# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:22:44 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: cis-4-methylcyclohexanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC[C@H](N)CC1
#
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
 2MH  2MH  cis-4-methylcyclohexanamine  ligand  23  8  .  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_2MH
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
 2MH  N1    N  NH2   0  -0.799  -1.9752  -0.0189   1.1639
 2MH  C5    C  CH1   0  -0.085  -1.6316  -0.0004  -0.2540
 2MH  C6    C  CH2   0  -0.438  -0.8262  -1.2495  -0.6070
 2MH  C4    C  CH2   0  -0.438  -0.8182   1.2526  -0.5722
 2MH  C3    C  CH2   0  -0.398   0.5592   1.2420   0.0832
 2MH  C2    C  CH1   0  -0.229   1.3570  -0.0096  -0.2791
 2MH  C1    C  CH3   0  -0.652   2.7128  -0.0246   0.4138
 2MH  C7    C  CH2   0  -0.399   0.5511  -1.2656   0.0482
 2MH  HN11  H  HNH2  0   0.338  -2.5577   0.7820   1.3772
 2MH  HN12  H  HNH2  0   0.338  -2.5491  -0.8308   1.3587
 2MH  H5    H  HCH1  0   0.203  -2.5278   0.0106  -0.8934
 2MH  H61   H  HCH2  0   0.222  -1.3894  -2.1452  -0.3263
 2MH  H62   H  HCH2  0   0.212  -0.7121  -1.2910  -1.6950
 2MH  H41   H  HCH2  0   0.212  -0.7038   1.3238  -1.6587
 2MH  H42   H  HCH2  0   0.222  -1.3757   2.1439  -0.2671
 2MH  H31   H  HCH2  0   0.216   1.1146   2.1348  -0.2192
 2MH  H32   H  HCH2  0   0.203   0.4511   1.2978   1.1708
 2MH  H2    H  HCH1  0   0.201   1.5261   0.0051  -1.3647
 2MH  H11   H  HCH3  0   0.210   2.5908  -0.0425   1.4995
 2MH  H12   H  HCH3  0   0.221   3.2965  -0.9031   0.1314
 2MH  H13   H  HCH3  0   0.221   3.3018   0.8591   0.1604
 2MH  H71   H  HCH2  0   0.203   0.4425  -1.3512   1.1338
 2MH  H72   H  HCH2  0   0.216   1.1010  -2.1530  -0.2790

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
 2MH  N1  C5    single  1.459  0.020  1.459
 2MH  C5  C6    single  1.528  0.020  1.528
 2MH  C5  C4    single  1.527  0.020  1.527
 2MH  C6  C7    single  1.525  0.020  1.525
 2MH  C4  C3    single  1.525  0.020  1.525
 2MH  C3  C2    single  1.528  0.020  1.528
 2MH  C2  C1    single  1.523  0.020  1.523
 2MH  C2  C7    single  1.528  0.020  1.528
 2MH  N1  HN11  single  0.890  0.020  1.040
 2MH  N1  HN12  single  0.890  0.020  1.040
 2MH  C5  H5    single  0.970  0.020  1.090
 2MH  C6  H61   single  0.970  0.020  1.090
 2MH  C6  H62   single  0.970  0.020  1.090
 2MH  C4  H41   single  0.970  0.020  1.090
 2MH  C4  H42   single  0.970  0.020  1.090
 2MH  C3  H31   single  0.970  0.020  1.090
 2MH  C3  H32   single  0.970  0.020  1.090
 2MH  C2  H2    single  0.970  0.020  1.090
 2MH  C1  H11   single  0.970  0.020  1.090
 2MH  C1  H12   single  0.970  0.020  1.090
 2MH  C1  H13   single  0.970  0.020  1.090
 2MH  C7  H71   single  0.970  0.020  1.090
 2MH  C7  H72   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
 2MH  HN12  N1  HN11  105.51  3.000
 2MH  HN12  N1  C5    109.29  3.000
 2MH  HN11  N1  C5    109.27  3.000
 2MH  H5    C5  C4    107.72  3.000
 2MH  H5    C5  C6    107.65  3.000
 2MH  C4    C5  C6    109.99  3.000
 2MH  H5    C5  N1    111.89  3.000
 2MH  C4    C5  N1    109.77  3.000
 2MH  C6    C5  N1    109.77  3.000
 2MH  H62   C6  H61   106.10  3.000
 2MH  H62   C6  C7    109.41  3.000
 2MH  H61   C6  C7    110.23  3.000
 2MH  H62   C6  C5    108.40  3.000
 2MH  H61   C6  C5    109.79  3.000
 2MH  C7    C6  C5    112.68  3.000
 2MH  H42   C4  H41   106.07  3.000
 2MH  H42   C4  C3    110.23  3.000
 2MH  H41   C4  C3    109.42  3.000
 2MH  H42   C4  C5    109.79  3.000
 2MH  H41   C4  C5    108.40  3.000
 2MH  C3    C4  C5    112.69  3.000
 2MH  H32   C3  H31   106.45  3.000
 2MH  H32   C3  C2    109.21  3.000
 2MH  H31   C3  C2    109.75  3.000
 2MH  H32   C3  C4    109.72  3.000
 2MH  H31   C3  C4    109.50  3.000
 2MH  C2    C3  C4    112.05  3.000
 2MH  H2    C2  C7    107.68  3.000
 2MH  H2    C2  C1    108.22  3.000
 2MH  C7    C2  C1    111.36  3.000
 2MH  H2    C2  C3    107.68  3.000
 2MH  C7    C2  C3    110.32  3.000
 2MH  C1    C2  C3    111.42  3.000
 2MH  H13   C1  H12   107.63  3.000
 2MH  H13   C1  H11   107.70  3.000
 2MH  H12   C1  H11   107.67  3.000
 2MH  H13   C1  C2    111.52  3.000
 2MH  H12   C1  C2    111.48  3.000
 2MH  H11   C1  C2    110.66  3.000
 2MH  H72   C7  H71   106.45  3.000
 2MH  H72   C7  C2    109.73  3.000
 2MH  H71   C7  C2    109.22  3.000
 2MH  H72   C7  C6    109.51  3.000
 2MH  H71   C7  C6    109.71  3.000
 2MH  C2    C7  C6    112.06  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
 2MH  Var_01  C2  C7  C6  C5  -55.09  30.0  1
 2MH  Var_02  C2  C3  C4  C5   55.10  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
 2MH  chir_01  C5  N1  C6  C4  positiv
 2MH  chir_02  C2  C3  C1  C7  negativ

