# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:50:04 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-(4-{[(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)carbamoyl]amino}benzoyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(NC(=O)Nc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C(=O)N1)N
#
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
 9L9  9L9  'N-(4-{[(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)carbamoyl]amino}benzoyl)-L-glutamic acid'  ligand  50  31  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9L9
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
 9L9  N2A   N  NH2   0  -0.825   8.6112   2.2752  -1.1251
 9L9  N1    N  N     0  -0.531   7.2086   1.6155   0.5547
 9L9  C2    C  CR6   0   0.696   7.5895   1.5290  -0.6948
 9L9  N3    N  NR16  0  -0.720   7.0064   0.6914  -1.5822
 9L9  C4    C  CR6   0   0.525   5.9406  -0.1531  -1.2573
 9L9  O4A   O  O     0  -0.506   5.4549  -0.8699  -2.1268
 9L9  C5    C  CR6   0  -0.062   5.5401  -0.0649   0.0975
 9L9  C6    C  CR6   0   0.491   6.1860   0.8267   0.9510
 9L9  N7    N  NH2   0  -0.820   5.8340   0.9382   2.2377
 9L9  O8A   O  O     0  -0.497   2.8846   0.5967  -0.2067
 9L9  N9    N  NH1   0  -0.787   2.2580  -1.4366   0.6377
 9L9  C1B   C  CR6   0   0.387   0.8751  -1.3600   0.6084
 9L9  C2B   C  CR16  0  -0.346   0.1725  -2.4890   1.0509
 9L9  C3B   C  CR16  0  -0.255  -1.2052  -2.5029   1.0803
 9L9  C4B   C  CR6   0  -0.062  -1.9424  -1.3978   0.6561
 9L9  C5B   C  CR16  0  -0.277  -1.2412  -0.2780   0.2178
 9L9  C6B   C  CR16  0  -0.307   0.1430  -0.2455   0.1880
 9L9  C7B   C  C     0   0.557  -3.4248  -1.4565   0.7398
 9L9  O7B   O  O     0  -0.484  -3.9963  -2.2794   1.4416
 9L9  CAW   C  C     0   0.724   3.1783  -0.4792   0.2814
 9L9  N     N  NH1   0  -0.660  -4.1105  -0.5381   0.0231
 9L9  CA    C  CH1   0  -0.196  -5.5461  -0.5124   0.0322
 9L9  C     C  C     0   0.550  -6.1115  -1.6554  -0.8001
 9L9  O     O  O     0  -0.429  -5.4782  -2.2983  -1.5950
 9L9  CB    C  CH2   0  -0.462  -6.0657   0.8343  -0.4806
 9L9  CG    C  CH2   0  -0.576  -5.6006   1.9772   0.4072
 9L9  CD    C  C     0   0.554  -6.1433   3.3121  -0.0218
 9L9  OE1   O  O     0  -0.442  -6.8345   3.5027  -0.9912
 9L9  OE2   O  OH1   0  -0.595  -5.7630   4.2818   0.8029
 9L9  OXT   O  OH1   0  -0.591  -7.4000  -1.8390  -0.5523
 9L9  H2A1  H  HNH2  0   0.413   8.9829   2.9788  -0.5107
 9L9  H2A2  H  HNH2  0   0.416   8.8451   2.3422  -2.1006
 9L9  H71N  H  HNH2  0   0.397   6.2441   1.6597   2.8039
 9L9  H72N  H  HNH2  0   0.402   5.0317   0.4517   2.5960
 9L9  H9    H  HNH1  0   0.413   2.6217  -2.3013   1.0101
 9L9  H2B   H  HCR6  0   0.274   0.7184  -3.3636   1.3838
 9L9  H6B   H  HCR6  0   0.287   0.6379   0.6474  -0.1529
 9L9  H3B   H  HCR6  0   0.261  -1.7136  -3.3882   1.4374
 9L9  H5B   H  HCR6  0   0.252  -1.7614   0.6198  -0.0915
 9L9  H5A   H  HNH1  0   0.397   4.6514  -1.7856   0.8678
 9L9  HN3   H  HNR6  0   0.418   7.3353   0.6636  -2.5379
 9L9  H     H  HNH1  0   0.408  -3.6433  -0.0492  -0.7243
 9L9  HA    H  HCH1  0   0.294  -5.8929  -0.6474   1.0601
 9L9  HB1C  H  HCH2  0   0.259  -5.7356   0.9882  -1.5112
 9L9  HB2C  H  HCH2  0   0.273  -7.1550   0.8026  -0.4996
 9L9  HG1C  H  HCH2  0   0.287  -5.8971   1.8015   1.4457
 9L9  HG2C  H  HCH2  0   0.286  -4.5095   2.0499   0.4232
 9L9  HE2   H  HOH1  0   0.480  -6.1201   5.1314   0.5037
 9L9  HB    H  HOH1  0   0.486  -7.7537  -2.5461  -1.1131
 9L9  N5A   N  NH1   0  -0.759   4.4637  -0.8456   0.5521

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
 9L9  N2A  C2    single    1.336  0.020  1.336
 9L9  N1   C2    double    1.309  0.020  1.309
 9L9  N1   C6    single    1.351  0.020  1.351
 9L9  C2   N3    single    1.352  0.020  1.352
 9L9  N3   C4    single    1.398  0.020  1.398
 9L9  C4   O4A   double    1.227  0.020  1.227
 9L9  C4   C5    single    1.416  0.020  1.416
 9L9  N5A  C5    single    1.405  0.020  1.405
 9L9  N5A  CAW   single    1.364  0.020  1.364
 9L9  C5   C6    double    1.393  0.020  1.393
 9L9  C6   N7    single    1.339  0.020  1.339
 9L9  O8A  CAW   double    1.217  0.020  1.217
 9L9  N9   C1B   single    1.385  0.020  1.385
 9L9  N9   CAW   single    1.375  0.020  1.375
 9L9  C1B  C2B   aromatic  1.401  0.020  1.401
 9L9  C1B  C6B   aromatic  1.398  0.020  1.398
 9L9  C2B  C3B   aromatic  1.378  0.020  1.378
 9L9  C3B  C4B   aromatic  1.395  0.020  1.395
 9L9  C4B  C5B   aromatic  1.392  0.020  1.392
 9L9  C4B  C7B   single    1.486  0.020  1.486
 9L9  C5B  C6B   aromatic  1.385  0.020  1.385
 9L9  C7B  O7B   double    1.223  0.020  1.223
 9L9  C7B  N     single    1.352  0.020  1.352
 9L9  N    CA    single    1.436  0.020  1.436
 9L9  CB   CG    single    1.520  0.020  1.520
 9L9  CB   CA    single    1.532  0.020  1.532
 9L9  CG   CD    single    1.504  0.020  1.504
 9L9  CD   OE1   double    1.206  0.020  1.206
 9L9  CD   OE2   single    1.329  0.020  1.329
 9L9  C    OXT   single    1.325  0.020  1.325
 9L9  C    O     double    1.202  0.020  1.202
 9L9  C    CA    single    1.523  0.020  1.523
 9L9  N2A  H2A1  single    0.860  0.020  1.020
 9L9  N2A  H2A2  single    0.860  0.020  1.020
 9L9  N7   H71N  single    0.860  0.020  1.020
 9L9  N7   H72N  single    0.860  0.020  1.020
 9L9  N9   H9    single    0.860  0.020  1.020
 9L9  C2B  H2B   single    0.930  0.020  1.080
 9L9  C6B  H6B   single    0.930  0.020  1.080
 9L9  C3B  H3B   single    0.930  0.020  1.080
 9L9  C5B  H5B   single    0.930  0.020  1.080
 9L9  N    H     single    0.860  0.020  1.020
 9L9  CA   HA    single    0.970  0.020  1.090
 9L9  CB   HB1C  single    0.970  0.020  1.090
 9L9  CB   HB2C  single    0.970  0.020  1.090
 9L9  CG   HG1C  single    0.970  0.020  1.090
 9L9  CG   HG2C  single    0.970  0.020  1.090
 9L9  OE2  HE2   single    0.850  0.020  0.980
 9L9  OXT  HB    single    0.850  0.020  0.980
 9L9  N5A  H5A   single    0.860  0.020  1.020
 9L9  N3   HN3   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
 9L9  H2A2  N2A  H2A1  117.41  3.000
 9L9  H2A2  N2A  C2    121.84  3.000
 9L9  H2A1  N2A  C2    118.47  3.000
 9L9  C6    N1   C2    117.50  3.000
 9L9  N3    C2   N1    122.80  3.000
 9L9  N3    C2   N2A   117.66  3.000
 9L9  N1    C2   N2A   119.53  3.000
 9L9  HN3   N3   C4    116.81  3.000
 9L9  HN3   N3   C2    119.80  3.000
 9L9  C4    N3   C2    123.39  3.000
 9L9  C5    C4   O4A   127.06  3.000
 9L9  C5    C4   N3    113.61  3.000
 9L9  O4A   C4   N3    119.34  3.000
 9L9  C6    C5   N5A   120.83  3.000
 9L9  C6    C5   C4    119.68  3.000
 9L9  N5A   C5   C4    119.46  3.000
 9L9  N7    C6   C5    121.36  3.000
 9L9  N7    C6   N1    115.62  3.000
 9L9  C5    C6   N1    123.02  3.000
 9L9  H72N  N7   H71N  118.22  3.000
 9L9  H72N  N7   C6    120.83  3.000
 9L9  H71N  N7   C6    119.62  3.000
 9L9  H9    N9   CAW   116.81  3.000
 9L9  H9    N9   C1B   114.51  3.000
 9L9  CAW   N9   C1B   128.62  3.000
 9L9  C6B   C1B  C2B   118.33  3.000
 9L9  C6B   C1B  N9    124.97  3.000
 9L9  C2B   C1B  N9    116.70  3.000
 9L9  H2B   C2B  C3B   119.28  3.000
 9L9  H2B   C2B  C1B   119.65  3.000
 9L9  C3B   C2B  C1B   121.07  3.000
 9L9  H3B   C3B  C4B   120.03  3.000
 9L9  H3B   C3B  C2B   119.03  3.000
 9L9  C4B   C3B  C2B   120.94  3.000
 9L9  C7B   C4B  C5B   123.51  3.000
 9L9  C7B   C4B  C3B   118.62  3.000
 9L9  C5B   C4B  C3B   117.83  3.000
 9L9  H5B   C5B  C6B   117.04  3.000
 9L9  H5B   C5B  C4B   121.00  3.000
 9L9  C6B   C5B  C4B   121.95  3.000
 9L9  H6B   C6B  C5B   119.07  3.000
 9L9  H6B   C6B  C1B   121.05  3.000
 9L9  C5B   C6B  C1B   119.88  3.000
 9L9  N     C7B  O7B   121.61  3.000
 9L9  N     C7B  C4B   116.70  3.000
 9L9  O7B   C7B  C4B   121.67  3.000
 9L9  N9    CAW  O8A   123.91  3.000
 9L9  N9    CAW  N5A   113.10  3.000
 9L9  O8A   CAW  N5A   122.99  3.000
 9L9  H     N    CA    117.36  3.000
 9L9  H     N    C7B   119.18  3.000
 9L9  CA    N    C7B   121.06  3.000
 9L9  HA    CA   CB    108.40  3.000
 9L9  HA    CA   C     107.67  3.000
 9L9  CB    CA   C     110.55  3.000
 9L9  HA    CA   N     108.72  3.000
 9L9  C     CA   N     110.75  3.000
 9L9  CB    CA   N     110.65  3.000
 9L9  OXT   C    O     124.17  3.000
 9L9  O     C    CA    124.54  3.000
 9L9  OXT   C    CA    111.28  3.000
 9L9  HB2C  CB   HB1C  106.83  3.000
 9L9  HB2C  CB   CG    109.75  3.000
 9L9  HB1C  CB   CG    110.64  3.000
 9L9  HB2C  CB   CA    108.61  3.000
 9L9  HB1C  CB   CA    109.69  3.000
 9L9  CG    CB   CA    111.21  3.000
 9L9  HG2C  CG   HG1C  105.49  3.000
 9L9  HG2C  CG   CD    107.78  3.000
 9L9  HG1C  CG   CD    108.39  3.000
 9L9  HG2C  CG   CB    111.33  3.000
 9L9  HG1C  CG   CB    110.53  3.000
 9L9  CD    CG   CB    112.98  3.000
 9L9  OE2   CD   OE1   123.22  3.000
 9L9  OE2   CD   CG    111.56  3.000
 9L9  OE1   CD   CG    125.22  3.000
 9L9  HE2   OE2  CD    110.04  3.000
 9L9  HB    OXT  C     110.35  3.000
 9L9  H5A   N5A  CAW   119.19  3.000
 9L9  H5A   N5A  C5    118.43  3.000
 9L9  CAW   N5A  C5    120.57  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
 9L9  CONST_01  C4B   C3B  C2B  C1B     0.00   0.0  0
 9L9  CONST_02  C4B   C5B  C6B  C1B     0.00   0.0  0
 9L9  CONST_03  C5B   C6B  C1B  C2B     0.00   0.0  0
 9L9  CONST_04  C5B   C4B  C3B  C2B     0.00   0.0  0
 9L9  CONST_05  C6B   C1B  C2B  C3B     0.00   0.0  0
 9L9  CONST_06  C6B   C5B  C4B  C3B     0.00   0.0  0
 9L9  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 9L9  CONST_08  C5    C6   N1   C2      0.00   0.0  0
 9L9  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 9L9  CONST_10  C6    N1   C2   N3      0.00   0.0  0
 9L9  CONST_11  C3B   C2B  C1B  N9    180.00   0.0  0
 9L9  CONST_12  C5B   C6B  C1B  N9    180.00   0.0  0
 9L9  CONST_13  C7B   C4B  C3B  C2B   180.00   0.0  0
 9L9  CONST_14  C7B   C4B  C5B  C6B   180.00   0.0  0
 9L9  CONST_15  C6    N1   C2   N2A   180.00   0.0  0
 9L9  CONST_16  C4    N3   C2   N2A   180.00   0.0  0
 9L9  CONST_17  N7    C6   N1   C2    180.00   0.0  0
 9L9  CONST_18  O4A   C4   N3   C2    180.00   0.0  0
 9L9  CONST_19  H3B   C3B  C2B  C1B   180.00   0.0  0
 9L9  CONST_20  H5B   C5B  C6B  C1B   180.00   0.0  0
 9L9  CONST_21  H6B   C6B  C1B  C2B   180.00   0.0  0
 9L9  CONST_22  H2B   C2B  C3B  C4B   180.00   0.0  0
 9L9  CONST_23  HN3   N3   C2   N1    180.00   0.0  0
 9L9  CONST_24  CAW   N9   C1B  C2B   180.00   0.0  0
 9L9  CONST_25  CAW   N9   C1B  C6B     0.00   0.0  0
 9L9  CONST_26  H9    N9   C1B  C2B     0.00   0.0  0
 9L9  CONST_27  H2A1  N2A  C2   N1      0.00   0.0  0
 9L9  CONST_28  H2A2  N2A  C2   N1    180.00   0.0  0
 9L9  CONST_29  H71N  N7   C6   N1      0.00   0.0  0
 9L9  CONST_30  H72N  N7   C6   N1    180.00   0.0  0
 9L9  CONST_31  O8A   CAW  N5A  C5      0.00   0.0  0
 9L9  CONST_32  C1B   N9   CAW  O8A     0.00   0.0  0
 9L9  CONST_33  CA    N    C7B  C4B   180.00   0.0  0
 9L9  CONST_34  C1B   N9   CAW  N5A   180.00   0.0  0
 9L9  CONST_35  N9    CAW  N5A  C5    180.00   0.0  0
 9L9  CONST_37  CA    N    C7B  O7B     0.00   0.0  0
 9L9  CONST_38  H5A   N5A  CAW  O8A   180.00   0.0  0
 9L9  CONST_39  HB    OXT  C    CA    180.00   0.0  0
 9L9  CONST_40  HE2   OE2  CD   CG    180.00   0.0  0
 9L9  Var_01    CAW   N5A  C5   C4    -77.94  30.0  2
 9L9  Var_02    O7B   C7B  C4B  C3B    17.61  30.0  2
 9L9  Var_03    CD    CG   CB   CA   -177.21  30.0  3
 9L9  Var_04    OE1   CD   CG   CB     -2.74  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
 9L9  chir_01  CA  N  CB  C  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
 9L9  plan-1  N2A   0.020
 9L9  plan-1  N1    0.020
 9L9  plan-1  C2    0.020
 9L9  plan-1  N3    0.020
 9L9  plan-1  C4    0.020
 9L9  plan-1  O4A   0.020
 9L9  plan-1  C5    0.020
 9L9  plan-1  C6    0.020
 9L9  plan-1  N7    0.020
 9L9  plan-1  H2A1  0.020
 9L9  plan-1  H2A2  0.020
 9L9  plan-1  H71N  0.020
 9L9  plan-1  H72N  0.020
 9L9  plan-1  HN3   0.020
 9L9  plan-1  N5A   0.020
 9L9  plan-2  CA    0.020
 9L9  plan-2  C     0.020
 9L9  plan-2  O     0.020
 9L9  plan-2  OXT   0.020
 9L9  plan-2  HB    0.020
 9L9  plan-3  CG    0.020
 9L9  plan-3  CD    0.020
 9L9  plan-3  OE1   0.020
 9L9  plan-3  OE2   0.020
 9L9  plan-3  HE2   0.020
 9L9  plan-4  N9    0.020
 9L9  plan-4  C1B   0.020
 9L9  plan-4  C2B   0.020
 9L9  plan-4  C3B   0.020
 9L9  plan-4  C4B   0.020
 9L9  plan-4  C5B   0.020
 9L9  plan-4  C6B   0.020
 9L9  plan-4  C7B   0.020
 9L9  plan-4  H2B   0.020
 9L9  plan-4  H6B   0.020
 9L9  plan-4  H3B   0.020
 9L9  plan-4  H5B   0.020
 9L9  plan-5  C4B   0.020
 9L9  plan-5  C7B   0.020
 9L9  plan-5  O7B   0.020
 9L9  plan-5  N     0.020
 9L9  plan-5  CA    0.020
 9L9  plan-5  H     0.020
 9L9  plan-6  C5    0.020
 9L9  plan-6  O8A   0.020
 9L9  plan-6  N9    0.020
 9L9  plan-6  C1B   0.020
 9L9  plan-6  CAW   0.020
 9L9  plan-6  H9    0.020
 9L9  plan-6  H5A   0.020
 9L9  plan-6  N5A   0.020

