# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:33:56 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,2S,3S)-3-amino-5-(hydroxymethyl)cyclohex-4-ene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C=C(CO)C[C@H](O)[C@H]1O
#
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
 ADH  ADH  (1S,2S,3S)-3-amino-5-(hydroxymethyl)cyclohex-4-ene-1,2-diol  ligand  24  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ADH
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
 ADH  C1    C  CH1   0  -0.186  -1.3836   0.2729  -0.4307
 ADH  C2    C  CH1   0   0.058  -0.2264   0.5697  -1.3908
 ADH  C3    C  CH1   0   0.061   0.9355  -0.3602  -1.0947
 ADH  C4    C  CH2   0  -0.548   1.4597  -0.0525   0.3044
 ADH  C5    C  C     0   0.030   0.3712   0.0590   1.3324
 ADH  C6    C  CH2   0  -0.171   0.8544  -0.0028   2.7488
 ADH  C7    C  C1    0  -0.269  -0.9050   0.2180   0.9916
 ADH  N1    N  NH2   0  -0.791  -2.0162  -0.9989  -0.7783
 ADH  O2    O  OH1   0  -0.674  -0.6127   0.4178  -2.7367
 ADH  O3    O  OH1   0  -0.674   1.9357  -0.1711  -2.0710
 ADH  O6    O  OH1   0  -0.666  -0.1924   0.1969   3.6606
 ADH  H1    H  HCH1  0   0.220  -2.0919   1.1141  -0.5086
 ADH  H2    H  HCH1  0   0.204   0.1058   1.6025  -1.1989
 ADH  H3    H  HCH1  0   0.203   0.5620  -1.3934  -1.1123
 ADH  H41   H  HCH2  0   0.247   2.0249   0.8873   0.2757
 ADH  H42   H  HCH2  0   0.248   2.1790  -0.8226   0.6056
 ADH  H61   H  HCH2  0   0.211   1.3419  -0.9784   2.8975
 ADH  H62   H  HCH2  0   0.209   1.6500   0.7476   2.8715
 ADH  H71   H  H     0   0.244  -1.6684   0.2945   1.7577
 ADH  HN12  H  HNH2  0   0.345  -2.7375  -1.2058  -0.0982
 ADH  HN22  H  HNH2  0   0.341  -2.4945  -0.9067  -1.6658
 ADH  HO2   H  HOH1  0   0.449  -1.2731   1.0895  -2.9344
 ADH  HO3   H  HOH1  0   0.448   2.6618  -0.7691  -1.8678
 ADH  HO6   H  HOH1  0   0.460   0.1715   0.1385   4.5483

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
 ADH  C1  C2    single  1.533  0.020  1.533
 ADH  C1  C7    single  1.502  0.020  1.502
 ADH  C1  N1    single  1.462  0.020  1.462
 ADH  C1  H1    single  0.970  0.020  1.090
 ADH  C2  C3    single  1.517  0.020  1.517
 ADH  C2  O2    single  1.408  0.020  1.408
 ADH  C2  H2    single  0.970  0.020  1.090
 ADH  C3  C4    single  1.525  0.020  1.525
 ADH  C3  O3    single  1.410  0.020  1.410
 ADH  C3  H3    single  0.970  0.020  1.090
 ADH  C4  C5    single  1.501  0.020  1.501
 ADH  C4  H41   single  0.970  0.020  1.090
 ADH  C4  H42   single  0.970  0.020  1.090
 ADH  C5  C6    single  1.498  0.020  1.498
 ADH  C5  C7    double  1.330  0.020  1.330
 ADH  C6  O6    single  1.403  0.020  1.403
 ADH  C6  H61   single  0.970  0.020  1.090
 ADH  C6  H62   single  0.970  0.020  1.090
 ADH  C7  H71   single  0.930  0.020  1.080
 ADH  N1  HN12  single  0.890  0.020  1.040
 ADH  N1  HN22  single  0.890  0.020  1.040
 ADH  O2  HO2   single  0.850  0.020  0.980
 ADH  O3  HO3   single  0.850  0.020  0.980
 ADH  O6  HO6   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
 ADH  H1    C1  N1    111.65  3.000
 ADH  H1    C1  C7    107.43  3.000
 ADH  N1    C1  C7    109.34  3.000
 ADH  H1    C1  C2    107.04  3.000
 ADH  N1    C1  C2    110.25  3.000
 ADH  C7    C1  C2    111.09  3.000
 ADH  H2    C2  O2    110.50  3.000
 ADH  H2    C2  C3    108.03  3.000
 ADH  O2    C2  C3    109.29  3.000
 ADH  H2    C2  C1    107.46  3.000
 ADH  O2    C2  C1    111.76  3.000
 ADH  C3    C2  C1    109.71  3.000
 ADH  H3    C3  O3    110.85  3.000
 ADH  H3    C3  C4    108.74  3.000
 ADH  O3    C3  C4    111.36  3.000
 ADH  H3    C3  C2    108.23  3.000
 ADH  O3    C3  C2    109.01  3.000
 ADH  C4    C3  C2    108.58  3.000
 ADH  H42   C4  H41   105.72  3.000
 ADH  H42   C4  C5    109.86  3.000
 ADH  H41   C4  C5    109.13  3.000
 ADH  H42   C4  C3    109.63  3.000
 ADH  H41   C4  C3    109.02  3.000
 ADH  C5    C4  C3    113.20  3.000
 ADH  C7    C5  C6    123.82  3.000
 ADH  C7    C5  C4    121.93  3.000
 ADH  C6    C5  C4    114.24  3.000
 ADH  H62   C6  H61   105.61  3.000
 ADH  H62   C6  O6    111.71  3.000
 ADH  H61   C6  O6    111.65  3.000
 ADH  H62   C6  C5    108.09  3.000
 ADH  H61   C6  C5    107.89  3.000
 ADH  O6    C6  C5    111.60  3.000
 ADH  H71   C7  C5    120.19  3.000
 ADH  H71   C7  C1    116.25  3.000
 ADH  C5    C7  C1    123.55  3.000
 ADH  HN22  N1  HN12  105.71  3.000
 ADH  HN22  N1  C1    109.48  3.000
 ADH  HN12  N1  C1    109.04  3.000
 ADH  HO2   O2  C2    108.01  3.000
 ADH  HO3   O3  C3    107.79  3.000
 ADH  HO6   O6  C6    108.01  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
 ADH  Var_01  C4  C5  C7  C1    1.29  30.0  1
 ADH  Var_02  C7  C5  C4  C3  -16.28  30.0  1
 ADH  Var_03  O6  C6  C5  C4  175.98  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
 ADH  chir_01  C1  C2  C7  N1  positiv
 ADH  chir_02  C2  O2  C1  C3  negativ
 ADH  chir_03  C3  O3  C2  C4  positiv

