# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:12:32 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2ncnc(Nc3ccc(cc3Cl)C(N)=N)c2O
#
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
 UQD  UQD  3-chloro-4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide  ligand  41  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UQD
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
 UQD  N    N   N     0  -0.461  23.9902   8.2485  28.3295
 UQD  O    O   OH1   0  -0.623  24.2219   8.4687  24.7764
 UQD  C1   C   CR6   0   0.093  19.6000   6.9995  23.0098
 UQD  C10  C   CR16  0   0.046  22.7570   7.7648  28.4263
 UQD  C11  C   CR6   0   0.448  26.7020   9.3220  27.8074
 UQD  C12  C   CR16  0  -0.309  26.5928   9.2250  29.1972
 UQD  C13  C   CR16  0  -0.276  27.6328   9.6152  30.0236
 UQD  C14  C   CR6   0   0.025  28.8235  10.1173  29.5112
 UQD  C15  C   CR16  0  -0.231  28.9431  10.2258  28.1290
 UQD  C16  C   CR6   0  -0.144  27.9123   9.8334  27.3038
 UQD  C17  C   C     0   0.342  29.9480  10.5635  30.3754
 UQD  C2   C   CR16  0  -0.280  20.3328   8.1823  23.0409
 UQD  C3   C   CR16  0  -0.302  21.2423   8.4368  24.0575
 UQD  C4   C   CR6   0   0.014  21.4374   7.5107  25.0815
 UQD  C5   C   CR16  0  -0.269  20.6898   6.3332  25.0669
 UQD  C6   C   CR16  0  -0.282  19.7924   6.0823  24.0436
 UQD  C7   C   CR6   0   0.139  22.3736   7.7723  26.1923
 UQD  C8   C   CR6   0   0.185  23.6576   8.2327  25.9762
 UQD  C9   C   CR6   0   0.510  24.4573   8.4797  27.1168
 UQD  N1   N   N     0  -0.425  21.9344   7.5157  27.4370
 UQD  N2   N   NH1   0  -0.782  25.7170   8.9593  26.9095
 UQD  N3   N   N     0  -0.653  30.8066  11.3768  29.8906
 UQD  N4   N   NH2   0  -0.826  29.9238  10.0921  31.6563
 UQD  CL   CL  CL    0  -0.115  28.1325   9.9884  25.5864
 UQD  H3   H   HCH3  0   0.253  19.1363   6.1267  21.1063
 UQD  H4   H   HCH3  0   0.247  17.7904   6.1281  22.2333
 UQD  H2   H   HCH3  0   0.246  18.2750   7.6239  21.4306
 UQD  H16  H   HOH1  0   0.489  23.7333   8.0361  24.0638
 UQD  H9   H   HCR6  0   0.258  22.4004   7.5627  29.4299
 UQD  H11  H   HCR6  0   0.304  25.6837   8.8459  29.6316
 UQD  H12  H   HCR6  0   0.263  27.4799   9.5345  31.0917
 UQD  H13  H   HCR6  0   0.278  29.8548  10.6190  27.7009
 UQD  H5   H   HCR6  0   0.255  20.1879   8.9236  22.2645
 UQD  H6   H   HCR6  0   0.273  21.7682   9.3840  24.0647
 UQD  H7   H   HCR6  0   0.256  20.8172   5.6085  25.8606
 UQD  H8   H   HCR6  0   0.253  19.2270   5.1579  24.0499
 UQD  H10  H   HNH1  0   0.408  25.9595   9.0761  25.9367
 UQD  H    H   H     0   0.326  31.5385  11.5818  30.5653
 UQD  H14  H   HNH2  0   0.392  30.7310  10.2777  32.2300
 UQD  H15  H   HNH2  0   0.396  29.5015   9.1961  31.8354
 UQD  C    C   CH3   0  -0.722  18.6463   6.7085  21.8898

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
 UQD  C    C1   single    1.500  0.020  1.500
 UQD  C2   C1   aromatic  1.392  0.020  1.392
 UQD  C2   C3   aromatic  1.388  0.020  1.388
 UQD  C1   C6   aromatic  1.395  0.020  1.395
 UQD  C3   C4   aromatic  1.394  0.020  1.394
 UQD  C6   C5   aromatic  1.384  0.020  1.384
 UQD  O    C8   single    1.347  0.020  1.347
 UQD  C5   C4   aromatic  1.395  0.020  1.395
 UQD  C4   C7   single    1.476  0.020  1.476
 UQD  CL   C16  single    1.738  0.020  1.738
 UQD  C8   C7   aromatic  1.381  0.020  1.381
 UQD  C8   C9   aromatic  1.415  0.020  1.415
 UQD  C7   N1   aromatic  1.345  0.020  1.345
 UQD  N2   C9   single    1.364  0.020  1.364
 UQD  N2   C11  single    1.381  0.020  1.381
 UQD  C9   N    aromatic  1.320  0.020  1.320
 UQD  C16  C11  aromatic  1.407  0.020  1.407
 UQD  C16  C15  aromatic  1.377  0.020  1.377
 UQD  N1   C10  aromatic  1.311  0.020  1.311
 UQD  C11  C12  aromatic  1.397  0.020  1.397
 UQD  C15  C14  aromatic  1.392  0.020  1.392
 UQD  N    C10  aromatic  1.328  0.020  1.328
 UQD  C12  C13  aromatic  1.385  0.020  1.385
 UQD  C14  C13  aromatic  1.390  0.020  1.390
 UQD  C14  C17  single    1.487  0.020  1.487
 UQD  N3   C17  double    1.278  0.020  1.278
 UQD  C17  N4   single    1.365  0.020  1.365
 UQD  C    H3   single    0.970  0.020  1.090
 UQD  C    H4   single    0.970  0.020  1.090
 UQD  C    H2   single    0.970  0.020  1.090
 UQD  O    H16  single    0.850  0.020  0.980
 UQD  C10  H9   single    0.930  0.020  1.080
 UQD  C12  H11  single    0.930  0.020  1.080
 UQD  C13  H12  single    0.930  0.020  1.080
 UQD  C15  H13  single    0.930  0.020  1.080
 UQD  C2   H5   single    0.930  0.020  1.080
 UQD  C3   H6   single    0.930  0.020  1.080
 UQD  C5   H7   single    0.930  0.020  1.080
 UQD  C6   H8   single    0.930  0.020  1.080
 UQD  N2   H10  single    0.860  0.020  1.020
 UQD  N3   H    single    0.890  0.020  1.040
 UQD  N4   H14  single    0.890  0.020  1.040
 UQD  N4   H15  single    0.890  0.020  1.040

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
 UQD  C9   N    C10  117.34  3.000
 UQD  H16  O    C8   111.51  3.000
 UQD  C6   C1   C2   118.00  3.000
 UQD  C6   C1   C    120.90  3.000
 UQD  C2   C1   C    121.10  3.000
 UQD  H9   C10  N1   117.19  3.000
 UQD  H9   C10  N    116.15  3.000
 UQD  N1   C10  N    126.66  3.000
 UQD  N2   C11  C16  118.44  3.000
 UQD  C16  C11  C12  116.64  3.000
 UQD  N2   C11  C12  124.92  3.000
 UQD  H11  C12  C13  119.52  3.000
 UQD  H11  C12  C11  119.46  3.000
 UQD  C13  C12  C11  121.03  3.000
 UQD  H12  C13  C14  120.79  3.000
 UQD  H12  C13  C12  117.52  3.000
 UQD  C14  C13  C12  121.67  3.000
 UQD  C17  C14  C15  119.27  3.000
 UQD  C17  C14  C13  122.82  3.000
 UQD  C15  C14  C13  117.90  3.000
 UQD  H13  C15  C16  119.83  3.000
 UQD  H13  C15  C14  119.61  3.000
 UQD  C16  C15  C14  120.56  3.000
 UQD  CL   C16  C15  118.14  3.000
 UQD  C15  C16  C11  122.20  3.000
 UQD  CL   C16  C11  119.66  3.000
 UQD  N4   C17  N3   125.98  3.000
 UQD  N4   C17  C14  115.36  3.000
 UQD  N3   C17  C14  118.59  3.000
 UQD  H5   C2   C3   119.16  3.000
 UQD  H5   C2   C1   119.68  3.000
 UQD  C3   C2   C1   121.16  3.000
 UQD  H6   C3   C4   120.51  3.000
 UQD  H6   C3   C2   118.91  3.000
 UQD  C4   C3   C2   120.53  3.000
 UQD  C7   C4   C5   119.83  3.000
 UQD  C7   C4   C3   121.58  3.000
 UQD  C5   C4   C3   118.55  3.000
 UQD  H7   C5   C6   119.81  3.000
 UQD  H7   C5   C4   119.63  3.000
 UQD  C6   C5   C4   120.55  3.000
 UQD  H8   C6   C5   119.25  3.000
 UQD  H8   C6   C1   119.55  3.000
 UQD  C5   C6   C1   121.20  3.000
 UQD  N1   C7   C8   120.81  3.000
 UQD  N1   C7   C4   117.11  3.000
 UQD  C8   C7   C4   122.07  3.000
 UQD  C9   C8   C7   117.24  3.000
 UQD  C9   C8   O    116.79  3.000
 UQD  C7   C8   O    125.97  3.000
 UQD  N2   C9   C8   117.46  3.000
 UQD  N2   C9   N    121.88  3.000
 UQD  C8   C9   N    120.67  3.000
 UQD  C7   N1   C10  117.22  3.000
 UQD  H10  N2   C9   114.15  3.000
 UQD  H10  N2   C11  115.13  3.000
 UQD  C9   N2   C11  130.71  3.000
 UQD  H    N3   C17  111.12  3.000
 UQD  H15  N4   H14  113.50  3.000
 UQD  H15  N4   C17  118.80  3.000
 UQD  H14  N4   C17  117.16  3.000
 UQD  H2   C    H4   108.22  3.000
 UQD  H2   C    H3   107.35  3.000
 UQD  H4   C    H3   107.15  3.000
 UQD  H2   C    C1   111.63  3.000
 UQD  H4   C    C1   111.56  3.000
 UQD  H3   C    C1   110.73  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
 UQD  CONST_01  C7   C8   C9   N       0.00   0.0  0
 UQD  CONST_02  C7   N1   C10  N       0.00   0.0  0
 UQD  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 UQD  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 UQD  CONST_05  C4   C7   N1   C10   180.00   0.0  0
 UQD  CONST_06  C8   C7   N1   C10     0.00   0.0  0
 UQD  CONST_07  C8   C9   N    C10     0.00   0.0  0
 UQD  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 UQD  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 UQD  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 UQD  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 UQD  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 UQD  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 UQD  CONST_14  C5   C6   C1   C2      0.00   0.0  0
 UQD  CONST_15  C5   C4   C3   C2      0.00   0.0  0
 UQD  CONST_16  C7   C4   C3   C2    180.00   0.0  0
 UQD  CONST_17  C6   C1   C2   C3      0.00   0.0  0
 UQD  CONST_18  C6   C5   C4   C3      0.00   0.0  0
 UQD  CONST_21  C9   C8   C7   C4    180.00   0.0  0
 UQD  CONST_24  C7   C4   C5   C6    180.00   0.0  0
 UQD  CONST_25  N1   C7   C8   C9      0.00   0.0  0
 UQD  CONST_26  N1   C10  N    C9      0.00   0.0  0
 UQD  CONST_27  O    C8   C9   N     180.00   0.0  0
 UQD  CONST_28  C3   C2   C1   C     180.00   0.0  0
 UQD  CONST_29  C5   C6   C1   C     180.00   0.0  0
 UQD  CONST_30  C4   C7   C8   O       0.00   0.0  0
 UQD  CONST_31  N1   C7   C8   O     180.00   0.0  0
 UQD  CONST_32  N2   C9   N    C10   180.00   0.0  0
 UQD  CONST_33  CL   C16  C11  C12   180.00   0.0  0
 UQD  CONST_34  C17  C14  C13  C12   180.00   0.0  0
 UQD  CONST_35  N2   C11  C12  C13   180.00   0.0  0
 UQD  CONST_36  CL   C16  C15  C14   180.00   0.0  0
 UQD  CONST_37  N2   C11  C16  C15   180.00   0.0  0
 UQD  CONST_38  C17  C14  C15  C16   180.00   0.0  0
 UQD  CONST_39  N2   C9   C8   C7    180.00   0.0  0
 UQD  CONST_40  H6   C3   C2   C1    180.00   0.0  0
 UQD  CONST_41  H7   C5   C6   C1    180.00   0.0  0
 UQD  CONST_42  H13  C15  C16  C11   180.00   0.0  0
 UQD  CONST_43  H12  C13  C12  C11   180.00   0.0  0
 UQD  CONST_44  H11  C12  C13  C14   180.00   0.0  0
 UQD  CONST_45  H8   C6   C1   C2    180.00   0.0  0
 UQD  CONST_46  H5   C2   C3   C4    180.00   0.0  0
 UQD  CONST_47  H9   C10  N1   C7    180.00   0.0  0
 UQD  CONST_48  H    N3   C17  C14   180.00   0.0  0
 UQD  CONST_49  H14  N4   C17  C14   180.00   0.0  0
 UQD  Var_01    C11  N2   C9   N      -1.92  30.0  2
 UQD  Var_02    C9   N2   C11  C12     1.84  30.0  2
 UQD  Var_03    N3   C17  C14  C13  -158.31  30.0  2
 UQD  Var_04    H3   C    C1   C2     93.56  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
 UQD  plan-1  C11  0.020
 UQD  plan-1  C12  0.020
 UQD  plan-1  C13  0.020
 UQD  plan-1  C14  0.020
 UQD  plan-1  C15  0.020
 UQD  plan-1  C16  0.020
 UQD  plan-1  C17  0.020
 UQD  plan-1  N2   0.020
 UQD  plan-1  CL   0.020
 UQD  plan-1  H11  0.020
 UQD  plan-1  H12  0.020
 UQD  plan-1  H13  0.020
 UQD  plan-2  C1   0.020
 UQD  plan-2  C2   0.020
 UQD  plan-2  C3   0.020
 UQD  plan-2  C4   0.020
 UQD  plan-2  C5   0.020
 UQD  plan-2  C6   0.020
 UQD  plan-2  C7   0.020
 UQD  plan-2  H5   0.020
 UQD  plan-2  H6   0.020
 UQD  plan-2  H7   0.020
 UQD  plan-2  H8   0.020
 UQD  plan-2  C    0.020
 UQD  plan-3  N    0.020
 UQD  plan-3  O    0.020
 UQD  plan-3  C10  0.020
 UQD  plan-3  C4   0.020
 UQD  plan-3  C7   0.020
 UQD  plan-3  C8   0.020
 UQD  plan-3  C9   0.020
 UQD  plan-3  N1   0.020
 UQD  plan-3  N2   0.020
 UQD  plan-3  H9   0.020
 UQD  plan-4  C14  0.020
 UQD  plan-4  C17  0.020
 UQD  plan-4  N3   0.020
 UQD  plan-4  N4   0.020
 UQD  plan-4  H    0.020
 UQD  plan-4  H14  0.020
 UQD  plan-4  H15  0.020

