# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:01:13 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-(biphenyl-4-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1ccc(cc1)c2ccccc2
#
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
 0YF  0YF  '3-(biphenyl-4-yl)propanoic acid'  ligand  31  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0YF
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
 0YF  C1   C  CH2   0  -0.574  -3.5598   0.1077  -0.5133
 0YF  C2   C  C     0   0.552  -5.0580   0.0758  -0.3889
 0YF  O2   O  O     0  -0.445  -5.6668  -0.0989   0.6373
 0YF  C14  C  CH2   0  -0.511  -2.8378  -0.1594   0.8030
 0YF  C15  C  CR16  0  -0.293  -0.6213   1.0453   0.7924
 0YF  C16  C  CR16  0  -0.294   0.7487   1.0793   0.5821
 0YF  C17  C  CR6   0   0.072   1.4424  -0.0634   0.1821
 0YF  C18  C  CR6   0   0.114  -1.3469  -0.1290   0.6127
 0YF  C19  C  CR6   0   0.090   2.9027  -0.0283  -0.0347
 0YF  C20  C  CR16  0  -0.313   3.7068  -1.1134   0.3203
 0YF  C21  C  CR16  0  -0.239   5.0792  -1.0778   0.1210
 0YF  C22  C  CR16  0  -0.240   4.8880   1.1307  -0.7951
 0YF  C23  C  CR16  0  -0.312   3.5155   1.0938  -0.5962
 0YF  C27  C  CR16  0  -0.268   5.6764   0.0449  -0.4371
 0YF  C30  C  CR16  0  -0.296   0.7141  -1.2402   0.0011
 0YF  C31  C  CR16  0  -0.289  -0.6553  -1.2695   0.2125
 0YF  H1   H  HCH2  0   0.286  -3.2615  -0.6229  -1.2711
 0YF  H2   H  HCH2  0   0.288  -3.2722   1.0833  -0.9173
 0YF  H16  H  HCH2  0   0.255  -3.1312   0.5872   1.5432
 0YF  H17  H  HCH2  0   0.254  -3.1385  -1.1329   1.1955
 0YF  H18  H  HCR6  0   0.249  -1.1299   1.9460   1.1158
 0YF  H19  H  HCR6  0   0.252   1.2865   2.0034   0.7556
 0YF  H20  H  HCR6  0   0.253   3.2611  -1.9887   0.7762
 0YF  H21  H  HCR6  0   0.257   5.6840  -1.9271   0.4118
 0YF  H22  H  HCR6  0   0.257   5.3408   2.0086  -1.2372
 0YF  H23  H  HCR6  0   0.253   2.9137   1.9415  -0.9002
 0YF  H24  H  HCR6  0   0.257   6.7472   0.0734  -0.5919
 0YF  H25  H  HCR6  0   0.252   1.2162  -2.1424  -0.3255
 0YF  H26  H  HCR6  0   0.249  -1.1955  -2.1970   0.0603
 0YF  OXT  O  OH1   0  -0.596  -5.6540   0.2677  -1.5616
 0YF  HXT  H  HOH1  0   0.479  -6.6161   0.2426  -1.4513

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
 0YF  C1   C2   single    1.504  0.020  1.504
 0YF  C1   C14  single    1.525  0.020  1.525
 0YF  C2   O2   double    1.206  0.020  1.206
 0YF  C14  C18  single    1.503  0.020  1.503
 0YF  C31  C18  aromatic  1.393  0.020  1.393
 0YF  C31  C30  aromatic  1.386  0.020  1.386
 0YF  C18  C15  aromatic  1.392  0.020  1.392
 0YF  C30  C17  aromatic  1.396  0.020  1.396
 0YF  C15  C16  aromatic  1.386  0.020  1.386
 0YF  C23  C22  aromatic  1.387  0.020  1.387
 0YF  C23  C19  aromatic  1.396  0.020  1.396
 0YF  C17  C16  aromatic  1.395  0.020  1.395
 0YF  C17  C19  single    1.477  0.020  1.477
 0YF  C22  C27  aromatic  1.389  0.020  1.389
 0YF  C19  C20  aromatic  1.396  0.020  1.396
 0YF  C27  C21  aromatic  1.389  0.020  1.389
 0YF  C20  C21  aromatic  1.387  0.020  1.387
 0YF  C1   H1   single    0.970  0.020  1.090
 0YF  C1   H2   single    0.970  0.020  1.090
 0YF  C14  H16  single    0.970  0.020  1.090
 0YF  C14  H17  single    0.970  0.020  1.090
 0YF  C15  H18  single    0.930  0.020  1.080
 0YF  C16  H19  single    0.930  0.020  1.080
 0YF  C20  H20  single    0.930  0.020  1.080
 0YF  C21  H21  single    0.930  0.020  1.080
 0YF  C22  H22  single    0.930  0.020  1.080
 0YF  C23  H23  single    0.930  0.020  1.080
 0YF  C27  H24  single    0.930  0.020  1.080
 0YF  C30  H25  single    0.930  0.020  1.080
 0YF  C31  H26  single    0.930  0.020  1.080
 0YF  C2   OXT  single    1.329  0.020  1.329
 0YF  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
 0YF  H2   C1   H1   105.54  3.000
 0YF  H2   C1   C14  110.51  3.000
 0YF  H1   C1   C14  110.60  3.000
 0YF  H2   C1   C2   108.14  3.000
 0YF  H1   C1   C2   108.35  3.000
 0YF  C14  C1   C2   113.37  3.000
 0YF  OXT  C2   O2   123.05  3.000
 0YF  OXT  C2   C1   111.75  3.000
 0YF  O2   C2   C1   125.20  3.000
 0YF  H17  C14  H16  106.98  3.000
 0YF  H17  C14  C18  109.67  3.000
 0YF  H16  C14  C18  109.79  3.000
 0YF  H17  C14  C1   109.64  3.000
 0YF  H16  C14  C1   109.77  3.000
 0YF  C18  C14  C1   110.90  3.000
 0YF  H18  C15  C18  119.67  3.000
 0YF  H18  C15  C16  119.25  3.000
 0YF  C18  C15  C16  121.08  3.000
 0YF  H19  C16  C17  119.85  3.000
 0YF  H19  C16  C15  119.16  3.000
 0YF  C17  C16  C15  120.97  3.000
 0YF  C30  C17  C19  121.13  3.000
 0YF  C19  C17  C16  120.95  3.000
 0YF  C30  C17  C16  117.92  3.000
 0YF  C31  C18  C15  117.97  3.000
 0YF  C15  C18  C14  121.18  3.000
 0YF  C31  C18  C14  120.83  3.000
 0YF  C23  C19  C20  118.29  3.000
 0YF  C20  C19  C17  120.90  3.000
 0YF  C23  C19  C17  120.81  3.000
 0YF  H20  C20  C21  119.23  3.000
 0YF  H20  C20  C19  119.88  3.000
 0YF  C21  C20  C19  120.88  3.000
 0YF  H21  C21  C27  120.13  3.000
 0YF  H21  C21  C20  119.61  3.000
 0YF  C27  C21  C20  120.26  3.000
 0YF  H22  C22  C27  120.13  3.000
 0YF  H22  C22  C23  119.61  3.000
 0YF  C27  C22  C23  120.26  3.000
 0YF  H23  C23  C22  119.26  3.000
 0YF  H23  C23  C19  119.85  3.000
 0YF  C22  C23  C19  120.88  3.000
 0YF  H24  C27  C22  120.28  3.000
 0YF  H24  C27  C21  120.28  3.000
 0YF  C22  C27  C21  119.44  3.000
 0YF  H25  C30  C31  119.11  3.000
 0YF  H25  C30  C17  119.97  3.000
 0YF  C31  C30  C17  120.91  3.000
 0YF  H26  C31  C30  119.28  3.000
 0YF  H26  C31  C18  119.57  3.000
 0YF  C30  C31  C18  121.15  3.000
 0YF  HXT  OXT  C2   109.94  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
 0YF  CONST_01  C30  C31  C18  C15    0.00   0.0  0
 0YF  CONST_02  C30  C17  C16  C15    0.00   0.0  0
 0YF  CONST_03  C19  C17  C16  C15  180.00   0.0  0
 0YF  CONST_04  C31  C18  C15  C16    0.00   0.0  0
 0YF  CONST_05  C31  C30  C17  C16    0.00   0.0  0
 0YF  CONST_08  C18  C31  C30  C17    0.00   0.0  0
 0YF  CONST_09  C18  C15  C16  C17    0.00   0.0  0
 0YF  CONST_10  C22  C23  C19  C17  180.00   0.0  0
 0YF  CONST_11  C21  C20  C19  C17  180.00   0.0  0
 0YF  CONST_12  C27  C22  C23  C19    0.00   0.0  0
 0YF  CONST_13  C31  C30  C17  C19  180.00   0.0  0
 0YF  CONST_14  C27  C21  C20  C19    0.00   0.0  0
 0YF  CONST_15  C22  C23  C19  C20    0.00   0.0  0
 0YF  CONST_17  C22  C27  C21  C20    0.00   0.0  0
 0YF  CONST_18  C23  C22  C27  C21    0.00   0.0  0
 0YF  CONST_19  C23  C19  C20  C21    0.00   0.0  0
 0YF  CONST_21  C30  C31  C18  C14  180.00   0.0  0
 0YF  CONST_22  C16  C15  C18  C14  180.00   0.0  0
 0YF  CONST_23  H26  C31  C18  C15  180.00   0.0  0
 0YF  CONST_24  H25  C30  C17  C16  180.00   0.0  0
 0YF  CONST_25  H18  C15  C16  C17  180.00   0.0  0
 0YF  CONST_26  H23  C23  C19  C17    0.00   0.0  0
 0YF  CONST_27  H20  C20  C19  C17    0.00   0.0  0
 0YF  CONST_28  H19  C16  C15  C18  180.00   0.0  0
 0YF  CONST_29  H22  C22  C23  C19  180.00   0.0  0
 0YF  CONST_30  H21  C21  C20  C19  180.00   0.0  0
 0YF  CONST_31  H24  C27  C21  C20  180.00   0.0  0
 0YF  CONST_32  HXT  OXT  C2   C1   180.00   0.0  0
 0YF  Var_01    C31  C18  C14  C1   -86.26  30.0  2
 0YF  Var_02    C18  C14  C1   C2   179.40  30.0  3
 0YF  Var_03    C14  C1   C2   O2     2.19  30.0  1

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
 0YF  plan-1  C17  0.020
 0YF  plan-1  C19  0.020
 0YF  plan-1  C20  0.020
 0YF  plan-1  C21  0.020
 0YF  plan-1  C22  0.020
 0YF  plan-1  C23  0.020
 0YF  plan-1  C27  0.020
 0YF  plan-1  H20  0.020
 0YF  plan-1  H21  0.020
 0YF  plan-1  H22  0.020
 0YF  plan-1  H23  0.020
 0YF  plan-1  H24  0.020
 0YF  plan-2  C14  0.020
 0YF  plan-2  C15  0.020
 0YF  plan-2  C16  0.020
 0YF  plan-2  C17  0.020
 0YF  plan-2  C18  0.020
 0YF  plan-2  C19  0.020
 0YF  plan-2  C30  0.020
 0YF  plan-2  C31  0.020
 0YF  plan-2  H18  0.020
 0YF  plan-2  H19  0.020
 0YF  plan-2  H25  0.020
 0YF  plan-2  H26  0.020
 0YF  plan-3  C1   0.020
 0YF  plan-3  C2   0.020
 0YF  plan-3  O2   0.020
 0YF  plan-3  OXT  0.020
 0YF  plan-3  HXT  0.020

