# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:08:15 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (2~{S})-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl)carbamoylamino]phenyl]carbonylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(O)c1NC(=O)Nc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)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
 J49  J49  '(2~{S})-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl)carbamoylamino]phenyl]carbonylamino]pentanedioic acid'  ligand  46  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J49
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
 J49  C1   C  CR16   0   0.061  -59.1261  24.2131  23.3960
 J49  C3   C  CR6    0   0.492  -57.3843  24.0638  21.9862
 J49  C4   C  CR6    0   0.038  -56.7618  25.1320  22.6135
 J49  C5   C  CR6    0   0.491  -57.4610  25.7184  23.6809
 J49  C8   C  C      0   0.707  -55.4408  26.5339  21.1732
 J49  C10  C  C      0   0.369  -53.7770  27.8746  19.9427
 J49  C11  C  C1     0  -0.286  -54.4904  28.1433  18.7727
 J49  C12  C  C1     0  -0.269  -54.0378  29.1143  17.8967
 J49  C13  C  C      0  -0.052  -52.8646  29.8261  18.1310
 J49  C14  C  C1     0  -0.288  -52.1517  29.5416  19.2941
 J49  C15  C  C1     0  -0.322  -52.6008  28.5860  20.1865
 J49  C16  C  C      0   0.530  -52.4571  30.8817  17.1514
 J49  C19  C  CH1    0  -0.218  -50.5556  32.2539  16.3519
 J49  C23  C  C      0   0.422  -49.1512  31.7557  15.9224
 J49  C26  C  CH2    0  -0.396  -50.4232  33.6076  17.0642
 J49  C27  C  CH2    0  -0.567  -51.7438  34.2232  17.5002
 J49  C28  C  C      0   0.404  -51.6289  35.5774  18.2289
 J49  N2   N  N      0  -0.480  -58.5662  23.5923  22.3703
 J49  N6   N  N      0  -0.464  -58.6541  25.2383  24.0711
 J49  N9   N  NH1    0  -0.779  -54.1547  26.9059  20.8706
 J49  N17  N  NH1    0  -0.643  -51.1752  31.2636  17.2049
 J49  N21  N  NH1    0  -0.771  -55.5176  25.6294  22.1954
 J49  N22  N  NH2    0  -0.816  -56.9802  26.7841  24.3327
 J49  O7   O  O      0  -0.486  -56.4263  26.9639  20.6052
 J49  O18  O  O      0  -0.500  -53.2772  31.3461  16.3644
 J49  O20  O  OH1    0  -0.592  -56.7774  23.4835  20.9621
 J49  O24  O  OC    -1  -0.595  -48.6658  30.8072  16.5717
 J49  O25  O  O      0  -0.599  -48.6229  32.3782  14.9840
 J49  O29  O  OC    -1  -0.610  -50.5692  35.8092  18.8464
 J49  O30  O  O      0  -0.621  -52.6283  36.3239  18.1699
 J49  H1   H  HCR6   0   0.258  -60.0912  23.8322  23.7151
 J49  H2   H  H      0   0.270  -55.3897  27.5989  18.5331
 J49  H3   H  H      0   0.254  -54.6110  29.3124  17.0008
 J49  H4   H  H      0   0.255  -51.2492  30.0836  19.5471
 J49  H5   H  H      0   0.270  -52.0384  28.3996  21.0935
 J49  H6   H  HCH1   0   0.225  -51.1721  32.3787  15.4586
 J49  H7   H  HCH2   0   0.201  -49.7700  33.4834  17.9327
 J49  H8   H  HCH2   0   0.209  -49.9063  34.2913  16.3867
 J49  H9   H  HCH2   0   0.199  -52.4094  34.3320  16.6392
 J49  H10  H  HCH2   0   0.218  -52.2582  33.5362  18.1830
 J49  H12  H  HNH1   0   0.411  -53.4271  26.6207  21.5098
 J49  H13  H  HNH1   0   0.382  -50.5058  30.7002  17.7096
 J49  H14  H  HNH1   0   0.407  -54.6782  25.2267  22.5860
 J49  H15  H  HNH2   0   0.399  -57.4391  27.0847  25.1754
 J49  H16  H  HNH2   0   0.405  -56.0338  27.0895  24.1852
 J49  H11  H  HOH1   0   0.477  -57.3333  22.7621  20.6356

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
 J49  O25  C23  deloc     1.244  0.020  1.244
 J49  C23  C19  single    1.551  0.020  1.551
 J49  C23  O24  deloc     1.248  0.020  1.248
 J49  O18  C16  double    1.228  0.020  1.228
 J49  C19  C26  single    1.535  0.020  1.535
 J49  C19  N17  single    1.446  0.020  1.446
 J49  C26  C27  single    1.521  0.020  1.521
 J49  C16  N17  single    1.339  0.020  1.339
 J49  C16  C13  single    1.497  0.020  1.497
 J49  C27  C28  single    1.542  0.020  1.542
 J49  C12  C13  aromatic  1.392  0.020  1.392
 J49  C12  C11  aromatic  1.384  0.020  1.384
 J49  C13  C14  aromatic  1.394  0.020  1.394
 J49  C28  O30  deloc     1.249  0.020  1.249
 J49  C28  O29  deloc     1.248  0.020  1.248
 J49  C11  C10  aromatic  1.396  0.020  1.396
 J49  C14  C15  aromatic  1.382  0.020  1.382
 J49  C10  C15  aromatic  1.396  0.020  1.396
 J49  C10  N9   single    1.394  0.020  1.394
 J49  O7   C8   double    1.216  0.020  1.216
 J49  O20  C3   single    1.324  0.020  1.324
 J49  N9   C8   single    1.373  0.020  1.373
 J49  C8   N21  single    1.367  0.020  1.367
 J49  C3   N2   aromatic  1.329  0.020  1.329
 J49  C3   C4   aromatic  1.386  0.020  1.386
 J49  N2   C1   aromatic  1.323  0.020  1.323
 J49  N21  C4   single    1.404  0.020  1.404
 J49  C4   C5   aromatic  1.404  0.020  1.404
 J49  C1   N6   aromatic  1.315  0.020  1.315
 J49  C5   N6   aromatic  1.344  0.020  1.344
 J49  C5   N22  single    1.339  0.020  1.339
 J49  C1   H1   single    0.930  0.020  1.080
 J49  C11  H2   single    0.930  0.020  1.080
 J49  C12  H3   single    0.930  0.020  1.080
 J49  C14  H4   single    0.930  0.020  1.080
 J49  C15  H5   single    0.930  0.020  1.080
 J49  C19  H6   single    0.970  0.020  1.090
 J49  C26  H7   single    0.970  0.020  1.090
 J49  C26  H8   single    0.970  0.020  1.090
 J49  C27  H9   single    0.970  0.020  1.090
 J49  C27  H10  single    0.970  0.020  1.090
 J49  N9   H12  single    0.860  0.020  1.020
 J49  N17  H13  single    0.860  0.020  1.020
 J49  N21  H14  single    0.860  0.020  1.020
 J49  N22  H15  single    0.890  0.020  1.040
 J49  N22  H16  single    0.890  0.020  1.040
 J49  O20  H11  single    0.850  0.020  0.980

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
 J49  H1   C1   N6   116.21  3.000
 J49  H1   C1   N2   116.07  3.000
 J49  N6   C1   N2   127.72  3.000
 J49  O20  C3   N2   118.39  3.000
 J49  N2   C3   C4   122.81  3.000
 J49  O20  C3   C4   118.80  3.000
 J49  N21  C4   C5   121.32  3.000
 J49  C5   C4   C3   116.23  3.000
 J49  N21  C4   C3   122.43  3.000
 J49  N22  C5   N6   117.51  3.000
 J49  N22  C5   C4   121.58  3.000
 J49  N6   C5   C4   120.90  3.000
 J49  O7   C8   N21  122.53  3.000
 J49  N21  C8   N9   113.38  3.000
 J49  O7   C8   N9   124.09  3.000
 J49  N9   C10  C15  117.80  3.000
 J49  N9   C10  C11  123.58  3.000
 J49  C15  C10  C11  118.60  3.000
 J49  H2   C11  C12  119.10  3.000
 J49  H2   C11  C10  121.01  3.000
 J49  C12  C11  C10  119.89  3.000
 J49  H3   C12  C13  119.49  3.000
 J49  H3   C12  C11  118.65  3.000
 J49  C13  C12  C11  121.85  3.000
 J49  C16  C13  C14  123.44  3.000
 J49  C14  C13  C12  117.85  3.000
 J49  C16  C13  C12  118.68  3.000
 J49  H4   C14  C15  117.78  3.000
 J49  H4   C14  C13  121.28  3.000
 J49  C15  C14  C13  120.91  3.000
 J49  H5   C15  C14  119.39  3.000
 J49  H5   C15  C10  119.73  3.000
 J49  C14  C15  C10  120.88  3.000
 J49  O18  C16  N17  123.87  3.000
 J49  N17  C16  C13  115.83  3.000
 J49  O18  C16  C13  120.29  3.000
 J49  H6   C19  N17  108.58  3.000
 J49  H6   C19  C26  109.10  3.000
 J49  N17  C19  C26  111.53  3.000
 J49  H6   C19  C23  108.74  3.000
 J49  N17  C19  C23  109.35  3.000
 J49  C26  C19  C23  109.49  3.000
 J49  O25  C23  O24  127.43  3.000
 J49  O24  C23  C19  116.89  3.000
 J49  O25  C23  C19  115.65  3.000
 J49  H8   C26  H7   106.31  3.000
 J49  H8   C26  C27  109.59  3.000
 J49  H7   C26  C27  109.69  3.000
 J49  H8   C26  C19  107.75  3.000
 J49  H7   C26  C19  108.65  3.000
 J49  C27  C26  C19  114.52  3.000
 J49  H10  C27  H9   105.49  3.000
 J49  H10  C27  C28  106.91  3.000
 J49  H9   C27  C28  109.27  3.000
 J49  H10  C27  C26  109.40  3.000
 J49  H9   C27  C26  110.06  3.000
 J49  C28  C27  C26  115.23  3.000
 J49  O30  C28  O29  126.29  3.000
 J49  O29  C28  C27  117.39  3.000
 J49  O30  C28  C27  116.29  3.000
 J49  C3   N2   C1   115.71  3.000
 J49  C5   N6   C1   116.62  3.000
 J49  H12  N9   C10  114.99  3.000
 J49  H12  N9   C8   117.33  3.000
 J49  C10  N9   C8   126.10  3.000
 J49  H13  N17  C19  113.12  3.000
 J49  H13  N17  C16  119.70  3.000
 J49  C19  N17  C16  125.59  3.000
 J49  H14  N21  C8   120.43  3.000
 J49  H14  N21  C4   118.71  3.000
 J49  C8   N21  C4   120.46  3.000
 J49  H16  N22  H15  117.50  3.000
 J49  H16  N22  C5   120.57  3.000
 J49  H15  N22  C5   118.83  3.000
 J49  H11  O20  C3   108.93  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
 J49  CONST_01  C4   C3   N2   C1     0.00   0.0  0
 J49  CONST_02  C4   C5   N6   C1     0.00   0.0  0
 J49  CONST_03  N6   C1   N2   C3     0.00   0.0  0
 J49  CONST_04  N6   C5   C4   C3     0.00   0.0  0
 J49  CONST_05  N2   C3   C4   C5     0.00   0.0  0
 J49  CONST_06  N2   C1   N6   C5     0.00   0.0  0
 J49  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 J49  CONST_08  C13  C14  C15  C10    0.00   0.0  0
 J49  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 J49  CONST_10  C14  C15  C10  C11    0.00   0.0  0
 J49  CONST_11  C15  C14  C13  C12    0.00   0.0  0
 J49  CONST_12  C15  C10  C11  C12    0.00   0.0  0
 J49  CONST_13  O20  C3   N2   C1   180.00   0.0  0
 J49  CONST_14  N22  C5   N6   C1   180.00   0.0  0
 J49  CONST_15  N22  C5   C4   C3   180.00   0.0  0
 J49  CONST_16  O20  C3   C4   C5   180.00   0.0  0
 J49  CONST_17  C16  C13  C12  C11  180.00   0.0  0
 J49  CONST_18  N9   C10  C11  C12  180.00   0.0  0
 J49  CONST_19  N9   C10  C15  C14  180.00   0.0  0
 J49  CONST_20  C16  C13  C14  C15  180.00   0.0  0
 J49  CONST_21  N21  C4   C3   N2   180.00   0.0  0
 J49  CONST_22  N21  C4   C5   N6   180.00   0.0  0
 J49  CONST_23  H1   C1   N2   C3   180.00   0.0  0
 J49  CONST_24  H3   C12  C11  C10  180.00   0.0  0
 J49  CONST_25  H4   C14  C15  C10  180.00   0.0  0
 J49  CONST_26  H5   C15  C10  C11  180.00   0.0  0
 J49  CONST_27  H2   C11  C12  C13  180.00   0.0  0
 J49  CONST_33  H15  N22  C5   C4   180.00   0.0  0
 J49  CONST_34  H16  N22  C5   C4     0.00   0.0  0
 J49  CONST_36  O7   C8   N21  C4     0.00   0.0  0
 J49  CONST_37  O7   C8   N9   C10    0.00   0.0  0
 J49  CONST_38  C19  N17  C16  C13  180.00   0.0  0
 J49  CONST_39  N9   C8   N21  C4   180.00   0.0  0
 J49  CONST_40  N21  C8   N9   C10  180.00   0.0  0
 J49  CONST_41  H13  N17  C16  C13    0.00   0.0  0
 J49  CONST_42  O18  C16  N17  C19    0.00   0.0  0
 J49  Var_01    O18  C16  C13  C12   18.24  30.0  2
 J49  Var_02    C28  C27  C26  C19  179.47  30.0  3
 J49  Var_03    O30  C28  C27  C26  154.91  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
 J49  chir_01  C19  C23  C26  N17  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
 J49  plan-1  C1   0.020
 J49  plan-1  C3   0.020
 J49  plan-1  C4   0.020
 J49  plan-1  C5   0.020
 J49  plan-1  N2   0.020
 J49  plan-1  N6   0.020
 J49  plan-1  N21  0.020
 J49  plan-1  N22  0.020
 J49  plan-1  O20  0.020
 J49  plan-1  H1   0.020
 J49  plan-2  C19  0.020
 J49  plan-2  C23  0.020
 J49  plan-2  O24  0.020
 J49  plan-2  O25  0.020
 J49  plan-3  C27  0.020
 J49  plan-3  C28  0.020
 J49  plan-3  O29  0.020
 J49  plan-3  O30  0.020
 J49  plan-4  C10  0.020
 J49  plan-4  C11  0.020
 J49  plan-4  C12  0.020
 J49  plan-4  C13  0.020
 J49  plan-4  C14  0.020
 J49  plan-4  C15  0.020
 J49  plan-4  C16  0.020
 J49  plan-4  N9   0.020
 J49  plan-4  H2   0.020
 J49  plan-4  H3   0.020
 J49  plan-4  H4   0.020
 J49  plan-4  H5   0.020
 J49  plan-5  C4   0.020
 J49  plan-5  C8   0.020
 J49  plan-5  C10  0.020
 J49  plan-5  N9   0.020
 J49  plan-5  N21  0.020
 J49  plan-5  O7   0.020
 J49  plan-5  H12  0.020
 J49  plan-5  H14  0.020
 J49  plan-6  C13  0.020
 J49  plan-6  C16  0.020
 J49  plan-6  C19  0.020
 J49  plan-6  N17  0.020
 J49  plan-6  O18  0.020
 J49  plan-6  H13  0.020
 J49  plan-7  C5   0.020
 J49  plan-7  N22  0.020
 J49  plan-7  H15  0.020
 J49  plan-7  H16  0.020

