# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 23:19:13 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 6-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(nc1)N2CCc3sccc3C2
#
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
 H29  H29  6-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)pyridin-3-amine  ligand  29  16  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H29
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
 H29  C1   C  CR6   0   0.194  -0.6982   4.9528  -11.3515
 H29  C2   C  CR16  0  -0.143  -1.9376   4.6243  -11.8852
 H29  C4   C  CR16  0  -0.371  -1.4196   7.2475  -11.5056
 H29  C5   C  CH2   0  -0.318  -3.3185   8.9910  -12.9715
 H29  C6   C  CH2   0  -0.478  -4.3398  10.0366  -12.5426
 H29  C7   C  CR5   0  -0.244  -5.6982   9.4848  -12.8107
 H29  C9   C  CH2   0  -0.301  -4.8762   7.1195  -12.9181
 H29  C11  C  CR15  0  -0.472  -8.0833   9.0248  -13.2720
 H29  N    N  N     0  -0.459  -2.8577   5.5162  -12.2409
 H29  C    C  CR16  0  -0.208  -0.4626   6.3198  -11.1616
 H29  C10  C  CR15  0  -0.208  -7.3260   7.8965  -13.2636
 H29  C3   C  CR6   0   0.493  -2.6311   6.8097  -12.0684
 H29  C8   C  CR5   0   0.134  -5.9507   8.1606  -12.9940
 H29  N1   N  NT    0  -0.518  -3.6486   7.6930  -12.4048
 H29  N2   N  NH2   0  -0.862   0.2666   3.9947  -11.0730
 H29  S    S  S2    0   0.198  -7.1344  10.4224  -12.9591
 H29  H1   H  HCR6  0   0.249  -2.1974   3.5810  -12.0430
 H29  H2   H  HCR6  0   0.265  -1.2269   8.2937  -11.3141
 H29  H4   H  HCH2  0   0.232  -3.2914   8.9360  -14.0685
 H29  H5   H  HCH2  0   0.255  -4.2137  10.2703  -11.4818
 H29  H6   H  HCH2  0   0.254  -4.1668  10.9623  -13.0955
 H29  H7   H  HCH2  0   0.257  -5.1976   6.3123  -12.2586
 H29  H8   H  HCH2  0   0.227  -4.7350   6.6629  -13.9095
 H29  H9   H  HCR5  0   0.289  -9.1453   9.1117  -13.4420
 H29  H10  H  HCR6  0   0.266   0.4725   6.6543  -10.7271
 H29  H11  H  HCR5  0   0.259  -7.7291   6.9079  -13.4377
 H29  H12  H  HNH2  0   0.373   0.9089   4.2522  -10.3395
 H29  H13  H  HNH2  0   0.372  -0.1005   3.0701  -10.9074
 H29  H3   H  HCH2  0   0.264  -2.3292   9.3032  -12.6499

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
 H29  C11  C10  aromatic  1.359  0.020  1.359
 H29  C11  S    aromatic  1.718  0.020  1.718
 H29  C10  C8   aromatic  1.426  0.020  1.426
 H29  S    C7   aromatic  1.722  0.020  1.722
 H29  C5   N1   single    1.454  0.020  1.454
 H29  C5   C6   single    1.523  0.020  1.523
 H29  C8   C7   aromatic  1.360  0.020  1.360
 H29  C8   C9   single    1.498  0.020  1.498
 H29  C7   C6   single    1.491  0.020  1.491
 H29  C9   N1   single    1.449  0.020  1.449
 H29  N1   C3   single    1.389  0.020  1.389
 H29  N    C3   aromatic  1.325  0.020  1.325
 H29  N    C2   aromatic  1.330  0.020  1.330
 H29  C3   C4   aromatic  1.406  0.020  1.406
 H29  C2   C1   aromatic  1.389  0.020  1.389
 H29  C4   C    aromatic  1.376  0.020  1.376
 H29  C1   C    aromatic  1.400  0.020  1.400
 H29  C1   N2   single    1.388  0.020  1.388
 H29  C2   H1   single    0.930  0.020  1.080
 H29  C4   H2   single    0.930  0.020  1.080
 H29  C5   H3   single    0.970  0.020  1.090
 H29  C5   H4   single    0.970  0.020  1.090
 H29  C6   H5   single    0.970  0.020  1.090
 H29  C6   H6   single    0.970  0.020  1.090
 H29  C9   H7   single    0.970  0.020  1.090
 H29  C9   H8   single    0.970  0.020  1.090
 H29  C11  H9   single    0.930  0.020  1.080
 H29  C    H10  single    0.930  0.020  1.080
 H29  C10  H11  single    0.930  0.020  1.080
 H29  N2   H12  single    0.890  0.020  1.040
 H29  N2   H13  single    0.890  0.020  1.040

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
 H29  N2   C1   C    121.99  3.000
 H29  N2   C1   C2   122.29  3.000
 H29  C    C1   C2   115.67  3.000
 H29  H1   C2   N    116.08  3.000
 H29  H1   C2   C1   119.75  3.000
 H29  N    C2   C1   124.17  3.000
 H29  H2   C4   C3   121.73  3.000
 H29  H2   C4   C    118.95  3.000
 H29  C3   C4   C    119.30  3.000
 H29  H4   C5   H3   106.72  3.000
 H29  H4   C5   N1   110.48  3.000
 H29  H3   C5   N1   110.35  3.000
 H29  H4   C5   C6   109.39  3.000
 H29  H3   C5   C6   109.27  3.000
 H29  N1   C5   C6   110.54  3.000
 H29  H6   C6   H5   106.96  3.000
 H29  H6   C6   C7   111.54  3.000
 H29  H5   C6   C7   111.02  3.000
 H29  H6   C6   C5   109.45  3.000
 H29  H5   C6   C5   110.03  3.000
 H29  C7   C6   C5   107.84  3.000
 H29  S    C7   C8   111.33  3.000
 H29  C8   C7   C6   123.62  3.000
 H29  S    C7   C6   125.04  3.000
 H29  H8   C9   H7   105.99  3.000
 H29  H8   C9   N1   112.00  3.000
 H29  H7   C9   N1   109.17  3.000
 H29  H8   C9   C8   109.56  3.000
 H29  H7   C9   C8   109.48  3.000
 H29  N1   C9   C8   110.52  3.000
 H29  H9   C11  S    120.45  3.000
 H29  H9   C11  C10  128.05  3.000
 H29  S    C11  C10  111.50  3.000
 H29  C3   N    C2   120.12  3.000
 H29  H10  C    C4   119.47  3.000
 H29  H10  C    C1   120.05  3.000
 H29  C4   C    C1   120.47  3.000
 H29  H11  C10  C8   123.99  3.000
 H29  H11  C10  C11  123.38  3.000
 H29  C8   C10  C11  112.63  3.000
 H29  N1   C3   N    117.66  3.000
 H29  N    C3   C4   120.25  3.000
 H29  N1   C3   C4   122.03  3.000
 H29  C10  C8   C9   124.93  3.000
 H29  C9   C8   C7   122.45  3.000
 H29  C10  C8   C7   112.62  3.000
 H29  C3   N1   C9   117.06  3.000
 H29  C3   N1   C5   119.72  3.000
 H29  C9   N1   C5   114.05  3.000
 H29  H13  N2   H12  110.28  3.000
 H29  H13  N2   C1   114.38  3.000
 H29  H12  N2   C1   114.36  3.000
 H29  C11  S    C7    91.92  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
 H29  CONST_01  C3   N    C2   C1      0.00   0.0  0
 H29  CONST_02  C3   C4   C    C1      0.00   0.0  0
 H29  CONST_03  C4   C3   N    C2      0.00   0.0  0
 H29  CONST_04  C4   C    C1   C2      0.00   0.0  0
 H29  CONST_05  C10  C11  S    C7      0.00   0.0  0
 H29  CONST_06  C11  C10  C8   C7      0.00   0.0  0
 H29  CONST_07  C8   C7   S    C11     0.00   0.0  0
 H29  CONST_08  C    C4   C3   N       0.00   0.0  0
 H29  CONST_09  C    C1   C2   N       0.00   0.0  0
 H29  CONST_10  S    C7   C8   C10     0.00   0.0  0
 H29  CONST_11  S    C11  C10  C8      0.00   0.0  0
 H29  CONST_12  N1   C3   N    C2    180.00   0.0  0
 H29  CONST_13  N1   C3   C4   C     180.00   0.0  0
 H29  CONST_14  N2   C1   C    C4    180.00   0.0  0
 H29  CONST_15  N2   C1   C2   N     180.00   0.0  0
 H29  CONST_16  H2   C4   C    C1    180.00   0.0  0
 H29  CONST_17  H10  C    C1   C2    180.00   0.0  0
 H29  CONST_18  H9   C11  S    C7    180.00   0.0  0
 H29  CONST_19  H11  C10  C8   C7    180.00   0.0  0
 H29  CONST_20  H1   C2   C1   C     180.00   0.0  0
 H29  Var_01    C5   N1   C3   C4     37.96  30.0  1
 H29  Var_02    C8   C9   N1   C5    -43.53  30.0  1
 H29  Var_03    S    C7   C6   C5   -160.14  30.0  1
 H29  Var_04    N1   C9   C8   C7     10.02  30.0  1
 H29  Var_05    N1   C5   C6   C7    -49.87  30.0  1

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
 H29  plan-1  C1   0.020
 H29  plan-1  C2   0.020
 H29  plan-1  C4   0.020
 H29  plan-1  N    0.020
 H29  plan-1  C    0.020
 H29  plan-1  C3   0.020
 H29  plan-1  N1   0.020
 H29  plan-1  N2   0.020
 H29  plan-1  H1   0.020
 H29  plan-1  H2   0.020
 H29  plan-1  H10  0.020
 H29  plan-2  C6   0.020
 H29  plan-2  C7   0.020
 H29  plan-2  C9   0.020
 H29  plan-2  C11  0.020
 H29  plan-2  C10  0.020
 H29  plan-2  C8   0.020
 H29  plan-2  S    0.020
 H29  plan-2  H9   0.020
 H29  plan-2  H11  0.020
 H29  plan-3  C1   0.020
 H29  plan-3  N2   0.020
 H29  plan-3  H12  0.020
 H29  plan-3  H13  0.020

