# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:58:39 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 5'-O-[(S)-{[(5S)-5-amino-6-oxohexyl]amino}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C=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
 APK  APK  5'-O-[(S)-{[(5S)-5-amino-6-oxohexyl]amino}(hydroxy)phosphoryl]adenosine  L-peptide  56  31  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_APK
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
 APK  O     O  O      0  -0.384   -5.0004  56.2321  133.8472
 APK  C     C  C1     0   0.174   -5.9369  56.9837  133.7264
 APK  CA    C  CH1    0  -0.206   -7.3869  56.5693  133.8485
 APK  N     N  NH2    0  -0.784   -7.5933  55.1700  134.1496
 APK  CB    C  CH2    0  -0.437   -8.0872  57.4737  134.8758
 APK  CG    C  CH2    0  -0.430   -8.3710  58.8842  134.3701
 APK  CD    C  CH2    0  -0.445   -9.0300  59.7559  135.4313
 APK  CE    C  CH2    0  -0.269   -9.4953  61.1144  134.9257
 APK  NZ    N  NH1    0  -0.793   -8.4029  61.9003  134.3784
 APK  P     P  P      0   1.341   -8.7448  63.3847  133.6204
 APK  O1P   O  O      0  -0.798   -7.4456  64.1076  133.4285
 APK  O2P   O  OP    -1  -0.791   -9.9448  64.0613  134.2111
 APK  O5'   O  O2     0  -0.640   -9.2896  62.8506  132.1387
 APK  C5'   C  CH2    0  -0.168   -8.3797  62.2325  131.2553
 APK  C4'   C  CH1    0  -0.000   -9.2311  61.4963  130.2404
 APK  O4'   O  O2     0  -0.499   -8.4058  60.7690  129.3313
 APK  C3'   C  CH1    0  -0.034  -10.1429  60.4412  130.8673
 APK  O3'   O  OH1    0  -0.665  -11.3759  60.9152  131.3223
 APK  C2'   C  CH1    0  -0.043  -10.3370  59.4771  129.7013
 APK  O2'   O  OH1    0  -0.661  -11.2341  59.9849  128.7522
 APK  C1'   C  CH1    0   0.185   -8.9435  59.5090  129.0693
 APK  N9    N  NR5    0  -0.539   -8.0680  58.4881  129.6424
 APK  C8    C  CR15   0   0.106   -6.9346  58.6587  130.3887
 APK  N7    N  N      0  -0.454   -6.3578  57.5375  130.7137
 APK  C5    C  CR5    0   0.007   -7.1476  56.5705  130.1521
 APK  C4    C  CR5    0   0.490   -8.2124  57.1416  129.4720
 APK  N3    N  N      0  -0.457   -9.1643  56.4926  128.8034
 APK  C2    C  C1     0   0.039   -8.9974  55.1830  128.8650
 APK  N1    N  N      0  -0.469   -8.0456  54.4995  129.4960
 APK  C6    C  C      0   0.459   -7.0985  55.1653  130.1642
 APK  N6    N  NH2    0  -0.821   -6.1659  54.4794  130.8334
 APK  HC    H  H      0   0.180   -5.7700  58.0580  133.5357
 APK  HA    H  HCH1   0   0.263   -7.8439  56.7789  132.8731
 APK  H     H  HNH2   0   0.339   -7.1309  54.9307  135.0191
 APK  H2    H  HNH2   0   0.345   -7.1569  54.5969  133.4374
 APK  HB2   H  HCH2   0   0.227   -7.4994  57.5145  135.8001
 APK  HB3   H  HCH2   0   0.241   -9.0317  56.9900  135.1361
 APK  HG2   H  HCH2   0   0.225   -9.0256  58.8200  133.4943
 APK  HG3   H  HCH2   0   0.221   -7.4540  59.3679  134.0268
 APK  HD2   H  HCH2   0   0.217   -8.3381  59.8940  136.2694
 APK  HD3   H  HCH2   0   0.221   -9.9001  59.2339  135.8414
 APK  HE2   H  HCH2   0   0.207  -10.0177  61.6311  135.7410
 APK  HE3   H  HCH2   0   0.213  -10.2381  60.9581  134.1383
 APK  HZ    H  HNH1   0   0.359   -7.6215  61.9643  135.0181
 APK  H5'1  H  HCH2   0   0.206   -7.7302  61.5199  131.7789
 APK  H5'2  H  HCH2   0   0.226   -7.7371  62.9696  130.7620
 APK  H4'   H  HCH1   0   0.239   -9.8354  62.2208  129.6798
 APK  H3'   H  HCH1   0   0.240   -9.5938  59.9195  131.6654
 APK  HO3'  H  HOH1   0   0.459  -11.2043  61.6875  131.8748
 APK  H2'   H  HCH1   0   0.261  -10.6181  58.4703  130.0306
 APK  HO2'  H  HOH1   0   0.453  -11.9695  60.3930  129.2241
 APK  H1'   H  HCH1   0   0.284   -8.9914  59.3301  127.9912
 APK  H8    H  HCR5   0   0.299   -6.5737  59.6361  130.6655
 APK  HC2   H  H      0   0.251   -9.7306  54.5822  128.3375
 APK  HN61  H  HNH2   0   0.402   -6.1137  53.4797  130.7334
 APK  HN62  H  HNH2   0   0.410   -5.3823  54.9510  131.2508

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
 APK  O    C     double    1.231  0.020  1.231
 APK  C    CA    single    1.525  0.021  1.525
 APK  C    HC    single    0.930  0.020  1.080
 APK  CA   N     single    1.458  0.019  1.458
 APK  CA   CB    single    1.530  0.020  1.530
 APK  CA   HA    single    0.970  0.020  0.970
 APK  N    H     single    0.860  0.020  0.860
 APK  N    H2    single    0.890  0.020  1.040
 APK  CB   CG    single    1.525  0.020  1.525
 APK  CB   HB2   single    0.970  0.020  1.090
 APK  CB   HB3   single    0.970  0.020  1.090
 APK  CG   CD    single    1.523  0.020  1.523
 APK  CG   HG2   single    0.970  0.020  1.090
 APK  CG   HG3   single    0.970  0.020  1.090
 APK  CD   CE    single    1.522  0.020  1.522
 APK  CD   HD2   single    0.970  0.020  1.090
 APK  CD   HD3   single    0.970  0.020  1.090
 APK  CE   NZ    single    1.453  0.020  1.453
 APK  CE   HE2   single    0.970  0.020  1.090
 APK  CE   HE3   single    0.970  0.020  1.090
 APK  NZ   P     single    1.702  0.020  1.702
 APK  NZ   HZ    single    0.890  0.020  1.040
 APK  P    O1P   deloc     1.499  0.020  1.499
 APK  P    O2P   deloc     1.499  0.020  1.499
 APK  P    O5'   single    1.667  0.020  1.667
 APK  O5'  C5'   single    1.411  0.020  1.411
 APK  C5'  C4'   single    1.516  0.020  1.516
 APK  C5'  H5'1  single    0.970  0.020  1.090
 APK  C5'  H5'2  single    0.970  0.020  1.090
 APK  C4'  O4'   single    1.427  0.020  1.427
 APK  C4'  C3'   single    1.529  0.020  1.529
 APK  C4'  H4'   single    0.970  0.020  1.090
 APK  O4'  C1'   single    1.395  0.020  1.395
 APK  C3'  O3'   single    1.397  0.020  1.397
 APK  C3'  C2'   single    1.525  0.020  1.525
 APK  C3'  H3'   single    0.970  0.020  1.090
 APK  O3'  HO3'  single    0.850  0.020  0.980
 APK  C2'  O2'   single    1.401  0.020  1.401
 APK  C2'  C1'   single    1.530  0.020  1.530
 APK  C2'  H2'   single    0.970  0.020  1.090
 APK  O2'  HO2'  single    0.850  0.020  0.980
 APK  C1'  N9    single    1.462  0.020  1.462
 APK  C1'  H1'   single    0.970  0.020  1.090
 APK  N9   C8    aromatic  1.368  0.020  1.368
 APK  N9   C4    aromatic  1.365  0.020  1.365
 APK  C8   N7    aromatic  1.302  0.020  1.302
 APK  C8   H8    single    0.930  0.020  1.080
 APK  N7   C5    aromatic  1.369  0.020  1.369
 APK  C5   C4    aromatic  1.387  0.020  1.387
 APK  C5   C6    aromatic  1.406  0.020  1.406
 APK  C4   N3    aromatic  1.332  0.020  1.332
 APK  N3   C2    aromatic  1.322  0.020  1.322
 APK  C2   N1    aromatic  1.331  0.020  1.331
 APK  C2   HC2   single    0.930  0.020  1.080
 APK  N1   C6    aromatic  1.337  0.020  1.337
 APK  C6   N6    single    1.337  0.020  1.337
 APK  N6   HN61  single    0.860  0.020  1.020
 APK  N6   HN62  single    0.860  0.020  1.020

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
 APK  HC    C    CA    115.18  3.000
 APK  HC    C    O     120.40  3.000
 APK  CA    C    O     120.80  1.700
 APK  HA    CA   CB    109.00  3.000
 APK  HA    CA   N     110.00  3.000
 APK  CB    CA   N     110.50  1.700
 APK  HA    CA   C     109.00  3.000
 APK  CB    CA   C     110.10  1.900
 APK  N     CA   C     111.00  2.800
 APK  H2    N    H     105.84  3.000
 APK  H2    N    CA    109.85  3.000
 APK  H     N    CA    114.00  3.000
 APK  HB3   CB   HB2   106.20  3.000
 APK  HB3   CB   CG    109.12  3.000
 APK  HB2   CB   CG    110.18  3.000
 APK  HB3   CB   CA    107.01  3.000
 APK  HB2   CB   CA    109.94  3.000
 APK  CG    CB   CA    114.04  3.000
 APK  HG3   CG   HG2   106.04  3.000
 APK  HG3   CG   CD    109.20  3.000
 APK  HG2   CG   CD    109.40  3.000
 APK  HG3   CG   CB    110.95  3.000
 APK  HG2   CG   CB    108.79  3.000
 APK  CD    CG   CB    112.26  3.000
 APK  HD3   CD   HD2   106.00  3.000
 APK  HD3   CD   CE    107.88  3.000
 APK  HD2   CD   CE    109.55  3.000
 APK  HD3   CD   CG    109.39  3.000
 APK  HD2   CD   CG    109.38  3.000
 APK  CE    CD   CG    114.30  3.000
 APK  HE3   CE   HE2   106.19  3.000
 APK  HE3   CE   NZ    108.47  3.000
 APK  HE2   CE   NZ    112.52  3.000
 APK  HE3   CE   CD    108.61  3.000
 APK  HE2   CE   CD    108.59  3.000
 APK  NZ    CE   CD    112.21  3.000
 APK  HZ    NZ   P     112.43  3.000
 APK  HZ    NZ   CE    112.14  3.000
 APK  P     NZ   CE    119.25  3.000
 APK  O5'   P    O2P   103.49  3.000
 APK  O5'   P    O1P   108.91  3.000
 APK  O2P   P    O1P   121.78  3.000
 APK  O5'   P    NZ    100.50  3.000
 APK  O2P   P    NZ    112.28  3.000
 APK  O1P   P    NZ    107.67  3.000
 APK  C5'   O5'  P     119.09  3.000
 APK  H5'2  C5'  H5'1  107.74  3.000
 APK  H5'2  C5'  C4'   110.78  3.000
 APK  H5'1  C5'  C4'   109.67  3.000
 APK  H5'2  C5'  O5'   111.44  3.000
 APK  H5'1  C5'  O5'   111.57  3.000
 APK  C4'   C5'  O5'   105.65  3.000
 APK  H4'   C4'  C3'   109.67  3.000
 APK  H4'   C4'  O4'   109.23  3.000
 APK  C3'   C4'  O4'   104.74  3.000
 APK  H4'   C4'  C5'   109.32  3.000
 APK  C3'   C4'  C5'   113.31  3.000
 APK  O4'   C4'  C5'   110.44  3.000
 APK  C1'   O4'  C4'   110.92  3.000
 APK  H3'   C3'  C2'   108.56  3.000
 APK  H3'   C3'  O3'   111.41  3.000
 APK  C2'   C3'  O3'   110.55  3.000
 APK  H3'   C3'  C4'   109.09  3.000
 APK  C2'   C3'  C4'   101.46  3.000
 APK  O3'   C3'  C4'   115.19  3.000
 APK  HO3'  O3'  C3'   107.52  3.000
 APK  H2'   C2'  C1'   112.13  3.000
 APK  H2'   C2'  O2'   111.85  3.000
 APK  C1'   C2'  O2'   107.20  3.000
 APK  H2'   C2'  C3'   112.55  3.000
 APK  C1'   C2'  C3'   100.76  3.000
 APK  O2'   C2'  C3'   111.73  3.000
 APK  HO2'  O2'  C2'   108.07  3.000
 APK  H1'   C1'  N9    107.36  3.000
 APK  H1'   C1'  C2'   111.33  3.000
 APK  N9    C1'  C2'   111.65  3.000
 APK  H1'   C1'  O4'   110.47  3.000
 APK  N9    C1'  O4'   109.05  3.000
 APK  C2'   C1'  O4'   106.99  3.000
 APK  C4    N9   C8    106.19  3.000
 APK  C4    N9   C1'   125.21  3.000
 APK  C8    N9   C1'   128.54  3.000
 APK  H8    C8   N7    124.64  3.000
 APK  H8    C8   N9    122.05  3.000
 APK  N7    C8   N9    113.32  3.000
 APK  C5    N7   C8    104.50  3.000
 APK  C6    C5   C4    116.28  3.000
 APK  C6    C5   N7    133.01  3.000
 APK  C4    C5   N7    110.69  3.000
 APK  N3    C4   C5    126.46  3.000
 APK  N3    C4   N9    128.24  3.000
 APK  C5    C4   N9    105.30  3.000
 APK  C2    N3   C4    111.66  3.000
 APK  HC2   C2   N1    115.44  3.000
 APK  HC2   C2   N3    116.15  3.000
 APK  N1    C2   N3    128.41  3.000
 APK  C6    N1   C2    119.20  3.000
 APK  N6    C6   N1    119.27  3.000
 APK  N6    C6   C5    122.77  3.000
 APK  N1    C6   C5    117.95  3.000
 APK  HN62  N6   HN61  117.84  3.000
 APK  HN62  N6   C6    120.72  3.000
 APK  HN61  N6   C6    119.75  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
 APK  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 APK  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 APK  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 APK  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 APK  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 APK  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 APK  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 APK  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 APK  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 APK  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 APK  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 APK  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 APK  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 APK  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 APK  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 APK  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 APK  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 APK  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 APK  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 APK  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 APK  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 APK  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 APK  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 APK  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 APK  CONST_25  HC2   C2   N3   C4    180.00   0.0  0
 APK  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 APK  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 APK  Var_01    C4'   C5'  O5'  P     162.73  30.0  3
 APK  Var_02    CD    CG   CB   CA   -178.44  30.0  3
 APK  Var_03    CE    CD   CG   CB   -172.59  30.0  3
 APK  Var_04    NZ    CE   CD   CG    -59.07  30.0  3
 APK  Var_05    P     NZ   CE   CD    173.91  30.0  3
 APK  Var_06    O1P   P    NZ   CE    167.77  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
 APK  chir_01  CA   C    N    CB   negativ
 APK  chir_03  C4'  C5'  O4'  C3'  negativ
 APK  chir_04  C3'  O3'  C4'  C2'  positiv
 APK  chir_05  C2'  O2'  C3'  C1'  positiv
 APK  chir_06  C1'  O4'  N9   C2'  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
 APK  plan-1  C1'   0.020
 APK  plan-1  N9    0.020
 APK  plan-1  C8    0.020
 APK  plan-1  N7    0.020
 APK  plan-1  C5    0.020
 APK  plan-1  C4    0.020
 APK  plan-1  N3    0.020
 APK  plan-1  C2    0.020
 APK  plan-1  N1    0.020
 APK  plan-1  C6    0.020
 APK  plan-1  N6    0.020
 APK  plan-1  H8    0.020
 APK  plan-1  HC2   0.020
 APK  plan-2  C6    0.020
 APK  plan-2  N6    0.020
 APK  plan-2  HN61  0.020
 APK  plan-2  HN62  0.020
 APK  plan-3  O     0.020
 APK  plan-3  C     0.020
 APK  plan-3  CA    0.020
 APK  plan-3  HC    0.020

