# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 04:29:43 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  48  31  .  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_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  -0.824   8.6067   2.0011  -1.5273
 9L9  N1    N  N      0  -0.530   7.1776   1.7280   0.2347
 9L9  C2    C  C      0   0.695   7.5962   1.3469  -0.9455
 9L9  N3    N  NH1    0  -0.719   7.0316   0.3249  -1.6283
 9L9  C4    C  C      0   0.525   5.9549  -0.4221  -1.1411
 9L9  O4A   O  O      0  -0.505   5.4927  -1.3289  -1.8262
 9L9  C5    C  C      0  -0.062   5.5176  -0.0174   0.1433
 9L9  C6    C  C      0   0.486   6.1365   1.0582   0.7748
 9L9  N7    N  NH2    0  -0.817   5.7139   1.5051   1.9661
 9L9  O8A   O  O      0  -0.497   2.8557   0.5941  -0.2587
 9L9  N9    N  NH1    0  -0.787   2.2384  -1.2771   0.9066
 9L9  C1B   C  CR6    0   0.383   0.8541  -1.2384   0.8203
 9L9  C2B   C  CR16   0  -0.344   0.1635  -2.3837   1.2334
 9L9  C3B   C  CR16   0  -0.260  -1.2148  -2.4284   1.2141
 9L9  C4B   C  CR6    0  -0.062  -1.9648  -1.3408   0.7699
 9L9  C5B   C  CR16   0  -0.287  -1.2728  -0.2013   0.3680
 9L9  C6B   C  CR16   0  -0.303   0.1114  -0.1370   0.3865
 9L9  C7B   C  C      0   0.546  -3.4540  -1.4498   0.7890
 9L9  O7B   O  O      0  -0.507  -4.0062  -2.3408   1.4277
 9L9  CAW   C  C      0   0.717   3.1522  -0.3830   0.4043
 9L9  N     N  NH1    0  -0.639  -4.1371  -0.5169   0.1112
 9L9  CA    C  CH1    0  -0.191  -5.5732  -0.5732  -0.0442
 9L9  C     C  C      0   0.410  -6.0172  -1.6412  -1.0756
 9L9  O     O  O     -1  -0.600  -5.1550  -2.0898  -1.8504
 9L9  CB    C  CH2    0  -0.443  -6.1022   0.8080  -0.4358
 9L9  CG    C  CH2    0  -0.576  -5.8392   1.8726   0.6171
 9L9  CD    C  C      0   0.411  -6.4247   3.2654   0.3240
 9L9  OE1   O  O      0  -0.609  -7.1229   3.4040  -0.6996
 9L9  OE2   O  OC    -1  -0.634  -6.1487   4.1569   1.1551
 9L9  OXT   O  OC     0  -0.620  -7.2306  -1.9311  -1.0465
 9L9  H2A1  H  HNH2   0   0.412   9.1027   2.6862  -0.9836
 9L9  H2A2  H  HNH2   0   0.415   9.0659   1.6447  -2.3478
 9L9  H71N  H  HNH2   0   0.396   6.2737   2.1767   2.4616
 9L9  H72N  H  HNH2   0   0.400   5.0497   0.9706   2.4977
 9L9  H9    H  HNH1   0   0.411   2.6072  -2.1001   1.3592
 9L9  H2B   H  HCR6   0   0.270   0.7172  -3.2489   1.5787
 9L9  H6B   H  HCR6   0   0.281   0.5964   0.7722   0.0733
 9L9  H3B   H  HCR6   0   0.257  -1.7151  -3.3273   1.5478
 9L9  H5B   H  HCR6   0   0.251  -1.8007   0.6887   0.0490
 9L9  H5A   H  HNH1   0   0.396   4.6244  -1.5627   1.2110
 9L9  HN3   H  HNH1   0   0.418   7.3822   0.0770  -2.5439
 9L9  H     H  HNH1   0   0.389  -3.6390   0.0454  -0.5598
 9L9  HA    H  HCH1   0   0.226  -6.0052  -0.8384   0.9245
 9L9  HB1C  H  HCH2   0   0.209  -5.6638   1.1067  -1.3947
 9L9  HB2C  H  HCH2   0   0.226  -7.1743   0.7160  -0.6085
 9L9  HG1C  H  HCH2   0   0.219  -6.2372   1.5321   1.5812
 9L9  HG2C  H  HCH2   0   0.220  -4.7632   1.9858   0.7833
 9L9  N5A   N  NH1    0  -0.756   4.4387  -0.6860   0.7462

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    1.337  0.020  1.337
 9L9  N1   C2    double    1.309  0.020  1.309
 9L9  N1   C6    single    1.351  0.020  1.351
 9L9  C2   N3    single    1.353  0.020  1.353
 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    1.365  0.020  1.365
 9L9  C5   C6    double    1.392  0.020  1.392
 9L9  C6   N7    single    1.341  0.020  1.341
 9L9  O8A  CAW   double    1.217  0.020  1.217
 9L9  N9   C1B   single    1.388  0.020  1.388
 9L9  N9   CAW   single    1.374  0.020  1.374
 9L9  C1B  C2B   aromatic  1.400  0.020  1.400
 9L9  C1B  C6B   aromatic  1.397  0.020  1.397
 9L9  C2B  C3B   aromatic  1.379  0.020  1.379
 9L9  C3B  C4B   aromatic  1.394  0.020  1.394
 9L9  C4B  C5B   aromatic  1.392  0.020  1.392
 9L9  C4B  C7B   single    1.493  0.020  1.493
 9L9  C5B  C6B   aromatic  1.386  0.020  1.386
 9L9  C7B  O7B   double    1.228  0.020  1.228
 9L9  C7B  N     single    1.340  0.020  1.340
 9L9  N    CA    single    1.446  0.020  1.446
 9L9  CB   CG    single    1.520  0.020  1.520
 9L9  CB   CA    single    1.530  0.020  1.530
 9L9  CG   CD    single    1.539  0.020  1.539
 9L9  CD   OE1   deloc     1.247  0.020  1.247
 9L9  CD   OE2   deloc     1.250  0.020  1.250
 9L9  C    OXT   deloc     1.248  0.020  1.248
 9L9  C    O     deloc     1.243  0.020  1.243
 9L9  C    CA    single    1.550  0.020  1.550
 9L9  N2A  H2A1  single    0.860  0.020  1.020
 9L9  N2A  H2A2  single    0.860  0.020  1.020
 9L9  N7   H71N  single    0.890  0.020  1.040
 9L9  N7   H72N  single    0.890  0.020  1.040
 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  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  117.22  3.000
 9L9  H2A2  N2A  C2    121.79  3.000
 9L9  H2A1  N2A  C2    118.10  3.000
 9L9  C6    N1   C2    117.56  3.000
 9L9  N3    C2   N1    122.80  3.000
 9L9  N3    C2   N2A   117.75  3.000
 9L9  N1    C2   N2A   119.44  3.000
 9L9  HN3   N3   C4    116.84  3.000
 9L9  HN3   N3   C2    119.84  3.000
 9L9  C4    N3   C2    123.32  3.000
 9L9  C5    C4   O4A   126.98  3.000
 9L9  C5    C4   N3    113.65  3.000
 9L9  O4A   C4   N3    119.37  3.000
 9L9  C6    C5   N5A   120.95  3.000
 9L9  C6    C5   C4    119.67  3.000
 9L9  N5A   C5   C4    119.36  3.000
 9L9  N7    C6   C5    121.36  3.000
 9L9  N7    C6   N1    115.66  3.000
 9L9  C5    C6   N1    122.98  3.000
 9L9  H72N  N7   H71N  117.57  3.000
 9L9  H72N  N7   C6    120.08  3.000
 9L9  H71N  N7   C6    119.03  3.000
 9L9  H9    N9   CAW   116.86  3.000
 9L9  H9    N9   C1B   114.54  3.000
 9L9  CAW   N9   C1B   128.52  3.000
 9L9  C6B   C1B  C2B   118.31  3.000
 9L9  C6B   C1B  N9    124.86  3.000
 9L9  C2B   C1B  N9    116.81  3.000
 9L9  H2B   C2B  C3B   119.29  3.000
 9L9  H2B   C2B  C1B   119.68  3.000
 9L9  C3B   C2B  C1B   121.03  3.000
 9L9  H3B   C3B  C4B   119.86  3.000
 9L9  H3B   C3B  C2B   119.01  3.000
 9L9  C4B   C3B  C2B   121.13  3.000
 9L9  C7B   C4B  C5B   123.99  3.000
 9L9  C7B   C4B  C3B   118.40  3.000
 9L9  C5B   C4B  C3B   117.59  3.000
 9L9  H5B   C5B  C6B   116.92  3.000
 9L9  H5B   C5B  C4B   121.02  3.000
 9L9  C6B   C5B  C4B   122.04  3.000
 9L9  H6B   C6B  C5B   119.01  3.000
 9L9  H6B   C6B  C1B   121.09  3.000
 9L9  C5B   C6B  C1B   119.89  3.000
 9L9  N     C7B  O7B   122.62  3.000
 9L9  N     C7B  C4B   116.80  3.000
 9L9  O7B   C7B  C4B   120.55  3.000
 9L9  N9    CAW  O8A   124.03  3.000
 9L9  N9    CAW  N5A   113.00  3.000
 9L9  O8A   CAW  N5A   122.96  3.000
 9L9  H     N    CA    116.19  3.000
 9L9  H     N    C7B   118.26  3.000
 9L9  CA    N    C7B   122.24  3.000
 9L9  HA    CA   CB    108.01  3.000
 9L9  HA    CA   C     108.02  3.000
 9L9  CB    CA   C     110.66  3.000
 9L9  HA    CA   N     107.86  3.000
 9L9  C     CA   N     112.52  3.000
 9L9  CB    CA   N     109.62  3.000
 9L9  OXT   C    O     127.25  3.000
 9L9  O     C    CA    117.70  3.000
 9L9  OXT   C    CA    115.03  3.000
 9L9  HB2C  CB   HB1C  106.14  3.000
 9L9  HB2C  CB   CG    109.82  3.000
 9L9  HB1C  CB   CG    110.24  3.000
 9L9  HB2C  CB   CA    107.72  3.000
 9L9  HB1C  CB   CA    109.37  3.000
 9L9  CG    CB   CA    113.27  3.000
 9L9  HG2C  CG   HG1C  104.79  3.000
 9L9  HG2C  CG   CD    108.02  3.000
 9L9  HG1C  CG   CD    108.07  3.000
 9L9  HG2C  CG   CB    110.34  3.000
 9L9  HG1C  CG   CB    109.18  3.000
 9L9  CD    CG   CB    115.85  3.000
 9L9  OE2   CD   OE1   126.18  3.000
 9L9  OE2   CD   CG    115.78  3.000
 9L9  OE1   CD   CG    118.04  3.000
 9L9  H5A   N5A  CAW   118.78  3.000
 9L9  H5A   N5A  C5    118.00  3.000
 9L9  CAW   N5A  C5    120.69  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  Var_01    CAW   N5A  C5   C4    -80.56  30.0  3
 9L9  Var_02    O7B   C7B  C4B  C3B    14.96  30.0  2
 9L9  Var_03    CD    CG   CB   CA   -176.28  30.0  3
 9L9  Var_04    OE1   CD   CG   CB      3.81  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-3  CG    0.020
 9L9  plan-3  CD    0.020
 9L9  plan-3  OE1   0.020
 9L9  plan-3  OE2   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

