# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:54:22 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@](O)(CC(=O)C(O)=O)C(O)=O
#
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
 7QD  7QD  '(2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid'  ligand  23  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7QD
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
 7QD  O01   O  O     0  -0.331   1.9169   1.2507   0.3466
 7QD  C02   C  C     0   0.297   1.9417   0.0803   0.0822
 7QD  C03   C  C     0   0.488   3.2867  -0.6629   0.0232
 7QD  O04   O  O     0  -0.399   3.3694  -1.8175  -0.2989
 7QD  O05   O  OH1   0  -0.568   4.2851   0.1216   0.3543
 7QD  C06   C  CH2   0  -0.580   0.7406  -0.7480  -0.2524
 7QD  C07   C  CT    0   0.095  -0.6016  -0.1373   0.1762
 7QD  O08   O  OH1   0  -0.650  -0.6711   0.0262   1.5617
 7QD  C09   C  C     0   0.560  -0.7843   1.2634  -0.4145
 7QD  O10   O  O     0  -0.425  -0.9855   2.2586   0.2222
 7QD  O11   O  OH1   0  -0.596  -0.6811   1.2283  -1.7362
 7QD  C12   C  CH2   0  -0.585  -1.7011  -1.0912  -0.3220
 7QD  C13   C  C     0   0.558  -3.0870  -0.6280   0.0361
 7QD  O14   O  OH1   0  -0.585  -3.8651  -1.6230   0.4337
 7QD  O15   O  O     0  -0.433  -3.4612   0.5136  -0.0613
 7QD  H1    H  HOH1  0   0.496   5.1261  -0.3597   0.3079
 7QD  H062  H  HCH2  0   0.319   0.7663  -0.9325  -1.3316
 7QD  H061  H  HCH2  0   0.307   0.8436  -1.7392   0.1979
 7QD  H081  H  HOH1  0   0.459  -0.5258  -0.8286   1.9820
 7QD  H2    H  HOH1  0   0.487  -0.8035   2.1167  -2.1030
 7QD  H121  H  HCH2  0   0.309  -1.6597  -1.1950  -1.4098
 7QD  H122  H  HCH2  0   0.292  -1.5146  -2.0877   0.0836
 7QD  H3    H  HOH1  0   0.484  -4.7607  -1.2964   0.6111

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
 7QD  O04  C03   double  1.202  0.020  1.202
 7QD  O05  C03   single  1.312  0.020  1.312
 7QD  C03  C02   single  1.538  0.020  1.538
 7QD  C02  C06   single  1.497  0.020  1.497
 7QD  C02  O01   double  1.200  0.020  1.200
 7QD  C06  C07   single  1.536  0.020  1.536
 7QD  O08  C07   single  1.397  0.020  1.397
 7QD  C07  C12   single  1.539  0.020  1.539
 7QD  C07  C09   single  1.531  0.020  1.531
 7QD  C12  C13   single  1.505  0.020  1.505
 7QD  O15  C13   double  1.205  0.020  1.205
 7QD  C13  O14   single  1.324  0.020  1.324
 7QD  C09  O10   double  1.198  0.020  1.198
 7QD  C09  O11   single  1.326  0.020  1.326
 7QD  O05  H1    single  0.850  0.020  0.980
 7QD  C06  H062  single  0.970  0.020  1.090
 7QD  C06  H061  single  0.970  0.020  1.090
 7QD  O08  H081  single  0.850  0.020  0.980
 7QD  O11  H2    single  0.850  0.020  0.980
 7QD  C12  H121  single  0.970  0.020  1.090
 7QD  C12  H122  single  0.970  0.020  1.090
 7QD  O14  H3    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
 7QD  C06   C02  C03   115.20  3.000
 7QD  C06   C02  O01   124.91  3.000
 7QD  C03   C02  O01   119.86  3.000
 7QD  O05   C03  O04   126.14  3.000
 7QD  O05   C03  C02   111.52  3.000
 7QD  O04   C03  C02   122.34  3.000
 7QD  H1    O05  C03   110.54  3.000
 7QD  H061  C06  H062  104.53  3.000
 7QD  H061  C06  C07   109.14  3.000
 7QD  H062  C06  C07   111.26  3.000
 7QD  H061  C06  C02   109.51  3.000
 7QD  H062  C06  C02   107.14  3.000
 7QD  C07   C06  C02   114.76  3.000
 7QD  C12   C07  C09   110.92  3.000
 7QD  C09   C07  O08   105.64  3.000
 7QD  C12   C07  O08   110.99  3.000
 7QD  C09   C07  C06   111.13  3.000
 7QD  C12   C07  C06   106.72  3.000
 7QD  O08   C07  C06   111.53  3.000
 7QD  H081  O08  C07   108.74  3.000
 7QD  O11   C09  O10   124.37  3.000
 7QD  O11   C09  C07   110.55  3.000
 7QD  O10   C09  C07   125.08  3.000
 7QD  H2    O11  C09   110.07  3.000
 7QD  H122  C12  H121  106.05  3.000
 7QD  H122  C12  C13   110.48  3.000
 7QD  H121  C12  C13   107.51  3.000
 7QD  H122  C12  C07   108.87  3.000
 7QD  H121  C12  C07   110.73  3.000
 7QD  C13   C12  C07   112.98  3.000
 7QD  O15   C13  O14   123.61  3.000
 7QD  O14   C13  C12   112.42  3.000
 7QD  O15   C13  C12   123.94  3.000
 7QD  H3    O14  C13   110.15  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
 7QD  CONST_01  H1   O05  C03  C02   180.00   0.0  0
 7QD  CONST_02  H2   O11  C09  C07   180.00   0.0  0
 7QD  CONST_03  H3   O14  C13  C12   180.00   0.0  0
 7QD  Var_01    O04  C03  C02  O01  -176.37  30.0  2
 7QD  Var_02    C07  C06  C02  O01   -18.27  30.0  3
 7QD  Var_03    O15  C13  C12  C07    43.15  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
 7QD  chir_01  C07  O08  C12  C09  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
 7QD  plan-1  O01  0.020
 7QD  plan-1  C02  0.020
 7QD  plan-1  C03  0.020
 7QD  plan-1  C06  0.020
 7QD  plan-2  C02  0.020
 7QD  plan-2  C03  0.020
 7QD  plan-2  O04  0.020
 7QD  plan-2  O05  0.020
 7QD  plan-2  H1   0.020
 7QD  plan-3  C07  0.020
 7QD  plan-3  C09  0.020
 7QD  plan-3  O10  0.020
 7QD  plan-3  O11  0.020
 7QD  plan-3  H2   0.020
 7QD  plan-4  C12  0.020
 7QD  plan-4  C13  0.020
 7QD  plan-4  O14  0.020
 7QD  plan-4  O15  0.020
 7QD  plan-4  H3   0.020

