# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 02:32:17 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(Cc1ccccc1c2ccccc2)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
 6HM  6HM  '[([1,1'-biphenyl]-2-yl)methyl]propanedioic acid'  ligand  32  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6HM
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
 6HM  C10  C  CR16   0  -0.255   0.2399  -3.7219  -0.4096
 6HM  C13  C  CH2    0  -0.508  -0.8280  -0.1525  -1.1337
 6HM  C15  C  C      0   0.412  -2.3282   1.7698  -0.3444
 6HM  C01  C  CR16   0  -0.267   3.1633   2.6721   0.3201
 6HM  C02  C  CR16   0  -0.246   2.7952   1.9230   1.4296
 6HM  C03  C  CR16   0  -0.286   2.1864   0.6861   1.2646
 6HM  C04  C  CR6    0   0.049   1.9315   0.1802  -0.0089
 6HM  C05  C  CR16   0  -0.293   2.3108   0.9379  -1.1156
 6HM  C06  C  CR16   0  -0.246   2.9205   2.1742  -0.9538
 6HM  C07  C  CR6    0   0.015   1.3072  -1.1568  -0.1681
 6HM  C08  C  CR16   0  -0.283   2.0242  -2.2738   0.2596
 6HM  C09  C  CR16   0  -0.266   1.5024  -3.5536   0.1400
 6HM  C11  C  CR16   0  -0.293  -0.4828  -2.6130  -0.8255
 6HM  C12  C  CR6    0   0.111   0.0270  -1.3196  -0.7196
 6HM  C14  C  CH1    0  -0.468  -1.4790   0.5468   0.0594
 6HM  O16  O  O      0  -0.607  -2.4055   2.0723  -1.5520
 6HM  O17  O  OC    -1  -0.629  -2.8860   2.3736   0.5975
 6HM  C18  C  C      0   0.419  -2.3856  -0.4107   0.8520
 6HM  O19  O  OC    -1  -0.622  -2.1942  -0.5280   2.0783
 6HM  O20  O  O      0  -0.627  -3.2732  -0.9938   0.1901
 6HM  H1   H  HCR6   0   0.246  -0.1834  -4.7130  -0.5132
 6HM  H2   H  HCH2   0   0.227  -0.2380   0.5743  -1.6926
 6HM  H3   H  HCH2   0   0.219  -1.6065  -0.5060  -1.8101
 6HM  H4   H  HCR6   0   0.253   3.6393   3.6359   0.4475
 6HM  H5   H  HCR6   0   0.253   2.9792   2.3023   2.4266
 6HM  H6   H  HCR6   0   0.246   1.8950   0.1108   2.1351
 6HM  H7   H  HCR6   0   0.249   2.1370   0.5531  -2.1131
 6HM  H8   H  HCR6   0   0.253   3.2102   2.7473  -1.8254
 6HM  H9   H  HCR6   0   0.242   3.0127  -2.1355   0.6820
 6HM  H10  H  HCR6   0   0.247   2.0791  -4.4090   0.4680
 6HM  H11  H  HCR6   0   0.238  -1.4775  -2.7471  -1.2324
 6HM  H12  H  HCH1   0   0.214  -0.6877   0.9065   0.7256

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
 6HM  C02  C01  aromatic  1.388  0.020  1.388
 6HM  C02  C03  aromatic  1.388  0.020  1.388
 6HM  C01  C06  aromatic  1.389  0.020  1.389
 6HM  C03  C04  aromatic  1.394  0.020  1.394
 6HM  C06  C05  aromatic  1.388  0.020  1.388
 6HM  O20  C18  deloc     1.251  0.020  1.251
 6HM  C04  C05  aromatic  1.394  0.020  1.394
 6HM  C04  C07  single    1.484  0.020  1.484
 6HM  O16  C15  deloc     1.247  0.020  1.247
 6HM  C13  C14  single    1.529  0.020  1.529
 6HM  C13  C12  single    1.505  0.020  1.505
 6HM  C18  C14  single    1.539  0.020  1.539
 6HM  C18  O19  deloc     1.247  0.020  1.247
 6HM  C07  C12  aromatic  1.403  0.020  1.403
 6HM  C07  C08  aromatic  1.395  0.020  1.395
 6HM  C15  C14  single    1.543  0.020  1.543
 6HM  C15  O17  deloc     1.250  0.020  1.250
 6HM  C12  C11  aromatic  1.394  0.020  1.394
 6HM  C08  C09  aromatic  1.387  0.020  1.387
 6HM  C11  C10  aromatic  1.387  0.020  1.387
 6HM  C09  C10  aromatic  1.387  0.020  1.387
 6HM  C10  H1   single    0.930  0.020  1.080
 6HM  C13  H2   single    0.970  0.020  1.090
 6HM  C13  H3   single    0.970  0.020  1.090
 6HM  C01  H4   single    0.930  0.020  1.080
 6HM  C02  H5   single    0.930  0.020  1.080
 6HM  C03  H6   single    0.930  0.020  1.080
 6HM  C05  H7   single    0.930  0.020  1.080
 6HM  C06  H8   single    0.930  0.020  1.080
 6HM  C08  H9   single    0.930  0.020  1.080
 6HM  C09  H10  single    0.930  0.020  1.080
 6HM  C11  H11  single    0.930  0.020  1.080
 6HM  C14  H12  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
 6HM  H1   C10  C11  119.95  3.000
 6HM  H1   C10  C09  120.32  3.000
 6HM  C11  C10  C09  119.73  3.000
 6HM  H3   C13  H2   106.53  3.000
 6HM  H3   C13  C14  109.17  3.000
 6HM  H2   C13  C14  109.00  3.000
 6HM  H3   C13  C12  108.97  3.000
 6HM  H2   C13  C12  110.53  3.000
 6HM  C14  C13  C12  112.46  3.000
 6HM  O17  C15  O16  125.78  3.000
 6HM  O17  C15  C14  115.55  3.000
 6HM  O16  C15  C14  118.67  3.000
 6HM  H4   C01  C06  120.27  3.000
 6HM  H4   C01  C02  120.19  3.000
 6HM  C06  C01  C02  119.54  3.000
 6HM  H5   C02  C03  119.74  3.000
 6HM  H5   C02  C01  120.13  3.000
 6HM  C03  C02  C01  120.13  3.000
 6HM  H6   C03  C04  119.49  3.000
 6HM  H6   C03  C02  119.71  3.000
 6HM  C04  C03  C02  120.80  3.000
 6HM  C07  C04  C05  121.26  3.000
 6HM  C07  C04  C03  120.13  3.000
 6HM  C05  C04  C03  118.58  3.000
 6HM  H7   C05  C06  119.62  3.000
 6HM  H7   C05  C04  119.64  3.000
 6HM  C06  C05  C04  120.74  3.000
 6HM  H8   C06  C05  119.68  3.000
 6HM  H8   C06  C01  120.12  3.000
 6HM  C05  C06  C01  120.20  3.000
 6HM  C12  C07  C08  119.78  3.000
 6HM  C08  C07  C04  118.19  3.000
 6HM  C12  C07  C04  122.03  3.000
 6HM  H9   C08  C09  119.63  3.000
 6HM  H9   C08  C07  119.09  3.000
 6HM  C09  C08  C07  121.27  3.000
 6HM  H10  C09  C08  120.16  3.000
 6HM  H10  C09  C10  120.60  3.000
 6HM  C08  C09  C10  119.24  3.000
 6HM  H11  C11  C12  118.63  3.000
 6HM  H11  C11  C10  119.48  3.000
 6HM  C12  C11  C10  121.88  3.000
 6HM  C11  C12  C07  118.10  3.000
 6HM  C11  C12  C13  119.39  3.000
 6HM  C07  C12  C13  122.45  3.000
 6HM  H12  C14  C18  108.47  3.000
 6HM  H12  C14  C15  107.25  3.000
 6HM  C18  C14  C15  107.69  3.000
 6HM  H12  C14  C13  108.50  3.000
 6HM  C15  C14  C13  113.13  3.000
 6HM  C18  C14  C13  111.61  3.000
 6HM  O20  C18  O19  125.83  3.000
 6HM  O19  C18  C14  118.35  3.000
 6HM  O20  C18  C14  115.82  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
 6HM  CONST_01  C07  C12  C11  C10    0.00   0.0  0
 6HM  CONST_02  C07  C08  C09  C10    0.00   0.0  0
 6HM  CONST_03  C04  C03  C02  C01    0.00   0.0  0
 6HM  CONST_04  C04  C05  C06  C01    0.00   0.0  0
 6HM  CONST_05  C05  C06  C01  C02    0.00   0.0  0
 6HM  CONST_06  C05  C04  C03  C02    0.00   0.0  0
 6HM  CONST_07  C07  C04  C03  C02  180.00   0.0  0
 6HM  CONST_08  C06  C01  C02  C03    0.00   0.0  0
 6HM  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 6HM  CONST_12  C11  C12  C07  C04  180.00   0.0  0
 6HM  CONST_13  C09  C08  C07  C04  180.00   0.0  0
 6HM  CONST_16  C07  C04  C05  C06  180.00   0.0  0
 6HM  CONST_17  C11  C12  C07  C08    0.00   0.0  0
 6HM  CONST_18  C11  C10  C09  C08    0.00   0.0  0
 6HM  CONST_19  C12  C07  C08  C09    0.00   0.0  0
 6HM  CONST_20  C12  C11  C10  C09    0.00   0.0  0
 6HM  CONST_21  C13  C12  C11  C10  180.00   0.0  0
 6HM  CONST_22  C04  C07  C12  C13    0.00   0.0  0
 6HM  CONST_23  C08  C07  C12  C13  180.00   0.0  0
 6HM  CONST_24  H9   C08  C09  C10  180.00   0.0  0
 6HM  CONST_25  H6   C03  C02  C01  180.00   0.0  0
 6HM  CONST_26  H7   C05  C06  C01  180.00   0.0  0
 6HM  CONST_27  H8   C06  C01  C02  180.00   0.0  0
 6HM  CONST_28  H4   C01  C02  C03  180.00   0.0  0
 6HM  CONST_29  H5   C02  C03  C04  180.00   0.0  0
 6HM  CONST_30  H11  C11  C12  C07  180.00   0.0  0
 6HM  CONST_31  H10  C09  C08  C07  180.00   0.0  0
 6HM  CONST_32  H1   C10  C09  C08  180.00   0.0  0
 6HM  Var_01    C14  C13  C12  C07  -76.94  30.0  2
 6HM  Var_02    C12  C13  C14  C15  178.41  30.0  2
 6HM  Var_03    O20  C18  C14  C13  -54.63  30.0  2
 6HM  Var_04    O16  C15  C14  C13   -0.17  30.0  2

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
 6HM  plan-1  C01  0.020
 6HM  plan-1  C02  0.020
 6HM  plan-1  C03  0.020
 6HM  plan-1  C04  0.020
 6HM  plan-1  C05  0.020
 6HM  plan-1  C06  0.020
 6HM  plan-1  C07  0.020
 6HM  plan-1  H4   0.020
 6HM  plan-1  H5   0.020
 6HM  plan-1  H6   0.020
 6HM  plan-1  H7   0.020
 6HM  plan-1  H8   0.020
 6HM  plan-2  C10  0.020
 6HM  plan-2  C13  0.020
 6HM  plan-2  C04  0.020
 6HM  plan-2  C07  0.020
 6HM  plan-2  C08  0.020
 6HM  plan-2  C09  0.020
 6HM  plan-2  C11  0.020
 6HM  plan-2  C12  0.020
 6HM  plan-2  H1   0.020
 6HM  plan-2  H9   0.020
 6HM  plan-2  H10  0.020
 6HM  plan-2  H11  0.020
 6HM  plan-3  C15  0.020
 6HM  plan-3  C14  0.020
 6HM  plan-3  O16  0.020
 6HM  plan-3  O17  0.020
 6HM  plan-4  C14  0.020
 6HM  plan-4  C18  0.020
 6HM  plan-4  O19  0.020
 6HM  plan-4  O20  0.020

