# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 14:00:30 2020
#   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  53  34  .  2021-08-12  2021-08-12  
;
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  -0.531   7.2436   0.2814  -0.9639
 LUD  C2   C  CR6    0  -0.053   5.1516   0.5158   0.2146
 LUD  N3   N  NH1    0  -0.670   5.9337  -1.5619  -0.6191
 LUD  C4   C  CH2    0  -0.247   4.7780  -2.2758  -0.1309
 LUD  N5   N  NH1    0  -0.637  -4.3914  -0.5435  -0.0764
 LUD  C6   C  CR5    0   0.706   2.7585   0.0840   0.3003
 LUD  C7   C  CR6    0   0.371   0.6104  -1.1132   0.5487
 LUD  C9   C  CR16   0  -0.290  -1.5005  -0.5359  -0.4659
 LUD  C    C  CR6    0   0.697   7.4476   1.5607  -0.7756
 LUD  O    O  O      0  -0.478   2.3851   1.0739  -0.2897
 LUD  C19  C  CR6    0   0.503   5.4059   1.8761   0.5042
 LUD  N6   N  NR16   0  -0.721   6.5869   2.3449  -0.0839
 LUD  N2   N  NR5    0  -0.560   4.0335  -0.1480   0.7516
 LUD  N4   N  NR5    0  -0.616   1.9948  -1.0113   0.6545
 LUD  C5   C  CH2    0  -0.315   2.7823  -1.9667   1.4168
 LUD  C3   C  CR15   0  -0.166   4.2068  -1.5484   1.0844
 LUD  C1   C  CR6    0   0.522   6.1017  -0.2376  -0.4651
 LUD  C12  C  CR16   0  -0.330  -0.0743  -1.9958   1.3905
 LUD  C11  C  CR16   0  -0.265  -1.4467  -2.1382   1.2990
 LUD  C10  C  CR6    0  -0.055  -2.1891  -1.3955   0.3869
 LUD  C8   C  CR16   0  -0.293  -0.1256  -0.3952  -0.4006
 LUD  C13  C  C      0   0.538  -3.6690  -1.5892   0.3393
 LUD  O1   O  O      0  -0.511  -4.1742  -2.6436   0.7143
 LUD  C14  C  CH1    0  -0.185  -5.8043  -0.6343  -0.3637
 LUD  C18  C  C      0   0.411  -6.0907  -1.4288  -1.6655
 LUD  O5   O  O      0  -0.595  -5.1274  -1.7110  -2.3971
 LUD  O4   O  OC    -1  -0.619  -7.2935  -1.6979  -1.8603
 LUD  C15  C  CH2    0  -0.453  -6.4040   0.7705  -0.4339
 LUD  C16  C  CH2    0  -0.578  -6.2762   1.5472   0.8667
 LUD  C17  C  C      0   0.412  -6.9303   2.9405   0.8785
 LUD  O3   O  OC    -1  -0.633  -6.7111   3.6357   1.8934
 LUD  O2   O  O      0  -0.609  -7.6316   3.2655  -0.0999
 LUD  H2   H  HCH2   0   0.242   4.0043  -2.3611  -0.9037
 LUD  H3   H  HCH2   0   0.271   5.0765  -3.2874   0.1444
 LUD  H4   H  HNH1   0   0.394  -3.9098   0.2800  -0.3984
 LUD  H5   H  HCR6   0   0.256  -2.0270   0.0180  -1.2336
 LUD  H6   H  HNH2   0   0.414   9.1975   1.5743  -1.7944
 LUD  H7   H  HNH2   0   0.416   8.7396   3.1146  -1.1726
 LUD  H8   H  HNR6   0   0.417   6.8105   3.3189   0.0713
 LUD  H9   H  HCH2   0   0.276   2.5899  -1.8816   2.4893
 LUD  H10  H  HCH2   0   0.277   2.5680  -2.9904   1.1077
 LUD  H11  H  HCR5   0   0.293   4.8736  -1.6593   1.9397
 LUD  H12  H  HCR6   0   0.279   0.4543  -2.5760   2.1343
 LUD  H13  H  HCR6   0   0.258  -1.9464  -2.8299   1.9644
 LUD  H14  H  HCR6   0   0.277   0.3650   0.2596  -1.1017
 LUD  H15  H  HCH1   0   0.228  -6.2854  -1.1661   0.4630
 LUD  H17  H  HCH2   0   0.211  -5.9295   1.3241  -1.2522
 LUD  H18  H  HCH2   0   0.229  -7.4547   0.6709  -0.7035
 LUD  H19  H  HCH2   0   0.221  -6.7212   0.9622   1.6813
 LUD  H20  H  HCH2   0   0.218  -5.2241   1.6623   1.1449
 LUD  H1   H  HNH1   0   0.400   6.6535  -2.0677  -1.1084
 LUD  N    N  NH2    0  -0.830   8.5483   2.1330  -1.2692
 LUD  O6   O  O      0  -0.498   4.7250   2.6390   1.1799

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    1.335  0.020  1.335
 LUD  C    N1   double    1.309  0.020  1.309
 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    1.344  0.020  1.344
 LUD  C19  O6   double    1.226  0.020  1.226
 LUD  C19  C2   single    1.414  0.020  1.414
 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    1.372  0.020  1.372
 LUD  C6   N4   single    1.381  0.020  1.381
 LUD  N2   C3   single    1.450  0.020  1.450
 LUD  C12  C11  aromatic  1.383  0.020  1.383
 LUD  C12  C7   aromatic  1.399  0.020  1.399
 LUD  C4   C3   single    1.527  0.020  1.527
 LUD  C11  C10  aromatic  1.391  0.020  1.391
 LUD  N4   C7   single    1.392  0.020  1.392
 LUD  N4   C5   single    1.454  0.020  1.454
 LUD  C3   C5   single    1.521  0.020  1.521
 LUD  C7   C8   aromatic  1.399  0.020  1.399
 LUD  O1   C13  double    1.228  0.020  1.228
 LUD  C10  C13  single    1.493  0.020  1.493
 LUD  C10  C9   aromatic  1.393  0.020  1.393
 LUD  C13  N5   single    1.337  0.020  1.337
 LUD  C8   C9   aromatic  1.384  0.020  1.384
 LUD  N5   C14  single    1.445  0.020  1.445
 LUD  O2   C17  deloc     1.247  0.020  1.247
 LUD  C15  C14  single    1.529  0.020  1.529
 LUD  C15  C16  single    1.520  0.020  1.520
 LUD  C14  C18  single    1.552  0.020  1.552
 LUD  C16  C17  single    1.539  0.020  1.539
 LUD  C17  O3   deloc     1.250  0.020  1.250
 LUD  C18  O5   deloc     1.242  0.020  1.242
 LUD  C18  O4   deloc     1.248  0.020  1.248
 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  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  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    117.03  3.000
 LUD  C1   C2   N2   118.30  3.000
 LUD  N2   C2   C19  121.25  3.000
 LUD  C1   C2   C19  119.91  3.000
 LUD  H1   N3   C1   117.48  3.000
 LUD  H1   N3   C4   119.23  3.000
 LUD  C1   N3   C4   123.28  3.000
 LUD  H3   C4   H2   107.40  3.000
 LUD  H3   C4   C3   110.09  3.000
 LUD  H2   C4   C3   109.50  3.000
 LUD  H3   C4   N3   108.97  3.000
 LUD  H2   C4   N3   111.41  3.000
 LUD  C3   C4   N3   109.45  3.000
 LUD  H4   N5   C14  117.10  3.000
 LUD  H4   N5   C13  118.73  3.000
 LUD  C14  N5   C13  122.75  3.000
 LUD  N4   C6   N2   107.18  3.000
 LUD  N4   C6   O    127.04  3.000
 LUD  N2   C6   O    125.78  3.000
 LUD  C8   C7   C12  118.33  3.000
 LUD  C8   C7   N4   122.48  3.000
 LUD  C12  C7   N4   119.16  3.000
 LUD  H5   C9   C8   117.68  3.000
 LUD  H5   C9   C10  120.60  3.000
 LUD  C8   C9   C10  121.68  3.000
 LUD  N6   C    N    117.68  3.000
 LUD  N6   C    N1   122.70  3.000
 LUD  N    C    N1   119.62  3.000
 LUD  N6   C19  O6   119.46  3.000
 LUD  O6   C19  C2   127.72  3.000
 LUD  N6   C19  C2   112.82  3.000
 LUD  H8   N6   C19  116.40  3.000
 LUD  H8   N6   C    119.70  3.000
 LUD  C19  N6   C    123.83  3.000
 LUD  C3   N2   C6   110.47  3.000
 LUD  C3   N2   C2   116.64  3.000
 LUD  C6   N2   C2   122.22  3.000
 LUD  C5   N4   C7   122.03  3.000
 LUD  C5   N4   C6   110.86  3.000
 LUD  C7   N4   C6   126.03  3.000
 LUD  H10  C5   H9   108.46  3.000
 LUD  H10  C5   C3   112.34  3.000
 LUD  H9   C5   C3   110.97  3.000
 LUD  H10  C5   N4   111.21  3.000
 LUD  H9   C5   N4   111.59  3.000
 LUD  C3   C5   N4   102.24  3.000
 LUD  H11  C3   C5   111.92  3.000
 LUD  H11  C3   N2   110.57  3.000
 LUD  C5   C3   N2   101.76  3.000
 LUD  H11  C3   C4   110.31  3.000
 LUD  C5   C3   C4   113.15  3.000
 LUD  N2   C3   C4   108.79  3.000
 LUD  N3   C1   C2   120.31  3.000
 LUD  N3   C1   N1   116.25  3.000
 LUD  C2   C1   N1   123.40  3.000
 LUD  H12  C12  C11  118.39  3.000
 LUD  H12  C12  C7   120.88  3.000
 LUD  C11  C12  C7   120.73  3.000
 LUD  H13  C11  C10  119.87  3.000
 LUD  H13  C11  C12  118.91  3.000
 LUD  C10  C11  C12  121.21  3.000
 LUD  C13  C10  C11  118.73  3.000
 LUD  C13  C10  C9   123.40  3.000
 LUD  C11  C10  C9   117.84  3.000
 LUD  H14  C8   C9   118.92  3.000
 LUD  H14  C8   C7   120.91  3.000
 LUD  C9   C8   C7   120.17  3.000
 LUD  O1   C13  C10  120.62  3.000
 LUD  C10  C13  N5   116.35  3.000
 LUD  O1   C13  N5   122.97  3.000
 LUD  H15  C14  C15  107.98  3.000
 LUD  H15  C14  C18  107.68  3.000
 LUD  C15  C14  C18  111.07  3.000
 LUD  H15  C14  N5   108.07  3.000
 LUD  C18  C14  N5   112.30  3.000
 LUD  C15  C14  N5   109.57  3.000
 LUD  O4   C18  O5   127.34  3.000
 LUD  O4   C18  C14  114.79  3.000
 LUD  O5   C18  C14  117.86  3.000
 LUD  H18  C15  H17  106.20  3.000
 LUD  H18  C15  C16  109.85  3.000
 LUD  H17  C15  C16  110.14  3.000
 LUD  H18  C15  C14  107.80  3.000
 LUD  H17  C15  C14  109.18  3.000
 LUD  C16  C15  C14  113.40  3.000
 LUD  H20  C16  H19  104.90  3.000
 LUD  H20  C16  C17  108.14  3.000
 LUD  H19  C16  C17  107.73  3.000
 LUD  H20  C16  C15  110.61  3.000
 LUD  H19  C16  C15  109.19  3.000
 LUD  C17  C16  C15  115.68  3.000
 LUD  O2   C17  O3   126.22  3.000
 LUD  O3   C17  C16  115.81  3.000
 LUD  O2   C17  C16  117.96  3.000
 LUD  H7   N    H6   118.07  3.000
 LUD  H7   N    C    122.70  3.000
 LUD  H6   N    C    119.18  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_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  Var_01    C1   C2   N2   C6   -114.86  30.0  1
 LUD  Var_02    C12  C7   N4   C6   -154.74  30.0  2
 LUD  Var_03    C1   N3   C4   C3    -27.91  30.0  1
 LUD  Var_04    H9   C5   N4   C6    100.36  30.0  1
 LUD  Var_05    C11  C10  C13  N5    152.40  30.0  2
 LUD  Var_06    C17  C16  C15  C14  -176.82  30.0  3
 LUD  Var_07    O2   C17  C16  C15     7.83  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-3  C16  0.020
 LUD  plan-3  C17  0.020
 LUD  plan-3  O3   0.020
 LUD  plan-3  O2   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

