# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:41:00 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-methyl-1-(piperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2cnc3[nH]ccc3c2n1C4CCNCC4
#
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
 JAK  JAK  2-methyl-1-(piperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine  ligand  36  19  .  2022-07-25  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_JAK
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
 JAK  C1    C  CH3   0  -0.778   1.0354   3.5804   0.0237
 JAK  C2    C  CR5   0   0.417   0.0285   2.4874   0.0213
 JAK  N3    N  N     0  -0.479  -1.2601   2.6708   0.0285
 JAK  C4    C  CR56  0   0.007  -1.8059   1.4107   0.0230
 JAK  C5    C  CR16  0  -0.145  -3.1542   1.0338   0.0267
 JAK  N6    N  N     0  -0.433  -3.5243  -0.2307   0.0206
 JAK  C7    C  CR56  0   0.415  -2.5428  -1.1341   0.0108
 JAK  C8    C  CR56  0   0.011  -1.1443  -0.9154   0.0053
 JAK  C9    C  CR56  0   0.364  -0.7916   0.4439   0.0121
 JAK  N10   N  NR5   0  -0.553   0.3766   1.1579   0.0106
 JAK  C11   C  CH1   0  -0.118   1.7327   0.6293   0.0020
 JAK  C12   C  CH2   0  -0.434   2.0251  -0.1693   1.2713
 JAK  C13   C  CH2   0  -0.300   3.4025  -0.8097   1.1855
 JAK  N14   N  NH1   0  -0.590   3.4914  -1.6186  -0.0159
 JAK  C15   C  CH2   0  -0.300   3.3924  -0.7989  -1.2091
 JAK  C16   C  CH2   0  -0.434   2.0145  -0.1571  -1.2773
 JAK  C17   C  CR15  0  -0.464  -0.5274  -2.2041  -0.0035
 JAK  C18   C  CR15  0  -0.009  -1.5418  -3.1212  -0.0039
 JAK  N19   N  NR15  0  -0.655  -2.7434  -2.4824   0.0049
 JAK  H1    H  HCH3  0   0.265   1.6713   3.5485  -0.8621
 JAK  H1A   H  HCH3  0   0.276   0.5196   4.5372   0.0352
 JAK  H1B   H  HCH3  0   0.264   1.6835   3.5329   0.8999
 JAK  H5    H  HCR6  0   0.256  -3.9342   1.7876   0.0348
 JAK  H11   H  HCH1  0   0.273   2.4021   1.4923   0.0030
 JAK  H12   H  HCH2  0   0.247   1.9734   0.4947   2.1370
 JAK  H12A  H  HCH2  0   0.242   1.2756  -0.9485   1.4178
 JAK  H13   H  HCH2  0   0.194   4.1703  -0.0184   1.2175
 JAK  H13A  H  HCH2  0   0.241   3.5642  -1.4445   2.0582
 JAK  HN14  H  HNH1  0   0.357   4.3694  -2.1210  -0.0217
 JAK  H15   H  HCH2  0   0.194   4.1605  -0.0079  -1.2410
 JAK  H15A  H  HCH2  0   0.241   3.5457  -1.4259  -2.0890
 JAK  H16   H  HCH2  0   0.242   1.2637  -0.9344  -1.4257
 JAK  H16A  H  HCH2  0   0.247   1.9564   0.5157  -2.1357
 JAK  H17   H  HCR5  0   0.246   0.5245  -2.4404  -0.0097
 JAK  H18   H  HCR5  0   0.287  -1.4901  -4.1975  -0.0094
 JAK  H171  H  HNR5  0   0.410  -3.6449  -2.9311   0.0068

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
 JAK  C1   C2    single    1.486  0.020  1.486
 JAK  C1   H1    single    0.970  0.020  1.090
 JAK  C1   H1A   single    0.970  0.020  1.090
 JAK  C1   H1B   single    0.970  0.020  1.090
 JAK  C2   N10   aromatic  1.374  0.020  1.374
 JAK  N3   C2    aromatic  1.302  0.020  1.302
 JAK  N3   C4    aromatic  1.373  0.020  1.373
 JAK  C4   C9    aromatic  1.401  0.020  1.401
 JAK  C5   C4    aromatic  1.400  0.020  1.400
 JAK  C5   N6    aromatic  1.318  0.020  1.318
 JAK  C5   H5    single    0.930  0.020  1.080
 JAK  N6   C7    aromatic  1.334  0.020  1.334
 JAK  C7   C8    aromatic  1.416  0.020  1.416
 JAK  C7   N19   aromatic  1.363  0.020  1.363
 JAK  C8   C17   aromatic  1.429  0.020  1.429
 JAK  C9   C8    aromatic  1.404  0.020  1.404
 JAK  C9   N10   aromatic  1.369  0.020  1.369
 JAK  N10  C11   single    1.455  0.020  1.455
 JAK  C11  C12   single    1.528  0.020  1.528
 JAK  C11  H11   single    0.970  0.020  1.090
 JAK  C12  C13   single    1.521  0.020  1.521
 JAK  C12  H12   single    0.970  0.020  1.090
 JAK  C12  H12A  single    0.970  0.020  1.090
 JAK  C13  H13   single    0.970  0.020  1.090
 JAK  C13  H13A  single    0.970  0.020  1.090
 JAK  N14  C13   single    1.451  0.020  1.451
 JAK  N14  HN14  single    0.890  0.020  1.040
 JAK  C15  N14   single    1.451  0.020  1.451
 JAK  C15  H15   single    0.970  0.020  1.090
 JAK  C15  H15A  single    0.970  0.020  1.090
 JAK  C16  C11   single    1.528  0.020  1.528
 JAK  C16  C15   single    1.522  0.020  1.522
 JAK  C16  H16   single    0.970  0.020  1.090
 JAK  C16  H16A  single    0.970  0.020  1.090
 JAK  C17  C18   aromatic  1.368  0.020  1.368
 JAK  C17  H17   single    0.930  0.020  1.080
 JAK  C18  H18   single    0.930  0.020  1.080
 JAK  N19  C18   aromatic  1.361  0.020  1.361
 JAK  N19  H171  single    0.860  0.020  1.020

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
 JAK  H1B   C1   H1A  108.16  3.000
 JAK  H1B   C1   H1   107.73  3.000
 JAK  H1A   C1   H1   108.11  3.000
 JAK  H1B   C1   C2   111.84  3.000
 JAK  H1A   C1   C2   109.02  3.000
 JAK  H1    C1   C2   111.85  3.000
 JAK  N10   C2   N3   112.78  3.000
 JAK  N3    C2   C1   124.55  3.000
 JAK  N10   C2   C1   122.67  3.000
 JAK  C4    N3   C2   105.32  3.000
 JAK  C9    C4   C5   120.76  3.000
 JAK  C5    C4   N3   129.04  3.000
 JAK  C9    C4   N3   110.20  3.000
 JAK  H5    C5   N6   117.71  3.000
 JAK  H5    C5   C4   120.37  3.000
 JAK  N6    C5   C4   121.93  3.000
 JAK  C7    N6   C5   116.32  3.000
 JAK  N19   C7   C8   107.35  3.000
 JAK  N19   C7   N6   124.17  3.000
 JAK  C8    C7   N6   128.49  3.000
 JAK  C17   C8   C9   139.88  3.000
 JAK  C9    C8   C7   113.43  3.000
 JAK  C17   C8   C7   106.69  3.000
 JAK  N10   C9   C8   135.97  3.000
 JAK  N10   C9   C4   104.95  3.000
 JAK  C8    C9   C4   119.08  3.000
 JAK  C11   N10  C9   127.27  3.000
 JAK  C11   N10  C2   125.97  3.000
 JAK  C9    N10  C2   106.76  3.000
 JAK  H11   C11  C16  107.12  3.000
 JAK  C16   C11  C12  113.04  3.000
 JAK  H11   C11  C12  107.16  3.000
 JAK  C16   C11  N10  111.33  3.000
 JAK  H11   C11  N10  106.50  3.000
 JAK  C12   C11  N10  111.30  3.000
 JAK  H12A  C12  H12  107.18  3.000
 JAK  H12A  C12  C13  109.20  3.000
 JAK  H12   C12  C13  110.09  3.000
 JAK  H12A  C12  C11  110.69  3.000
 JAK  H12   C12  C11  109.37  3.000
 JAK  C13   C12  C11  110.26  3.000
 JAK  H13A  C13  H13  106.91  3.000
 JAK  H13A  C13  N14  109.20  3.000
 JAK  H13   C13  N14  112.42  3.000
 JAK  N14   C13  C12  109.68  3.000
 JAK  H13A  C13  C12  109.50  3.000
 JAK  H13   C13  C12  109.06  3.000
 JAK  HN14  N14  C15  109.58  3.000
 JAK  C15   N14  C13  111.21  3.000
 JAK  HN14  N14  C13  109.56  3.000
 JAK  H15A  C15  H15  106.91  3.000
 JAK  H15A  C15  C16  109.47  3.000
 JAK  H15   C15  C16  109.07  3.000
 JAK  C16   C15  N14  109.69  3.000
 JAK  H15A  C15  N14  109.20  3.000
 JAK  H15   C15  N14  112.42  3.000
 JAK  H16A  C16  H16  107.18  3.000
 JAK  H16A  C16  C15  110.07  3.000
 JAK  H16   C16  C15  109.20  3.000
 JAK  H16A  C16  C11  109.35  3.000
 JAK  H16   C16  C11  110.71  3.000
 JAK  C15   C16  C11  110.28  3.000
 JAK  H17   C17  C18  125.22  3.000
 JAK  H17   C17  C8   128.24  3.000
 JAK  C18   C17  C8   106.54  3.000
 JAK  H18   C18  N19  120.74  3.000
 JAK  N19   C18  C17  109.89  3.000
 JAK  H18   C18  C17  129.37  3.000
 JAK  H171  N19  C18  125.54  3.000
 JAK  H171  N19  C7   124.92  3.000
 JAK  C18   N19  C7   109.53  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
 JAK  CONST_01  C4    C9   N10  C2      0.00   0.0  0
 JAK  CONST_02  C8    C9   N10  C2    180.00   0.0  0
 JAK  CONST_03  C9    C4   N3   C2      0.00   0.0  0
 JAK  CONST_04  C5    C4   N3   C2    180.00   0.0  0
 JAK  CONST_05  C9    N10  C2   N3      0.00   0.0  0
 JAK  CONST_06  C8    C9   C4   N3    180.00   0.0  0
 JAK  CONST_07  N10   C9   C4   N3      0.00   0.0  0
 JAK  CONST_08  N6    C5   C4   N3    180.00   0.0  0
 JAK  CONST_09  N10   C2   N3   C4      0.00   0.0  0
 JAK  CONST_10  C7    C8   C9   C4      0.00   0.0  0
 JAK  CONST_11  C17   C8   C9   C4    180.00   0.0  0
 JAK  CONST_12  C7    N6   C5   C4      0.00   0.0  0
 JAK  CONST_13  C8    C9   C4   C5      0.00   0.0  0
 JAK  CONST_14  N10   C9   C4   C5    180.00   0.0  0
 JAK  CONST_15  C8    C7   N6   C5      0.00   0.0  0
 JAK  CONST_16  N19   C7   N6   C5    180.00   0.0  0
 JAK  CONST_17  C9    C4   C5   N6      0.00   0.0  0
 JAK  CONST_18  C17   C8   C7   N6    180.00   0.0  0
 JAK  CONST_19  C9    C8   C7   N6      0.00   0.0  0
 JAK  CONST_20  C18   N19  C7   N6    180.00   0.0  0
 JAK  CONST_21  C18   C17  C8   C7      0.00   0.0  0
 JAK  CONST_22  N10   C9   C8   C7    180.00   0.0  0
 JAK  CONST_23  C17   C18  N19  C7      0.00   0.0  0
 JAK  CONST_24  C18   N19  C7   C8      0.00   0.0  0
 JAK  CONST_25  N19   C18  C17  C8      0.00   0.0  0
 JAK  CONST_26  N19   C7   C8   C9    180.00   0.0  0
 JAK  CONST_27  C18   C17  C8   C9    180.00   0.0  0
 JAK  CONST_28  C17   C8   C9   N10     0.00   0.0  0
 JAK  CONST_29  N19   C7   C8   C17     0.00   0.0  0
 JAK  CONST_30  C11   N10  C2   N3    180.00   0.0  0
 JAK  CONST_31  C11   N10  C9   C4    180.00   0.0  0
 JAK  CONST_32  C11   N10  C9   C8      0.00   0.0  0
 JAK  CONST_33  C9    N10  C2   C1    180.00   0.0  0
 JAK  CONST_34  C11   N10  C2   C1      0.00   0.0  0
 JAK  CONST_35  C4    N3   C2   C1    180.00   0.0  0
 JAK  CONST_36  H5    C5   C4   N3      0.00   0.0  0
 JAK  CONST_37  H171  N19  C7   N6      0.00   0.0  0
 JAK  CONST_38  H17   C17  C8   C7    180.00   0.0  0
 JAK  CONST_39  H18   C18  N19  C7    180.00   0.0  0
 JAK  Var_01    N14   C13  C12  C11   -55.41  30.0  1
 JAK  Var_02    N14   C15  C16  C11    55.36  30.0  1
 JAK  Var_03    C15   N14  C13  C12    64.71  30.0  1
 JAK  Var_04    C16   C15  N14  C13   -64.68  30.0  1
 JAK  Var_05    H1    C1   C2   N3   -119.35  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JAK  chir_01  C11  N10  C12  C16  negativ

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
 JAK  plan-1  C1    0.020
 JAK  plan-1  C2    0.020
 JAK  plan-1  N3    0.020
 JAK  plan-1  C4    0.020
 JAK  plan-1  C5    0.020
 JAK  plan-1  N6    0.020
 JAK  plan-1  C7    0.020
 JAK  plan-1  C8    0.020
 JAK  plan-1  C9    0.020
 JAK  plan-1  N10   0.020
 JAK  plan-1  C11   0.020
 JAK  plan-1  C17   0.020
 JAK  plan-1  C18   0.020
 JAK  plan-1  N19   0.020
 JAK  plan-1  H5    0.020
 JAK  plan-1  H17   0.020
 JAK  plan-1  H18   0.020
 JAK  plan-1  H171  0.020

