# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 10:38:52 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: ~{N}-[(2~{R})-2,3-bis(azanyl)-3-oxidanylidene-propyl]-2-[(4~{R})-4-methanoyl-4,5-dihydro-1,3-thiazol-2-yl]pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CNC(=O)c1ccnc(c1)C2=N[C@@H](CS2)C=O)C(N)=O
#
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
 HHC  HHC  ~{N}-[(2~{R})-2,3-bis(azanyl)-3-oxidanylidene-propyl]-2-[(4~{R})-4-methanoyl-4,5-dihydro-1,3-thiazol-2-yl]pyridine-4-carboxamide  ligand  37  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HHC
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
 HHC  C10   C  CR6   0   0.073  -17.5439  -31.3389  36.1210
 HHC  C13   C  C     0   0.046  -16.8207  -31.0399  39.7861
 HHC  C15   C  CH2   0  -0.597  -16.5818  -30.8839  42.2827
 HHC  C02   C  C     0   0.517  -20.0842  -26.6963  33.2571
 HHC  C04   C  CH1   0  -0.225  -19.3363  -27.4742  34.3352
 HHC  C08   C  C     0   0.522  -18.1152  -30.5999  34.9444
 HHC  C11   C  CR16  0  -0.343  -17.4904  -30.8004  37.3987
 HHC  C12   C  CR6   0   0.259  -16.9129  -31.5575  38.4114
 HHC  C16   C  CH1   0  -0.226  -16.9322  -29.6000  41.5178
 HHC  C55   C  CR16  0  -0.056  -16.4534  -33.2766  36.9960
 HHC  C56   C  CR16  0  -0.330  -16.9980  -32.6004  35.9155
 HHC  N05   N  NH2   0  -0.781  -17.9161  -27.2591  34.1815
 HHC  N07   N  NH1   0  -0.638  -19.1391  -29.7768  35.2197
 HHC  N53   N  N     0  -0.369  -17.2229  -29.8918  40.1303
 HHC  N54   N  N     0  -0.419  -16.4117  -32.7700  38.2194
 HHC  O03   O  O     0  -0.479  -19.6413  -26.5995  32.1233
 HHC  O09   O  O     0  -0.463  -17.6582  -30.7819  33.8277
 HHC  S14   S  S2    0   0.085  -16.0924  -32.0829  41.0053
 HHC  H151  H  HCH2  0   0.303  -17.4441  -31.2728  42.8207
 HHC  H152  H  HCH2  0   0.297  -15.7687  -30.7370  42.9913
 HHC  H3    H  HCH1  0   0.262  -19.6266  -27.0972  35.3208
 HHC  H111  H  HCR6  0   0.285  -17.8595  -29.8088  37.6244
 HHC  H4    H  HCH1  0   0.315  -17.8084  -29.1196  41.9716
 HHC  H551  H  HCR6  0   0.278  -16.0341  -34.2669  36.8654
 HHC  H561  H  HCR6  0   0.283  -17.0013  -33.0586  34.9365
 HHC  H011  H  HNH2  0   0.400  -21.8560  -25.7140  32.9745
 HHC  H012  H  HNH2  0   0.408  -21.5946  -26.2593  34.5847
 HHC  H5    H  HNH2  0   0.356  -17.4176  -27.7205  34.9314
 HHC  H051  H  HNH2  0   0.344  -17.5919  -27.6722  33.3160
 HHC  H071  H  HNH1  0   0.415  -19.5082  -29.7465  36.1572
 HHC  C17   C  C1    0   0.183  -15.8394  -28.5448  41.5422
 HHC  O52   O  O     0  -0.352  -14.9486  -28.5141  42.3470
 HHC  C06   C  CH2   0  -0.295  -19.7913  -28.9458  34.2380
 HHC  N01   N  NH2   0  -0.798  -21.2654  -26.1904  33.6371
 HHC  H2    H  H     0   0.219  -15.9424  -27.7774  40.7563
 HHC  H061  H  HCH2  0   0.263  -20.8702  -29.0170  34.3877
 HHC  H062  H  HCH2  0   0.259  -19.5708  -29.3356  33.2444

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
 HHC  O03  C02   double    1.221  0.020  1.221
 HHC  O09  C08   double    1.220  0.020  1.220
 HHC  N01  C02   single    1.340  0.020  1.340
 HHC  C02  C04   single    1.525  0.020  1.525
 HHC  C06  C04   single    1.543  0.020  1.543
 HHC  C06  N07   single    1.442  0.020  1.442
 HHC  C08  N07   single    1.342  0.020  1.342
 HHC  C08  C10   single    1.502  0.020  1.502
 HHC  C04  N05   single    1.445  0.020  1.445
 HHC  C56  C10   aromatic  1.390  0.020  1.390
 HHC  C56  C55   aromatic  1.386  0.020  1.386
 HHC  C10  C11   aromatic  1.388  0.020  1.388
 HHC  C55  N54   aromatic  1.325  0.020  1.325
 HHC  C11  C12   aromatic  1.390  0.020  1.390
 HHC  N54  C12   aromatic  1.326  0.020  1.326
 HHC  C12  C13   single    1.472  0.020  1.472
 HHC  C13  N53   double    1.264  0.020  1.264
 HHC  C13  S14   single    1.762  0.020  1.762
 HHC  N53  C16   single    1.447  0.020  1.447
 HHC  S14  C15   single    1.819  0.020  1.819
 HHC  C17  C16   single    1.519  0.020  1.519
 HHC  C17  O52   double    1.201  0.020  1.201
 HHC  C16  C15   single    1.535  0.020  1.535
 HHC  C15  H151  single    0.970  0.020  1.090
 HHC  C15  H152  single    0.970  0.020  1.090
 HHC  C17  H2    single    0.930  0.020  1.080
 HHC  C04  H3    single    0.970  0.020  1.090
 HHC  C06  H061  single    0.970  0.020  1.090
 HHC  C06  H062  single    0.970  0.020  1.090
 HHC  C11  H111  single    0.930  0.020  1.080
 HHC  C16  H4    single    0.970  0.020  1.090
 HHC  C55  H551  single    0.930  0.020  1.080
 HHC  C56  H561  single    0.930  0.020  1.080
 HHC  N01  H011  single    0.860  0.020  1.020
 HHC  N01  H012  single    0.860  0.020  1.020
 HHC  N05  H5    single    0.890  0.020  1.040
 HHC  N05  H051  single    0.890  0.020  1.040
 HHC  N07  H071  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
 HHC  C56   C10  C11   118.24  3.000
 HHC  C11   C10  C08   123.02  3.000
 HHC  C56   C10  C08   118.69  3.000
 HHC  S14   C13  N53   118.73  3.000
 HHC  S14   C13  C12   117.65  3.000
 HHC  N53   C13  C12   123.62  3.000
 HHC  H152  C15  H151  108.56  3.000
 HHC  H152  C15  S14   110.19  3.000
 HHC  H151  C15  S14   108.95  3.000
 HHC  H152  C15  C16   112.46  3.000
 HHC  H151  C15  C16   111.37  3.000
 HHC  S14   C15  C16   105.23  3.000
 HHC  O03   C02  N01   123.59  3.000
 HHC  N01   C02  C04   115.10  3.000
 HHC  O03   C02  C04   121.25  3.000
 HHC  H3    C04  N05   107.77  3.000
 HHC  H3    C04  C06   107.88  3.000
 HHC  N05   C04  C06   115.16  3.000
 HHC  H3    C04  C02   109.31  3.000
 HHC  N05   C04  C02   109.32  3.000
 HHC  C06   C04  C02   107.29  3.000
 HHC  O09   C08  N07   124.40  3.000
 HHC  N07   C08  C10   115.53  3.000
 HHC  O09   C08  C10   120.06  3.000
 HHC  H111  C11  C12   119.27  3.000
 HHC  H111  C11  C10   122.32  3.000
 HHC  C12   C11  C10   118.39  3.000
 HHC  N54   C12  C11   123.34  3.000
 HHC  N54   C12  C13   115.66  3.000
 HHC  C11   C12  C13   121.00  3.000
 HHC  H4    C16  N53   108.93  3.000
 HHC  H4    C16  C17   105.28  3.000
 HHC  N53   C16  C17   107.45  3.000
 HHC  H4    C16  C15   110.01  3.000
 HHC  C17   C16  C15   114.12  3.000
 HHC  N53   C16  C15   110.79  3.000
 HHC  H551  C55  N54   116.66  3.000
 HHC  H551  C55  C56   120.27  3.000
 HHC  N54   C55  C56   123.07  3.000
 HHC  H561  C56  C55   120.03  3.000
 HHC  H561  C56  C10   121.16  3.000
 HHC  C55   C56  C10   118.81  3.000
 HHC  H051  N05  H5    106.84  3.000
 HHC  H051  N05  C04   110.19  3.000
 HHC  H5    N05  C04   109.73  3.000
 HHC  H071  N07  C08   119.25  3.000
 HHC  H071  N07  C06   116.75  3.000
 HHC  C08   N07  C06   123.97  3.000
 HHC  C16   N53  C13   112.34  3.000
 HHC  C55   N54  C12   118.13  3.000
 HHC  C15   S14  C13    89.11  3.000
 HHC  H2    C17  O52   121.93  3.000
 HHC  H2    C17  C16   113.86  3.000
 HHC  O52   C17  C16   124.20  3.000
 HHC  H062  C06  H061  107.56  3.000
 HHC  H062  C06  N07   108.84  3.000
 HHC  H061  C06  N07   108.43  3.000
 HHC  H062  C06  C04   109.80  3.000
 HHC  H061  C06  C04   110.18  3.000
 HHC  N07   C06  C04   111.91  3.000
 HHC  H012  N01  H011  117.41  3.000
 HHC  H012  N01  C02   122.01  3.000
 HHC  H011  N01  C02   120.58  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
 HHC  CONST_01  N54   C55  C56  C10     0.00   0.0  0
 HHC  CONST_02  N54   C12  C11  C10     0.00   0.0  0
 HHC  CONST_03  C55   C56  C10  C11     0.00   0.0  0
 HHC  CONST_04  C55   N54  C12  C11     0.00   0.0  0
 HHC  CONST_05  C56   C10  C11  C12     0.00   0.0  0
 HHC  CONST_06  C56   C55  N54  C12     0.00   0.0  0
 HHC  CONST_07  C13   C12  C11  C10   180.00   0.0  0
 HHC  CONST_08  C55   N54  C12  C13   180.00   0.0  0
 HHC  CONST_09  C55   C56  C10  C08   180.00   0.0  0
 HHC  CONST_10  C12   C11  C10  C08   180.00   0.0  0
 HHC  CONST_11  H551  C55  C56  C10   180.00   0.0  0
 HHC  CONST_12  H111  C11  C12  C13     0.00   0.0  0
 HHC  CONST_13  H561  C56  C10  C11   180.00   0.0  0
 HHC  CONST_14  C06   N07  C08  C10   180.00   0.0  0
 HHC  CONST_15  H071  N07  C08  C10     0.00   0.0  0
 HHC  CONST_16  O09   C08  N07  C06     0.00   0.0  0
 HHC  CONST_17  H011  N01  C02  C04   180.00   0.0  0
 HHC  CONST_18  H012  N01  C02  C04     0.00   0.0  0
 HHC  Var_01    C16   C15  S14  C13   -15.38  30.0  1
 HHC  Var_02    C12   C13  S14  C15  -172.45  30.0  1
 HHC  Var_03    O09   C08  C10  C11   147.66  30.0  2
 HHC  Var_04    C08   N07  C06  C04  -102.32  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
 HHC  chir_01  C04  C02  C06  N05  negativ
 HHC  chir_02  C16  N53  C17  C15  positiv

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
 HHC  plan-1  C10   0.020
 HHC  plan-1  C13   0.020
 HHC  plan-1  C08   0.020
 HHC  plan-1  C11   0.020
 HHC  plan-1  C12   0.020
 HHC  plan-1  C55   0.020
 HHC  plan-1  C56   0.020
 HHC  plan-1  N54   0.020
 HHC  plan-1  H111  0.020
 HHC  plan-1  H551  0.020
 HHC  plan-1  H561  0.020
 HHC  plan-2  C10   0.020
 HHC  plan-2  C08   0.020
 HHC  plan-2  N07   0.020
 HHC  plan-2  O09   0.020
 HHC  plan-2  H071  0.020
 HHC  plan-2  C06   0.020
 HHC  plan-3  C02   0.020
 HHC  plan-3  C04   0.020
 HHC  plan-3  O03   0.020
 HHC  plan-3  H011  0.020
 HHC  plan-3  H012  0.020
 HHC  plan-3  N01   0.020
 HHC  plan-4  C16   0.020
 HHC  plan-4  C17   0.020
 HHC  plan-4  O52   0.020
 HHC  plan-4  H2    0.020

