# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:22:20 2022
#   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  36  21  .  2022-03-18  2022-03-18
;
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  -0.589  -2.1488  -1.3518  14.5355
 D5U  C17  C  C      0   0.364  -2.7710  -0.3497  14.9411
 D5U  O4   O  OC    -1  -0.587  -3.0382  -0.0663  16.1241
 D5U  C12  C  C      0  -0.108  -3.3140   0.6150  13.8847
 D5U  C13  C  C1     0  -0.280  -4.5735   1.1708  14.1236
 D5U  C15  C  C1     0  -0.263  -5.1917   2.0103  13.2115
 D5U  C16  C  C1     0  -0.252  -4.5326   2.3360  12.0345
 D5U  C14  C  C1     0  -0.295  -3.2692   1.8188  11.7979
 D5U  C11  C  C      0   0.077  -2.6412   0.9562  12.7003
 D5U  C10  C  CH2    0  -0.522  -1.2515   0.4648  12.3645
 D5U  C9   C  CH2    0  -0.569  -0.2854   1.5774  11.9434
 D5U  C8   C  C      0   0.396  -0.2424   2.7554  12.8867
 D5U  O2   O  O      0  -0.394  -0.2944   3.8890  12.4548
 D5U  C3   C  CR6    0  -0.115  -0.2182   2.5529  14.3671
 D5U  C1   C  CR16   0  -0.258  -0.9892   3.4232  15.1361
 D5U  C2   C  CR16   0  -0.271  -1.0442   3.3192  16.5151
 D5U  C4   C  CR16   0  -0.234  -0.2890   2.3419  17.1461
 D5U  C6   C  CR16   0  -0.377   0.5085   1.4785  16.4106
 D5U  C5   C  CR6    0   0.381   0.5502   1.5764  15.0198
 D5U  O1   O  O2     0  -0.467   1.3301   0.7989  14.2526
 D5U  C7   C  CH3    0  -0.440   1.9935  -0.3030  14.8418
 D5U  H2   H  H      0   0.239  -5.0809   0.9284  15.0485
 D5U  H3   H  H      0   0.242  -6.1762   2.4106  13.4196
 D5U  H4   H  H      0   0.244  -4.9948   2.9920  11.3076
 D5U  H5   H  H      0   0.241  -2.7607   2.0902  10.8800
 D5U  H6   H  HCH2   0   0.251  -1.3109  -0.2467  11.5357
 D5U  H7   H  HCH2   0   0.268  -0.8440  -0.0938  13.1977
 D5U  H8   H  HCH2   0   0.276   0.7181   1.1553  11.8537
 D5U  H9   H  HCH2   0   0.253  -0.5383   1.9730  10.9586
 D5U  H10  H  HCR6   0   0.260  -1.5806   4.1789  14.6353
 D5U  H11  H  HCR6   0   0.255  -1.6663   3.9922  17.0894
 D5U  H12  H  HCR6   0   0.263  -0.3121   2.2464  18.2240
 D5U  H13  H  HCR6   0   0.284   1.0983   0.7385  16.9336
 D5U  H14  H  HCH3   0   0.261   2.4776  -0.8378  14.0288
 D5U  H15  H  HCH3   0   0.233   2.7565   0.0138  15.5568
 D5U  H16  H  HCH3   0   0.232   1.2925  -0.9759  15.3419

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  1.385  0.020  1.385
 D5U  C14  C11  aromatic  1.397  0.020  1.397
 D5U  C16  C15  aromatic  1.388  0.020  1.388
 D5U  C9   C10  single    1.532  0.020  1.532
 D5U  C9   C8   single    1.510  0.020  1.510
 D5U  C10  C11  single    1.512  0.020  1.512
 D5U  O2   C8   double    1.214  0.020  1.214
 D5U  C11  C12  aromatic  1.404  0.020  1.404
 D5U  C15  C13  aromatic  1.385  0.020  1.385
 D5U  C8   C3   single    1.494  0.020  1.494
 D5U  C12  C13  aromatic  1.397  0.020  1.397
 D5U  C12  C17  single    1.530  0.020  1.530
 D5U  O1   C7   single    1.415  0.020  1.415
 D5U  O1   C5   single    1.342  0.020  1.342
 D5U  C3   C5   aromatic  1.404  0.020  1.404
 D5U  C3   C1   aromatic  1.394  0.020  1.394
 D5U  O3   C17  deloc     1.247  0.020  1.247
 D5U  C17  O4   deloc     1.245  0.020  1.245
 D5U  C5   C6   aromatic  1.395  0.020  1.395
 D5U  C1   C2   aromatic  1.384  0.020  1.384
 D5U  C6   C4   aromatic  1.387  0.020  1.387
 D5U  C2   C4   aromatic  1.387  0.020  1.387
 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   115.86  3.000
 D5U  O4   C17  O3   126.78  3.000
 D5U  C12  C17  O3   117.32  3.000
 D5U  C11  C12  C13  118.65  3.000
 D5U  C13  C12  C17  116.91  3.000
 D5U  C11  C12  C17  124.44  3.000
 D5U  H2   C13  C15  119.28  3.000
 D5U  H2   C13  C12  118.66  3.000
 D5U  C15  C13  C12  122.06  3.000
 D5U  H3   C15  C16  120.53  3.000
 D5U  H3   C15  C13  120.21  3.000
 D5U  C16  C15  C13  119.26  3.000
 D5U  H4   C16  C14  120.05  3.000
 D5U  H4   C16  C15  120.58  3.000
 D5U  C14  C16  C15  119.36  3.000
 D5U  H5   C14  C11  119.38  3.000
 D5U  H5   C14  C16  118.62  3.000
 D5U  C11  C14  C16  122.00  3.000
 D5U  C10  C11  C14  118.05  3.000
 D5U  C10  C11  C12  123.29  3.000
 D5U  C14  C11  C12  118.64  3.000
 D5U  H7   C10  H6   105.54  3.000
 D5U  H7   C10  C9   110.41  3.000
 D5U  H6   C10  C9   107.35  3.000
 D5U  H7   C10  C11  110.04  3.000
 D5U  H6   C10  C11  109.26  3.000
 D5U  C9   C10  C11  113.87  3.000
 D5U  H9   C9   H8   106.20  3.000
 D5U  H9   C9   C8   106.72  3.000
 D5U  H8   C9   C8   109.06  3.000
 D5U  H9   C9   C10  111.42  3.000
 D5U  H8   C9   C10  108.73  3.000
 D5U  C8   C9   C10  114.38  3.000
 D5U  C3   C8   O2   118.66  3.000
 D5U  C3   C8   C9   120.91  3.000
 D5U  O2   C8   C9   120.33  3.000
 D5U  C5   C3   C1   118.73  3.000
 D5U  C1   C3   C8   116.93  3.000
 D5U  C5   C3   C8   124.32  3.000
 D5U  H10  C1   C2   119.46  3.000
 D5U  H10  C1   C3   118.87  3.000
 D5U  C2   C1   C3   121.64  3.000
 D5U  H11  C2   C4   120.67  3.000
 D5U  H11  C2   C1   120.34  3.000
 D5U  C4   C2   C1   118.99  3.000
 D5U  H12  C4   C6   119.05  3.000
 D5U  H12  C4   C2   120.24  3.000
 D5U  C6   C4   C2   120.71  3.000
 D5U  H13  C6   C5   120.94  3.000
 D5U  H13  C6   C4   118.91  3.000
 D5U  C5   C6   C4   120.16  3.000
 D5U  O1   C5   C6   123.14  3.000
 D5U  C6   C5   C3   119.75  3.000
 D5U  O1   C5   C3   117.08  3.000
 D5U  C7   O1   C5   119.05  3.000
 D5U  H16  C7   H15  109.09  3.000
 D5U  H16  C7   H14  108.96  3.000
 D5U  H15  C7   H14  108.73  3.000
 D5U  H16  C7   O1   111.68  3.000
 D5U  H15  C7   O1   111.98  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  Var_01    C11  C12  C17  O3    -37.97  30.0  2
 D5U  Var_02    C9   C10  C11  C12  -129.68  30.0  3
 D5U  Var_03    C5   C3   C8   C9     42.04  30.0  2
 D5U  Var_04    C8   C9   C10  C11    50.20  30.0  1
 D5U  Var_05    C3   C8   C9   C10    42.90  30.0  3
 D5U  Var_06    H14  C7   O1   C5    174.49  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

