# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:12:49 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{4-[3-(6-fluoropyridin-3-yl)-4-oxo-4,5,6,7-tetrahydro-1H-pyrrolo[3,2-c]pyridin-2-yl]pyridin-2-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(ccn1)c2[nH]c3CCNC(=O)c3c2c4ccc(F)nc4
#
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
 J2M  J2M  N-{4-[3-(6-fluoropyridin-3-yl)-4-oxo-4,5,6,7-tetrahydro-1H-pyrrolo[3,2-c]pyridin-2-yl]pyridin-2-yl}acetamide  ligand  43  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J2M
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
 J2M  N14  N  NH1   0  -0.650   4.4159  -2.4554  -0.3555
 J2M  C13  C  CH2   0  -0.284   3.6658  -3.6423  -0.7330
 J2M  C16  C  CR6   0  -0.125   1.6572   1.2078   0.0060
 J2M  C15  C  C     0   0.461   3.8571  -1.2368  -0.1521
 J2M  C19  C  CR16  0  -0.057   2.5196   1.9009   0.8466
 J2M  C21  C  CR6   0   0.572   2.1009   3.8614  -0.1773
 J2M  C22  C  CR16  0  -0.450   1.2126   3.3084  -1.0816
 J2M  C23  C  CR16  0  -0.175   0.9979   1.9469  -0.9768
 J2M  C24  C  C     0   0.497  -5.8891  -0.7798  -0.5043
 J2M  C12  C  CH2   0  -0.525   2.4124  -3.8003   0.1186
 J2M  N1   N  N     0  -0.430  -3.7105   0.7135   0.7711
 J2M  C2   C  CR6   0   0.548  -3.4987  -0.4261   0.1378
 J2M  C3   C  CR16  0  -0.485  -2.2243  -0.9760  -0.0374
 J2M  C4   C  CR6   0   0.145  -1.1215  -0.3079   0.4744
 J2M  C5   C  CR16  0  -0.404  -1.3491   0.8984   1.1472
 J2M  C6   C  CR16  0  -0.053  -2.6467   1.3502   1.2563
 J2M  C7   C  CR5   0   0.337   0.2185  -0.8574   0.3211
 J2M  C8   C  CR5   0   0.009   1.4404  -0.2366   0.1476
 J2M  C9   C  CR5   0  -0.155   2.4055  -1.2766   0.0334
 J2M  C10  C  CR5   0   0.360   1.7392  -2.4783   0.1439
 J2M  N11  N  NR15  0  -0.708   0.4343  -2.2146   0.3105
 J2M  O18  O  O     0  -0.486   4.5252  -0.2108  -0.0909
 J2M  N20  N  N     0  -0.427   2.7368   3.2094   0.7538
 J2M  C25  C  CH3   0  -0.797  -6.7227  -1.8540  -1.1597
 J2M  O26  O  O     0  -0.442  -6.3507   0.2711  -0.1166
 J2M  F27  F  F     0  -0.302   2.3477   5.1736  -0.2380
 J2M  H36  H  HNH1  0   0.397   5.4057  -2.4600  -0.5495
 J2M  H35  H  HCH2  0   0.242   3.3789  -3.5964  -1.7890
 J2M  H34  H  HCH2  0   0.266   4.3179  -4.5044  -0.6093
 J2M  H38  H  HCR6  0   0.265   3.0492   1.3810   1.6347
 J2M  H39  H  HCR6  0   0.291   0.7194   3.9091  -1.8323
 J2M  H40  H  HCR6  0   0.276   0.3213   1.4549  -1.6636
 J2M  H33  H  HCH2  0   0.276   1.7755  -4.5764  -0.3067
 J2M  H32  H  HCH2  0   0.271   2.6732  -4.1105   1.1350
 J2M  H28  H  HCR6  0   0.278  -2.1077  -1.8979  -0.5936
 J2M  H29  H  HCR6  0   0.266  -0.5417   1.4583   1.5958
 J2M  H30  H  HCR6  0   0.265  -2.8490   2.2791   1.7774
 J2M  H31  H  HNR5  0   0.423  -0.2769  -2.9123   0.4703
 J2M  H37  H  HNH1  0   0.423  -4.3244  -2.0259  -0.7959
 J2M  H41  H  HCH3  0   0.268  -7.7251  -1.4830  -1.3540
 J2M  H42  H  HCH3  0   0.267  -6.2792  -2.1844  -2.0993
 J2M  H43  H  HCH3  0   0.275  -6.7937  -2.7262  -0.5076
 J2M  N17  N  NH1   0  -0.722  -4.5698  -1.1344  -0.3926

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
 J2M  N1   C6   aromatic  1.331  0.020  1.331
 J2M  N1   C2   aromatic  1.321  0.020  1.321
 J2M  C25  C24  single    1.509  0.020  1.509
 J2M  N17  C2   single    1.389  0.020  1.389
 J2M  N17  C24  single    1.371  0.020  1.371
 J2M  C6   C5   aromatic  1.378  0.020  1.378
 J2M  C2   C3   aromatic  1.399  0.020  1.399
 J2M  C24  O26  double    1.212  0.020  1.212
 J2M  C5   C4   aromatic  1.400  0.020  1.400
 J2M  C3   C4   aromatic  1.387  0.020  1.387
 J2M  C22  C23  aromatic  1.382  0.020  1.382
 J2M  C22  C21  aromatic  1.383  0.020  1.383
 J2M  C4   C7   single    1.456  0.020  1.456
 J2M  F27  C21  single    1.337  0.020  1.337
 J2M  C23  C16  aromatic  1.395  0.020  1.395
 J2M  C21  N20  aromatic  1.303  0.020  1.303
 J2M  C7   C8   aromatic  1.381  0.020  1.381
 J2M  C7   N11  aromatic  1.374  0.020  1.374
 J2M  C16  C19  aromatic  1.390  0.020  1.390
 J2M  C16  C8   single    1.467  0.020  1.467
 J2M  N20  C19  aromatic  1.330  0.020  1.330
 J2M  C8   C9   aromatic  1.423  0.020  1.423
 J2M  N11  C10  aromatic  1.342  0.020  1.342
 J2M  C9   C10  aromatic  1.378  0.020  1.378
 J2M  C9   C15  single    1.464  0.020  1.464
 J2M  C10  C12  single    1.484  0.020  1.484
 J2M  C15  O18  double    1.226  0.020  1.226
 J2M  C15  N14  single    1.356  0.020  1.356
 J2M  C12  C13  single    1.524  0.020  1.524
 J2M  N14  C13  single    1.454  0.020  1.454
 J2M  N14  H36  single    0.890  0.020  1.040
 J2M  C13  H35  single    0.970  0.020  1.090
 J2M  C13  H34  single    0.970  0.020  1.090
 J2M  C19  H38  single    0.930  0.020  1.080
 J2M  C22  H39  single    0.930  0.020  1.080
 J2M  C23  H40  single    0.930  0.020  1.080
 J2M  C12  H33  single    0.970  0.020  1.090
 J2M  C12  H32  single    0.970  0.020  1.090
 J2M  C3   H28  single    0.930  0.020  1.080
 J2M  C5   H29  single    0.930  0.020  1.080
 J2M  C6   H30  single    0.930  0.020  1.080
 J2M  N11  H31  single    0.860  0.020  1.020
 J2M  N17  H37  single    0.860  0.020  1.020
 J2M  C25  H41  single    0.970  0.020  1.090
 J2M  C25  H42  single    0.970  0.020  1.090
 J2M  C25  H43  single    0.970  0.020  1.090

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
 J2M  H36  N14  C15  115.93  3.000
 J2M  H36  N14  C13  116.92  3.000
 J2M  C15  N14  C13  124.05  3.000
 J2M  H34  C13  H35  107.45  3.000
 J2M  H34  C13  C12  110.33  3.000
 J2M  H35  C13  C12  109.14  3.000
 J2M  H34  C13  N14  107.94  3.000
 J2M  H35  C13  N14  110.56  3.000
 J2M  C12  C13  N14  111.35  3.000
 J2M  C8   C16  C23  121.31  3.000
 J2M  C8   C16  C19  121.62  3.000
 J2M  C23  C16  C19  117.07  3.000
 J2M  O18  C15  C9   123.84  3.000
 J2M  O18  C15  N14  122.35  3.000
 J2M  C9   C15  N14  113.78  3.000
 J2M  H38  C19  N20  116.33  3.000
 J2M  H38  C19  C16  120.30  3.000
 J2M  N20  C19  C16  123.37  3.000
 J2M  F27  C21  N20  115.71  3.000
 J2M  N20  C21  C22  125.51  3.000
 J2M  F27  C21  C22  118.78  3.000
 J2M  H39  C22  C23  121.96  3.000
 J2M  H39  C22  C21  121.68  3.000
 J2M  C23  C22  C21  116.37  3.000
 J2M  H40  C23  C22  119.78  3.000
 J2M  H40  C23  C16  120.10  3.000
 J2M  C22  C23  C16  120.12  3.000
 J2M  O26  C24  C25  123.09  3.000
 J2M  O26  C24  N17  124.40  3.000
 J2M  C25  C24  N17  112.51  3.000
 J2M  H32  C12  H33  107.44  3.000
 J2M  H32  C12  C10  110.17  3.000
 J2M  H33  C12  C10  112.08  3.000
 J2M  H32  C12  C13  110.65  3.000
 J2M  H33  C12  C13  109.65  3.000
 J2M  C10  C12  C13  106.88  3.000
 J2M  C6   N1   C2   117.34  3.000
 J2M  N17  C2   C3   117.01  3.000
 J2M  C3   C2   N1   123.04  3.000
 J2M  N17  C2   N1   119.95  3.000
 J2M  H28  C3   C4   120.92  3.000
 J2M  H28  C3   C2   119.80  3.000
 J2M  C4   C3   C2   119.26  3.000
 J2M  C7   C4   C5   121.69  3.000
 J2M  C7   C4   C3   120.72  3.000
 J2M  C5   C4   C3   117.58  3.000
 J2M  H29  C5   C6   120.07  3.000
 J2M  H29  C5   C4   121.65  3.000
 J2M  C6   C5   C4   118.26  3.000
 J2M  H30  C6   C5   119.64  3.000
 J2M  H30  C6   N1   115.84  3.000
 J2M  C5   C6   N1   124.52  3.000
 J2M  N11  C7   C8   107.69  3.000
 J2M  N11  C7   C4   121.19  3.000
 J2M  C8   C7   C4   131.11  3.000
 J2M  C9   C8   C7   106.34  3.000
 J2M  C9   C8   C16  127.68  3.000
 J2M  C7   C8   C16  125.81  3.000
 J2M  C10  C9   C8   107.63  3.000
 J2M  C10  C9   C15  120.87  3.000
 J2M  C8   C9   C15  131.50  3.000
 J2M  N11  C10  C9   107.98  3.000
 J2M  C9   C10  C12  123.78  3.000
 J2M  N11  C10  C12  128.21  3.000
 J2M  H31  N11  C10  124.71  3.000
 J2M  H31  N11  C7   124.81  3.000
 J2M  C10  N11  C7   110.35  3.000
 J2M  C21  N20  C19  117.56  3.000
 J2M  H43  C25  H42  107.41  3.000
 J2M  H43  C25  H41  108.65  3.000
 J2M  H42  C25  H41  108.95  3.000
 J2M  H43  C25  C24  110.20  3.000
 J2M  H42  C25  C24  111.42  3.000
 J2M  H41  C25  C24  110.13  3.000
 J2M  H37  N17  C2   114.56  3.000
 J2M  H37  N17  C24  115.48  3.000
 J2M  C2   N17  C24  129.88  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
 J2M  CONST_01  C21  C22  C23  C16     0.00   0.0  0
 J2M  CONST_02  C21  N20  C19  C16     0.00   0.0  0
 J2M  CONST_03  C4   C7   C8   C16     0.00   0.0  0
 J2M  CONST_04  N11  C7   C8   C16   180.00   0.0  0
 J2M  CONST_05  C10  C9   C8   C16   180.00   0.0  0
 J2M  CONST_06  C22  C23  C16  C19     0.00   0.0  0
 J2M  CONST_09  C22  C21  N20  C19     0.00   0.0  0
 J2M  CONST_10  C8   C16  C23  C22   180.00   0.0  0
 J2M  CONST_11  N20  C21  C22  C23     0.00   0.0  0
 J2M  CONST_12  N20  C19  C16  C23     0.00   0.0  0
 J2M  CONST_15  C4   C5   C6   N1      0.00   0.0  0
 J2M  CONST_16  C4   C3   C2   N1      0.00   0.0  0
 J2M  CONST_17  C5   C6   N1   C2      0.00   0.0  0
 J2M  CONST_18  C5   C4   C3   C2      0.00   0.0  0
 J2M  CONST_19  C7   C4   C3   C2    180.00   0.0  0
 J2M  CONST_20  C6   N1   C2   C3      0.00   0.0  0
 J2M  CONST_21  C6   C5   C4   C3      0.00   0.0  0
 J2M  CONST_24  C9   C8   C7   C4    180.00   0.0  0
 J2M  CONST_25  C10  N11  C7   C4    180.00   0.0  0
 J2M  CONST_28  C7   C4   C5   C6    180.00   0.0  0
 J2M  CONST_29  C10  C9   C8   C7      0.00   0.0  0
 J2M  CONST_30  C9   C10  N11  C7      0.00   0.0  0
 J2M  CONST_31  C10  N11  C7   C8      0.00   0.0  0
 J2M  CONST_32  N20  C19  C16  C8    180.00   0.0  0
 J2M  CONST_33  N11  C10  C9   C8      0.00   0.0  0
 J2M  CONST_34  N11  C7   C8   C9      0.00   0.0  0
 J2M  CONST_35  C15  C9   C8   C16     0.00   0.0  0
 J2M  CONST_37  F27  C21  N20  C19   180.00   0.0  0
 J2M  CONST_38  F27  C21  C22  C23   180.00   0.0  0
 J2M  CONST_39  N17  C2   C3   C4    180.00   0.0  0
 J2M  CONST_40  N17  C2   N1   C6    180.00   0.0  0
 J2M  CONST_41  O18  C15  N14  C13   180.00   0.0  0
 J2M  CONST_42  H39  C22  C23  C16   180.00   0.0  0
 J2M  CONST_43  H40  C23  C16  C19   180.00   0.0  0
 J2M  CONST_44  H38  C19  N20  C21   180.00   0.0  0
 J2M  CONST_45  H31  N11  C10  C12     0.00   0.0  0
 J2M  CONST_46  H29  C5   C6   N1    180.00   0.0  0
 J2M  CONST_47  H28  C3   C2   N1    180.00   0.0  0
 J2M  CONST_48  H30  C6   N1   C2    180.00   0.0  0
 J2M  CONST_49  H36  N14  C15  C9    180.00   0.0  0
 J2M  CONST_50  N1   C2   N17  C24     0.00   0.0  0
 J2M  CONST_51  C3   C2   N17  C24   180.00   0.0  0
 J2M  CONST_52  H37  N17  C2   N1    180.00   0.0  0
 J2M  CONST_53  C25  C24  N17  C2    180.00   0.0  0
 J2M  CONST_54  O26  C24  N17  C2      0.00   0.0  0
 J2M  Var_01    C8   C9   C15  N14  -173.45  30.0  1
 J2M  Var_02    C10  C12  C13  N14    47.39  30.0  1
 J2M  Var_03    N11  C10  C12  C13   152.93  30.0  1
 J2M  Var_04    C12  C13  N14  C15   -46.26  30.0  1
 J2M  Var_05    H41  C25  C24  N17  -172.16  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
 J2M  plan-1  C16  0.020
 J2M  plan-1  C19  0.020
 J2M  plan-1  C21  0.020
 J2M  plan-1  C22  0.020
 J2M  plan-1  C23  0.020
 J2M  plan-1  C8   0.020
 J2M  plan-1  N20  0.020
 J2M  plan-1  F27  0.020
 J2M  plan-1  H38  0.020
 J2M  plan-1  H39  0.020
 J2M  plan-1  H40  0.020
 J2M  plan-2  N1   0.020
 J2M  plan-2  C2   0.020
 J2M  plan-2  C3   0.020
 J2M  plan-2  C4   0.020
 J2M  plan-2  C5   0.020
 J2M  plan-2  C6   0.020
 J2M  plan-2  C7   0.020
 J2M  plan-2  H28  0.020
 J2M  plan-2  H29  0.020
 J2M  plan-2  H30  0.020
 J2M  plan-2  N17  0.020
 J2M  plan-3  C16  0.020
 J2M  plan-3  C15  0.020
 J2M  plan-3  C12  0.020
 J2M  plan-3  C4   0.020
 J2M  plan-3  C7   0.020
 J2M  plan-3  C8   0.020
 J2M  plan-3  C9   0.020
 J2M  plan-3  C10  0.020
 J2M  plan-3  N11  0.020
 J2M  plan-3  H31  0.020
 J2M  plan-4  C24  0.020
 J2M  plan-4  C2   0.020
 J2M  plan-4  C25  0.020
 J2M  plan-4  O26  0.020
 J2M  plan-4  H37  0.020
 J2M  plan-4  N17  0.020
 J2M  plan-5  N14  0.020
 J2M  plan-5  C13  0.020
 J2M  plan-5  C15  0.020
 J2M  plan-5  C9   0.020
 J2M  plan-5  O18  0.020
 J2M  plan-5  H36  0.020

