# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:56:30 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N3CN(C[C@H]3CN2)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
 MEF  MEF  'N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid'  ligand  56  33  .  2022-11-17  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_MEF
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
 MEF  OE2   O  O     0  -0.442  46.3235  25.4145  47.7823
 MEF  CD    C  C     0   0.560  46.9218  24.8130  46.9258
 MEF  OE1   O  OH1   0  -0.596  47.7081  23.7730  47.1836
 MEF  CG    C  CH2   0  -0.598  46.8805  25.1252  45.4551
 MEF  CB    C  CH2   0  -0.418  45.9979  26.3173  45.1267
 MEF  CA    C  CH1   0  -0.238  45.8909  26.6013  43.6276
 MEF  CT    C  C     0   0.557  47.2077  27.0720  43.0313
 MEF  O1    O  OH1   0  -0.579  47.3107  26.8183  41.7376
 MEF  O2    O  O     0  -0.437  48.0464  27.6587  43.6671
 MEF  N     N  NH1   0  -0.668  45.3189  25.5093  42.8849
 MEF  C     C  C     0   0.556  44.0131  25.4749  42.5323
 MEF  O     O  O     0  -0.494  43.2407  26.3784  42.8302
 MEF  N10   N  NT    0  -0.541  42.0802  20.9667  39.6979
 MEF  CM    C  CH2   0  -0.101  42.9178  19.9430  39.1210
 MEF  N5    N  NT    0  -0.499  41.9711  18.8804  38.8353
 MEF  C9    C  CH2   0  -0.296  40.6731  20.6796  39.5123
 MEF  C6    C  CH1   0  -0.167  40.6958  19.5111  38.5403
 MEF  C7    C  CH2   0  -0.266  40.6202  19.9569  37.0777
 MEF  N8    N  NH1   0  -0.664  40.9248  18.8261  36.2387
 MEF  C8A   C  CR6   0   0.511  41.8284  17.8997  36.6051
 MEF  C4A   C  CR6   0  -0.075  42.3776  17.9233  37.8814
 MEF  N1    N  N     0  -0.528  42.1173  16.9528  35.6813
 MEF  C2    C  CR6   0   0.676  42.9956  16.0461  36.0127
 MEF  NA2   N  NH2   0  -0.828  43.2967  15.0599  35.1502
 MEF  N3    N  NR16  0  -0.715  43.6054  16.0273  37.2206
 MEF  C4    C  CR6   0   0.499  43.3259  16.9382  38.2439
 MEF  O4    O  O     0  -0.509  43.9066  16.8301  39.3217
 MEF  C11   C  CR6   0  -0.087  43.5596  24.2839  41.7758
 MEF  C12   C  CR16  0  -0.277  44.4192  23.3880  41.1356
 MEF  C13   C  CR16  0  -0.352  43.9411  22.2954  40.4428
 MEF  C16   C  CR16  0  -0.252  42.1875  24.0449  41.6729
 MEF  C15   C  CR16  0  -0.350  41.6887  22.9551  40.9929
 MEF  C14   C  CR6   0   0.415  42.5573  22.0428  40.3623
 MEF  HOE1  H  HOH1  0   0.480  47.7090  23.5861  48.1342
 MEF  HG    H  HCH2  0   0.286  47.9089  25.2847  45.1180
 MEF  HGA   H  HCH2  0   0.279  46.5339  24.2238  44.9407
 MEF  HB    H  HCH2  0   0.258  44.9851  26.1442  45.4936
 MEF  HBA   H  HCH2  0   0.253  46.3621  27.2119  45.6319
 MEF  HA    H  HCH1  0   0.322  45.2119  27.4529  43.5130
 MEF  HO1   H  HOH1  0   0.485  48.1452  27.1765  41.3981
 MEF  HN    H  HNH1  0   0.409  45.8954  24.7027  42.7147
 MEF  HM    H  HCH2  0   0.213  43.4353  20.3117  38.2197
 MEF  HMA   H  HCH2  0   0.247  43.6827  19.5960  39.8216
 MEF  H9    H  HCH2  0   0.256  40.1886  20.4024  40.4538
 MEF  H9A   H  HCH2  0   0.252  40.1351  21.5389  39.1021
 MEF  H6    H  HCH1  0   0.279  39.8819  18.8095  38.7371
 MEF  H7    H  HCH2  0   0.265  39.6186  20.3151  36.8401
 MEF  H7A   H  HCH2  0   0.236  41.3151  20.7882  36.9027
 MEF  HN8   H  HNH1  0   0.394  40.5652  18.7873  35.2995
 MEF  HNA2  H  HNH2  0   0.410  44.1298  14.5107  35.2775
 MEF  HNAA  H  HNH2  0   0.407  42.9848  15.1709  34.2003
 MEF  HN3   H  HNR6  0   0.417  44.2768  15.3009  37.4315
 MEF  H12   H  HCR6  0   0.249  45.4919  23.5396  41.1369
 MEF  H13   H  HCR6  0   0.275  44.6478  21.6436  39.9469
 MEF  H16   H  HCR6  0   0.255  41.4916  24.7234  42.1485
 MEF  H15   H  HCR6  0   0.272  40.6180  22.8048  40.9596

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
 MEF  OE2  CD    double    1.206  0.020  1.206
 MEF  CG   CD    single    1.504  0.020  1.504
 MEF  CD   OE1   single    1.329  0.020  1.329
 MEF  OE1  HOE1  single    0.850  0.020  0.980
 MEF  CB   CG    single    1.519  0.020  1.519
 MEF  CG   HG    single    0.970  0.020  1.090
 MEF  CG   HGA   single    0.970  0.020  1.090
 MEF  CA   CB    single    1.530  0.020  1.530
 MEF  CB   HB    single    0.970  0.020  1.090
 MEF  CB   HBA   single    0.970  0.020  1.090
 MEF  CA   N     single    1.439  0.020  1.439
 MEF  CA   CT    single    1.520  0.020  1.520
 MEF  CA   HA    single    0.970  0.020  1.090
 MEF  O2   CT    double    1.205  0.020  1.205
 MEF  CT   O1    single    1.322  0.020  1.322
 MEF  O1   HO1   single    0.850  0.020  0.980
 MEF  C    N     single    1.353  0.020  1.353
 MEF  N    HN    single    0.860  0.020  1.020
 MEF  O    C     double    1.225  0.020  1.225
 MEF  C    C11   single    1.482  0.020  1.482
 MEF  CM   N10   single    1.443  0.020  1.443
 MEF  C9   N10   single    1.448  0.020  1.448
 MEF  C14  N10   single    1.352  0.020  1.352
 MEF  N5   CM    single    1.452  0.020  1.452
 MEF  CM   HM    single    0.970  0.020  1.090
 MEF  CM   HMA   single    0.970  0.020  1.090
 MEF  C4A  N5    single    1.411  0.020  1.411
 MEF  N5   C6    single    1.453  0.020  1.453
 MEF  C6   C9    single    1.520  0.020  1.520
 MEF  C9   H9    single    0.970  0.020  1.090
 MEF  C9   H9A   single    0.970  0.020  1.090
 MEF  C7   C6    single    1.531  0.020  1.531
 MEF  C6   H6    single    0.970  0.020  1.090
 MEF  N8   C7    single    1.441  0.020  1.441
 MEF  C7   H7    single    0.970  0.020  1.090
 MEF  C7   H7A   single    0.970  0.020  1.090
 MEF  C8A  N8    single    1.345  0.020  1.345
 MEF  N8   HN8   single    0.860  0.020  1.020
 MEF  N1   C8A   single    1.354  0.020  1.354
 MEF  C8A  C4A   double    1.390  0.020  1.390
 MEF  C4   C4A   single    1.415  0.020  1.415
 MEF  C2   N1    double    1.305  0.020  1.305
 MEF  NA2  C2    single    1.344  0.020  1.344
 MEF  C2   N3    single    1.353  0.020  1.353
 MEF  NA2  HNA2  single    0.890  0.020  1.040
 MEF  NA2  HNAA  single    0.890  0.020  1.040
 MEF  N3   C4    single    1.398  0.020  1.398
 MEF  N3   HN3   single    0.860  0.020  1.020
 MEF  C4   O4    double    1.229  0.020  1.229
 MEF  C16  C11   aromatic  1.396  0.020  1.396
 MEF  C11  C12   aromatic  1.397  0.020  1.397
 MEF  C12  C13   aromatic  1.379  0.020  1.379
 MEF  C12  H12   single    0.930  0.020  1.080
 MEF  C14  C13   aromatic  1.409  0.020  1.409
 MEF  C13  H13   single    0.930  0.020  1.080
 MEF  C16  C15   aromatic  1.378  0.020  1.378
 MEF  C16  H16   single    0.930  0.020  1.080
 MEF  C15  C14   aromatic  1.409  0.020  1.409
 MEF  C15  H15   single    0.930  0.020  1.080

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
 MEF  CG    CD   OE1   111.61  3.000
 MEF  OE1   CD   OE2   123.11  3.000
 MEF  CG    CD   OE2   125.28  3.000
 MEF  HOE1  OE1  CD    109.99  3.000
 MEF  HGA   CG   HG    105.84  3.000
 MEF  HGA   CG   CB    111.15  3.000
 MEF  HG    CG   CB    111.42  3.000
 MEF  HGA   CG   CD    107.30  3.000
 MEF  HG    CG   CD    107.81  3.000
 MEF  CB    CG   CD    112.97  3.000
 MEF  HBA   CB   HB    106.53  3.000
 MEF  HBA   CB   CA    108.98  3.000
 MEF  HB    CB   CA    107.11  3.000
 MEF  HBA   CB   CG    110.47  3.000
 MEF  HB    CB   CG    110.01  3.000
 MEF  CA    CB   CG    113.47  3.000
 MEF  HA    CA   N     106.83  3.000
 MEF  HA    CA   CT    104.79  3.000
 MEF  N     CA   CT    112.13  3.000
 MEF  HA    CA   CB    106.88  3.000
 MEF  CT    CA   CB    112.42  3.000
 MEF  N     CA   CB    113.12  3.000
 MEF  O2    CT   O1    123.74  3.000
 MEF  O1    CT   CA    113.07  3.000
 MEF  O2    CT   CA    123.14  3.000
 MEF  HO1   O1   CT    109.80  3.000
 MEF  HN    N    C     119.24  3.000
 MEF  HN    N    CA    117.90  3.000
 MEF  C     N    CA    122.51  3.000
 MEF  C11   C    O     121.58  3.000
 MEF  C11   C    N     116.67  3.000
 MEF  O     C    N     121.75  3.000
 MEF  C14   N10  C9    124.32  3.000
 MEF  C14   N10  CM    123.81  3.000
 MEF  C9    N10  CM    111.85  3.000
 MEF  HMA   CM   HM    107.54  3.000
 MEF  HMA   CM   N5    110.49  3.000
 MEF  HM    CM   N5    112.95  3.000
 MEF  HMA   CM   N10   112.02  3.000
 MEF  HM    CM   N10   111.22  3.000
 MEF  N5    CM   N10   102.68  3.000
 MEF  C4A   N5   C6    114.21  3.000
 MEF  C6    N5   CM    107.14  3.000
 MEF  C4A   N5   CM    116.21  3.000
 MEF  H9A   C9   H9    107.68  3.000
 MEF  H9A   C9   C6    111.81  3.000
 MEF  H9    C9   C6    111.23  3.000
 MEF  H9A   C9   N10   111.74  3.000
 MEF  H9    C9   N10   111.72  3.000
 MEF  C6    C9   N10   102.70  3.000
 MEF  H6    C6   C7    108.81  3.000
 MEF  H6    C6   C9    111.55  3.000
 MEF  C7    C6   C9    112.73  3.000
 MEF  H6    C6   N5    109.79  3.000
 MEF  C7    C6   N5    111.33  3.000
 MEF  C9    C6   N5    102.53  3.000
 MEF  H7A   C7   H7    107.35  3.000
 MEF  H7A   C7   N8    111.58  3.000
 MEF  H7    C7   N8    108.98  3.000
 MEF  H7A   C7   C6    109.98  3.000
 MEF  H7    C7   C6    110.45  3.000
 MEF  N8    C7   C6    108.50  3.000
 MEF  HN8   N8   C8A   117.88  3.000
 MEF  HN8   N8   C7    119.88  3.000
 MEF  C8A   N8   C7    121.61  3.000
 MEF  N1    C8A  C4A   123.66  3.000
 MEF  C4A   C8A  N8    120.26  3.000
 MEF  N1    C8A  N8    116.05  3.000
 MEF  C4    C4A  C8A   119.24  3.000
 MEF  C4    C4A  N5    119.49  3.000
 MEF  C8A   C4A  N5    121.24  3.000
 MEF  C2    N1   C8A   117.14  3.000
 MEF  N3    C2   NA2   117.49  3.000
 MEF  N3    C2   N1    122.65  3.000
 MEF  NA2   C2   N1    119.84  3.000
 MEF  HNAA  NA2  HNA2  115.88  3.000
 MEF  HNAA  NA2  C2    117.10  3.000
 MEF  HNA2  NA2  C2    120.33  3.000
 MEF  HN3   N3   C4    116.61  3.000
 MEF  HN3   N3   C2    119.69  3.000
 MEF  C4    N3   C2    123.65  3.000
 MEF  O4    C4   N3    119.35  3.000
 MEF  O4    C4   C4A   127.06  3.000
 MEF  N3    C4   C4A   113.58  3.000
 MEF  C16   C11  C12   117.46  3.000
 MEF  C12   C11  C     124.12  3.000
 MEF  C16   C11  C     118.41  3.000
 MEF  H12   C12  C13   117.04  3.000
 MEF  H12   C12  C11   121.27  3.000
 MEF  C13   C12  C11   121.66  3.000
 MEF  H13   C13  C14   120.49  3.000
 MEF  H13   C13  C12   118.76  3.000
 MEF  C14   C13  C12   120.74  3.000
 MEF  H16   C16  C15   118.68  3.000
 MEF  H16   C16  C11   119.49  3.000
 MEF  C15   C16  C11   121.82  3.000
 MEF  H15   C15  C14   120.43  3.000
 MEF  H15   C15  C16   118.91  3.000
 MEF  C14   C15  C16   120.66  3.000
 MEF  C15   C14  C13   117.64  3.000
 MEF  C15   C14  N10   121.20  3.000
 MEF  C13   C14  N10   121.16  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
 MEF  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 MEF  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 MEF  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 MEF  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 MEF  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 MEF  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 MEF  CONST_07  C12   C13  C14  N10   180.00   0.0  0
 MEF  CONST_08  C16   C15  C14  N10   180.00   0.0  0
 MEF  CONST_09  N1    C8A  N8   C7    180.00   0.0  0
 MEF  CONST_10  C4A   C8A  N8   C7      0.00   0.0  0
 MEF  CONST_11  C2    N1   C8A  N8    180.00   0.0  0
 MEF  CONST_12  N3    C2   N1   C8A     0.00   0.0  0
 MEF  CONST_13  C2    N1   C8A  C4A     0.00   0.0  0
 MEF  CONST_14  C2    N3   C4   C4A     0.00   0.0  0
 MEF  CONST_15  C4    N3   C2   N1      0.00   0.0  0
 MEF  CONST_16  C15   C16  C11  C     180.00   0.0  0
 MEF  CONST_17  C13   C12  C11  C     180.00   0.0  0
 MEF  CONST_18  NA2   C2   N1   C8A   180.00   0.0  0
 MEF  CONST_19  O4    C4   N3   C2    180.00   0.0  0
 MEF  CONST_20  C4    N3   C2   NA2   180.00   0.0  0
 MEF  CONST_21  H13   C13  C14  N10     0.00   0.0  0
 MEF  CONST_22  H15   C15  C14  N10     0.00   0.0  0
 MEF  CONST_23  H16   C16  C11  C12   180.00   0.0  0
 MEF  CONST_24  H12   C12  C11  C16   180.00   0.0  0
 MEF  CONST_25  HN8   N8   C8A  C4A   180.00   0.0  0
 MEF  CONST_26  HN3   N3   C4   C4A   180.00   0.0  0
 MEF  CONST_28  HNAA  NA2  C2   N1      0.00   0.0  0
 MEF  CONST_29  C11   C    N    CA    180.00   0.0  0
 MEF  CONST_30  HN    N    C    C11     0.00   0.0  0
 MEF  CONST_31  O     C    N    CA      0.00   0.0  0
 MEF  CONST_32  HOE1  OE1  CD   OE2     0.00   0.0  0
 MEF  CONST_33  HO1   O1   CT   CA    180.00   0.0  0
 MEF  Var_01    C4A   N5   CM   N10   159.85  30.0  1
 MEF  Var_02    C6    C9   N10  CM    -10.10  30.0  1
 MEF  Var_03    C13   C14  N10  CM      5.29  30.0  2
 MEF  Var_04    C8A   C4A  N5   CM   -106.82  30.0  1
 MEF  Var_05    C9    N10  CM   N5    -11.99  30.0  1
 MEF  Var_06    C8A   N8   C7   C6    -35.15  30.0  1
 MEF  Var_07    C16   C11  C    N     164.72  30.0  2
 MEF  Var_08    CB    CG   CD   OE2     0.59  30.0  1
 MEF  Var_09    CA    CB   CG   CD   -177.07  30.0  2

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
 MEF  chir_01  CA  CB  N   CT  positiv
 MEF  chir_02  C6  N5  C9  C7  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
 MEF  plan-1  C     0.020
 MEF  plan-1  N10   0.020
 MEF  plan-1  C11   0.020
 MEF  plan-1  C12   0.020
 MEF  plan-1  C13   0.020
 MEF  plan-1  C16   0.020
 MEF  plan-1  C15   0.020
 MEF  plan-1  C14   0.020
 MEF  plan-1  H12   0.020
 MEF  plan-1  H13   0.020
 MEF  plan-1  H16   0.020
 MEF  plan-1  H15   0.020
 MEF  plan-2  OE2   0.020
 MEF  plan-2  CD    0.020
 MEF  plan-2  OE1   0.020
 MEF  plan-2  CG    0.020
 MEF  plan-2  HOE1  0.020
 MEF  plan-3  CA    0.020
 MEF  plan-3  CT    0.020
 MEF  plan-3  O1    0.020
 MEF  plan-3  O2    0.020
 MEF  plan-3  HO1   0.020
 MEF  plan-4  CA    0.020
 MEF  plan-4  N     0.020
 MEF  plan-4  C     0.020
 MEF  plan-4  O     0.020
 MEF  plan-4  C11   0.020
 MEF  plan-4  HN    0.020
 MEF  plan-5  N5    0.020
 MEF  plan-5  C7    0.020
 MEF  plan-5  N8    0.020
 MEF  plan-5  C8A   0.020
 MEF  plan-5  C4A   0.020
 MEF  plan-5  N1    0.020
 MEF  plan-5  C2    0.020
 MEF  plan-5  NA2   0.020
 MEF  plan-5  N3    0.020
 MEF  plan-5  C4    0.020
 MEF  plan-5  O4    0.020
 MEF  plan-5  HN8   0.020
 MEF  plan-5  HNA2  0.020
 MEF  plan-5  HNAA  0.020
 MEF  plan-5  HN3   0.020
 MEF  plan-6  CM    0.020
 MEF  plan-6  N5    0.020
 MEF  plan-6  C6    0.020
 MEF  plan-6  C4A   0.020

