# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 20:43:37 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (3R,5R,7S)-octane-1,3,5,7-tetracarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C[C@H](C[C@@H](CCC(O)=O)C(O)=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
 PAY  PAY  '(3R,5R,7S)-octane-1,3,5,7-tetracarboxylic acid'  ligand  34  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PAY
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
 PAY  O42   O  OC    -1  -0.639   6.0257   0.7287  -0.2330
 PAY  O41   O  O      0  -0.611   4.5303   2.0831  -1.1701
 PAY  C4    C  C      0   0.409   4.8573   1.0670  -0.5251
 PAY  C41   C  CH2    0  -0.588   3.7433   0.1298  -0.0280
 PAY  C32   C  CH2    0  -0.387   2.3215   0.5099  -0.4090
 PAY  C31   C  CH1    0  -0.319   1.2710  -0.5193   0.0153
 PAY  C3    C  C      0   0.410   1.2663  -0.7022   1.5417
 PAY  O31   O  O      0  -0.624   1.0096   0.3138   2.2273
 PAY  O32   O  OC    -1  -0.626   1.5200  -1.8376   1.9968
 PAY  C22   C  CH2    0  -0.378  -0.1110  -0.0932  -0.4848
 PAY  C21   C  CH1    0  -0.359  -1.2547  -1.0170  -0.0874
 PAY  C2    C  C      0   0.420  -1.1262  -2.4352  -0.6735
 PAY  O21   O  O      0  -0.621  -0.5945  -2.5559  -1.7987
 PAY  O22   O  OC    -1  -0.632  -1.6166  -3.3688  -0.0012
 PAY  C12   C  CH2    0  -0.385  -2.6274  -0.4661  -0.5099
 PAY  C11   C  CH1    0  -0.379  -2.9673   0.9376  -0.0088
 PAY  C10   C  CH3    0  -0.676  -2.8027   1.0657   1.5051
 PAY  C1    C  C      0   0.424  -4.3758   1.4145  -0.4354
 PAY  O12   O  OC    -1  -0.630  -4.6946   2.5710  -0.0809
 PAY  O11   O  O      0  -0.607  -5.0924   0.6380  -1.0992
 PAY  H411  H  HCH2   0   0.208   3.9641  -0.8806  -0.3925
 PAY  H412  H  HCH2   0   0.217   3.8334   0.0597   1.0621
 PAY  H321  H  HCH2   0   0.187   2.0636   1.4782   0.0294
 PAY  H322  H  HCH2   0   0.190   2.2617   0.6470  -1.4936
 PAY  H31   H  HCH1   0   0.176   1.5257  -1.4787  -0.4469
 PAY  H221  H  HCH2   0   0.198  -0.3056   0.9138  -0.1062
 PAY  H222  H  HCH2   0   0.183  -0.0845  -0.0091  -1.5760
 PAY  H21   H  HCH1   0   0.198  -1.2604  -1.1176   1.0021
 PAY  H121  H  HCH2   0   0.192  -2.6867  -0.4772  -1.6036
 PAY  H122  H  HCH2   0   0.195  -3.3959  -1.1613  -0.1582
 PAY  H11   H  HCH1   0   0.208  -2.2667   1.6486  -0.4650
 PAY  H101  H  HCH3   0   0.201  -3.4385   0.3487   2.0324
 PAY  H102  H  HCH3   0   0.229  -1.7727   0.8845   1.8172
 PAY  H103  H  HCH3   0   0.217  -3.0796   2.0642   1.8411

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
 PAY  O42  C4    deloc   1.251  0.020  1.251
 PAY  O41  C4    deloc   1.247  0.020  1.247
 PAY  C4   C41   single  1.538  0.020  1.538
 PAY  C41  C32   single  1.520  0.020  1.520
 PAY  C32  C31   single  1.531  0.020  1.531
 PAY  C31  C3    single  1.537  0.020  1.537
 PAY  C31  C22   single  1.530  0.020  1.530
 PAY  C3   O31   deloc   1.252  0.020  1.252
 PAY  C3   O32   deloc   1.249  0.020  1.249
 PAY  C22  C21   single  1.523  0.020  1.523
 PAY  C21  C2    single  1.540  0.020  1.540
 PAY  C21  C12   single  1.538  0.020  1.538
 PAY  C2   O21   deloc   1.250  0.020  1.250
 PAY  C2   O22   deloc   1.251  0.020  1.251
 PAY  C12  C11   single  1.529  0.020  1.529
 PAY  C11  C10   single  1.528  0.020  1.528
 PAY  C11  C1    single  1.547  0.020  1.547
 PAY  C1   O12   deloc   1.251  0.020  1.251
 PAY  C1   O11   deloc   1.248  0.020  1.248
 PAY  C41  H411  single  0.970  0.020  1.090
 PAY  C41  H412  single  0.970  0.020  1.090
 PAY  C32  H321  single  0.970  0.020  1.090
 PAY  C32  H322  single  0.970  0.020  1.090
 PAY  C31  H31   single  0.970  0.020  1.090
 PAY  C22  H221  single  0.970  0.020  1.090
 PAY  C22  H222  single  0.970  0.020  1.090
 PAY  C21  H21   single  0.970  0.020  1.090
 PAY  C12  H121  single  0.970  0.020  1.090
 PAY  C12  H122  single  0.970  0.020  1.090
 PAY  C11  H11   single  0.970  0.020  1.090
 PAY  C10  H101  single  0.970  0.020  1.090
 PAY  C10  H102  single  0.970  0.020  1.090
 PAY  C10  H103  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
 PAY  C41   C4   O41   118.27  3.000
 PAY  C41   C4   O42   115.86  3.000
 PAY  O41   C4   O42   125.87  3.000
 PAY  H412  C41  H411  104.78  3.000
 PAY  H412  C41  C32   110.01  3.000
 PAY  H411  C41  C32   109.59  3.000
 PAY  H412  C41  C4    107.51  3.000
 PAY  H411  C41  C4    107.94  3.000
 PAY  C32   C41  C4    116.36  3.000
 PAY  H322  C32  H321  105.86  3.000
 PAY  H322  C32  C31   108.74  3.000
 PAY  H321  C32  C31   108.80  3.000
 PAY  H322  C32  C41   109.31  3.000
 PAY  H321  C32  C41   109.96  3.000
 PAY  C31   C32  C41   113.85  3.000
 PAY  H31   C31  C22   108.43  3.000
 PAY  H31   C31  C3    108.40  3.000
 PAY  C22   C31  C3    110.78  3.000
 PAY  H31   C31  C32   108.21  3.000
 PAY  C22   C31  C32   110.00  3.000
 PAY  C3    C31  C32   110.93  3.000
 PAY  O32   C3   O31   125.42  3.000
 PAY  O32   C3   C31   117.98  3.000
 PAY  O31   C3   C31   116.60  3.000
 PAY  H222  C22  H221  106.18  3.000
 PAY  H222  C22  C21   108.95  3.000
 PAY  H221  C22  C21   109.56  3.000
 PAY  H222  C22  C31   108.98  3.000
 PAY  H221  C22  C31   107.70  3.000
 PAY  C21   C22  C31   115.09  3.000
 PAY  H21   C21  C12   107.57  3.000
 PAY  H21   C21  C2    107.14  3.000
 PAY  C12   C21  C2    107.44  3.000
 PAY  H21   C21  C22   108.63  3.000
 PAY  C12   C21  C22   112.41  3.000
 PAY  C2    C21  C22   113.37  3.000
 PAY  O22   C2   O21   125.34  3.000
 PAY  O22   C2   C21   116.76  3.000
 PAY  O21   C2   C21   117.83  3.000
 PAY  H122  C12  H121  106.05  3.000
 PAY  H122  C12  C11   108.77  3.000
 PAY  H121  C12  C11   108.94  3.000
 PAY  H122  C12  C21   108.11  3.000
 PAY  H121  C12  C21   108.60  3.000
 PAY  C11   C12  C21   115.93  3.000
 PAY  H11   C11  C1    105.47  3.000
 PAY  H11   C11  C10   106.79  3.000
 PAY  C1    C11  C10   110.21  3.000
 PAY  H11   C11  C12   108.46  3.000
 PAY  C1    C11  C12   113.27  3.000
 PAY  C10   C11  C12   112.20  3.000
 PAY  H103  C10  H102  107.69  3.000
 PAY  H103  C10  H101  107.73  3.000
 PAY  H102  C10  H101  107.57  3.000
 PAY  H103  C10  C11   110.80  3.000
 PAY  H102  C10  C11   111.78  3.000
 PAY  H101  C10  C11   111.10  3.000
 PAY  O11   C1   O12   125.43  3.000
 PAY  O11   C1   C11   118.53  3.000
 PAY  O12   C1   C11   116.03  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
 PAY  Var_01  C32  C41  C4   O42  -178.39  30.0  3
 PAY  Var_02  C31  C32  C41  C4    175.25  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
 PAY  chir_01  C31  C32  C3   C22  negativ
 PAY  chir_02  C21  C12  C2   C22  negativ
 PAY  chir_03  C11  C1   C10  C12  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
 PAY  plan-1  O42  0.020
 PAY  plan-1  O41  0.020
 PAY  plan-1  C4   0.020
 PAY  plan-1  C41  0.020
 PAY  plan-2  C31  0.020
 PAY  plan-2  C3   0.020
 PAY  plan-2  O31  0.020
 PAY  plan-2  O32  0.020
 PAY  plan-3  C21  0.020
 PAY  plan-3  C2   0.020
 PAY  plan-3  O21  0.020
 PAY  plan-3  O22  0.020
 PAY  plan-4  C11  0.020
 PAY  plan-4  C1   0.020
 PAY  plan-4  O12  0.020
 PAY  plan-4  O11  0.020

