# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 12 07:53:38 2020
#   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  61  35  .  2021-08-05  2021-08-05  
;
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   0.544  -1.5657   0.6334  -0.0218
 7MD  N     N  NH2    0  -0.796  -0.7711   2.8597  -0.7982
 7MD  O     O  O      0  -0.430  -1.1006   0.0435  -0.9709
 7MD  P     P  P      0   1.465  -2.3963  -1.6886   1.1636
 7MD  N1    N  N      0  -0.473   4.8995   1.6922  -2.4821
 7MD  C2    C  CR16   0   0.048   5.2291   0.4277  -2.2347
 7MD  N3    N  N      0  -0.457   4.6745  -0.4139  -1.3790
 7MD  C4    C  CR56   0   0.489   3.6650   0.1485  -0.7215
 7MD  C5    C  CR56   0   0.015   3.2073   1.4472  -0.8692
 7MD  C6    C  CR6    0   0.468   3.8819   2.2444  -1.8120
 7MD  N6    N  NH2    0  -0.816   3.5431   3.5092  -2.0622
 7MD  N7    N  N      0  -0.472   2.1418   1.6825  -0.0370
 7MD  C8    C  CR15   0   0.140   1.9645   0.5595   0.5902
 7MD  N8    N  NH1    0  -0.841  -2.0743  -0.0352   1.0724
 7MD  N9    N  NR5    0  -0.541   2.8589  -0.4103   0.2314
 7MD  CA    C  CH1    0  -0.232  -1.6944   2.1511   0.0525
 7MD  CB    C  CH2    0  -0.569  -3.1332   2.5240  -0.3132
 7MD  CG    C  C      0   0.423  -3.4436   4.0110  -0.0427
 7MD  C1'   C  CR15   0   0.205   2.8884  -1.7782   0.6810
 7MD  O1P   O  O      0  -0.696  -3.0943  -1.9757   2.4330
 7MD  C2'   C  CR15   0  -0.059   2.9986  -1.9274   2.1998
 7MD  O2'   O  OH1    0  -0.652   4.3399  -1.8920   2.5808
 7MD  C3'   C  CR15   0  -0.025   2.3004  -3.2723   2.4194
 7MD  O3'   O  OH1    0  -0.666   3.1424  -4.3375   2.0689
 7MD  O31   O  O2     0  -0.576  -3.1132  -2.0918  -0.1911
 7MD  C32   C  CH2    0  -0.176  -4.4084  -1.5540  -0.5151
 7MD  C33   C  CH2    0  -0.469  -4.4543  -1.2373  -1.9933
 7MD  C34   C  CH2    0  -0.278  -5.8370  -0.7621  -2.4150
 7MD  N35   N  NH2    0  -0.797  -5.8492  -0.4276  -3.8303
 7MD  C4'   C  CR15   0  -0.054   1.1788  -3.1895   1.3919
 7MD  O4'   O  O      0  -0.479   1.6979  -2.4180   0.3109
 7MD  C5'   C  CH2    0  -0.172  -0.0695  -2.5476   1.9601
 7MD  O5'   O  O2     0  -0.572  -1.0308  -2.4673   0.9088
 7MD  OD1   O  OC    -1  -0.613  -4.0987   4.6144  -0.9133
 7MD  OD2   O  O      0  -0.611  -3.0460   4.4693   1.0456
 7MD  HN    H  HNH2   0   0.364   0.1858   2.6312  -0.5482
 7MD  HNA   H  HNH2   0   0.334  -0.8934   2.5629  -1.7592
 7MD  HN6   H  HNH2   0   0.405   4.0550   4.0478  -2.7393
 7MD  HN6A  H  HNH2   0   0.410   2.8040   3.9619  -1.5545
 7MD  HN8   H  HNH1   0   0.430  -2.3987   0.5226   1.8518
 7MD  HA    H  HCH1   0   0.253  -1.5238   2.4642   1.0871
 7MD  HB    H  HCH2   0   0.220  -3.3155   2.2733  -1.3627
 7MD  HBA   H  HCH2   0   0.239  -3.8387   1.9247   0.2740
 7MD  H1'   H  HCR5   0   0.268   3.7536  -2.2376   0.1919
 7MD  H2'   H  HCR5   0   0.255   2.4195  -1.1403   2.6996
 7MD  HO2'  H  HOH1   0   0.472   4.3922  -1.6970   3.5221
 7MD  H3'   H  HCR5   0   0.258   1.9175  -3.3737   3.4435
 7MD  HO3'  H  HOH1   0   0.451   4.0099  -4.1714   2.4566
 7MD  H32   H  HCH2   0   0.250  -5.1600  -2.2986  -0.2465
 7MD  H32A  H  HCH2   0   0.229  -4.6166  -0.6521   0.0703
 7MD  H33   H  HCH2   0   0.234  -3.7177  -0.4668  -2.2314
 7MD  H33A  H  HCH2   0   0.237  -4.1837  -2.1314  -2.5630
 7MD  H34   H  HCH2   0   0.196  -6.5790  -1.5244  -2.1364
 7MD  H34A  H  HCH2   0   0.219  -6.0970   0.1377  -1.8505
 7MD  HN35  H  HNH2   0   0.339  -5.7245  -1.2720  -4.3755
 7MD  HN3A  H  HNH2   0   0.348  -6.7632  -0.0747  -4.0831
 7MD  H4'   H  HCR5   0   0.277   0.9221  -4.1849   1.0173
 7MD  H5'   H  HCH2   0   0.263  -0.4501  -3.1633   2.7786
 7MD  H5'A  H  HCH2   0   0.233   0.1439  -1.5516   2.3630
 7MD  H2    H  HCR6   0   0.254   6.0617   0.0410  -2.8125
 7MD  H8    H  HCR5   0   0.286   1.1951   0.3830   1.3266

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    1.525  0.020  1.525
 7MD  O    C     double    1.210  0.020  1.210
 7MD  C    N8    single    1.380  0.020  1.380
 7MD  N    CA    single    1.442  0.020  1.442
 7MD  N    HN    single    0.890  0.020  1.040
 7MD  N    HNA   single    0.890  0.020  1.040
 7MD  O31  P     single    1.585  0.020  1.585
 7MD  N8   P     single    1.687  0.020  1.687
 7MD  P    O5'   single    1.592  0.020  1.592
 7MD  P    O1P   double    1.477  0.020  1.477
 7MD  C6   N1    aromatic  1.338  0.020  1.338
 7MD  N1   C2    aromatic  1.330  0.020  1.330
 7MD  C2   N3    aromatic  1.322  0.020  1.322
 7MD  C2   H2    single    0.930  0.020  1.080
 7MD  C4   N3    aromatic  1.330  0.020  1.330
 7MD  C5   C4    aromatic  1.385  0.020  1.385
 7MD  N9   C4    aromatic  1.367  0.020  1.367
 7MD  N7   C5    aromatic  1.372  0.020  1.372
 7MD  C6   C5    aromatic  1.407  0.020  1.407
 7MD  N6   C6    single    1.333  0.020  1.333
 7MD  N6   HN6   single    0.860  0.020  1.020
 7MD  N6   HN6A  single    0.860  0.020  1.020
 7MD  N7   C8    aromatic  1.298  0.020  1.298
 7MD  C8   N9    aromatic  1.367  0.020  1.367
 7MD  C8   H8    single    0.930  0.020  1.080
 7MD  N8   HN8   single    0.860  0.020  1.020
 7MD  N9   C1'   single    1.440  0.020  1.440
 7MD  CB   CA    single    1.531  0.020  1.531
 7MD  CA   HA    single    0.970  0.020  1.090
 7MD  CG   CB    single    1.543  0.020  1.543
 7MD  CB   HB    single    0.970  0.020  1.090
 7MD  CB   HBA   single    0.970  0.020  1.090
 7MD  OD2  CG    deloc     1.246  0.020  1.246
 7MD  CG   OD1   deloc     1.246  0.020  1.246
 7MD  C2'  C1'   single    1.530  0.020  1.530
 7MD  C1'  O4'   single    1.401  0.020  1.401
 7MD  C1'  H1'   single    0.970  0.020  1.090
 7MD  C2'  O2'   single    1.395  0.020  1.395
 7MD  C2'  C3'   single    1.531  0.020  1.531
 7MD  C2'  H2'   single    0.970  0.020  1.090
 7MD  O2'  HO2'  single    0.850  0.020  0.980
 7MD  C3'  C4'   single    1.523  0.020  1.523
 7MD  C3'  O3'   single    1.402  0.020  1.402
 7MD  C3'  H3'   single    0.970  0.020  1.090
 7MD  O3'  HO3'  single    0.850  0.020  0.980
 7MD  C32  O31   single    1.439  0.020  1.439
 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    1.522  0.020  1.522
 7MD  C33  H33   single    0.970  0.020  1.090
 7MD  C33  H33A  single    0.970  0.020  1.090
 7MD  N35  C34   single    1.454  0.020  1.454
 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    1.514  0.020  1.514
 7MD  O4'  C4'   single    1.426  0.020  1.426
 7MD  C4'  H4'   single    0.970  0.020  1.090
 7MD  O5'  C5'   single    1.427  0.020  1.427
 7MD  C5'  H5'   single    0.970  0.020  1.090
 7MD  C5'  H5'A  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
 7MD  CA    C    N8    114.37  3.000
 7MD  N8    C    O     121.83  3.000
 7MD  CA    C    O     123.76  3.000
 7MD  HNA   N    HN    106.34  3.000
 7MD  HNA   N    CA    109.78  3.000
 7MD  HN    N    CA    110.35  3.000
 7MD  O5'   P    O31    97.28  3.000
 7MD  O5'   P    O1P   116.60  3.000
 7MD  O31   P    O1P   118.13  3.000
 7MD  O1P   P    N8    109.10  3.000
 7MD  O5'   P    N8    107.88  3.000
 7MD  O31   P    N8    106.83  3.000
 7MD  C6    N1   C2    119.20  3.000
 7MD  H2    C2   N3    116.09  3.000
 7MD  H2    C2   N1    115.48  3.000
 7MD  N3    C2   N1    128.43  3.000
 7MD  C4    N3   C2    111.67  3.000
 7MD  N9    C4   C5    105.23  3.000
 7MD  N9    C4   N3    128.27  3.000
 7MD  C5    C4   N3    126.50  3.000
 7MD  N7    C5   C6    132.96  3.000
 7MD  C6    C5   C4    116.39  3.000
 7MD  N7    C5   C4    110.65  3.000
 7MD  N6    C6   C5    122.79  3.000
 7MD  N6    C6   N1    119.40  3.000
 7MD  C5    C6   N1    117.81  3.000
 7MD  HN6A  N6   HN6   118.27  3.000
 7MD  HN6A  N6   C6    121.31  3.000
 7MD  HN6   N6   C6    120.36  3.000
 7MD  C8    N7   C5    104.52  3.000
 7MD  H8    C8   N9    121.95  3.000
 7MD  H8    C8   N7    124.63  3.000
 7MD  N9    C8   N7    113.42  3.000
 7MD  HN8   N8   P     115.94  3.000
 7MD  HN8   N8   C     117.52  3.000
 7MD  P     N8   C     126.03  3.000
 7MD  C1'   N9   C8    127.25  3.000
 7MD  C1'   N9   C4    126.41  3.000
 7MD  C8    N9   C4    106.18  3.000
 7MD  HA    CA   CB    107.62  3.000
 7MD  HA    CA   N     108.51  3.000
 7MD  CB    CA   N     109.96  3.000
 7MD  HA    CA   C     108.52  3.000
 7MD  CB    CA   C     108.07  3.000
 7MD  N     CA   C     113.98  3.000
 7MD  HBA   CB   HB    106.33  3.000
 7MD  HBA   CB   CG    107.67  3.000
 7MD  HB    CB   CG    110.82  3.000
 7MD  HBA   CB   CA    110.11  3.000
 7MD  HB    CB   CA    109.26  3.000
 7MD  CG    CB   CA    112.46  3.000
 7MD  OD2   CG   OD1   126.88  3.000
 7MD  OD1   CG   CB    116.76  3.000
 7MD  OD2   CG   CB    116.32  3.000
 7MD  H1'   C1'  O4'   111.22  3.000
 7MD  H1'   C1'  C2'   110.22  3.000
 7MD  O4'   C1'  C2'   106.19  3.000
 7MD  H1'   C1'  N9    105.98  3.000
 7MD  O4'   C1'  N9    109.50  3.000
 7MD  C2'   C1'  N9    113.83  3.000
 7MD  H2'   C2'  C3'   108.91  3.000
 7MD  H2'   C2'  O2'   111.39  3.000
 7MD  C3'   C2'  O2'   114.94  3.000
 7MD  H2'   C2'  C1'   110.12  3.000
 7MD  C3'   C2'  C1'   101.26  3.000
 7MD  O2'   C2'  C1'   109.75  3.000
 7MD  HO2'  O2'  C2'   108.93  3.000
 7MD  H3'   C3'  C4'   112.17  3.000
 7MD  H3'   C3'  O3'   111.86  3.000
 7MD  C4'   C3'  O3'   108.35  3.000
 7MD  H3'   C3'  C2'   111.96  3.000
 7MD  O3'   C3'  C2'   110.95  3.000
 7MD  C4'   C3'  C2'   101.03  3.000
 7MD  HO3'  O3'  C3'   107.99  3.000
 7MD  C32   O31  P     120.29  3.000
 7MD  H32A  C32  H32   107.41  3.000
 7MD  H32A  C32  C33   110.13  3.000
 7MD  H32   C32  C33   111.25  3.000
 7MD  H32A  C32  O31   111.01  3.000
 7MD  H32   C32  O31   108.02  3.000
 7MD  C33   C32  O31   109.00  3.000
 7MD  H33A  C33  H33   107.23  3.000
 7MD  H33A  C33  C34   109.61  3.000
 7MD  H33   C33  C34   109.40  3.000
 7MD  H33A  C33  C32   109.28  3.000
 7MD  H33   C33  C32   109.90  3.000
 7MD  C34   C33  C32   111.34  3.000
 7MD  H34A  C34  H34   106.21  3.000
 7MD  H34A  C34  N35   108.12  3.000
 7MD  H34   C34  N35   113.60  3.000
 7MD  H34A  C34  C33   109.27  3.000
 7MD  H34   C34  C33   109.05  3.000
 7MD  N35   C34  C33   110.43  3.000
 7MD  HN3A  N35  HN35  105.52  3.000
 7MD  HN3A  N35  C34   109.32  3.000
 7MD  HN35  N35  C34   109.33  3.000
 7MD  H4'   C4'  C5'   108.71  3.000
 7MD  H4'   C4'  O4'   108.55  3.000
 7MD  C5'   C4'  O4'   110.81  3.000
 7MD  H4'   C4'  C3'   110.75  3.000
 7MD  O4'   C4'  C3'   105.82  3.000
 7MD  C5'   C4'  C3'   112.14  3.000
 7MD  C4'   O4'  C1'   110.86  3.000
 7MD  H5'A  C5'  H5'   107.74  3.000
 7MD  H5'A  C5'  O5'   110.55  3.000
 7MD  H5'   C5'  O5'   110.43  3.000
 7MD  H5'A  C5'  C4'   111.28  3.000
 7MD  H5'   C5'  C4'   109.23  3.000
 7MD  O5'   C5'  C4'   107.62  3.000
 7MD  C5'   O5'  P     119.16  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  Var_01    C4'   C5'  O5'  P    -173.35  30.0  3
 7MD  Var_02    O31   P    N8   C     -43.85  30.0  3
 7MD  Var_03    C33   C32  O31  P     140.69  30.0  1
 7MD  Var_04    OD2   CG   CB   CA    -44.74  30.0  2
 7MD  Var_05    C34   C33  C32  O31   175.73  30.0  1
 7MD  Var_06    N35   C34  C33  C32   178.41  30.0  1
 7MD  Var_07    HN35  N35  C34  C33    67.48  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
 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  H2    0.020
 7MD  plan-1  H8    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

