# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:43:19 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N[C@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)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
 1YJ  1YJ  'N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid'  ligand  55  32  .  2022-07-22  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_1YJ
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
 1YJ  N3   N  NR16  0  -0.714   5.2569  -2.3690  -0.5138
 1YJ  C2   C  CR6   0   0.673   5.9040  -1.7458  -1.5246
 1YJ  N1   N  N     0  -0.529   6.1872  -0.4725  -1.4992
 1YJ  C8A  C  CR6   0   0.517   5.8288   0.2160  -0.3889
 1YJ  C4A  C  CR6   0  -0.075   5.1667  -0.3481   0.6940
 1YJ  C4   C  CR6   0   0.493   4.8131  -1.7175   0.6438
 1YJ  N8   N  NH1   0  -0.658   6.1131   1.5300  -0.3983
 1YJ  C7   C  CH2   0  -0.266   5.7759   2.3959   0.7053
 1YJ  C6   C  CH1   0  -0.207   4.5539   1.8383   1.4403
 1YJ  N5   N  NH1   0  -0.657   4.7380   0.4421   1.7897
 1YJ  C9   C  CH2   0  -0.257   3.2826   2.0083   0.6076
 1YJ  N10  N  NH1   0  -0.682   2.2034   1.2899   1.2345
 1YJ  C4'  C  CR6   0   0.385   0.9608   1.2061   0.6946
 1YJ  C3'  C  CR16  0  -0.344   0.5417   2.0329  -0.3622
 1YJ  C2'  C  CR16  0  -0.255  -0.7383   1.9280  -0.8700
 1YJ  C1'  C  CR6   0  -0.084  -1.6609   1.0194  -0.3531
 1YJ  C6'  C  CR16  0  -0.278  -1.2396   0.1895   0.6923
 1YJ  C5'  C  CR16  0  -0.336   0.0355   0.2746   1.2041
 1YJ  C11  C  C     0   0.552  -3.0119   0.9568  -0.9516
 1YJ  N    N  NH1   0  -0.665  -3.9733   0.3331  -0.2292
 1YJ  CA   C  CH1   0  -0.183  -5.3207   0.2590  -0.7214
 1YJ  C    C  C     0   0.544  -5.9643   1.6385  -0.7479
 1YJ  OX2  O  OH1   0  -0.590  -6.9729   1.6826  -1.6061
 1YJ  OX1  O  O     0  -0.434  -5.6265   2.5604  -0.0531
 1YJ  CB   C  CH2   0  -0.468  -6.1557  -0.6855   0.1480
 1YJ  CG   C  CH2   0  -0.577  -5.6501  -2.1160   0.0542
 1YJ  CD   C  C     0   0.554  -6.4326  -3.0720   0.9112
 1YJ  OE1  O  O     0  -0.442  -7.3840  -2.7772   1.5904
 1YJ  OE2  O  OH1   0  -0.595  -5.9472  -4.3064   0.8360
 1YJ  O11  O  O     0  -0.494  -3.2611   1.4292  -2.0546
 1YJ  O4   O  O     0  -0.512   4.1963  -2.3585   1.4910
 1YJ  N2   N  NH2   0  -0.828   6.2965  -2.4969  -2.5697
 1YJ  H3   H  HCH2  0   0.247   6.6058   2.4750   1.4150
 1YJ  H4   H  HCH2  0   0.252   5.5820   3.3995   0.3231
 1YJ  H5   H  HCH1  0   0.270   4.4330   2.3961   2.3709
 1YJ  H6   H  HNH1  0   0.366   5.3417   0.3490   2.5965
 1YJ  H8   H  HCH2  0   0.247   3.0534   3.0760   0.5520
 1YJ  H9   H  HCR6  0   0.268   1.2173   2.7585  -0.7944
 1YJ  H10  H  HCR6  0   0.253  -1.0270   2.5734  -1.6894
 1YJ  H11  H  HCR6  0   0.247  -1.8983  -0.5626   1.1093
 1YJ  H12  H  HCR6  0   0.261   0.3352  -0.3891   2.0063
 1YJ  H13  H  HNH1  0   0.406  -3.8330   0.1980   0.7596
 1YJ  H14  H  HCH1  0   0.288  -5.3085  -0.1280  -1.7436
 1YJ  H15  H  HOH1  0   0.485  -7.4036   2.5505  -1.5784
 1YJ  H16  H  HCH2  0   0.259  -6.1402  -0.3372   1.1839
 1YJ  H17  H  HCH2  0   0.273  -7.1937  -0.6410  -0.1829
 1YJ  H18  H  HCH2  0   0.290  -5.6969  -2.4674  -0.9813
 1YJ  H19  H  HCH2  0   0.285  -4.5973  -2.1882   0.3401
 1YJ  H20  H  HOH1  0   0.480  -6.4632  -4.9009   1.4008
 1YJ  H21  H  HNH2  0   0.409   5.8803  -3.3983  -2.7321
 1YJ  H22  H  HNH2  0   0.406   6.6090  -2.0061  -3.3902
 1YJ  H23  H  HNR6  0   0.415   5.0485  -3.3558  -0.5851
 1YJ  H1   H  HNH1  0   0.392   6.5468   1.9118  -1.2217
 1YJ  H2   H  HCH2  0   0.231   3.4443   1.6675  -0.4240
 1YJ  H7   H  HNH1  0   0.383   2.5209   0.4999   1.7821

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
 1YJ  C7   N8   single    1.443  0.020  1.443
 1YJ  C7   C6   single    1.531  0.020  1.531
 1YJ  N8   C8A  single    1.344  0.020  1.344
 1YJ  C6   N5   single    1.451  0.020  1.451
 1YJ  C6   C9   single    1.529  0.020  1.529
 1YJ  N10  C9   single    1.440  0.020  1.440
 1YJ  N10  C4'  single    1.357  0.020  1.357
 1YJ  C3'  C4'  aromatic  1.406  0.020  1.406
 1YJ  C3'  C2'  aromatic  1.381  0.020  1.381
 1YJ  C8A  C4A  double    1.389  0.020  1.389
 1YJ  C8A  N1   single    1.355  0.020  1.355
 1YJ  N5   C4A  single    1.417  0.020  1.417
 1YJ  C4'  C5'  aromatic  1.408  0.020  1.408
 1YJ  C4A  C4   single    1.415  0.020  1.415
 1YJ  N1   C2   double    1.305  0.020  1.305
 1YJ  C2'  C1'  aromatic  1.394  0.020  1.394
 1YJ  C2   N3   single    1.352  0.020  1.352
 1YJ  C2   N2   single    1.346  0.020  1.346
 1YJ  C4   N3   single    1.400  0.020  1.400
 1YJ  C4   O4   double    1.228  0.020  1.228
 1YJ  C5'  C6'  aromatic  1.377  0.020  1.377
 1YJ  C1'  C6'  aromatic  1.400  0.020  1.400
 1YJ  C1'  C11  single    1.479  0.020  1.479
 1YJ  O11  C11  double    1.225  0.020  1.225
 1YJ  C11  N    single    1.355  0.020  1.355
 1YJ  N    CA   single    1.436  0.020  1.436
 1YJ  CA   C    single    1.522  0.020  1.522
 1YJ  CA   CB   single    1.531  0.020  1.531
 1YJ  C    OX1  double    1.203  0.020  1.203
 1YJ  C    OX2  single    1.325  0.020  1.325
 1YJ  CG   CB   single    1.520  0.020  1.520
 1YJ  CG   CD   single    1.504  0.020  1.504
 1YJ  OE1  CD   double    1.206  0.020  1.206
 1YJ  CD   OE2  single    1.329  0.020  1.329
 1YJ  C7   H3   single    0.970  0.020  1.090
 1YJ  C7   H4   single    0.970  0.020  1.090
 1YJ  C6   H5   single    0.970  0.020  1.090
 1YJ  N5   H6   single    0.890  0.020  1.040
 1YJ  C9   H8   single    0.970  0.020  1.090
 1YJ  C3'  H9   single    0.930  0.020  1.080
 1YJ  C2'  H10  single    0.930  0.020  1.080
 1YJ  C6'  H11  single    0.930  0.020  1.080
 1YJ  C5'  H12  single    0.930  0.020  1.080
 1YJ  N    H13  single    0.890  0.020  1.040
 1YJ  CA   H14  single    0.970  0.020  1.090
 1YJ  OX2  H15  single    0.850  0.020  0.980
 1YJ  CB   H16  single    0.970  0.020  1.090
 1YJ  CB   H17  single    0.970  0.020  1.090
 1YJ  CG   H18  single    0.970  0.020  1.090
 1YJ  CG   H19  single    0.970  0.020  1.090
 1YJ  OE2  H20  single    0.850  0.020  0.980
 1YJ  N2   H21  single    0.890  0.020  1.040
 1YJ  N2   H22  single    0.890  0.020  1.040
 1YJ  N3   H23  single    0.860  0.020  1.020
 1YJ  N8   H1   single    0.860  0.020  1.020
 1YJ  C9   H2   single    0.970  0.020  1.090
 1YJ  N10  H7   single    0.890  0.020  1.040

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
 1YJ  H23  N3   C4   116.56  3.000
 1YJ  H23  N3   C2   119.71  3.000
 1YJ  C4   N3   C2   123.71  3.000
 1YJ  N2   C2   N1   119.78  3.000
 1YJ  N2   C2   N3   117.58  3.000
 1YJ  N1   C2   N3   122.62  3.000
 1YJ  C8A  N1   C2   117.04  3.000
 1YJ  N8   C8A  C4A  120.21  3.000
 1YJ  C4A  C8A  N1   123.96  3.000
 1YJ  N8   C8A  N1   115.79  3.000
 1YJ  N5   C4A  C4   119.43  3.000
 1YJ  C4   C4A  C8A  118.97  3.000
 1YJ  N5   C4A  C8A  121.36  3.000
 1YJ  O4   C4   C4A  127.29  3.000
 1YJ  O4   C4   N3   119.10  3.000
 1YJ  C4A  C4   N3   113.60  3.000
 1YJ  H1   N8   C7   119.94  3.000
 1YJ  H1   N8   C8A  117.90  3.000
 1YJ  C7   N8   C8A  122.13  3.000
 1YJ  H4   C7   H3   107.18  3.000
 1YJ  H4   C7   C6   111.18  3.000
 1YJ  H3   C7   C6   108.67  3.000
 1YJ  H4   C7   N8   109.00  3.000
 1YJ  H3   C7   N8   111.23  3.000
 1YJ  C6   C7   N8   109.58  3.000
 1YJ  H5   C6   C9   108.38  3.000
 1YJ  H5   C6   N5   107.49  3.000
 1YJ  C9   C6   N5   110.09  3.000
 1YJ  H5   C6   C7   108.15  3.000
 1YJ  C9   C6   C7   111.20  3.000
 1YJ  N5   C6   C7   111.40  3.000
 1YJ  H6   N5   C6   110.87  3.000
 1YJ  H6   N5   C4A  112.61  3.000
 1YJ  C6   N5   C4A  112.87  3.000
 1YJ  H2   C9   H8   106.61  3.000
 1YJ  H2   C9   N10  111.37  3.000
 1YJ  H8   C9   N10  110.62  3.000
 1YJ  H2   C9   C6   110.77  3.000
 1YJ  H8   C9   C6   108.09  3.000
 1YJ  N10  C9   C6   109.30  3.000
 1YJ  H7   N10  C4'  117.01  3.000
 1YJ  H7   N10  C9   112.93  3.000
 1YJ  C4'  N10  C9   122.94  3.000
 1YJ  C5'  C4'  C3'  117.71  3.000
 1YJ  C5'  C4'  N10  119.89  3.000
 1YJ  C3'  C4'  N10  122.39  3.000
 1YJ  H9   C3'  C2'  118.88  3.000
 1YJ  H9   C3'  C4'  120.58  3.000
 1YJ  C2'  C3'  C4'  120.54  3.000
 1YJ  H10  C2'  C1'  119.52  3.000
 1YJ  H10  C2'  C3'  118.71  3.000
 1YJ  C1'  C2'  C3'  121.77  3.000
 1YJ  C11  C1'  C6'  123.51  3.000
 1YJ  C11  C1'  C2'  118.82  3.000
 1YJ  C6'  C1'  C2'  117.65  3.000
 1YJ  H11  C6'  C5'  117.58  3.000
 1YJ  H11  C6'  C1'  121.08  3.000
 1YJ  C5'  C6'  C1'  121.32  3.000
 1YJ  H12  C5'  C6'  119.58  3.000
 1YJ  H12  C5'  C4'  119.42  3.000
 1YJ  C6'  C5'  C4'  120.99  3.000
 1YJ  O11  C11  N    120.87  3.000
 1YJ  N    C11  C1'  116.87  3.000
 1YJ  O11  C11  C1'  122.25  3.000
 1YJ  H13  N    CA   117.38  3.000
 1YJ  H13  N    C11  119.09  3.000
 1YJ  CA   N    C11  120.44  3.000
 1YJ  H14  CA   CB   108.58  3.000
 1YJ  H14  CA   C    108.02  3.000
 1YJ  CB   CA   C    109.77  3.000
 1YJ  H14  CA   N    109.16  3.000
 1YJ  CB   CA   N    110.41  3.000
 1YJ  C    CA   N    110.84  3.000
 1YJ  OX1  C    OX2  124.22  3.000
 1YJ  OX2  C    CA   111.29  3.000
 1YJ  OX1  C    CA   124.45  3.000
 1YJ  H15  OX2  C    110.46  3.000
 1YJ  H17  CB   H16  106.75  3.000
 1YJ  H17  CB   CG   109.65  3.000
 1YJ  H16  CB   CG   110.72  3.000
 1YJ  H17  CB   CA   108.75  3.000
 1YJ  H16  CB   CA   109.50  3.000
 1YJ  CG   CB   CA   111.35  3.000
 1YJ  H19  CG   H18  105.51  3.000
 1YJ  H19  CG   CD   108.07  3.000
 1YJ  H18  CG   CD   108.23  3.000
 1YJ  H19  CG   CB   111.49  3.000
 1YJ  H18  CG   CB   110.26  3.000
 1YJ  CD   CG   CB   112.96  3.000
 1YJ  OE2  CD   OE1  123.19  3.000
 1YJ  OE2  CD   CG   111.61  3.000
 1YJ  OE1  CD   CG   125.19  3.000
 1YJ  H20  OE2  CD   110.03  3.000
 1YJ  H22  N2   H21  115.73  3.000
 1YJ  H22  N2   C2   116.87  3.000
 1YJ  H21  N2   C2   120.32  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
 1YJ  CONST_01  C1'  C2'  C3'  C4'     0.00   0.0  0
 1YJ  CONST_02  C1'  C6'  C5'  C4'     0.00   0.0  0
 1YJ  CONST_03  C6'  C5'  C4'  C3'     0.00   0.0  0
 1YJ  CONST_04  C6'  C1'  C2'  C3'     0.00   0.0  0
 1YJ  CONST_05  C5'  C4'  C3'  C2'     0.00   0.0  0
 1YJ  CONST_06  C5'  C6'  C1'  C2'     0.00   0.0  0
 1YJ  CONST_07  C8A  N1   C2   N3      0.00   0.0  0
 1YJ  CONST_08  N8   C8A  N1   C2    180.00   0.0  0
 1YJ  CONST_09  C4A  C8A  N1   C2      0.00   0.0  0
 1YJ  CONST_10  C4A  C4   N3   C2      0.00   0.0  0
 1YJ  CONST_11  C7   N8   C8A  N1    180.00   0.0  0
 1YJ  CONST_12  C4   N3   C2   N1      0.00   0.0  0
 1YJ  CONST_13  C7   N8   C8A  C4A     0.00   0.0  0
 1YJ  CONST_14  C2'  C3'  C4'  N10   180.00   0.0  0
 1YJ  CONST_15  C6'  C5'  C4'  N10   180.00   0.0  0
 1YJ  CONST_16  C11  C1'  C2'  C3'   180.00   0.0  0
 1YJ  CONST_17  C11  C1'  C6'  C5'   180.00   0.0  0
 1YJ  CONST_18  O4   C4   N3   C2    180.00   0.0  0
 1YJ  CONST_19  N2   C2   N1   C8A   180.00   0.0  0
 1YJ  CONST_20  N2   C2   N3   C4    180.00   0.0  0
 1YJ  CONST_21  H10  C2'  C3'  C4'   180.00   0.0  0
 1YJ  CONST_22  H11  C6'  C5'  C4'   180.00   0.0  0
 1YJ  CONST_23  H12  C5'  C4'  C3'   180.00   0.0  0
 1YJ  CONST_24  H9   C3'  C2'  C1'   180.00   0.0  0
 1YJ  CONST_25  H1   N8   C8A  N1      0.00   0.0  0
 1YJ  CONST_26  H23  N3   C2   N1    180.00   0.0  0
 1YJ  CONST_27  C3'  C4'  N10  C9      0.00   0.0  0
 1YJ  CONST_28  C5'  C4'  N10  C9    180.00   0.0  0
 1YJ  CONST_31  H22  N2   C2   N3    180.00   0.0  0
 1YJ  CONST_32  CA   N    C11  C1'   180.00   0.0  0
 1YJ  CONST_34  O11  C11  N    CA      0.00   0.0  0
 1YJ  CONST_35  H15  OX2  C    CA    180.00   0.0  0
 1YJ  CONST_36  H20  OE2  CD   CG    180.00   0.0  0
 1YJ  Var_01    C6   C7   N8   C8A   -27.72  30.0  1
 1YJ  Var_02    C6   N5   C4A  C8A    23.70  30.0  1
 1YJ  Var_03    C4'  N10  C9   C6   -177.01  30.0  2
 1YJ  Var_04    O11  C11  C1'  C2'    17.28  30.0  2
 1YJ  Var_05    CD   CG   CB   CA    179.14  30.0  2
 1YJ  Var_06    OE1  CD   CG   CB      1.58  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
 1YJ  chir_01  C6  C7  N5  C9  positiv
 1YJ  chir_02  CA  N   C   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
 1YJ  plan-1  N10  0.020
 1YJ  plan-1  C4'  0.020
 1YJ  plan-1  C3'  0.020
 1YJ  plan-1  C2'  0.020
 1YJ  plan-1  C1'  0.020
 1YJ  plan-1  C6'  0.020
 1YJ  plan-1  C5'  0.020
 1YJ  plan-1  C11  0.020
 1YJ  plan-1  H9   0.020
 1YJ  plan-1  H10  0.020
 1YJ  plan-1  H11  0.020
 1YJ  plan-1  H12  0.020
 1YJ  plan-2  C4A  0.020
 1YJ  plan-2  C6   0.020
 1YJ  plan-2  N5   0.020
 1YJ  plan-2  H6   0.020
 1YJ  plan-3  CA   0.020
 1YJ  plan-3  C    0.020
 1YJ  plan-3  OX2  0.020
 1YJ  plan-3  OX1  0.020
 1YJ  plan-3  H15  0.020
 1YJ  plan-4  CG   0.020
 1YJ  plan-4  CD   0.020
 1YJ  plan-4  OE1  0.020
 1YJ  plan-4  OE2  0.020
 1YJ  plan-4  H20  0.020
 1YJ  plan-5  C1'  0.020
 1YJ  plan-5  C11  0.020
 1YJ  plan-5  N    0.020
 1YJ  plan-5  CA   0.020
 1YJ  plan-5  O11  0.020
 1YJ  plan-5  H13  0.020
 1YJ  plan-6  C9   0.020
 1YJ  plan-6  N10  0.020
 1YJ  plan-6  C4'  0.020
 1YJ  plan-6  H7   0.020
 1YJ  plan-7  N3   0.020
 1YJ  plan-7  C2   0.020
 1YJ  plan-7  N1   0.020
 1YJ  plan-7  C8A  0.020
 1YJ  plan-7  C4A  0.020
 1YJ  plan-7  C4   0.020
 1YJ  plan-7  N8   0.020
 1YJ  plan-7  C7   0.020
 1YJ  plan-7  N5   0.020
 1YJ  plan-7  O4   0.020
 1YJ  plan-7  N2   0.020
 1YJ  plan-7  H21  0.020
 1YJ  plan-7  H22  0.020
 1YJ  plan-7  H23  0.020
 1YJ  plan-7  H1   0.020

