# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:48:55 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  21  11  .  2021-08-19  2021-08-19  
;
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   0.408   0.0826  -0.0118   3.8712
 PML  O11   O  O      0  -0.611   1.3098   0.2057   3.8335
 PML  O12   O  OC    -1  -0.635  -0.5964  -0.2186   4.9003
 PML  C2    C  CH2    0  -0.578  -0.6907  -0.0117   2.5411
 PML  C3    C  CH2    0  -0.401   0.1507   0.0134   1.2754
 PML  C4    C  CH2    0  -0.406  -0.6910   0.0080   0.0045
 PML  C5    C  CH2    0  -0.401   0.1429   0.0078  -1.2716
 PML  C6    C  CH2    0  -0.578  -0.7061   0.0129  -2.5325
 PML  C7    C  C      0   0.409   0.0593  -0.0082  -3.8672
 PML  O71   O  O      0  -0.611   1.2893  -0.2109  -3.8321
 PML  O72   O  OC    -1  -0.635  -0.6281   0.1675  -4.8965
 PML  HC21  H  HCH2   0   0.210  -1.3554  -0.8829   2.5258
 PML  HC22  H  HCH2   0   0.217  -1.3646   0.8548   2.5460
 PML  HC31  H  HCH2   0   0.198   0.7959   0.8969   1.2763
 PML  HC32  H  HCH2   0   0.197   0.8251  -0.8490   1.2622
 PML  HC41  H  HCH2   0   0.197  -1.3497  -0.8690   0.0069
 PML  HC42  H  HCH2   0   0.197  -1.3571   0.8794   0.0062
 PML  HC51  H  HCH2   0   0.197   0.8058   0.8792  -1.2674
 PML  HC52  H  HCH2   0   0.198   0.7998  -0.8668  -1.2717
 PML  HC61  H  HCH2   0   0.217  -1.3791  -0.8541  -2.5199
 PML  HC62  H  HCH2   0   0.211  -1.3717   0.8836  -2.5270

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   deloc   1.247  0.020  1.247
 PML  C1  O12   deloc   1.250  0.020  1.250
 PML  C1  C2    single  1.539  0.020  1.539
 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  1.524  0.020  1.524
 PML  C3  HC31  single  0.970  0.020  1.090
 PML  C3  HC32  single  0.970  0.020  1.090
 PML  C4  C5    single  1.524  0.020  1.524
 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  1.539  0.020  1.539
 PML  C6  HC61  single  0.970  0.020  1.090
 PML  C6  HC62  single  0.970  0.020  1.090
 PML  C7  O71   deloc   1.247  0.020  1.247
 PML  C7  O72   deloc   1.250  0.020  1.250

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   116.02  3.000
 PML  C2    C1  O11   117.94  3.000
 PML  O12   C1  O11   126.03  3.000
 PML  HC22  C2  HC21  104.79  3.000
 PML  HC22  C2  C3    109.30  3.000
 PML  HC21  C2  C3    109.71  3.000
 PML  HC22  C2  C1    107.74  3.000
 PML  HC21  C2  C1    108.47  3.000
 PML  C3    C2  C1    116.21  3.000
 PML  HC32  C3  HC31  105.84  3.000
 PML  HC32  C3  C4    109.10  3.000
 PML  HC31  C3  C4    109.22  3.000
 PML  HC32  C3  C2    109.76  3.000
 PML  HC31  C3  C2    109.83  3.000
 PML  C4    C3  C2    112.86  3.000
 PML  HC42  C4  HC41  105.70  3.000
 PML  HC42  C4  C5    109.49  3.000
 PML  HC41  C4  C5    109.29  3.000
 PML  HC42  C4  C3    109.34  3.000
 PML  HC41  C4  C3    109.43  3.000
 PML  C5    C4  C3    113.32  3.000
 PML  HC52  C5  HC51  105.83  3.000
 PML  HC52  C5  C6    109.75  3.000
 PML  HC51  C5  C6    109.80  3.000
 PML  HC52  C5  C4    109.19  3.000
 PML  HC51  C5  C4    109.14  3.000
 PML  C6    C5  C4    112.88  3.000
 PML  HC62  C6  HC61  104.78  3.000
 PML  HC62  C6  C7    108.50  3.000
 PML  HC61  C6  C7    107.71  3.000
 PML  HC62  C6  C5    109.73  3.000
 PML  HC61  C6  C5    109.29  3.000
 PML  C7    C6  C5    116.21  3.000
 PML  O72   C7  O71   126.04  3.000
 PML  O72   C7  C6    116.02  3.000
 PML  O71   C7  C6    117.93  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  Var_01  C4   C3  C2  C1    179.84  30.0  3
 PML  Var_02  C3   C2  C1  O11    10.33  30.0  3
 PML  Var_03  C5   C4  C3  C2   -178.97  30.0  3
 PML  Var_04  C6   C5  C4  C3   -179.57  30.0  3
 PML  Var_05  C7   C6  C5  C4   -179.12  30.0  3
 PML  Var_06  O71  C7  C6  C5      9.58  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-2  C6   0.020
 PML  plan-2  C7   0.020
 PML  plan-2  O71  0.020
 PML  plan-2  O72  0.020

