# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:01:52 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)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
 MTX  MTX  'N-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)carbonyl]-L-glutamic acid'  ligand  53  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MTX
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
 MTX  N1    N  N      0  -0.506  17.0643  64.5873  46.0756
 MTX  C2    C  CR6    0   0.548  16.4287  64.8743  47.2023
 MTX  NA2   N  NH2    0  -0.814  15.3161  64.1806  47.4819
 MTX  N3    N  N      0  -0.499  16.7660  65.8104  48.1190
 MTX  C4    C  CR6    0   0.481  17.8382  66.5328  47.8906
 MTX  NA4   N  NH2    0  -0.803  18.2199  67.4617  48.7590
 MTX  C4A   C  CR66   0   0.010  18.6171  66.3208  46.6938
 MTX  N5    N  N      0  -0.395  19.7003  67.0530  46.4466
 MTX  C6    C  CR6    0   0.170  20.3653  66.8085  45.3415
 MTX  C7    C  CR16   0  -0.084  19.9155  65.7982  44.4651
 MTX  N8    N  N      0  -0.387  18.8495  65.0725  44.6919
 MTX  C8A   C  CR66   0   0.386  18.1599  65.3157  45.8248
 MTX  C9    C  CH2    0  -0.405  21.6127  67.6176  45.0760
 MTX  N10   N  NT     0  -0.512  21.9829  67.6990  43.6868
 MTX  CM    C  CH3    0  -0.546  23.0579  66.8678  43.1927
 MTX  C11   C  CR6    0  -0.077  19.6659  69.9588  40.9859
 MTX  C12   C  CR16   0  -0.259  20.7316  69.1692  40.5560
 MTX  C13   C  CR16   0  -0.346  21.4904  68.4188  41.4316
 MTX  C14   C  CR6    0   0.392  21.2221  68.4261  42.8129
 MTX  C15   C  CR16   0  -0.322  20.1420  69.2175  43.2480
 MTX  C16   C  CR16   0  -0.284  19.3943  69.9589  42.3543
 MTX  O     O  O      0  -0.505  19.2837  70.7470  38.7916
 MTX  N     N  NH1    0  -0.657  17.8079  71.3783  40.3815
 MTX  CA    C  CH1    0  -0.214  16.9836  72.2546  39.5767
 MTX  CT    C  C      0   0.417  16.5888  73.4985  40.4125
 MTX  O1    O  O      0  -0.598  16.7121  73.4076  41.6515
 MTX  O2    O  OC    -1  -0.600  16.1445  74.4654  39.7680
 MTX  CB    C  CH2    0  -0.397  15.7072  71.5512  39.0954
 MTX  CG    C  CH2    0  -0.575  15.9325  70.3577  38.1810
 MTX  CD    C  C      0   0.411  16.4943  70.6747  36.7801
 MTX  OE1   O  O      0  -0.625  17.0294  69.7219  36.1754
 MTX  OE2   O  OC    -1  -0.612  16.3345  71.8328  36.3401
 MTX  HN21  H  HNH2   0   0.398  14.8540  64.3031  48.3650
 MTX  HN22  H  HNH2   0   0.398  15.0404  63.4113  46.8978
 MTX  HN41  H  HNH2   0   0.413  19.0366  68.0212  48.5814
 MTX  HN42  H  HNH2   0   0.406  17.6854  67.6328  49.5937
 MTX  H7    H  HCR6   0   0.274  20.4578  65.5884  43.5490
 MTX  H91   H  HCH2   0   0.273  21.4817  68.6123  45.5117
 MTX  H92   H  HCH2   0   0.293  22.4457  67.1695  45.6205
 MTX  HM1   H  HCH3   0   0.246  23.7993  67.4528  42.6444
 MTX  HM2   H  HCH3   0   0.262  23.5634  66.4025  44.0341
 MTX  HM3   H  HCH3   0   0.237  22.7031  66.0694  42.5336
 MTX  H12   H  HCR6   0   0.249  20.9744  69.1356  39.5022
 MTX  H13   H  HCR6   0   0.267  22.2976  67.8237  41.0290
 MTX  H15   H  HCR6   0   0.268  19.8716  69.2680  44.2930
 MTX  H16   H  HCR6   0   0.244  18.5871  70.5469  42.7725
 MTX  HN    H  HNH1   0   0.386  17.6026  71.4447  41.3667
 MTX  HA    H  HCH1   0   0.226  17.5569  72.5759  38.7066
 MTX  HB1   H  HCH2   0   0.198  15.1430  71.2310  39.9788
 MTX  HB2   H  HCH2   0   0.208  15.0857  72.2861  38.5825
 MTX  HG1   H  HCH2   0   0.207  16.5658  69.6123  38.6683
 MTX  HG2   H  HCH2   0   0.221  14.9680  69.8553  38.0321
 MTX  C     C  C      0   0.532  18.9029  70.7326  39.9605

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
 MTX  N1   C2    aromatic  1.325  0.020  1.325
 MTX  N1   C8A   aromatic  1.339  0.020  1.339
 MTX  C2   NA2   single    1.341  0.020  1.341
 MTX  C2   N3    aromatic  1.353  0.020  1.353
 MTX  NA2  HN21  single    0.860  0.020  1.020
 MTX  NA2  HN22  single    0.860  0.020  1.020
 MTX  N3   C4    aromatic  1.313  0.020  1.313
 MTX  C4   NA4   single    1.328  0.020  1.328
 MTX  C4   C4A   aromatic  1.444  0.020  1.444
 MTX  NA4  HN41  single    0.860  0.020  1.020
 MTX  NA4  HN42  single    0.860  0.020  1.020
 MTX  C4A  N5    aromatic  1.331  0.020  1.331
 MTX  C4A  C8A   aromatic  1.405  0.020  1.405
 MTX  N5   C6    aromatic  1.313  0.020  1.313
 MTX  C6   C7    aromatic  1.411  0.020  1.411
 MTX  C6   C9    single    1.510  0.020  1.510
 MTX  C7   N8    aromatic  1.309  0.020  1.309
 MTX  C7   H7    single    0.930  0.020  1.080
 MTX  N8   C8A   aromatic  1.348  0.020  1.348
 MTX  C9   N10   single    1.440  0.020  1.440
 MTX  C9   H91   single    0.970  0.020  1.090
 MTX  C9   H92   single    0.970  0.020  1.090
 MTX  N10  CM    single    1.446  0.020  1.446
 MTX  N10  C14   single    1.368  0.020  1.368
 MTX  CM   HM1   single    0.970  0.020  1.090
 MTX  CM   HM2   single    0.970  0.020  1.090
 MTX  CM   HM3   single    0.970  0.020  1.090
 MTX  C11  C12   aromatic  1.394  0.020  1.394
 MTX  C11  C16   aromatic  1.395  0.020  1.395
 MTX  C11  C     single    1.494  0.020  1.494
 MTX  C12  C13   aromatic  1.380  0.020  1.380
 MTX  C12  H12   single    0.930  0.020  1.080
 MTX  C13  C14   aromatic  1.407  0.020  1.407
 MTX  C13  H13   single    0.930  0.020  1.080
 MTX  C14  C15   aromatic  1.408  0.020  1.408
 MTX  C15  C16   aromatic  1.381  0.020  1.381
 MTX  C15  H15   single    0.930  0.020  1.080
 MTX  C16  H16   single    0.930  0.020  1.080
 MTX  C    O     double    1.230  0.020  1.230
 MTX  C    N     single    1.339  0.020  1.339
 MTX  N    CA    single    1.447  0.020  1.447
 MTX  N    HN    single    0.860  0.020  1.020
 MTX  CA   CT    single    1.550  0.020  1.550
 MTX  CA   CB    single    1.535  0.020  1.535
 MTX  CA   HA    single    0.970  0.020  1.090
 MTX  CT   O1    deloc     1.249  0.020  1.249
 MTX  CT   O2    deloc     1.244  0.020  1.244
 MTX  CB   CG    single    1.520  0.020  1.520
 MTX  CB   HB1   single    0.970  0.020  1.090
 MTX  CB   HB2   single    0.970  0.020  1.090
 MTX  CG   CD    single    1.542  0.020  1.542
 MTX  CG   HG1   single    0.970  0.020  1.090
 MTX  CG   HG2   single    0.970  0.020  1.090
 MTX  CD   OE1   deloc     1.249  0.020  1.249
 MTX  CD   OE2   deloc     1.249  0.020  1.249

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
 MTX  C8A   N1   C2    115.71  3.000
 MTX  N3    C2   NA2   115.06  3.000
 MTX  N3    C2   N1    127.33  3.000
 MTX  NA2   C2   N1    117.61  3.000
 MTX  HN22  NA2  HN21  118.58  3.000
 MTX  HN22  NA2  C2    120.19  3.000
 MTX  HN21  NA2  C2    120.15  3.000
 MTX  C4    N3   C2    117.80  3.000
 MTX  C4A   C4   NA4   119.33  3.000
 MTX  C4A   C4   N3    120.27  3.000
 MTX  NA4   C4   N3    120.40  3.000
 MTX  HN42  NA4  HN41  118.91  3.000
 MTX  HN42  NA4  C4    120.59  3.000
 MTX  HN41  NA4  C4    120.48  3.000
 MTX  C8A   C4A  N5    122.93  3.000
 MTX  C8A   C4A  C4    116.24  3.000
 MTX  N5    C4A  C4    120.83  3.000
 MTX  C6    N5   C4A   117.80  3.000
 MTX  C9    C6   C7    122.52  3.000
 MTX  C9    C6   N5    117.81  3.000
 MTX  C7    C6   N5    119.65  3.000
 MTX  H7    C7   N8    116.49  3.000
 MTX  H7    C7   C6    120.23  3.000
 MTX  N8    C7   C6    123.28  3.000
 MTX  C8A   N8   C7    117.51  3.000
 MTX  N8    C8A  C4A   118.83  3.000
 MTX  N8    C8A  N1    118.52  3.000
 MTX  C4A   C8A  N1    122.65  3.000
 MTX  H92   C9   H91   105.43  3.000
 MTX  H92   C9   N10   107.96  3.000
 MTX  H91   C9   N10   111.32  3.000
 MTX  H92   C9   C6    108.83  3.000
 MTX  H91   C9   C6    108.56  3.000
 MTX  N10   C9   C6    114.34  3.000
 MTX  C14   N10  CM    120.05  3.000
 MTX  C14   N10  C9    120.23  3.000
 MTX  CM    N10  C9    119.23  3.000
 MTX  HM3   CM   HM2   107.75  3.000
 MTX  HM3   CM   HM1   107.97  3.000
 MTX  HM2   CM   HM1   107.60  3.000
 MTX  HM3   CM   N10   112.60  3.000
 MTX  HM2   CM   N10   109.12  3.000
 MTX  HM1   CM   N10   111.61  3.000
 MTX  C     C11  C16   125.00  3.000
 MTX  C     C11  C12   118.17  3.000
 MTX  C16   C11  C12   116.83  3.000
 MTX  H12   C12  C13   118.52  3.000
 MTX  H12   C12  C11   119.31  3.000
 MTX  C13   C12  C11   122.17  3.000
 MTX  H13   C13  C14   120.73  3.000
 MTX  H13   C13  C12   118.27  3.000
 MTX  C14   C13  C12   121.00  3.000
 MTX  C15   C14  C13   116.91  3.000
 MTX  C15   C14  N10   121.87  3.000
 MTX  C13   C14  N10   121.22  3.000
 MTX  H15   C15  C16   117.72  3.000
 MTX  H15   C15  C14   121.14  3.000
 MTX  C16   C15  C14   121.13  3.000
 MTX  H16   C16  C15   116.44  3.000
 MTX  H16   C16  C11   121.61  3.000
 MTX  C15   C16  C11   121.96  3.000
 MTX  HN    N    CA    112.79  3.000
 MTX  HN    N    C     120.36  3.000
 MTX  CA    N    C     125.65  3.000
 MTX  HA    CA   CB    108.79  3.000
 MTX  HA    CA   CT    109.13  3.000
 MTX  CB    CA   CT    108.97  3.000
 MTX  HA    CA   N     108.83  3.000
 MTX  CB    CA   N     111.75  3.000
 MTX  CT    CA   N     109.34  3.000
 MTX  O2    CT   O1    127.30  3.000
 MTX  O2    CT   CA    115.82  3.000
 MTX  O1    CT   CA    116.85  3.000
 MTX  HB2   CB   HB1   106.41  3.000
 MTX  HB2   CB   CG    109.30  3.000
 MTX  HB1   CB   CG    109.37  3.000
 MTX  HB2   CB   CA    108.22  3.000
 MTX  HB1   CB   CA    108.02  3.000
 MTX  CG    CB   CA    115.16  3.000
 MTX  HG2   CG   HG1   104.92  3.000
 MTX  HG2   CG   CD    106.91  3.000
 MTX  HG1   CG   CD    109.52  3.000
 MTX  HG2   CG   CB    108.10  3.000
 MTX  HG1   CG   CB    110.68  3.000
 MTX  CD    CG   CB    116.04  3.000
 MTX  OE2   CD   OE1   126.26  3.000
 MTX  OE2   CD   CG    117.64  3.000
 MTX  OE1   CD   CG    116.05  3.000
 MTX  N     C    O     123.13  3.000
 MTX  N     C    C11   116.85  3.000
 MTX  O     C    C11   120.02  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
 MTX  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 MTX  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 MTX  CONST_03  N5    C4A  C8A  N1    180.00   0.0  0
 MTX  CONST_04  C7    N8   C8A  N1    180.00   0.0  0
 MTX  CONST_05  C4A   C8A  N1   C2      0.00   0.0  0
 MTX  CONST_06  N8    C8A  N1   C2    180.00   0.0  0
 MTX  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 MTX  CONST_08  C8A   N1   C2   N3      0.00   0.0  0
 MTX  CONST_09  N5    C4A  C4   N3    180.00   0.0  0
 MTX  CONST_10  C8A   C4A  C4   N3      0.00   0.0  0
 MTX  CONST_11  C6    N5   C4A  C4    180.00   0.0  0
 MTX  CONST_12  N8    C8A  C4A  C4    180.00   0.0  0
 MTX  CONST_13  C7    C6   N5   C4A     0.00   0.0  0
 MTX  CONST_14  C7    N8   C8A  C4A     0.00   0.0  0
 MTX  CONST_15  N8    C8A  C4A  N5      0.00   0.0  0
 MTX  CONST_16  N8    C7   C6   N5      0.00   0.0  0
 MTX  CONST_17  C8A   C4A  N5   C6      0.00   0.0  0
 MTX  CONST_18  C8A   N8   C7   C6      0.00   0.0  0
 MTX  CONST_19  C14   C13  C12  C11     0.00   0.0  0
 MTX  CONST_20  C14   C15  C16  C11     0.00   0.0  0
 MTX  CONST_21  C15   C16  C11  C12     0.00   0.0  0
 MTX  CONST_22  C15   C14  C13  C12     0.00   0.0  0
 MTX  CONST_23  C16   C11  C12  C13     0.00   0.0  0
 MTX  CONST_24  C16   C15  C14  C13     0.00   0.0  0
 MTX  CONST_25  NA4   C4   N3   C2    180.00   0.0  0
 MTX  CONST_26  C8A   N1   C2   NA2   180.00   0.0  0
 MTX  CONST_27  C4    N3   C2   NA2   180.00   0.0  0
 MTX  CONST_28  N5    C4A  C4   NA4     0.00   0.0  0
 MTX  CONST_29  C8A   C4A  C4   NA4   180.00   0.0  0
 MTX  CONST_30  C9    C6   N5   C4A   180.00   0.0  0
 MTX  CONST_31  C9    C6   C7   N8    180.00   0.0  0
 MTX  CONST_32  C12   C13  C14  N10   180.00   0.0  0
 MTX  CONST_33  C16   C15  C14  N10   180.00   0.0  0
 MTX  CONST_34  C     C11  C12  C13   180.00   0.0  0
 MTX  CONST_35  C     C11  C16  C15   180.00   0.0  0
 MTX  CONST_36  H7    C7   C6   N5    180.00   0.0  0
 MTX  CONST_37  H13   C13  C12  C11   180.00   0.0  0
 MTX  CONST_38  H15   C15  C16  C11   180.00   0.0  0
 MTX  CONST_39  H16   C16  C11  C12   180.00   0.0  0
 MTX  CONST_40  H12   C12  C13  C14   180.00   0.0  0
 MTX  CONST_41  C13   C14  N10  C9    180.00   0.0  0
 MTX  CONST_42  C15   C14  N10  C9      0.00   0.0  0
 MTX  CONST_43  C13   C14  N10  CM      0.00   0.0  0
 MTX  CONST_44  C15   C14  N10  CM    180.00   0.0  0
 MTX  CONST_45  HN21  NA2  C2   N1    180.00   0.0  0
 MTX  CONST_46  HN22  NA2  C2   N1      0.00   0.0  0
 MTX  CONST_47  HN41  NA4  C4   N3    180.00   0.0  0
 MTX  CONST_48  HN42  NA4  C4   N3      0.00   0.0  0
 MTX  CONST_49  CA    N    C    C11   180.00   0.0  0
 MTX  CONST_50  HN    N    C    C11     0.00   0.0  0
 MTX  CONST_51  CA    N    C    O       0.00   0.0  0
 MTX  Var_01    N10   C9   C6   N5   -156.59  30.0  2
 MTX  Var_02    C14   N10  C9   C6     69.96  30.0  3
 MTX  Var_03    O     C    C11  C12    -5.75  30.0  2
 MTX  Var_04    HM1   CM   N10  C14    59.17  30.0  3
 MTX  Var_05    CD    CG   CB   CA    -68.44  30.0  3
 MTX  Var_06    OE1   CD   CG   CB    160.48  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
 MTX  chir_01  CA  N  CT  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
 MTX  plan-1  N10   0.020
 MTX  plan-1  C11   0.020
 MTX  plan-1  C12   0.020
 MTX  plan-1  C13   0.020
 MTX  plan-1  C14   0.020
 MTX  plan-1  C15   0.020
 MTX  plan-1  C16   0.020
 MTX  plan-1  H12   0.020
 MTX  plan-1  H13   0.020
 MTX  plan-1  H15   0.020
 MTX  plan-1  H16   0.020
 MTX  plan-1  C     0.020
 MTX  plan-2  CA    0.020
 MTX  plan-2  CT    0.020
 MTX  plan-2  O1    0.020
 MTX  plan-2  O2    0.020
 MTX  plan-3  CG    0.020
 MTX  plan-3  CD    0.020
 MTX  plan-3  OE1   0.020
 MTX  plan-3  OE2   0.020
 MTX  plan-4  N1    0.020
 MTX  plan-4  C2    0.020
 MTX  plan-4  NA2   0.020
 MTX  plan-4  N3    0.020
 MTX  plan-4  C4    0.020
 MTX  plan-4  NA4   0.020
 MTX  plan-4  C4A   0.020
 MTX  plan-4  N5    0.020
 MTX  plan-4  C6    0.020
 MTX  plan-4  C7    0.020
 MTX  plan-4  N8    0.020
 MTX  plan-4  C8A   0.020
 MTX  plan-4  C9    0.020
 MTX  plan-4  H7    0.020
 MTX  plan-5  C11   0.020
 MTX  plan-5  O     0.020
 MTX  plan-5  N     0.020
 MTX  plan-5  CA    0.020
 MTX  plan-5  HN    0.020
 MTX  plan-5  C     0.020
 MTX  plan-6  C2    0.020
 MTX  plan-6  NA2   0.020
 MTX  plan-6  HN21  0.020
 MTX  plan-6  HN22  0.020
 MTX  plan-7  C4    0.020
 MTX  plan-7  NA4   0.020
 MTX  plan-7  HN41  0.020
 MTX  plan-7  HN42  0.020
 MTX  plan-8  C9    0.020
 MTX  plan-8  N10   0.020
 MTX  plan-8  CM    0.020
 MTX  plan-8  C14   0.020

