# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 21:28:52 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 1-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)Nc1cccc(c1)C(F)(F)F
#
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
 GF6  GF6  "1-[3-(trifluoromethyl)phenyl]urea"
  ligand  21  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GF6
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
 GF6  C4  C  CR16  0  -0.231   1.1194  7.3587  -57.3900
 GF6  C5  C  CR16  0  -0.301   0.2618  6.6434  -56.5646
 GF6  C6  C  CR6   0  -0.178  -0.6131  5.7315  -57.1355
 GF6  C7  C  CT    0   1.050  -1.5879  4.9660  -56.2941
 GF6  C8  C  CR16  0  -0.334  -0.6418  5.5353  -58.5119
 GF6  N1  N  NH2   0  -0.825   0.1239  3.7546  -60.8126
 GF6  C3  C  CR16  0  -0.299   1.1216  7.1495  -58.7566
 GF6  C1  C  C     0   0.611   0.1463  4.9344  -61.4799
 GF6  O1  O  O     0  -0.508   0.0685  5.0124  -62.6963
 GF6  C2  C  CR6   0   0.353   0.2436  6.2288  -59.3315
 GF6  F1  F  F     0  -0.312  -1.5655  3.6560  -56.5748
 GF6  F2  F  F     0  -0.314  -2.8488  5.3775  -56.4983
 GF6  F3  F  F     0  -0.302  -1.3470  5.0906  -54.9867
 GF6  H5  H  HCR6  0   0.271   1.8045  8.0759  -56.9584
 GF6  H6  H  HCR6  0   0.271   0.2871  6.8093  -55.4971
 GF6  H7  H  HCR6  0   0.295  -1.3592  4.8555  -58.9528
 GF6  H2  H  HNH2  0   0.404   0.1936  2.9253  -61.3786
 GF6  H1  H  HNH2  0   0.407   0.5079  3.6711  -59.8853
 GF6  H3  H  HNH1  0   0.407   0.4531  6.9043  -61.2601
 GF6  H4  H  HCR6  0   0.279   1.8088  7.6976  -59.3892
 GF6  N2  N  NH1   0  -0.743   0.2393  6.0791  -60.7205

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
 GF6  O1  C1  double    1.221  0.020  1.221
 GF6  C1  N1  single    1.356  0.020  1.356
 GF6  C1  N2  single    1.377  0.020  1.377
 GF6  N2  C2  single    1.397  0.020  1.397
 GF6  C2  C3  aromatic  1.396  0.020  1.396
 GF6  C2  C8  aromatic  1.392  0.020  1.392
 GF6  C3  C4  aromatic  1.383  0.020  1.383
 GF6  C8  C6  aromatic  1.391  0.020  1.391
 GF6  C4  C5  aromatic  1.389  0.020  1.389
 GF6  C6  C5  aromatic  1.387  0.020  1.387
 GF6  C6  C7  single    1.498  0.020  1.498
 GF6  F1  C7  single    1.340  0.020  1.340
 GF6  C7  F2  single    1.342  0.020  1.342
 GF6  C7  F3  single    1.335  0.020  1.335
 GF6  C4  H5  single    0.930  0.020  1.080
 GF6  C5  H6  single    0.930  0.020  1.080
 GF6  C8  H7  single    0.930  0.020  1.080
 GF6  N1  H2  single    0.890  0.020  1.040
 GF6  N1  H1  single    0.890  0.020  1.040
 GF6  N2  H3  single    0.860  0.020  1.020
 GF6  C3  H4  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
 GF6  H5  C4  C3  119.59  3.000
 GF6  H5  C4  C5  119.70  3.000
 GF6  C3  C4  C5  120.70  3.000
 GF6  H6  C5  C6  121.50  3.000
 GF6  H6  C5  C4  119.58  3.000
 GF6  C6  C5  C4  118.93  3.000
 GF6  C8  C6  C7  118.06  3.000
 GF6  C7  C6  C5  121.02  3.000
 GF6  C8  C6  C5  120.88  3.000
 GF6  F3  C7  F2  106.85  3.000
 GF6  F3  C7  F1  107.06  3.000
 GF6  F2  C7  F1  106.48  3.000
 GF6  F3  C7  C6  112.64  3.000
 GF6  F2  C7  C6  111.67  3.000
 GF6  F1  C7  C6  111.78  3.000
 GF6  H7  C8  C2  119.66  3.000
 GF6  H7  C8  C6  120.37  3.000
 GF6  C2  C8  C6  119.97  3.000
 GF6  H1  N1  H2  115.02  3.000
 GF6  H1  N1  C1  121.27  3.000
 GF6  H2  N1  C1  116.05  3.000
 GF6  H4  C3  C2  119.49  3.000
 GF6  H4  C3  C4  120.12  3.000
 GF6  C2  C3  C4  120.39  3.000
 GF6  O1  C1  N2  120.03  3.000
 GF6  N2  C1  N1  116.95  3.000
 GF6  O1  C1  N1  123.01  3.000
 GF6  C3  C2  N2  118.82  3.000
 GF6  C3  C2  C8  119.09  3.000
 GF6  N2  C2  C8  122.02  3.000
 GF6  H3  N2  C2  116.33  3.000
 GF6  H3  N2  C1  113.53  3.000
 GF6  C2  N2  C1  129.62  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
 GF6  CONST_01  C8  C2  C3  C4     0.00   0.0  0
 GF6  CONST_02  C8  C6  C5  C4     0.00   0.0  0
 GF6  CONST_03  C2  C3  C4  C5     0.00   0.0  0
 GF6  CONST_04  C2  C8  C6  C5     0.00   0.0  0
 GF6  CONST_05  C3  C2  C8  C6     0.00   0.0  0
 GF6  CONST_06  C3  C4  C5  C6     0.00   0.0  0
 GF6  CONST_07  N2  C2  C3  C4   180.00   0.0  0
 GF6  CONST_08  C7  C6  C5  C4   180.00   0.0  0
 GF6  CONST_09  N2  C2  C8  C6   180.00   0.0  0
 GF6  CONST_10  C2  C8  C6  C7   180.00   0.0  0
 GF6  CONST_11  H4  C3  C4  C5   180.00   0.0  0
 GF6  CONST_12  H7  C8  C6  C5   180.00   0.0  0
 GF6  CONST_13  H5  C4  C5  C6   180.00   0.0  0
 GF6  CONST_14  H4  C3  C2  C8   180.00   0.0  0
 GF6  CONST_15  H6  C5  C6  C8   180.00   0.0  0
 GF6  CONST_16  H7  C8  C2  C3   180.00   0.0  0
 GF6  CONST_17  H6  C5  C4  C3   180.00   0.0  0
 GF6  CONST_18  H5  C4  C3  C2   180.00   0.0  0
 GF6  CONST_23  C2  N2  C1  O1   180.00   0.0  0
 GF6  CONST_24  C2  N2  C1  N1     0.00   0.0  0
 GF6  CONST_25  H2  N1  C1  O1     0.00   0.0  0
 GF6  CONST_27  H3  N2  C1  O1     0.00   0.0  0
 GF6  CONST_28  H3  N2  C1  N1   180.00   0.0  0
 GF6  CONST_29  H2  N1  C1  N2   180.00   0.0  0
 GF6  Var_01    F1  C7  C6  C5  -131.51  30.0  2
 GF6  Var_02    F2  C7  C6  C5   109.33  30.0  2
 GF6  Var_03    F3  C7  C6  C5   -10.92  30.0  2
 GF6  Var_04    F1  C7  C6  C8    50.65  30.0  2
 GF6  Var_05    F2  C7  C6  C8   -68.51  30.0  2
 GF6  Var_06    F3  C7  C6  C8   171.24  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
 GF6  plan-1  C4  0.020
 GF6  plan-1  C5  0.020
 GF6  plan-1  C6  0.020
 GF6  plan-1  C7  0.020
 GF6  plan-1  C8  0.020
 GF6  plan-1  C3  0.020
 GF6  plan-1  C2  0.020
 GF6  plan-1  H5  0.020
 GF6  plan-1  H6  0.020
 GF6  plan-1  H7  0.020
 GF6  plan-1  H4  0.020
 GF6  plan-1  N2  0.020
 GF6  plan-2  N1  0.020
 GF6  plan-2  C1  0.020
 GF6  plan-2  O1  0.020
 GF6  plan-2  C2  0.020
 GF6  plan-2  H2  0.020
 GF6  plan-2  H1  0.020
 GF6  plan-2  H3  0.020
 GF6  plan-2  N2  0.020

