# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:30:45 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (1-methylcyclohexyl)carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(CCCCC1)NC(O)=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
 12K  12K  '(1-methylcyclohexyl)carbamic acid'  ligand  26  11  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_12K
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
 12K  C1   C  C     0   0.679   1.9705   0.3498  -0.1641
 12K  O2   O  O     0  -0.519   2.4180   0.0306   0.9214
 12K  N3   N  NH1   0  -0.659   0.7633   0.0320  -0.6548
 12K  C4   C  CT    0   0.114  -0.2370  -0.8147   0.0005
 12K  C5   C  CH3   0  -0.643   0.2997  -2.2323   0.1935
 12K  C6   C  CH2   0  -0.453  -1.4490  -0.8580  -0.9419
 12K  C7   C  CH2   0  -0.438  -2.1573   0.4863  -1.0922
 12K  C8   C  CH2   0  -0.429  -2.5600   1.0507   0.2653
 12K  C9   C  CH2   0  -0.432  -1.3575   1.1382   1.1981
 12K  C10  C  CH2   0  -0.417  -0.6806  -0.2188   1.3456
 12K  H1   H  HNH1  0   0.398   0.5599   0.3416  -1.5921
 12K  H2   H  HCH3  0   0.237   1.1567  -2.2512   0.8657
 12K  H3   H  HCH3  0   0.223  -0.4753  -2.8702   0.6212
 12K  H4   H  HCH3  0   0.227   0.6031  -2.6655  -0.7614
 12K  H5   H  HCH2  0   0.240  -1.1393  -1.2433  -1.9188
 12K  H6   H  HCH2  0   0.235  -2.1553  -1.5868  -0.5343
 12K  H7   H  HCH2  0   0.213  -1.5134   1.2066  -1.6073
 12K  H8   H  HCH2  0   0.235  -3.0355   0.3603  -1.7295
 12K  H9   H  HCH2  0   0.228  -3.0247   2.0324   0.1456
 12K  H10  H  HCH2  0   0.210  -3.3166   0.3983   0.7154
 12K  H11  H  HCH2  0   0.213  -0.6426   1.8696   0.8084
 12K  H12  H  HCH2  0   0.228  -1.6657   1.5012   2.1814
 12K  H13  H  HCH2  0   0.217  -1.3872  -0.9230   1.7978
 12K  H14  H  HCH2  0   0.240   0.1682  -0.1590   2.0276
 12K  OXT  O  OH1   0  -0.628   2.6628   1.0960  -1.0403
 12K  HXT  H  HOH1  0   0.479   3.5216   1.3126  -0.6555

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
 12K  C5   C4   single  1.528  0.020  1.528
 12K  C1   N3   single  1.341  0.020  1.341
 12K  C1   O2   double  1.217  0.020  1.217
 12K  N3   C4   single  1.465  0.020  1.465
 12K  C4   C6   single  1.536  0.020  1.536
 12K  C4   C10  single  1.537  0.020  1.537
 12K  C6   C7   single  1.527  0.020  1.527
 12K  C7   C8   single  1.524  0.020  1.524
 12K  C10  C9   single  1.524  0.020  1.524
 12K  C9   C8   single  1.524  0.020  1.524
 12K  N3   H1   single  0.860  0.020  1.020
 12K  C5   H2   single  0.970  0.020  1.090
 12K  C5   H3   single  0.970  0.020  1.090
 12K  C5   H4   single  0.970  0.020  1.090
 12K  C6   H5   single  0.970  0.020  1.090
 12K  C6   H6   single  0.970  0.020  1.090
 12K  C7   H7   single  0.970  0.020  1.090
 12K  C7   H8   single  0.970  0.020  1.090
 12K  C8   H9   single  0.970  0.020  1.090
 12K  C8   H10  single  0.970  0.020  1.090
 12K  C9   H11  single  0.970  0.020  1.090
 12K  C9   H12  single  0.970  0.020  1.090
 12K  C10  H13  single  0.970  0.020  1.090
 12K  C10  H14  single  0.970  0.020  1.090
 12K  C1   OXT  single  1.343  0.020  1.343
 12K  OXT  HXT  single  0.850  0.020  0.980

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
 12K  OXT  C1   N3   110.91  3.000
 12K  OXT  C1   O2   122.56  3.000
 12K  N3   C1   O2   126.53  3.000
 12K  H1   N3   C4   117.11  3.000
 12K  H1   N3   C1   116.69  3.000
 12K  C4   N3   C1   125.99  3.000
 12K  C10  C4   C6   108.68  3.000
 12K  C10  C4   C5   110.52  3.000
 12K  C6   C4   C5   109.18  3.000
 12K  C10  C4   N3   111.37  3.000
 12K  C6   C4   N3   106.30  3.000
 12K  C5   C4   N3   110.66  3.000
 12K  H4   C5   H3   107.96  3.000
 12K  H4   C5   H2   108.32  3.000
 12K  H3   C5   H2   107.87  3.000
 12K  H4   C5   C4   110.81  3.000
 12K  H3   C5   C4   110.02  3.000
 12K  H2   C5   C4   111.74  3.000
 12K  H6   C6   H5   106.30  3.000
 12K  H6   C6   C7   108.89  3.000
 12K  H5   C6   C7   110.68  3.000
 12K  H6   C6   C4   107.44  3.000
 12K  H5   C6   C4   109.52  3.000
 12K  C7   C6   C4   113.68  3.000
 12K  H8   C7   H7   105.91  3.000
 12K  H8   C7   C8   110.48  3.000
 12K  H7   C7   C8   109.31  3.000
 12K  H8   C7   C6   109.20  3.000
 12K  H7   C7   C6   110.65  3.000
 12K  C8   C7   C6   111.15  3.000
 12K  H10  C8   H9   106.64  3.000
 12K  H10  C8   C9   109.12  3.000
 12K  H9   C8   C9   110.55  3.000
 12K  H10  C8   C7   109.13  3.000
 12K  H9   C8   C7   110.33  3.000
 12K  C9   C8   C7   110.96  3.000
 12K  H12  C9   H11  106.42  3.000
 12K  H12  C9   C10  109.52  3.000
 12K  H11  C9   C10  109.84  3.000
 12K  H12  C9   C8   110.32  3.000
 12K  H11  C9   C8   109.62  3.000
 12K  C10  C9   C8   111.01  3.000
 12K  H14  C10  H13  106.21  3.000
 12K  H14  C10  C9   110.95  3.000
 12K  H13  C10  C9   109.02  3.000
 12K  H14  C10  C4   110.12  3.000
 12K  H13  C10  C4   107.35  3.000
 12K  C9   C10  C4   112.89  3.000
 12K  HXT  OXT  C1   108.85  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
 12K  CONST_01  HXT  OXT  C1   O2    0.00   0.0  0
 12K  Var_01    C8   C7   C6   C4  -54.72  30.0  1
 12K  Var_02    C8   C9   C10  C4   56.90  30.0  1
 12K  Var_03    C9   C8   C7   C6   54.58  30.0  1
 12K  Var_04    C10  C9   C8   C7  -55.86  30.0  1
 12K  Var_05    C4   N3   C1   O2   -2.81  30.0  2

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
 12K  chir_01  C4  N3  C6  C10  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
 12K  plan-1  C1   0.020
 12K  plan-1  O2   0.020
 12K  plan-1  N3   0.020
 12K  plan-1  OXT  0.020
 12K  plan-1  HXT  0.020

