# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 19:38:47 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: N-{4-[(6aR)-3-amino-1,9-dioxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzene-1-carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N3[C@H](CN2)CN(C3=O)c4ccc(cc4)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
 LUD  LUD  'N-{4-[(6aR)-3-amino-1,9-dioxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzene-1-carbonyl}-L-glutamic acid'  ligand  55  34  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LUD
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
 LUD  N1   N  N     0  -0.529  -1.2345  51.6970  15.4741
 LUD  C2   C  CR6   0  -0.051   0.2861  52.5144  17.1592
 LUD  N3   N  NH1   0  -0.669  -1.9179  53.3510  16.8969
 LUD  C4   C  CH2   0  -0.247  -1.7708  54.2851  17.9865
 LUD  N5   N  NH1   0  -0.660   3.1733  60.6295  22.0497
 LUD  C6   C  CR5   0   0.713   1.3629  54.3968  18.2664
 LUD  C7   C  CR6   0   0.380   1.6821  56.3925  19.6973
 LUD  C9   C  CR16  0  -0.274   2.0236  58.0540  21.4235
 LUD  C    C  CR6   0   0.692  -0.3083  50.8497  15.1056
 LUD  O    O  O     0  -0.477   2.3353  54.4839  17.5493
 LUD  C19  C  CR6   0   0.504   1.2526  51.5328  16.8375
 LUD  N6   N  NR16  0  -0.719   0.8860  50.7511  15.7359
 LUD  N2   N  NR5   0  -0.561   0.4537  53.3709  18.2630
 LUD  N4   N  NR5   0  -0.618   0.9631  55.2956  19.2393
 LUD  C5   C  CH2   0  -0.320  -0.2239  54.8164  19.9301
 LUD  C3   C  CR15  0  -0.164  -0.7467  53.7477  18.9830
 LUD  C1   C  CR6   0   0.522  -0.9375  52.5232  16.4994
 LUD  C12  C  CR16  0  -0.301   2.7068  56.9956  18.9543
 LUD  C11  C  CR16  0  -0.261   3.3783  58.0922  19.4592
 LUD  C10  C  CR6   0  -0.054   3.0466  58.6493  20.6920
 LUD  C8   C  CR16  0  -0.337   1.3556  56.9430  20.9415
 LUD  C13  C  C     0   0.543   3.8160  59.8265  21.1778
 LUD  O1   O  O     0  -0.486   4.9601  60.0443  20.8028
 LUD  C14  C  CH1   0  -0.181   3.7847  61.8061  22.6142
 LUD  C18  C  C     0   0.549   3.1467  62.0645  23.9662
 LUD  O5   O  O     0  -0.431   2.0149  61.7565  24.2414
 LUD  O4   O  OH1   0  -0.580   3.9671  62.6925  24.7892
 LUD  C15  C  CH2   0  -0.448   3.6112  63.0166  21.6773
 LUD  C16  C  CH2   0  -0.558   4.3069  64.2917  22.1632
 LUD  C17  C  C     0   0.533   4.3319  65.3465  21.0904
 LUD  O3   O  OH1   0  -0.591   3.1088  65.7412  20.7521
 LUD  O2   O  O     0  -0.442   5.3306  65.7887  20.5794
 LUD  H2   H  HCH2  0   0.242  -1.4487  55.2698  17.6270
 LUD  H3   H  HCH2  0   0.272  -2.7362  54.4154  18.4755
 LUD  H4   H  HNH1  0   0.407   2.1838  60.5097  22.2012
 LUD  H5   H  HCR6  0   0.259   1.7506  58.4221  22.4045
 LUD  H6   H  HNH2  0   0.413  -1.4443  50.0181  13.6561
 LUD  H7   H  HNH2  0   0.415   0.1054  49.2975  13.8298
 LUD  H8   H  HNR6  0   0.419   1.5548  50.0562  15.4319
 LUD  H9   H  HCH2  0   0.279   0.0256  54.3919  20.9057
 LUD  H10  H  HCH2  0   0.279  -0.9447  55.6218  20.0790
 LUD  H11  H  HCR5  0   0.295  -1.1561  52.8926  19.5218
 LUD  H12  H  HCR6  0   0.282   2.9791  56.6196  17.9826
 LUD  H13  H  HCR6  0   0.260   4.1667  58.5348  18.8647
 LUD  H14  H  HCR6  0   0.286   0.5831  56.5049  21.5572
 LUD  H15  H  HCH1  0   0.295   4.8500  61.6148  22.7538
 LUD  H16  H  HOH1  0   0.489   3.5176  62.9007  25.6232
 LUD  H17  H  HCH2  0   0.272   4.0295  62.7178  20.7145
 LUD  H18  H  HCH2  0   0.257   2.5454  63.1960  21.5249
 LUD  H19  H  HCH2  0   0.279   3.7922  64.7019  23.0348
 LUD  H20  H  HCH2  0   0.270   5.3360  64.0821  22.4540
 LUD  H21  H  HOH1  0   0.482   3.1567  66.4078  20.0503
 LUD  H1   H  HNH1  0   0.400  -2.7887  53.3168  16.3926
 LUD  N    N  NH2   0  -0.827  -0.5224  50.0493  14.0556
 LUD  O6   O  O     0  -0.497   2.3215  51.3220  17.3984

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
 LUD  N    C    single    1.337  0.020  1.337
 LUD  C    N1   double    1.308  0.020  1.308
 LUD  C    N6   single    1.354  0.020  1.354
 LUD  N1   C1   single    1.350  0.020  1.350
 LUD  N6   C19  single    1.400  0.020  1.400
 LUD  C1   C2   double    1.390  0.020  1.390
 LUD  C1   N3   single    1.343  0.020  1.343
 LUD  C19  O6   double    1.225  0.020  1.225
 LUD  C19  C2   single    1.415  0.020  1.415
 LUD  O    C6   double    1.211  0.020  1.211
 LUD  C2   N2   single    1.407  0.020  1.407
 LUD  N3   C4   single    1.443  0.020  1.443
 LUD  C6   N2   single    1.371  0.020  1.371
 LUD  C6   N4   single    1.384  0.020  1.384
 LUD  N2   C3   single    1.450  0.020  1.450
 LUD  C12  C11  aromatic  1.381  0.020  1.381
 LUD  C12  C7   aromatic  1.402  0.020  1.402
 LUD  C4   C3   single    1.527  0.020  1.527
 LUD  C11  C10  aromatic  1.393  0.020  1.393
 LUD  N4   C7   single    1.389  0.020  1.389
 LUD  N4   C5   single    1.455  0.020  1.455
 LUD  C3   C5   single    1.521  0.020  1.521
 LUD  C7   C8   aromatic  1.399  0.020  1.399
 LUD  O1   C13  double    1.224  0.020  1.224
 LUD  C10  C13  single    1.488  0.020  1.488
 LUD  C10  C9   aromatic  1.391  0.020  1.391
 LUD  C13  N5   single    1.348  0.020  1.348
 LUD  C8   C9   aromatic  1.383  0.020  1.383
 LUD  N5   C14  single    1.441  0.020  1.441
 LUD  O2   C17  double    1.206  0.020  1.206
 LUD  C15  C14  single    1.540  0.020  1.540
 LUD  C15  C16  single    1.532  0.020  1.532
 LUD  C14  C18  single    1.517  0.020  1.517
 LUD  C16  C17  single    1.505  0.020  1.505
 LUD  C17  O3   single    1.329  0.020  1.329
 LUD  C18  O5   double    1.205  0.020  1.205
 LUD  C18  O4   single    1.321  0.020  1.321
 LUD  C4   H2   single    0.970  0.020  1.090
 LUD  C4   H3   single    0.970  0.020  1.090
 LUD  N5   H4   single    0.860  0.020  1.020
 LUD  C9   H5   single    0.930  0.020  1.080
 LUD  N    H6   single    0.860  0.020  1.020
 LUD  N    H7   single    0.860  0.020  1.020
 LUD  N6   H8   single    0.860  0.020  1.020
 LUD  C5   H9   single    0.970  0.020  1.090
 LUD  C5   H10  single    0.970  0.020  1.090
 LUD  C3   H11  single    0.970  0.020  1.090
 LUD  C12  H12  single    0.930  0.020  1.080
 LUD  C11  H13  single    0.930  0.020  1.080
 LUD  C8   H14  single    0.930  0.020  1.080
 LUD  C14  H15  single    0.970  0.020  1.090
 LUD  O4   H16  single    0.850  0.020  0.980
 LUD  C15  H17  single    0.970  0.020  1.090
 LUD  C15  H18  single    0.970  0.020  1.090
 LUD  C16  H19  single    0.970  0.020  1.090
 LUD  C16  H20  single    0.970  0.020  1.090
 LUD  O3   H21  single    0.850  0.020  0.980
 LUD  N3   H1   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
 LUD  C1   N1   C    117.04  3.000
 LUD  C1   C2   N2   118.25  3.000
 LUD  N2   C2   C19  121.29  3.000
 LUD  C1   C2   C19  119.86  3.000
 LUD  H1   N3   C1   117.52  3.000
 LUD  H1   N3   C4   119.24  3.000
 LUD  C1   N3   C4   123.23  3.000
 LUD  H3   C4   H2   107.45  3.000
 LUD  H3   C4   C3   110.08  3.000
 LUD  H2   C4   C3   109.45  3.000
 LUD  H3   C4   N3   109.02  3.000
 LUD  H2   C4   N3   111.33  3.000
 LUD  C3   C4   N3   109.48  3.000
 LUD  H4   N5   C14  117.03  3.000
 LUD  H4   N5   C13  119.62  3.000
 LUD  C14  N5   C13  122.50  3.000
 LUD  N4   C6   N2   107.23  3.000
 LUD  N4   C6   O    126.98  3.000
 LUD  N2   C6   O    125.79  3.000
 LUD  C8   C7   C12  118.20  3.000
 LUD  C8   C7   N4   118.88  3.000
 LUD  C12  C7   N4   122.91  3.000
 LUD  H5   C9   C8   117.84  3.000
 LUD  H5   C9   C10  121.08  3.000
 LUD  C8   C9   C10  121.04  3.000
 LUD  N6   C    N    117.59  3.000
 LUD  N6   C    N1   122.72  3.000
 LUD  N    C    N1   119.69  3.000
 LUD  N6   C19  O6   119.52  3.000
 LUD  O6   C19  C2   127.68  3.000
 LUD  N6   C19  C2   112.80  3.000
 LUD  H8   N6   C19  116.56  3.000
 LUD  H8   N6   C    119.57  3.000
 LUD  C19  N6   C    123.83  3.000
 LUD  C3   N2   C6   110.70  3.000
 LUD  C3   N2   C2   116.69  3.000
 LUD  C6   N2   C2   122.44  3.000
 LUD  C5   N4   C7   121.73  3.000
 LUD  C5   N4   C6   110.84  3.000
 LUD  C7   N4   C6   126.52  3.000
 LUD  H10  C5   H9   108.40  3.000
 LUD  H10  C5   C3   112.13  3.000
 LUD  H9   C5   C3   111.19  3.000
 LUD  H10  C5   N4   111.15  3.000
 LUD  H9   C5   N4   111.44  3.000
 LUD  C3   C5   N4   102.49  3.000
 LUD  H11  C3   C5   111.87  3.000
 LUD  H11  C3   N2   110.64  3.000
 LUD  C5   C3   N2   101.96  3.000
 LUD  H11  C3   C4   110.28  3.000
 LUD  C5   C3   C4   112.94  3.000
 LUD  N2   C3   C4   108.83  3.000
 LUD  N3   C1   C2   120.39  3.000
 LUD  N3   C1   N1   116.19  3.000
 LUD  C2   C1   N1   123.39  3.000
 LUD  H12  C12  C11  118.95  3.000
 LUD  H12  C12  C7   120.85  3.000
 LUD  C11  C12  C7   120.20  3.000
 LUD  H13  C11  C10  119.75  3.000
 LUD  H13  C11  C12  118.56  3.000
 LUD  C10  C11  C12  121.69  3.000
 LUD  C13  C10  C11  118.84  3.000
 LUD  C13  C10  C9   123.16  3.000
 LUD  C11  C10  C9   117.99  3.000
 LUD  H14  C8   C9   118.19  3.000
 LUD  H14  C8   C7   120.93  3.000
 LUD  C9   C8   C7   120.88  3.000
 LUD  O1   C13  C10  121.62  3.000
 LUD  C10  C13  N5   115.84  3.000
 LUD  O1   C13  N5   122.54  3.000
 LUD  H15  C14  C15  109.00  3.000
 LUD  H15  C14  C18  109.05  3.000
 LUD  C15  C14  C18  111.15  3.000
 LUD  H15  C14  N5   108.73  3.000
 LUD  C18  C14  N5   108.04  3.000
 LUD  C15  C14  N5   110.83  3.000
 LUD  O4   C18  O5   124.24  3.000
 LUD  O4   C18  C14  112.03  3.000
 LUD  O5   C18  C14  123.72  3.000
 LUD  H16  O4   C18  110.48  3.000
 LUD  H18  C15  H17  107.22  3.000
 LUD  H18  C15  C16  110.55  3.000
 LUD  H17  C15  C16  109.49  3.000
 LUD  H18  C15  C14  108.91  3.000
 LUD  H17  C15  C14  106.15  3.000
 LUD  C16  C15  C14  114.21  3.000
 LUD  H20  C16  H19  107.72  3.000
 LUD  H20  C16  C17  108.02  3.000
 LUD  H19  C16  C17  108.27  3.000
 LUD  H20  C16  C15  110.70  3.000
 LUD  H19  C16  C15  110.60  3.000
 LUD  C17  C16  C15  111.40  3.000
 LUD  O2   C17  O3   123.05  3.000
 LUD  O3   C17  C16  111.99  3.000
 LUD  O2   C17  C16  124.96  3.000
 LUD  H21  O3   C17  110.07  3.000
 LUD  H7   N    H6   117.41  3.000
 LUD  H7   N    C    121.60  3.000
 LUD  H6   N    C    118.51  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
 LUD  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 LUD  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 LUD  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 LUD  CONST_04  C12  C7   C8   C9      0.00   0.0  0
 LUD  CONST_05  C8   C7   C12  C11     0.00   0.0  0
 LUD  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 LUD  CONST_07  N4   C7   C8   C9    180.00   0.0  0
 LUD  CONST_08  C11  C12  C7   N4    180.00   0.0  0
 LUD  CONST_09  C19  N6   C    N1      0.00   0.0  0
 LUD  CONST_10  C4   N3   C1   N1    180.00   0.0  0
 LUD  CONST_11  C    N1   C1   C2      0.00   0.0  0
 LUD  CONST_12  C4   N3   C1   C2      0.00   0.0  0
 LUD  CONST_13  C    N6   C19  C2      0.00   0.0  0
 LUD  CONST_15  C    N1   C1   N3    180.00   0.0  0
 LUD  CONST_17  N2   C6   N4   C7    180.00   0.0  0
 LUD  CONST_18  C3   C5   N4   C7    180.00   0.0  0
 LUD  CONST_19  C1   N1   C    N6      0.00   0.0  0
 LUD  CONST_20  C5   N4   C6   N2      0.00   0.0  0
 LUD  CONST_22  C13  C10  C11  C12   180.00   0.0  0
 LUD  CONST_23  C13  C10  C9   C8    180.00   0.0  0
 LUD  CONST_25  O    C6   N4   C7      0.00   0.0  0
 LUD  CONST_26  C1   N1   C    N     180.00   0.0  0
 LUD  CONST_27  C19  N6   C    N     180.00   0.0  0
 LUD  CONST_28  O6   C19  N6   C     180.00   0.0  0
 LUD  CONST_29  C3   N2   C6   O     180.00   0.0  0
 LUD  CONST_30  C5   N4   C6   O     180.00   0.0  0
 LUD  CONST_31  H13  C11  C12  C7    180.00   0.0  0
 LUD  CONST_32  H5   C9   C8   C7    180.00   0.0  0
 LUD  CONST_33  H12  C12  C7   N4      0.00   0.0  0
 LUD  CONST_34  H14  C8   C7   N4      0.00   0.0  0
 LUD  CONST_35  H8   N6   C    N1    180.00   0.0  0
 LUD  CONST_36  H1   N3   C1   N1      0.00   0.0  0
 LUD  CONST_37  H6   N    C    N1      0.00   0.0  0
 LUD  CONST_38  H7   N    C    N1    180.00   0.0  0
 LUD  CONST_39  C14  N5   C13  C10   180.00   0.0  0
 LUD  CONST_40  H4   N5   C13  C10     0.00   0.0  0
 LUD  CONST_41  C14  N5   C13  O1      0.00   0.0  0
 LUD  CONST_42  H16  O4   C18  C14   180.00   0.0  0
 LUD  CONST_43  H21  O3   C17  C16   180.00   0.0  0
 LUD  Var_01    C1   C2   N2   C6   -116.04  30.0  1
 LUD  Var_02    C12  C7   N4   C6     21.50  30.0  2
 LUD  Var_03    C1   N3   C4   C3    -28.02  30.0  1
 LUD  Var_04    H9   C5   N4   C6    101.90  30.0  1
 LUD  Var_05    C11  C10  C13  N5    154.86  30.0  2
 LUD  Var_06    C17  C16  C15  C14   168.78  30.0  3
 LUD  Var_07    O2   C17  C16  C15  -116.29  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
 LUD  chir_01  C3   N2  C4   C5   positiv
 LUD  chir_02  C14  N5  C15  C18  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
 LUD  plan-1  C7   0.020
 LUD  plan-1  C9   0.020
 LUD  plan-1  N4   0.020
 LUD  plan-1  C12  0.020
 LUD  plan-1  C11  0.020
 LUD  plan-1  C10  0.020
 LUD  plan-1  C8   0.020
 LUD  plan-1  C13  0.020
 LUD  plan-1  H5   0.020
 LUD  plan-1  H12  0.020
 LUD  plan-1  H13  0.020
 LUD  plan-1  H14  0.020
 LUD  plan-2  C14  0.020
 LUD  plan-2  C18  0.020
 LUD  plan-2  O5   0.020
 LUD  plan-2  O4   0.020
 LUD  plan-2  H16  0.020
 LUD  plan-3  C16  0.020
 LUD  plan-3  C17  0.020
 LUD  plan-3  O3   0.020
 LUD  plan-3  O2   0.020
 LUD  plan-3  H21  0.020
 LUD  plan-4  N5   0.020
 LUD  plan-4  C10  0.020
 LUD  plan-4  C13  0.020
 LUD  plan-4  O1   0.020
 LUD  plan-4  C14  0.020
 LUD  plan-4  H4   0.020
 LUD  plan-5  C2   0.020
 LUD  plan-5  C6   0.020
 LUD  plan-5  C7   0.020
 LUD  plan-5  O    0.020
 LUD  plan-5  N2   0.020
 LUD  plan-5  N4   0.020
 LUD  plan-5  C5   0.020
 LUD  plan-5  C3   0.020
 LUD  plan-6  N1   0.020
 LUD  plan-6  C2   0.020
 LUD  plan-6  N3   0.020
 LUD  plan-6  C4   0.020
 LUD  plan-6  C    0.020
 LUD  plan-6  C19  0.020
 LUD  plan-6  N6   0.020
 LUD  plan-6  N2   0.020
 LUD  plan-6  C1   0.020
 LUD  plan-6  H6   0.020
 LUD  plan-6  H7   0.020
 LUD  plan-6  H8   0.020
 LUD  plan-6  H1   0.020
 LUD  plan-6  N    0.020
 LUD  plan-6  O6   0.020

