# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:35:36 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-(4-fluorophenyl)-3-(3-hydroxyphenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(NC(=O)Nc2ccc(F)cc2)c1
#
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
 LV1  LV1  1-(4-fluorophenyl)-3-(3-hydroxyphenyl)urea  ligand  29  18  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LV1
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
 LV1  N1   N  NH1   0  -0.753  -13.0476  -21.7600  -0.8456
 LV1  C4   C  CR6   0   0.378  -11.0802  -19.4790   4.0560
 LV1  C5   C  CR16  0  -0.407  -11.3637  -18.1245   4.1958
 LV1  C6   C  C     0   0.675  -12.3656  -21.3931   0.2827
 LV1  C7   C  CR6   0   0.262  -14.0617  -21.0549  -1.5212
 LV1  C8   C  CR16  0  -0.265  -13.9171  -20.7788  -2.8785
 LV1  C10  C  CR6   0   0.525  -16.0573  -19.7358  -2.8976
 LV1  N    N  NH1   0  -0.777  -12.6662  -20.1502   0.7645
 LV1  C    C  CR16  0  -0.231  -12.0701  -17.4858   3.1866
 LV1  O    O  OH1   0  -0.634  -10.4027  -20.1751   4.9912
 LV1  C1   C  CR16  0  -0.384  -12.4838  -18.1678   2.0577
 LV1  C11  C  CR16  0  -0.404  -16.2282  -19.9915  -1.5511
 LV1  C12  C  CR16  0  -0.277  -15.2314  -20.6712  -0.8677
 LV1  C2   C  CR6   0   0.401  -12.1918  -19.5299   1.9203
 LV1  C3   C  CR16  0  -0.417  -11.4899  -20.1867   2.9274
 LV1  C9   C  CR16  0  -0.407  -14.9210  -20.1283  -3.5783
 LV1  F    F  F     0  -0.313  -17.0275  -19.0930  -3.5651
 LV1  O1   O  O     0  -0.504  -11.5482  -22.1439   0.7898
 LV1  H1   H  HNH1  0   0.410  -12.6765  -22.5800  -1.3021
 LV1  H2   H  HCR6  0   0.268  -11.0397  -17.5768   5.0729
 LV1  H3   H  HCR6  0   0.282  -13.0134  -21.0777  -3.3937
 LV1  H4   H  HNH1  0   0.418  -13.2308  -19.5538   0.1790
 LV1  H5   H  HCR6  0   0.262  -12.3009  -16.4330   3.2839
 LV1  H6   H  HOH1  0   0.474  -10.1768  -19.6041   5.7335
 LV1  H7   H  HCR6  0   0.265  -13.0307  -17.6477   1.2807
 LV1  H8   H  HCR6  0   0.288  -17.1334  -19.6851  -1.0437
 LV1  H9   H  HCR6  0   0.292  -15.3777  -20.9125   0.1772
 LV1  H10  H  HCR6  0   0.283  -11.2503  -21.2353   2.8532
 LV1  H11  H  HCR6  0   0.287  -14.8112  -19.9201  -4.6341

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
 LV1  F    C10  single    1.342  0.020  1.342
 LV1  C9   C10  aromatic  1.382  0.020  1.382
 LV1  C9   C8   aromatic  1.386  0.020  1.386
 LV1  C10  C11  aromatic  1.381  0.020  1.381
 LV1  C8   C7   aromatic  1.393  0.020  1.393
 LV1  C11  C12  aromatic  1.387  0.020  1.387
 LV1  C7   C12  aromatic  1.394  0.020  1.394
 LV1  C7   N1   single    1.408  0.020  1.408
 LV1  N1   C6   single    1.368  0.020  1.368
 LV1  C6   O1   double    1.220  0.020  1.220
 LV1  C6   N    single    1.367  0.020  1.367
 LV1  N    C2   single    1.395  0.020  1.395
 LV1  C2   C1   aromatic  1.400  0.020  1.400
 LV1  C2   C3   aromatic  1.392  0.020  1.392
 LV1  C1   C    aromatic  1.382  0.020  1.382
 LV1  C3   C4   aromatic  1.394  0.020  1.394
 LV1  C    C5   aromatic  1.388  0.020  1.388
 LV1  C4   C5   aromatic  1.391  0.020  1.391
 LV1  C4   O    single    1.348  0.020  1.348
 LV1  N1   H1   single    0.860  0.020  1.020
 LV1  C5   H2   single    0.930  0.020  1.080
 LV1  C8   H3   single    0.930  0.020  1.080
 LV1  N    H4   single    0.860  0.020  1.020
 LV1  C    H5   single    0.930  0.020  1.080
 LV1  O    H6   single    0.850  0.020  0.980
 LV1  C1   H7   single    0.930  0.020  1.080
 LV1  C11  H8   single    0.930  0.020  1.080
 LV1  C12  H9   single    0.930  0.020  1.080
 LV1  C3   H10  single    0.930  0.020  1.080
 LV1  C9   H11  single    0.930  0.020  1.080

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
 LV1  H1   N1   C7   117.04  3.000
 LV1  H1   N1   C6   114.05  3.000
 LV1  C7   N1   C6   128.34  3.000
 LV1  C3   C4   O    116.56  3.000
 LV1  O    C4   C5   122.38  3.000
 LV1  C3   C4   C5   121.06  3.000
 LV1  H2   C5   C    120.54  3.000
 LV1  H2   C5   C4   120.84  3.000
 LV1  C    C5   C4   118.62  3.000
 LV1  O1   C6   N    124.09  3.000
 LV1  N    C6   N1   115.14  3.000
 LV1  O1   C6   N1   120.76  3.000
 LV1  C12  C7   C8   119.31  3.000
 LV1  C12  C7   N1   121.16  3.000
 LV1  C8   C7   N1   119.49  3.000
 LV1  H3   C8   C9   119.61  3.000
 LV1  H3   C8   C7   119.73  3.000
 LV1  C9   C8   C7   120.66  3.000
 LV1  F    C10  C9   119.06  3.000
 LV1  C9   C10  C11  121.97  3.000
 LV1  F    C10  C11  118.97  3.000
 LV1  H4   N    C2   114.11  3.000
 LV1  H4   N    C6   117.14  3.000
 LV1  C2   N    C6   128.45  3.000
 LV1  H5   C    C1   119.31  3.000
 LV1  H5   C    C5   119.41  3.000
 LV1  C1   C    C5   121.28  3.000
 LV1  H6   O    C4   110.26  3.000
 LV1  H7   C1   C2   120.13  3.000
 LV1  H7   C1   C    120.01  3.000
 LV1  C2   C1   C    119.86  3.000
 LV1  H8   C11  C12  120.60  3.000
 LV1  H8   C11  C10  120.55  3.000
 LV1  C12  C11  C10  118.84  3.000
 LV1  H9   C12  C11  119.21  3.000
 LV1  H9   C12  C7   120.31  3.000
 LV1  C11  C12  C7   120.47  3.000
 LV1  C3   C2   C1   119.55  3.000
 LV1  C3   C2   N    124.13  3.000
 LV1  C1   C2   N    116.30  3.000
 LV1  H10  C3   C2   121.40  3.000
 LV1  H10  C3   C4   118.96  3.000
 LV1  C2   C3   C4   119.63  3.000
 LV1  H11  C9   C10  120.64  3.000
 LV1  H11  C9   C8   120.64  3.000
 LV1  C10  C9   C8   118.71  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
 LV1  CONST_01  C1   C2   C3   C4     0.00  0.0  0
 LV1  CONST_02  C1   C    C5   C4     0.00  0.0  0
 LV1  CONST_03  C2   C1   C    C5     0.00  0.0  0
 LV1  CONST_04  C2   C3   C4   C5     0.00  0.0  0
 LV1  CONST_05  C10  C9   C8   C7     0.00  0.0  0
 LV1  CONST_06  C10  C11  C12  C7     0.00  0.0  0
 LV1  CONST_07  C11  C10  C9   C8     0.00  0.0  0
 LV1  CONST_08  C11  C12  C7   C8     0.00  0.0  0
 LV1  CONST_09  C3   C2   C1   C      0.00  0.0  0
 LV1  CONST_10  C3   C4   C5   C      0.00  0.0  0
 LV1  CONST_11  C9   C10  C11  C12    0.00  0.0  0
 LV1  CONST_12  C9   C8   C7   C12    0.00  0.0  0
 LV1  CONST_13  C9   C8   C7   N1   180.00  0.0  0
 LV1  CONST_14  C11  C12  C7   N1   180.00  0.0  0
 LV1  CONST_15  N    C2   C3   C4   180.00  0.0  0
 LV1  CONST_16  F    C10  C9   C8   180.00  0.0  0
 LV1  CONST_17  C    C1   C2   N    180.00  0.0  0
 LV1  CONST_18  O    C4   C5   C    180.00  0.0  0
 LV1  CONST_19  C2   C3   C4   O    180.00  0.0  0
 LV1  CONST_20  F    C10  C11  C12  180.00  0.0  0
 LV1  CONST_21  H5   C    C5   C4   180.00  0.0  0
 LV1  CONST_22  H7   C1   C    C5   180.00  0.0  0
 LV1  CONST_23  H10  C3   C4   C5   180.00  0.0  0
 LV1  CONST_24  H11  C9   C8   C7   180.00  0.0  0
 LV1  CONST_25  H8   C11  C12  C7   180.00  0.0  0
 LV1  CONST_26  H9   C12  C7   C8   180.00  0.0  0
 LV1  CONST_27  H3   C8   C9   C10  180.00  0.0  0
 LV1  CONST_28  H2   C5   C    C1   180.00  0.0  0
 LV1  CONST_31  C1   C2   N    C6   180.00  0.0  0
 LV1  CONST_32  C3   C2   N    C6     0.00  0.0  0
 LV1  CONST_34  H4   N    C2   C1     0.00  0.0  0
 LV1  CONST_35  O1   C6   N1   C7   180.00  0.0  0
 LV1  CONST_36  O1   C6   N    C2     0.00  0.0  0
 LV1  CONST_37  C2   N    C6   N1   180.00  0.0  0
 LV1  CONST_38  N    C6   N1   C7     0.00  0.0  0

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
 LV1  plan-1  C4   0.020
 LV1  plan-1  C5   0.020
 LV1  plan-1  N    0.020
 LV1  plan-1  C    0.020
 LV1  plan-1  O    0.020
 LV1  plan-1  C1   0.020
 LV1  plan-1  C2   0.020
 LV1  plan-1  C3   0.020
 LV1  plan-1  H2   0.020
 LV1  plan-1  H5   0.020
 LV1  plan-1  H7   0.020
 LV1  plan-1  H10  0.020
 LV1  plan-2  N1   0.020
 LV1  plan-2  C7   0.020
 LV1  plan-2  C8   0.020
 LV1  plan-2  C10  0.020
 LV1  plan-2  C11  0.020
 LV1  plan-2  C12  0.020
 LV1  plan-2  C9   0.020
 LV1  plan-2  F    0.020
 LV1  plan-2  H3   0.020
 LV1  plan-2  H8   0.020
 LV1  plan-2  H9   0.020
 LV1  plan-2  H11  0.020
 LV1  plan-3  N1   0.020
 LV1  plan-3  C6   0.020
 LV1  plan-3  C7   0.020
 LV1  plan-3  N    0.020
 LV1  plan-3  C2   0.020
 LV1  plan-3  O1   0.020
 LV1  plan-3  H1   0.020
 LV1  plan-3  H4   0.020

