# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 16:40:41 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(1H-indazol-5-yl)-3-(2-phenylethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCc1ccccc1)Nc2ccc3[nH]ncc3c2
#
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
 0HD  0HD  1-(1H-indazol-5-yl)-3-(2-phenylethyl)urea  ligand  37  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0HD
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
 0HD  C10  C  CR16  0  -0.240   6.7460   0.7118   0.9950
 0HD  N12  N  NH1   0  -0.786  -1.1917  -0.9229   0.5186
 0HD  C13  C  CR6   0   0.363  -2.5360  -0.6295   0.2644
 0HD  C15  C  CR56  0  -0.070  -4.4021   0.7993  -0.1457
 0HD  C20  C  CR16  0  -0.278  -4.7719  -1.6064   0.0415
 0HD  C21  C  CR16  0  -0.351  -3.4211  -1.7398   0.2446
 0HD  O01  O  O     0  -0.523  -0.1752   0.8847  -0.4451
 0HD  C02  C  C     0   0.729  -0.0975  -0.1854   0.1414
 0HD  N03  N  NH1   0  -0.690   1.0853  -0.7666   0.4659
 0HD  C04  C  CH2   0  -0.236   2.3469  -0.0857   0.2788
 0HD  C05  C  CH2   0  -0.545   3.4921  -1.0945   0.2371
 0HD  C06  C  CR6   0   0.122   4.8144  -0.4032   0.0565
 0HD  C07  C  CR16  0  -0.306   5.3217  -0.1573  -1.2175
 0HD  C08  C  CR16  0  -0.240   6.5266   0.5121  -1.3867
 0HD  C09  C  CR16  0  -0.271   7.2427   0.9497  -0.2800
 0HD  C11  C  CR16  0  -0.307   5.5410   0.0414   1.1589
 0HD  C14  C  CR16  0  -0.394  -3.0260   0.6484   0.0773
 0HD  C16  C  CR56  0   0.398  -5.2584  -0.3114  -0.1622
 0HD  N17  N  NR15  0  -0.544  -6.5023   0.1760  -0.3897
 0HD  N18  N  N     0  -0.228  -6.5072   1.5020  -0.5187
 0HD  C19  C  CR15  0  -0.136  -5.2671   1.9027  -0.3772
 0HD  H1   H  HCR6  0   0.254   7.2992   1.0434   1.8645
 0HD  H2   H  HNH1  0   0.405  -1.0168  -1.8509   0.8708
 0HD  H3   H  HCR6  0   0.274  -5.4217  -2.4711   0.0340
 0HD  H4   H  HCR6  0   0.271  -3.0130  -2.7321   0.3977
 0HD  H5   H  HNH1  0   0.395   1.0833  -1.5397   1.1135
 0HD  H6   H  HCH2  0   0.246   2.3170   0.4673  -0.6598
 0HD  H7   H  HCH2  0   0.232   2.5282   0.6438   1.0765
 0HD  H8   H  HCH2  0   0.252   3.5017  -1.6750   1.1641
 0HD  H9   H  HCH2  0   0.254   3.3193  -1.7991  -0.5795
 0HD  H10  H  HCR6  0   0.248   4.7725  -0.4987  -2.0876
 0HD  H11  H  HCR6  0   0.254   6.9085   0.6883  -2.3840
 0HD  H12  H  HCR6  0   0.254   8.1827   1.4702  -0.4109
 0HD  H13  H  HCR6  0   0.248   5.1627  -0.1456   2.1574
 0HD  H14  H  HCR6  0   0.268  -2.3826   1.5131   0.1069
 0HD  H15  H  HNR5  0   0.415  -7.3644  -0.3374  -0.4711
 0HD  H16  H  HCR5  0   0.265  -5.0166   2.9509  -0.4401

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
 0HD  N17  N18  aromatic  1.332  0.020  1.332
 0HD  N17  C16  aromatic  1.355  0.020  1.355
 0HD  N18  C19  aromatic  1.311  0.020  1.311
 0HD  C16  C20  aromatic  1.398  0.020  1.398
 0HD  C16  C15  aromatic  1.403  0.020  1.403
 0HD  C19  C15  aromatic  1.421  0.020  1.421
 0HD  C20  C21  aromatic  1.372  0.020  1.372
 0HD  C15  C14  aromatic  1.402  0.020  1.402
 0HD  C21  C13  aromatic  1.420  0.020  1.420
 0HD  C14  C13  aromatic  1.381  0.020  1.381
 0HD  C13  N12  single    1.399  0.020  1.399
 0HD  N12  C02  single    1.372  0.020  1.372
 0HD  O01  C02  double    1.223  0.020  1.223
 0HD  C02  N03  single    1.357  0.020  1.357
 0HD  N03  C04  single    1.446  0.020  1.446
 0HD  C04  C05  single    1.527  0.020  1.527
 0HD  C05  C06  single    1.503  0.020  1.503
 0HD  C07  C06  aromatic  1.393  0.020  1.393
 0HD  C07  C08  aromatic  1.389  0.020  1.389
 0HD  C06  C11  aromatic  1.393  0.020  1.393
 0HD  C08  C09  aromatic  1.389  0.020  1.389
 0HD  C11  C10  aromatic  1.389  0.020  1.389
 0HD  C09  C10  aromatic  1.389  0.020  1.389
 0HD  C10  H1   single    0.930  0.020  1.080
 0HD  N12  H2   single    0.860  0.020  1.020
 0HD  C20  H3   single    0.930  0.020  1.080
 0HD  C21  H4   single    0.930  0.020  1.080
 0HD  N03  H5   single    0.890  0.020  1.040
 0HD  C04  H6   single    0.970  0.020  1.090
 0HD  C04  H7   single    0.970  0.020  1.090
 0HD  C05  H8   single    0.970  0.020  1.090
 0HD  C05  H9   single    0.970  0.020  1.090
 0HD  C07  H10  single    0.930  0.020  1.080
 0HD  C08  H11  single    0.930  0.020  1.080
 0HD  C09  H12  single    0.930  0.020  1.080
 0HD  C11  H13  single    0.930  0.020  1.080
 0HD  C14  H14  single    0.930  0.020  1.080
 0HD  N17  H15  single    0.860  0.020  1.020
 0HD  C19  H16  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
 0HD  H1   C10  C11  119.77  3.000
 0HD  H1   C10  C09  120.14  3.000
 0HD  C11  C10  C09  120.09  3.000
 0HD  H2   N12  C02  116.91  3.000
 0HD  H2   N12  C13  115.03  3.000
 0HD  C02  N12  C13  127.12  3.000
 0HD  C14  C13  C21  120.02  3.000
 0HD  C14  C13  N12  124.01  3.000
 0HD  C21  C13  N12  115.94  3.000
 0HD  C19  C15  C16  103.97  3.000
 0HD  C19  C15  C14  134.98  3.000
 0HD  C16  C15  C14  121.05  3.000
 0HD  H3   C20  C16  122.02  3.000
 0HD  H3   C20  C21  120.97  3.000
 0HD  C16  C20  C21  117.00  3.000
 0HD  H4   C21  C20  118.72  3.000
 0HD  H4   C21  C13  118.63  3.000
 0HD  C20  C21  C13  122.65  3.000
 0HD  N03  C02  O01  123.01  3.000
 0HD  N03  C02  N12  113.52  3.000
 0HD  O01  C02  N12  123.46  3.000
 0HD  H5   N03  C04  116.48  3.000
 0HD  H5   N03  C02  118.69  3.000
 0HD  C04  N03  C02  121.86  3.000
 0HD  H7   C04  H6   107.08  3.000
 0HD  H7   C04  C05  109.60  3.000
 0HD  H6   C04  C05  109.41  3.000
 0HD  H7   C04  N03  111.32  3.000
 0HD  H6   C04  N03  109.06  3.000
 0HD  C05  C04  N03  110.30  3.000
 0HD  H9   C05  H8   107.02  3.000
 0HD  H9   C05  C06  110.24  3.000
 0HD  H8   C05  C06  109.77  3.000
 0HD  H9   C05  C04  109.15  3.000
 0HD  H8   C05  C04  109.52  3.000
 0HD  C06  C05  C04  111.05  3.000
 0HD  C11  C06  C07  118.52  3.000
 0HD  C11  C06  C05  120.70  3.000
 0HD  C07  C06  C05  120.76  3.000
 0HD  H10  C07  C08  119.57  3.000
 0HD  H10  C07  C06  119.60  3.000
 0HD  C08  C07  C06  120.83  3.000
 0HD  H11  C08  C09  120.06  3.000
 0HD  H11  C08  C07  119.80  3.000
 0HD  C09  C08  C07  120.14  3.000
 0HD  H12  C09  C08  120.19  3.000
 0HD  H12  C09  C10  120.26  3.000
 0HD  C08  C09  C10  119.54  3.000
 0HD  H13  C11  C06  119.46  3.000
 0HD  H13  C11  C10  119.66  3.000
 0HD  C06  C11  C10  120.88  3.000
 0HD  H14  C14  C15  120.24  3.000
 0HD  H14  C14  C13  121.77  3.000
 0HD  C15  C14  C13  117.99  3.000
 0HD  N17  C16  C20  132.60  3.000
 0HD  C20  C16  C15  121.29  3.000
 0HD  N17  C16  C15  106.11  3.000
 0HD  H15  N17  N18  119.77  3.000
 0HD  H15  N17  C16  128.04  3.000
 0HD  N18  N17  C16  112.19  3.000
 0HD  C19  N18  N17  106.87  3.000
 0HD  H16  C19  N18  120.66  3.000
 0HD  H16  C19  C15  128.48  3.000
 0HD  N18  C19  C15  110.86  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
 0HD  CONST_01  C07  C06  C11  C10     0.00   0.0  0
 0HD  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 0HD  CONST_03  C16  C20  C21  C13     0.00   0.0  0
 0HD  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 0HD  CONST_05  C19  C15  C14  C13   180.00   0.0  0
 0HD  CONST_06  N18  N17  C16  C15     0.00   0.0  0
 0HD  CONST_07  C21  C20  C16  C15     0.00   0.0  0
 0HD  CONST_08  N17  N18  C19  C15     0.00   0.0  0
 0HD  CONST_09  C21  C13  C14  C15     0.00   0.0  0
 0HD  CONST_10  N18  N17  C16  C20   180.00   0.0  0
 0HD  CONST_11  C19  C15  C16  C20   180.00   0.0  0
 0HD  CONST_12  C14  C15  C16  C20     0.00   0.0  0
 0HD  CONST_13  C14  C13  C21  C20     0.00   0.0  0
 0HD  CONST_14  N17  C16  C20  C21   180.00   0.0  0
 0HD  CONST_15  C09  C08  C07  C06     0.00   0.0  0
 0HD  CONST_16  C09  C10  C11  C06     0.00   0.0  0
 0HD  CONST_17  C11  C06  C07  C08     0.00   0.0  0
 0HD  CONST_18  C11  C10  C09  C08     0.00   0.0  0
 0HD  CONST_19  N17  C16  C15  C14   180.00   0.0  0
 0HD  CONST_20  N18  C19  C15  C14   180.00   0.0  0
 0HD  CONST_21  C19  N18  N17  C16     0.00   0.0  0
 0HD  CONST_22  N18  C19  C15  C16     0.00   0.0  0
 0HD  CONST_23  C19  C15  C16  N17     0.00   0.0  0
 0HD  CONST_24  C05  C06  C11  C10   180.00   0.0  0
 0HD  CONST_25  C20  C21  C13  N12   180.00   0.0  0
 0HD  CONST_26  C15  C14  C13  N12   180.00   0.0  0
 0HD  CONST_27  C08  C07  C06  C05   180.00   0.0  0
 0HD  CONST_28  H11  C08  C09  C10   180.00   0.0  0
 0HD  CONST_29  H3   C20  C21  C13   180.00   0.0  0
 0HD  CONST_30  H15  N17  C16  C15   180.00   0.0  0
 0HD  CONST_31  H14  C14  C13  C21   180.00   0.0  0
 0HD  CONST_32  H1   C10  C11  C06   180.00   0.0  0
 0HD  CONST_33  H13  C11  C06  C07   180.00   0.0  0
 0HD  CONST_34  H12  C09  C08  C07   180.00   0.0  0
 0HD  CONST_35  H10  C07  C08  C09   180.00   0.0  0
 0HD  CONST_36  H16  C19  C15  C14     0.00   0.0  0
 0HD  CONST_37  H4   C21  C13  C14   180.00   0.0  0
 0HD  CONST_40  H2   N12  C13  C21     0.00   0.0  0
 0HD  CONST_41  O01  C02  N12  C13     0.00   0.0  0
 0HD  CONST_42  N03  C02  N12  C13   180.00   0.0  0
 0HD  CONST_43  C04  N03  C02  O01     0.00   0.0  0
 0HD  CONST_44  C04  N03  C02  N12   180.00   0.0  0
 0HD  CONST_45  H5   N03  C02  O01   180.00   0.0  0
 0HD  Var_01    C07  C06  C05  C04   -89.84  30.0  2
 0HD  Var_02    C06  C05  C04  N03  -179.44  30.0  3
 0HD  Var_03    C05  C04  N03  C02  -159.67  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
 0HD  plan-1  C10  0.020
 0HD  plan-1  C05  0.020
 0HD  plan-1  C06  0.020
 0HD  plan-1  C07  0.020
 0HD  plan-1  C08  0.020
 0HD  plan-1  C09  0.020
 0HD  plan-1  C11  0.020
 0HD  plan-1  H1   0.020
 0HD  plan-1  H10  0.020
 0HD  plan-1  H11  0.020
 0HD  plan-1  H12  0.020
 0HD  plan-1  H13  0.020
 0HD  plan-2  N12  0.020
 0HD  plan-2  C13  0.020
 0HD  plan-2  C15  0.020
 0HD  plan-2  C20  0.020
 0HD  plan-2  C21  0.020
 0HD  plan-2  C14  0.020
 0HD  plan-2  C16  0.020
 0HD  plan-2  N17  0.020
 0HD  plan-2  N18  0.020
 0HD  plan-2  C19  0.020
 0HD  plan-2  H3   0.020
 0HD  plan-2  H4   0.020
 0HD  plan-2  H14  0.020
 0HD  plan-2  H15  0.020
 0HD  plan-2  H16  0.020
 0HD  plan-3  N12  0.020
 0HD  plan-3  C13  0.020
 0HD  plan-3  O01  0.020
 0HD  plan-3  C02  0.020
 0HD  plan-3  N03  0.020
 0HD  plan-3  C04  0.020
 0HD  plan-3  H2   0.020
 0HD  plan-3  H5   0.020

