# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:54:47 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2N[C@@H](CCc2n1)CNc3ccc(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
 VMV  VMV  'N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic acid'  ligand  55  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VMV
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
 VMV  C2    C  CR6    0   0.489   -9.9817  21.2578  13.1823
 VMV  C6    C  CR16   0  -0.129   -5.2808  21.3891  14.6635
 VMV  C8    C  C      0  -0.520   -7.5019  21.1882  15.8381
 VMV  C4    C  CR6    0   0.408   -8.0295  21.8247  12.1722
 VMV  C9    C  CH2    0  -0.297   -4.9961  19.8769  14.5972
 VMV  C12   C  CR6    0  -0.072   -5.6406  17.0042  18.9096
 VMV  C15   C  CR6    0   0.399   -4.7469  18.6224  16.7525
 VMV  C16   C  CR16   0  -0.344   -4.0010  18.5010  17.9400
 VMV  C17   C  CR16   0  -0.288   -4.4397  17.7151  18.9846
 VMV  N     N  NH1    0  -0.666   -5.6521  16.3371  21.2210
 VMV  CA    C  CH1    0  -0.175   -6.0413  15.6043  22.4073
 VMV  O     O  O      0  -0.512   -7.0204  15.2809  19.7700
 VMV  CB    C  CH2    0  -0.414   -5.3347  14.2377  22.4673
 VMV  CG    C  CH2    0  -0.585   -5.9743  13.2340  23.4130
 VMV  CD    C  C      0   0.406   -5.3677  11.8168  23.4007
 VMV  OE1   O  O      0  -0.628   -5.9825  10.9610  24.0728
 VMV  OE2   O  OC    -1  -0.607   -4.3215  11.6298  22.7467
 VMV  C13   C  CR16   0  -0.266   -6.3656  17.1046  17.7236
 VMV  C14   C  CR16   0  -0.336   -5.9448  17.8922  16.6693
 VMV  C4A   C  CR66   0   0.138   -7.3359  21.6395  13.3904
 VMV  C7    C  C      0  -0.460   -6.1052  21.7947  15.8773
 VMV  C8A   C  CR66   0   0.234   -8.1215  21.3215  14.4797
 VMV  CT    C  C      0   0.414   -5.7185  16.4805  23.6451
 VMV  N1    N  N      0  -0.498   -9.4451  21.1304  14.3834
 VMV  N10   N  NH1    0  -0.699   -4.2647  19.3942  15.7388
 VMV  N3    N  N      0  -0.489   -9.3320  21.6149  12.0726
 VMV  N5    N  NR16   0  -0.680   -5.9495  21.8511  13.4567
 VMV  NA2   N  NH2    0  -0.829  -11.3321  21.0705  13.0655
 VMV  NA4   N  NH2    0  -0.830   -7.3528  22.1828  11.0475
 VMV  O1    O  OC    -1  -0.589   -6.1894  16.0980  24.7303
 VMV  O2    O  O      0  -0.596   -5.0031  17.4862  23.4500
 VMV  H61   H  HCR6   0   0.249   -4.3161  21.9043  14.7150
 VMV  H82   H  H      0   0.260   -8.1490  21.6718  16.5731
 VMV  H81   H  H      0   0.257   -7.4751  20.1315  16.1209
 VMV  H92   H  HCH2   0   0.248   -5.9264  19.3213  14.4874
 VMV  H91   H  HCH2   0   0.249   -4.4199  19.6791  13.6873
 VMV  H161  H  HCR6   0   0.257   -3.0627  19.0356  18.0327
 VMV  H171  H  HCR6   0   0.246   -3.8085  17.6523  19.8628
 VMV  H     H  HNH1   0   0.384   -5.0721  17.1399  21.4221
 VMV  HA    H  HCH1   0   0.218   -7.1230  15.4323  22.3797
 VMV  HB2   H  HCH2   0   0.200   -4.2821  14.3918  22.7231
 VMV  HB3   H  HCH2   0   0.212   -5.3366  13.8178  21.4588
 VMV  HG2   H  HCH2   0   0.203   -7.0426  13.1489  23.1815
 VMV  HG3   H  HCH2   0   0.227   -5.9391  13.6096  24.4382
 VMV  H131  H  HCR6   0   0.247   -7.2900  16.5516  17.6194
 VMV  H141  H  HCR6   0   0.263   -6.5505  17.9197  15.7736
 VMV  H72   H  H      0   0.249   -5.5893  21.5062  16.7936
 VMV  H71   H  H      0   0.249   -6.1777  22.8850  15.8934
 VMV  H101  H  HNH1   0   0.386   -3.3989  19.8749  15.9284
 VMV  H2    H  HNR6   0   0.364   -5.4734  21.5110  12.6298
 VMV  HA21  H  HNH2   0   0.378  -11.6715  20.8623  12.1411
 VMV  HA22  H  HNH2   0   0.378  -11.7648  20.5278  13.7943
 VMV  HA42  H  HNH2   0   0.387   -7.9242  22.4651  10.2667
 VMV  HA41  H  HNH2   0   0.390   -6.5226  22.7428  11.1612
 VMV  C     C  C      0   0.521   -6.1616  16.1320  19.9996

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
 VMV  NA4  C4    single    1.361  0.020  1.361
 VMV  C4   N3    aromatic  1.323  0.020  1.323
 VMV  C4   C4A   aromatic  1.414  0.020  1.414
 VMV  N3   C2    aromatic  1.335  0.020  1.335
 VMV  N5   C4A   single    1.404  0.020  1.404
 VMV  N5   C6    single    1.455  0.020  1.455
 VMV  C4A  C8A   aromatic  1.380  0.020  1.380
 VMV  C2   NA2   single    1.368  0.020  1.368
 VMV  C2   N1    aromatic  1.322  0.020  1.322
 VMV  C8A  N1    aromatic  1.341  0.020  1.341
 VMV  C8A  C8    single    1.499  0.020  1.499
 VMV  C6   C9    single    1.540  0.020  1.540
 VMV  C6   C7    single    1.522  0.020  1.522
 VMV  C9   N10   single    1.439  0.020  1.439
 VMV  N10  C15   single    1.362  0.020  1.362
 VMV  C8   C7    single    1.523  0.020  1.523
 VMV  C14  C15   aromatic  1.405  0.020  1.405
 VMV  C14  C13   aromatic  1.382  0.020  1.382
 VMV  C15  C16   aromatic  1.408  0.020  1.408
 VMV  C13  C12   aromatic  1.394  0.020  1.394
 VMV  C16  C17   aromatic  1.379  0.020  1.379
 VMV  C12  C17   aromatic  1.398  0.020  1.398
 VMV  C12  C     single    1.490  0.020  1.490
 VMV  O    C     double    1.231  0.020  1.231
 VMV  C    N     single    1.339  0.020  1.339
 VMV  N    CA    single    1.448  0.020  1.448
 VMV  CG   CD    single    1.542  0.020  1.542
 VMV  CG   CB    single    1.520  0.020  1.520
 VMV  OE1  CD    deloc     1.250  0.020  1.250
 VMV  CD   OE2   deloc     1.248  0.020  1.248
 VMV  CB   CA    single    1.540  0.020  1.540
 VMV  CA   CT    single    1.550  0.020  1.550
 VMV  O2   CT    deloc     1.250  0.020  1.250
 VMV  CT   O1    deloc     1.243  0.020  1.243
 VMV  C6   H61   single    0.970  0.020  1.090
 VMV  C8   H82   single    0.970  0.020  1.090
 VMV  C8   H81   single    0.970  0.020  1.090
 VMV  C9   H92   single    0.970  0.020  1.090
 VMV  C9   H91   single    0.970  0.020  1.090
 VMV  C16  H161  single    0.930  0.020  1.080
 VMV  C17  H171  single    0.930  0.020  1.080
 VMV  N    H     single    0.860  0.020  1.020
 VMV  CA   HA    single    0.970  0.020  1.090
 VMV  CB   HB2   single    0.970  0.020  1.090
 VMV  CB   HB3   single    0.970  0.020  1.090
 VMV  CG   HG2   single    0.970  0.020  1.090
 VMV  CG   HG3   single    0.970  0.020  1.090
 VMV  C13  H131  single    0.930  0.020  1.080
 VMV  C14  H141  single    0.930  0.020  1.080
 VMV  C7   H72   single    0.970  0.020  1.090
 VMV  C7   H71   single    0.970  0.020  1.090
 VMV  N10  H101  single    0.860  0.020  1.020
 VMV  N5   H2    single    0.890  0.020  1.040
 VMV  NA2  HA21  single    0.890  0.020  1.040
 VMV  NA2  HA22  single    0.890  0.020  1.040
 VMV  NA4  HA42  single    0.890  0.020  1.040
 VMV  NA4  HA41  single    0.890  0.020  1.040

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
 VMV  NA2   C2   N3    116.49  3.000
 VMV  NA2   C2   N1    117.71  3.000
 VMV  N3    C2   N1    125.72  3.000
 VMV  H61   C6   N5    107.13  3.000
 VMV  H61   C6   C7    108.31  3.000
 VMV  N5    C6   C7    109.14  3.000
 VMV  H61   C6   C9    107.53  3.000
 VMV  C7    C6   C9    113.33  3.000
 VMV  N5    C6   C9    111.16  3.000
 VMV  H81   C8   H82   105.56  3.000
 VMV  H81   C8   C8A   109.28  3.000
 VMV  H82   C8   C8A   109.00  3.000
 VMV  H81   C8   C7    110.82  3.000
 VMV  H82   C8   C7    110.47  3.000
 VMV  C8A   C8   C7    111.52  3.000
 VMV  NA4   C4   N3    117.98  3.000
 VMV  N3    C4   C4A   121.80  3.000
 VMV  NA4   C4   C4A   120.18  3.000
 VMV  H91   C9   H92   105.88  3.000
 VMV  H91   C9   N10   109.33  3.000
 VMV  H92   C9   N10   110.06  3.000
 VMV  H91   C9   C6    108.09  3.000
 VMV  H92   C9   C6    110.32  3.000
 VMV  N10   C9   C6    112.90  3.000
 VMV  C13   C12  C     118.87  3.000
 VMV  C     C12  C17   123.98  3.000
 VMV  C13   C12  C17   117.13  3.000
 VMV  N10   C15  C14   123.51  3.000
 VMV  C14   C15  C16   117.18  3.000
 VMV  N10   C15  C16   119.28  3.000
 VMV  H161  C16  C17   119.45  3.000
 VMV  H161  C16  C15   119.24  3.000
 VMV  C17   C16  C15   121.31  3.000
 VMV  H171  C17  C16   117.50  3.000
 VMV  H171  C17  C12   120.97  3.000
 VMV  C16   C17  C12   121.51  3.000
 VMV  H     N    C     121.43  3.000
 VMV  H     N    CA    113.17  3.000
 VMV  C     N    CA    124.58  3.000
 VMV  HA    CA   CT    108.33  3.000
 VMV  HA    CA   CB    108.34  3.000
 VMV  CT    CA   CB    112.02  3.000
 VMV  HA    CA   N     108.92  3.000
 VMV  CT    CA   N     108.19  3.000
 VMV  CB    CA   N     110.97  3.000
 VMV  HB3   CB   HB2   105.76  3.000
 VMV  HB3   CB   CG    108.66  3.000
 VMV  HB2   CB   CG    110.63  3.000
 VMV  HB3   CB   CA    107.72  3.000
 VMV  HB2   CB   CA    109.00  3.000
 VMV  CG    CB   CA    114.66  3.000
 VMV  HG3   CG   HG2   104.85  3.000
 VMV  HG3   CG   CD    108.11  3.000
 VMV  HG2   CG   CD    108.08  3.000
 VMV  HG3   CG   CB    110.08  3.000
 VMV  HG2   CG   CB    109.26  3.000
 VMV  CD    CG   CB    115.87  3.000
 VMV  OE2   CD   OE1   126.27  3.000
 VMV  OE2   CD   CG    118.15  3.000
 VMV  OE1   CD   CG    115.57  3.000
 VMV  H131  C13  C14   118.55  3.000
 VMV  H131  C13  C12   119.31  3.000
 VMV  C14   C13  C12   122.14  3.000
 VMV  H141  C14  C13   118.42  3.000
 VMV  H141  C14  C15   120.87  3.000
 VMV  C13   C14  C15   120.70  3.000
 VMV  N5    C4A  C8A   124.02  3.000
 VMV  C8A   C4A  C4    115.53  3.000
 VMV  N5    C4A  C4    120.35  3.000
 VMV  H71   C7   H72   106.44  3.000
 VMV  H71   C7   C8    109.68  3.000
 VMV  H72   C7   C8    110.49  3.000
 VMV  H71   C7   C6    108.27  3.000
 VMV  H72   C7   C6    110.08  3.000
 VMV  C8    C7   C6    111.71  3.000
 VMV  N1    C8A  C4A   122.55  3.000
 VMV  N1    C8A  C8    117.42  3.000
 VMV  C4A   C8A  C8    120.03  3.000
 VMV  O2    CT   O1    126.92  3.000
 VMV  O1    CT   CA    116.37  3.000
 VMV  O2    CT   CA    116.70  3.000
 VMV  C8A   N1   C2    116.89  3.000
 VMV  H101  N10  C15   115.73  3.000
 VMV  H101  N10  C9    115.19  3.000
 VMV  C15   N10  C9    126.90  3.000
 VMV  C4    N3   C2    117.33  3.000
 VMV  H2    N5   C4A   112.02  3.000
 VMV  H2    N5   C6    110.76  3.000
 VMV  C4A   N5   C6    116.43  3.000
 VMV  HA22  NA2  HA21  114.11  3.000
 VMV  HA22  NA2  C2    115.86  3.000
 VMV  HA21  NA2  C2    116.07  3.000
 VMV  HA41  NA4  HA42  113.50  3.000
 VMV  HA41  NA4  C4    117.56  3.000
 VMV  HA42  NA4  C4    115.61  3.000
 VMV  O     C    N     122.79  3.000
 VMV  N     C    C12   116.39  3.000
 VMV  O     C    C12   120.82  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
 VMV  CONST_01  C4A   C4   N3   C2      0.00   0.0  0
 VMV  CONST_02  C4A   C8A  N1   C2      0.00   0.0  0
 VMV  CONST_03  N1    C2   N3   C4      0.00   0.0  0
 VMV  CONST_04  N1    C8A  C4A  C4      0.00   0.0  0
 VMV  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 VMV  CONST_06  C15   C16  C17  C12     0.00   0.0  0
 VMV  CONST_07  C13   C14  C15  C16     0.00   0.0  0
 VMV  CONST_08  C13   C12  C17  C16     0.00   0.0  0
 VMV  CONST_09  C14   C15  C16  C17     0.00   0.0  0
 VMV  CONST_10  C14   C13  C12  C17     0.00   0.0  0
 VMV  CONST_11  N3    C4   C4A  C8A     0.00   0.0  0
 VMV  CONST_12  N3    C2   N1   C8A     0.00   0.0  0
 VMV  CONST_13  NA4   C4   N3   C2    180.00   0.0  0
 VMV  CONST_14  NA2   C2   N3   C4    180.00   0.0  0
 VMV  CONST_15  C     C12  C17  C16   180.00   0.0  0
 VMV  CONST_16  N10   C15  C16  C17   180.00   0.0  0
 VMV  CONST_17  C14   C13  C12  C     180.00   0.0  0
 VMV  CONST_18  N10   C15  C14  C13   180.00   0.0  0
 VMV  CONST_19  NA4   C4   C4A  C8A   180.00   0.0  0
 VMV  CONST_20  NA2   C2   N1   C8A   180.00   0.0  0
 VMV  CONST_21  NA4   C4   C4A  N5      0.00   0.0  0
 VMV  CONST_22  H141  C14  C13  C12   180.00   0.0  0
 VMV  CONST_23  H161  C16  C17  C12   180.00   0.0  0
 VMV  CONST_24  H131  C13  C14  C15   180.00   0.0  0
 VMV  CONST_25  H171  C17  C16  C15   180.00   0.0  0
 VMV  CONST_27  C16   C15  N10  C9    180.00   0.0  0
 VMV  CONST_28  H101  N10  C15  C16     0.00   0.0  0
 VMV  CONST_29  HA42  NA4  C4   C4A   180.00   0.0  0
 VMV  CONST_33  CA    N    C    C12   180.00   0.0  0
 VMV  CONST_34  H     N    C    C12     0.00   0.0  0
 VMV  CONST_35  O     C    N    CA      0.00   0.0  0
 VMV  Var_01    C4    C4A  N5   C6   -168.30  30.0  1
 VMV  Var_02    C8A   C8   C7   C6    -45.03  30.0  1
 VMV  Var_03    C7    C8   C8A  C4A    15.25  30.0  1
 VMV  Var_04    C15   N10  C9   C6    107.79  30.0  3
 VMV  Var_05    O     C    C12  C17  -161.43  30.0  2
 VMV  Var_06    CD    CG   CB   CA    174.68  30.0  1
 VMV  Var_07    OE1   CD   CG   CB   -172.81  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
 VMV  chir_01  C6  N5  C9  C7  positiv
 VMV  chir_02  CA  N   CB  CT  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
 VMV  plan-1  C12   0.020
 VMV  plan-1  C15   0.020
 VMV  plan-1  C16   0.020
 VMV  plan-1  C17   0.020
 VMV  plan-1  C13   0.020
 VMV  plan-1  C14   0.020
 VMV  plan-1  N10   0.020
 VMV  plan-1  H161  0.020
 VMV  plan-1  H171  0.020
 VMV  plan-1  H131  0.020
 VMV  plan-1  H141  0.020
 VMV  plan-1  C     0.020
 VMV  plan-2  CG    0.020
 VMV  plan-2  CD    0.020
 VMV  plan-2  OE1   0.020
 VMV  plan-2  OE2   0.020
 VMV  plan-3  CA    0.020
 VMV  plan-3  CT    0.020
 VMV  plan-3  O1    0.020
 VMV  plan-3  O2    0.020
 VMV  plan-4  C12   0.020
 VMV  plan-4  N     0.020
 VMV  plan-4  CA    0.020
 VMV  plan-4  O     0.020
 VMV  plan-4  H     0.020
 VMV  plan-4  C     0.020
 VMV  plan-5  C9    0.020
 VMV  plan-5  C15   0.020
 VMV  plan-5  N10   0.020
 VMV  plan-5  H101  0.020
 VMV  plan-6  C2    0.020
 VMV  plan-6  NA2   0.020
 VMV  plan-6  HA21  0.020
 VMV  plan-6  HA22  0.020
 VMV  plan-7  C2    0.020
 VMV  plan-7  C8    0.020
 VMV  plan-7  C4    0.020
 VMV  plan-7  C4A   0.020
 VMV  plan-7  C8A   0.020
 VMV  plan-7  N1    0.020
 VMV  plan-7  N3    0.020
 VMV  plan-7  N5    0.020
 VMV  plan-7  NA2   0.020
 VMV  plan-7  NA4   0.020
 VMV  plan-8  C4    0.020
 VMV  plan-8  NA4   0.020
 VMV  plan-8  HA42  0.020
 VMV  plan-8  HA41  0.020

