# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 19:17:41 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 5'-O-[(R)-(3-aminopropoxy)(L-alpha-aspartylamino)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCO[P@](=O)(NC(=O)[C@@H](N)CC(O)=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 7MD  7MD  5'-O-[(R)-(3-aminopropoxy)(L-alpha-aspartylamino)phosphoryl]adenosine  ligand  62  35  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7MD
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
 7MD  C     C  C     0   0.624  12.9952  -3.1797  47.5645
 7MD  N     N  NH2   0  -0.791  11.4749  -2.1819  46.0233
 7MD  O     O  O     0  -0.438  14.0667  -3.6139  47.2054
 7MD  P     P  P     0   1.503  14.2436  -1.8985  49.5644
 7MD  N1    N  N     0  -0.475  14.4142   6.6423  49.3186
 7MD  C2    C  CR16  0   0.040  13.4368   6.4040  50.1906
 7MD  N3    N  N     0  -0.452  13.1247   5.2674  50.7875
 7MD  C4    C  CR56  0   0.490  13.9436   4.2814  50.4272
 7MD  C5    C  CR56  0  -0.001  15.0116   4.3800  49.5487
 7MD  C6    C  CR6   0   0.460  15.2310   5.6428  48.9693
 7MD  N6    N  NH2   0  -0.817  16.2132   5.8715  48.0962
 7MD  N7    N  N     0  -0.448  15.6489   3.1749  49.4178
 7MD  C8    C  CR15  0   0.102  14.9787   2.3683  50.1867
 7MD  N8    N  NH1   0  -0.857  12.8854  -2.3754  48.6663
 7MD  N9    N  NR5   0  -0.540  13.9342   2.9768  50.8293
 7MD  CA    C  CH1   0  -0.246  11.6853  -3.3921  46.8148
 7MD  CB    C  CH2   0  -0.554  11.8057  -4.6077  45.9063
 7MD  CG    C  C     0   0.532  10.5738  -4.9376  45.1042
 7MD  C1'   C  CH1   0   0.217  12.9599   2.3601  51.7006
 7MD  O1P   O  O     0  -0.676  14.9993  -2.9653  50.2414
 7MD  C2'   C  CH1   0  -0.001  11.8121   1.6793  50.9514
 7MD  O2'   O  OH1   0  -0.649  10.8352   2.6187  50.6385
 7MD  C3'   C  CH1   0  -0.050  11.4102   0.5819  51.9388
 7MD  O3'   O  OH1   0  -0.665  10.5513   1.1544  52.8887
 7MD  O31   O  O2    0  -0.579  15.1458  -1.0534  48.5760
 7MD  C32   C  CH2   0  -0.182  14.6346  -0.0818  47.6406
 7MD  C33   C  CH2   0  -0.481  15.8135   0.6296  47.0154
 7MD  C34   C  CH2   0  -0.299  15.3670   1.7485  46.0864
 7MD  N35   N  NH2   0  -0.791  14.5007   1.2464  45.0308
 7MD  C4'   C  CH1   0  -0.030  12.7666   0.2002  52.5498
 7MD  O4'   O  O2    0  -0.497  13.5941   1.3582  52.4366
 7MD  C5'   C  CH2   0  -0.193  13.4401  -1.0044  51.9362
 7MD  O5'   O  O2    0  -0.617  13.5561  -0.8152  50.5199
 7MD  OD1   O  OH1   0  -0.590   9.4457  -4.6827  45.7571
 7MD  OD2   O  O     0  -0.440  10.6007  -5.4181  43.9992
 7MD  HN    H  HNH2  0   0.364  10.5863  -2.2442  45.5409
 7MD  HNA   H  HNH2  0   0.358  11.3806  -1.3764  46.6299
 7MD  HN6   H  HNH2  0   0.404  16.3176   6.7771  47.6723
 7MD  HN6A  H  HNH2  0   0.409  16.8251   5.1321  47.7998
 7MD  H8    H  HCR5  0   0.293  15.2105   1.3266  50.3391
 7MD  HN8   H  HNH1  0   0.435  11.9642  -2.1107  48.9897
 7MD  HA    H  HCH1  0   0.262  10.8970  -3.5696  47.5591
 7MD  HB    H  HCH2  0   0.280  12.6348  -4.4812  45.2115
 7MD  HBA   H  HCH2  0   0.299  12.0283  -5.4929  46.5112
 7MD  H1'   H  HCH1  0   0.261  12.5677   3.1562  52.3440
 7MD  H2'   H  HCH1  0   0.241  12.2128   1.2013  50.0500
 7MD  HO2'  H  HOH1  0   0.463  10.1932   2.2103  50.0496
 7MD  H3'   H  HCH1  0   0.254  10.9419  -0.2738  51.4365
 7MD  HO3'  H  HOH1  0   0.458  10.3161   0.4771  53.5306
 7MD  H32   H  HCH2  0   0.247  14.0317  -0.5829  46.8821
 7MD  H32A  H  HCH2  0   0.228  13.9937   0.6382  48.1590
 7MD  H33   H  HCH2  0   0.244  16.4362   1.0663  47.7990
 7MD  H33A  H  HCH2  0   0.237  16.4317  -0.0891  46.4694
 7MD  H34   H  HCH2  0   0.221  14.8090   2.4867  46.6688
 7MD  H34A  H  HCH2  0   0.209  16.2641   2.2647  45.7184
 7MD  HN35  H  HNH2  0   0.348  14.2038   2.0153  44.4435
 7MD  HN3A  H  HNH2  0   0.338  15.0301   0.6292  44.4266
 7MD  H4'   H  HCH1  0   0.275  12.6440  -0.0398  53.6119
 7MD  H5'   H  HCH2  0   0.267  14.4277  -1.1476  52.3776
 7MD  H5'A  H  HCH2  0   0.258  12.8362  -1.8879  52.1555
 7MD  HOD1  H  HOH1  0   0.485   8.6828  -4.9224  45.2092
 7MD  H2    H  HCR6  0   0.251  12.8159   7.2588  50.4370

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
 7MD  CA   C     single    1.524  0.020  1.524
 7MD  O    C     double    1.211  0.020  1.211
 7MD  C    N8    single    1.369  0.020  1.369
 7MD  N    CA    single    1.461  0.020  1.461
 7MD  N    HN    single    0.890  0.020  1.040
 7MD  N    HNA   single    0.890  0.020  1.040
 7MD  O31  P     single    1.583  0.020  1.583
 7MD  N8   P     single    1.697  0.020  1.697
 7MD  P    O5'   single    1.600  0.020  1.600
 7MD  P    O1P   double    1.472  0.020  1.472
 7MD  C6   N1    aromatic  1.337  0.020  1.337
 7MD  N1   C2    aromatic  1.331  0.020  1.331
 7MD  C2   N3    aromatic  1.321  0.020  1.321
 7MD  C2   H2    single    0.930  0.020  1.080
 7MD  C4   N3    aromatic  1.331  0.020  1.331
 7MD  C5   C4    aromatic  1.386  0.020  1.386
 7MD  N9   C4    aromatic  1.365  0.020  1.365
 7MD  N7   C5    aromatic  1.370  0.020  1.370
 7MD  C6   C5    aromatic  1.407  0.020  1.407
 7MD  N6   C6    single    1.334  0.020  1.334
 7MD  N6   HN6   single    0.860  0.020  1.020
 7MD  N6   HN6A  single    0.860  0.020  1.020
 7MD  N7   C8    aromatic  1.300  0.020  1.300
 7MD  C8   N9    aromatic  1.369  0.020  1.369
 7MD  C8   H8    single    0.930  0.020  1.080
 7MD  N8   HN8   single    0.860  0.020  1.020
 7MD  N9   C1'   single    1.445  0.020  1.445
 7MD  CB   CA    single    1.522  0.020  1.522
 7MD  CA   HA    single    0.970  0.020  1.090
 7MD  CG   CB    single    1.507  0.020  1.507
 7MD  CB   HB    single    0.970  0.020  1.090
 7MD  CB   HBA   single    0.970  0.020  1.090
 7MD  OD2  CG    double    1.205  0.020  1.205
 7MD  CG   OD1   single    1.328  0.020  1.328
 7MD  C2'  C1'   single    1.530  0.020  1.530
 7MD  C1'  O4'   single    1.396  0.020  1.396
 7MD  C1'  H1'   single    0.970  0.020  1.090
 7MD  C2'  O2'   single    1.391  0.020  1.391
 7MD  C2'  C3'   single    1.530  0.020  1.530
 7MD  C2'  H2'   single    0.970  0.020  1.090
 7MD  O2'  HO2'  single    0.850  0.020  0.980
 7MD  C3'  C4'   single    1.536  0.020  1.536
 7MD  C3'  O3'   single    1.403  0.020  1.403
 7MD  C3'  H3'   single    0.970  0.020  1.090
 7MD  O3'  HO3'  single    0.850  0.020  0.980
 7MD  C32  O31   single    1.442  0.020  1.442
 7MD  C33  C32   single    1.512  0.020  1.512
 7MD  C32  H32   single    0.970  0.020  1.090
 7MD  C32  H32A  single    0.970  0.020  1.090
 7MD  C34  C33   single    1.521  0.020  1.521
 7MD  C33  H33   single    0.970  0.020  1.090
 7MD  C33  H33A  single    0.970  0.020  1.090
 7MD  N35  C34   single    1.455  0.020  1.455
 7MD  C34  H34   single    0.970  0.020  1.090
 7MD  C34  H34A  single    0.970  0.020  1.090
 7MD  N35  HN35  single    0.890  0.020  1.040
 7MD  N35  HN3A  single    0.890  0.020  1.040
 7MD  C5'  C4'   single    1.510  0.020  1.510
 7MD  O4'  C4'   single    1.428  0.020  1.428
 7MD  C4'  H4'   single    0.970  0.020  1.090
 7MD  O5'  C5'   single    1.434  0.020  1.434
 7MD  C5'  H5'   single    0.970  0.020  1.090
 7MD  C5'  H5'A  single    0.970  0.020  1.090
 7MD  OD1  HOD1  single    0.850  0.020  0.980

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
 7MD  CA    C    N8    114.14  3.000
 7MD  N8    C    O     121.37  3.000
 7MD  CA    C    O     124.39  3.000
 7MD  HNA   N    HN    104.62  3.000
 7MD  HNA   N    CA    110.35  3.000
 7MD  HN    N    CA    109.47  3.000
 7MD  O5'   P    O31   104.86  3.000
 7MD  O5'   P    O1P   115.89  3.000
 7MD  O31   P    O1P   112.43  3.000
 7MD  O1P   P    N8    116.78  3.000
 7MD  O5'   P    N8     99.35  3.000
 7MD  O31   P    N8    106.01  3.000
 7MD  C6    N1   C2    119.06  3.000
 7MD  H2    C2   N3    116.10  3.000
 7MD  H2    C2   N1    115.34  3.000
 7MD  N3    C2   N1    128.56  3.000
 7MD  C4    N3   C2    111.69  3.000
 7MD  N9    C4   C5    105.07  3.000
 7MD  N9    C4   N3    128.59  3.000
 7MD  C5    C4   N3    126.34  3.000
 7MD  N7    C5   C6    132.69  3.000
 7MD  C6    C5   C4    116.43  3.000
 7MD  N7    C5   C4    110.88  3.000
 7MD  N6    C6   C5    122.57  3.000
 7MD  N6    C6   N1    119.51  3.000
 7MD  C5    C6   N1    117.92  3.000
 7MD  HN6A  N6   HN6   118.38  3.000
 7MD  HN6A  N6   C6    121.03  3.000
 7MD  HN6   N6   C6    120.46  3.000
 7MD  C8    N7   C5    104.44  3.000
 7MD  H8    C8   N9    121.81  3.000
 7MD  H8    C8   N7    124.90  3.000
 7MD  N9    C8   N7    113.27  3.000
 7MD  HN8   N8   P     119.09  3.000
 7MD  HN8   N8   C     118.96  3.000
 7MD  P     N8   C     121.82  3.000
 7MD  C1'   N9   C8    127.42  3.000
 7MD  C1'   N9   C4    126.16  3.000
 7MD  C8    N9   C4    106.33  3.000
 7MD  HA    CA   CB    109.39  3.000
 7MD  HA    CA   N     113.42  3.000
 7MD  CB    CA   N     110.45  3.000
 7MD  HA    CA   C     107.82  3.000
 7MD  CB    CA   C     109.68  3.000
 7MD  N     CA   C     105.94  3.000
 7MD  HBA   CB   HB    106.95  3.000
 7MD  HBA   CB   CG    106.46  3.000
 7MD  HB    CB   CG    107.95  3.000
 7MD  HBA   CB   CA    109.39  3.000
 7MD  HB    CB   CA    110.38  3.000
 7MD  CG    CB   CA    115.34  3.000
 7MD  OD2   CG   OD1   123.10  3.000
 7MD  OD1   CG   CB    113.00  3.000
 7MD  OD2   CG   CB    123.87  3.000
 7MD  H1'   C1'  O4'   111.99  3.000
 7MD  H1'   C1'  C2'   110.00  3.000
 7MD  O4'   C1'  C2'   106.24  3.000
 7MD  H1'   C1'  N9    106.56  3.000
 7MD  O4'   C1'  N9    108.54  3.000
 7MD  C2'   C1'  N9    113.59  3.000
 7MD  H2'   C2'  C3'   108.30  3.000
 7MD  H2'   C2'  O2'   111.49  3.000
 7MD  C3'   C2'  O2'   116.43  3.000
 7MD  H2'   C2'  C1'   108.80  3.000
 7MD  C3'   C2'  C1'   101.54  3.000
 7MD  O2'   C2'  C1'   109.66  3.000
 7MD  HO2'  O2'  C2'   108.64  3.000
 7MD  H3'   C3'  C4'   111.42  3.000
 7MD  H3'   C3'  O3'   111.53  3.000
 7MD  C4'   C3'  O3'   111.88  3.000
 7MD  H3'   C3'  C2'   112.09  3.000
 7MD  O3'   C3'  C2'   107.76  3.000
 7MD  C4'   C3'  C2'   101.71  3.000
 7MD  HO3'  O3'  C3'   108.30  3.000
 7MD  C32   O31  P     124.24  3.000
 7MD  H32A  C32  H32   107.93  3.000
 7MD  H32A  C32  C33   110.05  3.000
 7MD  H32   C32  C33   111.07  3.000
 7MD  H32A  C32  O31   110.09  3.000
 7MD  H32   C32  O31   109.72  3.000
 7MD  C33   C32  O31   107.99  3.000
 7MD  H33A  C33  H33   107.38  3.000
 7MD  H33A  C33  C34   110.13  3.000
 7MD  H33   C33  C34   108.15  3.000
 7MD  H33A  C33  C32   109.74  3.000
 7MD  H33   C33  C32   109.64  3.000
 7MD  C34   C33  C32   111.70  3.000
 7MD  H34A  C34  H34   106.13  3.000
 7MD  H34A  C34  N35   113.91  3.000
 7MD  H34   C34  N35   108.39  3.000
 7MD  H34A  C34  C33   108.09  3.000
 7MD  H34   C34  C33   108.73  3.000
 7MD  N35   C34  C33   111.35  3.000
 7MD  HN3A  N35  HN35  105.67  3.000
 7MD  HN3A  N35  C34   109.38  3.000
 7MD  HN35  N35  C34   109.49  3.000
 7MD  H4'   C4'  C5'   105.60  3.000
 7MD  H4'   C4'  O4'   108.62  3.000
 7MD  C5'   C4'  O4'   110.87  3.000
 7MD  H4'   C4'  C3'   109.95  3.000
 7MD  O4'   C4'  C3'   106.19  3.000
 7MD  C5'   C4'  C3'   115.49  3.000
 7MD  C4'   O4'  C1'   111.14  3.000
 7MD  H5'A  C5'  H5'   108.24  3.000
 7MD  H5'A  C5'  O5'   110.48  3.000
 7MD  H5'   C5'  O5'   110.11  3.000
 7MD  H5'A  C5'  C4'   108.48  3.000
 7MD  H5'   C5'  C4'   110.11  3.000
 7MD  O5'   C5'  C4'   109.40  3.000
 7MD  C5'   O5'  P     122.37  3.000
 7MD  HOD1  OD1  CG    110.07  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
 7MD  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 7MD  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 7MD  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 7MD  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 7MD  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 7MD  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 7MD  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 7MD  CONST_08  N7    C5   C4   N3    180.00   0.0  0
 7MD  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 7MD  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 7MD  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 7MD  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 7MD  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 7MD  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 7MD  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 7MD  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 7MD  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 7MD  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 7MD  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 7MD  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 7MD  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 7MD  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 7MD  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 7MD  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 7MD  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 7MD  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 7MD  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 7MD  CONST_28  P     N8   C    O       0.00   0.0  0
 7MD  CONST_29  CA    C    N8   P     180.00   0.0  0
 7MD  CONST_30  HN8   N8   C    O     180.00   0.0  0
 7MD  CONST_31  HOD1  OD1  CG   CB    180.00   0.0  0
 7MD  Var_01    C4'   C5'  O5'  P     179.14  30.0  3
 7MD  Var_02    O31   P    N8   C      62.27  30.0  3
 7MD  Var_03    C33   C32  O31  P     172.76  30.0  2
 7MD  Var_04    OD2   CG   CB   CA    146.91  30.0  2
 7MD  Var_05    C34   C33  C32  O31  -175.79  30.0  1
 7MD  Var_06    N35   C34  C33  C32   -57.80  30.0  1
 7MD  Var_07    HN35  N35  C34  C33   178.69  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
 7MD  chir_02  CA   C    N    CB   negativ
 7MD  chir_03  C1'  N9   C2'  O4'  negativ
 7MD  chir_04  C2'  O2'  C3'  C1'  positiv
 7MD  chir_05  C3'  O3'  C4'  C2'  positiv
 7MD  chir_06  C4'  O4'  C3'  C5'  negativ
 7MD  chir_07  P    N8   O5'  O1P  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
 7MD  plan-1  N1    0.020
 7MD  plan-1  C2    0.020
 7MD  plan-1  N3    0.020
 7MD  plan-1  C4    0.020
 7MD  plan-1  C5    0.020
 7MD  plan-1  C6    0.020
 7MD  plan-1  N6    0.020
 7MD  plan-1  N7    0.020
 7MD  plan-1  C8    0.020
 7MD  plan-1  N9    0.020
 7MD  plan-1  C1'   0.020
 7MD  plan-1  H8    0.020
 7MD  plan-1  H2    0.020
 7MD  plan-2  C6    0.020
 7MD  plan-2  N6    0.020
 7MD  plan-2  HN6   0.020
 7MD  plan-2  HN6A  0.020
 7MD  plan-3  C     0.020
 7MD  plan-3  O     0.020
 7MD  plan-3  P     0.020
 7MD  plan-3  N8    0.020
 7MD  plan-3  CA    0.020
 7MD  plan-3  HN8   0.020
 7MD  plan-4  CB    0.020
 7MD  plan-4  CG    0.020
 7MD  plan-4  OD1   0.020
 7MD  plan-4  OD2   0.020
 7MD  plan-4  HOD1  0.020

