# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:59:03 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (1s,3R,5S)-3,5-diaminocyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@H](N)C[C@H](O)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
 GE2  GE2  (1s,3R,5S)-3,5-diaminocyclohexanol  ligand  23  9  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GE2
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
 GE2  C5    C  CH1   0  -0.093  -0.7235   0.3286  -1.2756
 GE2  C     C  CH2   0  -0.424  -1.4719  -0.1300  -0.0297
 GE2  C1    C  CH1   0  -0.072  -0.7832   0.3340   1.2476
 GE2  N1    N  NH2   0  -0.803  -1.5024  -0.1722   2.4093
 GE2  C2    C  CH2   0  -0.471   0.6577  -0.1635   1.2768
 GE2  C3    C  CH1   0   0.069   1.4315   0.2964   0.0469
 GE2  O32   O  OH1   0  -0.677   2.7488  -0.2206   0.0250
 GE2  C4    C  CH2   0  -0.461   0.7301  -0.1492  -1.2260
 GE2  N6    N  NH2   0  -0.790  -1.4445  -0.0919  -2.4694
 GE2  H5    H  HCH1  0   0.215  -0.7219   1.4255  -1.2815
 GE2  H1A   H  HCH2  0   0.209  -1.5328  -1.2255  -0.0218
 GE2  H2    H  HCH2  0   0.230  -2.4983   0.2474  -0.0629
 GE2  H1    H  HCH1  0   0.191  -0.7576   1.4367   1.2268
 GE2  HN11  H  HNH2  0   0.341  -1.0788   0.1973   3.2521
 GE2  HN12  H  HNH2  0   0.341  -2.4475   0.1929   2.4011
 GE2  H21   H  HCH2  0   0.231   1.1557   0.1974   2.1846
 GE2  H22   H  HCH2  0   0.215   0.6592  -1.2585   1.3222
 GE2  H3    H  HCH1  0   0.188   1.4596   1.3977   0.0533
 GE2  HOW   H  HOH1  0   0.445   3.2060   0.0947   0.8108
 GE2  H41   H  HCH2  0   0.212   0.7471  -1.2450  -1.2835
 GE2  H42   H  HCH2  0   0.232   1.2701   0.2278  -2.1004
 GE2  HN61  H  HNH2  0   0.342  -0.9724   0.2685  -3.2901
 GE2  HN62  H  HNH2  0   0.333  -1.3944  -1.1018  -2.5505

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
 GE2  C5   C     single  1.524  0.020  1.524
 GE2  C5   C4    single  1.531  0.020  1.531
 GE2  C5   N6    single  1.457  0.020  1.457
 GE2  C5   H5    single  0.970  0.020  1.090
 GE2  C    C1    single  1.524  0.020  1.524
 GE2  C    H1A   single  0.970  0.020  1.090
 GE2  C    H2    single  0.970  0.020  1.090
 GE2  C1   N1    single  1.457  0.020  1.457
 GE2  C1   C2    single  1.525  0.020  1.525
 GE2  C1   H1    single  0.970  0.020  1.090
 GE2  N1   HN11  single  0.890  0.020  1.040
 GE2  N1   HN12  single  0.890  0.020  1.040
 GE2  C2   C3    single  1.524  0.020  1.524
 GE2  C2   H21   single  0.970  0.020  1.090
 GE2  C2   H22   single  0.970  0.020  1.090
 GE2  C3   O32   single  1.415  0.020  1.415
 GE2  C3   C4    single  1.520  0.020  1.520
 GE2  C3   H3    single  0.970  0.020  1.090
 GE2  O32  HOW   single  0.850  0.020  0.980
 GE2  C4   H41   single  0.970  0.020  1.090
 GE2  C4   H42   single  0.970  0.020  1.090
 GE2  N6   HN61  single  0.890  0.020  1.040
 GE2  N6   HN62  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
 GE2  H5    C5   N6    106.56  3.000
 GE2  H5    C5   C4    108.11  3.000
 GE2  N6    C5   C4    113.98  3.000
 GE2  H5    C5   C     107.82  3.000
 GE2  N6    C5   C     109.88  3.000
 GE2  C4    C5   C     110.24  3.000
 GE2  H2    C    H1A   107.01  3.000
 GE2  H2    C    C1    110.15  3.000
 GE2  H1A   C    C1    108.85  3.000
 GE2  H2    C    C5    109.40  3.000
 GE2  H1A   C    C5    109.49  3.000
 GE2  C1    C    C5    111.82  3.000
 GE2  H1    C1   C2    107.73  3.000
 GE2  H1    C1   N1    111.95  3.000
 GE2  C2    C1   N1    109.74  3.000
 GE2  H1    C1   C     107.41  3.000
 GE2  C2    C1   C     110.11  3.000
 GE2  N1    C1   C     109.84  3.000
 GE2  HN12  N1   HN11  105.39  3.000
 GE2  HN12  N1   C1    109.19  3.000
 GE2  HN11  N1   C1    109.28  3.000
 GE2  H22   C2   H21   107.10  3.000
 GE2  H22   C2   C3    109.52  3.000
 GE2  H21   C2   C3    109.77  3.000
 GE2  H22   C2   C1    109.16  3.000
 GE2  H21   C2   C1    109.73  3.000
 GE2  C3    C2   C1    111.46  3.000
 GE2  H3    C3   C4    108.04  3.000
 GE2  H3    C3   O32   109.97  3.000
 GE2  C4    C3   O32   108.02  3.000
 GE2  H3    C3   C2    108.05  3.000
 GE2  C4    C3   C2    110.67  3.000
 GE2  O32   C3   C2    112.01  3.000
 GE2  HOW   O32  C3    108.05  3.000
 GE2  H42   C4   H41   107.12  3.000
 GE2  H42   C4   C3    109.89  3.000
 GE2  H41   C4   C3    109.23  3.000
 GE2  H42   C4   C5    109.58  3.000
 GE2  H41   C4   C5    108.94  3.000
 GE2  C3    C4   C5    111.95  3.000
 GE2  HN62  N6   HN61  105.45  3.000
 GE2  HN62  N6   C5    109.18  3.000
 GE2  HN61  N6   C5    109.31  3.000

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
 GE2  chir_01  C5  C    C4  N6  negativ
 GE2  chir_02  C1  N1   C2  C   negativ
 GE2  chir_03  C3  O32  C2  C4  positiv

