# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:22:51 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-(2-methylpropylamino)-1-[(4~{R})-4-(6-methylpyridin-2-yl)-6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CNCC(=O)N1CCc2sccc2[C@@H]1c3cccc(C)n3
#
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
 9V3  9V3  "2-(2-methylpropylamino)-1-[(4R)-4-(6-methylpyridin-2-yl)-6,7-dihydro-4H-thieno[3,2-c]pyridin-5-yl]ethanone"
  ligand  49  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9V3
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
 9V3  N1   N  NT    0  -0.476  168.6713  169.5504  187.5065
 9V3  C7   C  CH2   0  -0.490  166.8096  171.1433  187.3429
 9V3  C8   C  CR5   0  -0.275  167.5747  171.9474  188.3356
 9V3  N2   N  N     0  -0.425  170.8969  171.2024  186.5921
 9V3  C9   C  CR5   0   0.213  168.8062  171.6081  188.8009
 9V3  C1   C  CH1   0  -0.260  168.7464  163.9037  188.9571
 9V3  C5   C  C     0   0.525  168.7615  168.1967  187.4369
 9V3  C6   C  CH2   0  -0.320  167.8000  170.2709  186.5859
 9V3  C4   C  CH2   0  -0.430  169.7491  167.4995  188.3786
 9V3  C3   C  CH2   0  -0.240  168.6084  165.4239  188.9577
 9V3  C2   C  CH3   0  -0.642  169.9873  163.4438  189.7129
 9V3  N    N  NH1   0  -0.584  169.7416  166.0652  188.3156
 9V3  C    C  CH3   0  -0.652  167.4894  163.2693  189.5419
 9V3  O    O  O     0  -0.484  168.1095  167.5417  186.6386
 9V3  C10  C  CR15  0  -0.187  169.3286  172.5564  189.7292
 9V3  C11  C  CR15  0  -0.472  168.4765  173.5911  189.9481
 9V3  C12  C  CH1   0  -0.233  169.5109  170.3424  188.3956
 9V3  C13  C  CR6   0   0.276  170.8746  170.6574  187.8047
 9V3  C14  C  CR6   0   0.233  172.0616  171.5213  186.0415
 9V3  C15  C  CH3   0  -0.728  172.0444  172.1306  184.6722
 9V3  C16  C  CR16  0  -0.332  173.2702  171.3077  186.7085
 9V3  C17  C  CR16  0  -0.143  173.2491  170.7437  187.9686
 9V3  C18  C  CR16  0  -0.351  172.0255  170.4051  188.5331
 9V3  S    S  S2    0   0.210  167.0346  173.4263  189.0280
 9V3  H16  H  HCH2  0   0.261  166.2792  171.7826  186.6347
 9V3  H15  H  HCH2  0   0.260  166.0568  170.5238  187.8384
 9V3  H4   H  HCH1  0   0.213  168.8346  163.5756  187.9135
 9V3  H14  H  HCH2  0   0.271  167.2738  169.5471  185.9714
 9V3  H13  H  HCH2  0   0.254  168.4083  170.8917  185.9274
 9V3  H11  H  HCH2  0   0.276  170.7547  167.8661  188.1426
 9V3  H12  H  HCH2  0   0.261  169.5613  167.7985  189.4136
 9V3  H8   H  HCH2  0   0.207  168.5662  165.7715  189.9965
 9V3  H9   H  HCH2  0   0.201  167.6453  165.6925  188.5016
 9V3  H7   H  HCH3  0   0.219  170.0861  162.3574  189.6816
 9V3  H5   H  HCH3  0   0.224  170.8966  163.8750  189.2961
 9V3  H6   H  HCH3  0   0.207  169.9281  163.7405  190.7633
 9V3  H10  H  HNH1  0   0.339  169.8032  165.7606  187.3518
 9V3  H2   H  HCH3  0   0.226  167.5553  162.1805  189.5297
 9V3  H3   H  HCH3  0   0.212  167.3437  163.5790  190.5797
 9V3  H1   H  HCH3  0   0.223  166.5969  163.5541  188.9817
 9V3  H17  H  HCR5  0   0.264  170.2933  172.4678  190.2100
 9V3  H18  H  HCR5  0   0.292  168.6170  174.4402  190.5989
 9V3  H    H  HCH1  0   0.301  169.6769  169.7764  189.3145
 9V3  H21  H  HCH3  0   0.249  171.0245  172.2456  184.3120
 9V3  H20  H  HCH3  0   0.251  172.5224  173.1112  184.6754
 9V3  H19  H  HCH3  0   0.252  172.5938  171.5113  183.9615
 9V3  H22  H  HCR6  0   0.263  174.2052  171.5835  186.2382
 9V3  H23  H  HCR6  0   0.270  174.1703  170.5645  188.5076
 9V3  H24  H  HCR6  0   0.271  171.9681  169.9570  189.5168

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
 9V3  C15  C14  single    1.499  0.020  1.499
 9V3  C6   C7   single    1.522  0.020  1.522
 9V3  C6   N1   single    1.458  0.020  1.458
 9V3  C14  C16  aromatic  1.397  0.020  1.397
 9V3  C14  N2   aromatic  1.327  0.020  1.327
 9V3  O    C5   double    1.221  0.020  1.221
 9V3  C16  C17  aromatic  1.381  0.020  1.381
 9V3  C7   C8   single    1.489  0.020  1.489
 9V3  N2   C13  aromatic  1.330  0.020  1.330
 9V3  N1   C5   single    1.358  0.020  1.358
 9V3  N1   C12  single    1.457  0.020  1.457
 9V3  C5   C4   single    1.532  0.020  1.532
 9V3  C17  C18  aromatic  1.389  0.020  1.389
 9V3  C13  C18  aromatic  1.385  0.020  1.385
 9V3  C13  C12  single    1.519  0.020  1.519
 9V3  C8   S    aromatic  1.720  0.020  1.720
 9V3  C8   C9   aromatic  1.359  0.020  1.359
 9V3  N    C4   single    1.436  0.020  1.436
 9V3  N    C3   single    1.452  0.020  1.452
 9V3  C12  C9   single    1.504  0.020  1.504
 9V3  S    C11  aromatic  1.718  0.020  1.718
 9V3  C9   C10  aromatic  1.426  0.020  1.426
 9V3  C3   C1   single    1.526  0.020  1.526
 9V3  C1   C2   single    1.524  0.020  1.524
 9V3  C1   C    single    1.525  0.020  1.525
 9V3  C10  C11  aromatic  1.358  0.020  1.358
 9V3  C7   H16  single    0.970  0.020  1.090
 9V3  C7   H15  single    0.970  0.020  1.090
 9V3  C1   H4   single    0.970  0.020  1.090
 9V3  C6   H14  single    0.970  0.020  1.090
 9V3  C6   H13  single    0.970  0.020  1.090
 9V3  C4   H11  single    0.970  0.020  1.090
 9V3  C4   H12  single    0.970  0.020  1.090
 9V3  C3   H8   single    0.970  0.020  1.090
 9V3  C3   H9   single    0.970  0.020  1.090
 9V3  C2   H7   single    0.970  0.020  1.090
 9V3  C2   H5   single    0.970  0.020  1.090
 9V3  C2   H6   single    0.970  0.020  1.090
 9V3  N    H10  single    0.890  0.020  1.040
 9V3  C    H2   single    0.970  0.020  1.090
 9V3  C    H3   single    0.970  0.020  1.090
 9V3  C    H1   single    0.970  0.020  1.090
 9V3  C10  H17  single    0.930  0.020  1.080
 9V3  C11  H18  single    0.930  0.020  1.080
 9V3  C12  H    single    0.970  0.020  1.090
 9V3  C15  H21  single    0.970  0.020  1.090
 9V3  C15  H20  single    0.970  0.020  1.090
 9V3  C15  H19  single    0.970  0.020  1.090
 9V3  C16  H22  single    0.930  0.020  1.080
 9V3  C17  H23  single    0.930  0.020  1.080
 9V3  C18  H24  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
 9V3  C12  N1   C6   117.46  3.000
 9V3  C12  N1   C5   122.32  3.000
 9V3  C6   N1   C5   119.98  3.000
 9V3  H15  C7   H16  106.93  3.000
 9V3  H15  C7   C6   110.41  3.000
 9V3  H16  C7   C6   109.22  3.000
 9V3  H15  C7   C8   110.95  3.000
 9V3  H16  C7   C8   111.46  3.000
 9V3  C6   C7   C8   107.87  3.000
 9V3  S    C8   C9   111.18  3.000
 9V3  C9   C8   C7   123.97  3.000
 9V3  S    C8   C7   124.85  3.000
 9V3  C14  N2   C13  119.45  3.000
 9V3  C12  C9   C10  124.28  3.000
 9V3  C10  C9   C8   112.87  3.000
 9V3  C12  C9   C8   122.83  3.000
 9V3  H4   C1   C    107.85  3.000
 9V3  H4   C1   C2   108.42  3.000
 9V3  C    C1   C2   110.83  3.000
 9V3  H4   C1   C3   107.78  3.000
 9V3  C    C1   C3   109.85  3.000
 9V3  C2   C1   C3   111.96  3.000
 9V3  O    C5   C4   120.11  3.000
 9V3  C4   C5   N1   117.69  3.000
 9V3  O    C5   N1   122.17  3.000
 9V3  H13  C6   H14  107.95  3.000
 9V3  H13  C6   C7   109.70  3.000
 9V3  H14  C6   C7   110.39  3.000
 9V3  H13  C6   N1   109.23  3.000
 9V3  H14  C6   N1   108.52  3.000
 9V3  C7   C6   N1   110.99  3.000
 9V3  H12  C4   H11  105.65  3.000
 9V3  H12  C4   N    108.28  3.000
 9V3  H11  C4   N    109.24  3.000
 9V3  H12  C4   C5   110.28  3.000
 9V3  H11  C4   C5   107.87  3.000
 9V3  N    C4   C5   115.10  3.000
 9V3  H9   C3   H8   106.38  3.000
 9V3  H9   C3   N    113.11  3.000
 9V3  H8   C3   N    108.01  3.000
 9V3  H9   C3   C1   108.81  3.000
 9V3  H8   C3   C1   108.64  3.000
 9V3  N    C3   C1   111.66  3.000
 9V3  H6   C2   H5   107.79  3.000
 9V3  H6   C2   H7   107.61  3.000
 9V3  H5   C2   H7   107.91  3.000
 9V3  H6   C2   C1   110.52  3.000
 9V3  H5   C2   C1   111.75  3.000
 9V3  H7   C2   C1   111.09  3.000
 9V3  H10  N    C3   109.61  3.000
 9V3  H10  N    C4   109.99  3.000
 9V3  C3   N    C4   115.21  3.000
 9V3  H1   C    H3   107.73  3.000
 9V3  H1   C    H2   107.70  3.000
 9V3  H3   C    H2   107.55  3.000
 9V3  H1   C    C1   111.64  3.000
 9V3  H3   C    C1   110.87  3.000
 9V3  H2   C    C1   111.17  3.000
 9V3  H17  C10  C11  123.39  3.000
 9V3  H17  C10  C9   124.17  3.000
 9V3  C11  C10  C9   112.44  3.000
 9V3  H18  C11  S    120.51  3.000
 9V3  H18  C11  C10  127.96  3.000
 9V3  S    C11  C10  111.53  3.000
 9V3  H    C12  C13  107.36  3.000
 9V3  H    C12  C9   106.30  3.000
 9V3  C13  C12  C9   110.54  3.000
 9V3  H    C12  N1   108.63  3.000
 9V3  C9   C12  N1   110.60  3.000
 9V3  C13  C12  N1   113.12  3.000
 9V3  C18  C13  C12  120.23  3.000
 9V3  C12  C13  N2   117.05  3.000
 9V3  C18  C13  N2   122.70  3.000
 9V3  C16  C14  C15  120.55  3.000
 9V3  C16  C14  N2   121.63  3.000
 9V3  C15  C14  N2   117.81  3.000
 9V3  H19  C15  H20  106.95  3.000
 9V3  H19  C15  H21  108.44  3.000
 9V3  H20  C15  H21  108.47  3.000
 9V3  H19  C15  C14  111.01  3.000
 9V3  H20  C15  C14  110.96  3.000
 9V3  H21  C15  C14  110.87  3.000
 9V3  H22  C16  C17  120.92  3.000
 9V3  H22  C16  C14  120.07  3.000
 9V3  C17  C16  C14  119.01  3.000
 9V3  H23  C17  C18  120.46  3.000
 9V3  H23  C17  C16  120.60  3.000
 9V3  C18  C17  C16  118.93  3.000
 9V3  H24  C18  C17  121.11  3.000
 9V3  H24  C18  C13  120.61  3.000
 9V3  C17  C18  C13  118.27  3.000
 9V3  C11  S    C8    91.98  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
 9V3  CONST_01  C10  C11  S    C8      0.00   0.0  0
 9V3  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 9V3  CONST_03  C17  C16  C14  N2      0.00   0.0  0
 9V3  CONST_04  C17  C18  C13  N2      0.00   0.0  0
 9V3  CONST_05  C11  S    C8   C9      0.00   0.0  0
 9V3  CONST_06  S    C11  C10  C9      0.00   0.0  0
 9V3  CONST_07  S    C8   C9   C10     0.00   0.0  0
 9V3  CONST_08  C16  C14  N2   C13     0.00   0.0  0
 9V3  CONST_09  C16  C17  C18  C13     0.00   0.0  0
 9V3  CONST_10  C18  C17  C16  C14     0.00   0.0  0
 9V3  CONST_11  C18  C13  N2   C14     0.00   0.0  0
 9V3  CONST_12  C14  N2   C13  C12   180.00   0.0  0
 9V3  CONST_13  C17  C18  C13  C12   180.00   0.0  0
 9V3  CONST_14  C15  C14  N2   C13   180.00   0.0  0
 9V3  CONST_15  C17  C16  C14  C15   180.00   0.0  0
 9V3  CONST_16  H18  C11  S    C8    180.00   0.0  0
 9V3  CONST_17  H17  C10  C9   C8    180.00   0.0  0
 9V3  CONST_18  H22  C16  C14  N2    180.00   0.0  0
 9V3  CONST_19  H24  C18  C13  N2    180.00   0.0  0
 9V3  CONST_20  H18  C11  C10  C9    180.00   0.0  0
 9V3  CONST_21  H24  C18  C13  C12     0.00   0.0  0
 9V3  CONST_22  H17  C10  C9   C12     0.00   0.0  0
 9V3  CONST_23  H23  C17  C18  C13   180.00   0.0  0
 9V3  CONST_24  H23  C17  C16  C14   180.00   0.0  0
 9V3  CONST_25  H24  C18  C17  C16   180.00   0.0  0
 9V3  CONST_26  H22  C16  C17  C18   180.00   0.0  0
 9V3  CONST_27  H17  C10  C11  S     180.00   0.0  0
 9V3  CONST_28  O    C5   N1   C6      0.00   0.0  0
 9V3  CONST_29  C4   C5   N1   C6    180.00   0.0  0
 9V3  CONST_30  C12  N1   C5   C4      0.00   0.0  0
 9V3  CONST_31  C12  N1   C5   O     180.00   0.0  0
 9V3  Var_01    C8   C7   C6   N1     50.01  30.0  1
 9V3  Var_02    C12  N1   C6   C7    -60.71  30.0  1
 9V3  Var_03    C6   C7   C8   C9    -21.58  30.0  1
 9V3  Var_04    S    C8   C7   C6    157.64  30.0  1
 9V3  Var_05    C5   N1   C6   C7    124.76  30.0  1
 9V3  Var_06    H16  C7   C6   N1    171.32  30.0  1
 9V3  Var_07    H15  C7   C6   N1    -71.37  30.0  1
 9V3  Var_08    H14  C6   C7   C8    170.38  30.0  1
 9V3  Var_09    H13  C6   C7   C8    -70.78  30.0  1
 9V3  Var_10    H16  C7   C8   C9   -141.48  30.0  1
 9V3  Var_11    H15  C7   C8   C9     99.47  30.0  1
 9V3  Var_12    H14  C6   N1   C12   177.83  30.0  1
 9V3  Var_13    H13  C6   N1   C12    60.37  30.0  1
 9V3  Var_14    H16  C7   C8   S      37.74  30.0  1
 9V3  Var_15    H15  C7   C8   S     -81.31  30.0  1
 9V3  Var_16    H21  C15  C14  N2      0.96  30.0  2
 9V3  Var_17    H20  C15  C14  N2    121.57  30.0  2
 9V3  Var_18    H19  C15  C14  N2   -119.65  30.0  2
 9V3  Var_19    H14  C6   N1   C5      3.29  30.0  1
 9V3  Var_20    H13  C6   N1   C5   -114.17  30.0  1
 9V3  Var_21    H21  C15  C14  C16  -178.71  30.0  2
 9V3  Var_22    H20  C15  C14  C16   -58.10  30.0  2
 9V3  Var_23    H19  C15  C14  C16    60.68  30.0  2
 9V3  Var_24    N    C4   C5   N1    176.41  30.0  3
 9V3  Var_25    H11  C4   C5   N1    -61.36  30.0  3
 9V3  Var_26    H12  C4   C5   N1     53.56  30.0  3
 9V3  Var_27    C4   N    C3   C1   -174.69  30.0  2
 9V3  Var_28    C3   N    C4   C5    -75.08  30.0  1
 9V3  Var_29    N    C3   C1   C2     60.76  30.0  1
 9V3  Var_30    O    C5   C4   N      -5.17  30.0  2
 9V3  Var_31    C    C1   C3   N    -175.65  30.0  3
 9V3  Var_32    H10  N    C3   C1     60.64  30.0  2
 9V3  Var_33    H10  N    C4   C5     49.39  30.0  1
 9V3  Var_34    H8   C3   N    C4    -55.30  30.0  3
 9V3  Var_35    H9   C3   N    C4     62.16  30.0  3
 9V3  Var_36    H11  C4   N    C3    163.43  30.0  3
 9V3  Var_37    H12  C4   N    C3     48.83  30.0  3
 9V3  Var_38    H7   C2   C1   C3   -178.53  30.0  3
 9V3  Var_39    H5   C2   C1   C3    -57.95  30.0  3
 9V3  Var_40    H6   C2   C1   C3     62.08  30.0  3
 9V3  Var_41    H2   C    C1   C3    178.64  30.0  3
 9V3  Var_42    H3   C    C1   C3    -61.78  30.0  3
 9V3  Var_43    H1   C    C1   C3     58.35  30.0  3
 9V3  Var_44    H8   C3   C1   C2    -58.25  30.0  1
 9V3  Var_45    H9   C3   C1   C2   -173.68  30.0  1
 9V3  Var_46    H2   C    C1   C2    -57.11  30.0  3
 9V3  Var_47    H3   C    C1   C2     62.47  30.0  3
 9V3  Var_48    H1   C    C1   C2   -177.41  30.0  3
 9V3  Var_49    H4   C1   C3   N     -58.38  30.0  3
 9V3  Var_50    H8   C3   C1   C      65.34  30.0  1
 9V3  Var_51    H9   C3   C1   C     -50.09  30.0  1
 9V3  Var_52    H7   C2   C1   C      58.43  30.0  3
 9V3  Var_53    H5   C2   C1   C     179.01  30.0  3
 9V3  Var_54    H6   C2   C1   C     -60.95  30.0  3
 9V3  Var_55    H11  C4   C5   O     117.06  30.0  3
 9V3  Var_56    H12  C4   C5   O    -128.02  30.0  3

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
 9V3  chir_01  C12  N1  C13  C9  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
 9V3  plan-1  N2   0.020
 9V3  plan-1  C12  0.020
 9V3  plan-1  C13  0.020
 9V3  plan-1  C14  0.020
 9V3  plan-1  C15  0.020
 9V3  plan-1  C16  0.020
 9V3  plan-1  C17  0.020
 9V3  plan-1  C18  0.020
 9V3  plan-1  H22  0.020
 9V3  plan-1  H23  0.020
 9V3  plan-1  H24  0.020
 9V3  plan-2  C7   0.020
 9V3  plan-2  C8   0.020
 9V3  plan-2  C9   0.020
 9V3  plan-2  C10  0.020
 9V3  plan-2  C11  0.020
 9V3  plan-2  C12  0.020
 9V3  plan-2  S    0.020
 9V3  plan-2  H17  0.020
 9V3  plan-2  H18  0.020
 9V3  plan-3  N1   0.020
 9V3  plan-3  C5   0.020
 9V3  plan-3  C6   0.020
 9V3  plan-3  C4   0.020
 9V3  plan-3  O    0.020
 9V3  plan-3  C12  0.020

