# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:43:27 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (2E,4S)-4-({4-[2-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}amino)pent-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[C@@H](/C=C/C(O)=O)C(O)=O)c[nH]c2N1
#
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
 4DW  4DW  '(2E,4S)-4-({4-[2-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}amino)pent-2-enedioic acid'  ligand  48  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4DW
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
 4DW  C1   C  CR6    0   0.122   1.0101   0.4357   0.1124
 4DW  C2   C  CR16   0  -0.293   0.7443  -0.8617   0.5492
 4DW  C3   C  CR16   0  -0.258  -0.5423  -1.3707   0.5300
 4DW  C4   C  CR6    0  -0.049  -1.6075  -0.5882   0.0871
 4DW  C5   C  CR16   0  -0.281  -1.3457   0.7031  -0.3644
 4DW  C6   C  CR16   0  -0.300  -0.0522   1.2046  -0.3534
 4DW  C7   C  CH2    0  -0.505   2.4183   0.9518   0.1026
 4DW  C8   C  CH2    0  -0.514   3.1727   0.5220  -1.1647
 4DW  C9   C  CR5    0   0.009   4.6145   0.9016  -1.1138
 4DW  C10  C  CR15   0  -0.102   5.2245   1.9027  -1.8115
 4DW  N11  N  NR15   0  -0.665   6.5587   1.9649  -1.4498
 4DW  C12  C  CR56   0   0.648   6.7889   1.0157  -0.5323
 4DW  C13  C  CR56   0  -0.253   5.6258   0.3219  -0.2788
 4DW  C14  C  CR6    0   0.411   5.6652  -0.7653   0.6707
 4DW  O15  O  O      0  -0.498   4.6884  -1.4572   0.9550
 4DW  N16  N  N      0  -0.538   6.8825  -1.0105   1.2650
 4DW  C17  C  CR6    0   0.660   7.9450  -0.3047   0.9885
 4DW  N18  N  NR16   0  -0.731   7.9629   0.7201   0.0914
 4DW  N19  N  NH2    0  -0.826   9.0981  -0.5536   1.6345
 4DW  C20  C  C      0   0.541  -2.9764  -1.1873   0.0864
 4DW  O21  O  O      0  -0.504  -3.1346  -2.4017   0.0230
 4DW  N22  N  NH1    0  -0.661  -4.0032  -0.3358   0.1924
 4DW  C23  C  CH1    0  -0.189  -5.3754  -0.7889   0.1258
 4DW  C24  C  C1     0  -0.222  -6.2822   0.3957   0.2221
 4DW  C25  C  C1     0  -0.408  -7.2931   0.5072   1.0784
 4DW  C26  C  C      0   0.389  -8.2348   1.6891   1.1177
 4DW  O27  O  O      0  -0.605  -8.0408   2.6168   0.3064
 4DW  O28  O  OC    -1  -0.620  -9.1396   1.6289   1.9769
 4DW  C29  C  C      0   0.406  -5.6919  -1.5116  -1.2221
 4DW  O30  O  OC    -1  -0.603  -6.5742  -2.3856  -1.1581
 4DW  O31  O  O      0  -0.597  -5.0862  -1.1068  -2.2262
 4DW  H1   H  HCR6   0   0.250   1.5620  -1.4770   0.9078
 4DW  H2   H  HCR6   0   0.253  -0.7255  -2.3805   0.8730
 4DW  H3   H  HCR6   0   0.252  -2.1410   1.3281  -0.7518
 4DW  H4   H  HCR6   0   0.251   0.1321   2.2099  -0.7136
 4DW  H5   H  HCH2   0   0.242   2.4263   2.0418   0.1720
 4DW  H6   H  HCH2   0   0.255   2.9508   0.5668   0.9733
 4DW  H7   H  HCH2   0   0.241   3.0763  -0.5600  -1.2803
 4DW  H8   H  HCH2   0   0.242   2.6992   0.9761  -2.0386
 4DW  H9   H  HCR5   0   0.281   4.8259   2.5869  -2.5424
 4DW  H10  H  HNR5   0   0.420   7.2326   2.6139  -1.8221
 4DW  H11  H  HNR6   0   0.431   8.8047   1.2478  -0.0875
 4DW  H12  H  HNH2   0   0.407   9.1497  -1.4092   2.1604
 4DW  H13  H  HNH2   0   0.408   9.9712  -0.1894   1.2925
 4DW  H14  H  HNH1   0   0.398  -3.8262   0.6437   0.3409
 4DW  H15  H  HCH1   0   0.237  -5.5783  -1.4789   0.9504
 4DW  H16  H  H      0   0.246  -6.1059   1.1912  -0.4985
 4DW  H17  H  H      0   0.220  -7.4684  -0.2864   1.8005

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
 4DW  O27  C26  deloc     1.248  0.020  1.248
 4DW  O28  C26  deloc     1.249  0.020  1.249
 4DW  C26  C25  single    1.512  0.020  1.512
 4DW  C25  C24  double    1.330  0.020  1.330
 4DW  C24  C23  single    1.495  0.020  1.495
 4DW  C23  N22  single    1.447  0.020  1.447
 4DW  C23  C29  single    1.562  0.020  1.562
 4DW  O31  C29  deloc     1.240  0.020  1.240
 4DW  N22  C20  single    1.338  0.020  1.338
 4DW  C29  O30  deloc     1.244  0.020  1.244
 4DW  C20  O21  double    1.226  0.020  1.226
 4DW  C20  C4   single    1.494  0.020  1.494
 4DW  C5   C4   aromatic  1.393  0.020  1.393
 4DW  C5   C6   aromatic  1.387  0.020  1.387
 4DW  C4   C3   aromatic  1.394  0.020  1.394
 4DW  C6   C1   aromatic  1.392  0.020  1.392
 4DW  C3   C2   aromatic  1.384  0.020  1.384
 4DW  C1   C2   aromatic  1.394  0.020  1.394
 4DW  C1   C7   single    1.500  0.020  1.500
 4DW  C7   C8   single    1.536  0.020  1.536
 4DW  C8   C9   single    1.492  0.020  1.492
 4DW  C10  C9   aromatic  1.364  0.020  1.364
 4DW  C10  N11  aromatic  1.384  0.020  1.384
 4DW  C9   C13  aromatic  1.434  0.020  1.434
 4DW  N11  C12  aromatic  1.340  0.020  1.340
 4DW  C13  C12  aromatic  1.378  0.020  1.378
 4DW  C13  C14  single    1.444  0.020  1.444
 4DW  C12  N18  single    1.362  0.020  1.362
 4DW  O15  C14  double    1.230  0.020  1.230
 4DW  C14  N16  single    1.377  0.020  1.377
 4DW  N18  C17  single    1.362  0.020  1.362
 4DW  N16  C17  double    1.305  0.020  1.305
 4DW  C17  N19  single    1.345  0.020  1.345
 4DW  C2   H1   single    0.930  0.020  1.080
 4DW  C3   H2   single    0.930  0.020  1.080
 4DW  C5   H3   single    0.930  0.020  1.080
 4DW  C6   H4   single    0.930  0.020  1.080
 4DW  C7   H5   single    0.970  0.020  1.090
 4DW  C7   H6   single    0.970  0.020  1.090
 4DW  C8   H7   single    0.970  0.020  1.090
 4DW  C8   H8   single    0.970  0.020  1.090
 4DW  C10  H9   single    0.930  0.020  1.080
 4DW  N11  H10  single    0.860  0.020  1.020
 4DW  N18  H11  single    0.860  0.020  1.020
 4DW  N19  H12  single    0.890  0.020  1.040
 4DW  N19  H13  single    0.890  0.020  1.040
 4DW  N22  H14  single    0.860  0.020  1.020
 4DW  C23  H15  single    0.970  0.020  1.090
 4DW  C24  H16  single    0.930  0.020  1.080
 4DW  C25  H17  single    0.930  0.020  1.080

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
 4DW  C7   C1   C6   121.62  3.000
 4DW  C7   C1   C2   120.08  3.000
 4DW  C6   C1   C2   118.26  3.000
 4DW  H1   C2   C3   119.80  3.000
 4DW  H1   C2   C1   119.20  3.000
 4DW  C3   C2   C1   121.00  3.000
 4DW  H2   C3   C4   119.69  3.000
 4DW  H2   C3   C2   119.75  3.000
 4DW  C4   C3   C2   120.56  3.000
 4DW  C20  C4   C5   122.94  3.000
 4DW  C5   C4   C3   118.68  3.000
 4DW  C20  C4   C3   118.36  3.000
 4DW  H3   C5   C6   118.61  3.000
 4DW  H3   C5   C4   120.86  3.000
 4DW  C6   C5   C4   120.52  3.000
 4DW  H4   C6   C5   119.42  3.000
 4DW  H4   C6   C1   119.61  3.000
 4DW  C5   C6   C1   120.97  3.000
 4DW  H6   C7   H5   107.33  3.000
 4DW  H6   C7   C8   108.66  3.000
 4DW  H5   C7   C8   109.16  3.000
 4DW  H6   C7   C1   109.37  3.000
 4DW  H5   C7   C1   110.48  3.000
 4DW  C8   C7   C1   111.73  3.000
 4DW  H8   C8   H7   106.78  3.000
 4DW  H8   C8   C9   109.89  3.000
 4DW  H7   C8   C9   109.93  3.000
 4DW  H8   C8   C7   109.31  3.000
 4DW  H7   C8   C7   108.73  3.000
 4DW  C9   C8   C7   112.04  3.000
 4DW  C13  C9   C10  106.21  3.000
 4DW  C13  C9   C8   126.77  3.000
 4DW  C10  C9   C8   126.97  3.000
 4DW  H9   C10  N11  120.35  3.000
 4DW  H9   C10  C9   130.35  3.000
 4DW  N11  C10  C9   109.30  3.000
 4DW  H10  N11  C12  126.49  3.000
 4DW  H10  N11  C10  125.29  3.000
 4DW  C12  N11  C10  108.23  3.000
 4DW  N18  C12  C13  122.29  3.000
 4DW  N18  C12  N11  127.98  3.000
 4DW  C13  C12  N11  109.73  3.000
 4DW  C14  C13  C12  118.50  3.000
 4DW  C14  C13  C9   134.95  3.000
 4DW  C12  C13  C9   106.54  3.000
 4DW  N16  C14  O15  120.14  3.000
 4DW  N16  C14  C13  116.24  3.000
 4DW  O15  C14  C13  123.62  3.000
 4DW  C17  N16  C14  122.14  3.000
 4DW  N19  C17  N18  116.38  3.000
 4DW  N19  C17  N16  119.74  3.000
 4DW  N18  C17  N16  123.85  3.000
 4DW  H11  N18  C17  121.40  3.000
 4DW  H11  N18  C12  121.62  3.000
 4DW  C17  N18  C12  116.97  3.000
 4DW  H13  N19  H12  116.19  3.000
 4DW  H13  N19  C17  120.92  3.000
 4DW  H12  N19  C17  116.91  3.000
 4DW  N22  C20  O21  122.36  3.000
 4DW  O21  C20  C4   121.02  3.000
 4DW  N22  C20  C4   116.60  3.000
 4DW  H14  N22  C23  118.58  3.000
 4DW  H14  N22  C20  119.75  3.000
 4DW  C23  N22  C20  121.66  3.000
 4DW  H15  C23  C29  108.73  3.000
 4DW  H15  C23  C24  109.80  3.000
 4DW  C29  C23  C24  107.42  3.000
 4DW  H15  C23  N22  109.80  3.000
 4DW  C29  C23  N22  112.14  3.000
 4DW  C24  C23  N22  108.91  3.000
 4DW  H16  C24  C25  119.25  3.000
 4DW  H16  C24  C23  116.01  3.000
 4DW  C25  C24  C23  124.69  3.000
 4DW  H17  C25  C26  116.94  3.000
 4DW  H17  C25  C24  119.29  3.000
 4DW  C26  C25  C24  123.78  3.000
 4DW  O28  C26  O27  126.57  3.000
 4DW  O28  C26  C25  115.55  3.000
 4DW  O27  C26  C25  117.87  3.000
 4DW  O31  C29  O30  128.13  3.000
 4DW  O30  C29  C23  115.12  3.000
 4DW  O31  C29  C23  116.65  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
 4DW  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 4DW  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4DW  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 4DW  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 4DW  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 4DW  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 4DW  CONST_07  C12  N11  C10  C9      0.00   0.0  0
 4DW  CONST_08  N11  C12  C13  C9      0.00   0.0  0
 4DW  CONST_09  C12  C13  C9   C10     0.00   0.0  0
 4DW  CONST_10  C13  C12  N11  C10     0.00   0.0  0
 4DW  CONST_11  C13  C9   C10  N11     0.00   0.0  0
 4DW  CONST_12  N16  C17  N18  C12     0.00   0.0  0
 4DW  CONST_13  N18  C17  N16  C14     0.00   0.0  0
 4DW  CONST_14  C20  C4   C3   C2    180.00   0.0  0
 4DW  CONST_15  C7   C1   C2   C3    180.00   0.0  0
 4DW  CONST_16  C7   C1   C6   C5    180.00   0.0  0
 4DW  CONST_17  C20  C4   C5   C6    180.00   0.0  0
 4DW  CONST_18  N11  C10  C9   C8    180.00   0.0  0
 4DW  CONST_19  C12  C13  C9   C8    180.00   0.0  0
 4DW  CONST_20  C14  C13  C9   C8      0.00   0.0  0
 4DW  CONST_21  N19  C17  N18  C12   180.00   0.0  0
 4DW  CONST_22  N19  C17  N16  C14   180.00   0.0  0
 4DW  CONST_23  H3   C5   C6   C1    180.00   0.0  0
 4DW  CONST_24  H2   C3   C2   C1    180.00   0.0  0
 4DW  CONST_25  H4   C6   C1   C2    180.00   0.0  0
 4DW  CONST_26  H1   C2   C3   C4    180.00   0.0  0
 4DW  CONST_27  H10  N11  C10  C9    180.00   0.0  0
 4DW  CONST_28  H9   C10  N11  C12   180.00   0.0  0
 4DW  CONST_29  H11  N18  C17  N16   180.00   0.0  0
 4DW  CONST_30  H12  N19  C17  N16     0.00   0.0  0
 4DW  CONST_32  C23  N22  C20  C4    180.00   0.0  0
 4DW  CONST_33  H14  N22  C20  C4      0.00   0.0  0
 4DW  CONST_34  C23  N22  C20  O21     0.00   0.0  0
 4DW  Var_01    C9   C8   C7   C1   -173.69  30.0  3
 4DW  Var_02    C8   C7   C1   C2     83.30  30.0  2
 4DW  Var_03    N22  C20  C4   C3    153.75  30.0  2
 4DW  Var_04    C10  C9   C8   C7   -106.51  30.0  2
 4DW  Var_05    C26  C25  C24  C23  -177.22   0.0  2
 4DW  Var_06    O27  C26  C25  C24    -0.71  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
 4DW  chir_01  C23  C24  N22  C29  positiv

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
 4DW  plan-1  C1   0.020
 4DW  plan-1  C2   0.020
 4DW  plan-1  C3   0.020
 4DW  plan-1  C4   0.020
 4DW  plan-1  C5   0.020
 4DW  plan-1  C6   0.020
 4DW  plan-1  C7   0.020
 4DW  plan-1  C20  0.020
 4DW  plan-1  H1   0.020
 4DW  plan-1  H2   0.020
 4DW  plan-1  H3   0.020
 4DW  plan-1  H4   0.020
 4DW  plan-2  C23  0.020
 4DW  plan-2  C24  0.020
 4DW  plan-2  C25  0.020
 4DW  plan-2  C26  0.020
 4DW  plan-2  H16  0.020
 4DW  plan-2  H17  0.020
 4DW  plan-3  C8   0.020
 4DW  plan-3  C9   0.020
 4DW  plan-3  C10  0.020
 4DW  plan-3  N11  0.020
 4DW  plan-3  C12  0.020
 4DW  plan-3  C13  0.020
 4DW  plan-3  C14  0.020
 4DW  plan-3  O15  0.020
 4DW  plan-3  N16  0.020
 4DW  plan-3  C17  0.020
 4DW  plan-3  N18  0.020
 4DW  plan-3  N19  0.020
 4DW  plan-3  H9   0.020
 4DW  plan-3  H10  0.020
 4DW  plan-3  H11  0.020
 4DW  plan-3  H12  0.020
 4DW  plan-3  H13  0.020
 4DW  plan-4  C4   0.020
 4DW  plan-4  C20  0.020
 4DW  plan-4  O21  0.020
 4DW  plan-4  N22  0.020
 4DW  plan-4  C23  0.020
 4DW  plan-4  H14  0.020
 4DW  plan-5  C25  0.020
 4DW  plan-5  C26  0.020
 4DW  plan-5  O27  0.020
 4DW  plan-5  O28  0.020
 4DW  plan-6  C23  0.020
 4DW  plan-6  C29  0.020
 4DW  plan-6  O30  0.020
 4DW  plan-6  O31  0.020

