# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:07:00 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-amino-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}-3-fluorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1F)C(=O)NC2(CCCCC2)C(=O)NCC#N
#
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
 I37  I37  4-amino-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}-3-fluorobenzamide  ligand  42  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I37
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
 I37  N1   N  NS    0  -0.269   1.7971  -4.3343  -1.6029
 I37  C1   C  CSP   0   0.128   2.0884  -3.7986  -0.6285
 I37  C2   C  CH2   0  -0.378   2.4558  -3.1330   0.6269
 I37  N3   N  NH1   0  -0.634   2.0271  -1.7654   0.6653
 I37  C4   C  C     0   0.611   2.5953  -0.8405  -0.1360
 I37  O5   O  O     0  -0.467   3.5425  -1.1132  -0.8508
 I37  C6   C  CT    0  -0.018   2.0456   0.5853   0.0065
 I37  C7   C  CH2   0  -0.452   2.6395   1.1709   1.3048
 I37  C8   C  CH2   0  -0.454   2.3003   2.6473   1.5006
 I37  C9   C  CH2   0  -0.429   2.6979   3.4813   0.2903
 I37  C10  C  CH2   0  -0.441   2.0867   2.9163  -0.9858
 I37  C11  C  CH2   0  -0.413   2.4753   1.4559  -1.1831
 I37  N12  N  NH1   0  -0.705   0.5992   0.5377   0.1560
 I37  C13  C  C     0   0.542  -0.2105  -0.0604  -0.7482
 I37  O14  O  O     0  -0.474   0.2423  -0.6702  -1.7073
 I37  C15  C  CR6   0  -0.036  -1.6726   0.0426  -0.5120
 I37  C16  C  CR16  0  -0.468  -2.2297   0.3779   0.7251
 I37  C17  C  CR6   0   0.516  -3.5922   0.4397   0.8651
 I37  C18  C  CR6   0   0.175  -4.4847   0.1812  -0.1816
 I37  C19  C  CR16  0  -0.318  -3.9090  -0.1622  -1.4112
 I37  C20  C  CR16  0  -0.275  -2.5387  -0.2363  -1.5673
 I37  N21  N  NH2   0  -0.847  -5.8319   0.3071  -0.0143
 I37  F22  F  F     0  -0.322  -4.1161   0.7527   2.0673
 I37  H1   H  HCH2  0   0.332   1.9883  -3.6735   1.4484
 I37  H2   H  HCH2  0   0.314   3.5352  -3.2206   0.7549
 I37  H3   H  HNH1  0   0.414   1.1848  -1.5508   1.1736
 I37  H4   H  HCH2  0   0.256   2.3045   0.5885   2.1671
 I37  H5   H  HCH2  0   0.253   3.7259   1.0604   1.2523
 I37  H6   H  HCH2  0   0.220   1.2311   2.7786   1.6993
 I37  H7   H  HCH2  0   0.249   2.8102   3.0048   2.3975
 I37  H8   H  HCH2  0   0.234   2.3962   4.5211   0.4342
 I37  H9   H  HCH2  0   0.216   3.7890   3.4807   0.1960
 I37  H10  H  HCH2  0   0.216   0.9973   3.0194  -0.9554
 I37  H11  H  HCH2  0   0.237   2.4219   3.4919  -1.8515
 I37  H12  H  HCH2  0   0.233   3.5606   1.3898  -1.2850
 I37  H13  H  HCH2  0   0.249   2.0515   1.0658  -2.1079
 I37  H14  H  HNH1  0   0.408   0.1905   1.1326   0.8577
 I37  H15  H  HCR6  0   0.273  -1.6244   0.5699   1.6026
 I37  H16  H  HCR6  0   0.274  -4.5578  -0.3763  -2.2516
 I37  H17  H  HCR6  0   0.261  -2.1361  -0.5135  -2.5318
 I37  H18  H  HNH2  0   0.392  -6.2037   0.2248   0.9173
 I37  H19  H  HNH2  0   0.394  -6.4152  -0.1219  -0.7137

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
 I37  C10  C11  single    1.524  0.020  1.524
 I37  C10  C9   single    1.524  0.020  1.524
 I37  C11  C6   single    1.535  0.020  1.535
 I37  O14  C13  double    1.223  0.020  1.223
 I37  C9   C8   single    1.523  0.020  1.523
 I37  C13  C15  single    1.485  0.020  1.485
 I37  C13  N12  single    1.353  0.020  1.353
 I37  C16  C15  aromatic  1.398  0.020  1.398
 I37  C16  C17  aromatic  1.371  0.020  1.371
 I37  F22  C17  single    1.348  0.020  1.348
 I37  C15  C20  aromatic  1.393  0.020  1.393
 I37  C17  C18  aromatic  1.400  0.020  1.400
 I37  N12  C6   single    1.455  0.020  1.455
 I37  C6   C4   single    1.535  0.020  1.535
 I37  C6   C7   single    1.543  0.020  1.543
 I37  N3   C2   single    1.434  0.020  1.434
 I37  N3   C4   single    1.349  0.020  1.349
 I37  N1   C1   triple    1.150  0.020  1.150
 I37  C20  C19  aromatic  1.381  0.020  1.381
 I37  C1   C2   single    1.468  0.020  1.468
 I37  C18  C19  aromatic  1.400  0.020  1.400
 I37  C18  N21  single    1.363  0.020  1.363
 I37  C8   C7   single    1.528  0.020  1.528
 I37  C4   O5   double    1.218  0.020  1.218
 I37  C2   H1   single    0.970  0.020  1.090
 I37  C2   H2   single    0.970  0.020  1.090
 I37  N3   H3   single    0.860  0.020  1.020
 I37  C7   H4   single    0.970  0.020  1.090
 I37  C7   H5   single    0.970  0.020  1.090
 I37  C8   H6   single    0.970  0.020  1.090
 I37  C8   H7   single    0.970  0.020  1.090
 I37  C9   H8   single    0.970  0.020  1.090
 I37  C9   H9   single    0.970  0.020  1.090
 I37  C10  H10  single    0.970  0.020  1.090
 I37  C10  H11  single    0.970  0.020  1.090
 I37  C11  H12  single    0.970  0.020  1.090
 I37  C11  H13  single    0.970  0.020  1.090
 I37  N12  H14  single    0.860  0.020  1.020
 I37  C16  H15  single    0.930  0.020  1.080
 I37  C19  H16  single    0.930  0.020  1.080
 I37  C20  H17  single    0.930  0.020  1.080
 I37  N21  H18  single    0.890  0.020  1.040
 I37  N21  H19  single    0.890  0.020  1.040

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
 I37  C2   C1   N1   180.00  3.000
 I37  H2   C2   H1   107.25  3.000
 I37  H2   C2   N3   111.68  3.000
 I37  H1   C2   N3   108.96  3.000
 I37  H2   C2   C1   108.17  3.000
 I37  H1   C2   C1   108.22  3.000
 I37  N3   C2   C1   112.37  3.000
 I37  H3   N3   C4   120.40  3.000
 I37  H3   N3   C2   117.83  3.000
 I37  C4   N3   C2   120.80  3.000
 I37  C6   C4   O5   122.77  3.000
 I37  O5   C4   N3   121.52  3.000
 I37  C6   C4   N3   115.52  3.000
 I37  N12  C6   C11  112.11  3.000
 I37  N12  C6   C7   107.97  3.000
 I37  C11  C6   C7   109.21  3.000
 I37  C7   C6   C4   107.03  3.000
 I37  N12  C6   C4   109.59  3.000
 I37  C11  C6   C4   110.76  3.000
 I37  H5   C7   H4   106.77  3.000
 I37  H5   C7   C8   108.94  3.000
 I37  H4   C7   C8   110.23  3.000
 I37  H5   C7   C6   107.68  3.000
 I37  H4   C7   C6   110.10  3.000
 I37  C8   C7   C6   112.90  3.000
 I37  H7   C8   H6   105.52  3.000
 I37  H7   C8   C9   110.59  3.000
 I37  H6   C8   C9   109.48  3.000
 I37  H7   C8   C7   108.54  3.000
 I37  H6   C8   C7   110.84  3.000
 I37  C9   C8   C7   111.69  3.000
 I37  H9   C9   H8   106.69  3.000
 I37  H9   C9   C10  109.11  3.000
 I37  H8   C9   C10  110.65  3.000
 I37  H9   C9   C8   109.16  3.000
 I37  H8   C9   C8   110.15  3.000
 I37  C10  C9   C8   110.97  3.000
 I37  H11  C10  H10  106.13  3.000
 I37  H11  C10  C11  108.92  3.000
 I37  H10  C10  C11  110.34  3.000
 I37  H11  C10  C9   110.20  3.000
 I37  H10  C10  C9   109.94  3.000
 I37  C11  C10  C9   111.19  3.000
 I37  H13  C11  H12  106.60  3.000
 I37  H13  C11  C10  110.72  3.000
 I37  H12  C11  C10  108.87  3.000
 I37  H13  C11  C6   110.23  3.000
 I37  H12  C11  C6   108.43  3.000
 I37  C10  C11  C6   111.82  3.000
 I37  H14  N12  C13  118.95  3.000
 I37  H14  N12  C6   117.13  3.000
 I37  C13  N12  C6   122.73  3.000
 I37  C15  C13  O14  121.59  3.000
 I37  C15  C13  N12  116.89  3.000
 I37  O14  C13  N12  121.51  3.000
 I37  C20  C15  C16  118.07  3.000
 I37  C20  C15  C13  118.54  3.000
 I37  C16  C15  C13  123.37  3.000
 I37  H15  C16  C17  117.69  3.000
 I37  H15  C16  C15  122.47  3.000
 I37  C17  C16  C15  119.83  3.000
 I37  F22  C17  C18  117.51  3.000
 I37  C18  C17  C16  123.30  3.000
 I37  F22  C17  C16  119.19  3.000
 I37  N21  C18  C19  122.45  3.000
 I37  N21  C18  C17  121.42  3.000
 I37  C19  C18  C17  116.09  3.000
 I37  H16  C19  C20  119.74  3.000
 I37  H16  C19  C18  118.91  3.000
 I37  C20  C19  C18  121.35  3.000
 I37  H17  C20  C19  118.94  3.000
 I37  H17  C20  C15  119.70  3.000
 I37  C19  C20  C15  121.36  3.000
 I37  H19  N21  H18  113.21  3.000
 I37  H19  N21  C18  116.62  3.000
 I37  H18  N21  C18  118.11  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
 I37  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 I37  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 I37  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 I37  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 I37  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 I37  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 I37  CONST_07  C17  C16  C15  C13   180.00   0.0  0
 I37  CONST_08  C19  C20  C15  C13   180.00   0.0  0
 I37  CONST_09  F22  C17  C16  C15   180.00   0.0  0
 I37  CONST_10  N21  C18  C17  C16   180.00   0.0  0
 I37  CONST_11  F22  C17  C18  C19   180.00   0.0  0
 I37  CONST_12  N21  C18  C19  C20   180.00   0.0  0
 I37  CONST_13  H16  C19  C20  C15   180.00   0.0  0
 I37  CONST_14  H17  C20  C15  C16   180.00   0.0  0
 I37  CONST_15  H15  C16  C17  C18   180.00   0.0  0
 I37  CONST_16  C15  C13  N12  C6    180.00   0.0  0
 I37  CONST_19  C6   C4   N3   C2    180.00   0.0  0
 I37  CONST_20  O14  C13  N12  C6      0.00   0.0  0
 I37  CONST_21  H3   N3   C4   C6      0.00   0.0  0
 I37  CONST_22  H14  N12  C13  C15     0.00   0.0  0
 I37  CONST_23  O5   C4   N3   C2      0.00   0.0  0
 I37  Var_01    C9   C10  C11  C6     57.84  30.0  1
 I37  Var_02    C9   C8   C7   C6    -53.91  30.0  1
 I37  Var_03    C10  C9   C8   C7     54.08  30.0  1
 I37  Var_04    C11  C10  C9   C8    -56.16  30.0  1
 I37  Var_05    C16  C15  C13  N12   -18.13  30.0  2
 I37  Var_06    N3   C2   C1   N1   -141.80  30.0  3
 I37  Var_07    C4   N3   C2   C1    -68.85  30.0  1

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
 I37  chir_01  C6  C11  C4  C7  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
 I37  plan-1  C13  0.020
 I37  plan-1  C15  0.020
 I37  plan-1  C16  0.020
 I37  plan-1  C17  0.020
 I37  plan-1  C18  0.020
 I37  plan-1  C19  0.020
 I37  plan-1  C20  0.020
 I37  plan-1  N21  0.020
 I37  plan-1  F22  0.020
 I37  plan-1  H15  0.020
 I37  plan-1  H16  0.020
 I37  plan-1  H17  0.020
 I37  plan-2  C6   0.020
 I37  plan-2  N12  0.020
 I37  plan-2  C13  0.020
 I37  plan-2  O14  0.020
 I37  plan-2  C15  0.020
 I37  plan-2  H14  0.020
 I37  plan-3  C18  0.020
 I37  plan-3  N21  0.020
 I37  plan-3  H18  0.020
 I37  plan-3  H19  0.020
 I37  plan-4  C2   0.020
 I37  plan-4  N3   0.020
 I37  plan-4  C4   0.020
 I37  plan-4  O5   0.020
 I37  plan-4  C6   0.020
 I37  plan-4  H3   0.020

