# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:51:06 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-methoxy-N-({6-[1-methyl-4-(methylamino)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-7-yl]pyridin-2-yl}methyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc2[nH]c(cc2c3n(C)cnc13)c4cccc(CNC(=O)COC)n4
#
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
 3SM  3SM  2-methoxy-N-({6-[1-methyl-4-(methylamino)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-7-yl]pyridin-2-yl}methyl)acetamide  ligand  49  28  .  2022-07-22  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_3SM
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
 3SM  C13  C  CR6   0   0.225   2.9712   2.6064  -0.4348
 3SM  C17  C  CH2   0  -0.289   4.3145   1.9221  -0.3882
 3SM  C16  C  CR16  0  -0.344   0.5170   3.7777  -0.5209
 3SM  C15  C  CR16  0  -0.144   1.6460   4.5638  -0.6943
 3SM  C21  C  CH2   0  -0.246   4.7869  -1.7208   0.4544
 3SM  C23  C  CH3   0  -0.400   5.5671  -3.9016   0.6166
 3SM  C11  C  CR6   0   0.214   0.6824   2.4114  -0.3021
 3SM  N1   N  NR5   0  -0.502  -2.1475  -2.8053   0.3620
 3SM  C2   C  CR15  0   0.074  -3.3137  -3.4913   0.5328
 3SM  N3   N  N     0  -0.452  -4.3593  -2.7183   0.5898
 3SM  C4   C  CR56  0  -0.042  -3.8584  -1.4500   0.4487
 3SM  C5   C  CR56  0   0.376  -2.4786  -1.4882   0.3058
 3SM  C6   C  CR56  0  -0.004  -1.7462  -0.2969   0.1490
 3SM  C7   C  CR56  0   0.411  -2.5591   0.8523   0.1578
 3SM  N8   N  NR15  0  -0.746  -1.7396   1.9218  -0.0062
 3SM  C9   C  CR5   0   0.338  -0.4315   1.5008  -0.1097
 3SM  C10  C  CR15  0  -0.449  -0.4068   0.1280  -0.0168
 3SM  N12  N  N     0  -0.498   1.8996   1.8569  -0.2646
 3SM  C14  C  CR16  0  -0.337   2.8990   3.9802  -0.6526
 3SM  N18  N  NH1   0  -0.655   4.1573   0.5239  -0.0948
 3SM  O20  O  O     0  -0.492   6.3553   0.0219  -0.0950
 3SM  O22  O  O2    0  -0.476   5.8620  -2.5794   0.2398
 3SM  N24  N  N     0  -0.517  -3.8881   0.9362   0.3010
 3SM  C25  C  CR6   0   0.446  -4.5486  -0.2011   0.4428
 3SM  N26  N  NH1   0  -0.658  -5.8873  -0.1780   0.5736
 3SM  H35  H  HCH2  0   0.266   4.8191   2.0666  -1.3486
 3SM  H36  H  HCH2  0   0.265   4.9398   2.4127   0.3639
 3SM  H34  H  HCR6  0   0.260  -0.4638   4.2308  -0.5671
 3SM  H33  H  HCR6  0   0.276   1.5429   5.6276  -0.8625
 3SM  H38  H  HCH2  0   0.242   4.4859  -1.7008   1.5136
 3SM  H39  H  HCH2  0   0.228   3.8966  -2.0329  -0.1114
 3SM  H41  H  HCH3  0   0.208   4.7245  -4.3124   0.0483
 3SM  H40  H  HCH3  0   0.238   6.4478  -4.5102   0.4161
 3SM  H42  H  HCH3  0   0.208   5.3241  -3.9805   1.6828
 3SM  H45  H  HCH3  0   0.233  -6.5114   1.6797  -0.1821
 3SM  H44  H  HCH3  0   0.248  -7.6940   0.7875   0.7759
 3SM  H46  H  HCH3  0   0.227  -6.3564   1.6221   1.5746
 3SM  H29  H  HCR5  0   0.285  -3.3212  -4.5689   0.6073
 3SM  H30  H  HNR5  0   0.409  -2.0594   2.8768   0.0002
 3SM  H31  H  HCR5  0   0.248   0.4770  -0.4859  -0.0762
 3SM  H32  H  HCR6  0   0.269   3.7980   4.5675  -0.7847
 3SM  H37  H  HNH1  0   0.404   3.2048   0.2055   0.0225
 3SM  H43  H  HNH1  0   0.398  -6.3473  -1.0484   0.7774
 3SM  H48  H  HCH3  0   0.262  -0.3743  -3.1141  -0.7039
 3SM  H47  H  HCH3  0   0.262  -0.1819  -2.9783   1.0552
 3SM  H49  H  HCH3  0   0.274  -0.8766  -4.4418   0.3495
 3SM  C28  C  CH3   0  -0.535  -0.8182  -3.3608   0.2590
 3SM  C19  C  C     0   0.503   5.1911  -0.3128   0.0514
 3SM  C27  C  CH3   0  -0.512  -6.6410   1.0422   0.6931

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
 3SM  O20  C19  double    1.220  0.020  1.220
 3SM  O22  C21  single    1.392  0.020  1.392
 3SM  O22  C23  single    1.406  0.020  1.406
 3SM  C21  C19  single    1.519  0.020  1.519
 3SM  C19  N18  single    1.338  0.020  1.338
 3SM  C27  N26  single    1.439  0.020  1.439
 3SM  N18  C17  single    1.437  0.020  1.437
 3SM  C17  C13  single    1.508  0.020  1.508
 3SM  N26  C25  single    1.345  0.020  1.345
 3SM  N24  C25  aromatic  1.323  0.020  1.323
 3SM  N24  C7   aromatic  1.339  0.020  1.339
 3SM  C25  C4   aromatic  1.427  0.020  1.427
 3SM  C13  N12  aromatic  1.319  0.020  1.319
 3SM  C13  C14  aromatic  1.393  0.020  1.393
 3SM  N12  C11  aromatic  1.338  0.020  1.338
 3SM  N8   C7   aromatic  1.357  0.020  1.357
 3SM  N8   C9   aromatic  1.378  0.020  1.378
 3SM  C7   C6   aromatic  1.408  0.020  1.408
 3SM  C4   N3   aromatic  1.371  0.020  1.371
 3SM  C4   C5   aromatic  1.388  0.020  1.388
 3SM  C14  C15  aromatic  1.383  0.020  1.383
 3SM  C9   C11  single    1.451  0.020  1.451
 3SM  C9   C10  aromatic  1.376  0.020  1.376
 3SM  C11  C16  aromatic  1.394  0.020  1.394
 3SM  N3   C2   aromatic  1.302  0.020  1.302
 3SM  C6   C5   aromatic  1.407  0.020  1.407
 3SM  C6   C10  aromatic  1.415  0.020  1.415
 3SM  C5   N1   aromatic  1.359  0.020  1.359
 3SM  C15  C16  aromatic  1.387  0.020  1.387
 3SM  C2   N1   aromatic  1.364  0.020  1.364
 3SM  N1   C28  single    1.444  0.020  1.444
 3SM  C17  H35  single    0.970  0.020  1.090
 3SM  C17  H36  single    0.970  0.020  1.090
 3SM  C16  H34  single    0.930  0.020  1.080
 3SM  C15  H33  single    0.930  0.020  1.080
 3SM  C21  H38  single    0.970  0.020  1.090
 3SM  C21  H39  single    0.970  0.020  1.090
 3SM  C23  H41  single    0.970  0.020  1.090
 3SM  C23  H40  single    0.970  0.020  1.090
 3SM  C23  H42  single    0.970  0.020  1.090
 3SM  C27  H45  single    0.970  0.020  1.090
 3SM  C27  H44  single    0.970  0.020  1.090
 3SM  C27  H46  single    0.970  0.020  1.090
 3SM  C2   H29  single    0.930  0.020  1.080
 3SM  N8   H30  single    0.860  0.020  1.020
 3SM  C10  H31  single    0.930  0.020  1.080
 3SM  C14  H32  single    0.930  0.020  1.080
 3SM  N18  H37  single    0.860  0.020  1.020
 3SM  N26  H43  single    0.860  0.020  1.020
 3SM  C28  H48  single    0.970  0.020  1.090
 3SM  C28  H47  single    0.970  0.020  1.090
 3SM  C28  H49  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
 3SM  C14  C13  N12  122.59  3.000
 3SM  C14  C13  C17  119.90  3.000
 3SM  N12  C13  C17  117.51  3.000
 3SM  H36  C17  H35  106.29  3.000
 3SM  H36  C17  N18  111.00  3.000
 3SM  H35  C17  N18  110.98  3.000
 3SM  H36  C17  C13  109.07  3.000
 3SM  H35  C17  C13  108.88  3.000
 3SM  N18  C17  C13  110.50  3.000
 3SM  H34  C16  C11  121.68  3.000
 3SM  H34  C16  C15  119.70  3.000
 3SM  C11  C16  C15  118.61  3.000
 3SM  H33  C15  C14  120.40  3.000
 3SM  H33  C15  C16  119.95  3.000
 3SM  C14  C15  C16  119.65  3.000
 3SM  H39  C21  H38  106.17  3.000
 3SM  H39  C21  O22  111.76  3.000
 3SM  H38  C21  O22  111.74  3.000
 3SM  H39  C21  C19  109.99  3.000
 3SM  H38  C21  C19  108.11  3.000
 3SM  O22  C21  C19  108.98  3.000
 3SM  H42  C23  H40  108.55  3.000
 3SM  H42  C23  H41  107.87  3.000
 3SM  H40  C23  H41  108.46  3.000
 3SM  H42  C23  O22  112.01  3.000
 3SM  H40  C23  O22  107.85  3.000
 3SM  H41  C23  O22  112.00  3.000
 3SM  N12  C11  C9   115.75  3.000
 3SM  C9   C11  C16  123.01  3.000
 3SM  N12  C11  C16  121.24  3.000
 3SM  C28  N1   C5   126.43  3.000
 3SM  C28  N1   C2   127.05  3.000
 3SM  C5   N1   C2   106.52  3.000
 3SM  H29  C2   N3   125.72  3.000
 3SM  H29  C2   N1   121.09  3.000
 3SM  N3   C2   N1   113.18  3.000
 3SM  C4   N3   C2   104.56  3.000
 3SM  C25  C4   C5   120.31  3.000
 3SM  C5   C4   N3   110.39  3.000
 3SM  C25  C4   N3   129.30  3.000
 3SM  C6   C5   C4   120.37  3.000
 3SM  C6   C5   N1   134.29  3.000
 3SM  C4   C5   N1   105.34  3.000
 3SM  C10  C6   C7   107.59  3.000
 3SM  C10  C6   C5   139.45  3.000
 3SM  C7   C6   C5   112.95  3.000
 3SM  N24  C7   N8   124.24  3.000
 3SM  N8   C7   C6   107.09  3.000
 3SM  N24  C7   C6   128.66  3.000
 3SM  H30  N8   C9   126.27  3.000
 3SM  H30  N8   C7   123.69  3.000
 3SM  C9   N8   C7   109.97  3.000
 3SM  C10  C9   N8   108.46  3.000
 3SM  C10  C9   C11  128.39  3.000
 3SM  N8   C9   C11  123.14  3.000
 3SM  H31  C10  C9   125.39  3.000
 3SM  H31  C10  C6   127.72  3.000
 3SM  C9   C10  C6   106.88  3.000
 3SM  C11  N12  C13  120.00  3.000
 3SM  H32  C14  C15  121.34  3.000
 3SM  H32  C14  C13  120.76  3.000
 3SM  C15  C14  C13  117.90  3.000
 3SM  H37  N18  C19  121.22  3.000
 3SM  H37  N18  C17  115.66  3.000
 3SM  C19  N18  C17  123.10  3.000
 3SM  C23  O22  C21  112.12  3.000
 3SM  C25  N24  C7   116.94  3.000
 3SM  N26  C25  N24  119.51  3.000
 3SM  N24  C25  C4   120.76  3.000
 3SM  N26  C25  C4   119.73  3.000
 3SM  H43  N26  C25  117.39  3.000
 3SM  H43  N26  C27  118.53  3.000
 3SM  C25  N26  C27  122.94  3.000
 3SM  H49  C28  H47  108.68  3.000
 3SM  H49  C28  H48  108.73  3.000
 3SM  H47  C28  H48  109.21  3.000
 3SM  H49  C28  N1   109.10  3.000
 3SM  H47  C28  N1   110.53  3.000
 3SM  H48  C28  N1   110.56  3.000
 3SM  O20  C19  N18  123.55  3.000
 3SM  N18  C19  C21  113.77  3.000
 3SM  O20  C19  C21  122.67  3.000
 3SM  H46  C27  H44  108.37  3.000
 3SM  H46  C27  H45  107.83  3.000
 3SM  H44  C27  H45  108.27  3.000
 3SM  H46  C27  N26  112.36  3.000
 3SM  H44  C27  N26  108.37  3.000
 3SM  H45  C27  N26  111.52  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
 3SM  CONST_01  C9   C11  N12  C13   180.00   0.0  0
 3SM  CONST_02  C16  C11  N12  C13     0.00   0.0  0
 3SM  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 3SM  CONST_04  N8   C9   C11  C16     0.00   0.0  0
 3SM  CONST_05  C10  C9   C11  C16   180.00   0.0  0
 3SM  CONST_06  N12  C13  C14  C15     0.00   0.0  0
 3SM  CONST_07  N12  C11  C16  C15     0.00   0.0  0
 3SM  CONST_08  C9   C11  C16  C15   180.00   0.0  0
 3SM  CONST_09  C14  C13  N12  C11     0.00   0.0  0
 3SM  CONST_10  C7   N8   C9   C11   180.00   0.0  0
 3SM  CONST_11  C6   C10  C9   C11   180.00   0.0  0
 3SM  CONST_12  C14  C15  C16  C11     0.00   0.0  0
 3SM  CONST_13  C25  C4   C5   N1    180.00   0.0  0
 3SM  CONST_14  N3   C4   C5   N1      0.00   0.0  0
 3SM  CONST_15  C7   C6   C5   N1    180.00   0.0  0
 3SM  CONST_16  C10  C6   C5   N1      0.00   0.0  0
 3SM  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 3SM  CONST_18  C25  C4   N3   C2    180.00   0.0  0
 3SM  CONST_19  C5   C4   N3   C2      0.00   0.0  0
 3SM  CONST_20  C4   C5   N1   C2      0.00   0.0  0
 3SM  CONST_21  C6   C5   N1   C2    180.00   0.0  0
 3SM  CONST_22  N24  C25  C4   N3    180.00   0.0  0
 3SM  CONST_23  C6   C5   C4   N3    180.00   0.0  0
 3SM  CONST_24  C5   N1   C2   N3      0.00   0.0  0
 3SM  CONST_25  C7   N24  C25  C4      0.00   0.0  0
 3SM  CONST_26  C7   C6   C5   C4      0.00   0.0  0
 3SM  CONST_27  C10  C6   C5   C4    180.00   0.0  0
 3SM  CONST_28  N24  C25  C4   C5      0.00   0.0  0
 3SM  CONST_29  N24  C7   C6   C5      0.00   0.0  0
 3SM  CONST_30  N8   C7   C6   C5    180.00   0.0  0
 3SM  CONST_31  C9   C10  C6   C5    180.00   0.0  0
 3SM  CONST_32  C25  N24  C7   C6      0.00   0.0  0
 3SM  CONST_33  C9   N8   C7   C6      0.00   0.0  0
 3SM  CONST_34  C25  C4   C5   C6      0.00   0.0  0
 3SM  CONST_35  N8   C9   C10  C6      0.00   0.0  0
 3SM  CONST_36  C10  C9   N8   C7      0.00   0.0  0
 3SM  CONST_37  C9   C10  C6   C7      0.00   0.0  0
 3SM  CONST_38  C25  N24  C7   N8    180.00   0.0  0
 3SM  CONST_39  C10  C6   C7   N8      0.00   0.0  0
 3SM  CONST_40  N12  C11  C9   N8    180.00   0.0  0
 3SM  CONST_41  N24  C7   N8   C9    180.00   0.0  0
 3SM  CONST_42  N12  C11  C9   C10     0.00   0.0  0
 3SM  CONST_43  N24  C7   C6   C10   180.00   0.0  0
 3SM  CONST_44  C11  N12  C13  C17   180.00   0.0  0
 3SM  CONST_45  C15  C14  C13  C17   180.00   0.0  0
 3SM  CONST_46  N26  C25  C4   N3      0.00   0.0  0
 3SM  CONST_47  C28  N1   C2   N3    180.00   0.0  0
 3SM  CONST_48  C28  N1   C5   C4    180.00   0.0  0
 3SM  CONST_49  N26  C25  C4   C5    180.00   0.0  0
 3SM  CONST_50  C28  N1   C5   C6      0.00   0.0  0
 3SM  CONST_51  N26  C25  N24  C7    180.00   0.0  0
 3SM  CONST_52  H33  C15  C14  C13   180.00   0.0  0
 3SM  CONST_53  H32  C14  C15  C16   180.00   0.0  0
 3SM  CONST_54  H30  N8   C9   C11     0.00   0.0  0
 3SM  CONST_55  H31  C10  C9   C11     0.00   0.0  0
 3SM  CONST_56  H29  C2   N3   C4    180.00   0.0  0
 3SM  CONST_57  H34  C16  C11  C9      0.00   0.0  0
 3SM  CONST_58  N24  C25  N26  C27     0.00   0.0  0
 3SM  CONST_59  C4   C25  N26  C27   180.00   0.0  0
 3SM  CONST_60  H43  N26  C25  C4      0.00   0.0  0
 3SM  CONST_61  O20  C19  N18  C17     0.00   0.0  0
 3SM  CONST_62  C21  C19  N18  C17   180.00   0.0  0
 3SM  CONST_63  H37  N18  C19  C21     0.00   0.0  0
 3SM  Var_01    N18  C17  C13  N12    -2.61  30.0  3
 3SM  Var_02    H48  C28  N1   C2    118.96  30.0  2
 3SM  Var_03    C19  N18  C17  C13  -177.62  30.0  1
 3SM  Var_04    H45  C27  N26  C25    60.39  30.0  3
 3SM  Var_05    O22  C21  C19  N18   164.56  30.0  1
 3SM  Var_06    H41  C23  O22  C21    60.45  30.0  3
 3SM  Var_07    H38  C21  O22  C23    59.45  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
 3SM  plan-1  C13  0.020
 3SM  plan-1  C17  0.020
 3SM  plan-1  C16  0.020
 3SM  plan-1  C15  0.020
 3SM  plan-1  C11  0.020
 3SM  plan-1  C9   0.020
 3SM  plan-1  N12  0.020
 3SM  plan-1  C14  0.020
 3SM  plan-1  H34  0.020
 3SM  plan-1  H33  0.020
 3SM  plan-1  H32  0.020
 3SM  plan-2  C11  0.020
 3SM  plan-2  N1   0.020
 3SM  plan-2  C2   0.020
 3SM  plan-2  N3   0.020
 3SM  plan-2  C4   0.020
 3SM  plan-2  C5   0.020
 3SM  plan-2  C6   0.020
 3SM  plan-2  C7   0.020
 3SM  plan-2  N8   0.020
 3SM  plan-2  C9   0.020
 3SM  plan-2  C10  0.020
 3SM  plan-2  N24  0.020
 3SM  plan-2  C25  0.020
 3SM  plan-2  N26  0.020
 3SM  plan-2  H29  0.020
 3SM  plan-2  H30  0.020
 3SM  plan-2  H31  0.020
 3SM  plan-2  C28  0.020
 3SM  plan-3  C17  0.020
 3SM  plan-3  C21  0.020
 3SM  plan-3  N18  0.020
 3SM  plan-3  O20  0.020
 3SM  plan-3  H37  0.020
 3SM  plan-3  C19  0.020
 3SM  plan-4  C25  0.020
 3SM  plan-4  N26  0.020
 3SM  plan-4  H43  0.020
 3SM  plan-4  C27  0.020

