# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 14:50:59 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ccccc1C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P@@](O)(=O)O[P](O)(O)=O)n3cnc4c(N)ncnc34
#
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
 MNT  MNT  '2'-deoxy-3'-O-{[2-(methylamino)phenyl]carbonyl}adenosine 5'-(trihydrogen diphosphate)'  ligand  58  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNT
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
 MNT  PB    P  P     0   1.474  34.7416  55.4104  21.4737
 MNT  O1B   O  O     0  -0.686  35.8421  54.4418  21.4223
 MNT  O2B   O  OH1   0  -0.724  33.4862  54.9495  20.6244
 MNT  O3B   O  OH1   0  -0.719  34.2873  55.7501  22.9513
 MNT  PA    P  P     0   1.509  36.0450  57.1914  19.5975
 MNT  O1A   O  O     0  -0.674  35.7640  56.3339  18.4393
 MNT  O2A   O  OH1   0  -0.722  35.8752  58.7593  19.4512
 MNT  O3A   O  O2    0  -0.705  35.1224  56.8861  20.8995
 MNT  O5'   O  O2    0  -0.585  37.5357  57.0580  20.1070
 MNT  C5B   C  CH2   0  -0.214  38.0306  57.5887  21.3419
 MNT  C4B   C  CR15  0   0.005  39.4574  58.0481  21.1503
 MNT  O4'   O  O     0  -0.491  40.2919  56.9515  20.8145
 MNT  C3B   C  CR15  0  -0.042  39.6303  59.0841  20.0320
 MNT  O3'   O  O2    0  -0.481  40.6294  59.9987  20.4845
 MNT  C2B   C  CH2   0  -0.539  40.1355  58.2513  18.8679
 MNT  C1B   C  CR15  0   0.221  40.9236  57.1534  19.5725
 MNT  N9    N  NR5   0  -0.543  40.9707  55.9041  18.8597
 MNT  C8    C  CR15  0   0.115  39.9139  55.1343  18.4476
 MNT  N7    N  N     0  -0.448  40.2764  54.0288  17.8703
 MNT  C5    C  CR56  0  -0.011  41.6475  54.0593  17.9013
 MNT  C6    C  CR6   0   0.460  42.6357  53.1687  17.4430
 MNT  N6    N  NH2   0  -0.816  42.3456  52.0234  16.8248
 MNT  N1    N  N     0  -0.475  43.9171  53.5020  17.6366
 MNT  C2    C  CR16  0   0.047  44.2033  54.6480  18.2478
 MNT  N3    N  N     0  -0.458  43.3692  55.5591  18.7184
 MNT  C4    C  CR56  0   0.491  42.1000  55.2138  18.5185
 MNT  C'    C  C     0   0.640  40.7646  61.1598  19.8429
 MNT  O1'   O  O     0  -0.475  40.0514  61.4562  18.9040
 MNT  C1'   C  CR6   0  -0.200  41.8289  62.0017  20.3976
 MNT  C2'   C  CR6   0   0.397  42.0639  63.3108  19.8838
 MNT  N2'   N  NH1   0  -0.688  41.3401  63.8390  18.8780
 MNT  CM'   C  CH3   0  -0.533  41.5417  65.1581  18.3412
 MNT  C3'   C  CR16  0  -0.359  43.1014  64.0651  20.4778
 MNT  C4'   C  CR16  0  -0.232  43.8604  63.5565  21.5067
 MNT  C5'   C  CR16  0  -0.284  43.6340  62.2732  22.0051
 MNT  C6'   C  CR16  0  -0.274  42.6254  61.5203  21.4469
 MNT  HOB2  H  HOH1  0   0.506  32.7405  55.5603  20.5466
 MNT  HOB3  H  HOH1  0   0.507  33.5312  56.3406  23.0729
 MNT  HOA2  H  HOH1  0   0.512  35.0368  59.0606  19.0731
 MNT  H5'1  H  HCH2  0   0.261  37.4349  58.4355  21.6895
 MNT  H5'2  H  HCH2  0   0.276  37.9824  56.8038  22.0983
 MNT  H4B   H  HCR5  0   0.282  39.7753  58.4707  22.1093
 MNT  H3B   H  HCR5  0   0.289  38.7044  59.6160  19.8090
 MNT  H2'1  H  HCH2  0   0.280  39.2882  57.8440  18.3153
 MNT  H2'2  H  HCH2  0   0.297  40.7501  58.8070  18.1626
 MNT  H1'   H  HCR5  0   0.265  41.9658  57.4535  19.7152
 MNT  H8    H  HCR5  0   0.290  38.8911  55.4394  18.6060
 MNT  HN61  H  HNH2  0   0.404  43.0816  51.3951  16.5518
 MNT  HN62  H  HNH2  0   0.411  41.3947  51.7183  16.7153
 MNT  H2    H  HCR6  0   0.253  45.2602  54.8576  18.3738
 MNT  HN2'  H  HNH1  0   0.407  40.6262  63.2598  18.4700
 MNT  HM'1  H  HCH3  0   0.262  40.8146  65.3170  17.5497
 MNT  HM'2  H  HCH3  0   0.233  41.3954  65.9385  19.0922
 MNT  HM'3  H  HCH3  0   0.233  42.5386  65.2859  17.9111
 MNT  H3'   H  HCR6  0   0.275  43.3090  65.0639  20.1203
 MNT  H4'   H  HCR6  0   0.261  44.6451  64.1705  21.9307
 MNT  H5'   H  HCR6  0   0.252  44.2340  61.8764  22.8121
 MNT  H6'   H  HCR6  0   0.262  42.4463  60.5257  21.8302

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
 MNT  PB   O1B   double    1.467  0.020  1.467
 MNT  PB   O2B   single    1.584  0.020  1.584
 MNT  PB   O3B   single    1.583  0.020  1.583
 MNT  PB   O3A   single    1.629  0.020  1.629
 MNT  O2B  HOB2  single    0.850  0.020  0.980
 MNT  O3B  HOB3  single    0.850  0.020  0.980
 MNT  PA   O1A   double    1.468  0.020  1.468
 MNT  PA   O2A   single    1.584  0.020  1.584
 MNT  PA   O3A   single    1.625  0.020  1.625
 MNT  PA   O5'   single    1.581  0.020  1.581
 MNT  O2A  HOA2  single    0.850  0.020  0.980
 MNT  O5'  C5B   single    1.432  0.020  1.432
 MNT  C5B  C4B   single    1.511  0.020  1.511
 MNT  C5B  H5'1  single    0.970  0.020  1.090
 MNT  C5B  H5'2  single    0.970  0.020  1.090
 MNT  C4B  O4'   single    1.418  0.020  1.418
 MNT  C4B  C3B   single    1.534  0.020  1.534
 MNT  C4B  H4B   single    0.970  0.020  1.090
 MNT  O4'  C1B   single    1.408  0.020  1.408
 MNT  C3B  O3'   single    1.428  0.020  1.428
 MNT  C3B  C2B   single    1.518  0.020  1.518
 MNT  C3B  H3B   single    0.970  0.020  1.090
 MNT  O3'  C'    single    1.333  0.020  1.333
 MNT  C2B  C1B   single    1.524  0.020  1.524
 MNT  C2B  H2'1  single    0.970  0.020  1.090
 MNT  C2B  H2'2  single    0.970  0.020  1.090
 MNT  C1B  N9    single    1.439  0.020  1.439
 MNT  C1B  H1'   single    0.970  0.020  1.090
 MNT  N9   C8    aromatic  1.371  0.020  1.371
 MNT  N9   C4    aromatic  1.367  0.020  1.367
 MNT  C8   N7    aromatic  1.299  0.020  1.299
 MNT  C8   H8    single    0.930  0.020  1.080
 MNT  N7   C5    aromatic  1.372  0.020  1.372
 MNT  C5   C6    aromatic  1.407  0.020  1.407
 MNT  C5   C4    aromatic  1.385  0.020  1.385
 MNT  C6   N6    single    1.333  0.020  1.333
 MNT  C6   N1    aromatic  1.338  0.020  1.338
 MNT  N6   HN61  single    0.860  0.020  1.020
 MNT  N6   HN62  single    0.860  0.020  1.020
 MNT  N1   C2    aromatic  1.330  0.020  1.330
 MNT  C2   N3    aromatic  1.322  0.020  1.322
 MNT  C2   H2    single    0.930  0.020  1.080
 MNT  N3   C4    aromatic  1.330  0.020  1.330
 MNT  C'   O1'   double    1.216  0.020  1.216
 MNT  C'   C1'   single    1.466  0.020  1.466
 MNT  C1'  C2'   aromatic  1.426  0.020  1.426
 MNT  C1'  C6'   aromatic  1.403  0.020  1.403
 MNT  C2'  N2'   single    1.347  0.020  1.347
 MNT  C2'  C3'   aromatic  1.414  0.020  1.414
 MNT  N2'  CM'   single    1.438  0.020  1.438
 MNT  N2'  HN2'  single    0.860  0.020  1.020
 MNT  CM'  HM'1  single    0.970  0.020  1.090
 MNT  CM'  HM'2  single    0.970  0.020  1.090
 MNT  CM'  HM'3  single    0.970  0.020  1.090
 MNT  C3'  C4'   aromatic  1.376  0.020  1.376
 MNT  C3'  H3'   single    0.930  0.020  1.080
 MNT  C4'  C5'   aromatic  1.395  0.020  1.395
 MNT  C4'  H4'   single    0.930  0.020  1.080
 MNT  C5'  C6'   aromatic  1.377  0.020  1.377
 MNT  C5'  H5'   single    0.930  0.020  1.080
 MNT  C6'  H6'   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
 MNT  O3A   PB   O3B   101.64  3.000
 MNT  O3A   PB   O2B   105.06  3.000
 MNT  O3B   PB   O2B   109.60  3.000
 MNT  O3A   PB   O1B   114.24  3.000
 MNT  O3B   PB   O1B   112.94  3.000
 MNT  O2B   PB   O1B   112.56  3.000
 MNT  HOB2  O2B  PB    118.06  3.000
 MNT  HOB3  O3B  PB    118.23  3.000
 MNT  O5'   PA   O3A   105.15  3.000
 MNT  O5'   PA   O2A   102.38  3.000
 MNT  O3A   PA   O2A   101.49  3.000
 MNT  O5'   PA   O1A   112.67  3.000
 MNT  O3A   PA   O1A   114.44  3.000
 MNT  O2A   PA   O1A   119.00  3.000
 MNT  HOA2  O2A  PA    115.92  3.000
 MNT  PA    O3A  PB    125.84  3.000
 MNT  C5B   O5'  PA    124.92  3.000
 MNT  H5'2  C5B  H5'1  108.24  3.000
 MNT  H5'2  C5B  C4B   110.39  3.000
 MNT  H5'1  C5B  C4B   108.64  3.000
 MNT  H5'2  C5B  O5'   108.42  3.000
 MNT  H5'1  C5B  O5'   111.91  3.000
 MNT  C4B   C5B  O5'   109.24  3.000
 MNT  H4B   C4B  C3B   110.18  3.000
 MNT  H4B   C4B  O4'   109.56  3.000
 MNT  C3B   C4B  O4'   106.45  3.000
 MNT  H4B   C4B  C5B   106.29  3.000
 MNT  C3B   C4B  C5B   113.84  3.000
 MNT  O4'   C4B  C5B   110.52  3.000
 MNT  C1B   O4'  C4B   111.22  3.000
 MNT  H3B   C3B  C2B   113.16  3.000
 MNT  H3B   C3B  O3'   110.27  3.000
 MNT  C2B   C3B  O3'   111.19  3.000
 MNT  H3B   C3B  C4B   112.50  3.000
 MNT  C2B   C3B  C4B   103.06  3.000
 MNT  O3'   C3B  C4B   106.28  3.000
 MNT  C'    O3'  C3B   118.43  3.000
 MNT  H2'2  C2B  H2'1  107.53  3.000
 MNT  H2'2  C2B  C1B   112.05  3.000
 MNT  H2'1  C2B  C1B   111.53  3.000
 MNT  H2'2  C2B  C3B   113.88  3.000
 MNT  H2'1  C2B  C3B   109.57  3.000
 MNT  C1B   C2B  C3B   102.29  3.000
 MNT  H1'   C1B  N9    105.76  3.000
 MNT  H1'   C1B  C2B   110.81  3.000
 MNT  N9    C1B  C2B   114.41  3.000
 MNT  H1'   C1B  O4'   110.59  3.000
 MNT  N9    C1B  O4'   109.10  3.000
 MNT  C2B   C1B  O4'   106.21  3.000
 MNT  C4    N9   C8    106.15  3.000
 MNT  C4    N9   C1B   126.09  3.000
 MNT  C8    N9   C1B   127.68  3.000
 MNT  H8    C8   N7    124.79  3.000
 MNT  H8    C8   N9    121.85  3.000
 MNT  N7    C8   N9    113.36  3.000
 MNT  C5    N7   C8    104.48  3.000
 MNT  C4    C5   C6    116.32  3.000
 MNT  C4    C5   N7    110.80  3.000
 MNT  C6    C5   N7    132.88  3.000
 MNT  N1    C6   N6    119.30  3.000
 MNT  N1    C6   C5    117.89  3.000
 MNT  N6    C6   C5    122.82  3.000
 MNT  HN62  N6   HN61  118.26  3.000
 MNT  HN62  N6   C6    121.15  3.000
 MNT  HN61  N6   C6    120.22  3.000
 MNT  C2    N1   C6    119.16  3.000
 MNT  H2    C2   N3    116.12  3.000
 MNT  H2    C2   N1    115.44  3.000
 MNT  N3    C2   N1    128.44  3.000
 MNT  C4    N3   C2    111.69  3.000
 MNT  N3    C4   C5    126.50  3.000
 MNT  N3    C4   N9    128.29  3.000
 MNT  C5    C4   N9    105.21  3.000
 MNT  C1'   C'   O1'   125.32  3.000
 MNT  C1'   C'   O3'   113.05  3.000
 MNT  O1'   C'   O3'   121.63  3.000
 MNT  C6'   C1'  C2'   119.42  3.000
 MNT  C6'   C1'  C'    119.89  3.000
 MNT  C2'   C1'  C'    120.70  3.000
 MNT  C3'   C2'  N2'   119.92  3.000
 MNT  C3'   C2'  C1'   117.35  3.000
 MNT  N2'   C2'  C1'   122.72  3.000
 MNT  HN2'  N2'  CM'   118.44  3.000
 MNT  HN2'  N2'  C2'   117.29  3.000
 MNT  CM'   N2'  C2'   124.26  3.000
 MNT  HM'3  CM'  HM'2  108.00  3.000
 MNT  HM'3  CM'  HM'1  107.86  3.000
 MNT  HM'2  CM'  HM'1  107.85  3.000
 MNT  HM'3  CM'  N2'   112.45  3.000
 MNT  HM'2  CM'  N2'   112.31  3.000
 MNT  HM'1  CM'  N2'   108.19  3.000
 MNT  H3'   C3'  C4'   118.88  3.000
 MNT  H3'   C3'  C2'   119.67  3.000
 MNT  C4'   C3'  C2'   121.45  3.000
 MNT  H4'   C4'  C5'   119.95  3.000
 MNT  H4'   C4'  C3'   118.87  3.000
 MNT  C5'   C4'  C3'   121.17  3.000
 MNT  H5'   C5'  C6'   120.57  3.000
 MNT  H5'   C5'  C4'   120.94  3.000
 MNT  C6'   C5'  C4'   118.49  3.000
 MNT  H6'   C6'  C5'   118.74  3.000
 MNT  H6'   C6'  C1'   119.15  3.000
 MNT  C5'   C6'  C1'   122.11  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
 MNT  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 MNT  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 MNT  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 MNT  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 MNT  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 MNT  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 MNT  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 MNT  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 MNT  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 MNT  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 MNT  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 MNT  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 MNT  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 MNT  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 MNT  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 MNT  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 MNT  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 MNT  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 MNT  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 MNT  CONST_20  C5'   C6'  C1'  C2'     0.00   0.0  0
 MNT  CONST_21  C5'   C4'  C3'  C2'     0.00   0.0  0
 MNT  CONST_22  C6'   C1'  C2'  C3'     0.00   0.0  0
 MNT  CONST_23  C6'   C5'  C4'  C3'     0.00   0.0  0
 MNT  CONST_24  N7    C8   N9   C1B   180.00   0.0  0
 MNT  CONST_25  C5    C4   N9   C1B   180.00   0.0  0
 MNT  CONST_26  N3    C4   N9   C1B     0.00   0.0  0
 MNT  CONST_27  N6    C6   C5   N7      0.00   0.0  0
 MNT  CONST_28  C4    C5   C6   N6    180.00   0.0  0
 MNT  CONST_29  C2    N1   C6   N6    180.00   0.0  0
 MNT  CONST_30  C3'   C2'  C1'  C'    180.00   0.0  0
 MNT  CONST_31  C5'   C6'  C1'  C'    180.00   0.0  0
 MNT  CONST_32  C6'   C1'  C2'  N2'   180.00   0.0  0
 MNT  CONST_33  C4'   C3'  C2'  N2'   180.00   0.0  0
 MNT  CONST_34  H8    C8   N9   C1B     0.00   0.0  0
 MNT  CONST_35  H2    C2   N1   C6    180.00   0.0  0
 MNT  CONST_36  H3'   C3'  C2'  C1'   180.00   0.0  0
 MNT  CONST_37  H5'   C5'  C6'  C1'   180.00   0.0  0
 MNT  CONST_38  H6'   C6'  C1'  C2'   180.00   0.0  0
 MNT  CONST_39  H4'   C4'  C3'  C2'   180.00   0.0  0
 MNT  CONST_40  CM'   N2'  C2'  C1'   180.00   0.0  0
 MNT  CONST_41  C3'   C2'  N2'  CM'     0.00   0.0  0
 MNT  CONST_42  HN61  N6   C6   C5    180.00   0.0  0
 MNT  CONST_43  HN62  N6   C6   C5      0.00   0.0  0
 MNT  CONST_44  HN2'  N2'  C2'  C1'     0.00   0.0  0
 MNT  Var_01    C1'   C'   O3'  C3B  -179.56  30.0  3
 MNT  Var_02    C2'   C1'  C'   O3'  -176.43  30.0  2
 MNT  Var_03    C4B   C5B  O5'  PA   -145.12  30.0  3
 MNT  Var_04    HM'1  CM'  N2'  C2'  -179.56  30.0  3
 MNT  Var_05    O1A   PA   O3A  PB     43.18  30.0  1

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
 MNT  chir_02  C4B  C5B  O4'  C3B  negativ
 MNT  chir_03  C3B  O3'  C2B  C4B  negativ
 MNT  chir_04  C1B  O4'  N9   C2B  negativ
 MNT  chir_05  PA   O2A  O3A  O5'  both

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
 MNT  plan-1  C'    0.020
 MNT  plan-1  C1'   0.020
 MNT  plan-1  C2'   0.020
 MNT  plan-1  N2'   0.020
 MNT  plan-1  C3'   0.020
 MNT  plan-1  C4'   0.020
 MNT  plan-1  C5'   0.020
 MNT  plan-1  C6'   0.020
 MNT  plan-1  H3'   0.020
 MNT  plan-1  H4'   0.020
 MNT  plan-1  H5'   0.020
 MNT  plan-1  H6'   0.020
 MNT  plan-2  C1B   0.020
 MNT  plan-2  N9    0.020
 MNT  plan-2  C8    0.020
 MNT  plan-2  N7    0.020
 MNT  plan-2  C5    0.020
 MNT  plan-2  C6    0.020
 MNT  plan-2  N6    0.020
 MNT  plan-2  N1    0.020
 MNT  plan-2  C2    0.020
 MNT  plan-2  N3    0.020
 MNT  plan-2  C4    0.020
 MNT  plan-2  H8    0.020
 MNT  plan-2  H2    0.020
 MNT  plan-3  C6    0.020
 MNT  plan-3  N6    0.020
 MNT  plan-3  HN61  0.020
 MNT  plan-3  HN62  0.020
 MNT  plan-4  C2'   0.020
 MNT  plan-4  N2'   0.020
 MNT  plan-4  CM'   0.020
 MNT  plan-4  HN2'  0.020
 MNT  plan-5  O3'   0.020
 MNT  plan-5  C'    0.020
 MNT  plan-5  O1'   0.020
 MNT  plan-5  C1'   0.020

