# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:45:16 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  57  34  .  2021-08-04  2021-08-04  
;
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  -0.529  -7.0141  -1.2192  -0.0326
 1YA  C2   C  CR6   0   0.671  -7.6097  -0.1087  -0.3698
 1YA  NA2  N  NH2   0  -0.829  -8.8798  -0.1371  -0.8130
 1YA  N3   N  NR16  0  -0.714  -7.0140   1.1001  -0.2550
 1YA  C4   C  CR6   0   0.493  -5.7085   1.2827   0.2178
 1YA  O4   O  O     0  -0.508  -5.2395   2.4170   0.2537
 1YA  C4A  C  CR6   0  -0.076  -5.0791   0.0817   0.6284
 1YA  N5   N  NH1   0  -0.635  -3.7385   0.1196   1.0800
 1YA  C6   C  CH1   0  -0.183  -3.0341  -1.1292   0.9033
 1YA  C7   C  CH2   0  -0.264  -3.8569  -2.3236   1.4001
 1YA  N8   N  NH1   0  -0.660  -5.1672  -2.2802   0.8003
 1YA  C8A  C  CR6   0   0.510  -5.7630  -1.1173   0.4785
 1YA  C9   C  CH2   0  -0.312  -2.6538  -1.3128  -0.5694
 1YA  N10  N  NT    0  -0.505  -1.9699  -0.1521  -1.1040
 1YA  C11  C  CR6   0  -0.042   1.9229   0.5759   0.3023
 1YA  C12  C  CR16  0  -0.272   0.8565   1.3538   0.7487
 1YA  C13  C  CR16  0  -0.241  -0.4245   1.1290   0.2771
 1YA  C14  C  CR6   0   0.301  -0.6568   0.1128  -0.6439
 1YA  C15  C  CR16  0  -0.264   0.3975  -0.6757  -1.0841
 1YA  C16  C  CR16  0  -0.289   1.6799  -0.4472  -0.6104
 1YA  N    N  NH1   0  -0.654   4.3262   0.4338   0.1153
 1YA  CA   C  CH1   0  -0.196   5.6777   0.6875   0.5319
 1YA  CB   C  CH2   0  -0.465   6.6562  -0.1829  -0.2625
 1YA  CG   C  CH2   0  -0.576   6.4338  -1.6607   0.0181
 1YA  CD   C  C     0   0.555   7.4125  -2.5447  -0.7042
 1YA  OE1  O  OH1   0  -0.595   7.2244  -3.8267  -0.4112
 1YA  OE2  O  O     0  -0.442   8.2687  -2.1589  -1.4603
 1YA  CT   C  C     0   0.550   6.0218   2.1622   0.3688
 1YA  O2   O  O     0  -0.429   5.3957   2.9384  -0.3029
 1YA  O1   O  OH1   0  -0.590   7.1168   2.4748   1.0452
 1YA  C18  C  C1    0   0.265  -2.6679   0.8039  -1.7557
 1YA  O5   O  O     0  -0.477  -2.2174   1.8674  -2.1317
 1YA  O    O  O     0  -0.476   3.4298   1.4063   1.9360
 1YA  H1   H  HNH2  0   0.406  -9.2627  -1.0370  -1.0483
 1YA  H2   H  HNH2  0   0.408  -9.2628   0.6479  -1.3121
 1YA  H3   H  HNR6  0   0.414  -7.5166   1.9354  -0.5230
 1YA  H5   H  HNH1  0   0.362  -3.6520   0.4614   2.0275
 1YA  H7   H  HCH1  0   0.266  -2.1215  -1.0856   1.5013
 1YA  H8   H  HCH2  0   0.251  -3.3796  -3.2695   1.1388
 1YA  H9   H  HCH2  0   0.246  -3.9143  -2.2808   2.4926
 1YA  H10  H  HCH2  0   0.272  -2.0185  -2.1931  -0.6793
 1YA  H11  H  HCH2  0   0.263  -3.5420  -1.4895  -1.1789
 1YA  H12  H  HCR6  0   0.265   1.0270   2.1406   1.4710
 1YA  H13  H  HCR6  0   0.270  -1.2523   1.7242   0.6385
 1YA  H14  H  HCR6  0   0.274   0.2190  -1.4730  -1.7941
 1YA  H15  H  HCR6  0   0.261   2.4789  -1.0929  -0.9515
 1YA  H16  H  HNH1  0   0.410   4.1756   0.2116  -0.8566
 1YA  H17  H  HCH1  0   0.296   5.7728   0.4380   1.5922
 1YA  H18  H  HCH2  0   0.260   6.5494   0.0271  -1.3299
 1YA  H19  H  HCH2  0   0.274   7.6733   0.0933   0.0151
 1YA  H20  H  HCH2  0   0.288   6.5160  -1.8610   1.0906
 1YA  H21  H  HCH2  0   0.286   5.4247  -1.9742  -0.2634
 1YA  H22  H  HOH1  0   0.481   7.8703  -4.3730  -0.8837
 1YA  H23  H  HOH1  0   0.486   7.3450   3.4065   0.9070
 1YA  H24  H  H     0   0.191  -3.7027   0.4907  -1.9562
 1YA  H4   H  HNH1  0   0.391  -5.6862  -3.1307   0.6608
 1YA  C17  C  C     0   0.556   3.2797   0.8502   0.8589

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    1.442  0.020  1.442
 1YA  C7   C6   single    1.533  0.020  1.533
 1YA  N8   C8A  single    1.346  0.020  1.346
 1YA  O5   C18  double    1.215  0.020  1.215
 1YA  C6   N5   single    1.445  0.020  1.445
 1YA  C6   C9   single    1.532  0.020  1.532
 1YA  C18  N10  single    1.351  0.020  1.351
 1YA  C15  C16  aromatic  1.386  0.020  1.386
 1YA  C15  C14  aromatic  1.388  0.020  1.388
 1YA  C16  C11  aromatic  1.392  0.020  1.392
 1YA  N10  C14  single    1.416  0.020  1.416
 1YA  N10  C9   single    1.449  0.020  1.449
 1YA  N5   C4A  single    1.415  0.020  1.415
 1YA  C8A  C4A  double    1.389  0.020  1.389
 1YA  C8A  N1   single    1.355  0.020  1.355
 1YA  C14  C13  aromatic  1.391  0.020  1.391
 1YA  C4A  C4   single    1.417  0.020  1.417
 1YA  N1   C2   double    1.304  0.020  1.304
 1YA  C11  C17  single    1.492  0.020  1.492
 1YA  C11  C12  aromatic  1.393  0.020  1.393
 1YA  C13  C12  aromatic  1.383  0.020  1.383
 1YA  C2   N3   single    1.352  0.020  1.352
 1YA  C2   NA2  single    1.345  0.020  1.345
 1YA  C4   N3   single    1.400  0.020  1.400
 1YA  C4   O4   double    1.228  0.020  1.228
 1YA  O    C17  double    1.221  0.020  1.221
 1YA  C17  N    single    1.350  0.020  1.350
 1YA  N    CA   single    1.437  0.020  1.437
 1YA  CA   CT   single    1.523  0.020  1.523
 1YA  CA   CB   single    1.532  0.020  1.532
 1YA  CT   O2   double    1.202  0.020  1.202
 1YA  CT   O1   single    1.324  0.020  1.324
 1YA  CG   CB   single    1.521  0.020  1.521
 1YA  CG   CD   single    1.504  0.020  1.504
 1YA  OE2  CD   double    1.206  0.020  1.206
 1YA  CD   OE1  single    1.328  0.020  1.328
 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    0.860  0.020  1.020
 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  OE1  H22  single    0.850  0.020  0.980
 1YA  O1   H23  single    0.850  0.020  0.980
 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   117.06  3.000
 1YA  N3   C2   NA2  117.55  3.000
 1YA  NA2  C2   N1   119.88  3.000
 1YA  N3   C2   N1   122.53  3.000
 1YA  H2   NA2  H1   115.92  3.000
 1YA  H2   NA2  C2   120.42  3.000
 1YA  H1   NA2  C2   117.08  3.000
 1YA  H3   N3   C4   116.43  3.000
 1YA  H3   N3   C2   119.80  3.000
 1YA  C4   N3   C2   123.77  3.000
 1YA  C4A  C4   O4   127.22  3.000
 1YA  O4   C4   N3   119.10  3.000
 1YA  C4A  C4   N3   113.67  3.000
 1YA  C8A  C4A  N5   121.61  3.000
 1YA  C8A  C4A  C4   118.81  3.000
 1YA  N5   C4A  C4   119.38  3.000
 1YA  H5   N5   C6   111.42  3.000
 1YA  H5   N5   C4A  112.90  3.000
 1YA  C6   N5   C4A  113.56  3.000
 1YA  H7   C6   C9   108.89  3.000
 1YA  H7   C6   C7   107.59  3.000
 1YA  C9   C6   C7   110.57  3.000
 1YA  H7   C6   N5   107.82  3.000
 1YA  C9   C6   N5   110.01  3.000
 1YA  C7   C6   N5   111.85  3.000
 1YA  H9   C7   H8   107.20  3.000
 1YA  H9   C7   N8   111.49  3.000
 1YA  H8   C7   N8   108.90  3.000
 1YA  H9   C7   C6   108.72  3.000
 1YA  H8   C7   C6   111.28  3.000
 1YA  N8   C7   C6   109.24  3.000
 1YA  H4   N8   C8A  117.97  3.000
 1YA  H4   N8   C7   120.07  3.000
 1YA  C8A  N8   C7   121.86  3.000
 1YA  N8   C8A  C4A  120.16  3.000
 1YA  C4A  C8A  N1   124.08  3.000
 1YA  N8   C8A  N1   115.72  3.000
 1YA  H11  C9   H10  106.67  3.000
 1YA  H11  C9   N10  107.91  3.000
 1YA  H10  C9   N10  109.52  3.000
 1YA  H11  C9   C6   110.75  3.000
 1YA  H10  C9   C6   109.76  3.000
 1YA  N10  C9   C6   112.07  3.000
 1YA  C18  N10  C14  120.21  3.000
 1YA  C14  N10  C9   117.86  3.000
 1YA  C18  N10  C9   120.05  3.000
 1YA  C17  C11  C16  122.57  3.000
 1YA  C17  C11  C12  118.29  3.000
 1YA  C16  C11  C12  119.12  3.000
 1YA  H12  C12  C13  119.46  3.000
 1YA  H12  C12  C11  119.96  3.000
 1YA  C13  C12  C11  120.58  3.000
 1YA  H13  C13  C14  119.70  3.000
 1YA  H13  C13  C12  120.35  3.000
 1YA  C14  C13  C12  119.94  3.000
 1YA  C15  C14  C13  119.87  3.000
 1YA  C13  C14  N10  120.44  3.000
 1YA  C15  C14  N10  119.66  3.000
 1YA  H14  C15  C16  119.88  3.000
 1YA  H14  C15  C14  120.07  3.000
 1YA  C16  C15  C14  120.05  3.000
 1YA  H15  C16  C15  118.49  3.000
 1YA  H15  C16  C11  121.06  3.000
 1YA  C15  C16  C11  120.44  3.000
 1YA  H16  N    CA   117.31  3.000
 1YA  H16  N    C17  118.90  3.000
 1YA  CA   N    C17  121.01  3.000
 1YA  H17  CA   CT   107.77  3.000
 1YA  H17  CA   CB   108.53  3.000
 1YA  CT   CA   CB   110.51  3.000
 1YA  H17  CA   N    108.82  3.000
 1YA  CB   CA   N    110.50  3.000
 1YA  CT   CA   N    110.63  3.000
 1YA  H19  CB   H18  106.93  3.000
 1YA  H19  CB   CG   109.62  3.000
 1YA  H18  CB   CG   110.64  3.000
 1YA  H19  CB   CA   108.67  3.000
 1YA  H18  CB   CA   109.57  3.000
 1YA  CG   CB   CA   111.29  3.000
 1YA  H21  CG   H20  105.61  3.000
 1YA  H21  CG   CD   107.96  3.000
 1YA  H20  CG   CD   108.32  3.000
 1YA  H21  CG   CB   111.48  3.000
 1YA  H20  CG   CB   110.35  3.000
 1YA  CD   CG   CB   112.80  3.000
 1YA  OE2  CD   OE1  123.21  3.000
 1YA  OE1  CD   CG   111.67  3.000
 1YA  OE2  CD   CG   125.13  3.000
 1YA  H22  OE1  CD   110.01  3.000
 1YA  O1   CT   O2   124.30  3.000
 1YA  O1   CT   CA   111.14  3.000
 1YA  O2   CT   CA   124.56  3.000
 1YA  H23  O1   CT   110.41  3.000
 1YA  H24  C18  O5   122.82  3.000
 1YA  H24  C18  N10  111.87  3.000
 1YA  O5   C18  N10  125.25  3.000
 1YA  O    C17  N    122.08  3.000
 1YA  N    C17  C11  116.29  3.000
 1YA  O    C17  C11  121.63  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_31  H1   NA2  C2   N1      0.00   0.0  0
 1YA  CONST_33  CA   N    C17  C11   180.00   0.0  0
 1YA  CONST_34  O5   C18  N10  C14     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  CONST_38  O    C17  N    CA      0.00   0.0  0
 1YA  CONST_39  H23  O1   CT   CA    180.00   0.0  0
 1YA  CONST_40  H22  OE1  CD   CG    180.00   0.0  0
 1YA  Var_01    C6   N5   C4A  C4   -154.00  30.0  1
 1YA  Var_02    C8A  N8   C7   C6    -31.04  30.0  1
 1YA  Var_03    C14  N10  C9   C6     70.00  30.0  2
 1YA  Var_04    O    C17  C11  C12    22.81  30.0  2
 1YA  Var_05    CD   CG   CB   CA   -177.77  30.0  1
 1YA  Var_06    OE2  CD   CG   CB     -1.98  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-3  H22  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-4  H23  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

