# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:55:43 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-[[(4~{S})-5-chloranyl-6-methyl-1,2,3,4-tetrahydrothieno[2,3-d]pyrimidin-4-yl]sulfanyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc2NCN[C@@H](SCC(O)=O)c2c1Cl
#
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
 M9N  M9N  '2-[[(4~{S})-5-chloranyl-6-methyl-1,2,3,4-tetrahydrothieno[2,3-d]pyrimidin-4-yl]sulfanyl]ethanoic acid'  ligand  27  16  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M9N
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
 M9N  C10  C   CR5   0  -0.170   0.3048  -5.5746  5.3680
 M9N  C13  C   CR5   0   0.007   2.0194  -7.2601  6.0471
 M9N  C15  C   CH2   0  -0.188   3.8290  -8.0215  7.3220
 M9N  C01  C   CH1   0  -0.261   3.9329  -5.7385  6.5001
 M9N  C04  C   C     0   0.561   7.2095  -3.5936  5.2245
 M9N  C07  C   CR5   0   0.177   2.5157  -5.9855  6.0732
 M9N  C08  C   CR5   0  -0.027   1.5058  -5.0440  5.7059
 M9N  C11  C   CH3   0  -0.709  -0.9349  -4.8903  4.9041
 M9N  N14  N   NH1   0  -0.654   2.7282  -8.3729  6.4237
 M9N  N16  N   NH1   0  -0.576   4.6491  -6.9852  6.7592
 M9N  O05  O   OH1   0  -0.585   8.3359  -3.2847  5.8473
 M9N  O06  O   O     0  -0.432   6.9265  -3.2265  4.1133
 M9N  S02  S   S2    0   0.021   4.8066  -4.8351  5.1797
 M9N  S12  S   S2    0   0.210   0.3753  -7.3024  5.5247
 M9N  CL1  CL  CL    0  -0.126   1.7681  -3.3407  5.7223
 M9N  H1   H   HCH2  0   0.264   4.4342  -8.9111  7.4858
 M9N  H2   H   HCH2  0   0.241   3.4473  -7.6805  8.2915
 M9N  H3   H   HCH1  0   0.289   3.9565  -5.1076  7.3956
 M9N  H4   H   HCH2  0   0.315   6.8692  -5.3772  6.3441
 M9N  H5   H   HCH2  0   0.313   6.1018  -3.9456  7.0144
 M9N  H6   H   HCH3  0   0.254  -1.7988  -5.5514  4.9505
 M9N  H7   H   HCH3  0   0.255  -1.1555  -4.0222  5.5255
 M9N  H8   H   HCH3  0   0.258  -0.8411  -4.5438  3.8735
 M9N  H9   H   HNH1  0   0.389   2.1756  -9.1580  6.7371
 M9N  H10  H   HNH1  0   0.360   5.0552  -7.3170  5.8915
 M9N  H12  H   HOH1  0   0.487   8.8880  -2.7217  5.2835
 M9N  C03  C   CH2   0  -0.674   6.3321  -4.4643  6.0803

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
 M9N  C11  C10  single    1.490  0.020  1.490
 M9N  CL1  C08  single    1.723  0.020  1.723
 M9N  O06  C04  double    1.204  0.020  1.204
 M9N  C10  C08  aromatic  1.356  0.020  1.356
 M9N  C10  S12  aromatic  1.736  0.020  1.736
 M9N  C08  C07  aromatic  1.429  0.020  1.429
 M9N  C04  O05  single    1.324  0.020  1.324
 M9N  C04  C03  single    1.503  0.020  1.503
 M9N  S02  C03  single    1.810  0.020  1.810
 M9N  S02  C01  single    1.823  0.020  1.823
 M9N  S12  C13  aromatic  1.726  0.020  1.726
 M9N  C07  C13  aromatic  1.368  0.020  1.368
 M9N  C07  C01  single    1.501  0.020  1.501
 M9N  C13  N14  single    1.372  0.020  1.372
 M9N  N16  C01  single    1.461  0.020  1.461
 M9N  N16  C15  single    1.436  0.020  1.436
 M9N  N14  C15  single    1.464  0.020  1.464
 M9N  C15  H1   single    0.970  0.020  1.090
 M9N  C15  H2   single    0.970  0.020  1.090
 M9N  C01  H3   single    0.970  0.020  1.090
 M9N  C03  H4   single    0.970  0.020  1.090
 M9N  C03  H5   single    0.970  0.020  1.090
 M9N  C11  H6   single    0.970  0.020  1.090
 M9N  C11  H7   single    0.970  0.020  1.090
 M9N  C11  H8   single    0.970  0.020  1.090
 M9N  N14  H9   single    0.890  0.020  1.040
 M9N  N16  H10  single    0.890  0.020  1.040
 M9N  O05  H12  single    0.850  0.020  0.980

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
 M9N  S12  C10  C11  121.26  3.000
 M9N  S12  C10  C08  109.33  3.000
 M9N  C11  C10  C08  129.41  3.000
 M9N  S12  C13  N14  123.74  3.000
 M9N  N14  C13  C07  124.26  3.000
 M9N  S12  C13  C07  111.98  3.000
 M9N  H2   C15  H1   108.35  3.000
 M9N  H2   C15  N16  108.71  3.000
 M9N  H1   C15  N16  109.34  3.000
 M9N  H2   C15  N14  110.83  3.000
 M9N  H1   C15  N14  108.33  3.000
 M9N  N16  C15  N14  111.23  3.000
 M9N  H3   C01  S02  107.24  3.000
 M9N  H3   C01  N16  109.62  3.000
 M9N  S02  C01  N16  108.44  3.000
 M9N  H3   C01  C07  110.35  3.000
 M9N  N16  C01  C07  111.90  3.000
 M9N  S02  C01  C07  109.16  3.000
 M9N  O06  C04  O05  124.27  3.000
 M9N  O05  C04  C03  111.35  3.000
 M9N  O06  C04  C03  124.38  3.000
 M9N  C08  C07  C01  129.21  3.000
 M9N  C01  C07  C13  120.09  3.000
 M9N  C08  C07  C13  110.65  3.000
 M9N  CL1  C08  C07  122.77  3.000
 M9N  C07  C08  C10  115.62  3.000
 M9N  CL1  C08  C10  121.60  3.000
 M9N  H8   C11  H7   107.63  3.000
 M9N  H8   C11  H6   107.53  3.000
 M9N  H7   C11  H6   107.39  3.000
 M9N  H8   C11  C10  111.61  3.000
 M9N  H7   C11  C10  110.89  3.000
 M9N  H6   C11  C10  111.59  3.000
 M9N  H9   N14  C15  114.06  3.000
 M9N  H9   N14  C13  115.65  3.000
 M9N  C15  N14  C13  111.24  3.000
 M9N  H10  N16  C01  108.90  3.000
 M9N  H10  N16  C15  109.14  3.000
 M9N  C01  N16  C15  113.91  3.000
 M9N  H12  O05  C04  110.28  3.000
 M9N  C03  S02  C01   98.35  3.000
 M9N  C13  S12  C10   92.39  3.000
 M9N  H5   C03  H4   107.10  3.000
 M9N  H5   C03  S02  110.17  3.000
 M9N  H4   C03  S02  111.32  3.000
 M9N  H5   C03  C04  109.55  3.000
 M9N  H4   C03  C04  109.56  3.000
 M9N  S02  C03  C04  109.11  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
 M9N  CONST_01  C13  C07  C08  C10     0.00   0.0  0
 M9N  CONST_02  C07  C13  S12  C10     0.00   0.0  0
 M9N  CONST_03  C08  C10  S12  C13     0.00   0.0  0
 M9N  CONST_04  S12  C10  C08  C07     0.00   0.0  0
 M9N  CONST_05  S12  C13  C07  C08     0.00   0.0  0
 M9N  CONST_06  C11  C10  S12  C13   180.00   0.0  0
 M9N  CONST_07  CL1  C08  C07  C13   180.00   0.0  0
 M9N  CONST_08  CL1  C08  C07  C01     0.00   0.0  0
 M9N  CONST_09  C11  C10  C08  C07   180.00   0.0  0
 M9N  CONST_10  CL1  C08  C10  S12   180.00   0.0  0
 M9N  CONST_11  H12  O05  C04  C03   180.00   0.0  0
 M9N  Var_01    N16  C15  N14  C13   -52.50  30.0  1
 M9N  Var_02    S12  C13  N14  C15  -155.82  30.0  1
 M9N  Var_03    N14  C15  N16  C01    60.51  30.0  1
 M9N  Var_04    H6   C11  C10  C08  -165.73  30.0  2
 M9N  Var_05    C04  C03  S02  C01  -175.13  30.0  3
 M9N  Var_06    S02  C03  C04  O05   179.44  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
 M9N  chir_01  C01  S02  C07  N16  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
 M9N  plan-1  C04  0.020
 M9N  plan-1  O05  0.020
 M9N  plan-1  O06  0.020
 M9N  plan-1  H12  0.020
 M9N  plan-1  C03  0.020
 M9N  plan-2  C10  0.020
 M9N  plan-2  C13  0.020
 M9N  plan-2  C01  0.020
 M9N  plan-2  C07  0.020
 M9N  plan-2  C08  0.020
 M9N  plan-2  C11  0.020
 M9N  plan-2  N14  0.020
 M9N  plan-2  S12  0.020
 M9N  plan-2  CL1  0.020

