# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 13:45:58 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C1CCCCC1
#
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
 WM2  WM2  'cyclohexanecarboxamide   '  ligand  22  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WM2
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
 WM2  O9   O  O     0  -0.499   2.0475  -0.5108   1.2134
 WM2  C7   C  C     0   0.535   1.7320   0.0423   0.1673
 WM2  N8   N  NH2   0  -0.803   2.6299   0.6332  -0.6357
 WM2  C1   C  CH1   0  -0.373   0.2889   0.1332  -0.2900
 WM2  C6   C  CH2   0  -0.417  -0.4288  -1.2081  -0.1394
 WM2  C5   C  CH2   0  -0.435  -1.8951  -1.0991  -0.5451
 WM2  C4   C  CH2   0  -0.429  -2.6140  -0.0123   0.2472
 WM2  C3   C  CH2   0  -0.434  -1.8990   1.3276   0.1120
 WM2  C2   C  CH2   0  -0.416  -0.4325   1.2226   0.5162
 WM2  H1   H  HNH2  0   0.396   3.6026   0.6704  -0.3769
 WM2  H2   H  HNH2  0   0.405   2.3596   1.0967  -1.4854
 WM2  H3   H  HCH1  0   0.240   0.2624   0.4224  -1.3474
 WM2  H4   H  HCH2  0   0.234   0.0716  -1.9714  -0.7412
 WM2  H5   H  HCH2  0   0.218  -0.3617  -1.5349   0.9021
 WM2  H6   H  HCH2  0   0.211  -1.9622  -0.8713  -1.6148
 WM2  H7   H  HCH2  0   0.229  -2.3890  -2.0630  -0.4020
 WM2  H8   H  HCH2  0   0.228  -3.6499   0.0789  -0.0885
 WM2  H9   H  HCH2  0   0.210  -2.6537  -0.2986   1.3038
 WM2  H10  H  HCH2  0   0.212  -1.9644   1.6689  -0.9268
 WM2  H11  H  HCH2  0   0.231  -2.3944   2.0882   0.7201
 WM2  H12  H  HCH2  0   0.221  -0.3618   0.9818   1.5819
 WM2  H13  H  HCH2  0   0.236   0.0656   2.1852   0.3750

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
 WM2  C3  C2   single  1.525  0.020  1.525
 WM2  C3  C4   single  1.525  0.020  1.525
 WM2  C2  C1   single  1.535  0.020  1.535
 WM2  O9  C7   double  1.225  0.020  1.225
 WM2  C4  C5   single  1.525  0.020  1.525
 WM2  C1  C7   single  1.517  0.020  1.517
 WM2  C1  C6   single  1.529  0.020  1.529
 WM2  C7  N8   single  1.342  0.020  1.342
 WM2  C5  C6   single  1.525  0.020  1.525
 WM2  N8  H1   single  0.860  0.020  1.020
 WM2  N8  H2   single  0.860  0.020  1.020
 WM2  C1  H3   single  0.970  0.020  1.090
 WM2  C6  H4   single  0.970  0.020  1.090
 WM2  C6  H5   single  0.970  0.020  1.090
 WM2  C5  H6   single  0.970  0.020  1.090
 WM2  C5  H7   single  0.970  0.020  1.090
 WM2  C4  H8   single  0.970  0.020  1.090
 WM2  C4  H9   single  0.970  0.020  1.090
 WM2  C3  H10  single  0.970  0.020  1.090
 WM2  C3  H11  single  0.970  0.020  1.090
 WM2  C2  H12  single  0.970  0.020  1.090
 WM2  C2  H13  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
 WM2  C1   C7  N8   115.46  3.000
 WM2  N8   C7  O9   122.53  3.000
 WM2  C1   C7  O9   122.00  3.000
 WM2  H2   N8  H1   117.39  3.000
 WM2  H2   N8  C7   121.95  3.000
 WM2  H1   N8  C7   120.58  3.000
 WM2  H3   C1  C2   107.93  3.000
 WM2  H3   C1  C6   108.36  3.000
 WM2  C2   C1  C6   110.50  3.000
 WM2  H3   C1  C7   109.25  3.000
 WM2  C6   C1  C7   111.37  3.000
 WM2  C2   C1  C7   109.35  3.000
 WM2  H5   C6  H4   106.71  3.000
 WM2  H5   C6  C5   109.49  3.000
 WM2  H4   C6  C5   110.09  3.000
 WM2  H5   C6  C1   109.10  3.000
 WM2  H4   C6  C1   110.09  3.000
 WM2  C5   C6  C1   111.25  3.000
 WM2  H7   C5  H6   106.48  3.000
 WM2  H7   C5  C4   110.34  3.000
 WM2  H6   C5  C4   109.28  3.000
 WM2  H7   C5  C6   109.67  3.000
 WM2  H6   C5  C6   109.48  3.000
 WM2  C4   C5  C6   111.46  3.000
 WM2  H9   C4  H8   106.48  3.000
 WM2  H9   C4  C3   109.40  3.000
 WM2  H8   C4  C3   110.12  3.000
 WM2  H9   C4  C5   109.39  3.000
 WM2  H8   C4  C5   110.29  3.000
 WM2  C3   C4  C5   111.05  3.000
 WM2  H11  C3  H10  106.49  3.000
 WM2  H11  C3  C2   109.66  3.000
 WM2  H10  C3  C2   109.28  3.000
 WM2  H11  C3  C4   110.48  3.000
 WM2  H10  C3  C4   109.26  3.000
 WM2  C2   C3  C4   111.53  3.000
 WM2  H13  C2  H12  106.86  3.000
 WM2  H13  C2  C3   110.09  3.000
 WM2  H12  C2  C3   109.59  3.000
 WM2  H13  C2  C1   110.05  3.000
 WM2  H12  C2  C1   108.95  3.000
 WM2  C3   C2  C1   111.20  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
 WM2  CONST_01  H1  N8  C7  C1  180.00   0.0  0
 WM2  CONST_02  H2  N8  C7  C1    0.00   0.0  0
 WM2  Var_01    C4  C3  C2  C1   55.65  30.0  1
 WM2  Var_02    C4  C5  C6  C1  -55.97  30.0  1
 WM2  Var_03    C3  C4  C5  C6   55.19  30.0  1
 WM2  Var_04    C2  C3  C4  C5  -55.11  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
 WM2  chir_01  C1  C2  C7  C6  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
 WM2  plan-1  O9  0.020
 WM2  plan-1  C7  0.020
 WM2  plan-1  N8  0.020
 WM2  plan-1  C1  0.020
 WM2  plan-1  H1  0.020
 WM2  plan-1  H2  0.020

