# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 05:24:55 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (1~{R},3~{S})-3-(carboxycarbonyl)cyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC[C@@H](C1)C(=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
 QVQ  QVQ  "3-(carboxycarbonyl)cyclopentane-1-carboxylic acid"  ligand  21  13  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QVQ
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
 QVQ  C01  C  C      0   0.413  16.9592  -25.2933  8.0007
 QVQ  C02  C  C      0   0.343  22.4799  -25.0285  8.8891
 QVQ  C03  C  CH2    0  -0.425  19.4183  -24.4826  8.0619
 QVQ  C04  C  CH1    0  -0.372  18.1746  -24.7770  7.2129
 QVQ  C05  C  CH2    0  -0.418  18.7005  -25.6794  6.1007
 QVQ  C06  C  CH2    0  -0.435  20.0377  -25.0403  5.7452
 QVQ  C07  C  CH1    0  -0.335  20.6302  -24.5774  7.0853
 QVQ  C08  C  C      0   0.225  21.6429  -25.5314  7.6676
 QVQ  O01  O  OC    -1  -0.610  16.8153  -24.8490  9.1594
 QVQ  O02  O  O      0  -0.608  16.1974  -26.0895  7.4134
 QVQ  O03  O  O      0  -0.579  23.2982  -25.8391  9.3460
 QVQ  O04  O  OC    -1  -0.570  22.2409  -23.8678  9.2663
 QVQ  O05  O  O      0  -0.394  21.7993  -26.6540  7.2435
 QVQ  H04  H  HCH2   0   0.215  19.5011  -25.2237  8.8629
 QVQ  H03  H  HCH2   0   0.225  19.3767  -23.5115  8.5511
 QVQ  H05  H  HCH1   0   0.221  17.8669  -23.8325  6.7405
 QVQ  H07  H  HCH2   0   0.213  18.0255  -25.7472  5.2468
 QVQ  H06  H  HCH2   0   0.203  18.8517  -26.6965  6.4760
 QVQ  H09  H  HCH2   0   0.223  20.7035  -25.7024  5.1903
 QVQ  H08  H  HCH2   0   0.217  19.8616  -24.1659  5.1127
 QVQ  H10  H  HCH1   0   0.249  21.1029  -23.5988  6.9936

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
 QVQ  C06  C05  single  1.524  0.020  1.524
 QVQ  C06  C07  single  1.537  0.020  1.537
 QVQ  C05  C04  single  1.526  0.020  1.526
 QVQ  C07  C08  single  1.508  0.020  1.508
 QVQ  C07  C03  single  1.559  0.020  1.559
 QVQ  C04  C01  single  1.538  0.020  1.538
 QVQ  C04  C03  single  1.534  0.020  1.534
 QVQ  O05  C08  double  1.210  0.020  1.210
 QVQ  O02  C01  deloc   1.249  0.020  1.249
 QVQ  C08  C02  single  1.564  0.020  1.564
 QVQ  C01  O01  deloc   1.249  0.020  1.249
 QVQ  C02  O03  deloc   1.239  0.020  1.239
 QVQ  C02  O04  deloc   1.244  0.020  1.244
 QVQ  C03  H04  single  0.970  0.020  1.090
 QVQ  C03  H03  single  0.970  0.020  1.090
 QVQ  C04  H05  single  0.970  0.020  1.090
 QVQ  C05  H07  single  0.970  0.020  1.090
 QVQ  C05  H06  single  0.970  0.020  1.090
 QVQ  C06  H09  single  0.970  0.020  1.090
 QVQ  C06  H08  single  0.970  0.020  1.090
 QVQ  C07  H10  single  0.970  0.020  1.090

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
 QVQ  O02  C01  O01  126.35  3.000
 QVQ  O01  C01  C04  116.54  3.000
 QVQ  O02  C01  C04  117.09  3.000
 QVQ  O04  C02  O03  128.73  3.000
 QVQ  O04  C02  C08  115.74  3.000
 QVQ  O03  C02  C08  115.53  3.000
 QVQ  H03  C03  H04  106.15  3.000
 QVQ  H03  C03  C07  111.45  3.000
 QVQ  H04  C03  C07  111.01  3.000
 QVQ  H03  C03  C04  112.89  3.000
 QVQ  H04  C03  C04  109.65  3.000
 QVQ  C07  C03  C04  105.77  3.000
 QVQ  H05  C04  C05  106.93  3.000
 QVQ  H05  C04  C03  107.43  3.000
 QVQ  C05  C04  C03  103.73  3.000
 QVQ  H05  C04  C01  106.69  3.000
 QVQ  C03  C04  C01  114.94  3.000
 QVQ  C05  C04  C01  116.57  3.000
 QVQ  H06  C05  H07  107.22  3.000
 QVQ  H06  C05  C06  110.40  3.000
 QVQ  H07  C05  C06  112.74  3.000
 QVQ  H06  C05  C04  110.32  3.000
 QVQ  H07  C05  C04  113.21  3.000
 QVQ  C06  C05  C04  102.97  3.000
 QVQ  H08  C06  H09  106.83  3.000
 QVQ  H08  C06  C07  109.01  3.000
 QVQ  H09  C06  C07  113.03  3.000
 QVQ  H08  C06  C05  109.21  3.000
 QVQ  H09  C06  C05  113.56  3.000
 QVQ  C07  C06  C05  105.14  3.000
 QVQ  H10  C07  C08  108.00  3.000
 QVQ  H10  C07  C06  111.35  3.000
 QVQ  C08  C07  C06  113.89  3.000
 QVQ  H10  C07  C03  109.57  3.000
 QVQ  C08  C07  C03  108.58  3.000
 QVQ  C06  C07  C03  105.36  3.000
 QVQ  O05  C08  C07  122.56  3.000
 QVQ  O05  C08  C02  120.19  3.000
 QVQ  C07  C08  C02  117.23  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
 QVQ  Var_01  C07  C06  C05  C04    38.17  30.0  1
 QVQ  Var_02  H09  C06  C05  C04   162.22  30.0  1
 QVQ  Var_03  H08  C06  C05  C04   -78.68  30.0  1
 QVQ  Var_04  H07  C05  C06  C07   160.52  30.0  1
 QVQ  Var_05  H06  C05  C06  C07   -79.60  30.0  1
 QVQ  Var_06  O03  C02  C08  C07   179.71  30.0  2
 QVQ  Var_07  O04  C02  C08  C07    -0.70  30.0  2
 QVQ  Var_08  O05  C08  C02  O03     1.25  30.0  3
 QVQ  Var_09  O05  C08  C02  O04  -179.15  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
 QVQ  chir_01  C04  C05  C01  C03  negativ
 QVQ  chir_02  C07  C06  C08  C03  positiv

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
 QVQ  plan-1  C02  0.020
 QVQ  plan-1  C07  0.020
 QVQ  plan-1  C08  0.020
 QVQ  plan-1  O05  0.020
 QVQ  plan-2  C01  0.020
 QVQ  plan-2  C04  0.020
 QVQ  plan-2  O01  0.020
 QVQ  plan-2  O02  0.020
 QVQ  plan-3  C02  0.020
 QVQ  plan-3  C08  0.020
 QVQ  plan-3  O03  0.020
 QVQ  plan-3  O04  0.020

