# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:28:29 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-benzyl-3-(2-chloropyridin-4-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(NC(=O)NCc2ccccc2)ccn1
#
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
 246  246  1-benzyl-3-(2-chloropyridin-4-yl)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_246
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
 246  CL5  CL  CL    0  -0.110  -5.0276   1.7303   1.1766
 246  C1   C   C     0   0.762   0.6225  -1.0693   0.2505
 246  O1   O   O     0  -0.507   0.6423  -1.5613  -0.8654
 246  N2   N   NH1   0  -0.667   1.6599  -1.1175   1.1124
 246  C3   C   CR6   0   0.484  -1.7088  -0.2241   0.1807
 246  N3   N   NH1   0  -0.788  -0.4815  -0.4153   0.7698
 246  C4   C   CR16  0  -0.375  -2.6353   0.5598   0.8772
 246  C5   C   CR6   0   0.162  -3.8771   0.7569   0.3106
 246  N6   N   N     0  -0.411  -4.2782   0.2713  -0.8401
 246  C7   C   CR16  0  -0.069  -3.3912  -0.4744  -1.4955
 246  C8   C   CR16  0  -0.375  -2.1150  -0.7563  -1.0500
 246  C9   C   CH2   0  -0.396   2.9626  -1.6292   0.7412
 246  C10  C   CR6   0   0.127   3.8922  -0.5489   0.2457
 246  C11  C   CR16  0  -0.295   3.8293  -0.1067  -1.0746
 246  C12  C   CR16  0  -0.242   4.6604   0.9124  -1.5179
 246  C13  C   CR16  0  -0.265   5.5667   1.5038  -0.6459
 246  C14  C   CR16  0  -0.242   5.6386   1.0675   0.6698
 246  C15  C   CR16  0  -0.300   4.8051   0.0468   1.1104
 246  HN2  H   HNH1  0   0.404   1.6029  -0.6255   1.9897
 246  HN3  H   HNH1  0   0.418  -0.3790   0.0010   1.6838
 246  H4   H   HCR6  0   0.302  -2.3869   1.0008   1.8333
 246  H7   H   HCR6  0   0.276  -3.7200  -0.8805  -2.4447
 246  H8   H   HCR6  0   0.296  -1.4694  -1.3753  -1.6474
 246  H91  H   HCH2  0   0.272   3.3884  -2.1162   1.6190
 246  H92  H   HCH2  0   0.270   2.8305  -2.3999  -0.0160
 246  H11  H   HCR6  0   0.252   3.1267  -0.5642  -1.7602
 246  H12  H   HCR6  0   0.255   4.6034   1.2433  -2.5470
 246  H13  H   HCR6  0   0.256   6.2158   2.2977  -0.9926
 246  H14  H   HCR6  0   0.256   6.3452   1.5196   1.3538
 246  H15  H   HCR6  0   0.252   4.8692  -0.2903   2.1385

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
 246  CL5  C5   single    1.738  0.020  1.738
 246  C5   C4   aromatic  1.379  0.020  1.379
 246  C5   N6   aromatic  1.312  0.020  1.312
 246  C4   C3   aromatic  1.399  0.020  1.399
 246  N6   C7   aromatic  1.331  0.020  1.331
 246  O1   C1   double    1.220  0.020  1.220
 246  C11  C12  aromatic  1.388  0.020  1.388
 246  C11  C10  aromatic  1.394  0.020  1.394
 246  C12  C13  aromatic  1.390  0.020  1.390
 246  C3   N3   single    1.375  0.020  1.375
 246  C3   C8   aromatic  1.401  0.020  1.401
 246  C7   C8   aromatic  1.381  0.020  1.381
 246  C1   N3   single    1.384  0.020  1.384
 246  C1   N2   single    1.350  0.020  1.350
 246  C9   C10  single    1.509  0.020  1.509
 246  C9   N2   single    1.448  0.020  1.448
 246  C10  C15  aromatic  1.391  0.020  1.391
 246  C13  C14  aromatic  1.388  0.020  1.388
 246  C15  C14  aromatic  1.390  0.020  1.390
 246  N2   HN2  single    0.860  0.020  1.020
 246  N3   HN3  single    0.860  0.020  1.020
 246  C4   H4   single    0.930  0.020  1.080
 246  C7   H7   single    0.930  0.020  1.080
 246  C8   H8   single    0.930  0.020  1.080
 246  C9   H91  single    0.970  0.020  1.090
 246  C9   H92  single    0.970  0.020  1.090
 246  C11  H11  single    0.930  0.020  1.080
 246  C12  H12  single    0.930  0.020  1.080
 246  C13  H13  single    0.930  0.020  1.080
 246  C14  H14  single    0.930  0.020  1.080
 246  C15  H15  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
 246  N3   C1   N2   112.97  3.000
 246  N2   C1   O1   123.88  3.000
 246  N3   C1   O1   123.15  3.000
 246  HN2  N2   C9   116.54  3.000
 246  HN2  N2   C1   119.68  3.000
 246  C9   N2   C1   122.71  3.000
 246  C8   C3   C4   117.26  3.000
 246  C8   C3   N3   125.62  3.000
 246  C4   C3   N3   117.11  3.000
 246  HN3  N3   C3   114.91  3.000
 246  HN3  N3   C1   116.97  3.000
 246  C3   N3   C1   128.09  3.000
 246  H4   C4   C5   120.77  3.000
 246  H4   C4   C3   121.08  3.000
 246  C5   C4   C3   118.15  3.000
 246  N6   C5   C4   125.65  3.000
 246  N6   C5   CL5  116.23  3.000
 246  C4   C5   CL5  118.12  3.000
 246  C7   N6   C5   115.81  3.000
 246  H7   C7   C8   119.12  3.000
 246  H7   C7   N6   116.04  3.000
 246  C8   C7   N6   124.84  3.000
 246  H8   C8   C7   119.54  3.000
 246  H8   C8   C3   122.18  3.000
 246  C7   C8   C3   118.28  3.000
 246  H92  C9   H91  106.93  3.000
 246  H92  C9   C10  110.69  3.000
 246  H91  C9   C10  110.10  3.000
 246  H92  C9   N2   108.62  3.000
 246  H91  C9   N2   107.62  3.000
 246  C10  C9   N2   112.67  3.000
 246  C15  C10  C11  118.85  3.000
 246  C15  C10  C9   120.44  3.000
 246  C11  C10  C9   120.69  3.000
 246  H11  C11  C12  119.77  3.000
 246  H11  C11  C10  119.66  3.000
 246  C12  C11  C10  120.57  3.000
 246  H12  C12  C13  120.04  3.000
 246  H12  C12  C11  119.78  3.000
 246  C13  C12  C11  120.17  3.000
 246  H13  C13  C14  120.20  3.000
 246  H13  C13  C12  120.14  3.000
 246  C14  C13  C12  119.66  3.000
 246  H14  C14  C15  119.87  3.000
 246  H14  C14  C13  120.10  3.000
 246  C15  C14  C13  120.02  3.000
 246  H15  C15  C14  119.58  3.000
 246  H15  C15  C10  119.68  3.000
 246  C14  C15  C10  120.73  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
 246  CONST_01  N6   C5   C4   C3     0.00   0.0  0
 246  CONST_02  N6   C7   C8   C3     0.00   0.0  0
 246  CONST_03  C7   N6   C5   C4     0.00   0.0  0
 246  CONST_04  C7   C8   C3   C4     0.00   0.0  0
 246  CONST_05  C8   C3   C4   C5     0.00   0.0  0
 246  CONST_06  C8   C7   N6   C5     0.00   0.0  0
 246  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 246  CONST_08  C13  C14  C15  C10    0.00   0.0  0
 246  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 246  CONST_10  C14  C15  C10  C11    0.00   0.0  0
 246  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 246  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 246  CONST_13  C3   C4   C5   CL5  180.00   0.0  0
 246  CONST_14  C7   N6   C5   CL5  180.00   0.0  0
 246  CONST_15  C5   C4   C3   N3   180.00   0.0  0
 246  CONST_16  C7   C8   C3   N3   180.00   0.0  0
 246  CONST_17  C12  C11  C10  C9   180.00   0.0  0
 246  CONST_18  C14  C15  C10  C9   180.00   0.0  0
 246  CONST_19  H7   C7   C8   C3   180.00   0.0  0
 246  CONST_20  H8   C8   C3   C4   180.00   0.0  0
 246  CONST_21  H4   C4   C5   N6   180.00   0.0  0
 246  CONST_22  H12  C12  C11  C10  180.00   0.0  0
 246  CONST_23  H14  C14  C15  C10  180.00   0.0  0
 246  CONST_24  H13  C13  C12  C11  180.00   0.0  0
 246  CONST_25  H15  C15  C10  C11  180.00   0.0  0
 246  CONST_26  H11  C11  C12  C13  180.00   0.0  0
 246  CONST_27  C4   C3   N3   C1   180.00   0.0  0
 246  CONST_28  C8   C3   N3   C1     0.00   0.0  0
 246  CONST_29  HN3  N3   C3   C4     0.00   0.0  0
 246  CONST_30  C3   N3   C1   O1     0.00   0.0  0
 246  CONST_31  C3   N3   C1   N2   180.00   0.0  0
 246  CONST_32  C9   N2   C1   O1     0.00   0.0  0
 246  CONST_33  C9   N2   C1   N3   180.00   0.0  0
 246  CONST_34  HN2  N2   C1   O1   180.00   0.0  0
 246  Var_01    C11  C10  C9   N2   -82.28  30.0  2
 246  Var_02    C10  C9   N2   C1    92.21  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
 246  plan-1  CL5  0.020
 246  plan-1  C3   0.020
 246  plan-1  N3   0.020
 246  plan-1  C4   0.020
 246  plan-1  C5   0.020
 246  plan-1  N6   0.020
 246  plan-1  C7   0.020
 246  plan-1  C8   0.020
 246  plan-1  H4   0.020
 246  plan-1  H7   0.020
 246  plan-1  H8   0.020
 246  plan-2  C9   0.020
 246  plan-2  C10  0.020
 246  plan-2  C11  0.020
 246  plan-2  C12  0.020
 246  plan-2  C13  0.020
 246  plan-2  C14  0.020
 246  plan-2  C15  0.020
 246  plan-2  H11  0.020
 246  plan-2  H12  0.020
 246  plan-2  H13  0.020
 246  plan-2  H14  0.020
 246  plan-2  H15  0.020
 246  plan-3  C1   0.020
 246  plan-3  O1   0.020
 246  plan-3  N2   0.020
 246  plan-3  C3   0.020
 246  plan-3  N3   0.020
 246  plan-3  C9   0.020
 246  plan-3  HN2  0.020
 246  plan-3  HN3  0.020

