# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 07:18:00 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: heptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCC(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
 PML  PML  'heptanedioic acid        '  ligand  23  11  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PML
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
 PML  C1    C  C     0   0.550   0.0748   0.0014   3.8257
 PML  O11   O  O     0  -0.446   1.2781  -0.0069   3.9058
 PML  O12   O  OH1   0  -0.598  -0.7199   0.0066   4.8931
 PML  C2    C  CH2   0  -0.580  -0.7112   0.0076   2.5443
 PML  C3    C  CH2   0  -0.418   0.1516   0.0026   1.2935
 PML  C4    C  CH2   0  -0.418  -0.6922   0.0128   0.0251
 PML  C5    C  CH2   0  -0.419   0.1603   0.0117  -1.2374
 PML  C6    C  CH2   0  -0.580  -0.6927   0.0191  -2.4951
 PML  C7    C  C     0   0.550   0.1055   0.0236  -3.7689
 PML  O71   O  O     0  -0.447   1.3093   0.0557  -3.8367
 PML  O72   O  OH1   0  -0.598  -0.6761  -0.0103  -4.8445
 PML  H12   H  HOH1  0   0.478  -0.1865   0.0023   5.7018
 PML  HC21  H  HCH2  0   0.276  -1.3811  -0.8584   2.5525
 PML  HC22  H  HCH2  0   0.276  -1.3687   0.8832   2.5537
 PML  HC31  H  HCH2  0   0.227   0.8138   0.8725   1.2955
 PML  HC32  H  HCH2  0   0.227   0.7981  -0.8791   1.2915
 PML  HC41  H  HCH2  0   0.218  -1.3566  -0.8581   0.0198
 PML  HC42  H  HCH2  0   0.218  -1.3443   0.8931   0.0258
 PML  HC51  H  HCH2  0   0.227   0.8191   0.8840  -1.2301
 PML  HC52  H  HCH2  0   0.227   0.8101  -0.8677  -1.2350
 PML  HC61  H  HCH2  0   0.275  -1.3605  -0.8481  -2.5129
 PML  HC62  H  HCH2  0   0.277  -1.3519   0.8936  -2.5069
 PML  H72   H  HOH1  0   0.478  -0.1334  -0.0005  -5.6467

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
 PML  C1   O11   double  1.206  0.020  1.206
 PML  C1   O12   single  1.331  0.020  1.331
 PML  C1   C2    single  1.503  0.020  1.503
 PML  O12  H12   single  0.850  0.020  0.980
 PML  C2   C3    single  1.520  0.020  1.520
 PML  C2   HC21  single  0.970  0.020  1.090
 PML  C2   HC22  single  0.970  0.020  1.090
 PML  C3   C4    single  1.523  0.020  1.523
 PML  C3   HC31  single  0.970  0.020  1.090
 PML  C3   HC32  single  0.970  0.020  1.090
 PML  C4   C5    single  1.523  0.020  1.523
 PML  C4   HC41  single  0.970  0.020  1.090
 PML  C4   HC42  single  0.970  0.020  1.090
 PML  C5   C6    single  1.520  0.020  1.520
 PML  C5   HC51  single  0.970  0.020  1.090
 PML  C5   HC52  single  0.970  0.020  1.090
 PML  C6   C7    single  1.503  0.020  1.503
 PML  C6   HC61  single  0.970  0.020  1.090
 PML  C6   HC62  single  0.970  0.020  1.090
 PML  C7   O71   double  1.206  0.020  1.206
 PML  C7   O72   single  1.330  0.020  1.330
 PML  O72  H72   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
 PML  C2    C1   O12   111.80  3.000
 PML  C2    C1   O11   125.34  3.000
 PML  O12   C1   O11   122.86  3.000
 PML  H12   O12  C1    109.92  3.000
 PML  HC22  C2   HC21  105.37  3.000
 PML  HC22  C2   C3    110.53  3.000
 PML  HC21  C2   C3    110.54  3.000
 PML  HC22  C2   C1    108.06  3.000
 PML  HC21  C2   C1    108.07  3.000
 PML  C3    C2   C1    113.87  3.000
 PML  HC32  C3   HC31  106.48  3.000
 PML  HC32  C3   C4    109.36  3.000
 PML  HC31  C3   C4    109.37  3.000
 PML  HC32  C3   C2    109.87  3.000
 PML  HC31  C3   C2    109.86  3.000
 PML  C4    C3   C2    111.76  3.000
 PML  HC42  C4   HC41  106.13  3.000
 PML  HC42  C4   C5    109.53  3.000
 PML  HC41  C4   C5    109.56  3.000
 PML  HC42  C4   C3    109.55  3.000
 PML  HC41  C4   C3    109.55  3.000
 PML  C5    C4   C3    112.33  3.000
 PML  HC52  C5   HC51  106.48  3.000
 PML  HC52  C5   C6    109.84  3.000
 PML  HC51  C5   C6    109.87  3.000
 PML  HC52  C5   C4    109.35  3.000
 PML  HC51  C5   C4    109.34  3.000
 PML  C6    C5   C4    111.82  3.000
 PML  HC62  C6   HC61  105.38  3.000
 PML  HC62  C6   C7    107.95  3.000
 PML  HC61  C6   C7    108.21  3.000
 PML  HC62  C6   C5    110.53  3.000
 PML  HC61  C6   C5    110.61  3.000
 PML  C7    C6   C5    113.78  3.000
 PML  O72   C7   O71   122.80  3.000
 PML  O72   C7   C6    111.91  3.000
 PML  O71   C7   C6    125.29  3.000
 PML  H72   O72  C7    109.90  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
 PML  CONST_01  H12  O12  C1  O11     0.00   0.0  0
 PML  CONST_02  H72  O72  C7  C6    180.00   0.0  0
 PML  Var_01    C4   C3   C2  C1   -179.85  30.0  3
 PML  Var_02    C3   C2   C1  O11     0.00  30.0  3
 PML  Var_03    C5   C4   C3  C2    179.85  30.0  3
 PML  Var_04    C6   C5   C4  C3    179.89  30.0  3
 PML  Var_05    C7   C6   C5  C4    179.78  30.0  3
 PML  Var_06    O71  C7   C6  C5     -1.98  30.0  3

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
 PML  plan-1  C1   0.020
 PML  plan-1  O11  0.020
 PML  plan-1  O12  0.020
 PML  plan-1  C2   0.020
 PML  plan-1  H12  0.020
 PML  plan-2  C6   0.020
 PML  plan-2  C7   0.020
 PML  plan-2  O71  0.020
 PML  plan-2  O72  0.020
 PML  plan-2  H72  0.020

