# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:54:53 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-ethyl-3-naphthalen-1-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cccc2ccccc12
#
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
 W9L  W9L  1-ethyl-3-naphthalen-1-ylurea  ligand  30  16  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W9L
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
 W9L  C1   C  C     0   0.725   2.1659   0.2686  -0.1962
 W9L  N1   N  NH1   0  -0.794   0.9686  -0.1275   0.3557
 W9L  O1   O  O     0  -0.525   2.2838   1.2661  -0.8930
 W9L  C2   C  CR6   0   0.329  -0.2441   0.5585   0.2511
 W9L  N2   N  NH1   0  -0.679   3.2030  -0.5419   0.1085
 W9L  C3   C  CR66  0   0.050  -1.4407  -0.2022   0.0778
 W9L  C4   C  CR66  0   0.099  -2.6881   0.4788   0.0511
 W9L  C5   C  CR16  0  -0.330  -2.7196   1.8883   0.1498
 W9L  C6   C  CR16  0  -0.261  -1.5546   2.5895   0.2830
 W9L  C7   C  CR16  0  -0.303  -0.3151   1.9276   0.3501
 W9L  C8   C  CH2   0  -0.253   4.5280  -0.3321  -0.4375
 W9L  C9   C  CH3   0  -0.699   5.5354  -1.2147   0.2753
 W9L  C11  C  CR16  0  -0.257  -3.8465  -1.6309  -0.2206
 W9L  C12  C  CR16  0  -0.252  -2.6096  -2.3052  -0.2194
 W9L  C40  C  CR16  0  -0.304  -1.4390  -1.6102  -0.0760
 W9L  C80  C  CR16  0  -0.310  -3.8802  -0.2701  -0.0925
 W9L  HN1  H  HNH1  0   0.404   0.9503  -1.0042   0.8522
 W9L  HN2  H  HNH1  0   0.396   3.0386  -1.3958   0.6174
 W9L  H5   H  HCR6  0   0.253  -3.6736   2.4001   0.1183
 W9L  H6   H  HCR6  0   0.258  -1.5749   3.6687   0.3600
 W9L  H7   H  HCR6  0   0.264   0.5819   2.5095   0.4996
 W9L  H8   H  HCH2  0   0.227   4.5462  -0.5409  -1.5116
 W9L  H8A  H  HCH2  0   0.234   4.8056   0.7159  -0.3143
 W9L  H9   H  HCH3  0   0.244   6.5336  -1.0349  -0.1210
 W9L  H9A  H  HCH3  0   0.234   5.5547  -1.0075   1.3456
 W9L  H9B  H  HCH3  0   0.232   5.3105  -2.2733   0.1362
 W9L  H11  H  HCR6  0   0.259  -4.7648  -2.1923  -0.3328
 W9L  H12  H  HCR6  0   0.260  -2.5842  -3.3802  -0.3398
 W9L  H40  H  HCR6  0   0.245  -0.5061  -2.1579  -0.0985
 W9L  H80  H  HCR6  0   0.256  -4.8262   0.2581  -0.1039

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
 W9L  C1   N1   single    1.377  0.020  1.377
 W9L  C1   O1   double    1.223  0.020  1.223
 W9L  C1   N2   single    1.351  0.020  1.351
 W9L  N1   C2   single    1.397  0.020  1.397
 W9L  C2   C3   aromatic  1.429  0.020  1.429
 W9L  C2   C7   aromatic  1.374  0.020  1.374
 W9L  N2   C8   single    1.448  0.020  1.448
 W9L  C3   C4   aromatic  1.421  0.020  1.421
 W9L  C3   C40  aromatic  1.416  0.020  1.416
 W9L  C4   C5   aromatic  1.413  0.020  1.413
 W9L  C4   C80  aromatic  1.415  0.020  1.415
 W9L  C5   C6   aromatic  1.366  0.020  1.366
 W9L  C6   C7   aromatic  1.407  0.020  1.407
 W9L  C8   C9   single    1.517  0.020  1.517
 W9L  C11  C12  aromatic  1.409  0.020  1.409
 W9L  C11  C80  aromatic  1.367  0.020  1.367
 W9L  C12  C40  aromatic  1.369  0.020  1.369
 W9L  N1   HN1  single    0.860  0.020  1.020
 W9L  N2   HN2  single    0.860  0.020  1.020
 W9L  C5   H5   single    0.930  0.020  1.080
 W9L  C6   H6   single    0.930  0.020  1.080
 W9L  C7   H7   single    0.930  0.020  1.080
 W9L  C8   H8   single    0.970  0.020  1.090
 W9L  C8   H8A  single    0.970  0.020  1.090
 W9L  C9   H9   single    0.970  0.020  1.090
 W9L  C9   H9A  single    0.970  0.020  1.090
 W9L  C9   H9B  single    0.970  0.020  1.090
 W9L  C11  H11  single    0.930  0.020  1.080
 W9L  C12  H12  single    0.930  0.020  1.080
 W9L  C40  H40  single    0.930  0.020  1.080
 W9L  C80  H80  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
 W9L  N2   C1   O1   122.96  3.000
 W9L  N2   C1   N1   113.87  3.000
 W9L  O1   C1   N1   123.17  3.000
 W9L  HN1  N1   C2   116.63  3.000
 W9L  HN1  N1   C1   117.62  3.000
 W9L  C2   N1   C1   125.70  3.000
 W9L  C7   C2   C3   119.73  3.000
 W9L  C7   C2   N1   121.91  3.000
 W9L  C3   C2   N1   118.34  3.000
 W9L  HN2  N2   C8   117.55  3.000
 W9L  HN2  N2   C1   119.81  3.000
 W9L  C8   N2   C1   122.03  3.000
 W9L  C40  C3   C4   118.38  3.000
 W9L  C40  C3   C2   122.79  3.000
 W9L  C4   C3   C2   118.83  3.000
 W9L  C80  C4   C5   121.07  3.000
 W9L  C80  C4   C3   119.18  3.000
 W9L  C5   C4   C3   119.74  3.000
 W9L  H5   C5   C6   120.75  3.000
 W9L  H5   C5   C4   119.27  3.000
 W9L  C6   C5   C4   119.98  3.000
 W9L  H6   C6   C7   118.84  3.000
 W9L  H6   C6   C5   120.19  3.000
 W9L  C7   C6   C5   120.96  3.000
 W9L  H7   C7   C6   119.02  3.000
 W9L  H7   C7   C2   120.26  3.000
 W9L  C6   C7   C2   120.72  3.000
 W9L  H8A  C8   H8   106.85  3.000
 W9L  H8A  C8   C9   109.68  3.000
 W9L  H8   C8   C9   109.82  3.000
 W9L  H8A  C8   N2   109.23  3.000
 W9L  H8   C8   N2   110.95  3.000
 W9L  C9   C8   N2   110.24  3.000
 W9L  H9B  C9   H9A  108.25  3.000
 W9L  H9B  C9   H9   107.62  3.000
 W9L  H9A  C9   H9   108.03  3.000
 W9L  H9B  C9   C8   111.57  3.000
 W9L  H9A  C9   C8   111.25  3.000
 W9L  H9   C9   C8   109.97  3.000
 W9L  H11  C11  C80  120.34  3.000
 W9L  H11  C11  C12  119.80  3.000
 W9L  C80  C11  C12  119.86  3.000
 W9L  H12  C12  C40  119.74  3.000
 W9L  H12  C12  C11  119.74  3.000
 W9L  C40  C12  C11  120.53  3.000
 W9L  H40  C40  C12  118.56  3.000
 W9L  H40  C40  C3   120.43  3.000
 W9L  C12  C40  C3   121.00  3.000
 W9L  H80  C80  C11  120.38  3.000
 W9L  H80  C80  C4   118.59  3.000
 W9L  C11  C80  C4   121.03  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
 W9L  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 W9L  CONST_02  C80  C4   C3   C2    180.00   0.0  0
 W9L  CONST_03  C12  C40  C3   C2    180.00   0.0  0
 W9L  CONST_04  C5   C6   C7   C2      0.00   0.0  0
 W9L  CONST_05  C6   C7   C2   C3      0.00   0.0  0
 W9L  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 W9L  CONST_07  C11  C80  C4   C3      0.00   0.0  0
 W9L  CONST_08  C11  C12  C40  C3      0.00   0.0  0
 W9L  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 W9L  CONST_10  C12  C40  C3   C4      0.00   0.0  0
 W9L  CONST_11  C7   C6   C5   C4      0.00   0.0  0
 W9L  CONST_12  C12  C11  C80  C4      0.00   0.0  0
 W9L  CONST_13  C40  C3   C4   C5    180.00   0.0  0
 W9L  CONST_14  C11  C80  C4   C5    180.00   0.0  0
 W9L  CONST_15  C80  C4   C5   C6    180.00   0.0  0
 W9L  CONST_16  C40  C3   C2   C7    180.00   0.0  0
 W9L  CONST_17  C80  C4   C3   C40     0.00   0.0  0
 W9L  CONST_18  C80  C11  C12  C40     0.00   0.0  0
 W9L  CONST_19  C4   C3   C2   N1    180.00   0.0  0
 W9L  CONST_20  C40  C3   C2   N1      0.00   0.0  0
 W9L  CONST_21  C6   C7   C2   N1    180.00   0.0  0
 W9L  CONST_22  H40  C40  C3   C2      0.00   0.0  0
 W9L  CONST_23  H6   C6   C7   C2    180.00   0.0  0
 W9L  CONST_24  H7   C7   C2   C3    180.00   0.0  0
 W9L  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 W9L  CONST_26  H80  C80  C4   C3    180.00   0.0  0
 W9L  CONST_27  H12  C12  C40  C3    180.00   0.0  0
 W9L  CONST_28  H11  C11  C80  C4    180.00   0.0  0
 W9L  CONST_32  C2   N1   C1   O1      0.00   0.0  0
 W9L  CONST_33  N2   C1   N1   C2    180.00   0.0  0
 W9L  CONST_34  C8   N2   C1   O1      0.00   0.0  0
 W9L  CONST_35  C8   N2   C1   N1    180.00   0.0  0
 W9L  CONST_36  HN2  N2   C1   O1    180.00   0.0  0
 W9L  Var_01    C9   C8   N2   C1    169.11  30.0  3
 W9L  Var_02    H9   C9   C8   N2   -178.55  30.0  3

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
 W9L  plan-1  N1   0.020
 W9L  plan-1  C2   0.020
 W9L  plan-1  C3   0.020
 W9L  plan-1  C4   0.020
 W9L  plan-1  C5   0.020
 W9L  plan-1  C6   0.020
 W9L  plan-1  C7   0.020
 W9L  plan-1  C11  0.020
 W9L  plan-1  C12  0.020
 W9L  plan-1  C40  0.020
 W9L  plan-1  C80  0.020
 W9L  plan-1  H5   0.020
 W9L  plan-1  H6   0.020
 W9L  plan-1  H7   0.020
 W9L  plan-1  H11  0.020
 W9L  plan-1  H12  0.020
 W9L  plan-1  H40  0.020
 W9L  plan-1  H80  0.020
 W9L  plan-2  C1   0.020
 W9L  plan-2  N1   0.020
 W9L  plan-2  O1   0.020
 W9L  plan-2  C2   0.020
 W9L  plan-2  N2   0.020
 W9L  plan-2  C8   0.020
 W9L  plan-2  HN1  0.020
 W9L  plan-2  HN2  0.020

