNH2  0   0.397  -4.5974  -3.4076  -0.3551
 GYB  H19  H   HCR6  0   0.274  -2.3307  -3.4722  -0.9599
 GYB  H20  H   HCR6  0   0.267  -0.1832  -2.3412  -1.0937
 GYB  H5   H   HCH2  0   0.248   5.6022  -4.0380   1.1141

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
 GYB  NBA  CAX  single    1.359  0.020  1.359
 GYB  BR1  CAY  single    1.892  0.020  1.892
 GYB  CAX  CAY  aromatic  1.408  0.020  1.408
 GYB  CAX  CAW  aromatic  1.405  0.020  1.405
 GYB  CAY  CAV  aromatic  1.379  0.020  1.379
 GYB  CAW  CAT  aromatic  1.377  0.020  1.377
 GYB  CAV  CAU  aromatic  1.395  0.020  1.395
 GYB  CAT  CAU  aromatic  1.397  0.020  1.397
 GYB  CAU  CAM  single    1.471  0.020  1.471
 GYB  NAI  CAH  single    1.442  0.020  1.442
 GYB  NAI  CAJ  single    1.347  0.020  1.347
 GYB  CAM  NAL  double    1.283  0.020  1.283
 GYB  CAM  CAN  single    1.477  0.020  1.477
 GYB  NAL  NAK  single    1.395  0.020  1.395
 GYB  CAO  CAN  aromatic  1.406  0.020  1.406
 GYB  CAO  CAP  aromatic  1.369  0.020  1.369
 GYB  CAN  CAD  aromatic  1.394  0.020  1.394
 GYB  CAJ  NAK  single    1.383  0.020  1.383
 GYB  CAJ  OAS  double    1.227  0.020  1.227
 GYB  NAK  CAB  single    1.468  0.020  1.468
 GYB  OAQ  CAP  single    1.355  0.020  1.355
 GYB  OAQ  CAR  single    1.421  0.020  1.421
 GYB  CAP  CAF  aromatic  1.386  0.020  1.386
 GYB  CAD  CAC  single    1.499  0.020  1.499
 GYB  CAD  CAE  aromatic  1.400  0.020  1.400
 GYB  CAB  CAC  single    1.528  0.020  1.528
 GYB  CAB  CAA  single    1.524  0.020  1.524
 GYB  CAR  OAG  single    1.424  0.020  1.424
 GYB  CAF  CAE  aromatic  1.373  0.020  1.373
 GYB  CAF  OAG  single    1.350  0.020  1.350
 GYB  CAH  H1   single    0.970  0.020  1.090
 GYB  CAH  H2   single    0.970  0.020  1.090
 GYB  CAH  H3   single    0.970  0.020  1.090
 GYB  NAI  H4   single    0.860  0.020  1.020
 GYB  CAB  H6   single    0.970  0.020  1.090
 GYB  CAA  H7   single    0.970  0.020  1.090
 GYB  CAA  H8   single    0.970  0.020  1.090
 GYB  CAA  H9   single    0.970  0.020  1.090
 GYB  CAC  H10  single    0.970  0.020  1.090
 GYB  CAC  H11  single    0.970  0.020  1.090
 GYB  CAE  H12  single    0.930  0.020  1.080
 GYB  CAR  H13  single    0.970  0.020  1.090
 GYB  CAO  H14  single    0.930  0.020  1.080
 GYB  CAV  H16  single    0.930  0.020  1.080
 GYB  NBA  H17  single    0.890  0.020  1.040
 GYB  NBA  H18  single    0.890  0.020  1.040
 GYB  CAW  H19  single    0.930  0.020  1.080
 GYB  CAT  H20  single    0.930  0.020  1.080
 GYB  CAR  H5   single    0.970  0.020  1.090

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
 GYB  H3   CAH  H2   108.11  3.000
 GYB  H3   CAH  H1   108.19  3.000
 GYB  H2   CAH  H1   107.98  3.000
 GYB  H3   CAH  NAI  112.67  3.000
 GYB  H2   CAH  NAI  111.57  3.000
 GYB  H1   CAH  NAI  108.17  3.000
 GYB  H4   NAI  CAJ  118.69  3.000
 GYB  H4   NAI  CAH  118.71  3.000
 GYB  CAJ  NAI  CAH  121.19  3.000
 GYB  NAK  CAJ  OAS  121.35  3.000
 GYB  OAS  CAJ  NAI  122.62  3.000
 GYB  NAK  CAJ  NAI  115.95  3.000
 GYB  CAB  NAK  NAL  117.58  3.000
 GYB  CAB  NAK  CAJ  117.43  3.000
 GYB  NAL  NAK  CAJ  115.39  3.000
 GYB  CAM  NAL  NAK  116.06  3.000
 GYB  H6   CAB  CAC  107.96  3.000
 GYB  H6   CAB  CAA  109.49  3.000
 GYB  CAC  CAB  CAA  110.68  3.000
 GYB  H6   CAB  NAK  105.82  3.000
 GYB  CAA  CAB  NAK  112.74  3.000
 GYB  CAC  CAB  NAK  109.93  3.000
 GYB  H9   CAA  H8   107.85  3.000
 GYB  H9   CAA  H7   108.55  3.000
 GYB  H8   CAA  H7   107.64  3.000
 GYB  H9   CAA  CAB  110.92  3.000
 GYB  H8   CAA  CAB  110.29  3.000
 GYB  H7   CAA  CAB  111.46  3.000
 GYB  H11  CAC  H10  106.19  3.000
 GYB  H11  CAC  CAD  110.43  3.000
 GYB  H10  CAC  CAD  109.79  3.000
 GYB  H11  CAC  CAB  108.04  3.000
 GYB  H10  CAC  CAB  109.68  3.000
 GYB  CAD  CAC  CAB  112.50  3.000
 GYB  CAN  CAD  CAE  120.35  3.000
 GYB  CAE  CAD  CAC  120.86  3.000
 GYB  CAN  CAD  CAC  118.78  3.000
 GYB  H12  CAE  CAF  121.59  3.000
 GYB  H12  CAE  CAD  120.94  3.000
 GYB  CAF  CAE  CAD  117.47  3.000
 GYB  CAP  CAF  OAG  109.45  3.000
 GYB  OAG  CAF  CAE  128.57  3.000
 GYB  CAP  CAF  CAE  121.98  3.000
 GYB  CAR  OAG  CAF  106.34  3.000
 GYB  H5   CAR  H13  110.63  3.000
 GYB  H5   CAR  OAQ  109.89  3.000
 GYB  H13  CAR  OAQ  109.98  3.000
 GYB  H5   CAR  OAG  109.72  3.000
 GYB  H13  CAR  OAG  109.65  3.000
 GYB  OAQ  CAR  OAG  106.90  3.000
 GYB  CAP  OAQ  CAR  106.20  3.000
 GYB  CAO  CAP  OAQ  128.85  3.000
 GYB  OAQ  CAP  CAF  109.36  3.000
 GYB  CAO  CAP  CAF  121.79  3.000
 GYB  H14  CAO  CAN  121.47  3.000
 GYB  H14  CAO  CAP  121.56  3.000
 GYB  CAN  CAO  CAP  116.96  3.000
 GYB  CAM  CAN  CAO  119.25  3.000
 GYB  CAO  CAN  CAD  121.44  3.000
 GYB  CAM  CAN  CAD  119.29  3.000
 GYB  CAU  CAM  CAN  118.95  3.000
 GYB  CAN  CAM  NAL  123.70  3.000
 GYB  CAU  CAM  NAL  117.35  3.000
 GYB  CAT  CAU  CAV  117.83  3.000
 GYB  CAT  CAU  CAM  121.45  3.000
 GYB  CAV  CAU  CAM  120.70  3.000
 GYB  H16  CAV  CAY  119.80  3.000
 GYB  H16  CAV  CAU  119.29  3.000
 GYB  CAY  CAV  CAU  120.90  3.000
 GYB  CAX  CAY  BR1  119.49  3.000
 GYB  CAX  CAY  CAV  121.96  3.000
 GYB  BR1  CAY  CAV  118.55  3.000
 GYB  CAW  CAX  NBA  120.37  3.000
 GYB  CAW  CAX  CAY  116.31  3.000
 GYB  NBA  CAX  CAY  123.28  3.000
 GYB  H18  NBA  H17  113.37  3.000
 GYB  H18  NBA  CAX  116.71  3.000
 GYB  H17  NBA  CAX  119.40  3.000
 GYB  H19  CAW  CAT  119.63  3.000
 GYB  H19  CAW  CAX  118.57  3.000
 GYB  CAT  CAW  CAX  121.80  3.000
 GYB  H20  CAT  CAW  118.60  3.000
 GYB  H20  CAT  CAU  120.20  3.000
 GYB  CAW  CAT  CAU  121.19  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
 GYB  CONST_01  CAP  CAF  CAE  CAD     0.00   0.0  0
 GYB  CONST_02  CAO  CAP  CAF  CAE     0.00   0.0  0
 GYB  CONST_03  CAN  CAO  CAP  CAF     0.00   0.0  0
 GYB  CONST_04  CAX  CAY  CAV  CAU     0.00   0.0  0
 GYB  CONST_05  CAX  CAW  CAT  CAU     0.00   0.0  0
 GYB  CONST_06  CAW  CAX  CAY  CAV     0.00   0.0  0
 GYB  CONST_07  CAW  CAT  CAU  CAV     0.00   0.0  0
 GYB  CONST_08  CAT  CAW  CAX  CAY     0.00   0.0  0
 GYB  CONST_09  CAT  CAU  CAV  CAY     0.00   0.0  0
 GYB  CONST_10  CAY  CAV  CAU  CAM   180.00   0.0  0
 GYB  CONST_11  CAW  CAT  CAU  CAM   180.00   0.0  0
 GYB  CONST_12  BR1  CAY  CAV  CAU   180.00   0.0  0
 GYB  CONST_13  NBA  CAX  CAY  CAV   180.00   0.0  0
 GYB  CONST_14  CAW  CAX  CAY  BR1   180.00   0.0  0
 GYB  CONST_15  CAT  CAW  CAX  NBA   180.00   0.0  0
 GYB  CONST_16  H14  CAO  CAP  CAF   180.00   0.0  0
 GYB  CONST_17  H12  CAE  CAF  OAG     0.00   0.0  0
 GYB  CONST_18  H16  CAV  CAU  CAM     0.00   0.0  0
 GYB  CONST_19  H20  CAT  CAU  CAM     0.00   0.0  0
 GYB  CONST_20  H19  CAW  CAT  CAU   180.00   0.0  0
 GYB  CONST_22  H18  NBA  CAX  CAY   180.00   0.0  0
 GYB  CONST_23  NAK  CAJ  NAI  CAH   180.00   0.0  0
 GYB  CONST_24  H4   NAI  CAJ  NAK     0.00   0.0  0
 GYB  CONST_25  OAS  CAJ  NAI  CAH     0.00   0.0  0
 GYB  Var_01    OAQ  CAR  OAG  CAF   -12.78  30.0  1
 GYB  Var_02    CAO  CAP  OAQ  CAR   172.52  30.0  1
 GYB  Var_03    CAP  CAF  OAG  CAR     7.77  30.0  1
 GYB  Var_04    H1   CAH  NAI  CAJ  -178.40  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
 GYB  chir_01  CAB  NAK  CAC  CAA  negativ

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
 GYB  plan-1  CAM  0.020
 GYB  plan-1  CAU  0.020
 GYB  plan-1  CAV  0.020
 GYB  plan-1  CAY  0.020
 GYB  plan-1  BR1  0.020
 GYB  plan-1  CAX  0.020
 GYB  plan-1  NBA  0.020
 GYB  plan-1  CAW  0.020
 GYB  plan-1  CAT  0.020
 GYB  plan-1  H16  0.020
 GYB  plan-1  H19  0.020
 GYB  plan-1  H20  0.020
 GYB  plan-2  CAC  0.020
 GYB  plan-2  CAD  0.020
 GYB  plan-2  CAE  0.020
 GYB  plan-2  CAF  0.020
 GYB  plan-2  OAG  0.020
 GYB  plan-2  OAQ  0.020
 GYB  plan-2  CAP  0.020
 GYB  plan-2  CAO  0.020
 GYB  plan-2  CAN  0.020
 GYB  plan-2  CAM  0.020
 GYB  plan-2  H12  0.020
 GYB  plan-2  H14  0.020
 GYB  plan-3  CAH  0.020
 GYB  plan-3  NAI  0.020
 GYB  plan-3  CAJ  0.020
 GYB  plan-3  OAS  0.020
 GYB  plan-3  NAK  0.020
 GYB  plan-3  NAL  0.020
 GYB  plan-3  CAB  0.020
 GYB  plan-3  H4   0.020
 GYB  plan-4  CAX  0.020
 GYB  plan-4  NBA  0.020
 GYB  plan-4  H17  0.020
 GYB  plan-4  H18  0.020

