# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 07:57:47 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C(=O)NC(=O)C2=C1CSC2)C(O)=O
#
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
 CGW  CGW  '(2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid'  ligand  27  17  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CGW
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
 CGW  N    N  NH2    0  -0.778  -2.1241  -1.0499   1.3403
 CGW  CA   C  CH1    0  -0.223  -2.2239   0.1649   0.5588
 CGW  C    C  C      0   0.392  -3.6541   0.6415   0.1901
 CGW  OXT  O  OC     0  -0.614  -3.7143   1.7308  -0.4158
 CGW  CB   C  CH2    0  -0.345  -1.4292   0.0241  -0.7445
 CGW  O    O  O     -1  -0.595  -4.6052  -0.0922   0.5127
 CGW  CAF  C  CH2    0  -0.584   3.1580   1.0174   0.5821
 CGW  CAG  C  CH2    0  -0.631   0.7214   1.8716  -0.1644
 CGW  CAL  C  CR56   0  -0.183   2.1523  -0.0280   0.2386
 CGW  CAM  C  CR56   0   0.444   0.9247   0.3893  -0.1322
 CGW  CAN  C  CR6    0   0.560   2.4628  -1.4308   0.2396
 CGW  CAO  C  CR6    0   0.721   0.1534  -1.8215  -0.5669
 CGW  NAI  N  NR16   0  -0.732   1.4071  -2.2209  -0.1738
 CGW  NAQ  N  NR6    0  -0.559  -0.0696  -0.4602  -0.5200
 CGW  SAJ  S  S2     0  -0.001   2.2218   2.5864   0.5784
 CGW  H1   H  HNH2   0   0.344  -2.5198  -0.8772   2.2559
 CGW  H2   H  HNH2   0   0.330  -2.7225  -1.7547   0.9259
 CGW  H4   H  HCH1   0   0.231  -1.7639   0.9652   1.1504
 CGW  H6   H  HCH2   0   0.279  -1.9195  -0.6776  -1.4164
 CGW  H7   H  HCH2   0   0.279  -1.3827   0.9770  -1.2660
 CGW  H8   H  HCH2   0   0.285   3.5958   0.8658   1.5691
 CGW  H9   H  HCH2   0   0.282   3.9715   1.0558  -0.1446
 CGW  H10  H  HCH2   0   0.309   0.5867   2.2131  -1.1934
 CGW  H11  H  HCH2   0   0.304  -0.1507   2.1897   0.4062
 CGW  H12  H  HNR6   0   0.424   1.5711  -3.2195  -0.2116
 CGW  OAC  O  O      0  -0.459   3.5334  -1.9212   0.5543
 CGW  OAD  O  O      0  -0.481  -0.6746  -2.6220  -0.9485

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
 CGW  CAF  CAL  single  1.491  0.020  1.491
 CGW  CAF  SAJ  single  1.827  0.020  1.827
 CGW  CAG  CAM  single  1.497  0.020  1.497
 CGW  CAG  SAJ  single  1.820  0.020  1.820
 CGW  CAL  CAM  double  1.349  0.020  1.349
 CGW  CAL  CAN  single  1.437  0.020  1.437
 CGW  OAC  CAN  double  1.219  0.020  1.219
 CGW  CAM  NAQ  single  1.364  0.020  1.364
 CGW  CAN  NAI  single  1.382  0.020  1.382
 CGW  NAQ  CB   single  1.461  0.020  1.461
 CGW  NAQ  CAO  single  1.380  0.020  1.380
 CGW  NAI  CAO  single  1.373  0.020  1.373
 CGW  CB   CA   single  1.533  0.020  1.533
 CGW  CAO  OAD  double  1.213  0.020  1.213
 CGW  O    C    deloc   1.244  0.020  1.244
 CGW  CA   C    single  1.552  0.020  1.552
 CGW  CA   N    single  1.448  0.020  1.448
 CGW  C    OXT  deloc   1.248  0.020  1.248
 CGW  N    H1   single  0.890  0.020  1.040
 CGW  N    H2   single  0.890  0.020  1.040
 CGW  CA   H4   single  0.970  0.020  1.090
 CGW  CB   H6   single  0.970  0.020  1.090
 CGW  CB   H7   single  0.970  0.020  1.090
 CGW  CAF  H8   single  0.970  0.020  1.090
 CGW  CAF  H9   single  0.970  0.020  1.090
 CGW  CAG  H10  single  0.970  0.020  1.090
 CGW  CAG  H11  single  0.970  0.020  1.090
 CGW  NAI  H12  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
 CGW  H2   N    H1   104.94  3.000
 CGW  H2   N    CA   108.79  3.000
 CGW  H1   N    CA   108.55  3.000
 CGW  H4   CA   CB   107.96  3.000
 CGW  H4   CA   C    106.90  3.000
 CGW  CB   CA   C    107.70  3.000
 CGW  H4   CA   N    106.99  3.000
 CGW  C    CA   N    116.71  3.000
 CGW  CB   CA   N    110.25  3.000
 CGW  O    C    OXT  127.16  3.000
 CGW  OXT  C    CA   115.33  3.000
 CGW  O    C    CA   117.51  3.000
 CGW  H7   CB   H6   106.76  3.000
 CGW  H7   CB   NAQ  108.93  3.000
 CGW  H6   CB   NAQ  107.49  3.000
 CGW  H7   CB   CA   110.45  3.000
 CGW  H6   CB   CA   110.52  3.000
 CGW  NAQ  CB   CA   112.48  3.000
 CGW  H9   CAF  H8   107.96  3.000
 CGW  H9   CAF  SAJ  110.51  3.000
 CGW  H8   CAF  SAJ  109.09  3.000
 CGW  H9   CAF  CAL  111.96  3.000
 CGW  H8   CAF  CAL  112.45  3.000
 CGW  SAJ  CAF  CAL  104.84  3.000
 CGW  H11  CAG  H10  107.66  3.000
 CGW  H11  CAG  SAJ  109.35  3.000
 CGW  H10  CAG  SAJ  111.29  3.000
 CGW  H11  CAG  CAM  112.75  3.000
 CGW  H10  CAG  CAM  110.29  3.000
 CGW  SAJ  CAG  CAM  105.55  3.000
 CGW  CAN  CAL  CAM  119.94  3.000
 CGW  CAN  CAL  CAF  122.60  3.000
 CGW  CAM  CAL  CAF  117.41  3.000
 CGW  NAQ  CAM  CAL  123.30  3.000
 CGW  NAQ  CAM  CAG  120.78  3.000
 CGW  CAL  CAM  CAG  115.86  3.000
 CGW  OAC  CAN  NAI  121.21  3.000
 CGW  NAI  CAN  CAL  113.13  3.000
 CGW  OAC  CAN  CAL  125.65  3.000
 CGW  OAD  CAO  NAQ  123.45  3.000
 CGW  OAD  CAO  NAI  121.41  3.000
 CGW  NAQ  CAO  NAI  115.12  3.000
 CGW  H12  NAI  CAO  115.08  3.000
 CGW  H12  NAI  CAN  116.82  3.000
 CGW  CAO  NAI  CAN  128.09  3.000
 CGW  CAO  NAQ  CAM  120.41  3.000
 CGW  CAO  NAQ  CB   118.17  3.000
 CGW  CAM  NAQ  CB   121.05  3.000
 CGW  CAG  SAJ  CAF   94.93  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
 CGW  CONST_01  CAO  NAI  CAN  CAL    0.00   0.0  0
 CGW  CONST_02  NAI  CAO  NAQ  CAM    0.00   0.0  0
 CGW  CONST_03  NAQ  CAO  NAI  CAN    0.00   0.0  0
 CGW  CONST_04  NAI  CAO  NAQ  CB   180.00   0.0  0
 CGW  CONST_05  OAD  CAO  NAQ  CAM  180.00   0.0  0
 CGW  CONST_06  OAD  CAO  NAI  CAN  180.00   0.0  0
 CGW  CONST_07  OAC  CAN  NAI  CAO  180.00   0.0  0
 CGW  CONST_08  H12  NAI  CAN  CAL  180.00   0.0  0
 CGW  CONST_09  OAD  CAO  NAQ  CB     0.00   0.0  0
 CGW  Var_01    CAM  CAG  SAJ  CAF   10.65  30.0  1
 CGW  Var_02    CAL  CAF  SAJ  CAG  -10.34  30.0  1
 CGW  Var_03    SAJ  CAG  CAM  CAL   -8.28  30.0  1
 CGW  Var_04    SAJ  CAF  CAL  CAM    7.55  30.0  1
 CGW  Var_05    CAM  NAQ  CB   CA   -81.41  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
 CGW  chir_01  CA  CB  C  N  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
 CGW  plan-1  CB   0.020
 CGW  plan-1  CAF  0.020
 CGW  plan-1  CAG  0.020
 CGW  plan-1  CAL  0.020
 CGW  plan-1  CAM  0.020
 CGW  plan-1  CAN  0.020
 CGW  plan-1  CAO  0.020
 CGW  plan-1  NAI  0.020
 CGW  plan-1  NAQ  0.020
 CGW  plan-1  H12  0.020
 CGW  plan-1  OAC  0.020
 CGW  plan-1  OAD  0.020
 CGW  plan-2  CA   0.020
 CGW  plan-2  C    0.020
 CGW  plan-2  OXT  0.020
 CGW  plan-2  O    0.020

