# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:05:51 2020
#   Inital geometry file: a 145 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-butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)[C@H](CC)[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
 9HT  9HT  (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-butanamide  ligand  58  32  .  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_9HT
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
 9HT  CAA  C   CH3   0  -0.704  -0.8895  -3.5213  -2.3998
 9HT  CAN  C   CH2   0  -0.263  -0.0657  -3.8670  -1.1750
 9HT  NAS  N   NH1   0  -0.631   0.8313  -2.7775  -0.8409
 9HT  CAU  C   C     0   0.589   1.5120  -2.7153   0.3096
 9HT  OAE  O   O     0  -0.496   1.4585  -3.5894   1.1642
 9HT  CBD  C   CH1   0  -0.401   2.3486  -1.4604   0.5146
 9HT  CAO  C   CH2   0  -0.416   3.7995  -1.8173   0.8327
 9HT  CAB  C   CH3   0  -0.671   4.5074  -2.4968  -0.3307
 9HT  CBE  C   CH1   0  -0.230   1.7127  -0.6679   1.6811
 9HT  NAP  N   N     0  -0.338   0.2634  -0.5963   1.6205
 9HT  CBC  C   CR5   0   0.415   2.2563   0.7060   1.8547
 9HT  NAR  N   N     0  -0.319   2.8751   1.1755   2.8928
 9HT  NAQ  N   N     0  -0.337   3.0785   2.5017   2.6879
 9HT  CAY  C   CR5   0   0.396   2.5762   2.8229   1.5303
 9HT  CAD  C   CH3   0  -0.762   2.5490   4.1883   0.9551
 9HT  NBF  N   NR5   0  -0.588   2.0407   1.7051   0.9533
 9HT  CBB  C   CR6   0   0.282   1.4293   1.5491  -0.3062
 9HT  CAL  C   CR16  0  -0.250   1.9900   2.1434  -1.4247
 9HT  CAI  C   CR16  0  -0.386   1.4309   1.9794  -2.6808
 9HT  CAX  C   CR6   0   0.427   0.2948   1.1879  -2.8329
 9HT  OAT  O   O2    0  -0.463  -0.3167   0.9513  -3.9995
 9HT  CAC  C   CH3   0  -0.443   0.2288   1.5210  -5.1767
 9HT  CAM  C   CR16  0  -0.407  -0.2632   0.5837  -1.7079
 9HT  CBA  C   CR6   0   0.005   0.2855   0.7532  -0.4430
 9HT  CAV  C   C     0   0.229  -0.3423   0.0251   0.6923
 9HT  CAZ  C   CR6   0   0.030  -1.8251  -0.0286   0.7144
 9HT  CAJ  C   CR16  0  -0.287  -2.4664  -1.1850   1.1537
 9HT  CAG  C   CR16  0  -0.196  -3.8481  -1.2554   1.2008
 9HT  CAW  C   CR6   0  -0.047  -4.5935  -0.1491   0.8201
 9HT  CL   CL  CL    0  -0.118  -6.3210  -0.2278   0.8788
 9HT  CAH  C   CR16  0  -0.193  -3.9793   1.0166   0.3901
 9HT  CAK  C   CR16  0  -0.284  -2.5957   1.0666   0.3308
 9HT  HAA  H   HCH3  0   0.237  -0.2560  -3.3341  -3.2681
 9HT  HAB  H   HCH3  0   0.251  -1.5530  -4.3488  -2.6459
 9HT  HAC  H   HCH3  0   0.229  -1.5098  -2.6395  -2.2308
 9HT  HAT  H   HCH2  0   0.238  -0.7228  -4.0622  -0.3255
 9HT  HAU  H   HCH2  0   0.239   0.5041  -4.7827  -1.3522
 9HT  HBF  H   HNH1  0   0.397   0.9482  -2.0381  -1.5154
 9HT  HBD  H   HCH1  0   0.262   2.3412  -0.8605  -0.3989
 9HT  HAW  H   HCH2  0   0.244   4.3355  -0.9024   1.0978
 9HT  HAV  H   HCH2  0   0.234   3.8252  -2.4580   1.7171
 9HT  HAD  H   HCH3  0   0.227   4.0203  -3.4306  -0.6150
 9HT  HAF  H   HCH3  0   0.225   4.5310  -1.8534  -1.2116
 9HT  HAE  H   HCH3  0   0.240   5.5380  -2.7349  -0.0683
 9HT  HBE  H   HCH1  0   0.290   1.9633  -1.2049   2.5981
 9HT  HAJ  H   HCH3  0   0.270   3.3160   4.3310   0.1937
 9HT  HAK  H   HCH3  0   0.269   1.5821   4.4150   0.5067
 9HT  HAL  H   HCH3  0   0.281   2.7365   4.9065   1.7501
 9HT  HAR  H   HCR6  0   0.290   2.8937   2.7292  -1.3343
 9HT  HAO  H   HCR6  0   0.300   1.9061   2.4613  -3.5233
 9HT  HAG  H   HCH3  0   0.266  -0.4088   1.2004  -5.9961
 9HT  HAH  H   HCH3  0   0.236   0.2303   2.6127  -5.1353
 9HT  HAI  H   HCH3  0   0.236   1.2465   1.1696  -5.3613
 9HT  HAS  H   HCR6  0   0.284  -1.1428  -0.0352  -1.8331
 9HT  HAP  H   HCR6  0   0.267  -1.8805  -2.0435   1.4541
 9HT  HAM  H   HCR6  0   0.285  -4.3364  -2.1632   1.5274
 9HT  HAN  H   HCR6  0   0.286  -4.5674   1.8766   0.1009
 9HT  HAQ  H   HCR6  0   0.273  -2.1226   1.9789  -0.0083

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
 9HT  CL   CAW  single    1.730  0.020  1.730
 9HT  CAW  CAG  aromatic  1.387  0.020  1.387
 9HT  CAW  CAH  aromatic  1.386  0.020  1.386
 9HT  CAG  CAJ  aromatic  1.384  0.020  1.384
 9HT  CAH  CAK  aromatic  1.386  0.020  1.386
 9HT  CAJ  CAZ  aromatic  1.393  0.020  1.393
 9HT  CAK  CAZ  aromatic  1.393  0.020  1.393
 9HT  CAZ  CAV  single    1.484  0.020  1.484
 9HT  CAN  CAA  single    1.516  0.020  1.516
 9HT  CAN  NAS  single    1.450  0.020  1.450
 9HT  NAS  CAU  single    1.338  0.020  1.338
 9HT  CAV  NAP  double    1.271  0.020  1.271
 9HT  CAV  CBA  single    1.488  0.020  1.488
 9HT  NAP  CBE  single    1.452  0.020  1.452
 9HT  CAU  OAE  double    1.224  0.020  1.224
 9HT  CAU  CBD  single    1.522  0.020  1.522
 9HT  CAM  CBA  aromatic  1.389  0.020  1.389
 9HT  CAM  CAX  aromatic  1.394  0.020  1.394
 9HT  CBA  CBB  aromatic  1.400  0.020  1.400
 9HT  CBD  CBE  single    1.547  0.020  1.547
 9HT  CBD  CAO  single    1.528  0.020  1.528
 9HT  OAT  CAX  single    1.338  0.020  1.338
 9HT  OAT  CAC  single    1.417  0.020  1.417
 9HT  CBE  CBC  single    1.488  0.020  1.488
 9HT  CAX  CAI  aromatic  1.393  0.020  1.393
 9HT  CBC  NBF  aromatic  1.363  0.020  1.363
 9HT  CBC  NAR  aromatic  1.297  0.020  1.297
 9HT  CBB  NBF  aromatic  1.409  0.020  1.409
 9HT  CBB  CAL  aromatic  1.385  0.020  1.385
 9HT  CAO  CAB  single    1.522  0.020  1.522
 9HT  NBF  CAY  aromatic  1.367  0.020  1.367
 9HT  NAR  NAQ  aromatic  1.357  0.020  1.357
 9HT  CAI  CAL  aromatic  1.385  0.020  1.385
 9HT  NAQ  CAY  aromatic  1.302  0.020  1.302
 9HT  CAY  CAD  single    1.482  0.020  1.482
 9HT  CAA  HAA  single    0.970  0.020  1.090
 9HT  CAA  HAB  single    0.970  0.020  1.090
 9HT  CAA  HAC  single    0.970  0.020  1.090
 9HT  CAN  HAT  single    0.970  0.020  1.090
 9HT  CAN  HAU  single    0.970  0.020  1.090
 9HT  NAS  HBF  single    0.860  0.020  1.020
 9HT  CBD  HBD  single    0.970  0.020  1.090
 9HT  CAO  HAW  single    0.970  0.020  1.090
 9HT  CAO  HAV  single    0.970  0.020  1.090
 9HT  CAB  HAD  single    0.970  0.020  1.090
 9HT  CAB  HAF  single    0.970  0.020  1.090
 9HT  CAB  HAE  single    0.970  0.020  1.090
 9HT  CBE  HBE  single    0.970  0.020  1.090
 9HT  CAD  HAJ  single    0.970  0.020  1.090
 9HT  CAD  HAK  single    0.970  0.020  1.090
 9HT  CAD  HAL  single    0.970  0.020  1.090
 9HT  CAL  HAR  single    0.930  0.020  1.080
 9HT  CAI  HAO  single    0.930  0.020  1.080
 9HT  CAC  HAG  single    0.970  0.020  1.090
 9HT  CAC  HAH  single    0.970  0.020  1.090
 9HT  CAC  HAI  single    0.970  0.020  1.090
 9HT  CAM  HAS  single    0.930  0.020  1.080
 9HT  CAJ  HAP  single    0.930  0.020  1.080
 9HT  CAG  HAM  single    0.930  0.020  1.080
 9HT  CAH  HAN  single    0.930  0.020  1.080
 9HT  CAK  HAQ  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
 9HT  HAC  CAA  HAB  107.62  3.000
 9HT  HAC  CAA  HAA  108.34  3.000
 9HT  HAB  CAA  HAA  107.72  3.000
 9HT  HAC  CAA  CAN  111.60  3.000
 9HT  HAB  CAA  CAN  109.90  3.000
 9HT  HAA  CAA  CAN  111.51  3.000
 9HT  HAU  CAN  HAT  106.87  3.000
 9HT  HAU  CAN  NAS  110.14  3.000
 9HT  HAT  CAN  NAS  109.11  3.000
 9HT  HAU  CAN  CAA  110.08  3.000
 9HT  HAT  CAN  CAA  110.02  3.000
 9HT  NAS  CAN  CAA  110.54  3.000
 9HT  HBF  NAS  CAU  118.84  3.000
 9HT  HBF  NAS  CAN  117.96  3.000
 9HT  CAU  NAS  CAN  123.20  3.000
 9HT  CBD  CAU  OAE  121.26  3.000
 9HT  CBD  CAU  NAS  115.70  3.000
 9HT  OAE  CAU  NAS  123.02  3.000
 9HT  HBD  CBD  CBE  110.26  3.000
 9HT  HBD  CBD  CAO  107.98  3.000
 9HT  CBE  CBD  CAO  110.68  3.000
 9HT  HBD  CBD  CAU  109.65  3.000
 9HT  CAO  CBD  CAU  110.94  3.000
 9HT  CBE  CBD  CAU  107.34  3.000
 9HT  HAV  CAO  HAW  106.44  3.000
 9HT  HAV  CAO  CAB  110.25  3.000
 9HT  HAW  CAO  CAB  109.33  3.000
 9HT  HAV  CAO  CBD  109.15  3.000
 9HT  HAW  CAO  CBD  108.70  3.000
 9HT  CAB  CAO  CBD  112.77  3.000
 9HT  HAE  CAB  HAF  107.63  3.000
 9HT  HAE  CAB  HAD  107.34  3.000
 9HT  HAF  CAB  HAD  107.69  3.000
 9HT  HAE  CAB  CAO  110.70  3.000
 9HT  HAF  CAB  CAO  111.34  3.000
 9HT  HAD  CAB  CAO  111.94  3.000
 9HT  HBE  CBE  CBC  105.81  3.000
 9HT  HBE  CBE  NAP  106.76  3.000
 9HT  CBC  CBE  NAP  108.91  3.000
 9HT  HBE  CBE  CBD  106.68  3.000
 9HT  CBC  CBE  CBD  114.26  3.000
 9HT  NAP  CBE  CBD  113.82  3.000
 9HT  CAV  NAP  CBE  122.02  3.000
 9HT  NBF  CBC  NAR  109.85  3.000
 9HT  NAR  CBC  CBE  127.03  3.000
 9HT  NBF  CBC  CBE  122.83  3.000
 9HT  NAQ  NAR  CBC  107.73  3.000
 9HT  CAY  NAQ  NAR  108.51  3.000
 9HT  NBF  CAY  CAD  125.61  3.000
 9HT  CAD  CAY  NAQ  125.41  3.000
 9HT  NBF  CAY  NAQ  108.95  3.000
 9HT  HAL  CAD  HAK  108.44  3.000
 9HT  HAL  CAD  HAJ  107.62  3.000
 9HT  HAK  CAD  HAJ  108.04  3.000
 9HT  HAL  CAD  CAY  108.76  3.000
 9HT  HAK  CAD  CAY  111.58  3.000
 9HT  HAJ  CAD  CAY  112.26  3.000
 9HT  CBB  NBF  CAY  129.64  3.000
 9HT  CAY  NBF  CBC  104.97  3.000
 9HT  CBB  NBF  CBC  125.37  3.000
 9HT  CBA  CBB  CAL  119.71  3.000
 9HT  CAL  CBB  NBF  119.92  3.000
 9HT  CBA  CBB  NBF  120.32  3.000
 9HT  HAR  CAL  CAI  118.54  3.000
 9HT  HAR  CAL  CBB  120.23  3.000
 9HT  CAI  CAL  CBB  121.21  3.000
 9HT  HAO  CAI  CAX  121.80  3.000
 9HT  HAO  CAI  CAL  118.48  3.000
 9HT  CAX  CAI  CAL  119.72  3.000
 9HT  CAM  CAX  OAT  116.37  3.000
 9HT  OAT  CAX  CAI  124.63  3.000
 9HT  CAM  CAX  CAI  119.00  3.000
 9HT  CAC  OAT  CAX  118.51  3.000
 9HT  HAI  CAC  HAH  109.06  3.000
 9HT  HAI  CAC  HAG  108.93  3.000
 9HT  HAH  CAC  HAG  108.92  3.000
 9HT  HAI  CAC  OAT  111.69  3.000
 9HT  HAH  CAC  OAT  111.76  3.000
 9HT  HAG  CAC  OAT  106.38  3.000
 9HT  HAS  CAM  CBA  119.73  3.000
 9HT  HAS  CAM  CAX  118.66  3.000
 9HT  CBA  CAM  CAX  121.60  3.000
 9HT  CAV  CBA  CAM  117.94  3.000
 9HT  CAM  CBA  CBB  118.75  3.000
 9HT  CAV  CBA  CBB  123.26  3.000
 9HT  CAZ  CAV  CBA  116.79  3.000
 9HT  CBA  CAV  NAP  126.56  3.000
 9HT  CAZ  CAV  NAP  116.60  3.000
 9HT  CAK  CAZ  CAJ  119.00  3.000
 9HT  CAK  CAZ  CAV  121.34  3.000
 9HT  CAJ  CAZ  CAV  119.64  3.000
 9HT  HAP  CAJ  CAG  119.39  3.000
 9HT  HAP  CAJ  CAZ  119.79  3.000
 9HT  CAG  CAJ  CAZ  120.81  3.000
 9HT  HAM  CAG  CAW  120.65  3.000
 9HT  HAM  CAG  CAJ  120.24  3.000
 9HT  CAW  CAG  CAJ  119.11  3.000
 9HT  CAH  CAW  CL   119.42  3.000
 9HT  CAH  CAW  CAG  121.18  3.000
 9HT  CL   CAW  CAG  119.40  3.000
 9HT  HAN  CAH  CAK  120.19  3.000
 9HT  HAN  CAH  CAW  120.73  3.000
 9HT  CAK  CAH  CAW  119.08  3.000
 9HT  HAQ  CAK  CAH  118.71  3.000
 9HT  HAQ  CAK  CAZ  120.48  3.000
 9HT  CAH  CAK  CAZ  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
 9HT  CONST_01  CAY  NAQ  NAR  CBC     0.00   0.0  0
 9HT  CONST_02  NBF  CAY  NAQ  NAR     0.00   0.0  0
 9HT  CONST_03  CAX  CAI  CAL  CBB     0.00   0.0  0
 9HT  CONST_04  CAM  CAX  CAI  CAL     0.00   0.0  0
 9HT  CONST_05  CBA  CAM  CAX  CAI     0.00   0.0  0
 9HT  CONST_06  CAW  CAG  CAJ  CAZ     0.00   0.0  0
 9HT  CONST_07  CAW  CAH  CAK  CAZ     0.00   0.0  0
 9HT  CONST_08  CAH  CAW  CAG  CAJ     0.00   0.0  0
 9HT  CONST_09  CAH  CAK  CAZ  CAJ     0.00   0.0  0
 9HT  CONST_10  CAK  CAH  CAW  CAG     0.00   0.0  0
 9HT  CONST_11  CAK  CAZ  CAJ  CAG     0.00   0.0  0
 9HT  CONST_12  CAG  CAJ  CAZ  CAV   180.00   0.0  0
 9HT  CONST_13  CAH  CAK  CAZ  CAV   180.00   0.0  0
 9HT  CONST_14  CAD  CAY  NAQ  NAR   180.00   0.0  0
 9HT  CONST_15  OAT  CAX  CAI  CAL   180.00   0.0  0
 9HT  CONST_16  CBA  CAM  CAX  OAT   180.00   0.0  0
 9HT  CONST_17  CL   CAW  CAG  CAJ   180.00   0.0  0
 9HT  CONST_18  CAK  CAH  CAW  CL    180.00   0.0  0
 9HT  CONST_19  HAO  CAI  CAL  CBB   180.00   0.0  0
 9HT  CONST_20  HAS  CAM  CAX  CAI   180.00   0.0  0
 9HT  CONST_21  HAR  CAL  CAI  CAX   180.00   0.0  0
 9HT  CONST_22  HAP  CAJ  CAZ  CAV     0.00   0.0  0
 9HT  CONST_23  HAQ  CAK  CAZ  CAV     0.00   0.0  0
 9HT  CONST_24  HAM  CAG  CAJ  CAZ   180.00   0.0  0
 9HT  CONST_25  HAN  CAH  CAK  CAZ   180.00   0.0  0
 9HT  CONST_26  OAE  CAU  NAS  CAN     0.00   0.0  0
 9HT  CONST_27  CBD  CAU  NAS  CAN   180.00   0.0  0
 9HT  CONST_28  HBF  NAS  CAU  OAE   180.00   0.0  0
 9HT  Var_01    CAM  CAX  OAT  CAC  -178.72  30.0  2
 9HT  Var_02    HAJ  CAD  CAY  NAQ   102.42  30.0  2
 9HT  Var_03    HAG  CAC  OAT  CAX   179.56  30.0  3
 9HT  Var_04    CAU  NAS  CAN  CAA   168.66  30.0  3
 9HT  Var_05    HAA  CAA  CAN  NAS    60.18  30.0  3
 9HT  Var_06    HAD  CAB  CAO  CBD   -60.36  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
 9HT  chir_01  CBD  CAU  CBE  CAO  negativ
 9HT  chir_02  CBE  NAP  CBD  CBC  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
 9HT  plan-1  CAV  0.020
 9HT  plan-1  CAZ  0.020
 9HT  plan-1  CAJ  0.020
 9HT  plan-1  CAG  0.020
 9HT  plan-1  CAW  0.020
 9HT  plan-1  CL   0.020
 9HT  plan-1  CAH  0.020
 9HT  plan-1  CAK  0.020
 9HT  plan-1  HAP  0.020
 9HT  plan-1  HAM  0.020
 9HT  plan-1  HAN  0.020
 9HT  plan-1  HAQ  0.020
 9HT  plan-2  CBE  0.020
 9HT  plan-2  CBC  0.020
 9HT  plan-2  NAR  0.020
 9HT  plan-2  NAQ  0.020
 9HT  plan-2  CAY  0.020
 9HT  plan-2  CAD  0.020
 9HT  plan-2  NBF  0.020
 9HT  plan-2  CBB  0.020
 9HT  plan-3  NBF  0.020
 9HT  plan-3  CBB  0.020
 9HT  plan-3  CAL  0.020
 9HT  plan-3  CAI  0.020
 9HT  plan-3  CAX  0.020
 9HT  plan-3  OAT  0.020
 9HT  plan-3  CAM  0.020
 9HT  plan-3  CBA  0.020
 9HT  plan-3  CAV  0.020
 9HT  plan-3  HAR  0.020
 9HT  plan-3  HAO  0.020
 9HT  plan-3  HAS  0.020
 9HT  plan-4  CAN  0.020
 9HT  plan-4  NAS  0.020
 9HT  plan-4  CAU  0.020
 9HT  plan-4  OAE  0.020
 9HT  plan-4  CBD  0.020
 9HT  plan-4  HBF  0.020

