# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 04:26:08 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (3R,5R,7R)-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
 PRU  PRU  '(3R,5R,7R)-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_PRU
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
 PRU  O42  O  O      0  -0.611  -5.1251   1.9626  -0.8592
 PRU  O41  O  OC    -1  -0.638  -6.3880   0.4514   0.1755
 PRU  C4   C  C      0   0.408  -5.2898   0.9107  -0.2094
 PRU  C41  C  CH2    0  -0.587  -4.0459   0.0941   0.1809
 PRU  C32  C  CH2    0  -0.394  -2.7253   0.5627  -0.4093
 PRU  C3   C  C      0   0.413  -1.6055  -1.6792  -0.1895
 PRU  O31  O  OC    -1  -0.626  -1.8772  -2.4600   0.7466
 PRU  O32  O  O      0  -0.629  -1.4453  -2.0079  -1.3865
 PRU  C22  C  CH2    0  -0.371  -0.2249   0.4397  -0.4460
 PRU  C2   C  C      0   0.416   1.2137  -0.0104   1.5903
 PRU  O21  O  O      0  -0.633   1.1300   1.1510   2.0512
 PRU  O22  O  OC    -1  -0.621   1.4050  -1.0440   2.2652
 PRU  C10  C  CH3    0  -0.667   3.8447  -1.4217  -0.3245
 PRU  C11  C  CH1    0  -0.378   3.6548   0.0906  -0.2019
 PRU  C12  C  CH2    0  -0.374   2.2619   0.5320  -0.6432
 PRU  C1   C  C      0   0.421   4.7946   0.8325  -0.9394
 PRU  O12  O  O      0  -0.607   4.4900   1.6622  -1.8205
 PRU  O11  O  OC    -1  -0.631   5.9594   0.5417  -0.5884
 PRU  C21  C  CH1    0  -0.339   1.0878  -0.1531   0.0657
 PRU  C31  C  CH1    0  -0.326  -1.4965  -0.1786   0.1300
 PRU  H2   H  HCH2   0   0.211  -3.9750   0.1000   1.2760
 PRU  H3   H  HCH2   0   0.216  -4.2299  -0.9529  -0.0805
 PRU  H4   H  HCH2   0   0.190  -2.7465   0.4603  -1.4991
 PRU  H5   H  HCH2   0   0.195  -2.6038   1.6317  -0.2127
 PRU  H7   H  HCH2   0   0.184  -0.2286   1.5153  -0.2373
 PRU  H8   H  HCH2   0   0.186  -0.2549   0.3431  -1.5364
 PRU  H12  H  HCH3   0   0.199   3.6687  -1.7591  -1.3501
 PRU  H13  H  HCH1   0   0.207   3.7712   0.3427   0.8610
 PRU  H14  H  HCH2   0   0.190   2.1659   1.6120  -0.5001
 PRU  H15  H  HCH2   0   0.186   2.1574   0.3642  -1.7209
 PRU  H17  H  HCH1   0   0.191   1.1013  -1.2184  -0.1860
 PRU  H18  H  HCH1   0   0.180  -1.4849  -0.0554   1.2197
 PRU  H10  H  HCH3   0   0.215   4.8576  -1.7105  -0.0470
 PRU  H11  H  HCH3   0   0.222   3.1549  -1.9587   0.3261

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
 PRU  O42  C4   deloc   1.247  0.020  1.247
 PRU  O21  C2   deloc   1.252  0.020  1.252
 PRU  O32  C3   deloc   1.252  0.020  1.252
 PRU  C4   O41  deloc   1.251  0.020  1.251
 PRU  C4   C41  single  1.538  0.020  1.538
 PRU  C2   O22  deloc   1.249  0.020  1.249
 PRU  C2   C21  single  1.536  0.020  1.536
 PRU  C3   O31  deloc   1.249  0.020  1.249
 PRU  C3   C31  single  1.538  0.020  1.538
 PRU  C22  C21  single  1.529  0.020  1.529
 PRU  C22  C31  single  1.527  0.020  1.527
 PRU  C41  C32  single  1.520  0.020  1.520
 PRU  C21  C12  single  1.533  0.020  1.533
 PRU  C32  C31  single  1.533  0.020  1.533
 PRU  C12  C11  single  1.526  0.020  1.526
 PRU  C11  C1   single  1.547  0.020  1.547
 PRU  C11  C10  single  1.529  0.020  1.529
 PRU  C1   O12  deloc   1.248  0.020  1.248
 PRU  C1   O11  deloc   1.251  0.020  1.251
 PRU  C41  H2   single  0.970  0.020  1.090
 PRU  C41  H3   single  0.970  0.020  1.090
 PRU  C32  H4   single  0.970  0.020  1.090
 PRU  C32  H5   single  0.970  0.020  1.090
 PRU  C22  H7   single  0.970  0.020  1.090
 PRU  C22  H8   single  0.970  0.020  1.090
 PRU  C10  H10  single  0.970  0.020  1.090
 PRU  C10  H11  single  0.970  0.020  1.090
 PRU  C10  H12  single  0.970  0.020  1.090
 PRU  C11  H13  single  0.970  0.020  1.090
 PRU  C12  H14  single  0.970  0.020  1.090
 PRU  C12  H15  single  0.970  0.020  1.090
 PRU  C21  H17  single  0.970  0.020  1.090
 PRU  C31  H18  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
 PRU  C41  C4   O41  115.91  3.000
 PRU  C41  C4   O42  118.23  3.000
 PRU  O41  C4   O42  125.86  3.000
 PRU  H3   C41  H2   104.73  3.000
 PRU  H3   C41  C32  110.37  3.000
 PRU  H2   C41  C32  109.24  3.000
 PRU  H3   C41  C4   108.14  3.000
 PRU  H2   C41  C4   107.61  3.000
 PRU  C32  C41  C4   116.12  3.000
 PRU  H5   C32  H4   105.82  3.000
 PRU  H5   C32  C31  108.68  3.000
 PRU  H4   C32  C31  108.69  3.000
 PRU  H5   C32  C41  109.14  3.000
 PRU  H4   C32  C41  109.92  3.000
 PRU  C31  C32  C41  114.24  3.000
 PRU  C31  C3   O32  116.48  3.000
 PRU  C31  C3   O31  118.01  3.000
 PRU  O32  C3   O31  125.48  3.000
 PRU  H8   C22  H7   106.04  3.000
 PRU  H8   C22  C31  108.49  3.000
 PRU  H7   C22  C31  108.83  3.000
 PRU  H8   C22  C21  108.82  3.000
 PRU  H7   C22  C21  108.65  3.000
 PRU  C31  C22  C21  115.59  3.000
 PRU  C21  C2   O22  118.15  3.000
 PRU  C21  C2   O21  116.48  3.000
 PRU  O22  C2   O21  125.36  3.000
 PRU  H12  C10  H11  107.81  3.000
 PRU  H12  C10  H10  107.86  3.000
 PRU  H11  C10  H10  107.82  3.000
 PRU  H12  C10  C11  111.12  3.000
 PRU  H11  C10  C11  111.16  3.000
 PRU  H10  C10  C11  110.94  3.000
 PRU  H13  C11  C1   105.85  3.000
 PRU  H13  C11  C12  108.07  3.000
 PRU  C1   C11  C12  113.32  3.000
 PRU  H13  C11  C10  106.94  3.000
 PRU  C1   C11  C10  110.15  3.000
 PRU  C12  C11  C10  112.10  3.000
 PRU  H15  C12  H14  105.76  3.000
 PRU  H15  C12  C21  108.26  3.000
 PRU  H14  C12  C21  108.27  3.000
 PRU  H15  C12  C11  109.10  3.000
 PRU  H14  C12  C11  109.13  3.000
 PRU  C21  C12  C11  115.85  3.000
 PRU  O11  C1   O12  125.45  3.000
 PRU  O11  C1   C11  116.16  3.000
 PRU  O12  C1   C11  118.39  3.000
 PRU  H17  C21  C12  108.61  3.000
 PRU  H17  C21  C2   108.51  3.000
 PRU  C12  C21  C2   110.77  3.000
 PRU  H17  C21  C22  108.12  3.000
 PRU  C12  C21  C22  109.24  3.000
 PRU  C2   C21  C22  111.51  3.000
 PRU  H18  C31  C22  108.70  3.000
 PRU  H18  C31  C3   108.47  3.000
 PRU  C22  C31  C3   112.07  3.000
 PRU  H18  C31  C32  107.68  3.000
 PRU  C22  C31  C32  109.82  3.000
 PRU  C3   C31  C32  109.99  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
 PRU  Var_01  C32  C41  C4   O42   -7.07  30.0  3
 PRU  Var_02  C31  C32  C41  C4   173.40  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
 PRU  chir_01  C11  C12  C1   C10  positiv
 PRU  chir_02  C21  C12  C22  C2   positiv
 PRU  chir_03  C31  C3   C22  C32  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
 PRU  plan-1  O42  0.020
 PRU  plan-1  O41  0.020
 PRU  plan-1  C4   0.020
 PRU  plan-1  C41  0.020
 PRU  plan-2  C3   0.020
 PRU  plan-2  O31  0.020
 PRU  plan-2  O32  0.020
 PRU  plan-2  C31  0.020
 PRU  plan-3  C2   0.020
 PRU  plan-3  O21  0.020
 PRU  plan-3  O22  0.020
 PRU  plan-3  C21  0.020
 PRU  plan-4  C11  0.020
 PRU  plan-4  C1   0.020
 PRU  plan-4  O12  0.020
 PRU  plan-4  O11  0.020

