# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 02:21:09 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-{2-[(4'-cyanobiphenyl-4-yl)oxy]ethyl}-3-hydroxy-1-methylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCOc1ccc(cc1)c2ccc(cc2)C#N)C(=O)NO
#
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
 2NI  2NI  1-{2-[(4'-cyanobiphenyl-4-yl)oxy]ethyl}-3-hydroxy-1-methylurea  ligand  40  23  .  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_2NI
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
 2NI  C1    C  CR16  0  -0.294  -1.2651  -1.3612  -0.2374
 2NI  C2    C  CR16  0  -0.365   0.1081  -1.5123  -0.3636
 2NI  C3    C  CR6   0   0.402   0.9200  -0.3851  -0.4529
 2NI  C4    C  CR16  0  -0.330   0.3372   0.8827  -0.4151
 2NI  C5    C  CR16  0  -0.291  -1.0305   1.0150  -0.2872
 2NI  C6    C  CR6   0   0.070  -1.8644  -0.1046  -0.1970
 2NI  C7    C  CR6   0   0.117  -3.3236   0.0398  -0.0641
 2NI  C8    C  CR16  0  -0.307  -4.1921  -0.8996  -0.6284
 2NI  C9    C  CR16  0  -0.222  -5.5622  -0.7730  -0.5031
 2NI  C10   C  CR6   0  -0.014  -6.0950   0.3127   0.1918
 2NI  C11   C  CR16  0  -0.221  -5.2453   1.2630   0.7576
 2NI  C12   C  CR16  0  -0.308  -3.8769   1.1205   0.6295
 2NI  C13   C  CSP   0   0.054  -7.5079   0.4514   0.3226
 2NI  N1    N  NS    0  -0.254  -8.6504   0.5627   0.4280
 2NI  O1    O  O2    0  -0.484   2.2594  -0.4256  -0.5778
 2NI  C14   C  CH2   0  -0.178   2.9152  -1.6805  -0.6290
 2NI  C15   C  CH2   0  -0.380   4.4036  -1.4245  -0.7535
 2NI  N2    N  NT    0  -0.475   4.9856  -0.7477   0.3869
 2NI  C16   C  CH3   0  -0.522   5.2702  -1.5790   1.5374
 2NI  C17   C  C     0   0.678   5.2170   0.5919   0.4486
 2NI  O2    O  O     0  -0.513   5.7920   1.1317   1.3781
 2NI  N3    N  NH1   0  -0.436   4.8127   1.3029  -0.6764
 2NI  O3    O  OH1   0  -0.552   4.8848   2.6704  -0.5281
 2NI  H1    H  HCR6  0   0.264  -1.8706  -2.2541  -0.1465
 2NI  H2    H  HCR6  0   0.286   0.5213  -2.5114  -0.3844
 2NI  H4    H  HCR6  0   0.269   0.9641   1.7619  -0.4958
 2NI  H5    H  HCR6  0   0.261  -1.4537   2.0117  -0.2799
 2NI  H8    H  HCR6  0   0.270  -3.7979  -1.7347  -1.1919
 2NI  H9    H  HCR6  0   0.282  -6.2171  -1.5083  -0.9504
 2NI  H11   H  HCR6  0   0.282  -5.6542   2.1040   1.3008
 2NI  H12   H  HCR6  0   0.269  -3.2329   1.8548   1.0949
 2NI  H141  H  HCH2  0   0.245   2.5798  -2.2609  -1.4947
 2NI  H142  H  HCH2  0   0.237   2.6975  -2.2653   0.2711
 2NI  H151  H  HCH2  0   0.275   4.6220  -0.8825  -1.6746
 2NI  H152  H  HCH2  0   0.279   4.8910  -2.3969  -0.8600
 2NI  H161  H  HCH3  0   0.263   5.8382  -1.0248   2.2762
 2NI  H162  H  HCH3  0   0.237   4.3527  -1.9392   2.0093
 2NI  H163  H  HCH3  0   0.240   5.8549  -2.4475   1.2311
 2NI  HN3   H  HNH1  0   0.398   3.9124   1.0556  -1.0645
 2NI  HO3   H  HOH1  0   0.472   5.6051   2.9449  -1.1061

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
 2NI  C1   C2    aromatic  1.387  0.020  1.387
 2NI  C1   C6    aromatic  1.393  0.020  1.393
 2NI  C1   H1    single    0.930  0.020  1.080
 2NI  C2   C3    aromatic  1.392  0.020  1.392
 2NI  C2   H2    single    0.930  0.020  1.080
 2NI  C3   C4    aromatic  1.396  0.020  1.396
 2NI  C3   O1    single    1.346  0.020  1.346
 2NI  C4   C5    aromatic  1.380  0.020  1.380
 2NI  C4   H4    single    0.930  0.020  1.080
 2NI  C5   C6    aromatic  1.399  0.020  1.399
 2NI  C5   H5    single    0.930  0.020  1.080
 2NI  C6   C7    single    1.472  0.020  1.472
 2NI  C7   C8    aromatic  1.398  0.020  1.398
 2NI  C7   C12   aromatic  1.398  0.020  1.398
 2NI  C8   C9    aromatic  1.382  0.020  1.382
 2NI  C8   H8    single    0.930  0.020  1.080
 2NI  C9   C10   aromatic  1.395  0.020  1.395
 2NI  C9   H9    single    0.930  0.020  1.080
 2NI  C10  C11   aromatic  1.395  0.020  1.395
 2NI  C10  C13   single    1.426  0.020  1.426
 2NI  C11  C12   aromatic  1.382  0.020  1.382
 2NI  C11  H11   single    0.930  0.020  1.080
 2NI  C12  H12   single    0.930  0.020  1.080
 2NI  C13  N1    triple    1.153  0.020  1.153
 2NI  O1   C14   single    1.417  0.020  1.417
 2NI  C14  C15   single    1.515  0.020  1.515
 2NI  C14  H141  single    0.970  0.020  1.090
 2NI  C14  H142  single    0.970  0.020  1.090
 2NI  C15  N2    single    1.448  0.020  1.448
 2NI  C15  H151  single    0.970  0.020  1.090
 2NI  C15  H152  single    0.970  0.020  1.090
 2NI  N2   C16   single    1.448  0.020  1.448
 2NI  N2   C17   single    1.361  0.020  1.361
 2NI  C16  H161  single    0.970  0.020  1.090
 2NI  C16  H162  single    0.970  0.020  1.090
 2NI  C16  H163  single    0.970  0.020  1.090
 2NI  C17  O2    double    1.219  0.020  1.219
 2NI  C17  N3    single    1.391  0.020  1.391
 2NI  N3   O3    single    1.377  0.020  1.377
 2NI  N3   HN3   single    0.890  0.020  1.040
 2NI  O3   HO3   single    0.850  0.020  0.980

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
 2NI  H1    C1   C6    120.07  3.000
 2NI  H1    C1   C2    118.13  3.000
 2NI  C6    C1   C2    121.79  3.000
 2NI  H2    C2   C3    121.61  3.000
 2NI  H2    C2   C1    118.72  3.000
 2NI  C3    C2   C1    119.67  3.000
 2NI  O1    C3   C4    116.45  3.000
 2NI  O1    C3   C2    124.20  3.000
 2NI  C4    C3   C2    119.35  3.000
 2NI  H4    C4   C5    120.19  3.000
 2NI  H4    C4   C3    119.58  3.000
 2NI  C5    C4   C3    120.23  3.000
 2NI  H5    C5   C6    120.21  3.000
 2NI  H5    C5   C4    118.44  3.000
 2NI  C6    C5   C4    121.33  3.000
 2NI  C7    C6   C5    121.21  3.000
 2NI  C7    C6   C1    121.17  3.000
 2NI  C5    C6   C1    117.63  3.000
 2NI  C12   C7   C8    118.27  3.000
 2NI  C12   C7   C6    120.85  3.000
 2NI  C8    C7   C6    120.88  3.000
 2NI  H8    C8   C9    118.64  3.000
 2NI  H8    C8   C7    120.17  3.000
 2NI  C9    C8   C7    121.18  3.000
 2NI  H9    C9   C10   120.26  3.000
 2NI  H9    C9   C8    120.04  3.000
 2NI  C10   C9   C8    119.69  3.000
 2NI  C13   C10  C11   120.02  3.000
 2NI  C13   C10  C9    120.00  3.000
 2NI  C11   C10  C9    119.98  3.000
 2NI  H11   C11  C12   120.08  3.000
 2NI  H11   C11  C10   120.22  3.000
 2NI  C12   C11  C10   119.70  3.000
 2NI  H12   C12  C11   118.66  3.000
 2NI  H12   C12  C7    120.16  3.000
 2NI  C11   C12  C7    121.17  3.000
 2NI  N1    C13  C10   180.00  3.000
 2NI  C14   O1   C3    119.38  3.000
 2NI  H142  C14  H141  107.81  3.000
 2NI  H142  C14  C15   110.67  3.000
 2NI  H141  C14  C15   108.99  3.000
 2NI  H142  C14  O1    110.56  3.000
 2NI  H141  C14  O1    110.88  3.000
 2NI  C15   C14  O1    107.93  3.000
 2NI  H152  C15  H151  105.70  3.000
 2NI  H152  C15  N2    108.26  3.000
 2NI  H151  C15  N2    110.63  3.000
 2NI  H152  C15  C14   107.20  3.000
 2NI  H151  C15  C14   110.48  3.000
 2NI  N2    C15  C14   114.14  3.000
 2NI  C17   N2   C16   119.72  3.000
 2NI  C17   N2   C15   124.34  3.000
 2NI  C16   N2   C15   115.88  3.000
 2NI  H163  C16  H162  107.99  3.000
 2NI  H163  C16  H161  108.51  3.000
 2NI  H162  C16  H161  108.30  3.000
 2NI  H163  C16  N2    109.85  3.000
 2NI  H162  C16  N2    111.56  3.000
 2NI  H161  C16  N2    110.55  3.000
 2NI  N3    C17  O2    121.83  3.000
 2NI  N3    C17  N2    114.65  3.000
 2NI  O2    C17  N2    123.42  3.000
 2NI  HN3   N3   O3    109.32  3.000
 2NI  HN3   N3   C17   116.37  3.000
 2NI  O3    N3   C17   113.91  3.000
 2NI  HO3   O3   N3    104.92  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
 2NI  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 2NI  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 2NI  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 2NI  CONST_06  C7    C6   C1   C2    180.00   0.0  0
 2NI  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 2NI  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 2NI  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 2NI  CONST_10  C7    C6   C5   C4    180.00   0.0  0
 2NI  CONST_13  C9    C8   C7   C6    180.00   0.0  0
 2NI  CONST_14  C11   C12  C7   C6    180.00   0.0  0
 2NI  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 2NI  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 2NI  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 2NI  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 2NI  CONST_19  C12   C7   C8   C9      0.00   0.0  0
 2NI  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 2NI  CONST_21  O1    C3   C2   C1    180.00   0.0  0
 2NI  CONST_22  O1    C3   C4   C5    180.00   0.0  0
 2NI  CONST_23  C13   C10  C9   C8    180.00   0.0  0
 2NI  CONST_24  C13   C10  C11  C12   180.00   0.0  0
 2NI  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 2NI  CONST_26  H4    C4   C3   C2    180.00   0.0  0
 2NI  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 2NI  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 2NI  CONST_29  H8    C8   C7   C6      0.00   0.0  0
 2NI  CONST_30  H12   C12  C7   C6      0.00   0.0  0
 2NI  CONST_31  H9    C9   C8   C7    180.00   0.0  0
 2NI  CONST_32  H11   C11  C12  C7    180.00   0.0  0
 2NI  CONST_33  O2    C17  N2   C15   180.00   0.0  0
 2NI  CONST_34  O2    C17  N2   C16     0.00   0.0  0
 2NI  CONST_35  O3    N3   C17  O2      0.00   0.0  0
 2NI  CONST_36  N3    C17  N2   C15     0.00   0.0  0
 2NI  CONST_37  O3    N3   C17  N2    180.00   0.0  0
 2NI  CONST_38  N3    C17  N2   C16   180.00   0.0  0
 2NI  Var_01    C15   C14  O1   C3   -179.34  30.0  3
 2NI  Var_02    N2    C15  C14  O1     63.87  30.0  3
 2NI  Var_03    C16   N2   C15  C14    79.64  30.0  3
 2NI  Var_04    H161  C16  N2   C15   171.29  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
 2NI  plan-1  C1   0.020
 2NI  plan-1  C2   0.020
 2NI  plan-1  C3   0.020
 2NI  plan-1  C4   0.020
 2NI  plan-1  C5   0.020
 2NI  plan-1  C6   0.020
 2NI  plan-1  C7   0.020
 2NI  plan-1  O1   0.020
 2NI  plan-1  H1   0.020
 2NI  plan-1  H2   0.020
 2NI  plan-1  H4   0.020
 2NI  plan-1  H5   0.020
 2NI  plan-2  C6   0.020
 2NI  plan-2  C7   0.020
 2NI  plan-2  C8   0.020
 2NI  plan-2  C9   0.020
 2NI  plan-2  C10  0.020
 2NI  plan-2  C11  0.020
 2NI  plan-2  C12  0.020
 2NI  plan-2  C13  0.020
 2NI  plan-2  N1   0.020
 2NI  plan-2  H8   0.020
 2NI  plan-2  H9   0.020
 2NI  plan-2  H11  0.020
 2NI  plan-2  H12  0.020
 2NI  plan-3  C15  0.020
 2NI  plan-3  N2   0.020
 2NI  plan-3  C16  0.020
 2NI  plan-3  C17  0.020
 2NI  plan-3  O2   0.020
 2NI  plan-3  N3   0.020
 2NI  plan-3  O3   0.020
 2NI  plan-3  HN3  0.020

