# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:42:05 2020
#   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  26  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.158   2.5956  -1.6369  -0.1208
 M9N  C13  C   CR5    0   0.004   2.1164   0.8119  -0.2692
 M9N  C15  C   CH2    0  -0.187   1.1541   2.8192   0.4530
 M9N  C01  C   CH1    0  -0.256  -0.2352   0.8229   0.5467
 M9N  C04  C   C      0   0.431  -4.3371   0.4487  -0.1764
 M9N  C07  C   CR5    0   0.175   1.0382   0.1091   0.1908
 M9N  C08  C   CR5    0  -0.035   1.3525  -1.2827   0.2913
 M9N  C11  C   CH3    0  -0.705   3.2508  -2.9723  -0.1712
 M9N  N14  N   NH1    0  -0.654   2.1512   2.1775  -0.4070
 M9N  N16  N   NH1    0  -0.574  -0.1490   2.2531   0.2548
 M9N  O05  O   OC    -1  -0.611  -5.3625   0.9241   0.3427
 M9N  O06  O   O      0  -0.598  -4.2659  -0.3630  -1.1169
 M9N  S02  S   S2     0  -0.016  -1.6206   0.1165  -0.4062
 M9N  S12  S   S2     0   0.196   3.4576  -0.2153  -0.6300
 M9N  CL1  CL  CL     0  -0.131   0.2387  -2.4288   0.9419
 M9N  H1   H   HCH2   0   0.236   1.4271   2.7129   1.5096
 M9N  H2   H   HCH2   0   0.260   1.1286   3.8806   0.2125
 M9N  H3   H   HCH1   0   0.273  -0.4613   0.6828   1.6102
 M9N  H4   H   HCH2   0   0.267  -2.9254   2.0213   0.3103
 M9N  H5   H   HCH2   0   0.263  -2.9698   0.7259   1.4929
 M9N  H6   H   HCH3   0   0.255   3.5860  -3.2184  -1.1796
 M9N  H7   H   HCH3   0   0.255   4.1200  -3.0229   0.4865
 M9N  H8   H   HCH3   0   0.251   2.5519  -3.7454   0.1425
 M9N  H9   H   HNH1   0   0.386   3.0695   2.5948  -0.3535
 M9N  H10  H   HNH1   0   0.355  -0.4429   2.4100  -0.7024
 M9N  C03  C   CH2    0  -0.684  -3.0057   0.9382   0.4210

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    1.488  0.020  1.488
 M9N  CL1  C08  single    1.725  0.020  1.725
 M9N  O06  C04  deloc     1.244  0.020  1.244
 M9N  C10  C08  aromatic  1.357  0.020  1.357
 M9N  C10  S12  aromatic  1.739  0.020  1.739
 M9N  C08  C07  aromatic  1.430  0.020  1.430
 M9N  C04  O05  deloc     1.244  0.020  1.244
 M9N  C04  C03  single    1.539  0.020  1.539
 M9N  S02  C03  single    1.811  0.020  1.811
 M9N  S02  C01  single    1.824  0.020  1.824
 M9N  S12  C13  aromatic  1.727  0.020  1.727
 M9N  C07  C13  aromatic  1.367  0.020  1.367
 M9N  C07  C01  single    1.503  0.020  1.503
 M9N  C13  N14  single    1.373  0.020  1.373
 M9N  N16  C01  single    1.462  0.020  1.462
 M9N  N16  C15  single    1.434  0.020  1.434
 M9N  N14  C15  single    1.465  0.020  1.465
 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

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  120.36  3.000
 M9N  S12  C10  C08  109.25  3.000
 M9N  C11  C10  C08  130.38  3.000
 M9N  S12  C13  N14  123.42  3.000
 M9N  N14  C13  C07  124.42  3.000
 M9N  S12  C13  C07  112.15  3.000
 M9N  H2   C15  H1   108.25  3.000
 M9N  H2   C15  N16  109.45  3.000
 M9N  H1   C15  N16  108.73  3.000
 M9N  H2   C15  N14  108.27  3.000
 M9N  H1   C15  N14  110.71  3.000
 M9N  N16  C15  N14  111.37  3.000
 M9N  H3   C01  S02  107.50  3.000
 M9N  H3   C01  N16  109.31  3.000
 M9N  S02  C01  N16  108.62  3.000
 M9N  H3   C01  C07  110.12  3.000
 M9N  N16  C01  C07  111.55  3.000
 M9N  S02  C01  C07  109.64  3.000
 M9N  O06  C04  O05  127.73  3.000
 M9N  O05  C04  C03  115.44  3.000
 M9N  O06  C04  C03  116.83  3.000
 M9N  C08  C07  C01  129.18  3.000
 M9N  C01  C07  C13  120.27  3.000
 M9N  C08  C07  C13  110.53  3.000
 M9N  CL1  C08  C07  122.07  3.000
 M9N  C07  C08  C10  115.72  3.000
 M9N  CL1  C08  C10  122.18  3.000
 M9N  H8   C11  H7   107.75  3.000
 M9N  H8   C11  H6   107.67  3.000
 M9N  H7   C11  H6   107.57  3.000
 M9N  H8   C11  C10  110.18  3.000
 M9N  H7   C11  C10  111.83  3.000
 M9N  H6   C11  C10  111.65  3.000
 M9N  H9   N14  C15  114.00  3.000
 M9N  H9   N14  C13  115.39  3.000
 M9N  C15  N14  C13  111.07  3.000
 M9N  H10  N16  C01  108.83  3.000
 M9N  H10  N16  C15  109.44  3.000
 M9N  C01  N16  C15  114.33  3.000
 M9N  C03  S02  C01   99.60  3.000
 M9N  C13  S12  C10   92.30  3.000
 M9N  H5   C03  H4   106.84  3.000
 M9N  H5   C03  S02  109.55  3.000
 M9N  H4   C03  S02  110.34  3.000
 M9N  H5   C03  C04  110.32  3.000
 M9N  H4   C03  C04  109.86  3.000
 M9N  S02  C03  C04  109.88  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  Var_01    N16  C15  N14  C13   -52.19  30.0  1
 M9N  Var_02    S12  C13  N14  C15  -156.39  30.0  1
 M9N  Var_03    N14  C15  N16  C01    60.23  30.0  1
 M9N  Var_04    H6   C11  C10  C08   122.67  30.0  2
 M9N  Var_05    C04  C03  S02  C01  -177.48  30.0  3
 M9N  Var_06    S02  C03  C04  O05   178.22  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  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

