# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 13:15:40 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[[methyl(thiophen-3-ylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC1=NC(=O)NC(=O)C1)Cc2cscc2
#
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
 M4Q  M4Q  6-[[methyl(thiophen-3-ylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione  ligand  30  17  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M4Q
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
 M4Q  CAA  C  CH3   0  -0.533  -0.6873   0.0141   1.5774
 M4Q  CAD  C  CR15  0  -0.460  -4.2957  -0.8391  -1.0893
 M4Q  CAE  C  CR15  0  -0.201  -3.0478  -0.3010  -1.0650
 M4Q  CAF  C  CR15  0  -0.534  -4.1104   1.0529   0.4768
 M4Q  CAG  C  CH2   0  -0.668   3.2143   1.2647   0.1242
 M4Q  CAH  C  CH2   0  -0.335  -1.6707   1.5767   0.0392
 M4Q  CAI  C  CH2   0  -0.318   0.7044   1.4105   0.2247
 M4Q  CAM  C  CR5   0   0.152  -2.9345   0.7979  -0.1610
 M4Q  CAN  C  C     0   0.263   1.9098   0.5509  -0.0040
 M4Q  CAO  C  C     0   0.582   4.4203   0.4430  -0.2116
 M4Q  CAP  C  C     0   0.606   2.9055  -1.4562  -0.5574
 M4Q  NAJ  N  N     0  -0.431   1.7794  -0.6799  -0.3018
 M4Q  NAK  N  NH1   0  -0.694   4.1545  -0.8620  -0.5155
 M4Q  NAQ  N  NT    0  -0.400  -0.5422   0.7018   0.3099
 M4Q  OAB  O  O     0  -0.431   5.5464   0.8839  -0.2083
 M4Q  OAC  O  O     0  -0.427   2.8000  -2.6295  -0.8212
 M4Q  SAL  S  S2    0   0.199  -5.3546  -0.0205  -0.0156
 M4Q  H1   H  HCH3  0   0.199  -0.7138   0.7040   2.4347
 M4Q  H2   H  HCH3  0   0.244  -1.6116  -0.5630   1.5860
 M4Q  H3   H  HCH3  0   0.244   0.1327  -0.6863   1.7272
 M4Q  H5   H  HCR5  0   0.258  -2.2255  -0.6700  -1.6617
 M4Q  H6   H  HCR5  0   0.290  -4.3054   1.8159   1.2160
 M4Q  H7   H  HCH2  0   0.333   3.2088   2.1594  -0.5053
 M4Q  H8   H  HCH2  0   0.340   3.3205   1.6335   1.1495
 M4Q  H9   H  HCH2  0   0.256  -1.4518   2.1355  -0.8757
 M4Q  H10  H  HCH2  0   0.217  -1.8221   2.3261   0.8331
 M4Q  H11  H  HCH2  0   0.241   0.9028   2.0557   1.0989
 M4Q  H12  H  HCH2  0   0.292   0.6752   2.0983  -0.6295
 M4Q  H13  H  HNH1  0   0.426   4.9448  -1.4589  -0.7312
 M4Q  H4   H  HCR5  0   0.293  -4.6509  -1.6706  -1.6783

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
 M4Q  OAC  CAP  double    1.207  0.020  1.207
 M4Q  CAP  NAK  single    1.384  0.020  1.384
 M4Q  CAP  NAJ  single    1.391  0.020  1.391
 M4Q  NAK  CAO  single    1.366  0.020  1.366
 M4Q  NAJ  CAN  double    1.273  0.020  1.273
 M4Q  CAO  OAB  double    1.209  0.020  1.209
 M4Q  CAO  CAG  single    1.498  0.020  1.498
 M4Q  CAN  CAG  single    1.493  0.020  1.493
 M4Q  CAN  CAI  single    1.498  0.020  1.498
 M4Q  CAA  NAQ  single    1.449  0.020  1.449
 M4Q  CAF  SAL  aromatic  1.715  0.020  1.715
 M4Q  CAF  CAM  aromatic  1.362  0.020  1.362
 M4Q  NAQ  CAI  single    1.436  0.020  1.436
 M4Q  NAQ  CAH  single    1.453  0.020  1.453
 M4Q  SAL  CAD  aromatic  1.716  0.020  1.716
 M4Q  CAH  CAM  single    1.498  0.020  1.498
 M4Q  CAM  CAE  aromatic  1.427  0.020  1.427
 M4Q  CAD  CAE  aromatic  1.359  0.020  1.359
 M4Q  CAA  H1   single    0.970  0.020  1.090
 M4Q  CAA  H2   single    0.970  0.020  1.090
 M4Q  CAA  H3   single    0.970  0.020  1.090
 M4Q  CAD  H4   single    0.930  0.020  1.080
 M4Q  CAE  H5   single    0.930  0.020  1.080
 M4Q  CAF  H6   single    0.930  0.020  1.080
 M4Q  CAG  H7   single    0.970  0.020  1.090
 M4Q  CAG  H8   single    0.970  0.020  1.090
 M4Q  CAH  H9   single    0.970  0.020  1.090
 M4Q  CAH  H10  single    0.970  0.020  1.090
 M4Q  CAI  H11  single    0.970  0.020  1.090
 M4Q  CAI  H12  single    0.970  0.020  1.090
 M4Q  NAK  H13  single    0.860  0.020  1.020

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
 M4Q  H3   CAA  H2   107.28  3.000
 M4Q  H3   CAA  H1   108.31  3.000
 M4Q  H2   CAA  H1   107.78  3.000
 M4Q  H3   CAA  NAQ  110.50  3.000
 M4Q  H2   CAA  NAQ  110.07  3.000
 M4Q  H1   CAA  NAQ  112.71  3.000
 M4Q  H4   CAD  SAL  120.40  3.000
 M4Q  H4   CAD  CAE  128.10  3.000
 M4Q  SAL  CAD  CAE  111.50  3.000
 M4Q  H5   CAE  CAM  123.51  3.000
 M4Q  H5   CAE  CAD  123.60  3.000
 M4Q  CAM  CAE  CAD  112.89  3.000
 M4Q  H6   CAF  SAL  120.50  3.000
 M4Q  H6   CAF  CAM  127.49  3.000
 M4Q  SAL  CAF  CAM  112.01  3.000
 M4Q  H8   CAG  H7   105.30  3.000
 M4Q  H8   CAG  CAO  108.46  3.000
 M4Q  H7   CAG  CAO  108.89  3.000
 M4Q  H8   CAG  CAN  109.05  3.000
 M4Q  H7   CAG  CAN  109.71  3.000
 M4Q  CAO  CAG  CAN  114.97  3.000
 M4Q  H10  CAH  H9   106.41  3.000
 M4Q  H10  CAH  NAQ  112.45  3.000
 M4Q  H9   CAH  NAQ  107.93  3.000
 M4Q  H10  CAH  CAM  109.50  3.000
 M4Q  H9   CAH  CAM  108.82  3.000
 M4Q  NAQ  CAH  CAM  111.53  3.000
 M4Q  H12  CAI  H11  104.76  3.000
 M4Q  H12  CAI  NAQ  109.41  3.000
 M4Q  H11  CAI  NAQ  113.40  3.000
 M4Q  H12  CAI  CAN  105.21  3.000
 M4Q  H11  CAI  CAN  108.15  3.000
 M4Q  NAQ  CAI  CAN  115.10  3.000
 M4Q  CAH  CAM  CAF  124.65  3.000
 M4Q  CAH  CAM  CAE  123.50  3.000
 M4Q  CAF  CAM  CAE  111.85  3.000
 M4Q  NAJ  CAN  CAI  120.54  3.000
 M4Q  CAI  CAN  CAG  114.56  3.000
 M4Q  NAJ  CAN  CAG  124.89  3.000
 M4Q  OAB  CAO  NAK  122.01  3.000
 M4Q  OAB  CAO  CAG  123.32  3.000
 M4Q  NAK  CAO  CAG  114.67  3.000
 M4Q  OAC  CAP  NAK  120.19  3.000
 M4Q  NAK  CAP  NAJ  119.04  3.000
 M4Q  OAC  CAP  NAJ  120.77  3.000
 M4Q  CAP  NAJ  CAN  119.97  3.000
 M4Q  H13  NAK  CAP  116.39  3.000
 M4Q  H13  NAK  CAO  117.27  3.000
 M4Q  CAP  NAK  CAO  126.34  3.000
 M4Q  CAI  NAQ  CAH  111.46  3.000
 M4Q  CAH  NAQ  CAA  111.76  3.000
 M4Q  CAI  NAQ  CAA  111.89  3.000
 M4Q  CAF  SAL  CAD   91.75  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
 M4Q  CONST_01  CAM  CAF  SAL  CAD     0.00   0.0  0
 M4Q  CONST_02  CAF  CAM  CAE  CAD     0.00   0.0  0
 M4Q  CONST_03  SAL  CAF  CAM  CAE     0.00   0.0  0
 M4Q  CONST_04  CAF  SAL  CAD  CAE     0.00   0.0  0
 M4Q  CONST_05  SAL  CAD  CAE  CAM     0.00   0.0  0
 M4Q  CONST_06  CAP  NAK  CAO  CAG     0.00   0.0  0
 M4Q  CONST_07  NAK  CAP  NAJ  CAN     0.00   0.0  0
 M4Q  CONST_08  NAJ  CAP  NAK  CAO     0.00   0.0  0
 M4Q  CONST_09  CAH  CAM  CAE  CAD   180.00   0.0  0
 M4Q  CONST_10  SAL  CAF  CAM  CAH   180.00   0.0  0
 M4Q  CONST_11  OAC  CAP  NAJ  CAN   180.00   0.0  0
 M4Q  CONST_12  OAC  CAP  NAK  CAO   180.00   0.0  0
 M4Q  CONST_13  OAB  CAO  NAK  CAP   180.00   0.0  0
 M4Q  CONST_14  H6   CAF  SAL  CAD   180.00   0.0  0
 M4Q  CONST_15  H4   CAD  SAL  CAF   180.00   0.0  0
 M4Q  CONST_16  H5   CAE  CAM  CAF   180.00   0.0  0
 M4Q  CONST_17  H13  NAK  CAO  CAG   180.00   0.0  0
 M4Q  Var_01    CAO  CAG  CAN  CAI  -175.23  30.0  1
 M4Q  Var_02    NAQ  CAH  CAM  CAE   -51.17  30.0  2
 M4Q  Var_03    NAQ  CAI  CAN  CAG  -170.79  30.0  3
 M4Q  Var_04    CAN  CAI  NAQ  CAA    75.08  30.0  3
 M4Q  Var_05    CAM  CAH  NAQ  CAA   -66.07  30.0  3
 M4Q  Var_06    H1   CAA  NAQ  CAH   -62.61  30.0  3

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
 M4Q  plan-1  CAD  0.020
 M4Q  plan-1  CAE  0.020
 M4Q  plan-1  CAF  0.020
 M4Q  plan-1  CAH  0.020
 M4Q  plan-1  CAM  0.020
 M4Q  plan-1  SAL  0.020
 M4Q  plan-1  H5   0.020
 M4Q  plan-1  H6   0.020
 M4Q  plan-1  H4   0.020
 M4Q  plan-2  CAG  0.020
 M4Q  plan-2  CAN  0.020
 M4Q  plan-2  CAO  0.020
 M4Q  plan-2  CAP  0.020
 M4Q  plan-2  NAJ  0.020
 M4Q  plan-2  NAK  0.020
 M4Q  plan-2  OAB  0.020
 M4Q  plan-2  OAC  0.020
 M4Q  plan-2  H13  0.020

