# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:56:11 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-~{N}-ethyl-pent-4-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@H](CC=C)[C@@H]1N=C(c2ccc(Cl)cc2)c3cc(OC)ccc3n4c(C)nnc14
#
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
 9J8  9J8  (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-~{N}-ethyl-pent-4-enamide  ligand  59  33  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9J8
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
 9J8  CBG  C   CH3   0  -0.706   0.5696   3.6075  -2.3201
 9J8  CBF  C   CH2   0  -0.263  -0.2304   3.8587  -1.0568
 9J8  NBE  N   NH1   0  -0.630  -1.0121   2.6864  -0.7113
 9J8  CAZ  C   C     0   0.586  -1.6220   2.5363   0.4700
 9J8  OBD  O   O     0  -0.493  -1.6137   3.3965   1.3397
 9J8  CAS  C   CH1   0  -0.403  -2.3167   1.2001   0.6912
 9J8  CBA  C   CH2   0  -0.483  -3.7772   1.4021   1.1108
 9J8  CBB  C   C1    0  -0.160  -4.5828   2.0818   0.0486
 9J8  CBC  C   C2    0  -0.532  -5.5702   1.5092  -0.6294
 9J8  CAJ  C   CH1   0  -0.230  -1.5452   0.4524   1.8050
 9J8  NAI  N   N     0  -0.337  -0.1014   0.5339   1.6800
 9J8  CAK  C   CR5   0   0.415  -1.9355  -0.9753   1.9591
 9J8  NAO  N   N     0  -0.318  -2.4559  -1.5339   3.0070
 9J8  NAP  N   N     0  -0.337  -2.5307  -2.8682   2.7699
 9J8  CAQ  C   CR5   0   0.396  -2.0504  -3.1048   1.5831
 9J8  CAR  C   CH3   0  -0.761  -1.9066  -4.4438   0.9644
 9J8  NAL  N   NR5   0  -0.588  -1.6591  -1.9225   1.0188
 9J8  CAM  C   CR6   0   0.283  -1.1298  -1.6688  -0.2620
 9J8  CAT  C   CR16  0  -0.248  -1.6800  -2.2856  -1.3739
 9J8  CAU  C   CR16  0  -0.385  -1.2073  -2.0212  -2.6483
 9J8  CAV  C   CR6   0   0.427  -0.1738  -1.1041  -2.8249
 9J8  OAX  O   O2    0  -0.462   0.3441  -0.7590  -4.0094
 9J8  CAY  C   CH3   0  -0.443  -0.1948  -1.3445  -5.1816
 9J8  CAW  C   CR16  0  -0.409   0.3753  -0.4813  -1.7057
 9J8  CAN  C   CR6   0   0.002  -0.0865  -0.7500  -0.4238
 9J8  CAH  C   C     0   0.230   0.5195   0.0032   0.7068
 9J8  CAA  C   CR6   0   0.031   1.9902   0.1936   0.6717
 9J8  CAB  C   CR16  0  -0.287   2.5449   1.3850   1.1347
 9J8  CAC  C   CR16  0  -0.197   3.9162   1.5749   1.1359
 9J8  CAD  C   CR6   0  -0.046   4.7395   0.5534   0.6847
 9J8  CLA  CL  CL    0  -0.118   6.4546   0.7808   0.6873
 9J8  CAE  C   CR16  0  -0.192   4.2126  -0.6447   0.2286
 9J8  CAF  C   CR16  0  -0.284   2.8373  -0.8140   0.2160
 9J8  HBI  H   HCH3  0   0.252   1.1598   4.4886  -2.5669
 9J8  HBJ  H   HCH3  0   0.231   1.2584   2.7706  -2.1946
 9J8  HBH  H   HCH3  0   0.238  -0.0798   3.3944  -3.1703
 9J8  HBG  H   HCH2  0   0.238   0.4419   4.0943  -0.2298
 9J8  HBF  H   HCH2  0   0.240  -0.8861   4.7227  -1.1902
 9J8  HBK  H   HNH1  0   0.398  -1.0889   1.9522  -1.3969
 9J8  HAU  H   HCH1  0   0.274  -2.3127   0.6175  -0.2326
 9J8  HBB  H   HCH2  0   0.260  -4.2184   0.4304   1.3457
 9J8  HBA  H   HCH2  0   0.251  -3.7982   1.9935   2.0308
 9J8  HBC  H   H     0   0.249  -4.3245   3.1144  -0.1702
 9J8  HBE  H   H     0   0.236  -5.8685   0.4835  -0.4455
 9J8  HBD  H   H     0   0.239  -6.1185   2.0465  -1.3921
 9J8  HAJ  H   HCH1  0   0.293  -1.8083   0.9369   2.7473
 9J8  HAS  H   HCH3  0   0.269  -2.6815  -4.6404   0.2235
 9J8  HAT  H   HCH3  0   0.269  -0.9391  -4.5549   0.4754
 9J8  HAR  H   HCH3  0   0.282  -1.9912  -5.2004   1.7408
 9J8  HAV  H   HCR6  0   0.289  -2.5096  -2.9691  -1.2633
 9J8  HAW  H   HCR6  0   0.300  -1.6709  -2.5253  -3.4845
 9J8  HA0  H   HCH3  0   0.235  -0.0775  -2.4306  -5.1832
 9J8  HAZ  H   HCH3  0   0.236  -1.2519  -1.0994  -5.3069
 9J8  HAY  H   HCH3  0   0.266   0.3641  -0.9296  -6.0158
 9J8  HAX  H   HCR6  0   0.286   1.1781   0.2308  -1.8498
 9J8  HAB  H   HCR6  0   0.267   1.8986   2.1769   1.4894
 9J8  HAC  H   HCR6  0   0.286   4.3366   2.5084   1.4835
 9J8  HAE  H   HCR6  0   0.286   4.8615  -1.4387  -0.1144
 9J8  HAF  H   HCR6  0   0.274   2.4320  -1.7515  -0.1418

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
 9J8  CLA  CAD  single    1.730  0.020  1.730
 9J8  CAD  CAE  aromatic  1.386  0.020  1.386
 9J8  CAD  CAC  aromatic  1.387  0.020  1.387
 9J8  CAE  CAF  aromatic  1.386  0.020  1.386
 9J8  CAC  CAB  aromatic  1.384  0.020  1.384
 9J8  CAF  CAA  aromatic  1.393  0.020  1.393
 9J8  CAB  CAA  aromatic  1.393  0.020  1.393
 9J8  CAA  CAH  single    1.483  0.020  1.483
 9J8  OBD  CAZ  double    1.223  0.020  1.223
 9J8  CBG  CBF  single    1.516  0.020  1.516
 9J8  NBE  CAZ  single    1.338  0.020  1.338
 9J8  NBE  CBF  single    1.451  0.020  1.451
 9J8  CAH  NAI  double    1.271  0.020  1.271
 9J8  CAH  CAN  single    1.488  0.020  1.488
 9J8  NAI  CAJ  single    1.451  0.020  1.451
 9J8  CAZ  CAS  single    1.522  0.020  1.522
 9J8  CAW  CAN  aromatic  1.389  0.020  1.389
 9J8  CAW  CAV  aromatic  1.393  0.020  1.393
 9J8  OAX  CAV  single    1.338  0.020  1.338
 9J8  OAX  CAY  single    1.417  0.020  1.417
 9J8  CAN  CAM  aromatic  1.400  0.020  1.400
 9J8  CAS  CAJ  single    1.548  0.020  1.548
 9J8  CAS  CBA  single    1.533  0.020  1.533
 9J8  CAJ  CAK  single    1.488  0.020  1.488
 9J8  CAV  CAU  aromatic  1.393  0.020  1.393
 9J8  CAK  NAL  aromatic  1.363  0.020  1.363
 9J8  CAK  NAO  aromatic  1.296  0.020  1.296
 9J8  CAM  NAL  aromatic  1.409  0.020  1.409
 9J8  CAM  CAT  aromatic  1.385  0.020  1.385
 9J8  CBA  CBB  single    1.496  0.020  1.496
 9J8  CAU  CAT  aromatic  1.385  0.020  1.385
 9J8  NAL  CAQ  aromatic  1.367  0.020  1.367
 9J8  NAO  NAP  aromatic  1.357  0.020  1.357
 9J8  CBB  CBC  double    1.328  0.020  1.328
 9J8  CAQ  NAP  aromatic  1.302  0.020  1.302
 9J8  CAQ  CAR  single    1.482  0.020  1.482
 9J8  CBG  HBI  single    0.970  0.020  1.090
 9J8  CBG  HBJ  single    0.970  0.020  1.090
 9J8  CBG  HBH  single    0.970  0.020  1.090
 9J8  CBF  HBG  single    0.970  0.020  1.090
 9J8  CBF  HBF  single    0.970  0.020  1.090
 9J8  NBE  HBK  single    0.860  0.020  1.020
 9J8  CAS  HAU  single    0.970  0.020  1.090
 9J8  CBA  HBB  single    0.970  0.020  1.090
 9J8  CBA  HBA  single    0.970  0.020  1.090
 9J8  CBB  HBC  single    0.930  0.020  1.080
 9J8  CBC  HBE  single    0.930  0.020  1.080
 9J8  CBC  HBD  single    0.930  0.020  1.080
 9J8  CAJ  HAJ  single    0.970  0.020  1.090
 9J8  CAR  HAS  single    0.970  0.020  1.090
 9J8  CAR  HAT  single    0.970  0.020  1.090
 9J8  CAR  HAR  single    0.970  0.020  1.090
 9J8  CAT  HAV  single    0.930  0.020  1.080
 9J8  CAU  HAW  single    0.930  0.020  1.080
 9J8  CAY  HA0  single    0.970  0.020  1.090
 9J8  CAY  HAZ  single    0.970  0.020  1.090
 9J8  CAY  HAY  single    0.970  0.020  1.090
 9J8  CAW  HAX  single    0.930  0.020  1.080
 9J8  CAB  HAB  single    0.930  0.020  1.080
 9J8  CAC  HAC  single    0.930  0.020  1.080
 9J8  CAE  HAE  single    0.930  0.020  1.080
 9J8  CAF  HAF  single    0.930  0.020  1.080

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
 9J8  HBH  CBG  HBJ  108.39  3.000
 9J8  HBH  CBG  HBI  107.71  3.000
 9J8  HBJ  CBG  HBI  107.73  3.000
 9J8  HBH  CBG  CBF  111.57  3.000
 9J8  HBJ  CBG  CBF  111.36  3.000
 9J8  HBI  CBG  CBF  109.93  3.000
 9J8  HBF  CBF  HBG  106.94  3.000
 9J8  HBF  CBF  NBE  110.16  3.000
 9J8  HBG  CBF  NBE  109.02  3.000
 9J8  HBF  CBF  CBG  110.23  3.000
 9J8  HBG  CBF  CBG  110.00  3.000
 9J8  NBE  CBF  CBG  110.42  3.000
 9J8  HBK  NBE  CAZ  118.97  3.000
 9J8  HBK  NBE  CBF  117.90  3.000
 9J8  CAZ  NBE  CBF  123.13  3.000
 9J8  CAS  CAZ  OBD  121.14  3.000
 9J8  CAS  CAZ  NBE  115.78  3.000
 9J8  OBD  CAZ  NBE  123.08  3.000
 9J8  HAU  CAS  CAJ  110.44  3.000
 9J8  HAU  CAS  CBA  107.78  3.000
 9J8  CAJ  CAS  CBA  109.98  3.000
 9J8  HAU  CAS  CAZ  110.10  3.000
 9J8  CBA  CAS  CAZ  111.03  3.000
 9J8  CAJ  CAS  CAZ  107.52  3.000
 9J8  HBA  CBA  HBB  107.00  3.000
 9J8  HBA  CBA  CBB  109.94  3.000
 9J8  HBB  CBA  CBB  109.82  3.000
 9J8  HBA  CBA  CAS  108.64  3.000
 9J8  HBB  CBA  CAS  109.05  3.000
 9J8  CBB  CBA  CAS  112.24  3.000
 9J8  HBC  CBB  CBC  118.93  3.000
 9J8  HBC  CBB  CBA  116.53  3.000
 9J8  CBC  CBB  CBA  124.54  3.000
 9J8  HBD  CBC  HBE  116.74  3.000
 9J8  HBD  CBC  CBB  121.51  3.000
 9J8  HBE  CBC  CBB  121.75  3.000
 9J8  HAJ  CAJ  CAK  105.85  3.000
 9J8  HAJ  CAJ  NAI  106.80  3.000
 9J8  CAK  CAJ  NAI  108.89  3.000
 9J8  HAJ  CAJ  CAS  106.66  3.000
 9J8  CAK  CAJ  CAS  114.03  3.000
 9J8  NAI  CAJ  CAS  114.01  3.000
 9J8  CAH  NAI  CAJ  121.91  3.000
 9J8  NAL  CAK  NAO  109.85  3.000
 9J8  NAO  CAK  CAJ  127.04  3.000
 9J8  NAL  CAK  CAJ  122.83  3.000
 9J8  NAP  NAO  CAK  107.73  3.000
 9J8  CAQ  NAP  NAO  108.51  3.000
 9J8  NAL  CAQ  CAR  125.53  3.000
 9J8  CAR  CAQ  NAP  125.49  3.000
 9J8  NAL  CAQ  NAP  108.94  3.000
 9J8  HAR  CAR  HAT  108.58  3.000
 9J8  HAR  CAR  HAS  107.72  3.000
 9J8  HAT  CAR  HAS  107.92  3.000
 9J8  HAR  CAR  CAQ  108.85  3.000
 9J8  HAT  CAR  CAQ  111.45  3.000
 9J8  HAS  CAR  CAQ  112.20  3.000
 9J8  CAM  NAL  CAQ  129.68  3.000
 9J8  CAQ  NAL  CAK  104.96  3.000
 9J8  CAM  NAL  CAK  125.32  3.000
 9J8  CAN  CAM  CAT  119.70  3.000
 9J8  CAT  CAM  NAL  120.02  3.000
 9J8  CAN  CAM  NAL  120.22  3.000
 9J8  HAV  CAT  CAU  118.50  3.000
 9J8  HAV  CAT  CAM  120.28  3.000
 9J8  CAU  CAT  CAM  121.20  3.000
 9J8  HAW  CAU  CAV  121.82  3.000
 9J8  HAW  CAU  CAT  118.46  3.000
 9J8  CAV  CAU  CAT  119.71  3.000
 9J8  CAW  CAV  OAX  116.31  3.000
 9J8  OAX  CAV  CAU  124.69  3.000
 9J8  CAW  CAV  CAU  119.00  3.000
 9J8  CAY  OAX  CAV  118.60  3.000
 9J8  HAY  CAY  HAZ  108.91  3.000
 9J8  HAY  CAY  HA0  108.86  3.000
 9J8  HAZ  CAY  HA0  109.07  3.000
 9J8  HAY  CAY  OAX  106.36  3.000
 9J8  HAZ  CAY  OAX  111.74  3.000
 9J8  HA0  CAY  OAX  111.79  3.000
 9J8  HAX  CAW  CAN  119.77  3.000
 9J8  HAX  CAW  CAV  118.63  3.000
 9J8  CAN  CAW  CAV  121.59  3.000
 9J8  CAH  CAN  CAW  117.92  3.000
 9J8  CAW  CAN  CAM  118.79  3.000
 9J8  CAH  CAN  CAM  123.24  3.000
 9J8  CAA  CAH  CAN  116.80  3.000
 9J8  CAN  CAH  NAI  126.49  3.000
 9J8  CAA  CAH  NAI  116.68  3.000
 9J8  CAF  CAA  CAB  119.02  3.000
 9J8  CAB  CAA  CAH  119.77  3.000
 9J8  CAF  CAA  CAH  121.19  3.000
 9J8  HAB  CAB  CAC  119.41  3.000
 9J8  HAB  CAB  CAA  119.80  3.000
 9J8  CAC  CAB  CAA  120.79  3.000
 9J8  HAC  CAC  CAD  120.63  3.000
 9J8  HAC  CAC  CAB  120.26  3.000
 9J8  CAD  CAC  CAB  119.11  3.000
 9J8  CAE  CAD  CLA  119.41  3.000
 9J8  CAE  CAD  CAC  121.19  3.000
 9J8  CLA  CAD  CAC  119.41  3.000
 9J8  HAE  CAE  CAF  120.20  3.000
 9J8  HAE  CAE  CAD  120.73  3.000
 9J8  CAF  CAE  CAD  119.07  3.000
 9J8  HAF  CAF  CAE  118.72  3.000
 9J8  HAF  CAF  CAA  120.47  3.000
 9J8  CAE  CAF  CAA  120.81  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
 9J8  CONST_01  CAQ  NAP  NAO  CAK     0.00   0.0  0
 9J8  CONST_02  NAL  CAQ  NAP  NAO     0.00   0.0  0
 9J8  CONST_03  CAV  CAU  CAT  CAM     0.00   0.0  0
 9J8  CONST_04  CAW  CAV  CAU  CAT     0.00   0.0  0
 9J8  CONST_05  CAN  CAW  CAV  CAU     0.00   0.0  0
 9J8  CONST_06  CAD  CAE  CAF  CAA     0.00   0.0  0
 9J8  CONST_07  CAD  CAC  CAB  CAA     0.00   0.0  0
 9J8  CONST_08  CAE  CAD  CAC  CAB     0.00   0.0  0
 9J8  CONST_09  CAE  CAF  CAA  CAB     0.00   0.0  0
 9J8  CONST_10  CAF  CAE  CAD  CAC     0.00   0.0  0
 9J8  CONST_11  CAF  CAA  CAB  CAC     0.00   0.0  0
 9J8  CONST_12  CAE  CAF  CAA  CAH   180.00   0.0  0
 9J8  CONST_13  CAC  CAB  CAA  CAH   180.00   0.0  0
 9J8  CONST_14  CAR  CAQ  NAP  NAO   180.00   0.0  0
 9J8  CONST_15  OAX  CAV  CAU  CAT   180.00   0.0  0
 9J8  CONST_16  CAN  CAW  CAV  OAX   180.00   0.0  0
 9J8  CONST_17  CLA  CAD  CAC  CAB   180.00   0.0  0
 9J8  CONST_18  CAF  CAE  CAD  CLA   180.00   0.0  0
 9J8  CONST_19  HAW  CAU  CAT  CAM   180.00   0.0  0
 9J8  CONST_20  HAX  CAW  CAV  CAU   180.00   0.0  0
 9J8  CONST_21  HAV  CAT  CAU  CAV   180.00   0.0  0
 9J8  CONST_22  HAF  CAF  CAA  CAH     0.00   0.0  0
 9J8  CONST_23  HAB  CAB  CAA  CAH     0.00   0.0  0
 9J8  CONST_24  HAE  CAE  CAF  CAA   180.00   0.0  0
 9J8  CONST_25  HAC  CAC  CAB  CAA   180.00   0.0  0
 9J8  CONST_26  OBD  CAZ  NBE  CBF     0.00   0.0  0
 9J8  CONST_27  CAS  CAZ  NBE  CBF   180.00   0.0  0
 9J8  CONST_28  HBK  NBE  CAZ  OBD   180.00   0.0  0
 9J8  Var_01    CAW  CAV  OAX  CAY  -178.86  30.0  2
 9J8  Var_02    HAS  CAR  CAQ  NAP   103.09  30.0  2
 9J8  Var_03    HA0  CAY  OAX  CAV   -61.32  30.0  3
 9J8  Var_04    CAZ  NBE  CBF  CBG   167.74  30.0  1
 9J8  Var_05    CBC  CBB  CBA  CAS   112.95  30.0  3
 9J8  Var_06    HBE  CBC  CBB  CBA     0.44   0.0  2
 9J8  Var_07    HBI  CBG  CBF  NBE  -179.49  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
 9J8  chir_01  CAS  CAZ  CAJ  CBA  negativ
 9J8  chir_02  CAJ  NAI  CAS  CAK  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
 9J8  plan-1  CAH  0.020
 9J8  plan-1  CAA  0.020
 9J8  plan-1  CAB  0.020
 9J8  plan-1  CAC  0.020
 9J8  plan-1  CAD  0.020
 9J8  plan-1  CLA  0.020
 9J8  plan-1  CAE  0.020
 9J8  plan-1  CAF  0.020
 9J8  plan-1  HAB  0.020
 9J8  plan-1  HAC  0.020
 9J8  plan-1  HAE  0.020
 9J8  plan-1  HAF  0.020
 9J8  plan-2  CAJ  0.020
 9J8  plan-2  CAK  0.020
 9J8  plan-2  NAO  0.020
 9J8  plan-2  NAP  0.020
 9J8  plan-2  CAQ  0.020
 9J8  plan-2  CAR  0.020
 9J8  plan-2  NAL  0.020
 9J8  plan-2  CAM  0.020
 9J8  plan-3  NAL  0.020
 9J8  plan-3  CAM  0.020
 9J8  plan-3  CAT  0.020
 9J8  plan-3  CAU  0.020
 9J8  plan-3  CAV  0.020
 9J8  plan-3  OAX  0.020
 9J8  plan-3  CAW  0.020
 9J8  plan-3  CAN  0.020
 9J8  plan-3  CAH  0.020
 9J8  plan-3  HAV  0.020
 9J8  plan-3  HAW  0.020
 9J8  plan-3  HAX  0.020
 9J8  plan-4  CBF  0.020
 9J8  plan-4  NBE  0.020
 9J8  plan-4  CAZ  0.020
 9J8  plan-4  OBD  0.020
 9J8  plan-4  CAS  0.020
 9J8  plan-4  HBK  0.020
 9J8  plan-5  CBA  0.020
 9J8  plan-5  CBB  0.020
 9J8  plan-5  CBC  0.020
 9J8  plan-5  HBC  0.020
 9J8  plan-5  HBE  0.020
 9J8  plan-5  HBD  0.020

