# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:16:18 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-(5-chloro-2-methylphenyl)-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yl)-1H-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Cl)cc1n2cc(cc2C(N)=O)c3ncnn4cccc34
#
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
 QUP  QUP  1-(5-chloro-2-methylphenyl)-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yl)-1H-pyrrole-2-carboxamide  ligand  39  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QUP
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
 QUP  CL    CL  CL    0  -0.125  -5.1648  -2.1998   1.1263
 QUP  C19   C   CR6   0  -0.071  -4.2406  -1.1041   0.1540
 QUP  C18   C   CR16  0  -0.202  -2.9241  -0.8418   0.4914
 QUP  C21   C   CR16  0  -0.188  -4.8262  -0.4973  -0.9440
 QUP  C22   C   CR16  0  -0.331  -4.0708   0.3737  -1.7147
 QUP  C23   C   CR6   0   0.125  -2.7427   0.6598  -1.4146
 QUP  C24   C   CH3   0  -0.736  -1.9386   1.5926  -2.2682
 QUP  C17   C   CR6   0   0.262  -2.1982   0.0388  -0.2919
 QUP  N16   N   NR5   0  -0.576  -0.8338   0.2674   0.0453
 QUP  C12   C   CR5   0   0.252  -0.2872   1.4125   0.5835
 QUP  C13   C   C     0   0.461  -1.1229   2.5238   1.0750
 QUP  N15   N   NH2   0  -0.815  -0.4740   3.6870   1.2418
 QUP  O14   O   O     0  -0.469  -2.3104   2.3715   1.3234
 QUP  C11   C   CR15  0  -0.471   1.0725   1.2399   0.6341
 QUP  C25   C   CR15  0  -0.012   0.1496  -0.6085  -0.2391
 QUP  C1    C   CR5   0  -0.000   1.3633  -0.0452   0.1133
 QUP  C2    C   CR6   0   0.170   2.6360  -0.7239  -0.0326
 QUP  N10   N   N     0  -0.457   2.6134  -2.0240  -0.2352
 QUP  C9    C   CR16  0   0.044   3.7939  -2.6640  -0.3609
 QUP  N8    N   N     0  -0.252   4.9844  -2.1585  -0.2993
 QUP  N7    N   N     0  -0.347   5.0077  -0.8340  -0.1073
 QUP  C3    C   CR56  0   0.432   3.8725  -0.0374   0.0258
 QUP  C6    C   CR15  0  -0.041   6.1165  -0.0766  -0.0438
 QUP  C5    C   CR15  0  -0.325   5.7134   1.2371   0.1267
 QUP  C4    C   CR15  0  -0.431   4.3162   1.2712   0.1676
 QUP  H18   H   HCR6  0   0.290  -2.4662  -1.3034   1.3560
 QUP  H21   H   HCR6  0   0.283  -5.8553  -0.7037  -1.2045
 QUP  H22   H   HCR6  0   0.268  -4.5293   0.8376  -2.5787
 QUP  H241  H   HCH3  0   0.255  -1.7582   2.5451  -1.7673
 QUP  H242  H   HCH3  0   0.254  -0.9656   1.1712  -2.5225
 QUP  H243  H   HCH3  0   0.262  -2.4613   1.8110  -3.1974
 QUP  H25   H   HCR5  0   0.305  -0.0677  -1.5609  -0.6944
 QUP  H11   H   HCR5  0   0.268   1.7704   1.9357   1.0695
 QUP  H151  H   HNH2  0   0.414   0.4666   3.8355   0.9205
 QUP  H152  H   HNH2  0   0.408  -0.9715   4.4883   1.5937
 QUP  H9    H   HCR6  0   0.278   3.7524  -3.7334  -0.5245
 QUP  H6    H   HCR5  0   0.295   7.0971  -0.5137  -0.1302
 QUP  H4    H   HCR5  0   0.258   3.7062   2.1519   0.2715
 QUP  H5    H   HCR5  0   0.266   6.3775   2.0826   0.2070

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
 QUP  CL   C19   single    1.732  0.020  1.732
 QUP  C19  C18   aromatic  1.384  0.020  1.384
 QUP  C19  C21   aromatic  1.384  0.020  1.384
 QUP  C18  C17   aromatic  1.384  0.020  1.384
 QUP  C21  C22   aromatic  1.387  0.020  1.387
 QUP  C22  C23   aromatic  1.391  0.020  1.391
 QUP  C23  C24   single    1.498  0.020  1.498
 QUP  C23  C17   aromatic  1.394  0.020  1.394
 QUP  C17  N16   single    1.424  0.020  1.424
 QUP  N16  C12   aromatic  1.378  0.020  1.378
 QUP  N16  C25   aromatic  1.347  0.020  1.347
 QUP  C12  C13   single    1.475  0.020  1.475
 QUP  C12  C11   aromatic  1.372  0.020  1.372
 QUP  C13  N15   single    1.342  0.020  1.342
 QUP  C13  O14   double    1.223  0.020  1.223
 QUP  C11  C1    aromatic  1.417  0.020  1.417
 QUP  C25  C1    aromatic  1.384  0.020  1.384
 QUP  C1   C2    single    1.450  0.020  1.450
 QUP  C2   N10   aromatic  1.316  0.020  1.316
 QUP  C2   C3    aromatic  1.416  0.020  1.416
 QUP  N10  C9    aromatic  1.349  0.020  1.349
 QUP  C9   N8    aromatic  1.295  0.020  1.295
 QUP  N8   N7    aromatic  1.338  0.020  1.338
 QUP  N7   C3    aromatic  1.393  0.020  1.393
 QUP  N7   C6    aromatic  1.344  0.020  1.344
 QUP  C3   C4    aromatic  1.389  0.020  1.389
 QUP  C6   C5    aromatic  1.385  0.020  1.385
 QUP  C5   C4    aromatic  1.398  0.020  1.398
 QUP  C18  H18   single    0.930  0.020  1.080
 QUP  C21  H21   single    0.930  0.020  1.080
 QUP  C22  H22   single    0.930  0.020  1.080
 QUP  C24  H241  single    0.970  0.020  1.090
 QUP  C24  H242  single    0.970  0.020  1.090
 QUP  C24  H243  single    0.970  0.020  1.090
 QUP  C25  H25   single    0.930  0.020  1.080
 QUP  C11  H11   single    0.930  0.020  1.080
 QUP  N15  H151  single    0.860  0.020  1.020
 QUP  N15  H152  single    0.860  0.020  1.020
 QUP  C9   H9    single    0.930  0.020  1.080
 QUP  C6   H6    single    0.930  0.020  1.080
 QUP  C4   H4    single    0.930  0.020  1.080
 QUP  C5   H5    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
 QUP  C21   C19  C18   120.84  3.000
 QUP  C21   C19  CL    119.78  3.000
 QUP  C18   C19  CL    119.38  3.000
 QUP  H18   C18  C17   120.11  3.000
 QUP  H18   C18  C19   121.10  3.000
 QUP  C17   C18  C19   118.78  3.000
 QUP  H21   C21  C22   120.29  3.000
 QUP  H21   C21  C19   120.66  3.000
 QUP  C22   C21  C19   119.05  3.000
 QUP  H22   C22  C23   119.23  3.000
 QUP  H22   C22  C21   118.81  3.000
 QUP  C23   C22  C21   121.96  3.000
 QUP  C17   C23  C24   121.77  3.000
 QUP  C17   C23  C22   117.07  3.000
 QUP  C24   C23  C22   121.16  3.000
 QUP  H243  C24  H242  107.88  3.000
 QUP  H243  C24  H241  107.23  3.000
 QUP  H242  C24  H241  107.27  3.000
 QUP  H243  C24  C23   110.70  3.000
 QUP  H242  C24  C23   111.79  3.000
 QUP  H241  C24  C23   111.76  3.000
 QUP  N16   C17  C23   119.58  3.000
 QUP  N16   C17  C18   118.07  3.000
 QUP  C23   C17  C18   122.30  3.000
 QUP  C25   N16  C12   109.45  3.000
 QUP  C25   N16  C17   123.03  3.000
 QUP  C12   N16  C17   127.29  3.000
 QUP  C11   C12  C13   130.12  3.000
 QUP  C11   C12  N16   107.64  3.000
 QUP  C13   C12  N16   122.10  3.000
 QUP  O14   C13  N15   123.52  3.000
 QUP  O14   C13  C12   121.61  3.000
 QUP  N15   C13  C12   114.86  3.000
 QUP  H152  N15  H151  117.17  3.000
 QUP  H152  N15  C13   119.63  3.000
 QUP  H151  N15  C13   122.73  3.000
 QUP  H11   C11  C1    126.97  3.000
 QUP  H11   C11  C12   125.15  3.000
 QUP  C1    C11  C12   107.71  3.000
 QUP  H25   C25  C1    130.11  3.000
 QUP  H25   C25  N16   121.09  3.000
 QUP  C1    C25  N16   108.77  3.000
 QUP  C2    C1   C25   123.63  3.000
 QUP  C2    C1   C11   129.93  3.000
 QUP  C25   C1   C11   106.43  3.000
 QUP  C3    C2   N10   120.03  3.000
 QUP  C3    C2   C1    122.39  3.000
 QUP  N10   C2   C1    117.58  3.000
 QUP  C9    N10  C2    117.92  3.000
 QUP  H9    C9   N8    115.34  3.000
 QUP  H9    C9   N10   116.70  3.000
 QUP  N8    C9   N10   127.95  3.000
 QUP  N7    N8   C9    114.15  3.000
 QUP  C6    N7   C3    110.20  3.000
 QUP  C6    N7   N8    125.36  3.000
 QUP  C3    N7   N8    124.43  3.000
 QUP  C4    C3   N7    106.75  3.000
 QUP  C4    C3   C2    137.74  3.000
 QUP  N7    C3   C2    115.50  3.000
 QUP  H6    C6   C5    131.30  3.000
 QUP  H6    C6   N7    121.23  3.000
 QUP  C5    C6   N7    107.47  3.000
 QUP  H5    C5   C4    126.46  3.000
 QUP  H5    C5   C6    125.02  3.000
 QUP  C4    C5   C6    108.52  3.000
 QUP  H4    C4   C5    126.09  3.000
 QUP  H4    C4   C3    126.85  3.000
 QUP  C5    C4   C3    107.05  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
 QUP  CONST_01  C23   C17  C18  C19     0.00   0.0  0
 QUP  CONST_02  N16   C17  C18  C19   180.00   0.0  0
 QUP  CONST_03  C23   C22  C21  C19     0.00   0.0  0
 QUP  CONST_04  C22   C21  C19  C18     0.00   0.0  0
 QUP  CONST_05  C22   C23  C17  C18     0.00   0.0  0
 QUP  CONST_08  C17   C18  C19  C21     0.00   0.0  0
 QUP  CONST_09  C17   C23  C22  C21     0.00   0.0  0
 QUP  CONST_10  N16   C17  C23  C22   180.00   0.0  0
 QUP  CONST_13  C11   C12  N16  C17   180.00   0.0  0
 QUP  CONST_14  C1    C25  N16  C17   180.00   0.0  0
 QUP  CONST_15  C1    C11  C12  N16     0.00   0.0  0
 QUP  CONST_16  C11   C1   C25  N16     0.00   0.0  0
 QUP  CONST_17  C2    C1   C25  N16   180.00   0.0  0
 QUP  CONST_18  C1    C25  N16  C12     0.00   0.0  0
 QUP  CONST_19  C25   C1   C11  C12     0.00   0.0  0
 QUP  CONST_20  C2    C1   C11  C12   180.00   0.0  0
 QUP  CONST_21  C25   N16  C12  C11     0.00   0.0  0
 QUP  CONST_26  C9    N10  C2   C1    180.00   0.0  0
 QUP  CONST_27  N7    C3   C2   C1    180.00   0.0  0
 QUP  CONST_28  C4    C3   C2   C1      0.00   0.0  0
 QUP  CONST_29  N8    C9   N10  C2      0.00   0.0  0
 QUP  CONST_30  N8    N7   C3   C2      0.00   0.0  0
 QUP  CONST_31  C6    N7   C3   C2    180.00   0.0  0
 QUP  CONST_32  C5    C4   C3   C2    180.00   0.0  0
 QUP  CONST_33  N7    C3   C2   N10     0.00   0.0  0
 QUP  CONST_34  C4    C3   C2   N10   180.00   0.0  0
 QUP  CONST_35  N7    N8   C9   N10     0.00   0.0  0
 QUP  CONST_36  C3    C2   N10  C9      0.00   0.0  0
 QUP  CONST_37  C3    N7   N8   C9      0.00   0.0  0
 QUP  CONST_38  C6    N7   N8   C9    180.00   0.0  0
 QUP  CONST_39  C4    C3   N7   N8    180.00   0.0  0
 QUP  CONST_40  C5    C6   N7   N8    180.00   0.0  0
 QUP  CONST_41  C5    C4   C3   N7      0.00   0.0  0
 QUP  CONST_42  C4    C5   C6   N7      0.00   0.0  0
 QUP  CONST_43  C5    C6   N7   C3      0.00   0.0  0
 QUP  CONST_44  C6    C5   C4   C3      0.00   0.0  0
 QUP  CONST_45  C4    C3   N7   C6      0.00   0.0  0
 QUP  CONST_46  C17   C18  C19  CL    180.00   0.0  0
 QUP  CONST_47  C22   C21  C19  CL    180.00   0.0  0
 QUP  CONST_48  C24   C23  C17  C18   180.00   0.0  0
 QUP  CONST_49  C24   C23  C22  C21   180.00   0.0  0
 QUP  CONST_50  N16   C17  C23  C24     0.00   0.0  0
 QUP  CONST_51  C13   C12  N16  C17     0.00   0.0  0
 QUP  CONST_52  C25   N16  C12  C13   180.00   0.0  0
 QUP  CONST_53  C1    C11  C12  C13   180.00   0.0  0
 QUP  CONST_54  H22   C22  C21  C19   180.00   0.0  0
 QUP  CONST_55  H21   C21  C19  C18   180.00   0.0  0
 QUP  CONST_56  H18   C18  C19  C21   180.00   0.0  0
 QUP  CONST_57  H25   C25  N16  C17     0.00   0.0  0
 QUP  CONST_58  H11   C11  C12  N16   180.00   0.0  0
 QUP  CONST_59  H9    C9   N10  C2    180.00   0.0  0
 QUP  CONST_60  H4    C4   C3   C2      0.00   0.0  0
 QUP  CONST_61  H6    C6   N7   N8      0.00   0.0  0
 QUP  CONST_62  H5    C5   C6   N7    180.00   0.0  0
 QUP  CONST_63  H151  N15  C13  C12     0.00   0.0  0
 QUP  CONST_64  H152  N15  C13  C12   180.00   0.0  0
 QUP  Var_01    N15   C13  C12  N16  -163.45  30.0  2
 QUP  Var_02    H241  C24  C23  C22   107.92  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
 QUP  plan-1  C17   0.020
 QUP  plan-1  N16   0.020
 QUP  plan-1  C12   0.020
 QUP  plan-1  C13   0.020
 QUP  plan-1  C11   0.020
 QUP  plan-1  C25   0.020
 QUP  plan-1  C1    0.020
 QUP  plan-1  C2    0.020
 QUP  plan-1  H25   0.020
 QUP  plan-1  H11   0.020
 QUP  plan-2  CL    0.020
 QUP  plan-2  C19   0.020
 QUP  plan-2  C18   0.020
 QUP  plan-2  C21   0.020
 QUP  plan-2  C22   0.020
 QUP  plan-2  C23   0.020
 QUP  plan-2  C24   0.020
 QUP  plan-2  C17   0.020
 QUP  plan-2  N16   0.020
 QUP  plan-2  H18   0.020
 QUP  plan-2  H21   0.020
 QUP  plan-2  H22   0.020
 QUP  plan-3  C1    0.020
 QUP  plan-3  C2    0.020
 QUP  plan-3  N10   0.020
 QUP  plan-3  C9    0.020
 QUP  plan-3  N8    0.020
 QUP  plan-3  N7    0.020
 QUP  plan-3  C3    0.020
 QUP  plan-3  C6    0.020
 QUP  plan-3  C5    0.020
 QUP  plan-3  C4    0.020
 QUP  plan-3  H9    0.020
 QUP  plan-3  H6    0.020
 QUP  plan-3  H4    0.020
 QUP  plan-3  H5    0.020
 QUP  plan-4  C12   0.020
 QUP  plan-4  C13   0.020
 QUP  plan-4  N15   0.020
 QUP  plan-4  O14   0.020
 QUP  plan-4  H151  0.020
 QUP  plan-4  H152  0.020

