# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 15:07:13 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: 5'-O-[(R)-{[(2S)-2,6-diaminohexanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)C(=O)O[P@@](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
 LAD  LAD  5'-O-[(R)-{[(2S)-2,6-diaminohexanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  58  32  .  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_LAD
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
 LAD  N     N  NH2   0  -0.800  21.0000  66.1702  32.7632
 LAD  CA    C  CH1   0  -0.220  20.5651  66.1729  34.1420
 LAD  CB    C  CH2   0  -0.438  19.8546  64.8522  34.4900
 LAD  CG    C  CH2   0  -0.465  18.6234  64.5686  33.6341
 LAD  CD    C  CH2   0  -0.429  17.5536  65.6534  33.7092
 LAD  CE    C  CH2   0  -0.289  16.2374  65.2417  33.0642
 LAD  NZ    N  NH2   0  -0.804  16.3831  65.0326  31.6301
 LAD  C     C  C     0   0.595  21.7728  66.3035  35.0378
 LAD  O     O  O     0  -0.386  22.9175  66.2058  34.7149
 LAD  PA    P  P     0   1.498  22.3752  66.4879  37.6300
 LAD  O5'   O  O2    0  -0.589  23.1226  65.0915  37.5232
 LAD  C5'   C  CH2   0  -0.234  22.4162  63.8535  37.6754
 LAD  C4'   C  CH1   0   0.036  22.9104  63.0820  38.8719
 LAD  O4'   O  O2    0  -0.496  24.2912  62.7708  38.7350
 LAD  C1'   C  CH1   0   0.180  24.9213  62.7545  39.9836
 LAD  N9    N  NR5   0  -0.536  25.9439  63.7903  40.0146
 LAD  C4    C  CR56  0   0.486  26.9603  63.8440  40.9222
 LAD  N3    N  N     0  -0.459  27.2209  62.9925  41.9128
 LAD  C2    C  CR16  0   0.040  28.2924  63.3556  42.5966
 LAD  N1    N  N     0  -0.474  29.0735  64.4160  42.4064
 LAD  C6    C  CR6   0   0.457  28.7953  65.2631  41.4087
 LAD  N6    N  NH2   0  -0.816  29.5788  66.3245  41.2160
 LAD  C5    C  CR56  0  -0.002  27.6780  64.9842  40.5998
 LAD  N7    N  N     0  -0.453  27.1224  65.6176  39.5200
 LAD  C8    C  CR15  0   0.096  26.0971  64.8807  39.2023
 LAD  C2'   C  CH1   0  -0.048  23.8379  62.9936  41.0375
 LAD  O2'   O  OH1   0  -0.663  23.3348  61.7433  41.4194
 LAD  C3'   C  CH1   0  -0.034  22.8051  63.7809  40.2236
 LAD  O3'   O  OH1   0  -0.656  21.4997  63.6882  40.7124
 LAD  O1A   O  O     0  -0.668  21.5522  66.7369  38.8225
 LAD  O2A   O  OH1   0  -0.713  23.5990  67.4441  37.3404
 LAD  O3A   O  O2    0  -0.589  21.3896  66.5337  36.3247
 LAD  H2A   H  HNH2  0   0.356  21.4029  67.0670  32.5214
 LAD  H1    H  HNH2  0   0.360  20.1940  66.0674  32.1603
 LAD  HA    H  HCH1  0   0.264  19.8869  67.0027  34.3921
 LAD  HB2   H  HCH2  0   0.244  20.5664  64.0289  34.3803
 LAD  HB1   H  HCH2  0   0.242  19.5494  64.8784  35.5380
 LAD  HG2   H  HCH2  0   0.225  18.9226  64.3915  32.5968
 LAD  HG1   H  HCH2  0   0.242  18.1978  63.6219  33.9810
 LAD  HD2   H  HCH2  0   0.222  17.3607  65.8949  34.7589
 LAD  HD1   H  HCH2  0   0.219  17.9046  66.5759  33.2360
 LAD  HE2   H  HCH2  0   0.189  15.8480  64.3627  33.5996
 LAD  HE1   H  HCH2  0   0.223  15.5075  66.0404  33.2157
 LAD  HZ2   H  HNH2  0   0.347  15.4809  64.8082  31.2303
 LAD  HZ1   H  HNH2  0   0.343  16.9600  64.2181  31.4607
 LAD  H5'2  H  HCH2  0   0.262  21.3404  64.0031  37.7964
 LAD  H5'1  H  HCH2  0   0.283  22.5703  63.2792  36.7610
 LAD  H4'   H  HCH1  0   0.258  22.3166  62.1587  38.8966
 LAD  H1'   H  HCH1  0   0.283  25.4281  61.7999  40.1487
 LAD  H2    H  HCR6  0   0.252  28.5759  62.7103  43.4214
 LAD  H62   H  HNH2  0   0.411  29.3695  67.0020  40.5042
 LAD  H61   H  HNH2  0   0.403  30.3470  66.5075  41.8382
 LAD  H8    H  HCR5  0   0.296  25.4284  65.0787  38.3813
 LAD  H2'   H  HCH1  0   0.263  24.2209  63.5595  41.8949
 LAD  H2O1  H  HOH1  0   0.454  22.4355  61.8737  41.7445
 LAD  H3'   H  HCH1  0   0.249  23.1357  64.8225  40.1423
 LAD  H3O1  H  HOH1  0   0.469  21.3480  64.4021  41.3391
 LAD  H2AO  H  HOH1  0   0.512  23.4976  68.3374  37.6988

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
 LAD  N    CA    single    1.446  0.020  1.446
 LAD  N    H2A   single    0.890  0.020  1.040
 LAD  N    H1    single    0.890  0.020  1.040
 LAD  CA   CB    single    1.540  0.020  1.540
 LAD  CA   C     single    1.509  0.020  1.509
 LAD  CA   HA    single    0.970  0.020  1.090
 LAD  CB   CG    single    1.526  0.020  1.526
 LAD  CB   HB2   single    0.970  0.020  1.090
 LAD  CB   HB1   single    0.970  0.020  1.090
 LAD  CG   CD    single    1.525  0.020  1.525
 LAD  CG   HG2   single    0.970  0.020  1.090
 LAD  CG   HG1   single    0.970  0.020  1.090
 LAD  CD   CE    single    1.522  0.020  1.522
 LAD  CD   HD2   single    0.970  0.020  1.090
 LAD  CD   HD1   single    0.970  0.020  1.090
 LAD  CE   NZ    single    1.457  0.020  1.457
 LAD  CE   HE2   single    0.970  0.020  1.090
 LAD  CE   HE1   single    0.970  0.020  1.090
 LAD  NZ   HZ2   single    0.890  0.020  1.040
 LAD  NZ   HZ1   single    0.890  0.020  1.040
 LAD  C    O     double    1.193  0.020  1.193
 LAD  C    O3A   single    1.362  0.020  1.362
 LAD  PA   O5'   single    1.587  0.020  1.587
 LAD  PA   O1A   double    1.470  0.020  1.470
 LAD  PA   O2A   single    1.580  0.020  1.580
 LAD  PA   O3A   single    1.636  0.020  1.636
 LAD  O5'  C5'   single    1.433  0.020  1.433
 LAD  C5'  C4'   single    1.507  0.020  1.507
 LAD  C5'  H5'2  single    0.970  0.020  1.090
 LAD  C5'  H5'1  single    0.970  0.020  1.090
 LAD  C4'  O4'   single    1.422  0.020  1.422
 LAD  C4'  C3'   single    1.525  0.020  1.525
 LAD  C4'  H4'   single    0.970  0.020  1.090
 LAD  O4'  C1'   single    1.399  0.020  1.399
 LAD  C1'  N9    single    1.456  0.020  1.456
 LAD  C1'  C2'   single    1.530  0.020  1.530
 LAD  C1'  H1'   single    0.970  0.020  1.090
 LAD  N9   C4    aromatic  1.364  0.020  1.364
 LAD  N9   C8    aromatic  1.368  0.020  1.368
 LAD  C4   N3    aromatic  1.332  0.020  1.332
 LAD  C4   C5    aromatic  1.385  0.020  1.385
 LAD  N3   C2    aromatic  1.322  0.020  1.322
 LAD  C2   N1    aromatic  1.331  0.020  1.331
 LAD  C2   H2    single    0.930  0.020  1.080
 LAD  N1   C6    aromatic  1.338  0.020  1.338
 LAD  C6   N6    single    1.333  0.020  1.333
 LAD  C6   C5    aromatic  1.407  0.020  1.407
 LAD  N6   H62   single    0.860  0.020  1.020
 LAD  N6   H61   single    0.860  0.020  1.020
 LAD  C5   N7    aromatic  1.370  0.020  1.370
 LAD  N7   C8    aromatic  1.302  0.020  1.302
 LAD  C8   H8    single    0.930  0.020  1.080
 LAD  C2'  O2'   single    1.401  0.020  1.401
 LAD  C2'  C3'   single    1.533  0.020  1.533
 LAD  C2'  H2'   single    0.970  0.020  1.090
 LAD  O2'  H2O1  single    0.850  0.020  0.980
 LAD  C3'  O3'   single    1.397  0.020  1.397
 LAD  C3'  H3'   single    0.970  0.020  1.090
 LAD  O3'  H3O1  single    0.850  0.020  0.980
 LAD  O2A  H2AO  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
 LAD  H1    N    H2A   105.35  3.000
 LAD  H1    N    CA    109.20  3.000
 LAD  H2A   N    CA    110.23  3.000
 LAD  HA    CA   C     107.04  3.000
 LAD  HA    CA   CB    108.13  3.000
 LAD  C     CA   CB    108.02  3.000
 LAD  HA    CA   N     113.79  3.000
 LAD  C     CA   N     109.00  3.000
 LAD  CB    CA   N     110.66  3.000
 LAD  HB1   CB   HB2   107.23  3.000
 LAD  HB1   CB   CG    108.50  3.000
 LAD  HB2   CB   CG    109.20  3.000
 LAD  HB1   CB   CA    108.98  3.000
 LAD  HB2   CB   CA    108.82  3.000
 LAD  CG    CB   CA    113.89  3.000
 LAD  HG1   CG   HG2   105.48  3.000
 LAD  HG1   CG   CD    109.08  3.000
 LAD  HG2   CG   CD    110.71  3.000
 LAD  HG1   CG   CB    107.26  3.000
 LAD  HG2   CG   CB    109.95  3.000
 LAD  CD    CG   CB    113.96  3.000
 LAD  HD1   CD   HD2   106.57  3.000
 LAD  HD1   CD   CE    108.78  3.000
 LAD  HD2   CD   CE    108.28  3.000
 LAD  HD1   CD   CG    110.69  3.000
 LAD  HD2   CD   CG    109.13  3.000
 LAD  CE    CD   CG    113.15  3.000
 LAD  HE1   CE   HE2   106.27  3.000
 LAD  HE1   CE   NZ    107.96  3.000
 LAD  HE2   CE   NZ    113.56  3.000
 LAD  HE1   CE   CD    108.73  3.000
 LAD  HE2   CE   CD    108.41  3.000
 LAD  NZ    CE   CD    111.68  3.000
 LAD  HZ1   NZ   HZ2   105.27  3.000
 LAD  HZ1   NZ   CE    109.72  3.000
 LAD  HZ2   NZ   CE    109.37  3.000
 LAD  O3A   C    O     122.64  3.000
 LAD  O3A   C    CA    110.50  3.000
 LAD  O     C    CA    126.86  3.000
 LAD  O3A   PA   O2A   107.66  3.000
 LAD  O3A   PA   O1A   107.76  3.000
 LAD  O2A   PA   O1A   118.67  3.000
 LAD  O3A   PA   O5'   104.75  3.000
 LAD  O2A   PA   O5'    98.94  3.000
 LAD  O1A   PA   O5'   117.85  3.000
 LAD  C5'   O5'  PA    121.37  3.000
 LAD  H5'1  C5'  H5'2  107.69  3.000
 LAD  H5'1  C5'  C4'   110.47  3.000
 LAD  H5'2  C5'  C4'   107.76  3.000
 LAD  H5'1  C5'  O5'   107.23  3.000
 LAD  H5'2  C5'  O5'   112.25  3.000
 LAD  C4'   C5'  O5'   111.40  3.000
 LAD  H4'   C4'  C3'   109.15  3.000
 LAD  H4'   C4'  O4'   110.07  3.000
 LAD  C3'   C4'  O4'   104.64  3.000
 LAD  H4'   C4'  C5'   105.72  3.000
 LAD  C3'   C4'  C5'   116.51  3.000
 LAD  O4'   C4'  C5'   110.73  3.000
 LAD  C1'   O4'  C4'   110.73  3.000
 LAD  H1'   C1'  C2'   111.14  3.000
 LAD  H1'   C1'  N9    107.00  3.000
 LAD  C2'   C1'  N9    111.81  3.000
 LAD  H1'   C1'  O4'   110.72  3.000
 LAD  C2'   C1'  O4'   107.10  3.000
 LAD  N9    C1'  O4'   109.09  3.000
 LAD  C8    N9   C4    106.27  3.000
 LAD  C8    N9   C1'   129.27  3.000
 LAD  C4    N9   C1'   124.45  3.000
 LAD  C5    C4   N3    126.72  3.000
 LAD  C5    C4   N9    105.29  3.000
 LAD  N3    C4   N9    127.99  3.000
 LAD  C2    N3   C4    111.57  3.000
 LAD  H2    C2   N1    115.43  3.000
 LAD  H2    C2   N3    116.21  3.000
 LAD  N1    C2   N3    128.37  3.000
 LAD  C6    N1   C2    119.27  3.000
 LAD  C5    C6   N6    122.77  3.000
 LAD  C5    C6   N1    117.92  3.000
 LAD  N6    C6   N1    119.31  3.000
 LAD  H61   N6   H62   118.35  3.000
 LAD  H61   N6   C6    120.30  3.000
 LAD  H62   N6   C6    121.12  3.000
 LAD  N7    C5   C6    133.13  3.000
 LAD  N7    C5   C4    110.73  3.000
 LAD  C6    C5   C4    116.15  3.000
 LAD  C8    N7   C5    104.49  3.000
 LAD  H8    C8   N7    124.81  3.000
 LAD  H8    C8   N9    121.96  3.000
 LAD  N7    C8   N9    113.23  3.000
 LAD  H2'   C2'  C3'   112.67  3.000
 LAD  H2'   C2'  O2'   111.90  3.000
 LAD  C3'   C2'  O2'   111.18  3.000
 LAD  H2'   C2'  C1'   111.84  3.000
 LAD  C3'   C2'  C1'   101.05  3.000
 LAD  O2'   C2'  C1'   107.61  3.000
 LAD  H2O1  O2'  C2'   107.81  3.000
 LAD  H3'   C3'  O3'   111.78  3.000
 LAD  H3'   C3'  C2'   108.93  3.000
 LAD  O3'   C3'  C2'   114.19  3.000
 LAD  H3'   C3'  C4'   110.42  3.000
 LAD  O3'   C3'  C4'   110.13  3.000
 LAD  C2'   C3'  C4'   100.87  3.000
 LAD  H3O1  O3'  C3'   109.03  3.000
 LAD  H2AO  O2A  PA    114.18  3.000
 LAD  PA    O3A  C     125.41  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
 LAD  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 LAD  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 LAD  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 LAD  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 LAD  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 LAD  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 LAD  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 LAD  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 LAD  CONST_09  C8   N9   C4   N3    180.00   0.0  0
 LAD  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 LAD  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 LAD  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 LAD  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 LAD  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 LAD  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 LAD  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 LAD  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 LAD  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 LAD  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 LAD  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 LAD  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 LAD  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 LAD  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 LAD  CONST_24  H8   C8   N9   C1'     0.00   0.0  0
 LAD  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 LAD  CONST_26  H62  N6   C6   N1    180.00   0.0  0
 LAD  CONST_27  H61  N6   C6   N1      0.00   0.0  0
 LAD  Var_01    C4'  C5'  O5'  PA   -117.04  30.0  3
 LAD  Var_02    CD   CG   CB   CA    -58.25  30.0  3
 LAD  Var_03    CE   CD   CG   CB   -169.32  30.0  3
 LAD  Var_04    NZ   CE   CD   CG    -64.64  30.0  3
 LAD  Var_05    O5'  PA   O3A  C     -51.37  30.0  2
 LAD  Var_06    HZ2  NZ   CE   CD   -177.08  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
 LAD  chir_01  CA   N    CB   C    negativ
 LAD  chir_03  C4'  C5'  O4'  C3'  negativ
 LAD  chir_04  C1'  O4'  N9   C2'  negativ
 LAD  chir_05  C2'  O2'  C1'  C3'  negativ
 LAD  chir_06  C3'  O3'  C4'  C2'  positiv
 LAD  chir_07  PA   O1A  O2A  O3A  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
 LAD  plan-1  C1'  0.020
 LAD  plan-1  N9   0.020
 LAD  plan-1  C4   0.020
 LAD  plan-1  N3   0.020
 LAD  plan-1  C2   0.020
 LAD  plan-1  N1   0.020
 LAD  plan-1  C6   0.020
 LAD  plan-1  N6   0.020
 LAD  plan-1  C5   0.020
 LAD  plan-1  N7   0.020
 LAD  plan-1  C8   0.020
 LAD  plan-1  H2   0.020
 LAD  plan-1  H8   0.020
 LAD  plan-2  C6   0.020
 LAD  plan-2  N6   0.020
 LAD  plan-2  H62  0.020
 LAD  plan-2  H61  0.020
 LAD  plan-3  CA   0.020
 LAD  plan-3  C    0.020
 LAD  plan-3  O    0.020
 LAD  plan-3  O3A  0.020

