# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 02:04:36 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(CNc2ccc(Cc3c[nH]c4ncc(Cl)cc34)cn2)cn1
#
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
 P31  P31  5-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]-N-{[6-(trifluoromethyl)pyridin-3-yl]methyl}pyridin-2-amine  ligand  44  29  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P31
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
 P31  C1   C   CR6   0  -0.123  -5.1562  -1.7597  -0.6129
 P31  C2   C   CR16  0  -0.063  -6.0351  -1.4887  -1.6683
 P31  N4   N   N     0  -0.419  -6.4207  -0.2652  -1.9878
 P31  C5   C   CR16  0  -0.197  -4.6348  -0.7432   0.1644
 P31  C7   C   CR56  0  -0.015  -5.0289   0.5519  -0.1564
 P31  C8   C   CR56  0   0.482  -5.9217   0.7073  -1.2436
 P31  N9   N   NR15  0  -0.669  -6.1728   2.0346  -1.3804
 P31  C11  C   CR5   0  -0.012  -4.7562   1.8577   0.3575
 P31  C12  C   CH2   0  -0.617  -3.8500   2.2023   1.4946
 P31  C15  C   CR6   0   0.029  -2.4170   1.8216   1.2266
 P31  C16  C   CR16  0  -0.129  -1.7374   0.9134   2.0210
 P31  N18  N   N     0  -0.459  -0.4813   0.5298   1.8267
 P31  C19  C   CR6   0   0.484   0.1946   1.0458   0.8031
 P31  C20  C   CR16  0  -0.391  -0.3956   1.9711  -0.0751
 P31  C22  C   CR16  0  -0.175  -1.7017   2.3480   0.1515
 P31  N24  N   NH1   0  -0.659   1.4951   0.6369   0.6804
 P31  C26  C   CH2   0  -0.342   2.2617   0.8526  -0.5241
 P31  C29  C   CR6   0   0.012   3.6921   0.4563  -0.3007
 P31  C30  C   CR15  0  -0.051  -5.4735   2.7197  -0.4228
 P31  C32  C   CR16  0  -0.106   4.2799  -0.5597  -1.0477
 P31  N34  N   N     0  -0.413   5.5365  -0.9451  -0.8965
 P31  C35  C   CR6   0  -0.012   6.2694  -0.3300   0.0175
 P31  C36  C   CR16  0  -0.303   5.7945   0.6880   0.8272
 P31  C38  C   CR16  0  -0.158   4.4760   1.0814   0.6590
 P31  C40  C   CT    0   1.048   7.6783  -0.8463   0.1214
 P31  F41  F   F     0  -0.300   8.4299  -0.1107   0.9438
 P31  F42  F   F     0  -0.312   7.6996  -2.1038   0.5798
 P31  F43  F   F     0  -0.308   8.2821  -0.8561  -1.0704
 P31  CL1  CL  CL    0  -0.130  -4.7283  -3.4086  -0.2926
 P31  H1   H   HCR6  0   0.276  -6.4291  -2.3030  -2.2650
 P31  H2   H   HCR6  0   0.277  -3.9554  -0.9510   0.9808
 P31  H3   H   HNR5  0   0.413  -6.7743   2.4488  -2.0735
 P31  H4   H   HCH2  0   0.266  -3.9212   3.2750   1.6931
 P31  H5   H   HCH2  0   0.259  -4.1848   1.7023   2.4080
 P31  H6   H   HCR6  0   0.251  -2.2415   0.4624   2.8717
 P31  H7   H   HCR6  0   0.271   0.1484   2.3801  -0.9147
 P31  H8   H   HCR6  0   0.256  -2.1748   3.0555  -0.5201
 P31  H9   H   HNH1  0   0.381   1.7002  -0.2147   1.1814
 P31  H10  H   HCH2  0   0.251   1.8562   0.3057  -1.3842
 P31  H11  H   HCH2  0   0.265   2.2325   1.9131  -0.7834
 P31  H12  H   HCR5  0   0.294  -5.5386   3.7949  -0.3639
 P31  H13  H   HCR6  0   0.275   3.7005  -1.0814  -1.8024
 P31  H14  H   HCR6  0   0.288   6.4182   1.1694   1.5663
 P31  H15  H   HCR6  0   0.281   4.0653   1.8753   1.2699

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
 P31  F43  C40  single    1.336  0.020  1.336
 P31  C40  F42  single    1.339  0.020  1.339
 P31  C40  C35  single    1.504  0.020  1.504
 P31  C40  F41  single    1.335  0.020  1.335
 P31  C35  C36  aromatic  1.385  0.020  1.385
 P31  C35  N34  aromatic  1.323  0.020  1.323
 P31  C36  C38  aromatic  1.386  0.020  1.386
 P31  N34  C32  aromatic  1.323  0.020  1.323
 P31  C38  C29  aromatic  1.388  0.020  1.388
 P31  C32  C29  aromatic  1.391  0.020  1.391
 P31  C29  C26  single    1.501  0.020  1.501
 P31  C26  N24  single    1.444  0.020  1.444
 P31  N18  C16  aromatic  1.328  0.020  1.328
 P31  N18  C19  aromatic  1.331  0.020  1.331
 P31  C16  C15  aromatic  1.385  0.020  1.385
 P31  N24  C19  single    1.369  0.020  1.369
 P31  C19  C20  aromatic  1.406  0.020  1.406
 P31  C15  C12  single    1.507  0.020  1.507
 P31  C15  C22  aromatic  1.394  0.020  1.394
 P31  C12  C11  single    1.494  0.020  1.494
 P31  C20  C22  aromatic  1.378  0.020  1.378
 P31  C11  C7   aromatic  1.430  0.020  1.430
 P31  C11  C30  aromatic  1.366  0.020  1.366
 P31  C5   C7   aromatic  1.391  0.020  1.391
 P31  C5   C1   aromatic  1.382  0.020  1.382
 P31  CL1  C1   single    1.733  0.020  1.733
 P31  C7   C8   aromatic  1.415  0.020  1.415
 P31  C1   C2   aromatic  1.400  0.020  1.400
 P31  C30  N9   aromatic  1.369  0.020  1.369
 P31  C8   N9   aromatic  1.358  0.020  1.358
 P31  C8   N4   aromatic  1.322  0.020  1.322
 P31  C2   N4   aromatic  1.322  0.020  1.322
 P31  C2   H1   single    0.930  0.020  1.080
 P31  C5   H2   single    0.930  0.020  1.080
 P31  N9   H3   single    0.860  0.020  1.020
 P31  C12  H4   single    0.970  0.020  1.090
 P31  C12  H5   single    0.970  0.020  1.090
 P31  C16  H6   single    0.930  0.020  1.080
 P31  C20  H7   single    0.930  0.020  1.080
 P31  C22  H8   single    0.930  0.020  1.080
 P31  N24  H9   single    0.890  0.020  1.040
 P31  C26  H10  single    0.970  0.020  1.090
 P31  C26  H11  single    0.970  0.020  1.090
 P31  C30  H12  single    0.930  0.020  1.080
 P31  C32  H13  single    0.930  0.020  1.080
 P31  C36  H14  single    0.930  0.020  1.080
 P31  C38  H15  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
 P31  CL1  C1   C5   120.18  3.000
 P31  CL1  C1   C2   118.58  3.000
 P31  C5   C1   C2   121.23  3.000
 P31  H1   C2   N4   117.15  3.000
 P31  H1   C2   C1   119.86  3.000
 P31  N4   C2   C1   122.99  3.000
 P31  C8   N4   C2   115.76  3.000
 P31  H2   C5   C7   122.04  3.000
 P31  H2   C5   C1   121.32  3.000
 P31  C7   C5   C1   116.63  3.000
 P31  C11  C7   C8   107.23  3.000
 P31  C8   C7   C5   117.26  3.000
 P31  C11  C7   C5   135.51  3.000
 P31  N9   C8   C7   107.54  3.000
 P31  N9   C8   N4   126.33  3.000
 P31  C7   C8   N4   126.13  3.000
 P31  H3   N9   C30  125.50  3.000
 P31  H3   N9   C8   125.58  3.000
 P31  C30  N9   C8   108.92  3.000
 P31  C30  C11  C12  127.41  3.000
 P31  C30  C11  C7   105.71  3.000
 P31  C12  C11  C7   126.86  3.000
 P31  H5   C12  H4   106.08  3.000
 P31  H5   C12  C15  108.92  3.000
 P31  H4   C12  C15  110.01  3.000
 P31  H5   C12  C11  110.14  3.000
 P31  H4   C12  C11  108.96  3.000
 P31  C15  C12  C11  112.53  3.000
 P31  C22  C15  C16  115.99  3.000
 P31  C22  C15  C12  121.98  3.000
 P31  C16  C15  C12  122.03  3.000
 P31  H6   C16  N18  115.69  3.000
 P31  H6   C16  C15  119.58  3.000
 P31  N18  C16  C15  124.74  3.000
 P31  C19  N18  C16  118.76  3.000
 P31  N24  C19  C20  122.66  3.000
 P31  C20  C19  N18  121.50  3.000
 P31  N24  C19  N18  115.83  3.000
 P31  H7   C20  C22  120.08  3.000
 P31  H7   C20  C19  121.54  3.000
 P31  C22  C20  C19  118.38  3.000
 P31  H8   C22  C20  119.35  3.000
 P31  H8   C22  C15  120.01  3.000
 P31  C20  C22  C15  120.64  3.000
 P31  H9   N24  C26  115.62  3.000
 P31  H9   N24  C19  113.62  3.000
 P31  C26  N24  C19  122.31  3.000
 P31  H11  C26  H10  106.74  3.000
 P31  H11  C26  C29  108.50  3.000
 P31  H10  C26  C29  109.71  3.000
 P31  H11  C26  N24  109.20  3.000
 P31  H10  C26  N24  112.54  3.000
 P31  C29  C26  N24  110.02  3.000
 P31  C38  C29  C32  117.49  3.000
 P31  C32  C29  C26  121.03  3.000
 P31  C38  C29  C26  121.48  3.000
 P31  H12  C30  C11  129.00  3.000
 P31  H12  C30  N9   120.40  3.000
 P31  C11  C30  N9   110.60  3.000
 P31  H13  C32  N34  116.52  3.000
 P31  H13  C32  C29  119.93  3.000
 P31  N34  C32  C29  123.55  3.000
 P31  C35  N34  C32  118.01  3.000
 P31  C40  C35  C36  122.22  3.000
 P31  C36  C35  N34  123.76  3.000
 P31  C40  C35  N34  114.01  3.000
 P31  H14  C36  C38  120.38  3.000
 P31  H14  C36  C35  121.98  3.000
 P31  C38  C36  C35  117.64  3.000
 P31  H15  C38  C36  120.03  3.000
 P31  H15  C38  C29  120.41  3.000
 P31  C36  C38  C29  119.55  3.000
 P31  F43  C40  F42  106.95  3.000
 P31  F42  C40  F41  107.32  3.000
 P31  F43  C40  F41  107.40  3.000
 P31  F41  C40  C35  112.38  3.000
 P31  F42  C40  C35  111.16  3.000
 P31  F43  C40  C35  111.36  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
 P31  CONST_01  C11  C7   C5   C1    180.00   0.0  0
 P31  CONST_02  C8   C7   C5   C1      0.00   0.0  0
 P31  CONST_03  C8   N4   C2   C1      0.00   0.0  0
 P31  CONST_04  C7   C5   C1   C2      0.00   0.0  0
 P31  CONST_05  C7   C8   N4   C2      0.00   0.0  0
 P31  CONST_06  N9   C8   N4   C2    180.00   0.0  0
 P31  CONST_07  C11  C7   C8   N4    180.00   0.0  0
 P31  CONST_08  C5   C7   C8   N4      0.00   0.0  0
 P31  CONST_09  C30  N9   C8   N4    180.00   0.0  0
 P31  CONST_10  C5   C1   C2   N4      0.00   0.0  0
 P31  CONST_11  C30  C11  C7   C5    180.00   0.0  0
 P31  CONST_12  N9   C8   C7   C5    180.00   0.0  0
 P31  CONST_13  N9   C30  C11  C7      0.00   0.0  0
 P31  CONST_14  C30  N9   C8   C7      0.00   0.0  0
 P31  CONST_15  C30  C11  C7   C8      0.00   0.0  0
 P31  CONST_16  C11  C30  N9   C8      0.00   0.0  0
 P31  CONST_17  C11  C7   C8   N9      0.00   0.0  0
 P31  CONST_18  C19  N18  C16  C15     0.00   0.0  0
 P31  CONST_19  C19  C20  C22  C15     0.00   0.0  0
 P31  CONST_20  C20  C19  N18  C16     0.00   0.0  0
 P31  CONST_21  C20  C22  C15  C16     0.00   0.0  0
 P31  CONST_22  C22  C15  C16  N18     0.00   0.0  0
 P31  CONST_23  C22  C20  C19  N18     0.00   0.0  0
 P31  CONST_24  C35  C36  C38  C29     0.00   0.0  0
 P31  CONST_25  C35  N34  C32  C29     0.00   0.0  0
 P31  CONST_26  C36  C35  N34  C32     0.00   0.0  0
 P31  CONST_27  C36  C38  C29  C32     0.00   0.0  0
 P31  CONST_28  C38  C36  C35  N34     0.00   0.0  0
 P31  CONST_29  C38  C29  C32  N34     0.00   0.0  0
 P31  CONST_30  CL1  C1   C2   N4    180.00   0.0  0
 P31  CONST_31  C12  C11  C7   C5      0.00   0.0  0
 P31  CONST_32  CL1  C1   C5   C7    180.00   0.0  0
 P31  CONST_33  C12  C11  C7   C8    180.00   0.0  0
 P31  CONST_34  C12  C11  C30  N9    180.00   0.0  0
 P31  CONST_35  N18  C16  C15  C12   180.00   0.0  0
 P31  CONST_36  C20  C22  C15  C12   180.00   0.0  0
 P31  CONST_37  N24  C19  N18  C16   180.00   0.0  0
 P31  CONST_38  N24  C19  C20  C22   180.00   0.0  0
 P31  CONST_39  C36  C38  C29  C26   180.00   0.0  0
 P31  CONST_40  N34  C32  C29  C26   180.00   0.0  0
 P31  CONST_41  C40  C35  N34  C32   180.00   0.0  0
 P31  CONST_42  C40  C35  C36  C38   180.00   0.0  0
 P31  CONST_43  H2   C5   C1   C2    180.00   0.0  0
 P31  CONST_44  H3   N9   C8   N4      0.00   0.0  0
 P31  CONST_45  H1   C2   C1   C5    180.00   0.0  0
 P31  CONST_46  H12  C30  C11  C7    180.00   0.0  0
 P31  CONST_47  H7   C20  C22  C15   180.00   0.0  0
 P31  CONST_48  H8   C22  C15  C16   180.00   0.0  0
 P31  CONST_49  H6   C16  N18  C19   180.00   0.0  0
 P31  CONST_50  H14  C36  C38  C29   180.00   0.0  0
 P31  CONST_51  H15  C38  C29  C32   180.00   0.0  0
 P31  CONST_52  H13  C32  N34  C35   180.00   0.0  0
 P31  CONST_53  C26  N24  C19  N18   180.00   0.0  0
 P31  Var_01    C15  C12  C11  C7     62.33  30.0  2
 P31  Var_02    C16  C15  C12  C11  -119.00  30.0  2
 P31  Var_03    C29  C26  N24  C19   172.89  30.0  2
 P31  Var_04    C38  C29  C26  N24   -61.00  30.0  2
 P31  Var_05    F43  C40  C35  N34    52.54  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
 P31  plan-1  C12  0.020
 P31  plan-1  C15  0.020
 P31  plan-1  C16  0.020
 P31  plan-1  N18  0.020
 P31  plan-1  C19  0.020
 P31  plan-1  C20  0.020
 P31  plan-1  C22  0.020
 P31  plan-1  N24  0.020
 P31  plan-1  H6   0.020
 P31  plan-1  H7   0.020
 P31  plan-1  H8   0.020
 P31  plan-2  C26  0.020
 P31  plan-2  C29  0.020
 P31  plan-2  C32  0.020
 P31  plan-2  N34  0.020
 P31  plan-2  C35  0.020
 P31  plan-2  C36  0.020
 P31  plan-2  C38  0.020
 P31  plan-2  C40  0.020
 P31  plan-2  H13  0.020
 P31  plan-2  H14  0.020
 P31  plan-2  H15  0.020
 P31  plan-3  C1   0.020
 P31  plan-3  C2   0.020
 P31  plan-3  N4   0.020
 P31  plan-3  C5   0.020
 P31  plan-3  C7   0.020
 P31  plan-3  C8   0.020
 P31  plan-3  N9   0.020
 P31  plan-3  C11  0.020
 P31  plan-3  C12  0.020
 P31  plan-3  C30  0.020
 P31  plan-3  CL1  0.020
 P31  plan-3  H1   0.020
 P31  plan-3  H2   0.020
 P31  plan-3  H3   0.020
 P31  plan-3  H12  0.020
 P31  plan-4  C19  0.020
 P31  plan-4  N24  0.020
 P31  plan-4  C26  0.020
 P31  plan-4  H9   0.020

