# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 05:57:14 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2E,4S,5R,6R,7S,8R)-5-(acetylamino)-4,6,7,8,9-pentahydroxy-2-(hydroxyimino)nonanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]([C@@H](O)C\C(=N/O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 OVY  OVY  '(2E,4S,5R,6R,7S,8R)-5-(acetylamino)-4,6,7,8,9-pentahydroxy-2-(hydroxyimino)nonanoic acid (non-preferred name)'  ligand  42  22  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OVY
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
 OVY  C01  C  C     0   0.523   0.1665   2.6573  -0.2466
 OVY  C02  C  CH3   0  -0.781   0.4192   3.8459   0.6459
 OVY  C03  C  CH1   0  -0.148   0.1613   0.1854  -0.2959
 OVY  C04  C  CH1   0   0.036   1.3668  -0.6844   0.1052
 OVY  C05  C  CH1   0  -0.025   2.7016   0.0369  -0.1307
 OVY  C06  C  CH1   0  -0.021   3.9067  -0.8303   0.2747
 OVY  C07  C  CH2   0  -0.157   5.2064  -0.0528   0.1320
 OVY  C08  C  CH1   0   0.057  -1.1722  -0.5277  -0.0269
 OVY  C09  C  CH2   0  -0.563  -2.3487   0.2617  -0.6130
 OVY  C10  C  C     0   0.091  -3.6400  -0.4610  -0.3958
 OVY  C11  C  C     0   0.523  -4.4400  -0.1323   0.8179
 OVY  N01  N  NH1   0  -0.645   0.2175   1.4611   0.3806
 OVY  N02  N  N     0  -0.084  -4.1313  -1.3683  -1.1424
 OVY  O01  O  O     0  -0.491  -0.0416   2.7740  -1.4440
 OVY  O02  O  OH1   0  -0.663   1.3196  -1.9283  -0.5576
 OVY  O03  O  OH1   0  -0.662   2.8214   0.4958  -1.4604
 OVY  O04  O  OH1   0  -0.660   3.7506  -1.3457   1.5764
 OVY  O06  O  OH1   0  -0.662  -1.3611  -0.8035   1.3418
 OVY  O07  O  OH1   0  -0.583  -5.5239  -0.8741   0.9634
 OVY  O08  O  O     0  -0.435  -4.1163   0.7387   1.5891
 OVY  O09  O  OH1   0  -0.523  -3.3775  -1.6533  -2.2190
 OVY  H03  H  HCH3  0   0.271   1.4828   4.0911   0.6202
 OVY  H01  H  HCH3  0   0.263  -0.1300   4.7112   0.2821
 OVY  H02  H  HCH3  0   0.253   0.1463   3.6637   1.6841
 OVY  H05  H  HCH1  0   0.263   0.2207   0.3841  -1.3686
 OVY  H06  H  HCH1  0   0.238   1.2904  -0.9107   1.1719
 OVY  H08  H  HCH1  0   0.232   2.7108   0.9366   0.4948
 OVY  H10  H  HCH1  0   0.229   3.9469  -1.7034  -0.3869
 OVY  H12  H  HCH2  0   0.205   5.2762   0.3549  -0.8819
 OVY  H13  H  HCH2  0   0.190   5.1826   0.8081   0.8186
 OVY  H15  H  HCH1  0   0.252  -1.1347  -1.4996  -0.5219
 OVY  H18  H  HCH2  0   0.268  -2.4058   1.2507  -0.1565
 OVY  H17  H  HCH2  0   0.276  -2.1770   0.4143  -1.6792
 OVY  H04  H  HNH1  0   0.399   0.4148   1.4613   1.3694
 OVY  H07  H  HOH1  0   0.444   1.2297  -1.7797  -1.5053
 OVY  H09  H  HOH1  0   0.444   3.0244  -0.2472  -2.0392
 OVY  H11  H  HOH1  0   0.445   3.7773  -0.6125   2.2015
 OVY  H14  H  HOH1  0   0.455   7.0979  -0.4203   0.2929
 OVY  H16  H  HOH1  0   0.441  -1.5460   0.0213   1.8042
 OVY  H1   H  HOH1  0   0.486  -5.9952  -0.6003   1.7644
 OVY  H19  H  HOH1  0   0.489  -3.8726  -2.3329  -2.6914
 OVY  O05  O  OH1   0  -0.671   6.2830  -0.9139   0.4194

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
 OVY  O09  N02  single  1.345  0.020  1.345
 OVY  N02  C10  double  1.274  0.020  1.274
 OVY  C02  C01  single  1.508  0.020  1.508
 OVY  O08  C11  double  1.208  0.020  1.208
 OVY  C10  C11  single  1.490  0.020  1.490
 OVY  C10  C09  single  1.496  0.020  1.496
 OVY  O01  C01  double  1.221  0.020  1.221
 OVY  C01  N01  single  1.352  0.020  1.352
 OVY  C11  O07  single  1.321  0.020  1.321
 OVY  C09  C08  single  1.533  0.020  1.533
 OVY  N01  C03  single  1.445  0.020  1.445
 OVY  O06  C08  single  1.409  0.020  1.409
 OVY  C08  C03  single  1.536  0.020  1.536
 OVY  C03  C04  single  1.540  0.020  1.540
 OVY  C04  C05  single  1.535  0.020  1.535
 OVY  C04  O02  single  1.410  0.020  1.410
 OVY  O03  C05  single  1.412  0.020  1.412
 OVY  C05  C06  single  1.539  0.020  1.539
 OVY  O04  C06  single  1.409  0.020  1.409
 OVY  C06  C07  single  1.521  0.020  1.521
 OVY  C07  O05  single  1.408  0.020  1.408
 OVY  C02  H03  single  0.970  0.020  1.090
 OVY  C02  H01  single  0.970  0.020  1.090
 OVY  C02  H02  single  0.970  0.020  1.090
 OVY  C03  H05  single  0.970  0.020  1.090
 OVY  C04  H06  single  0.970  0.020  1.090
 OVY  C05  H08  single  0.970  0.020  1.090
 OVY  C06  H10  single  0.970  0.020  1.090
 OVY  C07  H12  single  0.970  0.020  1.090
 OVY  C07  H13  single  0.970  0.020  1.090
 OVY  C08  H15  single  0.970  0.020  1.090
 OVY  C09  H18  single  0.970  0.020  1.090
 OVY  C09  H17  single  0.970  0.020  1.090
 OVY  N01  H04  single  0.860  0.020  1.020
 OVY  O02  H07  single  0.850  0.020  0.980
 OVY  O03  H09  single  0.850  0.020  0.980
 OVY  O04  H11  single  0.850  0.020  0.980
 OVY  O05  H14  single  0.850  0.020  0.980
 OVY  O06  H16  single  0.850  0.020  0.980
 OVY  O07  H1   single  0.850  0.020  0.980
 OVY  O09  H19  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
 OVY  O01  C01  N01  123.10  3.000
 OVY  N01  C01  C02  114.62  3.000
 OVY  O01  C01  C02  122.26  3.000
 OVY  H02  C02  H01  109.00  3.000
 OVY  H02  C02  H03  107.70  3.000
 OVY  H01  C02  H03  107.78  3.000
 OVY  H02  C02  C01  112.99  3.000
 OVY  H01  C02  C01  110.16  3.000
 OVY  H03  C02  C01  109.05  3.000
 OVY  H05  C03  N01  107.27  3.000
 OVY  H05  C03  C08  107.68  3.000
 OVY  N01  C03  C08  111.20  3.000
 OVY  H05  C03  C04  108.42  3.000
 OVY  C08  C03  C04  111.83  3.000
 OVY  N01  C03  C04  110.26  3.000
 OVY  H06  C04  O02  105.89  3.000
 OVY  H06  C04  C05  107.93  3.000
 OVY  O02  C04  C05  111.79  3.000
 OVY  H06  C04  C03  108.45  3.000
 OVY  O02  C04  C03  110.46  3.000
 OVY  C05  C04  C03  112.03  3.000
 OVY  H08  C05  O03  105.66  3.000
 OVY  H08  C05  C06  107.80  3.000
 OVY  O03  C05  C06  111.39  3.000
 OVY  H08  C05  C04  107.78  3.000
 OVY  C06  C05  C04  112.06  3.000
 OVY  O03  C05  C04  111.79  3.000
 OVY  H10  C06  O04  105.68  3.000
 OVY  H10  C06  C07  108.62  3.000
 OVY  O04  C06  C07  111.61  3.000
 OVY  H10  C06  C05  108.57  3.000
 OVY  C07  C06  C05  110.88  3.000
 OVY  O04  C06  C05  111.27  3.000
 OVY  H13  C07  H12  106.71  3.000
 OVY  H13  C07  O05  111.54  3.000
 OVY  H12  C07  O05  111.59  3.000
 OVY  H13  C07  C06  108.82  3.000
 OVY  H12  C07  C06  109.37  3.000
 OVY  O05  C07  C06  108.75  3.000
 OVY  H15  C08  O06  105.71  3.000
 OVY  H15  C08  C09  108.15  3.000
 OVY  O06  C08  C09  111.67  3.000
 OVY  H15  C08  C03  107.71  3.000
 OVY  O06  C08  C03  112.18  3.000
 OVY  C09  C08  C03  111.11  3.000
 OVY  H17  C09  H18  106.89  3.000
 OVY  H17  C09  C10  110.21  3.000
 OVY  H18  C09  C10  109.40  3.000
 OVY  H17  C09  C08  108.96  3.000
 OVY  H18  C09  C08  110.31  3.000
 OVY  C10  C09  C08  110.99  3.000
 OVY  N02  C10  C11  115.30  3.000
 OVY  C11  C10  C09  118.37  3.000
 OVY  N02  C10  C09  126.31  3.000
 OVY  O08  C11  O07  123.68  3.000
 OVY  O07  C11  C10  113.96  3.000
 OVY  O08  C11  C10  122.36  3.000
 OVY  H04  N01  C03  117.83  3.000
 OVY  H04  N01  C01  117.54  3.000
 OVY  C03  N01  C01  124.23  3.000
 OVY  O09  N02  C10  113.83  3.000
 OVY  H07  O02  C04  109.23  3.000
 OVY  H09  O03  C05  109.45  3.000
 OVY  H11  O04  C06  108.54  3.000
 OVY  H16  O06  C08  108.92  3.000
 OVY  H1   O07  C11  109.35  3.000
 OVY  H19  O09  N02  104.70  3.000
 OVY  H14  O05  C07  107.89  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
 OVY  CONST_01  C03  N01  C01  C02  180.00   0.0  0
 OVY  CONST_02  O01  C01  N01  C03    0.00   0.0  0
 OVY  CONST_03  H04  N01  C01  C02    0.00   0.0  0
 OVY  CONST_04  H1   O07  C11  C10  180.00   0.0  0
 OVY  Var_01    N02  C10  C09  C08  -85.51  30.0  2
 OVY  Var_02    O08  C11  C10  C09    3.83  30.0  2
 OVY  Var_03    H03  C02  C01  N01   92.46  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
 OVY  chir_01  C03  N01  C08  C04  positiv
 OVY  chir_02  C04  O02  C03  C05  positiv
 OVY  chir_03  C05  O03  C04  C06  negativ
 OVY  chir_04  C06  O04  C05  C07  negativ
 OVY  chir_05  C08  O06  C09  C03  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
 OVY  plan-1  C01  0.020
 OVY  plan-1  C02  0.020
 OVY  plan-1  C03  0.020
 OVY  plan-1  N01  0.020
 OVY  plan-1  O01  0.020
 OVY  plan-1  H04  0.020
 OVY  plan-2  C10  0.020
 OVY  plan-2  C11  0.020
 OVY  plan-2  O07  0.020
 OVY  plan-2  O08  0.020
 OVY  plan-2  H1   0.020
 OVY  plan-3  C09  0.020
 OVY  plan-3  C10  0.020
 OVY  plan-3  C11  0.020
 OVY  plan-3  N02  0.020
 OVY  plan-3  O09  0.020

