# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:15:20 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2Z,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-one oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NC(=N\O)/[C@H](O)[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
 GOX  GOX  '(2Z,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-one oxime'  ligand  25  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOX
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
 GOX  C1    C  C     0   0.413  -0.4232   1.1517   0.0134
 GOX  N1    N  N     0  -0.240  -1.2011   2.1239   0.3127
 GOX  C2    C  CH1   0  -0.050   0.9729   1.2458   0.5750
 GOX  N5    N  NH1   0  -0.646  -0.6965   0.1459  -0.8602
 GOX  O7    O  OH1   0  -0.591  -2.4313   2.0091  -0.3203
 GOX  O2    O  OH1   0  -0.656   1.8464   1.8453  -0.3515
 GOX  C3    C  CH1   0  -0.042   1.5069  -0.1395   0.9316
 GOX  O3    O  OH1   0  -0.662   0.8243  -0.6444   2.0526
 GOX  C4    C  CH1   0   0.035   1.3053  -1.1495  -0.2019
 GOX  O4    O  OH1   0  -0.662   2.1238  -0.8560  -1.3073
 GOX  C5    C  CH1   0  -0.145  -0.1342  -1.1879  -0.7092
 GOX  C6    C  CH2   0  -0.147  -1.0471  -2.0812   0.1249
 GOX  O6    O  OH1   0  -0.673  -2.2591  -2.2225  -0.5877
 GOX  HC2   H  HCH1  0   0.240   0.9170   1.8420   1.4954
 GOX  HN5   H  HNH1  0   0.383  -1.6417   0.1363  -1.2148
 GOX  HO7   H  HOH1  0   0.470  -2.9419   2.7404   0.0384
 GOX  HO2   H  HOH1  0   0.455   1.5783   2.7637  -0.4573
 GOX  HC3   H  HCH1  0   0.245   2.5844  -0.0513   1.1364
 GOX  HO3   H  HOH1  0   0.459   0.9866  -0.0631   2.8028
 GOX  HC4   H  HCH1  0   0.231   1.5435  -2.1449   0.2005
 GOX  HO4   H  HOH1  0   0.450   3.0260  -0.7258  -0.9988
 GOX  HC5   H  HCH1  0   0.262  -0.0902  -1.6375  -1.7071
 GOX  HC61  H  HCH2  0   0.198  -0.5579  -3.0527   0.2762
 GOX  HC62  H  HCH2  0   0.216  -1.2146  -1.6392   1.1097
 GOX  HO6   H  HOH1  0   0.458  -2.9448  -2.4861   0.0312

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
 GOX  C1  N1    double  1.281  0.020  1.281
 GOX  C1  C2    single  1.508  0.020  1.508
 GOX  C1  N5    single  1.360  0.020  1.360
 GOX  N1  O7    single  1.388  0.020  1.388
 GOX  C2  O2    single  1.407  0.020  1.407
 GOX  C2  C3    single  1.527  0.020  1.527
 GOX  C2  HC2   single  0.970  0.020  1.090
 GOX  N5  C5    single  1.455  0.020  1.455
 GOX  N5  HN5   single  0.890  0.020  1.040
 GOX  O7  HO7   single  0.850  0.020  0.980
 GOX  O2  HO2   single  0.850  0.020  0.980
 GOX  C3  O3    single  1.406  0.020  1.406
 GOX  C3  C4    single  1.531  0.020  1.531
 GOX  C3  HC3   single  0.970  0.020  1.090
 GOX  O3  HO3   single  0.850  0.020  0.980
 GOX  C4  O4    single  1.406  0.020  1.406
 GOX  C4  C5    single  1.527  0.020  1.527
 GOX  C4  HC4   single  0.970  0.020  1.090
 GOX  O4  HO4   single  0.850  0.020  0.980
 GOX  C5  C6    single  1.525  0.020  1.525
 GOX  C5  HC5   single  0.970  0.020  1.090
 GOX  C6  O6    single  1.413  0.020  1.413
 GOX  C6  HC61  single  0.970  0.020  1.090
 GOX  C6  HC62  single  0.970  0.020  1.090
 GOX  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
 GOX  N5    C1  C2    118.13  3.000
 GOX  N5    C1  N1    126.12  3.000
 GOX  C2    C1  N1    115.34  3.000
 GOX  O7    N1  C1    111.65  3.000
 GOX  HC2   C2  C3    108.34  3.000
 GOX  HC2   C2  O2    110.61  3.000
 GOX  C3    C2  O2    108.86  3.000
 GOX  HC2   C2  C1    107.39  3.000
 GOX  C3    C2  C1    110.74  3.000
 GOX  O2    C2  C1    110.86  3.000
 GOX  HN5   N5  C5    112.92  3.000
 GOX  HN5   N5  C1    114.89  3.000
 GOX  C5    N5  C1    122.24  3.000
 GOX  HO7   O7  N1    103.74  3.000
 GOX  HO2   O2  C2    107.81  3.000
 GOX  HC3   C3  C4    108.63  3.000
 GOX  HC3   C3  O3    110.83  3.000
 GOX  C4    C3  O3    106.82  3.000
 GOX  HC3   C3  C2    108.25  3.000
 GOX  C4    C3  C2    112.30  3.000
 GOX  O3    C3  C2    110.01  3.000
 GOX  HO3   O3  C3    108.82  3.000
 GOX  HC4   C4  C5    107.63  3.000
 GOX  HC4   C4  O4    110.51  3.000
 GOX  C5    C4  O4    107.02  3.000
 GOX  HC4   C4  C3    107.32  3.000
 GOX  C5    C4  C3    112.74  3.000
 GOX  O4    C4  C3    111.57  3.000
 GOX  HO4   O4  C4    108.78  3.000
 GOX  HC5   C5  C6    106.37  3.000
 GOX  HC5   C5  C4    105.97  3.000
 GOX  C6    C5  C4    113.41  3.000
 GOX  HC5   C5  N5    107.29  3.000
 GOX  C6    C5  N5    111.24  3.000
 GOX  C4    C5  N5    112.07  3.000
 GOX  HC62  C6  HC61  107.58  3.000
 GOX  HC62  C6  O6    111.32  3.000
 GOX  HC61  C6  O6    111.29  3.000
 GOX  HC62  C6  C5    110.35  3.000
 GOX  HC61  C6  C5    109.07  3.000
 GOX  O6    C6  C5    107.23  3.000
 GOX  HO6   O6  C6    108.34  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
 GOX  CONST_03  HN5  N5  C1  C2  180.00  0.0  0
 GOX  CONST_04  O7   N1  C1  C2  180.00  0.0  0
 GOX  CONST_05  O7   N1  C1  N5    0.00  0.0  0

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
 GOX  chir_01  C2  C1  O2  C3  positiv
 GOX  chir_02  C3  O3  C2  C4  positiv
 GOX  chir_03  C4  O4  C3  C5  negativ
 GOX  chir_04  C5  N5  C4  C6  negativ

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
 GOX  plan-1  C1   0.020
 GOX  plan-1  N1   0.020
 GOX  plan-1  C2   0.020
 GOX  plan-1  N5   0.020
 GOX  plan-1  O7   0.020
 GOX  plan-1  C5   0.020
 GOX  plan-1  HN5  0.020

