# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:11:57 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[(4-{[(2,5-diamino-6-hydroxypyrimidin-4-yl)carbamoyl]amino}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c(N)c(NC(=O)Nc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)n1
#
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
 L37  L37  'N-[(4-{[(2,5-diamino-6-hydroxypyrimidin-4-yl)carbamoyl]amino}phenyl)carbonyl]-L-glutamic acid'  ligand  48  31  .  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_L37
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
 L37  N2A   N  NH2    0  -0.820   3.3977  -1.0689   6.4557
 L37  N1    N  N      0  -0.489   1.5014  -0.4179   5.3643
 L37  C2    C  C      0   0.543   2.1147  -0.6701   6.5212
 L37  N3    N  N      0  -0.525   1.5826  -0.5404   7.7386
 L37  C4    C  C      0   0.492   0.3327  -0.1166   7.7879
 L37  O4A   O  OH1    0  -0.602  -0.2307   0.0261   8.9821
 L37  C5    C  C      0  -0.074  -0.4232   0.1906   6.6607
 L37  C6    C  C      0   0.545   0.2517   0.0068   5.4455
 L37  N7    N  NH1    0  -0.768  -0.4706   0.3078   4.3154
 L37  C8    C  C      0   0.740  -0.1066   0.1774   2.9950
 L37  O8A   O  O      0  -0.467   0.9477  -0.2793   2.6104
 L37  N9    N  NH1    0  -0.794  -1.0970   0.6297   2.1596
 L37  C1B   C  CR6    0   0.378  -1.1184   0.6274   0.7698
 L37  C2B   C  CR16   0  -0.342  -2.3117   1.0354   0.1623
 L37  C3B   C  CR16   0  -0.261  -2.4308   1.0789  -1.2110
 L37  C4B   C  CR6    0  -0.060  -1.3729   0.7023  -2.0366
 L37  C5B   C  CR16   0  -0.285  -0.1853   0.3086  -1.4272
 L37  C6B   C  CR16   0  -0.302  -0.0450   0.2678  -0.0489
 L37  C7B   C  C      0   0.543  -1.5592   0.7800  -3.5161
 L37  O7B   O  O      0  -0.505  -2.4602   1.4600  -3.9971
 L37  N     N  NH1    0  -0.635  -0.6796   0.1015  -4.2664
 L37  CA    C  CH1    0  -0.194  -0.8073  -0.0076  -5.7019
 L37  CB    C  CH2    0  -0.441   0.5473  -0.3709  -6.3133
 L37  CG    C  CH2    0  -0.576   1.6139   0.6863  -6.0751
 L37  CD    C  C      0   0.411   2.9763   0.4297  -6.7428
 L37  OE1   O  O      0  -0.609   3.1367  -0.6451  -7.3543
 L37  OE2   O  OC    -1  -0.634   3.8259   1.3367  -6.6124
 L37  C     C  C      0   0.411  -1.8942  -1.0283  -6.1256
 L37  O     O  O      0  -0.619  -2.2251  -0.9773  -7.3276
 L37  OXT   O  OC    -1  -0.600  -2.3176  -1.8141  -5.2610
 L37  HN21  H  HNH2   0   0.397   3.7941  -1.3141   5.5661
 L37  HN22  H  HNH2   0   0.396   3.8586  -1.4003   7.2843
 L37  HO4   H  HOH1   0   0.475   0.4157  -0.2086   9.6618
 L37  HN51  H  HNH2   0   0.368  -1.8694   1.5022   7.2042
 L37  HN52  H  HNH2   0   0.368  -2.4032  -0.0297   7.0401
 L37  HN7   H  HNH1   0   0.417  -1.3955   0.6537   4.5512
 L37  HN9   H  HNH1   0   0.417  -1.9382   0.9863   2.5875
 L37  H2B   H  HCR6   0   0.272  -3.1563   1.3230   0.7772
 L37  H3B   H  HCR6   0   0.258  -3.3648   1.4066  -1.6468
 L37  H5B   H  HCR6   0   0.253   0.6826   0.0446  -2.0187
 L37  H6B   H  HCR6   0   0.285   0.8987  -0.0354   0.3704
 L37  HN    H  HNH1   0   0.389  -0.1208  -0.6056  -3.8161
 L37  HA    H  HCH1   0   0.228  -1.0983   0.9736  -6.0863
 L37  HB1   H  HCH2   0   0.209   0.8787  -1.3388  -5.9215
 L37  HB2   H  HCH2   0   0.225   0.3988  -0.5131  -7.3840
 L37  HG1   H  HCH2   0   0.216   1.2425   1.6596  -6.4169
 L37  HG2   H  HCH2   0   0.223   1.7850   0.8146  -5.0007
 L37  N5A   N  NH2    0  -0.857  -1.7613   0.6552   6.6613

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
 L37  N2A  C2    single    1.345  0.020  1.345
 L37  N2A  HN21  single    0.860  0.020  1.020
 L37  N2A  HN22  single    0.860  0.020  1.020
 L37  N1   C2    aromatic  1.333  0.020  1.333
 L37  N1   C6    aromatic  1.322  0.020  1.322
 L37  C2   N3    aromatic  1.335  0.020  1.335
 L37  N3   C4    aromatic  1.321  0.020  1.321
 L37  C4   O4A   single    1.328  0.020  1.328
 L37  C4   C5    aromatic  1.392  0.020  1.392
 L37  O4A  HO4   single    0.850  0.020  0.980
 L37  N5A  C5    single    1.417  0.020  1.417
 L37  N5A  HN51  single    0.890  0.020  1.040
 L37  N5A  HN52  single    0.890  0.020  1.040
 L37  C5   C6    aromatic  1.402  0.020  1.402
 L37  C6   N7    single    1.375  0.020  1.375
 L37  N7   C8    single    1.376  0.020  1.376
 L37  N7   HN7   single    0.860  0.020  1.020
 L37  C8   O8A   double    1.212  0.020  1.212
 L37  C8   N9    single    1.372  0.020  1.372
 L37  N9   C1B   single    1.390  0.020  1.390
 L37  N9   HN9   single    0.860  0.020  1.020
 L37  C1B  C2B   aromatic  1.400  0.020  1.400
 L37  C1B  C6B   aromatic  1.397  0.020  1.397
 L37  C2B  C3B   aromatic  1.379  0.020  1.379
 L37  C2B  H2B   single    0.930  0.020  1.080
 L37  C3B  C4B   aromatic  1.394  0.020  1.394
 L37  C3B  H3B   single    0.930  0.020  1.080
 L37  C4B  C5B   aromatic  1.392  0.020  1.392
 L37  C4B  C7B   single    1.493  0.020  1.493
 L37  C5B  C6B   aromatic  1.386  0.020  1.386
 L37  C5B  H5B   single    0.930  0.020  1.080
 L37  C6B  H6B   single    0.930  0.020  1.080
 L37  C7B  O7B   double    1.227  0.020  1.227
 L37  C7B  N     single    1.341  0.020  1.341
 L37  N    CA    single    1.445  0.020  1.445
 L37  N    HN    single    0.890  0.020  1.040
 L37  CA   CB    single    1.530  0.020  1.530
 L37  CA   C     single    1.550  0.020  1.550
 L37  CA   HA    single    0.970  0.020  1.090
 L37  CB   CG    single    1.521  0.020  1.521
 L37  CB   HB1   single    0.970  0.020  1.090
 L37  CB   HB2   single    0.970  0.020  1.090
 L37  CG   CD    single    1.539  0.020  1.539
 L37  CG   HG1   single    0.970  0.020  1.090
 L37  CG   HG2   single    0.970  0.020  1.090
 L37  CD   OE1   deloc     1.247  0.020  1.247
 L37  CD   OE2   deloc     1.250  0.020  1.250
 L37  C    O     deloc     1.248  0.020  1.248
 L37  C    OXT   deloc     1.243  0.020  1.243

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
 L37  HN22  N2A  HN21  117.98  3.000
 L37  HN22  N2A  C2    119.69  3.000
 L37  HN21  N2A  C2    119.47  3.000
 L37  C6    N1   C2    116.24  3.000
 L37  N3    C2   N1    126.12  3.000
 L37  N3    C2   N2A   116.96  3.000
 L37  N1    C2   N2A   116.90  3.000
 L37  C4    N3   C2    116.26  3.000
 L37  C5    C4   O4A   118.31  3.000
 L37  C5    C4   N3    123.69  3.000
 L37  O4A   C4   N3    118.00  3.000
 L37  HO4   O4A  C4    108.81  3.000
 L37  C6    C5   N5A   119.87  3.000
 L37  C6    C5   C4    114.31  3.000
 L37  N5A   C5   C4    125.82  3.000
 L37  N7    C6   C5    115.53  3.000
 L37  N7    C6   N1    121.09  3.000
 L37  C5    C6   N1    123.38  3.000
 L37  HN7   N7   C8    119.75  3.000
 L37  HN7   N7   C6    111.24  3.000
 L37  C8    N7   C6    128.99  3.000
 L37  N9    C8   O8A   123.98  3.000
 L37  N9    C8   N7    111.23  3.000
 L37  O8A   C8   N7    124.80  3.000
 L37  HN9   N9   C1B   114.32  3.000
 L37  HN9   N9   C8    117.39  3.000
 L37  C1B   N9   C8    128.26  3.000
 L37  C6B   C1B  C2B   118.40  3.000
 L37  C6B   C1B  N9    125.07  3.000
 L37  C2B   C1B  N9    116.52  3.000
 L37  H2B   C2B  C3B   119.30  3.000
 L37  H2B   C2B  C1B   119.70  3.000
 L37  C3B   C2B  C1B   120.99  3.000
 L37  H3B   C3B  C4B   119.91  3.000
 L37  H3B   C3B  C2B   119.04  3.000
 L37  C4B   C3B  C2B   121.05  3.000
 L37  C7B   C4B  C5B   123.72  3.000
 L37  C7B   C4B  C3B   118.56  3.000
 L37  C5B   C4B  C3B   117.69  3.000
 L37  H5B   C5B  C6B   117.06  3.000
 L37  H5B   C5B  C4B   120.90  3.000
 L37  C6B   C5B  C4B   122.02  3.000
 L37  H6B   C6B  C5B   118.97  3.000
 L37  H6B   C6B  C1B   121.20  3.000
 L37  C5B   C6B  C1B   119.83  3.000
 L37  N     C7B  O7B   122.88  3.000
 L37  N     C7B  C4B   116.51  3.000
 L37  O7B   C7B  C4B   120.59  3.000
 L37  HN    N    CA    116.09  3.000
 L37  HN    N    C7B   117.97  3.000
 L37  CA    N    C7B   122.42  3.000
 L37  HA    CA   C     107.95  3.000
 L37  HA    CA   CB    107.95  3.000
 L37  C     CA   CB    110.81  3.000
 L37  HA    CA   N     107.76  3.000
 L37  C     CA   N     112.53  3.000
 L37  CB    CA   N     109.67  3.000
 L37  HB2   CB   HB1   106.09  3.000
 L37  HB2   CB   CG    109.88  3.000
 L37  HB1   CB   CG    110.25  3.000
 L37  HB2   CB   CA    107.63  3.000
 L37  HB1   CB   CA    109.55  3.000
 L37  CG    CB   CA    113.17  3.000
 L37  HG2   CG   HG1   104.75  3.000
 L37  HG2   CG   CD    107.87  3.000
 L37  HG1   CG   CD    108.22  3.000
 L37  HG2   CG   CB    110.16  3.000
 L37  HG1   CG   CB    109.31  3.000
 L37  CD    CG   CB    115.92  3.000
 L37  OE2   CD   OE1   126.11  3.000
 L37  OE2   CD   CG    115.83  3.000
 L37  OE1   CD   CG    118.06  3.000
 L37  OXT   C    O     127.28  3.000
 L37  OXT   C    CA    117.72  3.000
 L37  O     C    CA    114.99  3.000
 L37  HN52  N5A  HN51  107.33  3.000
 L37  HN52  N5A  C5    112.16  3.000
 L37  HN51  N5A  C5    112.07  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
 L37  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 L37  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 L37  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 L37  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 L37  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 L37  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 L37  CONST_07  C4B   C3B  C2B  C1B     0.00   0.0  0
 L37  CONST_08  C4B   C5B  C6B  C1B     0.00   0.0  0
 L37  CONST_09  C5B   C6B  C1B  C2B     0.00   0.0  0
 L37  CONST_10  C5B   C4B  C3B  C2B     0.00   0.0  0
 L37  CONST_11  C6B   C1B  C2B  C3B     0.00   0.0  0
 L37  CONST_12  C6B   C5B  C4B  C3B     0.00   0.0  0
 L37  CONST_13  C6    N1   C2   N2A   180.00   0.0  0
 L37  CONST_14  C4    N3   C2   N2A   180.00   0.0  0
 L37  CONST_15  N5A   C5   C6   N1    180.00   0.0  0
 L37  CONST_16  N7    C6   N1   C2    180.00   0.0  0
 L37  CONST_17  O4A   C4   N3   C2    180.00   0.0  0
 L37  CONST_18  N5A   C5   C4   N3    180.00   0.0  0
 L37  CONST_19  N7    C6   C5   C4    180.00   0.0  0
 L37  CONST_20  C6    C5   C4   O4A   180.00   0.0  0
 L37  CONST_21  C3B   C2B  C1B  N9    180.00   0.0  0
 L37  CONST_22  C5B   C6B  C1B  N9    180.00   0.0  0
 L37  CONST_23  C7B   C4B  C3B  C2B   180.00   0.0  0
 L37  CONST_24  C7B   C4B  C5B  C6B   180.00   0.0  0
 L37  CONST_25  H3B   C3B  C2B  C1B   180.00   0.0  0
 L37  CONST_26  H5B   C5B  C6B  C1B   180.00   0.0  0
 L37  CONST_27  H6B   C6B  C1B  C2B   180.00   0.0  0
 L37  CONST_28  H2B   C2B  C3B  C4B   180.00   0.0  0
 L37  CONST_29  C8    N7   C6   N1      0.00   0.0  0
 L37  CONST_30  C8    N7   C6   C5    180.00   0.0  0
 L37  CONST_31  C2B   C1B  N9   C8    180.00   0.0  0
 L37  CONST_32  C6B   C1B  N9   C8      0.00   0.0  0
 L37  CONST_33  HN21  N2A  C2   N1      0.00   0.0  0
 L37  CONST_34  HN22  N2A  C2   N1    180.00   0.0  0
 L37  CONST_35  HN7   N7   C6   N1    180.00   0.0  0
 L37  CONST_38  HN9   N9   C1B  C2B     0.00   0.0  0
 L37  CONST_39  O8A   C8   N7   C6      0.00   0.0  0
 L37  CONST_40  C1B   N9   C8   O8A     0.00   0.0  0
 L37  CONST_41  CA    N    C7B  C4B   180.00   0.0  0
 L37  CONST_42  N9    C8   N7   C6    180.00   0.0  0
 L37  CONST_43  C1B   N9   C8   N7    180.00   0.0  0
 L37  CONST_45  CA    N    C7B  O7B     0.00   0.0  0
 L37  Var_01    O7B   C7B  C4B  C3B    18.21  30.0  2
 L37  Var_02    CD    CG   CB   CA   -176.08  30.0  3
 L37  Var_03    OE1   CD   CG   CB     -4.20  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
 L37  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
 L37  plan-1  N2A   0.020
 L37  plan-1  N1    0.020
 L37  plan-1  C2    0.020
 L37  plan-1  N3    0.020
 L37  plan-1  C4    0.020
 L37  plan-1  O4A   0.020
 L37  plan-1  C5    0.020
 L37  plan-1  C6    0.020
 L37  plan-1  N7    0.020
 L37  plan-1  N5A   0.020
 L37  plan-2  C5    0.020
 L37  plan-2  HN51  0.020
 L37  plan-2  HN52  0.020
 L37  plan-2  N5A   0.020
 L37  plan-3  CG    0.020
 L37  plan-3  CD    0.020
 L37  plan-3  OE1   0.020
 L37  plan-3  OE2   0.020
 L37  plan-4  CA    0.020
 L37  plan-4  C     0.020
 L37  plan-4  O     0.020
 L37  plan-4  OXT   0.020
 L37  plan-5  N9    0.020
 L37  plan-5  C1B   0.020
 L37  plan-5  C2B   0.020
 L37  plan-5  C3B   0.020
 L37  plan-5  C4B   0.020
 L37  plan-5  C5B   0.020
 L37  plan-5  C6B   0.020
 L37  plan-5  C7B   0.020
 L37  plan-5  H2B   0.020
 L37  plan-5  H3B   0.020
 L37  plan-5  H5B   0.020
 L37  plan-5  H6B   0.020
 L37  plan-6  C6    0.020
 L37  plan-6  N7    0.020
 L37  plan-6  C8    0.020
 L37  plan-6  O8A   0.020
 L37  plan-6  N9    0.020
 L37  plan-6  C1B   0.020
 L37  plan-6  HN7   0.020
 L37  plan-6  HN9   0.020
 L37  plan-7  C4B   0.020
 L37  plan-7  C7B   0.020
 L37  plan-7  O7B   0.020
 L37  plan-7  N     0.020
 L37  plan-7  CA    0.020
 L37  plan-7  HN    0.020
 L37  plan-8  N2A   0.020
 L37  plan-8  C2    0.020
 L37  plan-8  HN21  0.020
 L37  plan-8  HN22  0.020

