# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:08:01 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: [(1R,3S,5R)-3-(aminomethyl)-5-methyl-cyclohexyl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](CN)C[C@H](CO)C1
#
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
 II6  II6  '[(1R,3S,5R)-3-(aminomethyl)-5-methyl-cyclohexyl]methanol'  ligand  30  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_II6
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
 II6  C1    C  C     0  -0.379   1.2578  -0.9292   0.1944
 II6  C2    C  C     0  -0.387  -1.2576  -0.9537   0.1765
 II6  C3    C  C     0  -0.411  -0.0192   1.2194   0.2760
 II6  C4    C  CR16  0  -0.234   0.0110  -1.6712  -0.2813
 II6  C5    C  CR16  0  -0.244   1.2553   0.5405  -0.2156
 II6  C6    C  CR16  0  -0.272  -1.2745   0.5171  -0.2346
 II6  C7    C  CH3   0  -0.652   0.0205  -3.1215   0.1843
 II6  C8    C  CH2   0  -0.261   2.4883   1.2882   0.2785
 II6  C9    C  CH2   0  -0.127  -2.5140   1.2453   0.2545
 II6  N10   N  NH2   0  -0.797   3.7157   0.7363  -0.2761
 II6  O11   O  OH1   0  -0.675  -3.6663   0.6636  -0.3169
 II6  H11C  H  H     0   0.193   1.3177  -0.9923   1.2898
 II6  H12C  H  H     0   0.222   2.1545  -1.4210  -0.1905
 II6  H4    H  HCR6  0   0.204   0.0182  -1.6633  -1.3795
 II6  H5    H  HCR6  0   0.204   1.2544   0.5915  -1.3145
 II6  H21C  H  H     0   0.224  -2.1343  -1.4704  -0.2228
 II6  H22C  H  H     0   0.195  -1.3321  -1.0185   1.2709
 II6  H6    H  HCR6  0   0.211  -1.2654   0.5735  -1.3318
 II6  H31C  H  H     0   0.204  -0.0259   1.2168   1.3740
 II6  H32C  H  H     0   0.223  -0.0268   2.2707  -0.0306
 II6  H71C  H  HCH3  0   0.210   0.0124  -3.1810   1.2756
 II6  H72C  H  HCH3  0   0.221  -0.8536  -3.6649  -0.1809
 II6  H73C  H  HCH3  0   0.222   0.9098  -3.6486  -0.1671
 II6  H81C  H  HCH2  0   0.194   2.3562   2.3579   0.0561
 II6  H82C  H  HCH2  0   0.205   2.5384   1.2080   1.3695
 II6  H91C  H  HCH2  0   0.180  -2.5455   1.2001   1.3530
 II6  H92C  H  HCH2  0   0.195  -2.4317   2.3078  -0.0147
 II6  H101  H  HNH2  0   0.335   3.7284   0.8975  -1.2762
 II6  H102  H  HNH2  0   0.345   4.5089   1.2470   0.0901
 II6  H11   H  HOH1  0   0.452  -4.4347   1.1415   0.0073

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
 II6  C1   C4    single  1.527  0.020  1.527
 II6  C1   C5    single  1.526  0.020  1.526
 II6  C2   C4    single  1.528  0.020  1.528
 II6  C2   C6    single  1.527  0.020  1.527
 II6  C3   C5    single  1.525  0.020  1.525
 II6  C3   C6    single  1.526  0.020  1.526
 II6  C4   C7    single  1.523  0.020  1.523
 II6  C5   C8    single  1.524  0.020  1.524
 II6  C6   C9    single  1.519  0.020  1.519
 II6  C8   N10   single  1.456  0.020  1.456
 II6  C9   O11   single  1.412  0.020  1.412
 II6  C1   H11C  single  0.970  0.020  1.090
 II6  C1   H12C  single  0.970  0.020  1.090
 II6  C4   H4    single  0.970  0.020  1.090
 II6  C5   H5    single  0.970  0.020  1.090
 II6  C2   H21C  single  0.970  0.020  1.090
 II6  C2   H22C  single  0.970  0.020  1.090
 II6  C6   H6    single  0.970  0.020  1.090
 II6  C3   H31C  single  0.970  0.020  1.090
 II6  C3   H32C  single  0.970  0.020  1.090
 II6  C7   H71C  single  0.970  0.020  1.090
 II6  C7   H72C  single  0.970  0.020  1.090
 II6  C7   H73C  single  0.970  0.020  1.090
 II6  C8   H81C  single  0.970  0.020  1.090
 II6  C8   H82C  single  0.970  0.020  1.090
 II6  C9   H91C  single  0.970  0.020  1.090
 II6  C9   H92C  single  0.970  0.020  1.090
 II6  N10  H101  single  0.890  0.020  1.040
 II6  N10  H102  single  0.890  0.020  1.040
 II6  O11  H11   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
 II6  H12C  C1   H11C  106.29  3.000
 II6  H12C  C1   C5    109.89  3.000
 II6  H11C  C1   C5    108.85  3.000
 II6  H12C  C1   C4    109.98  3.000
 II6  H11C  C1   C4    109.10  3.000
 II6  C5    C1   C4    112.52  3.000
 II6  H22C  C2   H21C  106.35  3.000
 II6  H22C  C2   C6    108.91  3.000
 II6  H21C  C2   C6    110.37  3.000
 II6  H22C  C2   C4    109.09  3.000
 II6  H21C  C2   C4    109.54  3.000
 II6  C6    C2   C4    112.39  3.000
 II6  H32C  C3   H31C  106.40  3.000
 II6  H32C  C3   C6    110.02  3.000
 II6  H31C  C3   C6    109.17  3.000
 II6  H32C  C3   C5    110.04  3.000
 II6  H31C  C3   C5    109.04  3.000
 II6  C6    C3   C5    112.00  3.000
 II6  H4    C4   C7    108.21  3.000
 II6  H4    C4   C2    107.56  3.000
 II6  C7    C4   C2    111.15  3.000
 II6  H4    C4   C1    107.61  3.000
 II6  C7    C4   C1    111.25  3.000
 II6  C2    C4   C1    110.89  3.000
 II6  H5    C5   C8    107.56  3.000
 II6  H5    C5   C3    107.49  3.000
 II6  C8    C5   C3    110.68  3.000
 II6  H5    C5   C1    108.24  3.000
 II6  C8    C5   C1    112.59  3.000
 II6  C3    C5   C1    110.08  3.000
 II6  H6    C6   C9    107.68  3.000
 II6  H6    C6   C3    107.68  3.000
 II6  C9    C6   C3    110.05  3.000
 II6  H6    C6   C2    108.55  3.000
 II6  C9    C6   C2    112.60  3.000
 II6  C3    C6   C2    110.12  3.000
 II6  H73C  C7   H72C  107.71  3.000
 II6  H73C  C7   H71C  107.52  3.000
 II6  H72C  C7   H71C  107.51  3.000
 II6  H73C  C7   C4    111.49  3.000
 II6  H72C  C7   C4    111.50  3.000
 II6  H71C  C7   C4    110.91  3.000
 II6  H82C  C8   H81C  106.14  3.000
 II6  H82C  C8   N10   108.26  3.000
 II6  H81C  C8   N10   113.13  3.000
 II6  H82C  C8   C5    108.90  3.000
 II6  H81C  C8   C5    108.31  3.000
 II6  N10   C8   C5    111.88  3.000
 II6  H92C  C9   H91C  106.64  3.000
 II6  H92C  C9   O11   111.12  3.000
 II6  H91C  C9   O11   111.34  3.000
 II6  H92C  C9   C6    108.88  3.000
 II6  H91C  C9   C6    108.99  3.000
 II6  O11   C9   C6    109.77  3.000
 II6  H102  N10  H101  105.50  3.000
 II6  H102  N10  C8    109.37  3.000
 II6  H101  N10  C8    109.05  3.000
 II6  H11   O11  C9    108.13  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
 II6  Var_01  H101  N10  C8  C5  66.24  30.0  3

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
 II6  chir_01  C4  C1  C2  C7  positiv
 II6  chir_02  C5  C8  C3  C1  positiv
 II6  chir_03  C6  C2  C3  C9  positiv

