# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:31:21 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[3-(2-methoxyphenyl)-3-oxidanylidene-propyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)CCc2ccccc2C(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
 D5U  D5U  '2-[3-(2-methoxyphenyl)-3-oxidanylidene-propyl]benzoic acid'  ligand  37  21  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D5U
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
 D5U  O3   O  O     0  -0.437  -1.9588  -0.8318  14.9463
 D5U  C17  C  C     0   0.497  -2.6723   0.1399  15.0249
 D5U  O4   O  OH1   0  -0.581  -3.0349   0.6687  16.1855
 D5U  C12  C  CR6   0  -0.094  -3.2879   0.8458  13.8671
 D5U  C13  C  CR16  0  -0.250  -4.5737   1.3705  14.0326
 D5U  C15  C  CR16  0  -0.259  -5.2460   1.9597  12.9778
 D5U  C16  C  CR16  0  -0.233  -4.6269   2.0457  11.7385
 D5U  C14  C  CR16  0  -0.290  -3.3458   1.5481  11.5762
 D5U  C11  C  CR6   0   0.124  -2.6507   0.9387  12.6209
 D5U  C10  C  CH2   0  -0.555  -1.2341   0.5008  12.3414
 D5U  C9   C  CH2   0  -0.560  -0.3209   1.6893  12.0079
 D5U  C8   C  C     0   0.399  -0.3454   2.8006  13.0309
 D5U  O2   O  O     0  -0.398  -0.5209   3.9478  12.6714
 D5U  C3   C  CR6   0  -0.143  -0.2364   2.5156  14.4928
 D5U  C1   C  CR16  0  -0.248  -0.9577   3.3490  15.3497
 D5U  C2   C  CR16  0  -0.260  -0.9382   3.1765  16.7208
 D5U  C4   C  CR16  0  -0.238  -0.1682   2.1553  17.2579
 D5U  C6   C  CR16  0  -0.377   0.5773   1.3239  16.4376
 D5U  C5   C  CR6   0   0.392   0.5580   1.5011  15.0539
 D5U  O1   O  O2    0  -0.468   1.2991   0.7646  14.2142
 D5U  C7   C  CH3   0  -0.441   2.0122  -0.3503  14.7156
 D5U  H1   H  HOH1  0   0.481  -2.6407   0.1626  16.9111
 D5U  H2   H  HCR6  0   0.266  -5.0678   1.3014  14.9920
 D5U  H3   H  HCR6  0   0.262  -6.2458   2.3461  13.1234
 D5U  H4   H  HCR6  0   0.263  -5.1392   2.5014  10.9012
 D5U  H5   H  HCR6  0   0.259  -2.8633   1.6324  10.6095
 D5U  H6   H  HCH2  0   0.270  -1.2353  -0.1607  11.4719
 D5U  H7   H  HCH2  0   0.284  -0.8194  -0.0770  13.1575
 D5U  H8   H  HCH2  0   0.281   0.7013   1.3260  11.8858
 D5U  H9   H  HCH2  0   0.258  -0.6102   2.1328  11.0537
 D5U  H10  H  HCR6  0   0.261  -1.5670   4.1331  14.9202
 D5U  H11  H  HCR6  0   0.255  -1.5225   3.8227  17.3612
 D5U  H12  H  HCR6  0   0.266  -0.1395   1.9988  18.3286
 D5U  H13  H  HCR6  0   0.284   1.1767   0.5459  16.8895
 D5U  H14  H  HCH3  0   0.263   2.4560  -0.8411  13.8536
 D5U  H15  H  HCH3  0   0.235   2.8099  -0.0496  15.3990
 D5U  H16  H  HCH3  0   0.233   1.3529  -1.0568  15.2245

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
 D5U  C14  C16  aromatic  1.384  0.020  1.384
 D5U  C14  C11  aromatic  1.395  0.020  1.395
 D5U  C16  C15  aromatic  1.388  0.020  1.388
 D5U  C9   C10  single    1.535  0.020  1.535
 D5U  C9   C8   single    1.511  0.020  1.511
 D5U  C10  C11  single    1.509  0.020  1.509
 D5U  O2   C8   double    1.215  0.020  1.215
 D5U  C11  C12  aromatic  1.403  0.020  1.403
 D5U  C15  C13  aromatic  1.383  0.020  1.383
 D5U  C8   C3   single    1.493  0.020  1.493
 D5U  C12  C13  aromatic  1.399  0.020  1.399
 D5U  C12  C17  single    1.489  0.020  1.489
 D5U  O1   C7   single    1.415  0.020  1.415
 D5U  O1   C5   single    1.340  0.020  1.340
 D5U  C3   C5   aromatic  1.405  0.020  1.405
 D5U  C3   C1   aromatic  1.396  0.020  1.396
 D5U  O3   C17  double    1.208  0.020  1.208
 D5U  C17  O4   single    1.326  0.020  1.326
 D5U  C5   C6   aromatic  1.395  0.020  1.395
 D5U  C1   C2   aromatic  1.382  0.020  1.382
 D5U  C6   C4   aromatic  1.386  0.020  1.386
 D5U  C2   C4   aromatic  1.387  0.020  1.387
 D5U  O4   H1   single    0.850  0.020  0.980
 D5U  C13  H2   single    0.930  0.020  1.080
 D5U  C15  H3   single    0.930  0.020  1.080
 D5U  C16  H4   single    0.930  0.020  1.080
 D5U  C14  H5   single    0.930  0.020  1.080
 D5U  C10  H6   single    0.970  0.020  1.090
 D5U  C10  H7   single    0.970  0.020  1.090
 D5U  C9   H8   single    0.970  0.020  1.090
 D5U  C9   H9   single    0.970  0.020  1.090
 D5U  C1   H10  single    0.930  0.020  1.080
 D5U  C2   H11  single    0.930  0.020  1.080
 D5U  C4   H12  single    0.930  0.020  1.080
 D5U  C6   H13  single    0.930  0.020  1.080
 D5U  C7   H14  single    0.970  0.020  1.090
 D5U  C7   H15  single    0.970  0.020  1.090
 D5U  C7   H16  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
 D5U  C12  C17  O4   112.23  3.000
 D5U  O4   C17  O3   122.63  3.000
 D5U  C12  C17  O3   125.09  3.000
 D5U  H1   O4   C17  109.63  3.000
 D5U  C11  C12  C13  119.86  3.000
 D5U  C13  C12  C17  117.77  3.000
 D5U  C11  C12  C17  122.30  3.000
 D5U  H2   C13  C15  118.81  3.000
 D5U  H2   C13  C12  120.07  3.000
 D5U  C15  C13  C12  121.11  3.000
 D5U  H3   C15  C16  120.69  3.000
 D5U  H3   C15  C13  119.93  3.000
 D5U  C16  C15  C13  119.39  3.000
 D5U  H4   C16  C14  119.93  3.000
 D5U  H4   C16  C15  120.38  3.000
 D5U  C14  C16  C15  119.69  3.000
 D5U  H5   C14  C11  118.70  3.000
 D5U  H5   C14  C16  119.26  3.000
 D5U  C11  C14  C16  122.04  3.000
 D5U  C10  C11  C14  117.12  3.000
 D5U  C10  C11  C12  124.88  3.000
 D5U  C14  C11  C12  117.90  3.000
 D5U  H7   C10  H6   106.09  3.000
 D5U  H7   C10  C9   110.43  3.000
 D5U  H6   C10  C9   107.25  3.000
 D5U  H7   C10  C11  112.02  3.000
 D5U  H6   C10  C11  108.79  3.000
 D5U  C9   C10  C11  111.97  3.000
 D5U  H9   C9   H8   106.60  3.000
 D5U  H9   C9   C8   106.79  3.000
 D5U  H8   C9   C8   109.62  3.000
 D5U  H9   C9   C10  110.29  3.000
 D5U  H8   C9   C10  108.88  3.000
 D5U  C8   C9   C10  114.38  3.000
 D5U  C3   C8   O2   118.71  3.000
 D5U  C3   C8   C9   121.42  3.000
 D5U  O2   C8   C9   119.78  3.000
 D5U  C5   C3   C1   118.55  3.000
 D5U  C1   C3   C8   116.69  3.000
 D5U  C5   C3   C8   124.74  3.000
 D5U  H10  C1   C2   119.49  3.000
 D5U  H10  C1   C3   118.68  3.000
 D5U  C2   C1   C3   121.81  3.000
 D5U  H11  C2   C4   120.70  3.000
 D5U  H11  C2   C1   120.35  3.000
 D5U  C4   C2   C1   118.94  3.000
 D5U  H12  C4   C6   118.98  3.000
 D5U  H12  C4   C2   120.28  3.000
 D5U  C6   C4   C2   120.74  3.000
 D5U  H13  C6   C5   120.91  3.000
 D5U  H13  C6   C4   118.86  3.000
 D5U  C5   C6   C4   120.23  3.000
 D5U  O1   C5   C6   122.95  3.000
 D5U  C6   C5   C3   119.70  3.000
 D5U  O1   C5   C3   117.33  3.000
 D5U  C7   O1   C5   119.30  3.000
 D5U  H16  C7   H15  109.11  3.000
 D5U  H16  C7   H14  108.90  3.000
 D5U  H15  C7   H14  108.80  3.000
 D5U  H16  C7   O1   111.75  3.000
 D5U  H15  C7   O1   111.88  3.000
 D5U  H14  C7   O1   106.29  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
 D5U  CONST_01  C16  C14  C11  C12     0.00   0.0  0
 D5U  CONST_02  C16  C15  C13  C12     0.00   0.0  0
 D5U  CONST_03  C14  C16  C15  C13     0.00   0.0  0
 D5U  CONST_04  C14  C11  C12  C13     0.00   0.0  0
 D5U  CONST_05  C11  C14  C16  C15     0.00   0.0  0
 D5U  CONST_06  C11  C12  C13  C15     0.00   0.0  0
 D5U  CONST_07  C4   C6   C5   C3      0.00   0.0  0
 D5U  CONST_08  C4   C2   C1   C3      0.00   0.0  0
 D5U  CONST_09  C6   C5   C3   C1      0.00   0.0  0
 D5U  CONST_10  C6   C4   C2   C1      0.00   0.0  0
 D5U  CONST_11  C5   C3   C1   C2      0.00   0.0  0
 D5U  CONST_12  C5   C6   C4   C2      0.00   0.0  0
 D5U  CONST_13  C14  C11  C12  C17   180.00   0.0  0
 D5U  CONST_14  C15  C13  C12  C17   180.00   0.0  0
 D5U  CONST_15  C10  C11  C12  C13   180.00   0.0  0
 D5U  CONST_16  C10  C11  C14  C16   180.00   0.0  0
 D5U  CONST_17  C6   C5   C3   C8    180.00   0.0  0
 D5U  CONST_18  C2   C1   C3   C8    180.00   0.0  0
 D5U  CONST_19  O1   C5   C3   C1    180.00   0.0  0
 D5U  CONST_20  O1   C5   C6   C4    180.00   0.0  0
 D5U  CONST_21  H5   C14  C11  C12   180.00   0.0  0
 D5U  CONST_22  H3   C15  C13  C12   180.00   0.0  0
 D5U  CONST_23  H4   C16  C15  C13   180.00   0.0  0
 D5U  CONST_24  H2   C13  C15  C16   180.00   0.0  0
 D5U  CONST_25  H13  C6   C5   C3    180.00   0.0  0
 D5U  CONST_26  H11  C2   C1   C3    180.00   0.0  0
 D5U  CONST_27  H12  C4   C2   C1    180.00   0.0  0
 D5U  CONST_28  H10  C1   C2   C4    180.00   0.0  0
 D5U  CONST_29  H1   O4   C17  C12   180.00   0.0  0
 D5U  Var_01    C11  C12  C17  O3    -33.02  30.0  2
 D5U  Var_02    C9   C10  C11  C12  -113.26  30.0  3
 D5U  Var_03    C5   C3   C8   C9     36.06  30.0  2
 D5U  Var_04    C8   C9   C10  C11    52.99  30.0  1
 D5U  Var_05    C3   C8   C9   C10    46.81  30.0  3
 D5U  Var_06    H14  C7   O1   C5    174.80  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
 D5U  plan-1  C17  0.020
 D5U  plan-1  C12  0.020
 D5U  plan-1  C13  0.020
 D5U  plan-1  C15  0.020
 D5U  plan-1  C16  0.020
 D5U  plan-1  C14  0.020
 D5U  plan-1  C11  0.020
 D5U  plan-1  C10  0.020
 D5U  plan-1  H2   0.020
 D5U  plan-1  H3   0.020
 D5U  plan-1  H4   0.020
 D5U  plan-1  H5   0.020
 D5U  plan-2  C8   0.020
 D5U  plan-2  C3   0.020
 D5U  plan-2  C1   0.020
 D5U  plan-2  C2   0.020
 D5U  plan-2  C4   0.020
 D5U  plan-2  C6   0.020
 D5U  plan-2  C5   0.020
 D5U  plan-2  O1   0.020
 D5U  plan-2  H10  0.020
 D5U  plan-2  H11  0.020
 D5U  plan-2  H12  0.020
 D5U  plan-2  H13  0.020
 D5U  plan-3  C9   0.020
 D5U  plan-3  C8   0.020
 D5U  plan-3  O2   0.020
 D5U  plan-3  C3   0.020
 D5U  plan-4  O3   0.020
 D5U  plan-4  C17  0.020
 D5U  plan-4  O4   0.020
 D5U  plan-4  C12  0.020
 D5U  plan-4  H1   0.020

