# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 11:13:43 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 2-cyclopropyl-4,5-dimethyl-thieno[2,3-d]pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc2sc(C(O)=O)c(C)c12)C3CC3
#
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
 8MW  8MW  '2-cyclopropyl-4,5-dimethyl-thieno[2,3-d]pyrimidine-6-carboxylic acid'  ligand  28  17  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8MW
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
 8MW  C4   C  CR6    0   0.406  -2.5433   0.1785   0.0105
 8MW  C5   C  CR56   0  -0.001  -0.4111  -0.4849   0.1072
 8MW  C6   C  CR5    0  -0.414   2.0582  -0.3522   0.1467
 8MW  N1   N  N      0  -0.446  -1.6899  -0.8265   0.1056
 8MW  C7   C  C      0   0.416   3.4816  -0.8584   0.2045
 8MW  C8   C  CH1    0  -0.371  -3.9867  -0.1272   0.0049
 8MW  C9   C  CH2    0  -0.468  -4.5116  -1.2724   0.8336
 8MW  C10  C  CH2    0  -0.468  -4.4805  -1.3941  -0.6464
 8MW  O1   O  O      0  -0.567   4.4119  -0.0360   0.1646
 8MW  O    O  OC    -1  -0.592   3.5659  -2.0998   0.2888
 8MW  C1   C  CR5    0   0.158   1.5147   0.8925   0.0482
 8MW  C    C  CH3    0  -0.770   2.2980   2.1642  -0.0224
 8MW  S    S  S2     0   0.197   0.8707  -1.6297   0.2145
 8MW  C2   C  CR56   0   0.050   0.0704   0.8315   0.0207
 8MW  N    N  N      0  -0.462  -2.2065   1.4700  -0.0830
 8MW  C3   C  CR6    0   0.248  -0.9270   1.8171  -0.0794
 8MW  H1   H  HCH1   0   0.270  -4.6215   0.7455  -0.0779
 8MW  H2   H  HCH2   0   0.255  -3.7880  -1.8366   1.4075
 8MW  H3   H  HCH2   0   0.261  -5.4662  -1.1247   1.3211
 8MW  H4   H  HCH2   0   0.261  -5.4130  -1.3342  -1.1923
 8MW  H5   H  HCH2   0   0.255  -3.7342  -2.0406  -1.0895
 8MW  H6   H  HCH3   0   0.257   0.0355   3.5019  -1.0076
 8MW  H7   H  HCH3   0   0.265  -1.5639   3.8308  -0.3285
 8MW  H8   H  HCH3   0   0.261  -0.1620   3.6490   0.7292
 8MW  H10  H  HCH3   0   0.239   2.0799   2.7116  -0.9398
 8MW  H11  H  HCH3   0   0.240   2.0577   2.8247   0.8122
 8MW  H12  H  HCH3   0   0.275   3.3611   1.9547   0.0060
 8MW  C11  C  CH3    0  -0.756  -0.6376   3.2808  -0.1804

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
 8MW  O1   C7   deloc     1.242  0.020  1.242
 8MW  C7   O    deloc     1.247  0.020  1.247
 8MW  C7   C6   single    1.512  0.020  1.512
 8MW  S    C6   aromatic  1.746  0.020  1.746
 8MW  S    C5   aromatic  1.722  0.020  1.722
 8MW  C6   C1   aromatic  1.362  0.020  1.362
 8MW  C5   N1   aromatic  1.324  0.020  1.324
 8MW  C5   C2   aromatic  1.404  0.020  1.404
 8MW  C1   C    single    1.495  0.020  1.495
 8MW  C1   C2   aromatic  1.446  0.020  1.446
 8MW  N1   C4   aromatic  1.322  0.020  1.322
 8MW  C2   C3   aromatic  1.406  0.020  1.406
 8MW  C10  C9   single    1.485  0.020  1.485
 8MW  C10  C8   single    1.508  0.020  1.508
 8MW  C4   C8   single    1.475  0.020  1.475
 8MW  C4   N    aromatic  1.338  0.020  1.338
 8MW  C9   C8   single    1.508  0.020  1.508
 8MW  C3   N    aromatic  1.326  0.020  1.326
 8MW  C3   C11  single    1.495  0.020  1.495
 8MW  C8   H1   single    0.970  0.020  1.090
 8MW  C9   H2   single    0.970  0.020  1.090
 8MW  C9   H3   single    0.970  0.020  1.090
 8MW  C10  H4   single    0.970  0.020  1.090
 8MW  C10  H5   single    0.970  0.020  1.090
 8MW  C11  H6   single    0.970  0.020  1.090
 8MW  C11  H7   single    0.970  0.020  1.090
 8MW  C11  H8   single    0.970  0.020  1.090
 8MW  C    H10  single    0.970  0.020  1.090
 8MW  C    H11  single    0.970  0.020  1.090
 8MW  C    H12  single    0.970  0.020  1.090

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
 8MW  N    C4   C8   116.49  3.000
 8MW  N    C4   N1   125.19  3.000
 8MW  C8   C4   N1   118.32  3.000
 8MW  C2   C5   S    111.83  3.000
 8MW  C2   C5   N1   124.97  3.000
 8MW  S    C5   N1   123.20  3.000
 8MW  S    C6   C1   113.59  3.000
 8MW  C1   C6   C7   133.20  3.000
 8MW  S    C6   C7   113.21  3.000
 8MW  C5   N1   C4   115.32  3.000
 8MW  O    C7   O1   127.63  3.000
 8MW  O    C7   C6   113.54  3.000
 8MW  O1   C7   C6   118.83  3.000
 8MW  H1   C8   C10  116.90  3.000
 8MW  H1   C8   C9   116.76  3.000
 8MW  C10  C8   C9    59.01  3.000
 8MW  H1   C8   C4   114.02  3.000
 8MW  C9   C8   C4   119.72  3.000
 8MW  C10  C8   C4   119.75  3.000
 8MW  H3   C9   H2   114.97  3.000
 8MW  H3   C9   C10  118.59  3.000
 8MW  H2   C9   C10  118.15  3.000
 8MW  H3   C9   C8   116.81  3.000
 8MW  H2   C9   C8   117.04  3.000
 8MW  C10  C9   C8    60.49  3.000
 8MW  H5   C10  H4   114.88  3.000
 8MW  H5   C10  C9   118.12  3.000
 8MW  H4   C10  C9   118.69  3.000
 8MW  H5   C10  C8   116.93  3.000
 8MW  H4   C10  C8   116.97  3.000
 8MW  C9   C10  C8    60.50  3.000
 8MW  C2   C1   C    123.93  3.000
 8MW  C2   C1   C6   111.20  3.000
 8MW  C    C1   C6   124.87  3.000
 8MW  H12  C    H11  108.24  3.000
 8MW  H12  C    H10  108.37  3.000
 8MW  H11  C    H10  107.20  3.000
 8MW  H12  C    C1   110.37  3.000
 8MW  H11  C    C1   111.31  3.000
 8MW  H10  C    C1   111.22  3.000
 8MW  C6   S    C5    91.00  3.000
 8MW  C3   C2   C1   132.89  3.000
 8MW  C3   C2   C5   114.73  3.000
 8MW  C1   C2   C5   112.38  3.000
 8MW  C3   N    C4   119.70  3.000
 8MW  N    C3   C2   120.10  3.000
 8MW  N    C3   C11  116.28  3.000
 8MW  C2   C3   C11  123.62  3.000
 8MW  H8   C11  H7   108.32  3.000
 8MW  H8   C11  H6   107.18  3.000
 8MW  H7   C11  H6   108.68  3.000
 8MW  H8   C11  C3   111.01  3.000
 8MW  H7   C11  C3   109.85  3.000
 8MW  H6   C11  C3   111.69  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
 8MW  CONST_01  S    C5   N1  C4    180.00   0.0  0
 8MW  CONST_02  C2   C5   N1  C4      0.00   0.0  0
 8MW  CONST_03  C2   C3   N   C4      0.00   0.0  0
 8MW  CONST_04  C1   C6   S   C5      0.00   0.0  0
 8MW  CONST_05  N    C4   N1  C5      0.00   0.0  0
 8MW  CONST_06  C6   C1   C2  C5      0.00   0.0  0
 8MW  CONST_07  N    C3   C2  C5      0.00   0.0  0
 8MW  CONST_08  N1   C5   S   C6    180.00   0.0  0
 8MW  CONST_09  C2   C5   S   C6      0.00   0.0  0
 8MW  CONST_10  C3   C2   C1  C6    180.00   0.0  0
 8MW  CONST_11  C1   C2   C5  N1    180.00   0.0  0
 8MW  CONST_12  C3   C2   C5  N1      0.00   0.0  0
 8MW  CONST_13  C3   N    C4  N1      0.00   0.0  0
 8MW  CONST_14  S    C5   C2  C1      0.00   0.0  0
 8MW  CONST_15  N    C3   C2  C1    180.00   0.0  0
 8MW  CONST_16  C2   C1   C6  S       0.00   0.0  0
 8MW  CONST_17  C3   C2   C5  S     180.00   0.0  0
 8MW  CONST_18  C8   C4   N1  C5    180.00   0.0  0
 8MW  CONST_19  C3   N    C4  C8    180.00   0.0  0
 8MW  CONST_20  C11  C3   N   C4    180.00   0.0  0
 8MW  CONST_21  C7   C6   S   C5    180.00   0.0  0
 8MW  CONST_22  C    C1   C2  C5    180.00   0.0  0
 8MW  CONST_23  C11  C3   C2  C5    180.00   0.0  0
 8MW  CONST_24  C2   C1   C6  C7    180.00   0.0  0
 8MW  CONST_25  C1   C2   C3  C11     0.00   0.0  0
 8MW  CONST_26  S    C6   C1  C     180.00   0.0  0
 8MW  CONST_27  C3   C2   C1  C       0.00   0.0  0
 8MW  Var_01    C9   C10  C8  C4    108.84  30.0  1
 8MW  Var_02    C10  C8   C4  N1    -34.26  30.0  2
 8MW  Var_03    S    C6   C7  O1   -179.94  30.0  2
 8MW  Var_04    H10  C    C1  C6    120.89  30.0  2
 8MW  Var_05    H6   C11  C3  C2     54.74  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
 8MW  chir_01  C8  C10  C4  C9  both

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
 8MW  plan-1  C4   0.020
 8MW  plan-1  C5   0.020
 8MW  plan-1  C6   0.020
 8MW  plan-1  N1   0.020
 8MW  plan-1  C7   0.020
 8MW  plan-1  C8   0.020
 8MW  plan-1  C1   0.020
 8MW  plan-1  C    0.020
 8MW  plan-1  S    0.020
 8MW  plan-1  C2   0.020
 8MW  plan-1  N    0.020
 8MW  plan-1  C3   0.020
 8MW  plan-1  C11  0.020
 8MW  plan-2  C6   0.020
 8MW  plan-2  C7   0.020
 8MW  plan-2  O1   0.020
 8MW  plan-2  O    0.020

