# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 20:55:06 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-(2-chlorophenyl)-3-(pyridin-3-ylmethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1NC(=O)NCc2cccnc2
#
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
 4VC  4VC  1-(2-chlorophenyl)-3-(pyridin-3-ylmethyl)urea  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VC
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
 4VC  C2   C   CR6   0  -0.123   2.9283  -0.7239   0.3796
 4VC  C3   C   CR16  0  -0.216   4.1961  -0.8409  -0.1681
 4VC  C5   C   CR16  0  -0.249   4.0500   1.4275  -0.9272
 4VC  C6   C   CR16  0  -0.293   2.7932   1.5458  -0.3582
 4VC  C7   C   CR6   0   0.431   2.1995   0.4653   0.2966
 4VC  C12  C   CH2   0  -0.385  -2.5365   1.6345   0.6363
 4VC  C13  C   CR6   0   0.035  -3.4595   0.5695   0.1040
 4VC  C14  C   CR16  0  -0.181  -3.1334  -0.1943  -1.0127
 4VC  C15  C   CR16  0  -0.317  -4.0234  -1.1579  -1.4541
 4VC  C16  C   CR16  0  -0.070  -5.2153  -1.3276  -0.7622
 4VC  CL1  CL  CL    0  -0.117   2.2364  -2.0955   1.1869
 4VC  C4   C   CR16  0  -0.274   4.7572   0.2364  -0.8344
 4VC  N8   N   NH1   0  -0.782   0.9459   0.5647   0.8962
 4VC  C9   C   C     0   0.738  -0.1472   1.1621   0.3091
 4VC  O10  O   O     0  -0.520  -0.1020   1.6907  -0.7914
 4VC  N11  N   NH1   0  -0.666  -1.2620   1.1181   1.0743
 4VC  N17  N   N     0  -0.401  -5.5414  -0.6106   0.3047
 4VC  C18  C   CR16  0  -0.106  -4.6777   0.3104   0.7192
 4VC  H19  H   HCR6  0   0.280   4.7346  -1.7749  -0.0828
 4VC  H21  H   HCR6  0   0.265   4.4841   2.2796  -1.4327
 4VC  H22  H   HCR6  0   0.274   2.2700   2.4890  -0.4089
 4VC  H25  H   HCH2  0   0.273  -2.3600   2.3911  -0.1273
 4VC  H26  H   HCH2  0   0.272  -3.0105   2.1423   1.4774
 4VC  H27  H   HCR6  0   0.269  -2.1983  -0.0327  -1.5347
 4VC  H28  H   HCR6  0   0.271  -3.8050  -1.7664  -2.3209
 4VC  H29  H   HCR6  0   0.264  -5.9333  -2.0732  -1.0860
 4VC  H20  H   HCR6  0   0.266   5.7422   0.1428  -1.2709
 4VC  H23  H   HNH1  0   0.400   0.7893  -0.0107   1.7101
 4VC  H24  H   HNH1  0   0.402  -1.2487   0.6221   1.9510
 4VC  H30  H   HCR6  0   0.259  -4.9682   0.8812   1.5970

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
 4VC  C5   C4   aromatic  1.388  0.020  1.388
 4VC  C5   C6   aromatic  1.385  0.020  1.385
 4VC  C4   C3   aromatic  1.385  0.020  1.385
 4VC  C6   C7   aromatic  1.396  0.020  1.396
 4VC  C3   C2   aromatic  1.386  0.020  1.386
 4VC  C7   C2   aromatic  1.397  0.020  1.397
 4VC  C7   N8   single    1.393  0.020  1.393
 4VC  C2   CL1  single    1.735  0.020  1.735
 4VC  O10  C9   double    1.222  0.020  1.222
 4VC  N8   C9   single    1.377  0.020  1.377
 4VC  C9   N11  single    1.353  0.020  1.353
 4VC  N11  C12  single    1.443  0.020  1.443
 4VC  C15  C14  aromatic  1.384  0.020  1.384
 4VC  C15  C16  aromatic  1.389  0.020  1.389
 4VC  C14  C13  aromatic  1.392  0.020  1.392
 4VC  C16  N17  aromatic  1.326  0.020  1.326
 4VC  N17  C18  aromatic  1.329  0.020  1.329
 4VC  C13  C18  aromatic  1.389  0.020  1.389
 4VC  C13  C12  single    1.507  0.020  1.507
 4VC  C3   H19  single    0.930  0.020  1.080
 4VC  C5   H21  single    0.930  0.020  1.080
 4VC  C6   H22  single    0.930  0.020  1.080
 4VC  C12  H25  single    0.970  0.020  1.090
 4VC  C12  H26  single    0.970  0.020  1.090
 4VC  C14  H27  single    0.930  0.020  1.080
 4VC  C15  H28  single    0.930  0.020  1.080
 4VC  C16  H29  single    0.930  0.020  1.080
 4VC  C4   H20  single    0.930  0.020  1.080
 4VC  N8   H23  single    0.860  0.020  1.020
 4VC  N11  H24  single    0.860  0.020  1.020
 4VC  C18  H30  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
 4VC  CL1  C2   C7   119.49  3.000
 4VC  CL1  C2   C3   118.80  3.000
 4VC  C7   C2   C3   121.70  3.000
 4VC  H19  C3   C4   120.51  3.000
 4VC  H19  C3   C2   119.82  3.000
 4VC  C4   C3   C2   119.66  3.000
 4VC  H21  C5   C4   120.18  3.000
 4VC  H21  C5   C6   119.27  3.000
 4VC  C4   C5   C6   120.54  3.000
 4VC  H22  C6   C7   119.48  3.000
 4VC  H22  C6   C5   119.67  3.000
 4VC  C7   C6   C5   120.84  3.000
 4VC  N8   C7   C6   121.96  3.000
 4VC  N8   C7   C2   120.30  3.000
 4VC  C6   C7   C2   117.70  3.000
 4VC  H26  C12  H25  106.71  3.000
 4VC  H26  C12  N11  108.44  3.000
 4VC  H25  C12  N11  108.55  3.000
 4VC  H26  C12  C13  109.59  3.000
 4VC  H25  C12  C13  110.04  3.000
 4VC  N11  C12  C13  113.29  3.000
 4VC  C18  C13  C14  117.30  3.000
 4VC  C18  C13  C12  120.84  3.000
 4VC  C14  C13  C12  121.86  3.000
 4VC  H27  C14  C15  120.36  3.000
 4VC  H27  C14  C13  120.48  3.000
 4VC  C15  C14  C13  119.16  3.000
 4VC  H28  C15  C16  120.26  3.000
 4VC  H28  C15  C14  121.17  3.000
 4VC  C16  C15  C14  118.57  3.000
 4VC  H29  C16  N17  116.69  3.000
 4VC  H29  C16  C15  120.23  3.000
 4VC  N17  C16  C15  123.08  3.000
 4VC  H20  C4   C5   120.74  3.000
 4VC  H20  C4   C3   119.72  3.000
 4VC  C5   C4   C3   119.53  3.000
 4VC  H23  N8   C9   117.91  3.000
 4VC  H23  N8   C7   116.50  3.000
 4VC  C9   N8   C7   124.18  3.000
 4VC  N11  C9   O10  123.65  3.000
 4VC  N11  C9   N8   113.51  3.000
 4VC  O10  C9   N8   122.84  3.000
 4VC  H24  N11  C9   119.83  3.000
 4VC  H24  N11  C12  116.87  3.000
 4VC  C9   N11  C12  122.98  3.000
 4VC  C18  N17  C16  117.77  3.000
 4VC  H30  C18  N17  116.26  3.000
 4VC  H30  C18  C13  119.62  3.000
 4VC  N17  C18  C13  124.13  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
 4VC  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 4VC  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 4VC  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 4VC  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 4VC  CONST_05  C4   C5   C6   C7     0.00   0.0  0
 4VC  CONST_06  C4   C3   C2   C7     0.00   0.0  0
 4VC  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 4VC  CONST_08  C16  N17  C18  C13    0.00   0.0  0
 4VC  CONST_09  N17  C16  C15  C14    0.00   0.0  0
 4VC  CONST_10  N17  C18  C13  C14    0.00   0.0  0
 4VC  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 4VC  CONST_12  C18  N17  C16  C15    0.00   0.0  0
 4VC  CONST_13  N8   C7   C2   C3   180.00   0.0  0
 4VC  CONST_14  N8   C7   C6   C5   180.00   0.0  0
 4VC  CONST_15  CL1  C2   C7   C6   180.00   0.0  0
 4VC  CONST_16  C15  C14  C13  C12  180.00   0.0  0
 4VC  CONST_17  N17  C18  C13  C12  180.00   0.0  0
 4VC  CONST_18  C4   C3   C2   CL1  180.00   0.0  0
 4VC  CONST_19  H20  C4   C3   C2   180.00   0.0  0
 4VC  CONST_20  H22  C6   C7   C2   180.00   0.0  0
 4VC  CONST_21  H21  C5   C4   C3   180.00   0.0  0
 4VC  CONST_22  H19  C3   C4   C5   180.00   0.0  0
 4VC  CONST_23  H28  C15  C14  C13  180.00   0.0  0
 4VC  CONST_24  H29  C16  C15  C14  180.00   0.0  0
 4VC  CONST_25  H30  C18  C13  C14  180.00   0.0  0
 4VC  CONST_26  H27  C14  C15  C16  180.00   0.0  0
 4VC  CONST_30  O10  C9   N8   C7     0.00   0.0  0
 4VC  CONST_31  N11  C9   N8   C7   180.00   0.0  0
 4VC  CONST_32  O10  C9   N11  C12    0.00   0.0  0
 4VC  CONST_33  N8   C9   N11  C12  180.00   0.0  0
 4VC  CONST_34  H24  N11  C9   O10  180.00   0.0  0
 4VC  Var_01    N11  C12  C13  C14  -61.81  30.0  2
 4VC  Var_02    C9   N11  C12  C13   98.41  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
 4VC  plan-1  C2   0.020
 4VC  plan-1  C3   0.020
 4VC  plan-1  C5   0.020
 4VC  plan-1  C6   0.020
 4VC  plan-1  C7   0.020
 4VC  plan-1  CL1  0.020
 4VC  plan-1  C4   0.020
 4VC  plan-1  N8   0.020
 4VC  plan-1  H19  0.020
 4VC  plan-1  H21  0.020
 4VC  plan-1  H22  0.020
 4VC  plan-1  H20  0.020
 4VC  plan-2  C12  0.020
 4VC  plan-2  C13  0.020
 4VC  plan-2  C14  0.020
 4VC  plan-2  C15  0.020
 4VC  plan-2  C16  0.020
 4VC  plan-2  N17  0.020
 4VC  plan-2  C18  0.020
 4VC  plan-2  H27  0.020
 4VC  plan-2  H28  0.020
 4VC  plan-2  H29  0.020
 4VC  plan-2  H30  0.020
 4VC  plan-3  C7   0.020
 4VC  plan-3  C12  0.020
 4VC  plan-3  N8   0.020
 4VC  plan-3  C9   0.020
 4VC  plan-3  O10  0.020
 4VC  plan-3  N11  0.020
 4VC  plan-3  H23  0.020
 4VC  plan-3  H24  0.020

