# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:36:38 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC(CC1)NC(=O)Nc2ccc(OC(F)(F)F)cc2
#
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
 2RV  2RV  1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea  ligand  45  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2RV
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
 2RV  F23  F  F     0  -0.300  -6.4603  -0.3836  -1.8133
 2RV  C20  C  CT    0   1.071  -6.7407  -0.2692  -0.5132
 2RV  F21  F  F     0  -0.278  -8.0492  -0.1149  -0.3820
 2RV  F22  F  F     0  -0.300  -6.3974  -1.4272   0.0561
 2RV  O19  O  O2    0  -0.523  -6.1477   0.7854   0.0553
 2RV  C18  C  CR6   0   0.293  -4.7562   0.8413   0.0225
 2RV  C17  C  CR16  0  -0.292  -4.0232   0.2769   1.0507
 2RV  C16  C  CR16  0  -0.302  -2.6414   0.3843   1.0566
 2RV  C24  C  CR16  0  -0.290  -4.1271   1.5235  -1.0034
 2RV  C25  C  CR16  0  -0.341  -2.7466   1.6214  -1.0020
 2RV  C1   C  CR6   0   0.380  -1.9842   1.0508   0.0197
 2RV  N2   N  NH1   0  -0.788  -0.6041   1.2314  -0.0228
 2RV  C3   C  C     0   0.729   0.3484   0.3677   0.4712
 2RV  O15  O  O     0  -0.519   0.0665  -0.6718   1.0490
 2RV  N4   N  NH1   0  -0.683   1.6168   0.7943   0.2703
 2RV  C5   C  CH1   0  -0.078   2.7822   0.0028   0.5964
 2RV  C14  C  CH2   0  -0.432   3.8118   0.8405   1.3484
 2RV  C13  C  CH2   0  -0.320   5.0660   0.0244   1.6378
 2RV  N8   N  NT    0  -0.452   5.6143  -0.5373   0.4162
 2RV  C7   C  CH2   0  -0.326   4.6770  -1.3911  -0.2894
 2RV  C6   C  CH2   0  -0.422   3.4105  -0.6227  -0.6486
 2RV  C9   C  C     0   0.564   6.8293  -0.1600  -0.0440
 2RV  O12  O  O     0  -0.506   7.5391   0.6246   0.5728
 2RV  C10  C  CH2   0  -0.597   7.2975  -0.7606  -1.3582
 2RV  C11  C  CH3   0  -0.649   8.6964  -0.3158  -1.7487
 2RV  H1   H  HCR6  0   0.280  -4.5209  -0.2261   1.8692
 2RV  H2   H  HCR6  0   0.278  -2.0909  -0.0419   1.8795
 2RV  H3   H  HCR6  0   0.281  -4.7000   1.9817  -1.7985
 2RV  H4   H  HCR6  0   0.278  -2.2537   2.1453  -1.8116
 2RV  H5   H  HNH1  0   0.408  -0.2877   1.9718  -0.6302
 2RV  H6   H  HNH1  0   0.394   1.7758   1.6352  -0.2634
 2RV  H7   H  HCH1  0   0.251   2.4489  -0.8039   1.2528
 2RV  H8   H  HCH2  0   0.230   4.0836   1.7219   0.7583
 2RV  H9   H  HCH2  0   0.249   3.3874   1.1981   2.2888
 2RV  H10  H  HCH2  0   0.267   5.8172   0.6378   2.1266
 2RV  H11  H  HCH2  0   0.240   4.8238  -0.7962   2.3220
 2RV  H12  H  HCH2  0   0.277   5.1273  -1.8101  -1.1837
 2RV  H13  H  HCH2  0   0.245   4.4213  -2.2376   0.3570
 2RV  H14  H  HCH2  0   0.248   2.6993  -1.3015  -1.1246
 2RV  H15  H  HCH2  0   0.229   3.6501   0.1592  -1.3765
 2RV  H16  H  HCH2  0   0.265   7.2641  -1.8514  -1.2904
 2RV  H17  H  HCH2  0   0.263   6.5909  -0.4927  -2.1492
 2RV  H18  H  HCH3  0   0.226   9.4342  -0.6019  -1.0001
 2RV  H19  H  HCH3  0   0.230   8.9807  -0.7864  -2.6894
 2RV  H20  H  HCH3  0   0.226   8.7570   0.7630  -1.8852

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
 2RV  F21  C20  single    1.324  0.020  1.324
 2RV  O19  C20  single    1.337  0.020  1.337
 2RV  O19  C18  single    1.393  0.020  1.393
 2RV  C20  F22  single    1.335  0.020  1.335
 2RV  C20  F23  single    1.335  0.020  1.335
 2RV  C18  C24  aromatic  1.383  0.020  1.383
 2RV  C18  C17  aromatic  1.383  0.020  1.383
 2RV  C24  C25  aromatic  1.384  0.020  1.384
 2RV  C17  C16  aromatic  1.386  0.020  1.386
 2RV  C25  C1   aromatic  1.397  0.020  1.397
 2RV  C16  C1   aromatic  1.397  0.020  1.397
 2RV  C1   N2   single    1.392  0.020  1.392
 2RV  N2   C3   single    1.377  0.020  1.377
 2RV  C3   O15  double    1.222  0.020  1.222
 2RV  C3   N4   single    1.353  0.020  1.353
 2RV  N4   C5   single    1.446  0.020  1.446
 2RV  C5   C14  single    1.526  0.020  1.526
 2RV  C5   C6   single    1.528  0.020  1.528
 2RV  C14  C13  single    1.524  0.020  1.524
 2RV  C6   C7   single    1.524  0.020  1.524
 2RV  C7   N8   single    1.451  0.020  1.451
 2RV  N8   C13  single    1.452  0.020  1.452
 2RV  N8   C9   single    1.353  0.020  1.353
 2RV  C10  C9   single    1.519  0.020  1.519
 2RV  C10  C11  single    1.519  0.020  1.519
 2RV  C9   O12  double    1.225  0.020  1.225
 2RV  C17  H1   single    0.930  0.020  1.080
 2RV  C16  H2   single    0.930  0.020  1.080
 2RV  C24  H3   single    0.930  0.020  1.080
 2RV  C25  H4   single    0.930  0.020  1.080
 2RV  N2   H5   single    0.860  0.020  1.020
 2RV  N4   H6   single    0.860  0.020  1.020
 2RV  C5   H7   single    0.970  0.020  1.090
 2RV  C14  H8   single    0.970  0.020  1.090
 2RV  C14  H9   single    0.970  0.020  1.090
 2RV  C13  H10  single    0.970  0.020  1.090
 2RV  C13  H11  single    0.970  0.020  1.090
 2RV  C7   H12  single    0.970  0.020  1.090
 2RV  C7   H13  single    0.970  0.020  1.090
 2RV  C6   H14  single    0.970  0.020  1.090
 2RV  C6   H15  single    0.970  0.020  1.090
 2RV  C10  H16  single    0.970  0.020  1.090
 2RV  C10  H17  single    0.970  0.020  1.090
 2RV  C11  H18  single    0.970  0.020  1.090
 2RV  C11  H19  single    0.970  0.020  1.090
 2RV  C11  H20  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
 2RV  O19  C20  F22  112.88  3.000
 2RV  F22  C20  F21  108.23  3.000
 2RV  O19  C20  F21  107.72  3.000
 2RV  F22  C20  F23  106.67  3.000
 2RV  O19  C20  F23  112.87  3.000
 2RV  F21  C20  F23  108.30  3.000
 2RV  C18  O19  C20  117.70  3.000
 2RV  C24  C18  C17  120.77  3.000
 2RV  C17  C18  O19  119.70  3.000
 2RV  C24  C18  O19  119.44  3.000
 2RV  H1   C17  C16  119.43  3.000
 2RV  H1   C17  C18  120.56  3.000
 2RV  C16  C17  C18  119.99  3.000
 2RV  H2   C16  C1   121.00  3.000
 2RV  H2   C16  C17  118.80  3.000
 2RV  C1   C16  C17  120.19  3.000
 2RV  H3   C24  C25  119.93  3.000
 2RV  H3   C24  C18  120.87  3.000
 2RV  C25  C24  C18  119.19  3.000
 2RV  H4   C25  C1   119.74  3.000
 2RV  H4   C25  C24  119.17  3.000
 2RV  C1   C25  C24  121.09  3.000
 2RV  N2   C1   C25  117.76  3.000
 2RV  N2   C1   C16  123.42  3.000
 2RV  C25  C1   C16  118.76  3.000
 2RV  H5   N2   C3   117.35  3.000
 2RV  H5   N2   C1   115.12  3.000
 2RV  C3   N2   C1   126.37  3.000
 2RV  N4   C3   O15  123.68  3.000
 2RV  N4   C3   N2   113.40  3.000
 2RV  O15  C3   N2   122.91  3.000
 2RV  H6   N4   C5   116.65  3.000
 2RV  H6   N4   C3   119.29  3.000
 2RV  C5   N4   C3   123.33  3.000
 2RV  H7   C5   C6   108.23  3.000
 2RV  H7   C5   C14  108.38  3.000
 2RV  C6   C5   C14  110.41  3.000
 2RV  H7   C5   N4   107.09  3.000
 2RV  C6   C5   N4   111.81  3.000
 2RV  C14  C5   N4   110.77  3.000
 2RV  H9   C14  H8   107.28  3.000
 2RV  H9   C14  C13  109.37  3.000
 2RV  H8   C14  C13  109.21  3.000
 2RV  H9   C14  C5   110.00  3.000
 2RV  H8   C14  C5   110.11  3.000
 2RV  C13  C14  C5   110.79  3.000
 2RV  H11  C13  H10  107.15  3.000
 2RV  H11  C13  N8   108.61  3.000
 2RV  H10  C13  N8   109.63  3.000
 2RV  H11  C13  C14  109.73  3.000
 2RV  H10  C13  C14  110.63  3.000
 2RV  N8   C13  C14  110.99  3.000
 2RV  C9   N8   C7   125.37  3.000
 2RV  C9   N8   C13  121.16  3.000
 2RV  C7   N8   C13  113.13  3.000
 2RV  H13  C7   H12  106.54  3.000
 2RV  H13  C7   C6   109.55  3.000
 2RV  H12  C7   C6   110.19  3.000
 2RV  H13  C7   N8   108.58  3.000
 2RV  H12  C7   N8   111.09  3.000
 2RV  C6   C7   N8   110.77  3.000
 2RV  H15  C6   H14  107.25  3.000
 2RV  H15  C6   C7   109.56  3.000
 2RV  H14  C6   C7   109.29  3.000
 2RV  H15  C6   C5   109.84  3.000
 2RV  H14  C6   C5   109.98  3.000
 2RV  C7   C6   C5   110.85  3.000
 2RV  C10  C9   O12  120.69  3.000
 2RV  O12  C9   N8   121.86  3.000
 2RV  C10  C9   N8   117.44  3.000
 2RV  H17  C10  H16  105.63  3.000
 2RV  H17  C10  C11  109.71  3.000
 2RV  H16  C10  C11  109.65  3.000
 2RV  H17  C10  C9   109.25  3.000
 2RV  H16  C10  C9   109.35  3.000
 2RV  C11  C10  C9   112.99  3.000
 2RV  H20  C11  H19  107.77  3.000
 2RV  H20  C11  H18  107.97  3.000
 2RV  H19  C11  H18  107.65  3.000
 2RV  H20  C11  C10  111.93  3.000
 2RV  H19  C11  C10  109.62  3.000
 2RV  H18  C11  C10  111.72  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
 2RV  CONST_01  C1   C25  C24  C18     0.00   0.0  0
 2RV  CONST_02  C1   C16  C17  C18     0.00   0.0  0
 2RV  CONST_03  C25  C24  C18  C17     0.00   0.0  0
 2RV  CONST_04  C25  C1   C16  C17     0.00   0.0  0
 2RV  CONST_05  C24  C18  C17  C16     0.00   0.0  0
 2RV  CONST_06  C24  C25  C1   C16     0.00   0.0  0
 2RV  CONST_07  C25  C24  C18  O19   180.00   0.0  0
 2RV  CONST_08  C16  C17  C18  O19   180.00   0.0  0
 2RV  CONST_09  N2   C1   C16  C17   180.00   0.0  0
 2RV  CONST_10  N2   C1   C25  C24   180.00   0.0  0
 2RV  CONST_11  H4   C25  C24  C18   180.00   0.0  0
 2RV  CONST_12  H2   C16  C17  C18   180.00   0.0  0
 2RV  CONST_13  H3   C24  C18  C17   180.00   0.0  0
 2RV  CONST_14  H1   C17  C18  C24   180.00   0.0  0
 2RV  CONST_15  C10  C9   N8   C13   180.00   0.0  0
 2RV  CONST_16  O12  C9   N8   C13     0.00   0.0  0
 2RV  CONST_17  C10  C9   N8   C7      0.00   0.0  0
 2RV  CONST_18  O12  C9   N8   C7    180.00   0.0  0
 2RV  CONST_22  O15  C3   N2   C1      0.00   0.0  0
 2RV  CONST_23  C5   N4   C3   O15     0.00   0.0  0
 2RV  CONST_24  N4   C3   N2   C1    180.00   0.0  0
 2RV  CONST_25  C5   N4   C3   N2    180.00   0.0  0
 2RV  CONST_26  H6   N4   C3   O15   180.00   0.0  0
 2RV  Var_01    N8   C13  C14  C5     55.10  30.0  1
 2RV  Var_02    N8   C7   C6   C5    -55.28  30.0  1
 2RV  Var_03    C7   N8   C13  C14   -58.43  30.0  1
 2RV  Var_04    C6   C7   N8   C13    58.45  30.0  1
 2RV  Var_05    C24  C18  O19  C20    93.49  30.0  2
 2RV  Var_06    C11  C10  C9   N8   -177.49  30.0  2
 2RV  Var_07    H18  C11  C10  C9     60.08  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2RV  chir_01  C5  N4  C14  C6  positiv

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
 2RV  plan-1  O19  0.020
 2RV  plan-1  C18  0.020
 2RV  plan-1  C17  0.020
 2RV  plan-1  C16  0.020
 2RV  plan-1  C24  0.020
 2RV  plan-1  C25  0.020
 2RV  plan-1  C1   0.020
 2RV  plan-1  N2   0.020
 2RV  plan-1  H1   0.020
 2RV  plan-1  H2   0.020
 2RV  plan-1  H3   0.020
 2RV  plan-1  H4   0.020
 2RV  plan-2  C1   0.020
 2RV  plan-2  N2   0.020
 2RV  plan-2  C3   0.020
 2RV  plan-2  O15  0.020
 2RV  plan-2  N4   0.020
 2RV  plan-2  C5   0.020
 2RV  plan-2  H5   0.020
 2RV  plan-2  H6   0.020
 2RV  plan-3  C13  0.020
 2RV  plan-3  N8   0.020
 2RV  plan-3  C7   0.020
 2RV  plan-3  C9   0.020
 2RV  plan-3  O12  0.020
 2RV  plan-3  C10  0.020

