# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:27:45 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-{4-[{[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}(formyl)amino]benzoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N[C@@H](CN2)CN(C=O)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C(=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
 1YA  1YA  'N-{4-[{[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}(formyl)amino]benzoyl}-L-glutamic acid'  ligand  55  34  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1YA
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
 1YA  N1   N  N      0  -0.520  -6.6186  -1.2159  -0.0822
 1YA  C2   C  CR6    0   0.665  -7.0221  -0.1643   0.5752
 1YA  NA2  N  NH2    0  -0.829  -8.3306   0.1623   0.5863
 1YA  N3   N  NR16   0  -0.709  -6.1778   0.6090   1.2972
 1YA  C4   C  CR6    0   0.479  -4.8092   0.3601   1.4112
 1YA  O4   O  O      0  -0.524  -4.0940   1.1338   2.0543
 1YA  C4A  C  CR6    0  -0.037  -4.3878  -0.8078   0.7447
 1YA  N5   N  NH1    0  -0.643  -3.0437  -1.2280   0.7830
 1YA  C6   C  CH1    0  -0.195  -2.6053  -1.7907  -0.4755
 1YA  C7   C  CH2    0  -0.256  -3.4985  -2.9973  -0.7652
 1YA  N8   N  NH1    0  -0.665  -4.8901  -2.6046  -0.7023
 1YA  C8A  C  CR6    0   0.493  -5.3051  -1.5323   0.0040
 1YA  C9   C  CH2    0  -0.324  -2.6567  -0.8141  -1.6667
 1YA  N10  N  NT     0  -0.524  -2.2421   0.5302  -1.3090
 1YA  C11  C  CR6    0  -0.043   1.7129   1.1467  -0.0200
 1YA  C12  C  CR16   0  -0.284   0.6422   1.5785   0.7581
 1YA  C13  C  CR16   0  -0.266  -0.6612   1.3662   0.3456
 1YA  C14  C  CR6    0   0.313  -0.9120   0.7486  -0.8775
 1YA  C15  C  CR16   0  -0.270   0.1521   0.3379  -1.6714
 1YA  C16  C  CR16   0  -0.290   1.4556   0.5286  -1.2399
 1YA  N    N  NH1    0  -0.618   3.9983   0.4502   0.2036
 1YA  CA   C  CH1    0  -0.204   5.4245   0.6683   0.2790
 1YA  CB   C  CH2    0  -0.442   6.1577  -0.6615   0.4395
 1YA  CG   C  CH2    0  -0.576   5.7803  -1.4162   1.7043
 1YA  CD   C  C      0   0.411   6.5865  -2.6993   1.9731
 1YA  OE1  O  OC    -1  -0.633   6.1368  -3.4536   2.8621
 1YA  OE2  O  O      0  -0.610   7.6261  -2.8843   1.3093
 1YA  CT   C  C      0   0.416   5.9487   1.4573  -0.9518
 1YA  O2   O  O      0  -0.593   5.1539   1.6712  -1.8829
 1YA  O1   O  OC    -1  -0.617   7.1466   1.7989  -0.8870
 1YA  C18  C  C1     0   0.249  -3.1233   1.5559  -1.3887
 1YA  O5   O  O      0  -0.465  -2.8780   2.7191  -1.1474
 1YA  O    O  O      0  -0.503   3.3727   2.4543   1.0451
 1YA  H1   H  HNH2   0   0.405  -8.9080  -0.2744  -0.1124
 1YA  H2   H  HNH2   0   0.407  -8.6121   1.0896   0.8578
 1YA  H3   H  HNR6   0   0.418  -6.5287   1.4310   1.7702
 1YA  H5   H  HNH1   0   0.370  -2.4321  -0.5047   1.1343
 1YA  H7   H  HCH1   0   0.274  -1.5830  -2.1500  -0.3461
 1YA  H8   H  HCH2   0   0.255  -3.2907  -3.3971  -1.7588
 1YA  H9   H  HCH2   0   0.252  -3.2752  -3.7867  -0.0429
 1YA  H10  H  HCH2   0   0.273  -2.0357  -1.2033  -2.4762
 1YA  H11  H  HCH2   0   0.269  -3.6693  -0.7471  -2.0679
 1YA  H12  H  HCR6   0   0.262   0.8274   2.0687   1.7047
 1YA  H13  H  HCR6   0   0.269  -1.4834   1.6676   0.9821
 1YA  H14  H  HCR6   0   0.275  -0.0307  -0.1194  -2.6351
 1YA  H15  H  HCR6   0   0.265   2.2720   0.2314  -1.8868
 1YA  H16  H  HNH1   0   0.392   3.6910  -0.3500  -0.3265
 1YA  H17  H  HCH1   0   0.233   5.6219   1.2705   1.1704
 1YA  H18  H  HCH2   0   0.209   5.9783  -1.2896  -0.4412
 1YA  H19  H  HCH2   0   0.227   7.2260  -0.4509   0.4448
 1YA  H20  H  HCH2   0   0.221   5.9095  -0.7516   2.5686
 1YA  H21  H  HCH2   0   0.216   4.7162  -1.6688   1.7013
 1YA  H24  H  H      0   0.199  -4.1149   1.2153  -1.7218
 1YA  H4   H  HNH1   0   0.392  -5.5571  -3.0542  -1.3067
 1YA  C17  C  C      0   0.528   3.1071   1.4173   0.4471

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
 1YA  C7   N8   single    1.447  0.020  1.447
 1YA  C7   C6   single    1.529  0.020  1.529
 1YA  N8   C8A  single    1.349  0.020  1.349
 1YA  O5   C18  double    1.213  0.020  1.213
 1YA  C6   N5   single    1.447  0.020  1.447
 1YA  C6   C9   single    1.541  0.020  1.541
 1YA  C18  N10  single    1.355  0.020  1.355
 1YA  C15  C16  aromatic  1.386  0.020  1.386
 1YA  C15  C14  aromatic  1.390  0.020  1.390
 1YA  C16  C11  aromatic  1.392  0.020  1.392
 1YA  N10  C14  single    1.415  0.020  1.415
 1YA  N10  C9   single    1.451  0.020  1.451
 1YA  N5   C4A  single    1.409  0.020  1.409
 1YA  C8A  C4A  double    1.384  0.020  1.384
 1YA  C8A  N1   single    1.354  0.020  1.354
 1YA  C14  C13  aromatic  1.393  0.020  1.393
 1YA  C4A  C4   single    1.409  0.020  1.409
 1YA  N1   C2   double    1.304  0.020  1.304
 1YA  C11  C17  single    1.495  0.020  1.495
 1YA  C11  C12  aromatic  1.392  0.020  1.392
 1YA  C13  C12  aromatic  1.383  0.020  1.383
 1YA  C2   N3   single    1.353  0.020  1.353
 1YA  C2   NA2  single    1.349  0.020  1.349
 1YA  C4   N3   single    1.396  0.020  1.396
 1YA  C4   O4   double    1.234  0.020  1.234
 1YA  O    C17  double    1.226  0.020  1.226
 1YA  C17  N    single    1.337  0.020  1.337
 1YA  N    CA   single    1.445  0.020  1.445
 1YA  CA   CT   single    1.553  0.020  1.553
 1YA  CA   CB   single    1.527  0.020  1.527
 1YA  CT   O2   deloc     1.243  0.020  1.243
 1YA  CT   O1   deloc     1.247  0.020  1.247
 1YA  CG   CB   single    1.520  0.020  1.520
 1YA  CG   CD   single    1.539  0.020  1.539
 1YA  OE2  CD   deloc     1.247  0.020  1.247
 1YA  CD   OE1  deloc     1.250  0.020  1.250
 1YA  NA2  H1   single    0.890  0.020  1.040
 1YA  NA2  H2   single    0.890  0.020  1.040
 1YA  N3   H3   single    0.860  0.020  1.020
 1YA  N5   H5   single    0.890  0.020  1.040
 1YA  C6   H7   single    0.970  0.020  1.090
 1YA  C7   H8   single    0.970  0.020  1.090
 1YA  C7   H9   single    0.970  0.020  1.090
 1YA  C9   H10  single    0.970  0.020  1.090
 1YA  C9   H11  single    0.970  0.020  1.090
 1YA  C12  H12  single    0.930  0.020  1.080
 1YA  C13  H13  single    0.930  0.020  1.080
 1YA  C15  H14  single    0.930  0.020  1.080
 1YA  C16  H15  single    0.930  0.020  1.080
 1YA  N    H16  single    0.890  0.020  1.040
 1YA  CA   H17  single    0.970  0.020  1.090
 1YA  CB   H18  single    0.970  0.020  1.090
 1YA  CB   H19  single    0.970  0.020  1.090
 1YA  CG   H20  single    0.970  0.020  1.090
 1YA  CG   H21  single    0.970  0.020  1.090
 1YA  C18  H24  single    0.930  0.020  1.080
 1YA  N8   H4   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
 1YA  C8A  N1   C2   117.16  3.000
 1YA  N3   C2   NA2  117.54  3.000
 1YA  NA2  C2   N1   119.97  3.000
 1YA  N3   C2   N1   122.45  3.000
 1YA  H2   NA2  H1   115.26  3.000
 1YA  H2   NA2  C2   119.78  3.000
 1YA  H1   NA2  C2   116.48  3.000
 1YA  H3   N3   C4   116.55  3.000
 1YA  H3   N3   C2   119.84  3.000
 1YA  C4   N3   C2   123.60  3.000
 1YA  C4A  C4   O4   126.35  3.000
 1YA  O4   C4   N3   119.93  3.000
 1YA  C4A  C4   N3   113.73  3.000
 1YA  C8A  C4A  N5   119.39  3.000
 1YA  C8A  C4A  C4   119.27  3.000
 1YA  N5   C4A  C4   121.31  3.000
 1YA  H5   N5   C6   113.42  3.000
 1YA  H5   N5   C4A  111.93  3.000
 1YA  C6   N5   C4A  112.43  3.000
 1YA  H7   C6   C9   109.37  3.000
 1YA  H7   C6   C7   108.05  3.000
 1YA  C9   C6   C7   109.52  3.000
 1YA  H7   C6   N5   107.98  3.000
 1YA  C9   C6   N5   114.57  3.000
 1YA  C7   C6   N5   107.14  3.000
 1YA  H9   C7   H8   107.35  3.000
 1YA  H9   C7   N8   111.33  3.000
 1YA  H8   C7   N8   108.79  3.000
 1YA  H9   C7   C6   108.99  3.000
 1YA  H8   C7   C6   110.52  3.000
 1YA  N8   C7   C6   109.84  3.000
 1YA  H4   N8   C8A  117.75  3.000
 1YA  H4   N8   C7   119.35  3.000
 1YA  C8A  N8   C7   122.28  3.000
 1YA  N8   C8A  C4A  119.50  3.000
 1YA  C4A  C8A  N1   123.70  3.000
 1YA  N8   C8A  N1   116.79  3.000
 1YA  H11  C9   H10  106.08  3.000
 1YA  H11  C9   N10  107.38  3.000
 1YA  H10  C9   N10  110.50  3.000
 1YA  H11  C9   C6   110.73  3.000
 1YA  H10  C9   C6   109.16  3.000
 1YA  N10  C9   C6   112.76  3.000
 1YA  C18  N10  C14  120.83  3.000
 1YA  C14  N10  C9   119.11  3.000
 1YA  C18  N10  C9   120.06  3.000
 1YA  C17  C11  C16  121.78  3.000
 1YA  C17  C11  C12  119.11  3.000
 1YA  C16  C11  C12  119.05  3.000
 1YA  H12  C12  C13  119.44  3.000
 1YA  H12  C12  C11  119.86  3.000
 1YA  C13  C12  C11  120.69  3.000
 1YA  H13  C13  C14  120.19  3.000
 1YA  H13  C13  C12  119.84  3.000
 1YA  C14  C13  C12  119.96  3.000
 1YA  C15  C14  C13  119.65  3.000
 1YA  C13  C14  N10  120.36  3.000
 1YA  C15  C14  N10  119.99  3.000
 1YA  H14  C15  C16  119.61  3.000
 1YA  H14  C15  C14  120.28  3.000
 1YA  C16  C15  C14  120.10  3.000
 1YA  H15  C16  C15  119.01  3.000
 1YA  H15  C16  C11  120.41  3.000
 1YA  C15  C16  C11  120.52  3.000
 1YA  H16  N    CA   116.63  3.000
 1YA  H16  N    C17  117.82  3.000
 1YA  CA   N    C17  122.62  3.000
 1YA  H17  CA   CT   107.77  3.000
 1YA  H17  CA   CB   107.89  3.000
 1YA  CT   CA   CB   111.33  3.000
 1YA  H17  CA   N    107.69  3.000
 1YA  CB   CA   N    110.37  3.000
 1YA  CT   CA   N    111.62  3.000
 1YA  H19  CB   H18  105.97  3.000
 1YA  H19  CB   CG   109.61  3.000
 1YA  H18  CB   CG   110.08  3.000
 1YA  H19  CB   CA   107.65  3.000
 1YA  H18  CB   CA   109.62  3.000
 1YA  CG   CB   CA   113.61  3.000
 1YA  H21  CG   H20  104.86  3.000
 1YA  H21  CG   CD   108.52  3.000
 1YA  H20  CG   CD   107.79  3.000
 1YA  H21  CG   CB   110.72  3.000
 1YA  H20  CG   CB   108.98  3.000
 1YA  CD   CG   CB   115.41  3.000
 1YA  OE2  CD   OE1  126.09  3.000
 1YA  OE1  CD   CG   116.04  3.000
 1YA  OE2  CD   CG   117.87  3.000
 1YA  O1   CT   O2   127.30  3.000
 1YA  O1   CT   CA   114.97  3.000
 1YA  O2   CT   CA   117.73  3.000
 1YA  H24  C18  O5   122.64  3.000
 1YA  H24  C18  N10  111.70  3.000
 1YA  O5   C18  N10  125.65  3.000
 1YA  O    C17  N    123.78  3.000
 1YA  N    C17  C11  115.70  3.000
 1YA  O    C17  C11  120.49  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
 1YA  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 1YA  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 1YA  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 1YA  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 1YA  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 1YA  CONST_06  C16  C11  C12  C13     0.00   0.0  0
 1YA  CONST_07  C7   N8   C8A  N1    180.00   0.0  0
 1YA  CONST_08  C4   N3   C2   N1      0.00   0.0  0
 1YA  CONST_09  N8   C8A  N1   C2    180.00   0.0  0
 1YA  CONST_10  C4A  C8A  N1   C2      0.00   0.0  0
 1YA  CONST_11  C4A  C4   N3   C2      0.00   0.0  0
 1YA  CONST_12  C8A  N1   C2   N3      0.00   0.0  0
 1YA  CONST_13  C7   N8   C8A  C4A     0.00   0.0  0
 1YA  CONST_14  C16  C15  C14  N10   180.00   0.0  0
 1YA  CONST_15  C12  C13  C14  N10   180.00   0.0  0
 1YA  CONST_16  C17  C11  C12  C13   180.00   0.0  0
 1YA  CONST_17  C17  C11  C16  C15   180.00   0.0  0
 1YA  CONST_18  O4   C4   N3   C2    180.00   0.0  0
 1YA  CONST_19  C8A  N1   C2   NA2   180.00   0.0  0
 1YA  CONST_20  C4   N3   C2   NA2   180.00   0.0  0
 1YA  CONST_21  H14  C15  C16  C11   180.00   0.0  0
 1YA  CONST_22  H13  C13  C12  C11   180.00   0.0  0
 1YA  CONST_23  H15  C16  C11  C12   180.00   0.0  0
 1YA  CONST_24  H12  C12  C13  C14   180.00   0.0  0
 1YA  CONST_25  H4   N8   C8A  N1      0.00   0.0  0
 1YA  CONST_26  H3   N3   C2   N1    180.00   0.0  0
 1YA  CONST_34  O5   C18  N10  C14     0.00   0.0  0
 1YA  CONST_35  H16  N    C17  C11     0.00   0.0  0
 1YA  CONST_36  H24  C18  N10  C14   180.00   0.0  0
 1YA  CONST_37  O5   C18  N10  C9    180.00   0.0  0
 1YA  Var_01    C6   N5   C4A  C4   -142.46  30.0  1
 1YA  Var_02    C8A  N8   C7   C6    -23.77  30.0  1
 1YA  Var_03    C14  N10  C9   C6     63.66  30.0  1
 1YA  Var_04    O    C17  C11  C12   -35.21  30.0  2
 1YA  Var_05    CD   CG   CB   CA   -174.68  30.0  2
 1YA  Var_06    OE2  CD   CG   CB     13.49  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
 1YA  chir_01  C6  C7  N5  C9  positiv
 1YA  chir_02  CA  N   CT  CB  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
 1YA  plan-1  N10  0.020
 1YA  plan-1  C11  0.020
 1YA  plan-1  C12  0.020
 1YA  plan-1  C13  0.020
 1YA  plan-1  C14  0.020
 1YA  plan-1  C15  0.020
 1YA  plan-1  C16  0.020
 1YA  plan-1  H12  0.020
 1YA  plan-1  H13  0.020
 1YA  plan-1  H14  0.020
 1YA  plan-1  H15  0.020
 1YA  plan-1  C17  0.020
 1YA  plan-2  C4A  0.020
 1YA  plan-2  N5   0.020
 1YA  plan-2  C6   0.020
 1YA  plan-2  H5   0.020
 1YA  plan-3  CG   0.020
 1YA  plan-3  CD   0.020
 1YA  plan-3  OE1  0.020
 1YA  plan-3  OE2  0.020
 1YA  plan-4  CA   0.020
 1YA  plan-4  CT   0.020
 1YA  plan-4  O2   0.020
 1YA  plan-4  O1   0.020
 1YA  plan-5  C9   0.020
 1YA  plan-5  N10  0.020
 1YA  plan-5  C14  0.020
 1YA  plan-5  C18  0.020
 1YA  plan-5  O5   0.020
 1YA  plan-5  H24  0.020
 1YA  plan-6  C11  0.020
 1YA  plan-6  N    0.020
 1YA  plan-6  CA   0.020
 1YA  plan-6  O    0.020
 1YA  plan-6  H16  0.020
 1YA  plan-6  C17  0.020
 1YA  plan-7  N1   0.020
 1YA  plan-7  C2   0.020
 1YA  plan-7  NA2  0.020
 1YA  plan-7  N3   0.020
 1YA  plan-7  C4   0.020
 1YA  plan-7  O4   0.020
 1YA  plan-7  C4A  0.020
 1YA  plan-7  N5   0.020
 1YA  plan-7  C7   0.020
 1YA  plan-7  N8   0.020
 1YA  plan-7  C8A  0.020
 1YA  plan-7  H1   0.020
 1YA  plan-7  H2   0.020
 1YA  plan-7  H3   0.020
 1YA  plan-7  H4   0.020

