# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 10:10:13 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: trans-4-(aminomethyl)-N-(phenylsulfonyl)cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CC[C@@H](CC1)C(=O)N[S](=O)(=O)c2ccccc2
#
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
 5C3  5C3  trans-4-(aminomethyl)-N-(phenylsulfonyl)cyclohexanecarboxamide  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5C3
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
 5C3  C01   C  CR16  0  -0.246   4.1569   1.7204   1.3009
 5C3  C02   C  CR16  0  -0.224   3.4475   0.5307   1.2935
 5C3  C03   C  CR6   0  -0.200   3.0685  -0.0151   0.0729
 5C3  C04   C  CR16  0  -0.213   3.3876   0.5944  -1.1315
 5C3  C05   C  CR16  0  -0.247   4.1042   1.7820  -1.1078
 5C3  C06   C  CR16  0  -0.232   4.4850   2.3442   0.1029
 5C3  O08   O  O     0  -0.432   0.2117   0.2181  -1.2733
 5C3  N09   N  NH2   0  -0.797  -6.8201  -0.2098  -0.1740
 5C3  C10   C  CH2   0  -0.261  -5.8792   0.7234   0.4278
 5C3  S11   S  S     0   1.396   2.1664  -1.5326   0.0756
 5C3  NP2   N  NC1   0  -0.818   0.6149  -1.0814   0.5234
 5C3  O13   O  OS    0  -0.626   2.1411  -2.0734  -1.2669
 5C3  O14   O  OS    0  -0.645   2.6206  -2.3581   1.1796
 5C3  C15   C  CH1   0  -0.242  -4.4566   0.4977  -0.0700
 5C3  C16   C  CH2   0  -0.427  -3.5108   1.5489   0.5061
 5C3  C17   C  CH2   0  -0.417  -2.0816   1.3631   0.0120
 5C3  C18   C  CH1   0  -0.395  -1.5674  -0.0379   0.3322
 5C3  C19   C  CH2   0  -0.419  -2.5116  -1.1108  -0.2363
 5C3  C11   C  C     0   0.624  -0.1844  -0.2539  -0.2313
 5C3  C20   C  CH2   0  -0.410  -3.9394  -0.9006   0.2548
 5C3  H01   H  HCR6  0   0.276   4.4550   2.1585   2.2435
 5C3  H02   H  HCR6  0   0.289   3.1983   0.0444   2.2272
 5C3  H06   H  HCR6  0   0.275   5.0418   3.2718   0.1144
 5C3  H04   H  HCR6  0   0.285   3.0902   0.1580  -2.0738
 5C3  H05   H  HCR6  0   0.275   4.3597   2.2686  -2.0391
 5C3  H091  H  HNH2  0   0.346  -7.7470  -0.0362   0.1936
 5C3  H092  H  HNH2  0   0.335  -6.8831  -0.0219  -1.1674
 5C3  H101  H  HCH2  0   0.196  -6.1445   1.7772   0.2541
 5C3  H102  H  HCH2  0   0.206  -5.9010   0.5787   1.5131
 5C3  H15   H  HCH1  0   0.210  -4.4577   0.6162  -1.1636
 5C3  HP2   H  HNC1  0   0.444   0.3042  -1.4153   1.4281
 5C3  H161  H  HCH2  0   0.231  -3.8558   2.5514   0.2392
 5C3  H162  H  HCH2  0   0.212  -3.5352   1.4939   1.6010
 5C3  H201  H  HCH2  0   0.208  -3.9758  -1.0498   1.3409
 5C3  H202  H  HCH2  0   0.236  -4.5910  -1.6566  -0.1857
 5C3  H171  H  HCH2  0   0.226  -2.0500   1.5228  -1.0692
 5C3  H172  H  HCH2  0   0.242  -1.4287   2.1139   0.4634
 5C3  H18   H  HCH1  0   0.264  -1.5334  -0.1627   1.4210
 5C3  H191  H  HCH2  0   0.229  -2.4866  -1.0659  -1.3298
 5C3  H192  H  HCH2  0   0.244  -2.1628  -2.1068   0.0471

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
 5C3  C01  C02   aromatic  1.385  0.020  1.385
 5C3  C01  C06   aromatic  1.390  0.020  1.390
 5C3  C02  C03   aromatic  1.390  0.020  1.390
 5C3  C03  C04   aromatic  1.387  0.020  1.387
 5C3  C03  S11   single    1.765  0.020  1.765
 5C3  C04  C05   aromatic  1.387  0.020  1.387
 5C3  C05  C06   aromatic  1.388  0.020  1.388
 5C3  O08  C11   double    1.210  0.020  1.210
 5C3  N09  C10   single    1.455  0.020  1.455
 5C3  C10  C15   single    1.524  0.020  1.524
 5C3  S11  NP2   single    1.677  0.020  1.677
 5C3  S11  O13   double    1.448  0.020  1.448
 5C3  S11  O14   double    1.451  0.020  1.451
 5C3  NP2  C11   single    1.376  0.020  1.376
 5C3  C15  C16   single    1.527  0.020  1.527
 5C3  C15  C20   single    1.526  0.020  1.526
 5C3  C16  C17   single    1.524  0.020  1.524
 5C3  C17  C18   single    1.526  0.020  1.526
 5C3  C18  C19   single    1.538  0.020  1.538
 5C3  C18  C11   single    1.509  0.020  1.509
 5C3  C19  C20   single    1.524  0.020  1.524
 5C3  C01  H01   single    0.930  0.020  1.080
 5C3  C02  H02   single    0.930  0.020  1.080
 5C3  C06  H06   single    0.930  0.020  1.080
 5C3  C04  H04   single    0.930  0.020  1.080
 5C3  C05  H05   single    0.930  0.020  1.080
 5C3  N09  H091  single    0.890  0.020  1.040
 5C3  N09  H092  single    0.890  0.020  1.040
 5C3  C10  H101  single    0.970  0.020  1.090
 5C3  C10  H102  single    0.970  0.020  1.090
 5C3  C15  H15   single    0.970  0.020  1.090
 5C3  NP2  HP2   single    0.860  0.020  1.020
 5C3  C16  H161  single    0.970  0.020  1.090
 5C3  C16  H162  single    0.970  0.020  1.090
 5C3  C20  H201  single    0.970  0.020  1.090
 5C3  C20  H202  single    0.970  0.020  1.090
 5C3  C17  H171  single    0.970  0.020  1.090
 5C3  C17  H172  single    0.970  0.020  1.090
 5C3  C18  H18   single    0.970  0.020  1.090
 5C3  C19  H191  single    0.970  0.020  1.090
 5C3  C19  H192  single    0.970  0.020  1.090

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
 5C3  H01   C01  C06   120.29  3.000
 5C3  H01   C01  C02   119.59  3.000
 5C3  C06   C01  C02   120.12  3.000
 5C3  H02   C02  C03   121.25  3.000
 5C3  H02   C02  C01   119.96  3.000
 5C3  C03   C02  C01   118.79  3.000
 5C3  S11   C03  C04   119.78  3.000
 5C3  S11   C03  C02   118.39  3.000
 5C3  C04   C03  C02   121.82  3.000
 5C3  H04   C04  C05   120.20  3.000
 5C3  H04   C04  C03   121.10  3.000
 5C3  C05   C04  C03   118.70  3.000
 5C3  H05   C05  C06   120.27  3.000
 5C3  H05   C05  C04   119.51  3.000
 5C3  C06   C05  C04   120.22  3.000
 5C3  H06   C06  C05   119.85  3.000
 5C3  H06   C06  C01   119.81  3.000
 5C3  C05   C06  C01   120.34  3.000
 5C3  H092  N09  H091  105.51  3.000
 5C3  H092  N09  C10   109.07  3.000
 5C3  H091  N09  C10   109.38  3.000
 5C3  H102  C10  H101  106.15  3.000
 5C3  H102  C10  C15   108.83  3.000
 5C3  H101  C10  C15   108.38  3.000
 5C3  H102  C10  N09   108.19  3.000
 5C3  H101  C10  N09   113.14  3.000
 5C3  C15   C10  N09   111.93  3.000
 5C3  O14   S11  O13   119.90  3.000
 5C3  O14   S11  NP2   103.85  3.000
 5C3  O13   S11  NP2   109.40  3.000
 5C3  O14   S11  C03   109.28  3.000
 5C3  O13   S11  C03   109.19  3.000
 5C3  NP2   S11  C03   104.00  3.000
 5C3  HP2   NP2  C11   120.65  3.000
 5C3  HP2   NP2  S11   115.70  3.000
 5C3  C11   NP2  S11   123.56  3.000
 5C3  H15   C15  C20   108.10  3.000
 5C3  H15   C15  C16   107.55  3.000
 5C3  C20   C15  C16   109.91  3.000
 5C3  H15   C15  C10   107.93  3.000
 5C3  C20   C15  C10   112.50  3.000
 5C3  C16   C15  C10   110.68  3.000
 5C3  H162  C16  H161  106.42  3.000
 5C3  H162  C16  C17   109.79  3.000
 5C3  H161  C16  C17   109.19  3.000
 5C3  H162  C16  C15   109.17  3.000
 5C3  H161  C16  C15   110.10  3.000
 5C3  C17   C16  C15   112.01  3.000
 5C3  H172  C17  H171  106.92  3.000
 5C3  H172  C17  C18   110.04  3.000
 5C3  H171  C17  C18   109.38  3.000
 5C3  H172  C17  C16   110.04  3.000
 5C3  H171  C17  C16   109.27  3.000
 5C3  C18   C17  C16   111.09  3.000
 5C3  H18   C18  C11   109.03  3.000
 5C3  H18   C18  C19   107.86  3.000
 5C3  C11   C18  C19   108.95  3.000
 5C3  H18   C18  C17   108.86  3.000
 5C3  C11   C18  C17   111.21  3.000
 5C3  C19   C18  C17   110.85  3.000
 5C3  H192  C19  H191  106.81  3.000
 5C3  H192  C19  C20   109.94  3.000
 5C3  H191  C19  C20   109.73  3.000
 5C3  H192  C19  C18   110.12  3.000
 5C3  H191  C19  C18   109.06  3.000
 5C3  C20   C19  C18   111.08  3.000
 5C3  C18   C11  NP2   114.44  3.000
 5C3  C18   C11  O08   124.44  3.000
 5C3  NP2   C11  O08   121.10  3.000
 5C3  H202  C20  H201  106.60  3.000
 5C3  H202  C20  C19   109.50  3.000
 5C3  H201  C20  C19   109.35  3.000
 5C3  H202  C20  C15   110.28  3.000
 5C3  H201  C20  C15   108.91  3.000
 5C3  C19   C20  C15   112.04  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
 5C3  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 5C3  CONST_02  C04   C05  C06  C01    0.00   0.0  0
 5C3  CONST_03  C05   C06  C01  C02    0.00   0.0  0
 5C3  CONST_04  C05   C04  C03  C02    0.00   0.0  0
 5C3  CONST_05  C06   C01  C02  C03    0.00   0.0  0
 5C3  CONST_06  C06   C05  C04  C03    0.00   0.0  0
 5C3  CONST_07  S11   C03  C02  C01  180.00   0.0  0
 5C3  CONST_08  S11   C03  C04  C05  180.00   0.0  0
 5C3  CONST_09  H05   C05  C06  C01  180.00   0.0  0
 5C3  CONST_10  H06   C06  C01  C02  180.00   0.0  0
 5C3  CONST_11  H04   C04  C03  C02  180.00   0.0  0
 5C3  CONST_12  H01   C01  C02  C03  180.00   0.0  0
 5C3  CONST_13  H02   C02  C03  C04  180.00   0.0  0
 5C3  CONST_14  C18   C11  NP2  S11  180.00   0.0  0
 5C3  CONST_15  HP2   NP2  C11  C18    0.00   0.0  0
 5C3  CONST_16  S11   NP2  C11  O08    0.00   0.0  0
 5C3  Var_01    C18   C17  C16  C15  -56.38  30.0  1
 5C3  Var_02    C18   C19  C20  C15   55.70  30.0  1
 5C3  Var_03    NP2   S11  C03  C02   76.25  30.0  2
 5C3  Var_04    C11   NP2  S11  C03   63.98  30.0  3
 5C3  Var_05    H091  N09  C10  C15  179.08  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
 5C3  chir_01  C15  C10  C16  C20  negativ
 5C3  chir_02  C18  C17  C19  C11  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
 5C3  plan-1  C01  0.020
 5C3  plan-1  C02  0.020
 5C3  plan-1  C03  0.020
 5C3  plan-1  C04  0.020
 5C3  plan-1  C05  0.020
 5C3  plan-1  C06  0.020
 5C3  plan-1  S11  0.020
 5C3  plan-1  H01  0.020
 5C3  plan-1  H02  0.020
 5C3  plan-1  H06  0.020
 5C3  plan-1  H04  0.020
 5C3  plan-1  H05  0.020
 5C3  plan-2  O08  0.020
 5C3  plan-2  S11  0.020
 5C3  plan-2  NP2  0.020
 5C3  plan-2  C18  0.020
 5C3  plan-2  C11  0.020
 5C3  plan-2  HP2  0.020

