# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:45:46 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc2ncnc(Oc3ccc(NC(=O)Nc4cccc(c4)C(F)(F)F)c(F)c3)c12
#
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
 42Q  42Q  1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea  ligand  47  32  .  2022-07-23  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_42Q
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
 42Q  C1    C  CR56  0   0.187  -7.3379   0.1735  -0.7749
 42Q  N2    N  N     0  -0.433  -7.1255  -0.3195  -2.0089
 42Q  C3    C  CR16  0   0.018  -5.8736  -0.5818  -2.2880
 42Q  N4    N  N     0  -0.454  -4.8083  -0.4134  -1.4885
 42Q  C5    C  CR6   0   0.520  -5.0046   0.0617  -0.2863
 42Q  C6    C  CR56  0   0.220  -6.2892   0.3862   0.1411
 42Q  N8    N  NR5   0  -0.507  -6.8175   0.8872   1.2958
 42Q  C9    C  CR15  0  -0.013  -8.1624   0.9901   1.1230
 42Q  C10   C  CR15  0  -0.412  -8.5341   0.5662  -0.1271
 42Q  C11   C  CH3   0  -0.522  -6.1038   1.2484   2.5022
 42Q  O17   O  O2    0  -0.509  -3.9747   0.2520   0.5516
 42Q  C18   C  CR6   0   0.377  -2.7107  -0.1363   0.1688
 42Q  C19   C  CR16  0  -0.324  -1.7847   0.8365  -0.1589
 42Q  C20   C  CR16  0  -0.278  -0.4866   0.4663  -0.4766
 42Q  C21   C  CR6   0   0.180  -0.0994  -0.8693  -0.4583
 42Q  C22   C  CR6   0   0.507  -1.0646  -1.8133  -0.1204
 42Q  C23   C  CR16  0  -0.461  -2.3655  -1.4775   0.1834
 42Q  N27   N  NH1   0  -0.777   1.1927  -1.2917  -0.7871
 42Q  C28   C  C     0   0.735   2.3235  -0.7392  -0.2477
 42Q  N29   N  NH1   0  -0.792   3.4676  -1.3562  -0.6762
 42Q  C30   C  CR6   0   0.402   4.7811  -1.0590  -0.3222
 42Q  O31   O  O     0  -0.492   2.3007   0.2044   0.5201
 42Q  F34   F  F     0  -0.304  -0.7092  -3.1050  -0.0983
 42Q  C35   C  CR16  0  -0.338   5.7529  -2.0141  -0.6394
 42Q  C36   C  CR16  0  -0.228   7.0837  -1.7904  -0.3487
 42Q  C37   C  CR16  0  -0.313   7.4869  -0.6141   0.2705
 42Q  C38   C  CR6   0  -0.169   6.5245   0.3329   0.5799
 42Q  C39   C  CR16  0  -0.343   5.1789   0.1269   0.2896
 42Q  C44   C  CT    0   1.047   6.8941   1.6210   1.2485
 42Q  F45   F  F     0  -0.302   8.2116   1.7590   1.4173
 42Q  F46   F  F     0  -0.315   6.4777   2.6846   0.5450
 42Q  F47   F  F     0  -0.315   6.3326   1.7267   2.4621
 42Q  H3    H  HCR6  0   0.254  -5.6585  -0.9808  -3.2729
 42Q  H9    H  HCR5  0   0.298  -8.7785   1.3679   1.9242
 42Q  H10   H  HCR5  0   0.261  -9.5361   0.5397  -0.5225
 42Q  H11   H  HCH3  0   0.261  -5.3697   2.0260   2.3036
 42Q  H11A  H  HCH3  0   0.263  -6.8218   1.6284   3.2231
 42Q  H11B  H  HCH3  0   0.260  -5.6034   0.3845   2.9341
 42Q  H19   H  HCR6  0   0.280  -2.0697   1.8799  -0.1711
 42Q  H20   H  HCR6  0   0.284   0.2273   1.2281  -0.7532
 42Q  H23   H  HCR6  0   0.299  -3.0815  -2.2467   0.4429
 42Q  HN27  H  HNH1  0   0.414   1.2729  -2.1502  -1.3101
 42Q  HN29  H  HNH1  0   0.418   3.3626  -2.1787  -1.2513
 42Q  H35   H  HCR6  0   0.281   5.4573  -2.9398  -1.1185
 42Q  H36   H  HCR6  0   0.272   7.8179  -2.5425  -0.6035
 42Q  H37   H  HCR6  0   0.271   8.5321  -0.4579   0.4954
 42Q  H39   H  HCR6  0   0.294   4.4491   0.8832   0.5307

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
 42Q  C1   N2    aromatic  1.346  0.020  1.346
 42Q  C1   C6    aromatic  1.409  0.020  1.409
 42Q  C1   C10   aromatic  1.416  0.020  1.416
 42Q  N2   C3    aromatic  1.309  0.020  1.309
 42Q  C3   N4    aromatic  1.343  0.020  1.343
 42Q  N4   C5    aromatic  1.307  0.020  1.307
 42Q  C5   C6    aromatic  1.392  0.020  1.392
 42Q  C5   O17   single    1.341  0.020  1.341
 42Q  C6   N8    aromatic  1.365  0.020  1.365
 42Q  N8   C9    aromatic  1.360  0.020  1.360
 42Q  N8   C11   single    1.448  0.020  1.448
 42Q  C9   C10   aromatic  1.371  0.020  1.371
 42Q  O17  C18   single    1.377  0.020  1.377
 42Q  C18  C19   aromatic  1.383  0.020  1.383
 42Q  C18  C23   aromatic  1.385  0.020  1.385
 42Q  C19  C20   aromatic  1.387  0.020  1.387
 42Q  C20  C21   aromatic  1.391  0.020  1.391
 42Q  C21  C22   aromatic  1.392  0.020  1.392
 42Q  C21  N27   single    1.399  0.020  1.399
 42Q  C22  C23   aromatic  1.378  0.020  1.378
 42Q  C22  F34   single    1.340  0.020  1.340
 42Q  N27  C28   single    1.369  0.020  1.369
 42Q  C28  N29   single    1.369  0.020  1.369
 42Q  C28  O31   double    1.217  0.020  1.217
 42Q  N29  C30   single    1.392  0.020  1.392
 42Q  C30  C35   aromatic  1.399  0.020  1.399
 42Q  C30  C39   aromatic  1.392  0.020  1.392
 42Q  C35  C36   aromatic  1.380  0.020  1.380
 42Q  C36  C37   aromatic  1.389  0.020  1.389
 42Q  C37  C38   aromatic  1.385  0.020  1.385
 42Q  C38  C39   aromatic  1.392  0.020  1.392
 42Q  C38  C44   single    1.498  0.020  1.498
 42Q  C44  F45   single    1.335  0.020  1.335
 42Q  C44  F46   single    1.341  0.020  1.341
 42Q  C44  F47   single    1.341  0.020  1.341
 42Q  C3   H3    single    0.930  0.020  1.080
 42Q  C9   H9    single    0.930  0.020  1.080
 42Q  C10  H10   single    0.930  0.020  1.080
 42Q  C11  H11   single    0.970  0.020  1.090
 42Q  C11  H11A  single    0.970  0.020  1.090
 42Q  C11  H11B  single    0.970  0.020  1.090
 42Q  C19  H19   single    0.930  0.020  1.080
 42Q  C20  H20   single    0.930  0.020  1.080
 42Q  C23  H23   single    0.930  0.020  1.080
 42Q  N27  HN27  single    0.860  0.020  1.020
 42Q  N29  HN29  single    0.860  0.020  1.020
 42Q  C35  H35   single    0.930  0.020  1.080
 42Q  C36  H36   single    0.930  0.020  1.080
 42Q  C37  H37   single    0.930  0.020  1.080
 42Q  C39  H39   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
 42Q  C10   C1   C6    106.83  3.000
 42Q  C10   C1   N2    130.89  3.000
 42Q  C6    C1   N2    122.28  3.000
 42Q  C3    N2   C1    114.83  3.000
 42Q  H3    C3   N4    115.45  3.000
 42Q  H3    C3   N2    117.21  3.000
 42Q  N4    C3   N2    127.35  3.000
 42Q  C5    N4   C3    118.30  3.000
 42Q  O17   C5   C6    118.93  3.000
 42Q  O17   C5   N4    120.71  3.000
 42Q  C6    C5   N4    120.36  3.000
 42Q  N8    C6   C5    134.62  3.000
 42Q  N8    C6   C1    108.50  3.000
 42Q  C5    C6   C1    116.88  3.000
 42Q  C11   N8   C9    125.07  3.000
 42Q  C11   N8   C6    127.28  3.000
 42Q  C9    N8   C6    107.64  3.000
 42Q  H9    C9   C10   129.07  3.000
 42Q  H9    C9   N8    119.79  3.000
 42Q  C10   C9   N8    111.13  3.000
 42Q  H10   C10  C9    126.46  3.000
 42Q  H10   C10  C1    127.65  3.000
 42Q  C9    C10  C1    105.89  3.000
 42Q  H11B  C11  H11A  108.56  3.000
 42Q  H11B  C11  H11   109.26  3.000
 42Q  H11A  C11  H11   108.50  3.000
 42Q  H11B  C11  N8    111.07  3.000
 42Q  H11A  C11  N8    108.34  3.000
 42Q  H11   C11  N8    111.04  3.000
 42Q  C18   O17  C5    119.43  3.000
 42Q  C23   C18  C19   121.13  3.000
 42Q  C23   C18  O17   119.94  3.000
 42Q  C19   C18  O17   118.85  3.000
 42Q  H19   C19  C20   120.11  3.000
 42Q  H19   C19  C18   120.32  3.000
 42Q  C20   C19  C18   119.57  3.000
 42Q  H20   C20  C21   119.78  3.000
 42Q  H20   C20  C19   119.28  3.000
 42Q  C21   C20  C19   120.93  3.000
 42Q  N27   C21  C22   119.53  3.000
 42Q  N27   C21  C20   122.97  3.000
 42Q  C22   C21  C20   117.48  3.000
 42Q  F34   C22  C23   118.81  3.000
 42Q  F34   C22  C21   118.29  3.000
 42Q  C23   C22  C21   122.90  3.000
 42Q  H23   C23  C22   120.28  3.000
 42Q  H23   C23  C18   121.73  3.000
 42Q  C22   C23  C18   117.98  3.000
 42Q  HN27  N27  C28   118.82  3.000
 42Q  HN27  N27  C21   116.91  3.000
 42Q  C28   N27  C21   123.26  3.000
 42Q  O31   C28  N29   124.26  3.000
 42Q  O31   C28  N27   123.09  3.000
 42Q  N29   C28  N27   112.65  3.000
 42Q  HN29  N29  C30   114.65  3.000
 42Q  HN29  N29  C28   117.32  3.000
 42Q  C30   N29  C28   127.78  3.000
 42Q  C39   C30  C35   118.86  3.000
 42Q  C39   C30  N29   124.26  3.000
 42Q  C35   C30  N29   116.86  3.000
 42Q  H35   C35  C36   119.65  3.000
 42Q  H35   C35  C30   119.61  3.000
 42Q  C36   C35  C30   120.75  3.000
 42Q  H36   C36  C37   119.79  3.000
 42Q  H36   C36  C35   119.48  3.000
 42Q  C37   C36  C35   120.73  3.000
 42Q  H37   C37  C38   121.79  3.000
 42Q  H37   C37  C36   119.74  3.000
 42Q  C38   C37  C36   118.48  3.000
 42Q  C44   C38  C39   117.32  3.000
 42Q  C44   C38  C37   121.08  3.000
 42Q  C39   C38  C37   121.59  3.000
 42Q  H39   C39  C38   120.26  3.000
 42Q  H39   C39  C30   120.15  3.000
 42Q  C38   C39  C30   119.59  3.000
 42Q  F47   C44  F46   106.38  3.000
 42Q  F47   C44  F45   106.89  3.000
 42Q  F46   C44  F45   106.89  3.000
 42Q  F47   C44  C38   111.62  3.000
 42Q  F46   C44  C38   111.79  3.000
 42Q  F45   C44  C38   112.88  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
 42Q  CONST_01  N4    C3   N2   C1     0.00   0.0  0
 42Q  CONST_02  N4    C5   C6   C1     0.00   0.0  0
 42Q  CONST_03  C9    N8   C6   C1     0.00   0.0  0
 42Q  CONST_04  N8    C9   C10  C1     0.00   0.0  0
 42Q  CONST_05  C5    C6   C1   N2     0.00   0.0  0
 42Q  CONST_06  N8    C6   C1   N2   180.00   0.0  0
 42Q  CONST_07  C9    C10  C1   N2   180.00   0.0  0
 42Q  CONST_08  C5    N4   C3   N2     0.00   0.0  0
 42Q  CONST_09  C6    C1   N2   C3     0.00   0.0  0
 42Q  CONST_10  C10   C1   N2   C3   180.00   0.0  0
 42Q  CONST_11  C6    C5   N4   C3     0.00   0.0  0
 42Q  CONST_12  N8    C6   C5   N4   180.00   0.0  0
 42Q  CONST_13  C10   C1   C6   C5   180.00   0.0  0
 42Q  CONST_14  C9    N8   C6   C5   180.00   0.0  0
 42Q  CONST_15  C9    C10  C1   C6     0.00   0.0  0
 42Q  CONST_16  C10   C9   N8   C6     0.00   0.0  0
 42Q  CONST_17  C10   C1   C6   N8     0.00   0.0  0
 42Q  CONST_18  C21   C20  C19  C18    0.00   0.0  0
 42Q  CONST_19  C21   C22  C23  C18    0.00   0.0  0
 42Q  CONST_20  C22   C23  C18  C19    0.00   0.0  0
 42Q  CONST_21  C22   C21  C20  C19    0.00   0.0  0
 42Q  CONST_22  C23   C18  C19  C20    0.00   0.0  0
 42Q  CONST_23  C23   C22  C21  C20    0.00   0.0  0
 42Q  CONST_24  C37   C36  C35  C30    0.00   0.0  0
 42Q  CONST_25  C37   C38  C39  C30    0.00   0.0  0
 42Q  CONST_26  C38   C39  C30  C35    0.00   0.0  0
 42Q  CONST_27  C38   C37  C36  C35    0.00   0.0  0
 42Q  CONST_28  C39   C30  C35  C36    0.00   0.0  0
 42Q  CONST_29  C39   C38  C37  C36    0.00   0.0  0
 42Q  CONST_30  O17   C5   C6   C1   180.00   0.0  0
 42Q  CONST_31  C11   N8   C6   C1   180.00   0.0  0
 42Q  CONST_32  O17   C5   N4   C3   180.00   0.0  0
 42Q  CONST_33  C11   N8   C6   C5     0.00   0.0  0
 42Q  CONST_34  O17   C5   C6   N8     0.00   0.0  0
 42Q  CONST_35  C11   N8   C9   C10  180.00   0.0  0
 42Q  CONST_36  C20   C19  C18  O17  180.00   0.0  0
 42Q  CONST_37  C22   C23  C18  O17  180.00   0.0  0
 42Q  CONST_38  F34   C22  C23  C18  180.00   0.0  0
 42Q  CONST_39  N27   C21  C20  C19  180.00   0.0  0
 42Q  CONST_40  F34   C22  C21  C20  180.00   0.0  0
 42Q  CONST_41  N27   C21  C22  C23  180.00   0.0  0
 42Q  CONST_42  C36   C35  C30  N29  180.00   0.0  0
 42Q  CONST_43  C38   C39  C30  N29  180.00   0.0  0
 42Q  CONST_44  C44   C38  C39  C30  180.00   0.0  0
 42Q  CONST_45  C44   C38  C37  C36  180.00   0.0  0
 42Q  CONST_46  H3    C3   N2   C1   180.00   0.0  0
 42Q  CONST_47  H9    C9   C10  C1   180.00   0.0  0
 42Q  CONST_48  H10   C10  C1   N2     0.00   0.0  0
 42Q  CONST_49  H20   C20  C19  C18  180.00   0.0  0
 42Q  CONST_50  H23   C23  C18  C19  180.00   0.0  0
 42Q  CONST_51  H19   C19  C20  C21  180.00   0.0  0
 42Q  CONST_52  H36   C36  C35  C30  180.00   0.0  0
 42Q  CONST_53  H39   C39  C30  C35  180.00   0.0  0
 42Q  CONST_54  H37   C37  C36  C35  180.00   0.0  0
 42Q  CONST_55  H35   C35  C36  C37  180.00   0.0  0
 42Q  CONST_58  C35   C30  N29  C28  180.00   0.0  0
 42Q  CONST_61  HN29  N29  C30  C35    0.00   0.0  0
 42Q  CONST_62  O31   C28  N27  C21    0.00   0.0  0
 42Q  CONST_63  O31   C28  N29  C30    0.00   0.0  0
 42Q  CONST_64  N29   C28  N27  C21  180.00   0.0  0
 42Q  CONST_65  C30   N29  C28  N27  180.00   0.0  0
 42Q  Var_01    C19   C18  O17  C5   107.47  30.0  2
 42Q  Var_02    F45   C44  C38  C37    3.81  30.0  2
 42Q  Var_03    H11   C11  N8   C6    60.05  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
 42Q  plan-1  O17   0.020
 42Q  plan-1  C18   0.020
 42Q  plan-1  C19   0.020
 42Q  plan-1  C20   0.020
 42Q  plan-1  C21   0.020
 42Q  plan-1  C22   0.020
 42Q  plan-1  C23   0.020
 42Q  plan-1  N27   0.020
 42Q  plan-1  F34   0.020
 42Q  plan-1  H19   0.020
 42Q  plan-1  H20   0.020
 42Q  plan-1  H23   0.020
 42Q  plan-2  N29   0.020
 42Q  plan-2  C30   0.020
 42Q  plan-2  C35   0.020
 42Q  plan-2  C36   0.020
 42Q  plan-2  C37   0.020
 42Q  plan-2  C38   0.020
 42Q  plan-2  C39   0.020
 42Q  plan-2  C44   0.020
 42Q  plan-2  H35   0.020
 42Q  plan-2  H36   0.020
 42Q  plan-2  H37   0.020
 42Q  plan-2  H39   0.020
 42Q  plan-3  C1    0.020
 42Q  plan-3  N2    0.020
 42Q  plan-3  C3    0.020
 42Q  plan-3  N4    0.020
 42Q  plan-3  C5    0.020
 42Q  plan-3  C6    0.020
 42Q  plan-3  N8    0.020
 42Q  plan-3  C9    0.020
 42Q  plan-3  C10   0.020
 42Q  plan-3  C11   0.020
 42Q  plan-3  O17   0.020
 42Q  plan-3  H3    0.020
 42Q  plan-3  H9    0.020
 42Q  plan-3  H10   0.020
 42Q  plan-4  C21   0.020
 42Q  plan-4  N27   0.020
 42Q  plan-4  C28   0.020
 42Q  plan-4  N29   0.020
 42Q  plan-4  C30   0.020
 42Q  plan-4  O31   0.020
 42Q  plan-4  HN27  0.020
 42Q  plan-4  HN29  0.020

