# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:39:12 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-({4-[(6aS)-3-amino-1-oxo-1,4,6a,7-tetrahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C2=C(N1)N=C[C@@H]3CN(CN23)c4ccc(cc4)C(=O)N[C@H](CCC(O)=O)C(O)=O
#
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
 TMF  TMF  'N-({4-[(6aS)-3-amino-1-oxo-1,4,6a,7-tetrahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-D-glutamic acid'  ligand  52  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TMF
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
 TMF  N1    N  NC1    0  -0.592   1.0954  -0.2387   7.3767
 TMF  C2    C  C      0   0.637   0.3681   0.7286   7.9849
 TMF  NA2   N  NH2    0  -0.821   0.6559   1.0033   9.2618
 TMF  N3    N  N      0  -0.562  -0.5895   1.3853   7.3828
 TMF  C4    C  C      0   0.396  -0.9485   1.0878   6.1034
 TMF  O4    O  OC     0  -0.468  -1.8107   1.7400   5.5139
 TMF  C4A   C  C      0   0.092  -0.2448  -0.0144   5.4549
 TMF  N5    N  NT     0  -0.555  -0.5897  -0.4541   4.1843
 TMF  C6    C  CH1    0  -0.102  -0.1339  -1.7947   3.8593
 TMF  C7    C  C1     0  -0.043   1.2678  -1.9975   4.3799
 TMF  N8    N  N      0  -0.423   1.6741  -1.4664   5.4639
 TMF  C8A   C  C      0   0.391   0.8018  -0.5966   6.0865
 TMF  C9    C  CH2    0  -0.370  -0.2373  -1.8304   2.3440
 TMF  N10   N  NT     0  -0.474   0.0187  -0.4535   1.9833
 TMF  C11   C  CR6    0   0.097   0.1014   0.8712  -1.9953
 TMF  C12   C  CR16   0  -0.336   0.0877   1.7728  -0.9315
 TMF  C13   C  CR16   0  -0.237   0.0533   1.3441   0.3775
 TMF  C14   C  CR6    0   0.104   0.0337  -0.0285   0.6839
 TMF  C15   C  CR16   0  -0.129   0.0442  -0.9391  -0.3855
 TMF  C16   C  CR16   0  -0.401   0.0756  -0.4907  -1.6920
 TMF  O     O  O      0  -0.426  -0.2121   2.5749  -3.6011
 TMF  N     N  NH1    0  -0.706   0.3808   0.5373  -4.3638
 TMF  CA    C  CH1    0  -0.149   0.5002   0.9580  -5.7351
 TMF  CB    C  CH2    0  -0.446   0.2427  -0.2107  -6.6797
 TMF  CG    C  CH2    0  -0.601  -1.1512  -0.7962  -6.5265
 TMF  CD    C  C      0   0.337  -1.5207  -1.9318  -7.4949
 TMF  OE1   O  O      0  -0.388  -0.7035  -2.2483  -8.3838
 TMF  OE2   O  OC    -1  -0.811  -2.7040  -2.3298  -7.4327
 TMF  CT    C  C      0   0.436   1.8652   1.5910  -6.0274
 TMF  O1    O  O      0  -0.634   1.9734   2.1257  -7.1551
 TMF  O2    O  OC    -1  -0.737   2.7540   1.4188  -5.2197
 TMF  CP1   C  CH2    0  -0.114  -0.3992   0.4399   3.0477
 TMF  HN1   H  HNC1   0   0.420   1.8512  -0.7109   7.8549
 TMF  HN21  H  HNH2   0   0.391   0.1924   1.7812   9.6997
 TMF  HN22  H  HNH2   0   0.398   1.4605   0.6211   9.7243
 TMF  H6    H  HCH1   0   0.286  -0.7869  -2.5501   4.3137
 TMF  H7    H  H      0   0.285   1.9704  -2.6034   3.8136
 TMF  H91   H  HCH2   0   0.294   0.5002  -2.5048   1.9066
 TMF  H92   H  HCH2   0   0.282  -1.2297  -2.1701   2.0285
 TMF  H12   H  HCR6   0   0.239   0.0920   2.8367  -1.1287
 TMF  H13   H  HCR6   0   0.266   0.0460   2.0867   1.1627
 TMF  H15   H  HCR6   0   0.305   0.0069  -2.0047  -0.2076
 TMF  H16   H  HCR6   0   0.236   0.0490  -1.2354  -2.4774
 TMF  HN    H  HNH1   0   0.360   0.8037  -0.3407  -4.1211
 TMF  HA    H  HCH1   0   0.253  -0.2613   1.7187  -5.9117
 TMF  HB1   H  HCH2   0   0.268   0.3916   0.1420  -7.7002
 TMF  HB2   H  HCH2   0   0.238   0.9970  -0.9891  -6.5163
 TMF  HG1   H  HCH2   0   0.211  -1.2920  -1.1749  -5.5101
 TMF  HG2   H  HCH2   0   0.251  -1.8945   0.0028  -6.6312
 TMF  HCP1  H  HCH2   0   0.286   0.3667   1.1995   3.2433
 TMF  HCP2  H  HCH2   0   0.240  -1.3309   0.9577   2.8000
 TMF  C     C  C      0   0.524   0.0985   1.4090  -3.3789

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
 TMF  N1   C2    aromatic  1.354  0.020  1.354
 TMF  N1   C8A   aromatic  1.371  0.020  1.371
 TMF  N1   HN1   single    0.860  0.020  1.020
 TMF  C2   NA2   single    1.337  0.020  1.337
 TMF  C2   N3    aromatic  1.308  0.020  1.308
 TMF  NA2  HN21  single    0.860  0.020  1.020
 TMF  NA2  HN22  single    0.860  0.020  1.020
 TMF  N3   C4    aromatic  1.362  0.020  1.362
 TMF  C4   O4    double    1.231  0.020  1.231
 TMF  C4   C4A   aromatic  1.460  0.020  1.460
 TMF  C4A  N5    single    1.388  0.020  1.388
 TMF  C4A  C8A   aromatic  1.354  0.020  1.354
 TMF  N5   C6    single    1.453  0.020  1.453
 TMF  N5   CP1   single    1.459  0.020  1.459
 TMF  C6   C7    single    1.509  0.020  1.509
 TMF  C6   C9    single    1.519  0.020  1.519
 TMF  C6   H6    single    0.970  0.020  1.090
 TMF  C7   N8    double    1.274  0.020  1.274
 TMF  C7   H7    single    0.930  0.020  1.080
 TMF  N8   C8A   single    1.380  0.020  1.380
 TMF  C9   N10   single    1.446  0.020  1.446
 TMF  C9   H91   single    0.970  0.020  1.090
 TMF  C9   H92   single    0.970  0.020  1.090
 TMF  N10  C14   single    1.367  0.020  1.367
 TMF  N10  CP1   single    1.451  0.020  1.451
 TMF  C11  C12   aromatic  1.394  0.020  1.394
 TMF  C11  C16   aromatic  1.395  0.020  1.395
 TMF  C11  C     single    1.484  0.020  1.484
 TMF  C12  C13   aromatic  1.378  0.020  1.378
 TMF  C12  H12   single    0.930  0.020  1.080
 TMF  C13  C14   aromatic  1.406  0.020  1.406
 TMF  C13  H13   single    0.930  0.020  1.080
 TMF  C14  C15   aromatic  1.405  0.020  1.405
 TMF  C15  C16   aromatic  1.382  0.020  1.382
 TMF  C15  H15   single    0.930  0.020  1.080
 TMF  C16  H16   single    0.930  0.020  1.080
 TMF  C    O     double    1.227  0.020  1.227
 TMF  C    N     single    1.345  0.020  1.345
 TMF  N    CA    single    1.439  0.020  1.439
 TMF  N    HN    single    0.890  0.020  1.040
 TMF  CA   CB    single    1.525  0.020  1.525
 TMF  CA   CT    single    1.533  0.020  1.533
 TMF  CA   HA    single    0.970  0.020  1.090
 TMF  CB   CG    single    1.520  0.020  1.520
 TMF  CB   HB1   single    0.970  0.020  1.090
 TMF  CB   HB2   single    0.970  0.020  1.090
 TMF  CG   CD    single    1.538  0.020  1.538
 TMF  CG   HG1   single    0.970  0.020  1.090
 TMF  CG   HG2   single    0.970  0.020  1.090
 TMF  CD   OE1   deloc     1.248  0.020  1.248
 TMF  CD   OE2   deloc     1.250  0.020  1.250
 TMF  CT   O1    deloc     1.253  0.020  1.253
 TMF  CT   O2    deloc     1.213  0.020  1.213
 TMF  CP1  HCP1  single    0.970  0.020  1.090
 TMF  CP1  HCP2  single    0.970  0.020  1.090

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
 TMF  HN1   N1   C8A   118.89  3.000
 TMF  HN1   N1   C2    121.49  3.000
 TMF  C8A   N1   C2    119.61  3.000
 TMF  N3    C2   NA2   119.60  3.000
 TMF  N3    C2   N1    123.02  3.000
 TMF  NA2   C2   N1    117.38  3.000
 TMF  HN22  NA2  HN21  117.60  3.000
 TMF  HN22  NA2  C2    122.29  3.000
 TMF  HN21  NA2  C2    118.38  3.000
 TMF  C4    N3   C2    121.05  3.000
 TMF  C4A   C4   O4    121.65  3.000
 TMF  C4A   C4   N3    117.09  3.000
 TMF  O4    C4   N3    121.24  3.000
 TMF  C8A   C4A  N5    118.87  3.000
 TMF  C8A   C4A  C4    119.35  3.000
 TMF  N5    C4A  C4    121.74  3.000
 TMF  CP1   N5   C6    110.50  3.000
 TMF  CP1   N5   C4A   119.13  3.000
 TMF  C6    N5   C4A   114.78  3.000
 TMF  H6    C6   C9    110.88  3.000
 TMF  H6    C6   C7    108.51  3.000
 TMF  C9    C6   C7    113.84  3.000
 TMF  H6    C6   N5    110.86  3.000
 TMF  C9    C6   N5    102.91  3.000
 TMF  C7    C6   N5    109.77  3.000
 TMF  H7    C7   N8    118.01  3.000
 TMF  H7    C7   C6    119.72  3.000
 TMF  N8    C7   C6    122.27  3.000
 TMF  C8A   N8   C7    116.43  3.000
 TMF  N8    C8A  C4A   123.30  3.000
 TMF  N8    C8A  N1    116.99  3.000
 TMF  C4A   C8A  N1    119.49  3.000
 TMF  H92   C9   H91   107.78  3.000
 TMF  H92   C9   N10   112.57  3.000
 TMF  H91   C9   N10   111.65  3.000
 TMF  H92   C9   C6    110.87  3.000
 TMF  H91   C9   C6    111.62  3.000
 TMF  N10   C9   C6    102.38  3.000
 TMF  CP1   N10  C14   120.59  3.000
 TMF  CP1   N10  C9    110.62  3.000
 TMF  C14   N10  C9    122.34  3.000
 TMF  C     C11  C16   123.79  3.000
 TMF  C     C11  C12   118.47  3.000
 TMF  C16   C11  C12   117.71  3.000
 TMF  H12   C12  C13   118.63  3.000
 TMF  H12   C12  C11   119.78  3.000
 TMF  C13   C12  C11   121.59  3.000
 TMF  H13   C13  C14   120.81  3.000
 TMF  H13   C13  C12   118.47  3.000
 TMF  C14   C13  C12   120.73  3.000
 TMF  C15   C14  C13   117.82  3.000
 TMF  C15   C14  N10   121.47  3.000
 TMF  C13   C14  N10   120.70  3.000
 TMF  H15   C15  C16   118.44  3.000
 TMF  H15   C15  C14   120.90  3.000
 TMF  C16   C15  C14   120.65  3.000
 TMF  H16   C16  C15   117.53  3.000
 TMF  H16   C16  C11   120.94  3.000
 TMF  C15   C16  C11   121.51  3.000
 TMF  HN    N    CA    116.80  3.000
 TMF  HN    N    C     118.55  3.000
 TMF  CA    N    C     121.71  3.000
 TMF  HA    CA   CT    107.62  3.000
 TMF  HA    CA   CB    108.44  3.000
 TMF  CT    CA   CB    110.42  3.000
 TMF  HA    CA   N     107.47  3.000
 TMF  CT    CA   N     112.10  3.000
 TMF  CB    CA   N     110.62  3.000
 TMF  HB2   CB   HB1   105.98  3.000
 TMF  HB2   CB   CG    110.04  3.000
 TMF  HB1   CB   CG    110.15  3.000
 TMF  HB2   CB   CA    109.62  3.000
 TMF  HB1   CB   CA    107.99  3.000
 TMF  CG    CB   CA    112.82  3.000
 TMF  HG2   CG   HG1   104.71  3.000
 TMF  HG2   CG   CD    108.38  3.000
 TMF  HG1   CG   CD    107.37  3.000
 TMF  HG2   CG   CB    109.36  3.000
 TMF  HG1   CG   CB    110.19  3.000
 TMF  CD    CG   CB    116.20  3.000
 TMF  OE2   CD   OE1   125.07  3.000
 TMF  OE2   CD   CG    115.55  3.000
 TMF  OE1   CD   CG    118.58  3.000
 TMF  O2    CT   O1    126.63  3.000
 TMF  O2    CT   CA    117.82  3.000
 TMF  O1    CT   CA    115.14  3.000
 TMF  HCP2  CP1  HCP1  107.90  3.000
 TMF  HCP2  CP1  N10   111.74  3.000
 TMF  HCP1  CP1  N10   110.87  3.000
 TMF  HCP2  CP1  N5    110.80  3.000
 TMF  HCP1  CP1  N5    112.15  3.000
 TMF  N10   CP1  N5    103.41  3.000
 TMF  N     C    O     122.43  3.000
 TMF  N     C    C11   116.57  3.000
 TMF  O     C    C11   120.90  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
 TMF  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 TMF  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 TMF  CONST_03  C4A   C8A  N1   C2      0.00   0.0  0
 TMF  CONST_04  C4A   C4   N3   C2      0.00   0.0  0
 TMF  CONST_05  C8A   N1   C2   N3      0.00   0.0  0
 TMF  CONST_06  C8A   C4A  C4   N3      0.00   0.0  0
 TMF  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 TMF  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 TMF  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 TMF  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 TMF  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 TMF  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 TMF  CONST_13  C12   C13  C14  N10   180.00   0.0  0
 TMF  CONST_14  C16   C15  C14  N10   180.00   0.0  0
 TMF  CONST_15  O4    C4   N3   C2    180.00   0.0  0
 TMF  CONST_16  C8A   N1   C2   NA2   180.00   0.0  0
 TMF  CONST_17  C4    N3   C2   NA2   180.00   0.0  0
 TMF  CONST_18  N5    C4A  C4   O4      0.00   0.0  0
 TMF  CONST_19  C8A   C4A  C4   O4    180.00   0.0  0
 TMF  CONST_20  C     C11  C12  C13   180.00   0.0  0
 TMF  CONST_21  C     C11  C16  C15   180.00   0.0  0
 TMF  CONST_22  HN1   N1   C2   N3    180.00   0.0  0
 TMF  CONST_23  H13   C13  C14  N10     0.00   0.0  0
 TMF  CONST_24  H15   C15  C14  N10     0.00   0.0  0
 TMF  CONST_25  H16   C16  C11  C12   180.00   0.0  0
 TMF  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 TMF  CONST_27  HN21  NA2  C2   N1    180.00   0.0  0
 TMF  CONST_28  HN22  NA2  C2   N1      0.00   0.0  0
 TMF  CONST_29  CA    N    C    C11   180.00   0.0  0
 TMF  CONST_31  CA    N    C    O       0.00   0.0  0
 TMF  Var_01    C6    N5   C4A  C4   -160.30  30.0  1
 TMF  Var_02    N10   CP1  N5   C4A   143.38  30.0  1
 TMF  Var_03    C9    N10  CP1  N5     14.17  30.0  1
 TMF  Var_04    C13   C14  N10  C9    168.87  30.0  2
 TMF  Var_05    H7    C7   N8   C8A   173.67  30.0  1
 TMF  Var_06    O     C    C11  C12   -16.39  30.0  2
 TMF  Var_07    CD    CG   CB   CA    176.85  30.0  3
 TMF  Var_08    OE1   CD   CG   CB     -4.10  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
 TMF  chir_01  C6  N5  C7  C9  positiv
 TMF  chir_02  CA  N   CB  CT  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
 TMF  plan-1  N10   0.020
 TMF  plan-1  C11   0.020
 TMF  plan-1  C12   0.020
 TMF  plan-1  C13   0.020
 TMF  plan-1  C14   0.020
 TMF  plan-1  C15   0.020
 TMF  plan-1  C16   0.020
 TMF  plan-1  H12   0.020
 TMF  plan-1  H13   0.020
 TMF  plan-1  H15   0.020
 TMF  plan-1  H16   0.020
 TMF  plan-1  C     0.020
 TMF  plan-2  CA    0.020
 TMF  plan-2  CT    0.020
 TMF  plan-2  O1    0.020
 TMF  plan-2  O2    0.020
 TMF  plan-3  C11   0.020
 TMF  plan-3  O     0.020
 TMF  plan-3  N     0.020
 TMF  plan-3  CA    0.020
 TMF  plan-3  HN    0.020
 TMF  plan-3  C     0.020
 TMF  plan-4  C2    0.020
 TMF  plan-4  NA2   0.020
 TMF  plan-4  HN21  0.020
 TMF  plan-4  HN22  0.020
 TMF  plan-5  N1    0.020
 TMF  plan-5  C2    0.020
 TMF  plan-5  NA2   0.020
 TMF  plan-5  N3    0.020
 TMF  plan-5  C4    0.020
 TMF  plan-5  O4    0.020
 TMF  plan-5  C4A   0.020
 TMF  plan-5  N5    0.020
 TMF  plan-5  N8    0.020
 TMF  plan-5  C8A   0.020
 TMF  plan-5  HN1   0.020
 TMF  plan-6  CG    0.020
 TMF  plan-6  CD    0.020
 TMF  plan-6  OE1   0.020
 TMF  plan-6  OE2   0.020

