# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:04:06 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 6-(2-{3-(aminomethyl)-5-[2-(1H-pyrrolo[2,3-b]pyridin-6-yl)ethyl]phenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(CN)cc(CCc3ccc4cc[nH]c4n3)c2)c1
#
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
 S97  S97  6-(2-{3-(aminomethyl)-5-[2-(1H-pyrrolo[2,3-b]pyridin-6-yl)ethyl]phenyl}ethyl)-4-methylpyridin-2-amine  ligand  56  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S97
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
 S97  C29   C  CH3   0  -0.725  -6.0618   4.3160  -0.4556
 S97  C26   C  CR6   0   0.204  -5.9711   2.8292  -0.2950
 S97  C27   C  CR16  0  -0.433  -4.7794   2.1521  -0.5800
 S97  C25   C  CR16  0  -0.446  -7.0547   2.0870   0.1272
 S97  C24   C  CR6   0   0.439  -6.9222   0.6926   0.2496
 S97  N28   N  NH2   0  -0.839  -7.9614  -0.0679   0.7059
 S97  N23   N  N     0  -0.483  -5.7871   0.0607  -0.0263
 S97  C22   C  CR6   0   0.274  -4.7359   0.7780  -0.4301
 S97  C21   C  CH2   0  -0.490  -3.4699   0.0093  -0.6784
 S97  C20   C  CH2   0  -0.512  -2.8277  -0.4554   0.6361
 S97  C16   C  CR6   0   0.178  -1.5664  -1.2388   0.4016
 S97  C17   C  CR16  0  -0.390  -0.3797  -0.5858   0.0856
 S97  C15   C  CR16  0  -0.405  -1.5667  -2.6298   0.4515
 S97  C14   C  CR6   0   0.135  -0.4125  -3.3648   0.1999
 S97  C18   C  CH2   0  -0.344  -0.4325  -4.8693   0.3079
 S97  N19   N  NH2   0  -0.792   0.3548  -5.5035  -0.7359
 S97  C13   C  CR16  0  -0.375   0.7587  -2.6848  -0.1214
 S97  C12   C  CR6   0   0.174   0.7884  -1.2948  -0.1791
 S97  C11   C  CH2   0  -0.512   2.0699  -0.5619  -0.4621
 S97  C10   C  CH2   0  -0.496   2.8469  -0.2602   0.8292
 S97  C07   C  CR6   0   0.233   4.0955   0.5244   0.5475
 S97  N06   N  N     0  -0.445   5.1689  -0.1616   0.1738
 S97  C05   C  CR56  0   0.445   6.2408   0.5565  -0.1218
 S97  N01   N  NR15  0  -0.666   7.4450   0.0649  -0.5208
 S97  C02   C  CR15  0  -0.007   8.3073   1.1064  -0.7352
 S97  C03   C  CR15  0  -0.445   7.6815   2.2917  -0.4792
 S97  C04   C  CR56  0   0.006   6.3489   1.9656  -0.0815
 S97  C09   C  CR16  0  -0.221   5.2102   2.6632   0.3151
 S97  C08   C  CR16  0  -0.358   4.0827   1.9278   0.6299
 S97  H291  H  HCH3  0   0.253  -5.9974   4.5945  -1.5091
 S97  H292  H  HCH3  0   0.246  -6.9980   4.7081  -0.0613
 S97  H293  H  HCH3  0   0.249  -5.2392   4.8159   0.0568
 S97  H27   H  HCR6  0   0.243  -3.9005   2.6916  -0.9105
 S97  H25   H  HCR6  0   0.255  -7.9960   2.5667   0.3679
 S97  H281  H  HNH2  0   0.387  -8.8900   0.3080   0.6098
 S97  H282  H  HNH2  0   0.379  -7.8985  -1.0561   0.5228
 S97  H211  H  HCH2  0   0.247  -3.6899  -0.8638  -1.2982
 S97  H212  H  HCH2  0   0.245  -2.7599   0.6275  -1.2322
 S97  H201  H  HCH2  0   0.246  -2.6109   0.4201   1.2542
 S97  H202  H  HCH2  0   0.247  -3.5484  -1.0623   1.1881
 S97  H17   H  HCR6  0   0.233  -0.3637   0.4990   0.0403
 S97  H15   H  HCR6  0   0.236  -2.4879  -3.1514   0.6922
 S97  H181  H  HCH2  0   0.238   0.0019  -5.1557   1.2705
 S97  H182  H  HCH2  0   0.213  -1.4786  -5.2026   0.3427
 S97  H13   H  HCR6  0   0.234   1.6596  -3.2492  -0.3327
 S97  H191  H  HNH2  0   0.352   0.3944  -6.4998  -0.5634
 S97  H192  H  HNH2  0   0.342  -0.1140  -5.3930  -1.6263
 S97  H111  H  HCH2  0   0.248   2.7060  -1.1496  -1.1282
 S97  H112  H  HCH2  0   0.248   1.8538   0.3784  -0.9760
 S97  H101  H  HCH2  0   0.248   2.2021   0.2953   1.5142
 S97  H102  H  HCH2  0   0.249   3.1072  -1.2008   1.3200
 S97  H08   H  HCR6  0   0.254   3.1761   2.4276   0.9454
 S97  H01   H  HNR5  0   0.409   7.6691  -0.9099  -0.6355
 S97  H02   H  HCR5  0   0.286   9.3175   0.9179  -1.0603
 S97  H03   H  HCR5  0   0.252   8.1176   3.2736  -0.5681
 S97  H09   H  HCR6  0   0.258   5.2028   3.7442   0.3794

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
 S97  C29  C26   single    1.498  0.020  1.498
 S97  C26  C27   aromatic  1.400  0.020  1.400
 S97  C26  C25   aromatic  1.380  0.020  1.380
 S97  C27  C22   aromatic  1.383  0.020  1.383
 S97  C25  C24   aromatic  1.406  0.020  1.406
 S97  C24  N28   single    1.366  0.020  1.366
 S97  C24  N23   aromatic  1.328  0.020  1.328
 S97  N23  C22   aromatic  1.335  0.020  1.335
 S97  C22  C21   single    1.502  0.020  1.502
 S97  C21  C20   single    1.535  0.020  1.535
 S97  C20  C16   single    1.503  0.020  1.503
 S97  C16  C17   aromatic  1.391  0.020  1.391
 S97  C16  C15   aromatic  1.392  0.020  1.392
 S97  C17  C12   aromatic  1.392  0.020  1.392
 S97  C15  C14   aromatic  1.391  0.020  1.391
 S97  C14  C18   single    1.508  0.020  1.508
 S97  C14  C13   aromatic  1.392  0.020  1.392
 S97  C18  N19   single    1.453  0.020  1.453
 S97  C13  C12   aromatic  1.392  0.020  1.392
 S97  C12  C11   single    1.503  0.020  1.503
 S97  C11  C10   single    1.537  0.020  1.537
 S97  C10  C07   single    1.501  0.020  1.501
 S97  C07  N06   aromatic  1.328  0.020  1.328
 S97  C07  C08   aromatic  1.406  0.020  1.406
 S97  N06  C05   aromatic  1.324  0.020  1.324
 S97  C05  N01   aromatic  1.361  0.020  1.361
 S97  C05  C04   aromatic  1.414  0.020  1.414
 S97  N01  C02   aromatic  1.369  0.020  1.369
 S97  C02  C03   aromatic  1.365  0.020  1.365
 S97  C03  C04   aromatic  1.428  0.020  1.428
 S97  C04  C09   aromatic  1.393  0.020  1.393
 S97  C09  C08   aromatic  1.382  0.020  1.382
 S97  C29  H291  single    0.970  0.020  1.090
 S97  C29  H292  single    0.970  0.020  1.090
 S97  C29  H293  single    0.970  0.020  1.090
 S97  C27  H27   single    0.930  0.020  1.080
 S97  C25  H25   single    0.930  0.020  1.080
 S97  N28  H281  single    0.890  0.020  1.040
 S97  N28  H282  single    0.890  0.020  1.040
 S97  C21  H211  single    0.970  0.020  1.090
 S97  C21  H212  single    0.970  0.020  1.090
 S97  C20  H201  single    0.970  0.020  1.090
 S97  C20  H202  single    0.970  0.020  1.090
 S97  C17  H17   single    0.930  0.020  1.080
 S97  C15  H15   single    0.930  0.020  1.080
 S97  C18  H181  single    0.970  0.020  1.090
 S97  C18  H182  single    0.970  0.020  1.090
 S97  C13  H13   single    0.930  0.020  1.080
 S97  N19  H191  single    0.890  0.020  1.040
 S97  N19  H192  single    0.890  0.020  1.040
 S97  C11  H111  single    0.970  0.020  1.090
 S97  C11  H112  single    0.970  0.020  1.090
 S97  C10  H101  single    0.970  0.020  1.090
 S97  C10  H102  single    0.970  0.020  1.090
 S97  C08  H08   single    0.930  0.020  1.080
 S97  N01  H01   single    0.860  0.020  1.020
 S97  C02  H02   single    0.930  0.020  1.080
 S97  C03  H03   single    0.930  0.020  1.080
 S97  C09  H09   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
 S97  H293  C29  H292  108.26  3.000
 S97  H293  C29  H291  106.98  3.000
 S97  H292  C29  H291  107.96  3.000
 S97  H293  C29  C26   111.03  3.000
 S97  H292  C29  C26   111.75  3.000
 S97  H291  C29  C26   110.68  3.000
 S97  C25   C26  C27   118.08  3.000
 S97  C25   C26  C29   121.28  3.000
 S97  C27   C26  C29   120.64  3.000
 S97  H27   C27  C22   120.17  3.000
 S97  H27   C27  C26   120.80  3.000
 S97  C22   C27  C26   119.03  3.000
 S97  H25   C25  C24   120.10  3.000
 S97  H25   C25  C26   120.81  3.000
 S97  C24   C25  C26   119.09  3.000
 S97  N23   C24  N28   117.05  3.000
 S97  N23   C24  C25   122.29  3.000
 S97  N28   C24  C25   120.63  3.000
 S97  H282  N28  H281  114.00  3.000
 S97  H282  N28  C24   115.98  3.000
 S97  H281  N28  C24   117.52  3.000
 S97  C22   N23  C24   118.69  3.000
 S97  C21   C22  N23   116.02  3.000
 S97  C21   C22  C27   121.14  3.000
 S97  N23   C22  C27   122.81  3.000
 S97  H212  C21  H211  107.18  3.000
 S97  H212  C21  C20   109.49  3.000
 S97  H211  C21  C20   109.14  3.000
 S97  H212  C21  C22   110.01  3.000
 S97  H211  C21  C22   109.45  3.000
 S97  C20   C21  C22   111.47  3.000
 S97  H202  C20  H201  106.87  3.000
 S97  H202  C20  C16   110.06  3.000
 S97  H201  C20  C16   109.83  3.000
 S97  H202  C20  C21   108.96  3.000
 S97  H201  C20  C21   108.94  3.000
 S97  C16   C20  C21   112.04  3.000
 S97  C15   C16  C17   118.53  3.000
 S97  C15   C16  C20   121.00  3.000
 S97  C17   C16  C20   120.44  3.000
 S97  H17   C17  C12   119.25  3.000
 S97  H17   C17  C16   119.42  3.000
 S97  C12   C17  C16   121.34  3.000
 S97  H15   C15  C14   119.36  3.000
 S97  H15   C15  C16   119.22  3.000
 S97  C14   C15  C16   121.42  3.000
 S97  C13   C14  C18   120.99  3.000
 S97  C13   C14  C15   118.79  3.000
 S97  C18   C14  C15   120.20  3.000
 S97  H182  C18  H181  105.71  3.000
 S97  H182  C18  N19   113.97  3.000
 S97  H181  C18  N19   107.61  3.000
 S97  H182  C18  C14   108.51  3.000
 S97  H181  C18  C14   108.59  3.000
 S97  N19   C18  C14   112.13  3.000
 S97  H192  N19  H191  105.99  3.000
 S97  H192  N19  C18   109.47  3.000
 S97  H191  N19  C18   109.18  3.000
 S97  H13   C13  C12   119.63  3.000
 S97  H13   C13  C14   119.34  3.000
 S97  C12   C13  C14   121.04  3.000
 S97  C11   C12  C13   120.87  3.000
 S97  C11   C12  C17   120.19  3.000
 S97  C13   C12  C17   118.88  3.000
 S97  H112  C11  H111  106.92  3.000
 S97  H112  C11  C10   109.04  3.000
 S97  H111  C11  C10   108.87  3.000
 S97  H112  C11  C12   109.84  3.000
 S97  H111  C11  C12   110.42  3.000
 S97  C10   C11  C12   111.63  3.000
 S97  H102  C10  H101  107.26  3.000
 S97  H102  C10  C07   109.64  3.000
 S97  H101  C10  C07   110.05  3.000
 S97  H102  C10  C11   109.21  3.000
 S97  H101  C10  C11   109.16  3.000
 S97  C07   C10  C11   111.43  3.000
 S97  C08   C07  N06   122.66  3.000
 S97  C08   C07  C10   120.20  3.000
 S97  N06   C07  C10   117.08  3.000
 S97  C05   N06  C07   115.93  3.000
 S97  C04   C05  N01   107.51  3.000
 S97  C04   C05  N06   126.60  3.000
 S97  N01   C05  N06   125.89  3.000
 S97  H01   N01  C02   125.35  3.000
 S97  H01   N01  C05   125.47  3.000
 S97  C02   N01  C05   109.18  3.000
 S97  H02   C02  C03   129.67  3.000
 S97  H02   C02  N01   120.30  3.000
 S97  C03   C02  N01   110.03  3.000
 S97  H03   C03  C04   127.47  3.000
 S97  H03   C03  C02   126.16  3.000
 S97  C04   C03  C02   106.37  3.000
 S97  C09   C04  C03   136.68  3.000
 S97  C09   C04  C05   116.41  3.000
 S97  C03   C04  C05   106.91  3.000
 S97  H09   C09  C08   120.79  3.000
 S97  H09   C09  C04   121.49  3.000
 S97  C08   C09  C04   117.72  3.000
 S97  H08   C08  C09   120.26  3.000
 S97  H08   C08  C07   119.06  3.000
 S97  C09   C08  C07   120.68  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
 S97  CONST_01  N23   C22  C27  C26     0.00   0.0  0
 S97  CONST_02  N23   C24  C25  C26     0.00   0.0  0
 S97  CONST_03  C24   C25  C26  C27     0.00   0.0  0
 S97  CONST_04  C24   N23  C22  C27     0.00   0.0  0
 S97  CONST_05  C22   C27  C26  C25     0.00   0.0  0
 S97  CONST_06  C22   N23  C24  C25     0.00   0.0  0
 S97  CONST_07  C13   C12  C17  C16     0.00   0.0  0
 S97  CONST_08  C13   C14  C15  C16     0.00   0.0  0
 S97  CONST_09  C14   C15  C16  C17     0.00   0.0  0
 S97  CONST_10  C14   C13  C12  C17     0.00   0.0  0
 S97  CONST_11  C12   C17  C16  C15     0.00   0.0  0
 S97  CONST_12  C12   C13  C14  C15     0.00   0.0  0
 S97  CONST_13  N01   C05  N06  C07   180.00   0.0  0
 S97  CONST_14  C04   C05  N06  C07     0.00   0.0  0
 S97  CONST_15  C04   C09  C08  C07     0.00   0.0  0
 S97  CONST_16  C09   C08  C07  N06     0.00   0.0  0
 S97  CONST_17  C02   N01  C05  N06   180.00   0.0  0
 S97  CONST_18  C03   C04  C05  N06   180.00   0.0  0
 S97  CONST_19  C09   C04  C05  N06     0.00   0.0  0
 S97  CONST_20  C08   C07  N06  C05     0.00   0.0  0
 S97  CONST_21  C03   C02  N01  C05     0.00   0.0  0
 S97  CONST_22  C02   C03  C04  C05     0.00   0.0  0
 S97  CONST_23  C08   C09  C04  C05     0.00   0.0  0
 S97  CONST_24  C03   C04  C05  N01     0.00   0.0  0
 S97  CONST_25  C09   C04  C05  N01   180.00   0.0  0
 S97  CONST_26  C04   C03  C02  N01     0.00   0.0  0
 S97  CONST_27  C04   C05  N01  C02     0.00   0.0  0
 S97  CONST_28  C09   C04  C03  C02   180.00   0.0  0
 S97  CONST_29  C08   C09  C04  C03   180.00   0.0  0
 S97  CONST_30  C22   C27  C26  C29   180.00   0.0  0
 S97  CONST_31  C24   C25  C26  C29   180.00   0.0  0
 S97  CONST_32  C21   C22  C27  C26   180.00   0.0  0
 S97  CONST_33  N28   C24  C25  C26   180.00   0.0  0
 S97  CONST_34  C21   C22  N23  C24   180.00   0.0  0
 S97  CONST_35  C22   N23  C24  N28   180.00   0.0  0
 S97  CONST_36  C12   C17  C16  C20   180.00   0.0  0
 S97  CONST_37  C14   C15  C16  C20   180.00   0.0  0
 S97  CONST_38  C11   C12  C17  C16   180.00   0.0  0
 S97  CONST_39  C18   C14  C15  C16   180.00   0.0  0
 S97  CONST_40  C11   C12  C13  C14   180.00   0.0  0
 S97  CONST_41  C12   C13  C14  C18   180.00   0.0  0
 S97  CONST_42  C05   N06  C07  C10   180.00   0.0  0
 S97  CONST_43  C09   C08  C07  C10   180.00   0.0  0
 S97  CONST_44  H25   C25  C26  C27   180.00   0.0  0
 S97  CONST_45  H27   C27  C26  C25   180.00   0.0  0
 S97  CONST_46  H15   C15  C16  C17   180.00   0.0  0
 S97  CONST_47  H13   C13  C12  C17   180.00   0.0  0
 S97  CONST_48  H17   C17  C16  C15   180.00   0.0  0
 S97  CONST_49  H09   C09  C08  C07   180.00   0.0  0
 S97  CONST_50  H08   C08  C07  N06   180.00   0.0  0
 S97  CONST_51  H01   N01  C05  N06     0.00   0.0  0
 S97  CONST_52  H02   C02  N01  C05   180.00   0.0  0
 S97  CONST_53  H03   C03  C04  C05   180.00   0.0  0
 S97  Var_01    C20   C21  C22  C27   105.85  30.0  2
 S97  Var_02    C16   C20  C21  C22   179.41  30.0  3
 S97  Var_03    C17   C16  C20  C21    77.73  30.0  2
 S97  Var_04    C10   C11  C12  C17    88.52  30.0  2
 S97  Var_05    N19   C18  C14  C15   140.80  30.0  2
 S97  Var_06    C07   C10  C11  C12  -177.50  30.0  3
 S97  Var_07    N06   C07  C10  C11   -83.38  30.0  2
 S97  Var_08    H291  C29  C26  C27    67.86  30.0  2
 S97  Var_09    H191  N19  C18  C14   173.86  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
 S97  plan-1  C29   0.020
 S97  plan-1  C26   0.020
 S97  plan-1  C27   0.020
 S97  plan-1  C25   0.020
 S97  plan-1  C24   0.020
 S97  plan-1  N28   0.020
 S97  plan-1  N23   0.020
 S97  plan-1  C22   0.020
 S97  plan-1  C21   0.020
 S97  plan-1  H27   0.020
 S97  plan-1  H25   0.020
 S97  plan-2  C20   0.020
 S97  plan-2  C16   0.020
 S97  plan-2  C17   0.020
 S97  plan-2  C15   0.020
 S97  plan-2  C14   0.020
 S97  plan-2  C18   0.020
 S97  plan-2  C13   0.020
 S97  plan-2  C12   0.020
 S97  plan-2  C11   0.020
 S97  plan-2  H17   0.020
 S97  plan-2  H15   0.020
 S97  plan-2  H13   0.020
 S97  plan-3  C10   0.020
 S97  plan-3  C07   0.020
 S97  plan-3  N06   0.020
 S97  plan-3  C05   0.020
 S97  plan-3  N01   0.020
 S97  plan-3  C02   0.020
 S97  plan-3  C03   0.020
 S97  plan-3  C04   0.020
 S97  plan-3  C09   0.020
 S97  plan-3  C08   0.020
 S97  plan-3  H08   0.020
 S97  plan-3  H01   0.020
 S97  plan-3  H02   0.020
 S97  plan-3  H03   0.020
 S97  plan-3  H09   0.020
 S97  plan-4  C24   0.020
 S97  plan-4  N28   0.020
 S97  plan-4  H281  0.020
 S97  plan-4  H282  0.020

