# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:11:48 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-(benzyloxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(OCc2ccccc2)cc1
#
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
 02S  02S  '4-(benzyloxy)benzoic acid'  ligand  29  17  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_02S
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
 02S  C8    C  CR6   0  -0.109  -3.2945  -0.0818   0.0589
 02S  C27   C  C     0   0.528  -4.7702  -0.0971   0.0751
 02S  O28   O  O     0  -0.448  -5.4351  -1.1042   0.1598
 02S  C34   C  CR16  0  -0.239  -2.6093  -1.2974   0.1411
 02S  C33   C  CR16  0  -0.334  -1.2329  -1.3350   0.1322
 02S  C30   C  CR16  0  -0.242  -2.5563   1.0950  -0.0332
 02S  C31   C  CR16  0  -0.370  -1.1712   1.0716  -0.0436
 02S  C32   C  CR6   0   0.402  -0.4982  -0.1475   0.0402
 02S  O35   O  O2    0  -0.458   0.8346  -0.2776   0.0391
 02S  C36   C  CH2   0  -0.277   1.6414   0.8925  -0.0737
 02S  C37   C  CR6   0   0.101   3.0729   0.4526  -0.0409
 02S  C38   C  CR16  0  -0.285   3.6766   0.1237   1.1704
 02S  C39   C  CR16  0  -0.242   4.9938  -0.3096   1.2053
 02S  C40   C  CR16  0  -0.261   5.7220  -0.4176   0.0264
 02S  C41   C  CR16  0  -0.241   5.1278  -0.0905  -1.1846
 02S  C42   C  CR16  0  -0.298   3.8074   0.3402  -1.2163
 02S  H34   H  HCR6  0   0.267  -3.1617  -2.2248   0.2140
 02S  H33   H  HCR6  0   0.271  -0.7101  -2.2807   0.1965
 02S  H30   H  HCR6  0   0.271  -3.0513   2.0541  -0.0998
 02S  H31   H  HCR6  0   0.290  -0.6360   2.0080  -0.1183
 02S  H36   H  HCH2  0   0.251   1.4183   1.4156  -1.0085
 02S  H36A  H  HCH2  0   0.248   1.4291   1.5774   0.7535
 02S  H38   H  HCR6  0   0.255   3.1161   0.2146   2.0935
 02S  H39   H  HCR6  0   0.259   5.4542  -0.5595   2.1523
 02S  H40   H  HCR6  0   0.259   6.7510  -0.7522   0.0531
 02S  H41   H  HCR6  0   0.259   5.6909  -0.1716  -2.1053
 02S  H42   H  HCR6  0   0.256   3.3480   0.5949  -2.1639
 02S  OXT   O  OH1   0  -0.597  -5.3075   1.1144  -0.0113
 02S  HXT   H  HOH1  0   0.486  -6.2732   1.0450   0.0039

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
 02S  C27  C8    single    1.476  0.020  1.476
 02S  C8   C34   aromatic  1.398  0.020  1.398
 02S  C8   C30   aromatic  1.392  0.020  1.392
 02S  O28  C27   double    1.210  0.020  1.210
 02S  C34  C33   aromatic  1.377  0.020  1.377
 02S  C34  H34   single    0.930  0.020  1.080
 02S  C33  C32   aromatic  1.399  0.020  1.399
 02S  C33  H33   single    0.930  0.020  1.080
 02S  C30  C31   aromatic  1.385  0.020  1.385
 02S  C30  H30   single    0.930  0.020  1.080
 02S  C31  C32   aromatic  1.395  0.020  1.395
 02S  C31  H31   single    0.930  0.020  1.080
 02S  C32  O35   single    1.339  0.020  1.339
 02S  O35  C36   single    1.426  0.020  1.426
 02S  C36  C37   single    1.498  0.020  1.498
 02S  C36  H36   single    0.970  0.020  1.090
 02S  C36  H36A  single    0.970  0.020  1.090
 02S  C37  C42   aromatic  1.391  0.020  1.391
 02S  C37  C38   aromatic  1.393  0.020  1.393
 02S  C38  C39   aromatic  1.387  0.020  1.387
 02S  C38  H38   single    0.930  0.020  1.080
 02S  C39  C40   aromatic  1.390  0.020  1.390
 02S  C39  H39   single    0.930  0.020  1.080
 02S  C41  C40   aromatic  1.388  0.020  1.388
 02S  C40  H40   single    0.930  0.020  1.080
 02S  C42  C41   aromatic  1.389  0.020  1.389
 02S  C41  H41   single    0.930  0.020  1.080
 02S  C42  H42   single    0.930  0.020  1.080
 02S  C27  OXT   single    1.328  0.020  1.328
 02S  OXT  HXT   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
 02S  C30   C8   C34  118.63  3.000
 02S  C30   C8   C27  122.66  3.000
 02S  C34   C8   C27  118.71  3.000
 02S  OXT   C27  O28  122.79  3.000
 02S  OXT   C27  C8   113.22  3.000
 02S  O28   C27  C8   123.99  3.000
 02S  H34   C34  C33  119.17  3.000
 02S  H34   C34  C8   119.94  3.000
 02S  C33   C34  C8   120.89  3.000
 02S  H33   C33  C32  119.45  3.000
 02S  H33   C33  C34  120.42  3.000
 02S  C32   C33  C34  120.14  3.000
 02S  H30   C30  C31  118.18  3.000
 02S  H30   C30  C8   120.74  3.000
 02S  C31   C30  C8   121.09  3.000
 02S  H31   C31  C32  121.48  3.000
 02S  H31   C31  C30  118.74  3.000
 02S  C32   C31  C30  119.78  3.000
 02S  O35   C32  C31  124.40  3.000
 02S  O35   C32  C33  116.11  3.000
 02S  C31   C32  C33  119.49  3.000
 02S  C36   O35  C32  118.92  3.000
 02S  H36A  C36  H36  107.87  3.000
 02S  H36A  C36  C37  110.64  3.000
 02S  H36   C36  C37  110.73  3.000
 02S  H36A  C36  O35  110.12  3.000
 02S  H36   C36  O35  110.16  3.000
 02S  C37   C36  O35  107.34  3.000
 02S  C42   C37  C38  119.15  3.000
 02S  C38   C37  C36  120.17  3.000
 02S  C42   C37  C36  120.66  3.000
 02S  H38   C38  C39  119.73  3.000
 02S  H38   C38  C37  119.79  3.000
 02S  C39   C38  C37  120.48  3.000
 02S  H39   C39  C40  120.09  3.000
 02S  H39   C39  C38  119.88  3.000
 02S  C40   C39  C38  120.03  3.000
 02S  H40   C40  C41  120.09  3.000
 02S  H40   C40  C39  120.08  3.000
 02S  C41   C40  C39  119.83  3.000
 02S  H41   C41  C42  119.89  3.000
 02S  H41   C41  C40  120.12  3.000
 02S  C42   C41  C40  119.99  3.000
 02S  H42   C42  C41  119.72  3.000
 02S  H42   C42  C37  119.76  3.000
 02S  C41   C42  C37  120.52  3.000
 02S  HXT   OXT  C27  109.70  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
 02S  CONST_01  C32  C33  C34  C8     0.00   0.0  0
 02S  CONST_02  C32  C31  C30  C8     0.00   0.0  0
 02S  CONST_03  C31  C30  C8   C34    0.00   0.0  0
 02S  CONST_04  C31  C32  C33  C34    0.00   0.0  0
 02S  CONST_05  C30  C8   C34  C33    0.00   0.0  0
 02S  CONST_06  C30  C31  C32  C33    0.00   0.0  0
 02S  CONST_07  C40  C41  C42  C37    0.00   0.0  0
 02S  CONST_08  C40  C39  C38  C37    0.00   0.0  0
 02S  CONST_09  C41  C42  C37  C38    0.00   0.0  0
 02S  CONST_10  C41  C40  C39  C38    0.00   0.0  0
 02S  CONST_11  C42  C37  C38  C39    0.00   0.0  0
 02S  CONST_12  C42  C41  C40  C39    0.00   0.0  0
 02S  CONST_13  C33  C34  C8   C27  180.00   0.0  0
 02S  CONST_14  C31  C30  C8   C27  180.00   0.0  0
 02S  CONST_15  O35  C32  C33  C34  180.00   0.0  0
 02S  CONST_16  O35  C32  C31  C30  180.00   0.0  0
 02S  CONST_17  C41  C42  C37  C36  180.00   0.0  0
 02S  CONST_18  C39  C38  C37  C36  180.00   0.0  0
 02S  CONST_19  H33  C33  C34  C8   180.00   0.0  0
 02S  CONST_20  H31  C31  C30  C8   180.00   0.0  0
 02S  CONST_21  H30  C30  C8   C34  180.00   0.0  0
 02S  CONST_22  H34  C34  C8   C30  180.00   0.0  0
 02S  CONST_23  H41  C41  C42  C37  180.00   0.0  0
 02S  CONST_24  H39  C39  C38  C37  180.00   0.0  0
 02S  CONST_25  H42  C42  C37  C38  180.00   0.0  0
 02S  CONST_26  H40  C40  C39  C38  180.00   0.0  0
 02S  CONST_27  H38  C38  C39  C40  180.00   0.0  0
 02S  CONST_28  HXT  OXT  C27  C8   180.00   0.0  0
 02S  Var_01    C34  C8   C27  O28    0.23  30.0  2
 02S  Var_02    C37  C36  O35  C32  179.72  30.0  3
 02S  Var_03    C42  C37  C36  O35  100.35  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
 02S  plan-1  C8   0.020
 02S  plan-1  C27  0.020
 02S  plan-1  C34  0.020
 02S  plan-1  C33  0.020
 02S  plan-1  C30  0.020
 02S  plan-1  C31  0.020
 02S  plan-1  C32  0.020
 02S  plan-1  O35  0.020
 02S  plan-1  H34  0.020
 02S  plan-1  H33  0.020
 02S  plan-1  H30  0.020
 02S  plan-1  H31  0.020
 02S  plan-2  C36  0.020
 02S  plan-2  C37  0.020
 02S  plan-2  C38  0.020
 02S  plan-2  C39  0.020
 02S  plan-2  C40  0.020
 02S  plan-2  C41  0.020
 02S  plan-2  C42  0.020
 02S  plan-2  H38  0.020
 02S  plan-2  H39  0.020
 02S  plan-2  H40  0.020
 02S  plan-2  H41  0.020
 02S  plan-2  H42  0.020
 02S  plan-3  C8   0.020
 02S  plan-3  C27  0.020
 02S  plan-3  O28  0.020
 02S  plan-3  OXT  0.020
 02S  plan-3  HXT  0.020

