# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:33:51 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (1R)-7-[3-(naphthalen-1-yloxy)propyl]-3,4-dihydro-2H-[1,4]thiazepino[2,3,4-hi]indole-6-carboxylic acid 1-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1n2CCC[S@@](=O)c3cccc(c1CCCOc4cccc5ccccc45)c23
#
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
 4M7  4M7  '(1R)-7-[3-(naphthalen-1-yloxy)propyl]-3,4-dihydro-2H-[1,4]thiazepino[2,3,4-hi]indole-6-carboxylic acid 1-oxide'  ligand  54  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4M7
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
 4M7  OAA  O  OH1   0  -0.591  -2.8903  -3.5243   0.5151
 4M7  CAU  C  C     0   0.482  -1.8373  -2.7207   0.4400
 4M7  OAC  O  O     0  -0.429  -0.6954  -3.1140   0.4695
 4M7  CAY  C  CR5   0   0.154  -2.1928  -1.2970   0.3812
 4M7  NBD  N  NR5   0  -0.583  -3.3959  -0.8039  -0.1080
 4M7  CBC  C  CR56  0   0.487  -3.4135   0.5364   0.1229
 4M7  CAR  C  CH2   0  -0.318  -4.2580  -1.4861  -1.0764
 4M7  CAO  C  CH2   0  -0.481  -4.5286  -0.6286  -2.3102
 4M7  CAS  C  CH2   0  -0.589  -5.7301   0.3035  -2.2435
 4M7  SBE  S  S3    0   0.739  -6.0453   1.1318  -0.6617
 4M7  OAB  O  O     0  -0.768  -6.5581   0.0810   0.2963
 4M7  CAX  C  CR6   0  -0.268  -4.3819   1.5118  -0.1625
 4M7  CAI  C  CR16  0  -0.283  -4.1138   2.8235   0.1776
 4M7  CAG  C  CR16  0  -0.261  -2.9012   3.1934   0.7781
 4M7  CAM  C  CR16  0  -0.356  -1.9557   2.2396   1.0822
 4M7  CBB  C  CR56  0   0.033  -2.2046   0.9033   0.7503
 4M7  CAW  C  CR5   0   0.075  -1.4344  -0.2832   0.9125
 4M7  CAQ  C  CH2   0  -0.542  -0.0883  -0.3490   1.5537
 4M7  CAN  C  CH2   0  -0.453   1.0436  -0.1804   0.5380
 4M7  CAP  C  CH2   0  -0.177   2.3933  -0.2774   1.2175
 4M7  OAT  O  O2    0  -0.467   3.3944  -0.0395   0.2415
 4M7  CAV  C  CR6   0   0.367   4.6847  -0.0393   0.6125
 4M7  CBA  C  CR66  0  -0.019   5.6148   0.2732  -0.4258
 4M7  CAL  C  CR16  0  -0.288   5.1989   0.5675  -1.7452
 4M7  CAE  C  CR16  0  -0.257   6.1185   0.8653  -2.7159
 4M7  CAD  C  CR16  0  -0.252   7.4941   0.8831  -2.4139
 4M7  CAJ  C  CR16  0  -0.317   7.9213   0.6040  -1.1443
 4M7  CAZ  C  CR66  0   0.126   6.9993   0.2928  -0.1177
 4M7  CAK  C  CR16  0  -0.345   7.4305   0.0047   1.2003
 4M7  CAF  C  CR16  0  -0.245   6.5125  -0.2875   2.1670
 4M7  CAH  C  CR16  0  -0.408   5.1307  -0.3116   1.8829
 4M7  H1   H  HOH1  0   0.491  -2.5988  -4.4488   0.5379
 4M7  H2   H  HCH2  0   0.277  -3.7380  -2.3800  -1.4015
 4M7  H3   H  HCH2  0   0.271  -5.1820  -1.8022  -0.5957
 4M7  H4   H  HCH2  0   0.266  -3.6288  -0.0643  -2.5615
 4M7  H5   H  HCH2  0   0.283  -4.6997  -1.3008  -3.1529
 4M7  H6   H  HCH2  0   0.300  -5.6439   1.0973  -2.9873
 4M7  H7   H  HCH2  0   0.296  -6.6641  -0.2273  -2.4392
 4M7  H9   H  HCR6  0   0.277  -4.8668   3.5806  -0.0039
 4M7  H10  H  HCR6  0   0.265  -2.7265   4.2319   1.0232
 4M7  H11  H  HCR6  0   0.258  -1.0311   2.5223   1.5702
 4M7  H12  H  HCH2  0   0.249  -0.0149   0.4375   2.3096
 4M7  H13  H  HCH2  0   0.254   0.0348  -1.2945   2.0838
 4M7  H14  H  HCH2  0   0.246   0.9596  -0.9520  -0.2295
 4M7  H15  H  HCH2  0   0.240   0.9531   0.7887   0.0404
 4M7  H16  H  HCH2  0   0.225   2.4731   0.4585   2.0264
 4M7  H17  H  HCH2  0   0.225   2.5223  -1.2711   1.6621
 4M7  H18  H  HCR6  0   0.253   4.1464   0.5623  -1.9932
 4M7  H19  H  HCR6  0   0.257   5.7872   1.0909  -3.7211
 4M7  H20  H  HCR6  0   0.258   8.2114   1.1195  -3.1891
 4M7  H21  H  HCR6  0   0.254   8.9785   0.6186  -0.9076
 4M7  H22  H  HCR6  0   0.250   8.4895   0.0192   1.4262
 4M7  H23  H  HCR6  0   0.259   6.8364  -0.5091   3.1756
 4M7  H24  H  HCR6  0   0.281   4.4420  -0.5474   2.6824

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
 4M7  OAC  CAU  double    1.208  0.020  1.208
 4M7  CAU  OAA  single    1.327  0.020  1.327
 4M7  CAU  CAY  single    1.469  0.020  1.469
 4M7  CAQ  CAW  single    1.492  0.020  1.492
 4M7  CAQ  CAN  single    1.530  0.020  1.530
 4M7  CAY  CAW  aromatic  1.373  0.020  1.373
 4M7  CAY  NBD  aromatic  1.389  0.020  1.389
 4M7  CAW  CBB  aromatic  1.424  0.020  1.424
 4M7  CAN  CAP  single    1.514  0.020  1.514
 4M7  CAO  CAR  single    1.527  0.020  1.527
 4M7  CAO  CAS  single    1.522  0.020  1.522
 4M7  NBD  CAR  single    1.465  0.020  1.465
 4M7  NBD  CBC  aromatic  1.360  0.020  1.360
 4M7  CAE  CAL  aromatic  1.370  0.020  1.370
 4M7  CAE  CAD  aromatic  1.408  0.020  1.408
 4M7  CBB  CBC  aromatic  1.411  0.020  1.411
 4M7  CBB  CAM  aromatic  1.399  0.020  1.399
 4M7  CAL  CBA  aromatic  1.414  0.020  1.414
 4M7  CBC  CAX  aromatic  1.404  0.020  1.404
 4M7  CAM  CAG  aromatic  1.377  0.020  1.377
 4M7  CAS  SBE  single    1.813  0.020  1.813
 4M7  OAT  CAP  single    1.418  0.020  1.418
 4M7  OAT  CAV  single    1.343  0.020  1.343
 4M7  CAD  CAJ  aromatic  1.368  0.020  1.368
 4M7  CAX  CAI  aromatic  1.381  0.020  1.381
 4M7  CAX  SBE  single    1.778  0.020  1.778
 4M7  CAG  CAI  aromatic  1.403  0.020  1.403
 4M7  CBA  CAV  aromatic  1.429  0.020  1.429
 4M7  CBA  CAZ  aromatic  1.419  0.020  1.419
 4M7  SBE  OAB  double    1.512  0.020  1.512
 4M7  CAV  CAH  aromatic  1.374  0.020  1.374
 4M7  CAJ  CAZ  aromatic  1.415  0.020  1.415
 4M7  CAZ  CAK  aromatic  1.416  0.020  1.416
 4M7  CAH  CAF  aromatic  1.411  0.020  1.411
 4M7  CAK  CAF  aromatic  1.365  0.020  1.365
 4M7  OAA  H1   single    0.850  0.020  0.980
 4M7  CAR  H2   single    0.970  0.020  1.090
 4M7  CAR  H3   single    0.970  0.020  1.090
 4M7  CAO  H4   single    0.970  0.020  1.090
 4M7  CAO  H5   single    0.970  0.020  1.090
 4M7  CAS  H6   single    0.970  0.020  1.090
 4M7  CAS  H7   single    0.970  0.020  1.090
 4M7  CAI  H9   single    0.930  0.020  1.080
 4M7  CAG  H10  single    0.930  0.020  1.080
 4M7  CAM  H11  single    0.930  0.020  1.080
 4M7  CAQ  H12  single    0.970  0.020  1.090
 4M7  CAQ  H13  single    0.970  0.020  1.090
 4M7  CAN  H14  single    0.970  0.020  1.090
 4M7  CAN  H15  single    0.970  0.020  1.090
 4M7  CAP  H16  single    0.970  0.020  1.090
 4M7  CAP  H17  single    0.970  0.020  1.090
 4M7  CAL  H18  single    0.930  0.020  1.080
 4M7  CAE  H19  single    0.930  0.020  1.080
 4M7  CAD  H20  single    0.930  0.020  1.080
 4M7  CAJ  H21  single    0.930  0.020  1.080
 4M7  CAK  H22  single    0.930  0.020  1.080
 4M7  CAF  H23  single    0.930  0.020  1.080
 4M7  CAH  H24  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
 4M7  H1   OAA  CAU  109.89  3.000
 4M7  CAY  CAU  OAC  123.05  3.000
 4M7  CAY  CAU  OAA  113.41  3.000
 4M7  OAC  CAU  OAA  123.48  3.000
 4M7  CAW  CAY  NBD  110.65  3.000
 4M7  NBD  CAY  CAU  124.60  3.000
 4M7  CAW  CAY  CAU  124.51  3.000
 4M7  CAR  NBD  CBC  124.29  3.000
 4M7  CBC  NBD  CAY  107.53  3.000
 4M7  CAR  NBD  CAY  125.25  3.000
 4M7  CBB  CBC  CAX  120.07  3.000
 4M7  CAX  CBC  NBD  131.23  3.000
 4M7  CBB  CBC  NBD  108.71  3.000
 4M7  H3   CAR  H2   107.47  3.000
 4M7  H3   CAR  CAO  111.69  3.000
 4M7  H2   CAR  CAO  107.81  3.000
 4M7  H3   CAR  NBD  110.05  3.000
 4M7  H2   CAR  NBD  107.45  3.000
 4M7  CAO  CAR  NBD  112.14  3.000
 4M7  H5   CAO  H4   105.66  3.000
 4M7  H5   CAO  CAS  106.69  3.000
 4M7  H4   CAO  CAS  110.14  3.000
 4M7  H5   CAO  CAR  107.80  3.000
 4M7  H4   CAO  CAR  109.29  3.000
 4M7  CAS  CAO  CAR  116.65  3.000
 4M7  H7   CAS  H6   107.40  3.000
 4M7  H7   CAS  SBE  103.28  3.000
 4M7  H6   CAS  SBE  106.02  3.000
 4M7  H7   CAS  CAO  111.70  3.000
 4M7  H6   CAS  CAO  110.68  3.000
 4M7  SBE  CAS  CAO  117.07  3.000
 4M7  CAX  SBE  OAB  106.74  3.000
 4M7  OAB  SBE  CAS  107.11  3.000
 4M7  CAX  SBE  CAS  100.37  3.000
 4M7  CAI  CAX  SBE  116.98  3.000
 4M7  SBE  CAX  CBC  123.65  3.000
 4M7  CAI  CAX  CBC  118.41  3.000
 4M7  H9   CAI  CAG  119.23  3.000
 4M7  H9   CAI  CAX  119.18  3.000
 4M7  CAG  CAI  CAX  121.58  3.000
 4M7  H10  CAG  CAM  120.28  3.000
 4M7  H10  CAG  CAI  119.34  3.000
 4M7  CAM  CAG  CAI  120.36  3.000
 4M7  H11  CAM  CBB  120.53  3.000
 4M7  H11  CAM  CAG  120.33  3.000
 4M7  CBB  CAM  CAG  119.14  3.000
 4M7  CAW  CBB  CAM  132.27  3.000
 4M7  CAM  CBB  CBC  120.42  3.000
 4M7  CAW  CBB  CBC  107.31  3.000
 4M7  CAQ  CAW  CBB  125.00  3.000
 4M7  CBB  CAW  CAY  105.81  3.000
 4M7  CAQ  CAW  CAY  129.19  3.000
 4M7  H13  CAQ  H12  106.26  3.000
 4M7  H13  CAQ  CAN  109.55  3.000
 4M7  H12  CAQ  CAN  109.27  3.000
 4M7  H13  CAQ  CAW  110.41  3.000
 4M7  H12  CAQ  CAW  109.02  3.000
 4M7  CAN  CAQ  CAW  112.16  3.000
 4M7  H15  CAN  H14  107.47  3.000
 4M7  H15  CAN  CAP  109.57  3.000
 4M7  H14  CAN  CAP  109.80  3.000
 4M7  H15  CAN  CAQ  109.79  3.000
 4M7  H14  CAN  CAQ  109.38  3.000
 4M7  CAP  CAN  CAQ  110.76  3.000
 4M7  H17  CAP  H16  107.49  3.000
 4M7  H17  CAP  OAT  110.37  3.000
 4M7  H16  CAP  OAT  110.11  3.000
 4M7  H17  CAP  CAN  110.18  3.000
 4M7  H16  CAP  CAN  110.67  3.000
 4M7  OAT  CAP  CAN  108.04  3.000
 4M7  CAV  OAT  CAP  119.23  3.000
 4M7  CAH  CAV  CBA  120.27  3.000
 4M7  CAH  CAV  OAT  124.58  3.000
 4M7  CBA  CAV  OAT  115.15  3.000
 4M7  CAZ  CBA  CAL  119.12  3.000
 4M7  CAZ  CBA  CAV  118.73  3.000
 4M7  CAL  CBA  CAV  122.15  3.000
 4M7  H18  CAL  CAE  119.46  3.000
 4M7  H18  CAL  CBA  119.94  3.000
 4M7  CAE  CAL  CBA  120.59  3.000
 4M7  H19  CAE  CAD  119.70  3.000
 4M7  H19  CAE  CAL  119.87  3.000
 4M7  CAD  CAE  CAL  120.42  3.000
 4M7  H20  CAD  CAJ  120.14  3.000
 4M7  H20  CAD  CAE  119.77  3.000
 4M7  CAJ  CAD  CAE  120.09  3.000
 4M7  H21  CAJ  CAZ  118.72  3.000
 4M7  H21  CAJ  CAD  120.30  3.000
 4M7  CAZ  CAJ  CAD  120.98  3.000
 4M7  CAK  CAZ  CAJ  121.44  3.000
 4M7  CAK  CAZ  CBA  119.77  3.000
 4M7  CAJ  CAZ  CBA  118.79  3.000
 4M7  H22  CAK  CAF  120.86  3.000
 4M7  H22  CAK  CAZ  119.28  3.000
 4M7  CAF  CAK  CAZ  119.86  3.000
 4M7  H23  CAF  CAH  118.51  3.000
 4M7  H23  CAF  CAK  120.17  3.000
 4M7  CAH  CAF  CAK  121.32  3.000
 4M7  H24  CAH  CAF  118.60  3.000
 4M7  H24  CAH  CAV  121.35  3.000
 4M7  CAF  CAH  CAV  120.05  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
 4M7  CONST_01  CBC  CBB  CAW  CAY     0.00   0.0  0
 4M7  CONST_02  CAM  CBB  CAW  CAY   180.00   0.0  0
 4M7  CONST_03  CBB  CAW  CAY  NBD     0.00   0.0  0
 4M7  CONST_04  CAG  CAM  CBB  CBC     0.00   0.0  0
 4M7  CONST_05  CAM  CAG  CAI  CAX     0.00   0.0  0
 4M7  CONST_06  CBB  CAM  CAG  CAI     0.00   0.0  0
 4M7  CONST_07  CAW  CBB  CAM  CAG   180.00   0.0  0
 4M7  CONST_08  CAE  CAL  CBA  CAV   180.00   0.0  0
 4M7  CONST_09  CAJ  CAZ  CBA  CAV   180.00   0.0  0
 4M7  CONST_10  CAK  CAZ  CBA  CAV     0.00   0.0  0
 4M7  CONST_11  CAK  CAF  CAH  CAV     0.00   0.0  0
 4M7  CONST_12  CAD  CAE  CAL  CBA     0.00   0.0  0
 4M7  CONST_13  CAF  CAH  CAV  CBA     0.00   0.0  0
 4M7  CONST_14  CAD  CAJ  CAZ  CBA     0.00   0.0  0
 4M7  CONST_15  CAF  CAK  CAZ  CBA     0.00   0.0  0
 4M7  CONST_16  CAJ  CAD  CAE  CAL     0.00   0.0  0
 4M7  CONST_17  CAH  CAV  CBA  CAL   180.00   0.0  0
 4M7  CONST_18  CAJ  CAZ  CBA  CAL     0.00   0.0  0
 4M7  CONST_19  CAK  CAZ  CBA  CAL   180.00   0.0  0
 4M7  CONST_20  CAZ  CBA  CAL  CAE     0.00   0.0  0
 4M7  CONST_21  CAZ  CAJ  CAD  CAE     0.00   0.0  0
 4M7  CONST_22  CAK  CAZ  CAJ  CAD   180.00   0.0  0
 4M7  CONST_23  CAF  CAK  CAZ  CAJ   180.00   0.0  0
 4M7  CONST_24  CAH  CAV  CBA  CAZ     0.00   0.0  0
 4M7  CONST_25  CAH  CAF  CAK  CAZ     0.00   0.0  0
 4M7  CONST_26  CBB  CAW  CAY  CAU   180.00   0.0  0
 4M7  CONST_27  CAQ  CAW  CAY  NBD   180.00   0.0  0
 4M7  CONST_28  CAQ  CAW  CBB  CBC   180.00   0.0  0
 4M7  CONST_29  CAQ  CAW  CBB  CAM     0.00   0.0  0
 4M7  CONST_30  CAL  CBA  CAV  OAT     0.00   0.0  0
 4M7  CONST_31  CAZ  CBA  CAV  OAT   180.00   0.0  0
 4M7  CONST_32  CAF  CAH  CAV  OAT   180.00   0.0  0
 4M7  CONST_33  H11  CAM  CBB  CBC   180.00   0.0  0
 4M7  CONST_34  H10  CAG  CAI  CAX   180.00   0.0  0
 4M7  CONST_35  H9   CAI  CAG  CAM   180.00   0.0  0
 4M7  CONST_36  H18  CAL  CBA  CAV     0.00   0.0  0
 4M7  CONST_37  H23  CAF  CAH  CAV   180.00   0.0  0
 4M7  CONST_38  H19  CAE  CAL  CBA   180.00   0.0  0
 4M7  CONST_39  H24  CAH  CAV  CBA   180.00   0.0  0
 4M7  CONST_40  H21  CAJ  CAZ  CBA   180.00   0.0  0
 4M7  CONST_41  H22  CAK  CAZ  CBA   180.00   0.0  0
 4M7  CONST_42  H20  CAD  CAE  CAL   180.00   0.0  0
 4M7  CONST_43  H1   OAA  CAU  CAY   180.00   0.0  0
 4M7  Var_01    CAW  CAY  CAU  OAA   147.62  30.0  2
 4M7  Var_02    CAN  CAQ  CAW  CAY    89.58  30.0  2
 4M7  Var_03    CBA  CAV  OAT  CAP  -177.10  30.0  2
 4M7  Var_04    CAP  CAN  CAQ  CAW  -178.97  30.0  3
 4M7  Var_05    H16  CAP  OAT  CAV    57.38  30.0  3
 4M7  Var_06    OAT  CAP  CAN  CAQ  -176.79  30.0  3

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
 4M7  plan-1  OAT  0.020
 4M7  plan-1  CAV  0.020
 4M7  plan-1  CBA  0.020
 4M7  plan-1  CAL  0.020
 4M7  plan-1  CAE  0.020
 4M7  plan-1  CAD  0.020
 4M7  plan-1  CAJ  0.020
 4M7  plan-1  CAZ  0.020
 4M7  plan-1  CAK  0.020
 4M7  plan-1  CAF  0.020
 4M7  plan-1  CAH  0.020
 4M7  plan-1  H18  0.020
 4M7  plan-1  H19  0.020
 4M7  plan-1  H20  0.020
 4M7  plan-1  H21  0.020
 4M7  plan-1  H22  0.020
 4M7  plan-1  H23  0.020
 4M7  plan-1  H24  0.020
 4M7  plan-2  CAU  0.020
 4M7  plan-2  CAY  0.020
 4M7  plan-2  NBD  0.020
 4M7  plan-2  CBC  0.020
 4M7  plan-2  CAR  0.020
 4M7  plan-2  SBE  0.020
 4M7  plan-2  CAX  0.020
 4M7  plan-2  CAI  0.020
 4M7  plan-2  CAG  0.020
 4M7  plan-2  CAM  0.020
 4M7  plan-2  CBB  0.020
 4M7  plan-2  CAW  0.020
 4M7  plan-2  CAQ  0.020
 4M7  plan-2  H9   0.020
 4M7  plan-2  H10  0.020
 4M7  plan-2  H11  0.020
 4M7  plan-3  OAA  0.020
 4M7  plan-3  CAU  0.020
 4M7  plan-3  OAC  0.020
 4M7  plan-3  CAY  0.020
 4M7  plan-3  H1   0.020

