# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:21:42 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-amino-4-bromo-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Br)ccc1C(=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
 3Y1  3Y1  2-amino-4-bromo-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}benzamide  ligand  42  23  .  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_3Y1
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
 3Y1  C1   C   CSP   0   0.127  -4.7302   3.1526   1.2110
 3Y1  C2   C   CH2   0  -0.374  -3.4247   3.0383   0.5519
 3Y1  C4   C   C     0   0.611  -3.4793   0.7100  -0.1042
 3Y1  C6   C   CT    0  -0.024  -2.8743  -0.6860   0.0924
 3Y1  C8   C   CH2   0  -0.442  -2.8827  -3.0738  -0.7612
 3Y1  C9   C   CH2   0  -0.429  -3.4281  -3.5790   0.5685
 3Y1  C10  C   CH2   0  -0.453  -3.0108  -2.6638   1.7115
 3Y1  C11  C   CH2   0  -0.452  -3.4019  -1.2120   1.4439
 3Y1  C15  C   CR6   0  -0.100   0.8016  -0.0314  -0.5436
 3Y1  C16  C   CR6   0   0.334   1.7003  -0.0741  -1.6350
 3Y1  C20  C   CR16  0  -0.295   1.3104   0.0396   0.7530
 3Y1  N1   N   NS    0  -0.267  -5.7487   3.2522   1.7349
 3Y1  N3   N   NH1   0  -0.635  -2.9063   1.7020   0.6052
 3Y1  O5   O   O     0  -0.466  -4.4721   0.9075  -0.7817
 3Y1  C7   C   CH2   0  -0.413  -3.3178  -1.6374  -1.0285
 3Y1  N12  N   NH1   0  -0.687  -1.4251  -0.5863   0.1847
 3Y1  O14  O   O     0  -0.486  -1.1703   0.5111  -1.7618
 3Y1  C17  C   CR16  0  -0.304   3.0796  -0.0844  -1.3587
 3Y1  C18  C   CR6   0  -0.104   3.5330  -0.0250  -0.0595
 3Y1  C19  C   CR16  0  -0.259   2.6652   0.0469   1.0236
 3Y1  N21  N   NH2   0  -0.862   1.2894  -0.1732  -2.9271
 3Y1  BR2  BR  BR    0  -0.040   5.3941  -0.0266   0.2570
 3Y1  H1   H   HCH2  0   0.315  -3.5300   3.3925  -0.4750
 3Y1  H2   H   HCH2  0   0.333  -2.7290   3.7071   1.0557
 3Y1  H3   H   HCH2  0   0.216  -1.7903  -3.1487  -0.7689
 3Y1  H4   H   HCH2  0   0.238  -3.2353  -3.7068  -1.5784
 3Y1  H5   H   HCH2  0   0.216  -4.5214  -3.6174   0.5184
 3Y1  H6   H   HCH2  0   0.235  -3.0869  -4.5985   0.7609
 3Y1  H7   H   HCH2  0   0.250  -3.4764  -2.9810   2.6467
 3Y1  H8   H   HCH2  0   0.222  -1.9315  -2.7525   1.8758
 3Y1  H9   H   HCH2  0   0.256  -3.0545  -0.5727   2.2597
 3Y1  H10  H   HCH2  0   0.255  -4.4925  -1.1365   1.4261
 3Y1  H11  H   HCR6  0   0.267   0.6317   0.1216   1.5926
 3Y1  H12  H   HNH1  0   0.413  -2.1094   1.5282   1.1948
 3Y1  H13  H   HCH2  0   0.234  -4.4071  -1.6047  -1.0963
 3Y1  H14  H   HCH2  0   0.251  -2.9358  -1.2910  -1.9885
 3Y1  H15  H   HNH1  0   0.411  -0.9662  -1.1384   0.8916
 3Y1  H16  H   HCR6  0   0.285   3.7753  -0.1316  -2.1871
 3Y1  H17  H   HCR6  0   0.277   3.0221   0.1151   2.0410
 3Y1  H18  H   HNH2  0   0.398   0.3603   0.1429  -3.1475
 3Y1  H19  H   HNH2  0   0.391   1.9757   0.0031  -3.6413
 3Y1  C13  C   C     0   0.557  -0.6664  -0.0132  -0.7743

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
 3Y1  C9   C10  single    1.523  0.020  1.523
 3Y1  C9   C8   single    1.523  0.020  1.523
 3Y1  C10  C11  single    1.527  0.020  1.527
 3Y1  C8   C7   single    1.524  0.020  1.524
 3Y1  C11  C6   single    1.543  0.020  1.543
 3Y1  C7   C6   single    1.536  0.020  1.536
 3Y1  C6   N12  single    1.455  0.020  1.455
 3Y1  C6   C4   single    1.534  0.020  1.534
 3Y1  N12  C13  single    1.350  0.020  1.350
 3Y1  C4   N3   single    1.347  0.020  1.347
 3Y1  C4   O5   double    1.218  0.020  1.218
 3Y1  C20  C19  aromatic  1.382  0.020  1.382
 3Y1  C20  C15  aromatic  1.395  0.020  1.395
 3Y1  N3   C2   single    1.434  0.020  1.434
 3Y1  C13  C15  single    1.486  0.020  1.486
 3Y1  C13  O14  double    1.226  0.020  1.226
 3Y1  C19  C18  aromatic  1.390  0.020  1.390
 3Y1  C15  C16  aromatic  1.414  0.020  1.414
 3Y1  C2   C1   single    1.467  0.020  1.467
 3Y1  C18  BR2  single    1.888  0.020  1.888
 3Y1  C18  C17  aromatic  1.377  0.020  1.377
 3Y1  C16  C17  aromatic  1.407  0.020  1.407
 3Y1  C16  N21  single    1.359  0.020  1.359
 3Y1  C1   N1   triple    1.150  0.020  1.150
 3Y1  C2   H1   single    0.970  0.020  1.090
 3Y1  C2   H2   single    0.970  0.020  1.090
 3Y1  C8   H3   single    0.970  0.020  1.090
 3Y1  C8   H4   single    0.970  0.020  1.090
 3Y1  C9   H5   single    0.970  0.020  1.090
 3Y1  C9   H6   single    0.970  0.020  1.090
 3Y1  C10  H7   single    0.970  0.020  1.090
 3Y1  C10  H8   single    0.970  0.020  1.090
 3Y1  C11  H9   single    0.970  0.020  1.090
 3Y1  C11  H10  single    0.970  0.020  1.090
 3Y1  C20  H11  single    0.930  0.020  1.080
 3Y1  N3   H12  single    0.860  0.020  1.020
 3Y1  C7   H13  single    0.970  0.020  1.090
 3Y1  C7   H14  single    0.970  0.020  1.090
 3Y1  N12  H15  single    0.860  0.020  1.020
 3Y1  C17  H16  single    0.930  0.020  1.080
 3Y1  C19  H17  single    0.930  0.020  1.080
 3Y1  N21  H18  single    0.890  0.020  1.040
 3Y1  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
 3Y1  N1   C1   C2   180.00  3.000
 3Y1  H2   C2   H1   107.33  3.000
 3Y1  H2   C2   N3   108.92  3.000
 3Y1  H1   C2   N3   111.85  3.000
 3Y1  H2   C2   C1   108.23  3.000
 3Y1  H1   C2   C1   108.16  3.000
 3Y1  N3   C2   C1   112.18  3.000
 3Y1  O5   C4   N3   121.33  3.000
 3Y1  O5   C4   C6   122.70  3.000
 3Y1  N3   C4   C6   115.77  3.000
 3Y1  N12  C6   C7   112.10  3.000
 3Y1  N12  C6   C11  107.95  3.000
 3Y1  C7   C6   C11  109.23  3.000
 3Y1  N12  C6   C4   109.78  3.000
 3Y1  C7   C6   C4   110.87  3.000
 3Y1  C11  C6   C4   106.71  3.000
 3Y1  H4   C8   H3   106.09  3.000
 3Y1  H4   C8   C7   108.83  3.000
 3Y1  H3   C8   C7   110.36  3.000
 3Y1  H4   C8   C9   110.20  3.000
 3Y1  H3   C8   C9   109.91  3.000
 3Y1  C7   C8   C9   111.31  3.000
 3Y1  H6   C9   H5   106.69  3.000
 3Y1  H6   C9   C10  110.07  3.000
 3Y1  H5   C9   C10  109.21  3.000
 3Y1  H6   C9   C8   110.58  3.000
 3Y1  H5   C9   C8   109.21  3.000
 3Y1  C10  C9   C8   110.96  3.000
 3Y1  H8   C10  H7   105.57  3.000
 3Y1  H8   C10  C11  110.83  3.000
 3Y1  H7   C10  C11  108.49  3.000
 3Y1  H8   C10  C9   109.51  3.000
 3Y1  H7   C10  C9   110.58  3.000
 3Y1  C11  C10  C9   111.69  3.000
 3Y1  H10  C11  H9   106.79  3.000
 3Y1  H10  C11  C10  108.90  3.000
 3Y1  H9   C11  C10  110.11  3.000
 3Y1  H10  C11  C6   107.65  3.000
 3Y1  H9   C11  C6   110.22  3.000
 3Y1  C10  C11  C6   112.95  3.000
 3Y1  C20  C15  C16  119.15  3.000
 3Y1  C16  C15  C13  120.55  3.000
 3Y1  C20  C15  C13  120.27  3.000
 3Y1  N21  C16  C17  118.85  3.000
 3Y1  N21  C16  C15  122.92  3.000
 3Y1  C17  C16  C15  118.14  3.000
 3Y1  H11  C20  C19  117.55  3.000
 3Y1  H11  C20  C15  119.74  3.000
 3Y1  C19  C20  C15  122.69  3.000
 3Y1  H12  N3   C4   121.20  3.000
 3Y1  H12  N3   C2   117.96  3.000
 3Y1  C4   N3   C2   120.84  3.000
 3Y1  H14  C7   H13  106.59  3.000
 3Y1  H14  C7   C8   110.73  3.000
 3Y1  H13  C7   C8   108.90  3.000
 3Y1  H14  C7   C6   110.17  3.000
 3Y1  H13  C7   C6   108.35  3.000
 3Y1  C8   C7   C6   111.92  3.000
 3Y1  H15  N12  C13  118.35  3.000
 3Y1  H15  N12  C6   117.42  3.000
 3Y1  C13  N12  C6   122.92  3.000
 3Y1  H16  C17  C18  120.80  3.000
 3Y1  H16  C17  C16  118.69  3.000
 3Y1  C18  C17  C16  120.52  3.000
 3Y1  BR2  C18  C19  119.01  3.000
 3Y1  BR2  C18  C17  118.86  3.000
 3Y1  C19  C18  C17  122.13  3.000
 3Y1  H17  C19  C18  122.07  3.000
 3Y1  H17  C19  C20  120.58  3.000
 3Y1  C18  C19  C20  117.35  3.000
 3Y1  H19  N21  H18  114.80  3.000
 3Y1  H19  N21  C16  117.11  3.000
 3Y1  H18  N21  C16  117.68  3.000
 3Y1  O14  C13  N12  121.49  3.000
 3Y1  O14  C13  C15  122.42  3.000
 3Y1  N12  C13  C15  116.08  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
 3Y1  CONST_01  C18  C19  C20  C15    0.00   0.0  0
 3Y1  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 3Y1  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 3Y1  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 3Y1  CONST_05  C17  C18  C19  C20    0.00   0.0  0
 3Y1  CONST_06  C17  C16  C15  C20    0.00   0.0  0
 3Y1  CONST_07  C19  C20  C15  C13  180.00   0.0  0
 3Y1  CONST_08  C17  C16  C15  C13  180.00   0.0  0
 3Y1  CONST_09  BR2  C18  C17  C16  180.00   0.0  0
 3Y1  CONST_10  BR2  C18  C19  C20  180.00   0.0  0
 3Y1  CONST_11  N21  C16  C15  C20  180.00   0.0  0
 3Y1  CONST_12  N21  C16  C17  C18  180.00   0.0  0
 3Y1  CONST_13  H17  C19  C20  C15  180.00   0.0  0
 3Y1  CONST_14  H16  C17  C16  C15  180.00   0.0  0
 3Y1  CONST_15  H11  C20  C15  C16  180.00   0.0  0
 3Y1  CONST_16  C15  C13  N12  C6   180.00   0.0  0
 3Y1  CONST_18  H19  N21  C16  C15  180.00   0.0  0
 3Y1  CONST_19  C6   C4   N3   C2   180.00   0.0  0
 3Y1  CONST_20  O14  C13  N12  C6     0.00   0.0  0
 3Y1  CONST_21  H12  N3   C4   C6     0.00   0.0  0
 3Y1  CONST_22  H15  N12  C13  C15    0.00   0.0  0
 3Y1  CONST_23  O5   C4   N3   C2     0.00   0.0  0
 3Y1  Var_01    C9   C10  C11  C6   -53.99  30.0  1
 3Y1  Var_02    C9   C8   C7   C6    57.54  30.0  1
 3Y1  Var_03    C11  C10  C9   C8    54.09  30.0  1
 3Y1  Var_04    C7   C8   C9   C10  -56.00  30.0  1
 3Y1  Var_05    N12  C13  C15  C16  149.82  30.0  2
 3Y1  Var_06    C4   N3   C2   C1    69.53  30.0  1
 3Y1  Var_07    N3   C2   C1   N1   127.40  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
 3Y1  chir_01  C6  C7  C11  C4  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
 3Y1  plan-1  C15  0.020
 3Y1  plan-1  C16  0.020
 3Y1  plan-1  C20  0.020
 3Y1  plan-1  C17  0.020
 3Y1  plan-1  C18  0.020
 3Y1  plan-1  C19  0.020
 3Y1  plan-1  N21  0.020
 3Y1  plan-1  BR2  0.020
 3Y1  plan-1  H11  0.020
 3Y1  plan-1  H16  0.020
 3Y1  plan-1  H17  0.020
 3Y1  plan-1  C13  0.020
 3Y1  plan-2  C6   0.020
 3Y1  plan-2  C15  0.020
 3Y1  plan-2  N12  0.020
 3Y1  plan-2  O14  0.020
 3Y1  plan-2  H15  0.020
 3Y1  plan-2  C13  0.020
 3Y1  plan-3  C16  0.020
 3Y1  plan-3  N21  0.020
 3Y1  plan-3  H18  0.020
 3Y1  plan-3  H19  0.020
 3Y1  plan-4  C2   0.020
 3Y1  plan-4  C4   0.020
 3Y1  plan-4  C6   0.020
 3Y1  plan-4  N3   0.020
 3Y1  plan-4  O5   0.020
 3Y1  plan-4  H12  0.020

