# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:14:32 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  53  32  .  2022-07-22  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_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   5.2231  -2.3572  -0.3423
 1YJ  C2   C  CR6    0   0.674   5.8718  -1.7882  -1.3838
 1YJ  N1   N  N      0  -0.529   6.1614  -0.5165  -1.4219
 1YJ  C8A  C  CR6    0   0.517   5.8098   0.2278  -0.3457
 1YJ  C4A  C  CR6    0  -0.075   5.1484  -0.2789   0.7653
 1YJ  C4   C  CR6    0   0.492   4.7889  -1.6476   0.7841
 1YJ  N8   N  NH1    0  -0.658   6.1025   1.5378  -0.4197
 1YJ  C7   C  CH2    0  -0.266   5.7738   2.4586   0.6412
 1YJ  C6   C  CH1    0  -0.205   4.5512   1.9449   1.4076
 1YJ  N5   N  NH1    0  -0.657   4.7277   0.5661   1.8224
 1YJ  C9   C  CH2    0  -0.258   3.2774   2.0854   0.5727
 1YJ  N10  N  NH1    0  -0.683   2.1956   1.3992   1.2310
 1YJ  C4'  C  CR6    0   0.375   0.9604   1.2773   0.6721
 1YJ  C3'  C  CR16   0  -0.343   0.5494   2.0547  -0.4227
 1YJ  C2'  C  CR16   0  -0.261  -0.7219   1.9128  -0.9473
 1YJ  C1'  C  CR6    0  -0.083  -1.6435   1.0154  -0.4123
 1YJ  C6'  C  CR16   0  -0.285  -1.2287   0.2350   0.6722
 1YJ  C5'  C  CR16   0  -0.336   0.0374   0.3570   1.2026
 1YJ  C11  C  C      0   0.541  -2.9903   0.9179  -1.0355
 1YJ  N    N  NH1    0  -0.644  -3.9469   0.3050  -0.3178
 1YJ  CA   C  CH1    0  -0.181  -5.3251   0.2803  -0.7534
 1YJ  C    C  C      0   0.407  -5.9907   1.6789  -0.7018
 1YJ  OX2  O  OC    -1  -0.620  -7.0395   1.7921  -1.3686
 1YJ  OX1  O  O      0  -0.603  -5.4585   2.5456   0.0130
 1YJ  CB   C  CH2    0  -0.448  -6.1152  -0.7115   0.1018
 1YJ  CG   C  CH2    0  -0.577  -5.6307  -2.1469  -0.0221
 1YJ  CD   C  C      0   0.411  -6.4193  -3.1886   0.7920
 1YJ  OE1  O  O      0  -0.609  -7.4416  -2.8077   1.3956
 1YJ  OE2  O  OC    -1  -0.634  -5.9653  -4.3527   0.7728
 1YJ  O11  O  O      0  -0.514  -3.1999   1.3555  -2.1643
 1YJ  O4   O  O      0  -0.512   4.1747  -2.2436   1.6655
 1YJ  N2   N  NH2    0  -0.829   6.2579  -2.5920  -2.3909
 1YJ  H3   H  HCH2   0   0.246   6.6068   2.5666   1.3435
 1YJ  H4   H  HCH2   0   0.252   5.5844   3.4433   0.2109
 1YJ  H5   H  HCH1   0   0.269   4.4404   2.5479   2.3107
 1YJ  H6   H  HNH1   0   0.366   5.3322   0.5073   2.6319
 1YJ  H8   H  HCH2   0   0.245   3.0536   3.1513   0.4733
 1YJ  H9   H  HCR6   0   0.264   1.2233   2.7716  -0.8721
 1YJ  H10  H  HCR6   0   0.249  -1.0046   2.5193  -1.7979
 1YJ  H11  H  HCR6   0   0.246  -1.8853  -0.5084   1.1078
 1YJ  H12  H  HCR6   0   0.258   0.3299  -0.2691   2.0374
 1YJ  H13  H  HNH1   0   0.387  -3.7896   0.1790   0.6689
 1YJ  H14  H  HCH1   0   0.221  -5.3486  -0.0684  -1.7897
 1YJ  H16  H  HCH2   0   0.209  -6.0828  -0.3895   1.1486
 1YJ  H17  H  HCH2   0   0.227  -7.1611  -0.6498  -0.1998
 1YJ  H18  H  HCH2   0   0.220  -5.6615  -2.4486  -1.0766
 1YJ  H19  H  HCH2   0   0.219  -4.5756  -2.2230   0.2594
 1YJ  H21  H  HNH2   0   0.409   5.8437  -3.5017  -2.5040
 1YJ  H22  H  HNH2   0   0.406   6.5774  -2.1465  -3.2341
 1YJ  H23  H  HNR6   0   0.415   5.0104  -3.3454  -0.3636
 1YJ  H1   H  HNH1   0   0.392   6.5316   1.8771  -1.2640
 1YJ  H2   H  HCH2   0   0.228   3.4361   1.7033  -0.4453
 1YJ  H7   H  HNH1   0   0.381   2.5147   0.6242   1.7987

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    1.532  0.020  1.532
 1YJ  N8   C8A  single    1.344  0.020  1.344
 1YJ  C6   N5   single    1.451  0.020  1.451
 1YJ  C6   C9   single    1.530  0.020  1.530
 1YJ  N10  C9   single    1.440  0.020  1.440
 1YJ  N10  C4'  single    1.361  0.020  1.361
 1YJ  C3'  C4'  aromatic  1.404  0.020  1.404
 1YJ  C3'  C2'  aromatic  1.383  0.020  1.383
 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  1.407  0.020  1.407
 1YJ  C4A  C4   single    1.415  0.020  1.415
 1YJ  N1   C2   double    1.305  0.020  1.305
 1YJ  C2'  C1'  aromatic  1.393  0.020  1.393
 1YJ  C2   N3   single    1.352  0.020  1.352
 1YJ  C2   N2   single    1.345  0.020  1.345
 1YJ  C4   N3   single    1.400  0.020  1.400
 1YJ  C4   O4   double    1.229  0.020  1.229
 1YJ  C5'  C6'  aromatic  1.378  0.020  1.378
 1YJ  C1'  C6'  aromatic  1.399  0.020  1.399
 1YJ  C1'  C11  single    1.487  0.020  1.487
 1YJ  O11  C11  double    1.229  0.020  1.229
 1YJ  C11  N    single    1.344  0.020  1.344
 1YJ  N    CA   single    1.446  0.020  1.446
 1YJ  CA   C    single    1.550  0.020  1.550
 1YJ  CA   CB   single    1.529  0.020  1.529
 1YJ  C    OX1  deloc     1.243  0.020  1.243
 1YJ  C    OX2  deloc     1.248  0.020  1.248
 1YJ  CG   CB   single    1.520  0.020  1.520
 1YJ  CG   CD   single    1.539  0.020  1.539
 1YJ  OE1  CD   deloc     1.247  0.020  1.247
 1YJ  CD   OE2  deloc     1.250  0.020  1.250
 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  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  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   116.55  3.000
 1YJ  H23  N3   C2   119.73  3.000
 1YJ  C4   N3   C2   123.71  3.000
 1YJ  N2   C2   N1   119.79  3.000
 1YJ  N2   C2   N3   117.57  3.000
 1YJ  N1   C2   N3   122.61  3.000
 1YJ  C8A  N1   C2   117.04  3.000
 1YJ  N8   C8A  C4A  120.22  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  118.98  3.000
 1YJ  N5   C4A  C8A  121.37  3.000
 1YJ  O4   C4   C4A  127.28  3.000
 1YJ  O4   C4   N3   119.10  3.000
 1YJ  C4A  C4   N3   113.62  3.000
 1YJ  H1   N8   C7   119.94  3.000
 1YJ  H1   N8   C8A  117.89  3.000
 1YJ  C7   N8   C8A  122.13  3.000
 1YJ  H4   C7   H3   107.22  3.000
 1YJ  H4   C7   C6   111.19  3.000
 1YJ  H3   C7   C6   108.63  3.000
 1YJ  H4   C7   N8   108.99  3.000
 1YJ  H3   C7   N8   111.18  3.000
 1YJ  C6   C7   N8   109.62  3.000
 1YJ  H5   C6   C9   108.44  3.000
 1YJ  H5   C6   N5   107.50  3.000
 1YJ  C9   C6   N5   110.16  3.000
 1YJ  H5   C6   C7   108.05  3.000
 1YJ  C9   C6   C7   111.16  3.000
 1YJ  N5   C6   C7   111.39  3.000
 1YJ  H6   N5   C6   110.90  3.000
 1YJ  H6   N5   C4A  112.62  3.000
 1YJ  C6   N5   C4A  112.92  3.000
 1YJ  H2   C9   H8   106.51  3.000
 1YJ  H2   C9   N10  111.49  3.000
 1YJ  H8   C9   N10  110.62  3.000
 1YJ  H2   C9   C6   110.70  3.000
 1YJ  H8   C9   C6   108.03  3.000
 1YJ  N10  C9   C6   109.41  3.000
 1YJ  H7   N10  C4'  116.60  3.000
 1YJ  H7   N10  C9   112.60  3.000
 1YJ  C4'  N10  C9   122.45  3.000
 1YJ  C5'  C4'  C3'  117.65  3.000
 1YJ  C5'  C4'  N10  119.93  3.000
 1YJ  C3'  C4'  N10  122.42  3.000
 1YJ  H9   C3'  C2'  118.90  3.000
 1YJ  H9   C3'  C4'  120.56  3.000
 1YJ  C2'  C3'  C4'  120.54  3.000
 1YJ  H10  C2'  C1'  119.34  3.000
 1YJ  H10  C2'  C3'  118.74  3.000
 1YJ  C1'  C2'  C3'  121.92  3.000
 1YJ  C11  C1'  C6'  123.83  3.000
 1YJ  C11  C1'  C2'  118.71  3.000
 1YJ  C6'  C1'  C2'  117.44  3.000
 1YJ  H11  C6'  C5'  117.57  3.000
 1YJ  H11  C6'  C1'  120.98  3.000
 1YJ  C5'  C6'  C1'  121.43  3.000
 1YJ  H12  C5'  C6'  119.56  3.000
 1YJ  H12  C5'  C4'  119.42  3.000
 1YJ  C6'  C5'  C4'  121.02  3.000
 1YJ  O11  C11  N    122.12  3.000
 1YJ  N    C11  C1'  116.79  3.000
 1YJ  O11  C11  C1'  121.07  3.000
 1YJ  H13  N    CA   116.23  3.000
 1YJ  H13  N    C11  117.98  3.000
 1YJ  CA   N    C11  121.71  3.000
 1YJ  H14  CA   CB   108.18  3.000
 1YJ  H14  CA   C    108.06  3.000
 1YJ  CB   CA   C    110.17  3.000
 1YJ  H14  CA   N    108.15  3.000
 1YJ  CB   CA   N    109.58  3.000
 1YJ  C    CA   N    112.58  3.000
 1YJ  OX1  C    OX2  127.14  3.000
 1YJ  OX2  C    CA   115.15  3.000
 1YJ  OX1  C    CA   117.67  3.000
 1YJ  H17  CB   H16  106.02  3.000
 1YJ  H17  CB   CG   109.68  3.000
 1YJ  H16  CB   CG   110.24  3.000
 1YJ  H17  CB   CA   107.71  3.000
 1YJ  H16  CB   CA   109.17  3.000
 1YJ  CG   CB   CA   113.71  3.000
 1YJ  H19  CG   H18  104.78  3.000
 1YJ  H19  CG   CD   108.11  3.000
 1YJ  H18  CG   CD   107.93  3.000
 1YJ  H19  CG   CB   110.60  3.000
 1YJ  H18  CG   CB   109.21  3.000
 1YJ  CD   CG   CB   115.63  3.000
 1YJ  OE2  CD   OE1  126.15  3.000
 1YJ  OE2  CD   CG   115.86  3.000
 1YJ  OE1  CD   CG   117.99  3.000
 1YJ  H22  N2   H21  115.92  3.000
 1YJ  H22  N2   C2   117.01  3.000
 1YJ  H21  N2   C2   120.42  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_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  Var_01    C6   C7   N8   C8A   -27.63  30.0  1
 1YJ  Var_02    C6   N5   C4A  C8A    23.63  30.0  1
 1YJ  Var_03    C4'  N10  C9   C6   -175.38  30.0  2
 1YJ  Var_04    O11  C11  C1'  C2'    17.29  30.0  2
 1YJ  Var_05    CD   CG   CB   CA   -178.45  30.0  2
 1YJ  Var_06    OE1  CD   CG   CB      5.57  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-4  CG   0.020
 1YJ  plan-4  CD   0.020
 1YJ  plan-4  OE1  0.020
 1YJ  plan-4  OE2  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

