# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 15:34:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (4Z)-4-(2-amino-5-oxo-3,5-dihydro-4H-imidazol-4-ylidene)-2,3-dichloro-4,5,6,7-tetrahydropyrrolo[2,3-c]azepin-8(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C(\N1)=C2/CCNC(=O)c3[nH]c(Cl)c(Cl)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
 HYM  HYM  (4Z)-4-(2-amino-5-oxo-3,5-dihydro-4H-imidazol-4-ylidene)-2,3-dichloro-4,5,6,7-tetrahydropyrrolo[2,3-c]azepin-8(1H)-one  ligand  29  20  .  2022-07-25  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_HYM
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
 HYM  CAI   C   CH2   0  -0.481   1.1356  -1.8597   1.4618
 HYM  CAH   C   CH2   0  -0.340   0.0297  -2.9009   1.4079
 HYM  NAG   N   NH1   0  -0.623  -0.2819  -3.3708   0.0671
 HYM  CAF   C   C     0   0.472  -1.1136  -2.7374  -0.7776
 HYM  OAK   O   O     0  -0.485  -1.6479  -3.2629  -1.7463
 HYM  CAD   C   CR5   0   0.184  -1.3418  -1.3214  -0.4559
 HYM  NAC   N   NR15  0  -0.646  -2.4902  -0.6960  -0.8227
 HYM  CAA   C   CR5   0   0.293  -2.4426   0.5939  -0.4378
 HYM  CLA   CL  CL    0  -0.056  -3.7278   1.6698  -0.6741
 HYM  CAB   C   CR5   0  -0.191  -1.2316   0.8194   0.1705
 HYM  CLB   CL  CL    0  -0.107  -0.7644   2.2959   0.8867
 HYM  CAE   C   CR5   0   0.128  -0.5073  -0.3995   0.1535
 HYM  CAJ   C   C     0  -0.041   0.8642  -0.6493   0.5996
 HYM  CAL   C   CR5   0   0.227   1.8535   0.1673   0.2026
 HYM  NAP   N   NR15  0  -0.731   1.7687   1.2208  -0.6974
 HYM  CAM   C   CR5   0   0.384   3.3041   0.1735   0.5975
 HYM  OAR   O   O     0  -0.463   3.8217  -0.5663   1.4173
 HYM  NAN   N   N     0  -0.546   3.9339   1.1601  -0.0967
 HYM  CAO   C   CR5   0   0.687   3.0153   1.7281  -0.8594
 HYM  NAQ   N   NH2   0  -0.825   3.2616   2.7089  -1.7091
 HYM  HAI1  H   HCH2  0   0.261   1.2515  -1.5549   2.5064
 HYM  HAI2  H   HCH2  0   0.256   2.0795  -2.3180   1.1719
 HYM  HAH1  H   HCH2  0   0.284   0.3472  -3.7697   1.9817
 HYM  HAH2  H   HCH2  0   0.258  -0.8772  -2.5273   1.8878
 HYM  HAG   H   HNH1  0   0.405  -0.0850  -4.3374  -0.1448
 HYM  HAC   H   HNR5  0   0.433  -3.2632  -1.1387  -1.2984
 HYM  HAP   H   HNR5  0   0.420   0.9935   1.4025  -1.3151
 HYM  HAQ1  H   HNH2  0   0.421   2.5397   3.1287  -2.2692
 HYM  HAQ2  H   HNH2  0   0.423   4.1976   3.0657  -1.7975

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
 HYM  CAI  CAH   single    1.520  0.020  1.520
 HYM  CAI  CAJ   single    1.511  0.020  1.511
 HYM  CAI  HAI1  single    0.970  0.020  1.090
 HYM  CAI  HAI2  single    0.970  0.020  1.090
 HYM  CAH  NAG   single    1.455  0.020  1.455
 HYM  CAH  HAH1  single    0.970  0.020  1.090
 HYM  CAH  HAH2  single    0.970  0.020  1.090
 HYM  NAG  CAF   single    1.344  0.020  1.344
 HYM  NAG  HAG   single    0.860  0.020  1.020
 HYM  CAF  OAK   double    1.225  0.020  1.225
 HYM  CAF  CAD   single    1.470  0.020  1.470
 HYM  CAD  NAC   aromatic  1.358  0.020  1.358
 HYM  CAD  CAE   aromatic  1.385  0.020  1.385
 HYM  NAC  CAA   aromatic  1.347  0.020  1.347
 HYM  NAC  HAC   single    0.860  0.020  1.020
 HYM  CAA  CLA   single    1.693  0.020  1.693
 HYM  CAA  CAB   aromatic  1.374  0.020  1.374
 HYM  CAB  CLB   single    1.706  0.020  1.706
 HYM  CAB  CAE   aromatic  1.418  0.020  1.418
 HYM  CAE  CAJ   single    1.464  0.020  1.464
 HYM  CAJ  CAL   double    1.343  0.020  1.343
 HYM  CAL  NAP   single    1.388  0.020  1.388
 HYM  CAL  CAM   single    1.503  0.020  1.503
 HYM  NAP  CAO   single    1.356  0.020  1.356
 HYM  NAP  HAP   single    0.860  0.020  1.020
 HYM  CAM  OAR   double    1.220  0.020  1.220
 HYM  CAM  NAN   single    1.361  0.020  1.361
 HYM  NAN  CAO   double    1.322  0.020  1.322
 HYM  CAO  NAQ   single    1.321  0.020  1.321
 HYM  NAQ  HAQ1  single    0.860  0.020  1.020
 HYM  NAQ  HAQ2  single    0.860  0.020  1.020

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
 HYM  HAI2  CAI  HAI1  106.24  3.000
 HYM  HAI2  CAI  CAJ   109.95  3.000
 HYM  HAI1  CAI  CAJ   109.92  3.000
 HYM  HAI2  CAI  CAH   109.45  3.000
 HYM  HAI1  CAI  CAH   107.56  3.000
 HYM  CAJ   CAI  CAH   113.45  3.000
 HYM  HAH2  CAH  HAH1  106.48  3.000
 HYM  HAH2  CAH  NAG   109.74  3.000
 HYM  HAH1  CAH  NAG   106.89  3.000
 HYM  HAH2  CAH  CAI   110.75  3.000
 HYM  HAH1  CAH  CAI   108.41  3.000
 HYM  NAG   CAH  CAI   114.19  3.000
 HYM  HAG   NAG  CAF   116.12  3.000
 HYM  HAG   NAG  CAH   117.47  3.000
 HYM  CAF   NAG  CAH   124.04  3.000
 HYM  CAD   CAF  OAK   121.25  3.000
 HYM  CAD   CAF  NAG   114.36  3.000
 HYM  OAK   CAF  NAG   124.39  3.000
 HYM  CAE   CAD  NAC   108.78  3.000
 HYM  CAE   CAD  CAF   130.09  3.000
 HYM  NAC   CAD  CAF   121.05  3.000
 HYM  HAC   NAC  CAA   125.55  3.000
 HYM  HAC   NAC  CAD   124.93  3.000
 HYM  CAA   NAC  CAD   109.51  3.000
 HYM  CAB   CAA  CLA   128.81  3.000
 HYM  CAB   CAA  NAC   108.35  3.000
 HYM  CLA   CAA  NAC   122.82  3.000
 HYM  CAE   CAB  CLB   127.52  3.000
 HYM  CAE   CAB  CAA   107.69  3.000
 HYM  CLB   CAB  CAA   124.70  3.000
 HYM  CAJ   CAE  CAB   128.44  3.000
 HYM  CAJ   CAE  CAD   125.82  3.000
 HYM  CAB   CAE  CAD   105.64  3.000
 HYM  CAL   CAJ  CAE   119.76  3.000
 HYM  CAL   CAJ  CAI   121.58  3.000
 HYM  CAE   CAJ  CAI   118.62  3.000
 HYM  CAM   CAL  NAP   103.07  3.000
 HYM  CAM   CAL  CAJ   129.47  3.000
 HYM  NAP   CAL  CAJ   127.46  3.000
 HYM  HAP   NAP  CAO   124.52  3.000
 HYM  HAP   NAP  CAL   125.53  3.000
 HYM  CAO   NAP  CAL   107.78  3.000
 HYM  NAN   CAM  OAR   125.89  3.000
 HYM  NAN   CAM  CAL   108.39  3.000
 HYM  OAR   CAM  CAL   125.70  3.000
 HYM  CAO   NAN  CAM   106.51  3.000
 HYM  NAQ   CAO  NAN   124.09  3.000
 HYM  NAQ   CAO  NAP   121.75  3.000
 HYM  NAN   CAO  NAP   114.15  3.000
 HYM  HAQ2  NAQ  HAQ1  118.10  3.000
 HYM  HAQ2  NAQ  CAO   119.58  3.000
 HYM  HAQ1  NAQ  CAO   122.31  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
 HYM  CONST_01  CAB   CAA  NAC  CAD    0.00  0.0  0
 HYM  CONST_02  CAE   CAB  CAA  NAC    0.00  0.0  0
 HYM  CONST_03  NAN   CAO  NAP  CAL    0.00  0.0  0
 HYM  CONST_04  CAO   NAN  CAM  CAL    0.00  0.0  0
 HYM  CONST_05  NAN   CAM  CAL  NAP    0.00  0.0  0
 HYM  CONST_06  CAM   NAN  CAO  NAP    0.00  0.0  0
 HYM  CONST_07  CAO   NAP  CAL  CAM    0.00  0.0  0
 HYM  CONST_08  CLA   CAA  NAC  CAD  180.00  0.0  0
 HYM  CONST_09  CLB   CAB  CAA  NAC  180.00  0.0  0
 HYM  CONST_10  CAE   CAB  CAA  CLA  180.00  0.0  0
 HYM  CONST_11  NAQ   CAO  NAP  CAL  180.00  0.0  0
 HYM  CONST_12  NAQ   CAO  NAN  CAM  180.00  0.0  0
 HYM  CONST_13  HAC   NAC  CAA  CAB  180.00  0.0  0
 HYM  CONST_14  HAP   NAP  CAL  CAM  180.00  0.0  0
 HYM  CONST_15  HAQ1  NAQ  CAO  NAP    0.00  0.0  0
 HYM  CONST_16  HAQ2  NAQ  CAO  NAP  180.00  0.0  0

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
 HYM  plan-1  CAJ   0.020
 HYM  plan-1  CAL   0.020
 HYM  plan-1  NAP   0.020
 HYM  plan-1  CAM   0.020
 HYM  plan-1  OAR   0.020
 HYM  plan-1  NAN   0.020
 HYM  plan-1  CAO   0.020
 HYM  plan-1  NAQ   0.020
 HYM  plan-1  HAP   0.020
 HYM  plan-1  HAQ1  0.020
 HYM  plan-1  HAQ2  0.020
 HYM  plan-2  CAF   0.020
 HYM  plan-2  CAD   0.020
 HYM  plan-2  NAC   0.020
 HYM  plan-2  CAA   0.020
 HYM  plan-2  CLA   0.020
 HYM  plan-2  CAB   0.020
 HYM  plan-2  CLB   0.020
 HYM  plan-2  CAE   0.020
 HYM  plan-2  CAJ   0.020
 HYM  plan-2  HAC   0.020
 HYM  plan-3  CAH   0.020
 HYM  plan-3  NAG   0.020
 HYM  plan-3  CAF   0.020
 HYM  plan-3  OAK   0.020
 HYM  plan-3  CAD   0.020
 HYM  plan-3  HAG   0.020

