# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:28:31 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-methyl-~{N}-[(1~{S})-1-thieno[3,2-b]pyridin-6-ylethyl]pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1cccnc1C)c2cnc3ccsc3c2
#
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
 6S0  6S0  2-methyl-~{N}-[(1~{S})-1-thieno[3,2-b]pyridin-6-ylethyl]pyridin-3-amine  ligand  34  19  .  2022-07-23  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_6S0
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
 6S0  C01  C  CH3   0  -0.658   0.9527  -0.7246   2.3692
 6S0  C02  C  CH1   0  -0.205   0.6195  -0.6236   0.8804
 6S0  N03  N  NH1   0  -0.692   1.5378   0.2261   0.1400
 6S0  C04  C  CR6   0   0.281   2.8447  -0.1299  -0.0937
 6S0  C05  C  CR6   0   0.171   3.7639   0.8413  -0.5596
 6S0  C06  C  CH3   0  -0.767   3.3288   2.2637  -0.7468
 6S0  N07  N  N     0  -0.409   5.0194   0.5425  -0.8490
 6S0  C08  C  CR16  0  -0.122   5.4564  -0.7061  -0.7063
 6S0  C09  C  CR16  0  -0.314   4.6367  -1.7233  -0.2574
 6S0  C10  C  CR16  0  -0.254   3.3178  -1.4338   0.0581
 6S0  C11  C  CR6   0   0.066  -0.7897  -0.1352   0.6418
 6S0  C12  C  CR16  0  -0.217  -1.6572  -0.8392  -0.1726
 6S0  C13  C  CR56  0  -0.208  -2.9346  -0.3263  -0.3524
 6S0  C14  C  CR56  0   0.246  -3.3018   0.8746   0.2806
 6S0  C15  C  CR15  0  -0.180  -4.6538   1.2480  -0.0177
 6S0  C16  C  CR15  0  -0.461  -5.2549   0.3588  -0.8374
 6S0  S17  S  S2    0   0.219  -4.2362  -0.9665  -1.2902
 6S0  N18  N  N     0  -0.424  -2.4597   1.5544   1.0627
 6S0  C19  C  CR16  0  -0.120  -1.2524   1.0537   1.2308
 6S0  H1   H  HCH3  0   0.231   0.8902   0.2449   2.8643
 6S0  H2   H  HCH3  0   0.241   0.2663  -1.4076   2.8699
 6S0  H3   H  HCH3  0   0.245   1.9647  -1.1029   2.5147
 6S0  H4   H  HCH1  0   0.268   0.6825  -1.6270   0.4520
 6S0  H5   H  HNH1  0   0.391   1.3754   1.2139   0.2579
 6S0  H6   H  HCH3  0   0.248   3.0278   2.7277   0.1970
 6S0  H7   H  HCH3  0   0.262   4.1460   2.8527  -1.1568
 6S0  H8   H  HCH3  0   0.249   2.4767   2.3424  -1.4264
 6S0  H9   H  HCR6  0   0.248   6.4936  -0.8932  -0.9591
 6S0  H10  H  HCR6  0   0.262   5.0166  -2.7305  -0.1490
 6S0  H11  H  HCR6  0   0.276   2.6743  -2.2273   0.4142
 6S0  H12  H  HCR6  0   0.281  -1.3486  -1.7624  -0.6479
 6S0  H13  H  HCR5  0   0.277  -5.1304   2.1360   0.3712
 6S0  H14  H  HCR5  0   0.307  -6.2644   0.3975  -1.2173
 6S0  H15  H  HCR6  0   0.261  -0.5950   1.6246   1.8791

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
 6S0  C01  C02  single    1.529  0.020  1.529
 6S0  C19  N18  aromatic  1.318  0.020  1.318
 6S0  C19  C11  aromatic  1.405  0.020  1.405
 6S0  C02  C11  single    1.510  0.020  1.510
 6S0  C02  N03  single    1.454  0.020  1.454
 6S0  N18  C14  aromatic  1.335  0.020  1.335
 6S0  C11  C12  aromatic  1.383  0.020  1.383
 6S0  N03  C04  single    1.375  0.020  1.375
 6S0  C10  C04  aromatic  1.395  0.020  1.395
 6S0  C10  C09  aromatic  1.387  0.020  1.387
 6S0  C04  C05  aromatic  1.416  0.020  1.416
 6S0  C09  C08  aromatic  1.381  0.020  1.381
 6S0  C05  C06  single    1.499  0.020  1.499
 6S0  C05  N07  aromatic  1.323  0.020  1.323
 6S0  C08  N07  aromatic  1.331  0.020  1.331
 6S0  C14  C15  aromatic  1.434  0.020  1.434
 6S0  C14  C13  aromatic  1.406  0.020  1.406
 6S0  C12  C13  aromatic  1.388  0.020  1.388
 6S0  C15  C16  aromatic  1.351  0.020  1.351
 6S0  C13  S17  aromatic  1.727  0.020  1.727
 6S0  C16  S17  aromatic  1.732  0.020  1.732
 6S0  C01  H1   single    0.970  0.020  1.090
 6S0  C01  H2   single    0.970  0.020  1.090
 6S0  C01  H3   single    0.970  0.020  1.090
 6S0  C02  H4   single    0.970  0.020  1.090
 6S0  N03  H5   single    0.890  0.020  1.040
 6S0  C06  H6   single    0.970  0.020  1.090
 6S0  C06  H7   single    0.970  0.020  1.090
 6S0  C06  H8   single    0.970  0.020  1.090
 6S0  C08  H9   single    0.930  0.020  1.080
 6S0  C09  H10  single    0.930  0.020  1.080
 6S0  C10  H11  single    0.930  0.020  1.080
 6S0  C12  H12  single    0.930  0.020  1.080
 6S0  C15  H13  single    0.930  0.020  1.080
 6S0  C16  H14  single    0.930  0.020  1.080
 6S0  C19  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
 6S0  H3   C01  H2   107.81  3.000
 6S0  H3   C01  H1   107.53  3.000
 6S0  H2   C01  H1   108.21  3.000
 6S0  H3   C01  C02  110.80  3.000
 6S0  H2   C01  C02  110.57  3.000
 6S0  H1   C01  C02  111.77  3.000
 6S0  H4   C02  C11  106.78  3.000
 6S0  H4   C02  N03  107.49  3.000
 6S0  C11  C02  N03  108.66  3.000
 6S0  H4   C02  C01  107.97  3.000
 6S0  N03  C02  C01  113.38  3.000
 6S0  C11  C02  C01  112.24  3.000
 6S0  H5   N03  C04  115.27  3.000
 6S0  H5   N03  C02  114.29  3.000
 6S0  C04  N03  C02  122.40  3.000
 6S0  C10  C04  C05  117.17  3.000
 6S0  C05  C04  N03  119.70  3.000
 6S0  C10  C04  N03  123.09  3.000
 6S0  N07  C05  C06  117.55  3.000
 6S0  N07  C05  C04  122.22  3.000
 6S0  C06  C05  C04  120.23  3.000
 6S0  H8   C06  H7   108.21  3.000
 6S0  H8   C06  H6   106.94  3.000
 6S0  H7   C06  H6   107.60  3.000
 6S0  H8   C06  C05  111.86  3.000
 6S0  H7   C06  C05  110.05  3.000
 6S0  H6   C06  C05  112.00  3.000
 6S0  C08  N07  C05  120.02  3.000
 6S0  H9   C08  C09  121.10  3.000
 6S0  H9   C08  N07  116.82  3.000
 6S0  C09  C08  N07  122.08  3.000
 6S0  H10  C09  C10  120.37  3.000
 6S0  H10  C09  C08  120.65  3.000
 6S0  C10  C09  C08  118.98  3.000
 6S0  H11  C10  C09  119.17  3.000
 6S0  H11  C10  C04  121.29  3.000
 6S0  C09  C10  C04  119.53  3.000
 6S0  C19  C11  C12  118.10  3.000
 6S0  C12  C11  C02  120.92  3.000
 6S0  C19  C11  C02  120.97  3.000
 6S0  H12  C12  C13  121.35  3.000
 6S0  H12  C12  C11  120.90  3.000
 6S0  C13  C12  C11  117.75  3.000
 6S0  S17  C13  C14  111.35  3.000
 6S0  S17  C13  C12  128.81  3.000
 6S0  C14  C13  C12  119.83  3.000
 6S0  N18  C14  C15  125.72  3.000
 6S0  C15  C14  C13  112.02  3.000
 6S0  N18  C14  C13  122.26  3.000
 6S0  H13  C15  C16  124.29  3.000
 6S0  H13  C15  C14  123.72  3.000
 6S0  C16  C15  C14  111.99  3.000
 6S0  H14  C16  S17  119.05  3.000
 6S0  H14  C16  C15  127.32  3.000
 6S0  S17  C16  C15  113.63  3.000
 6S0  C16  S17  C13   91.01  3.000
 6S0  C19  N18  C14  117.32  3.000
 6S0  H15  C19  N18  115.54  3.000
 6S0  H15  C19  C11  119.73  3.000
 6S0  N18  C19  C11  124.73  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
 6S0  CONST_01  C08  C09  C10  C04    0.00   0.0  0
 6S0  CONST_02  C08  N07  C05  C04    0.00   0.0  0
 6S0  CONST_03  C09  C10  C04  C05    0.00   0.0  0
 6S0  CONST_04  C09  C08  N07  C05    0.00   0.0  0
 6S0  CONST_05  C10  C04  C05  N07    0.00   0.0  0
 6S0  CONST_06  C10  C09  C08  N07    0.00   0.0  0
 6S0  CONST_07  C14  N18  C19  C11    0.00   0.0  0
 6S0  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 6S0  CONST_09  S17  C13  C12  C11  180.00   0.0  0
 6S0  CONST_10  N18  C19  C11  C12    0.00   0.0  0
 6S0  CONST_11  N18  C14  C13  C12    0.00   0.0  0
 6S0  CONST_12  C15  C14  C13  C12  180.00   0.0  0
 6S0  CONST_13  C16  S17  C13  C12  180.00   0.0  0
 6S0  CONST_14  C19  N18  C14  C13    0.00   0.0  0
 6S0  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 6S0  CONST_16  C19  C11  C12  C13    0.00   0.0  0
 6S0  CONST_17  C15  C16  S17  C13    0.00   0.0  0
 6S0  CONST_18  S17  C16  C15  C14    0.00   0.0  0
 6S0  CONST_19  C16  S17  C13  C14    0.00   0.0  0
 6S0  CONST_20  C19  N18  C14  C15  180.00   0.0  0
 6S0  CONST_21  S17  C13  C14  C15    0.00   0.0  0
 6S0  CONST_22  N18  C14  C15  C16  180.00   0.0  0
 6S0  CONST_23  N18  C14  C13  S17  180.00   0.0  0
 6S0  CONST_24  N18  C19  C11  C02  180.00   0.0  0
 6S0  CONST_25  C13  C12  C11  C02  180.00   0.0  0
 6S0  CONST_26  C09  C10  C04  N03  180.00   0.0  0
 6S0  CONST_27  N07  C05  C04  N03  180.00   0.0  0
 6S0  CONST_28  C10  C04  C05  C06  180.00   0.0  0
 6S0  CONST_29  C08  N07  C05  C06  180.00   0.0  0
 6S0  CONST_30  H10  C09  C10  C04  180.00   0.0  0
 6S0  CONST_31  H11  C10  C04  C05  180.00   0.0  0
 6S0  CONST_32  H9   C08  N07  C05  180.00   0.0  0
 6S0  CONST_33  H15  C19  C11  C12  180.00   0.0  0
 6S0  CONST_34  H13  C15  C14  C13  180.00   0.0  0
 6S0  CONST_35  H14  C16  S17  C13  180.00   0.0  0
 6S0  CONST_36  H12  C12  C13  C14  180.00   0.0  0
 6S0  CONST_38  C05  C04  N03  C02  180.00   0.0  0
 6S0  Var_01    H6   C06  C05  C04   63.29  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
 6S0  chir_01  C02  C01  C11  N03  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
 6S0  plan-1  N03  0.020
 6S0  plan-1  C04  0.020
 6S0  plan-1  C05  0.020
 6S0  plan-1  C06  0.020
 6S0  plan-1  N07  0.020
 6S0  plan-1  C08  0.020
 6S0  plan-1  C09  0.020
 6S0  plan-1  C10  0.020
 6S0  plan-1  H9   0.020
 6S0  plan-1  H10  0.020
 6S0  plan-1  H11  0.020
 6S0  plan-2  C02  0.020
 6S0  plan-2  C11  0.020
 6S0  plan-2  C12  0.020
 6S0  plan-2  C13  0.020
 6S0  plan-2  C14  0.020
 6S0  plan-2  C15  0.020
 6S0  plan-2  C16  0.020
 6S0  plan-2  S17  0.020
 6S0  plan-2  N18  0.020
 6S0  plan-2  C19  0.020
 6S0  plan-2  H12  0.020
 6S0  plan-2  H13  0.020
 6S0  plan-2  H14  0.020
 6S0  plan-2  H15  0.020
 6S0  plan-3  C02  0.020
 6S0  plan-3  N03  0.020
 6S0  plan-3  C04  0.020
 6S0  plan-3  H5   0.020

