# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:51:42 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](CC[C@H](N)C(O)=O)C[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
 4IK  4IK  '(2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid (non-preferred name)'  L-peptide  52  28  .  2016-04-22  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_4IK
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
 4IK  C     C  C      0   0.385  -15.3834  35.1035  88.9841
 4IK  N     N  NH2    0  -0.808  -17.3043  34.1241  90.2205
 4IK  O     O  O      0  -0.606  -16.1669  35.5682  88.1330
 4IK  N1    N  N      0  -0.471  -17.1498  23.1685  93.1817
 4IK  C2    C  CR16   0   0.044  -16.4196  24.1086  93.7762
 4IK  N3    N  N      0  -0.454  -15.8717  25.1850  93.2406
 4IK  C4    C  CR56   0   0.486  -16.1330  25.2746  91.9386
 4IK  C5    C  CR56   0  -0.009  -16.8774  24.3807  91.1844
 4IK  C6    C  CR6    0   0.454  -17.4019  23.2712  91.8722
 4IK  N6    N  NH2    0  -0.815  -18.1161  22.3176  91.2680
 4IK  N7    N  N      0  -0.447  -16.9487  24.7875  89.8768
 4IK  C8    C  CR15   0   0.107  -16.2632  25.8913  89.8442
 4IK  N9    N  NR5    0  -0.540  -15.7405  26.2432  91.0598
 4IK  CA    C  CH1    0  -0.151  -15.8999  33.9373  89.8624
 4IK  CB    C  CH2    0  -0.434  -15.7792  32.6056  89.1148
 4IK  O3'   O  OH1    0  -0.665  -12.8407  29.3569  91.8909
 4IK  O2'   O  OH1    0  -0.655  -12.5747  26.6839  91.3409
 4IK  CE    C  CH2    0  -0.278  -14.3666  30.7886  86.6705
 4IK  CG    C  CH2    0  -0.440  -14.3439  32.1686  88.8457
 4IK  C5'   C  CH2    0  -0.485  -14.9313  29.6565  88.8506
 4IK  O4'   O  O2     0  -0.495  -15.5802  28.5468  90.9013
 4IK  CD    C  CH1    0  -0.235  -14.1470  30.7930  88.1854
 4IK  C3'   C  CH1    0  -0.034  -13.2579  28.8899  90.6324
 4IK  C2'   C  CH1    0  -0.026  -13.5630  27.3962  90.6639
 4IK  C4'   C  CH1    0   0.017  -14.6369  29.4730  90.3330
 4IK  C1'   C  CH1    0   0.197  -14.9296  27.3984  91.3578
 4IK  OXT   O  OC    -1  -0.616  -14.2045  35.4650  89.1865
 4IK  H     H  HNH2   0   0.327  -17.5619  33.4141  90.8961
 4IK  H2    H  HNH2   0   0.330  -17.4193  35.0077  90.7020
 4IK  H62   H  HNH2   0   0.401  -18.5589  21.6020  91.8188
 4IK  H61   H  HNH2   0   0.409  -18.4168  22.4299  90.3154
 4IK  H8    H  HCR5   0   0.300  -16.1092  26.5005  88.9652
 4IK  HA    H  HCH1   0   0.164  -15.2499  33.8831  90.7502
 4IK  HB2   H  HCH2   0   0.206  -16.2839  31.8433  89.7209
 4IK  HB3   H  HCH2   0   0.219  -16.3362  32.6653  88.1789
 4IK  HZ2   H  HNH2   0   0.346  -15.7873  31.0702  85.2548
 4IK  HZ3   H  HNH2   0   0.341  -16.3178  30.2269  86.5192
 4IK  HO3'  H  HOH1   0   0.451  -12.0390  28.8861  92.1431
 4IK  HO2'  H  HOH1   0   0.465  -12.7051  25.7415  91.1941
 4IK  HE3   H  HCH2   0   0.193  -13.9600  29.8433  86.2793
 4IK  HE2   H  HCH2   0   0.219  -13.7522  31.5840  86.2396
 4IK  HG2   H  HCH2   0   0.224  -13.8410  32.9116  88.2213
 4IK  HG3   H  HCH2   0   0.210  -13.7947  32.1774  89.7941
 4IK  H5''  H  HCH2   0   0.243  -16.0062  29.8290  88.7469
 4IK  H5'   H  HCH2   0   0.238  -14.7201  28.7222  88.3169
 4IK  HD    H  HCH1   0   0.227  -13.0805  30.5615  88.2958
 4IK  H3'   H  HCH1   0   0.253  -12.5305  29.1368  89.8495
 4IK  H2'   H  HCH1   0   0.244  -13.6837  27.0406  89.6315
 4IK  H4'   H  HCH1   0   0.252  -14.7567  30.4256  90.8578
 4IK  H1'   H  HCH1   0   0.251  -14.7965  27.4038  92.4455
 4IK  NZ    N  NH2    0  -0.790  -15.7447  31.0214  86.2648
 4IK  H2A   H  HCR6   0   0.250  -16.2537  23.9669  94.8390

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
 4IK  O    C     deloc     1.231  0.020  1.231
 4IK  C    CA    single    1.525  0.021  1.525
 4IK  C    OXT   deloc     1.250  0.020  1.250
 4IK  CA   N     single    1.458  0.019  1.458
 4IK  N    H     single    0.860  0.020  0.860
 4IK  N    H2    single    0.890  0.020  1.040
 4IK  C6   N1    aromatic  1.338  0.020  1.338
 4IK  N1   C2    aromatic  1.331  0.020  1.331
 4IK  N3   C2    aromatic  1.321  0.020  1.321
 4IK  C2   H2A   single    0.930  0.020  1.080
 4IK  C4   N3    aromatic  1.331  0.020  1.331
 4IK  N9   C4    aromatic  1.365  0.020  1.365
 4IK  C5   C4    aromatic  1.386  0.020  1.386
 4IK  N7   C5    aromatic  1.371  0.020  1.371
 4IK  C5   C6    aromatic  1.407  0.020  1.407
 4IK  N6   C6    single    1.336  0.020  1.336
 4IK  N6   H62   single    0.860  0.020  1.020
 4IK  N6   H61   single    0.860  0.020  1.020
 4IK  C8   N7    aromatic  1.300  0.020  1.300
 4IK  C8   N9    aromatic  1.369  0.020  1.369
 4IK  C8   H8    single    0.930  0.020  1.080
 4IK  N9   C1'   single    1.442  0.020  1.442
 4IK  CB   CA    single    1.521  0.033  1.521
 4IK  CA   HA    single    0.970  0.020  0.970
 4IK  CG   CB    single    1.524  0.020  1.524
 4IK  CB   HB2   single    0.970  0.020  1.090
 4IK  CB   HB3   single    0.970  0.020  1.090
 4IK  NZ   CE    single    1.455  0.020  1.455
 4IK  NZ   HZ2   single    0.890  0.020  1.040
 4IK  NZ   HZ3   single    0.890  0.020  1.040
 4IK  C3'  O3'   single    1.406  0.020  1.406
 4IK  O3'  HO3'  single    0.850  0.020  0.980
 4IK  C2'  O2'   single    1.394  0.020  1.394
 4IK  O2'  HO2'  single    0.850  0.020  0.980
 4IK  CE   CD    single    1.531  0.020  1.531
 4IK  CE   HE3   single    0.970  0.020  1.090
 4IK  CE   HE2   single    0.970  0.020  1.090
 4IK  CD   CG    single    1.538  0.020  1.538
 4IK  CG   HG2   single    0.970  0.020  1.090
 4IK  CG   HG3   single    0.970  0.020  1.090
 4IK  CD   C5'   single    1.533  0.020  1.533
 4IK  C5'  C4'   single    1.522  0.020  1.522
 4IK  C5'  H5''  single    0.970  0.020  1.090
 4IK  C5'  H5'   single    0.970  0.020  1.090
 4IK  C4'  O4'   single    1.439  0.020  1.439
 4IK  O4'  C1'   single    1.397  0.020  1.397
 4IK  CD   HD    single    0.970  0.020  1.090
 4IK  C4'  C3'   single    1.527  0.020  1.527
 4IK  C3'  C2'   single    1.525  0.020  1.525
 4IK  C3'  H3'   single    0.970  0.020  1.090
 4IK  C2'  C1'   single    1.533  0.020  1.533
 4IK  C2'  H2'   single    0.970  0.020  1.090
 4IK  C4'  H4'   single    0.970  0.020  1.090
 4IK  C1'  H1'   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
 4IK  OXT   C    CA    120.80  1.700
 4IK  OXT   C    O     126.56  3.000
 4IK  CA    C    O     120.80  1.700
 4IK  H2    N    H     105.40  3.000
 4IK  H2    N    CA    109.71  3.000
 4IK  H     N    CA    114.00  3.000
 4IK  C6    N1   C2    119.12  3.000
 4IK  H2A   C2   N3    116.11  3.000
 4IK  H2A   C2   N1    115.42  3.000
 4IK  N3    C2   N1    128.47  3.000
 4IK  C4    N3   C2    111.72  3.000
 4IK  N9    C4   C5    105.17  3.000
 4IK  C5    C4   N3    126.45  3.000
 4IK  N9    C4   N3    128.38  3.000
 4IK  N7    C5   C6    132.90  3.000
 4IK  C6    C5   C4    116.28  3.000
 4IK  N7    C5   C4    110.82  3.000
 4IK  N6    C6   C5    122.77  3.000
 4IK  N6    C6   N1    119.26  3.000
 4IK  C5    C6   N1    117.96  3.000
 4IK  H61   N6   H62   117.83  3.000
 4IK  H61   N6   C6    120.58  3.000
 4IK  H62   N6   C6    119.71  3.000
 4IK  C8    N7   C5    104.39  3.000
 4IK  H8    C8   N9    121.53  3.000
 4IK  H8    C8   N7    125.06  3.000
 4IK  N9    C8   N7    113.41  3.000
 4IK  C1'   N9   C8    127.14  3.000
 4IK  C1'   N9   C4    126.63  3.000
 4IK  C8    N9   C4    106.22  3.000
 4IK  HA    CA   CB    109.00  3.000
 4IK  HA    CA   N     110.00  3.000
 4IK  CB    CA   N     110.40  1.500
 4IK  HA    CA   C     110.00  3.000
 4IK  CB    CA   C     110.50  1.500
 4IK  N     CA   C     111.00  2.800
 4IK  HB3   CB   HB2   106.09  3.000
 4IK  HB3   CB   CG    110.19  3.000
 4IK  HB2   CB   CG    109.36  3.000
 4IK  HB3   CB   CA    109.33  3.000
 4IK  HB2   CB   CA    107.35  3.000
 4IK  CG    CB   CA    114.18  3.000
 4IK  HO3'  O3'  C3'   108.61  3.000
 4IK  HO2'  O2'  C2'   109.28  3.000
 4IK  HE2   CE   HE3   106.08  3.000
 4IK  HE2   CE   CD    107.89  3.000
 4IK  HE3   CE   CD    107.53  3.000
 4IK  HE2   CE   NZ    107.81  3.000
 4IK  HE3   CE   NZ    112.83  3.000
 4IK  CD    CE   NZ    114.28  3.000
 4IK  HG3   CG   HG2   104.97  3.000
 4IK  HG3   CG   CD    108.33  3.000
 4IK  HG2   CG   CD    107.68  3.000
 4IK  HG3   CG   CB    108.47  3.000
 4IK  HG2   CG   CB    109.82  3.000
 4IK  CD    CG   CB    116.91  3.000
 4IK  H5'   C5'  H5''  106.11  3.000
 4IK  H5'   C5'  C4'   109.51  3.000
 4IK  H5''  C5'  C4'   107.54  3.000
 4IK  H5'   C5'  CD    108.79  3.000
 4IK  H5''  C5'  CD    110.17  3.000
 4IK  C4'   C5'  CD    114.39  3.000
 4IK  C1'   O4'  C4'   110.67  3.000
 4IK  HD    CD   C5'   107.30  3.000
 4IK  HD    CD   CG    105.66  3.000
 4IK  C5'   CD   CG    114.28  3.000
 4IK  HD    CD   CE    103.80  3.000
 4IK  C5'   CD   CE    110.73  3.000
 4IK  CG    CD   CE    114.14  3.000
 4IK  H3'   C3'  C4'   111.90  3.000
 4IK  H3'   C3'  C2'   111.59  3.000
 4IK  C4'   C3'  C2'   101.39  3.000
 4IK  H3'   C3'  O3'   111.56  3.000
 4IK  C2'   C3'  O3'   111.49  3.000
 4IK  C4'   C3'  O3'   108.47  3.000
 4IK  H2'   C2'  C1'   109.15  3.000
 4IK  H2'   C2'  C3'   108.64  3.000
 4IK  C1'   C2'  C3'   100.74  3.000
 4IK  H2'   C2'  O2'   111.65  3.000
 4IK  C1'   C2'  O2'   114.40  3.000
 4IK  C3'   C2'  O2'   111.64  3.000
 4IK  H4'   C4'  C3'   109.72  3.000
 4IK  H4'   C4'  O4'   107.41  3.000
 4IK  C3'   C4'  O4'   105.59  3.000
 4IK  H4'   C4'  C5'   109.93  3.000
 4IK  C3'   C4'  C5'   114.31  3.000
 4IK  O4'   C4'  C5'   109.59  3.000
 4IK  H1'   C1'  C2'   109.94  3.000
 4IK  H1'   C1'  O4'   112.15  3.000
 4IK  C2'   C1'  O4'   105.58  3.000
 4IK  H1'   C1'  N9    106.10  3.000
 4IK  C2'   C1'  N9    113.99  3.000
 4IK  O4'   C1'  N9    109.22  3.000
 4IK  HZ3   NZ   HZ2   105.35  3.000
 4IK  HZ3   NZ   CE    109.92  3.000
 4IK  HZ2   NZ   CE    109.01  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
 4IK  CONST_01  C4   C5  C6  N1    0.00   0.0  0
 4IK  CONST_02  N7   C5  C6  N1  180.00   0.0  0
 4IK  CONST_03  C4   N3  C2  N1    0.00   0.0  0
 4IK  CONST_04  C5   C6  N1  C2    0.00   0.0  0
 4IK  CONST_05  N9   C4  N3  C2  180.00   0.0  0
 4IK  CONST_06  C5   C4  N3  C2    0.00   0.0  0
 4IK  CONST_07  C6   N1  C2  N3    0.00   0.0  0
 4IK  CONST_08  C8   N9  C4  N3  180.00   0.0  0
 4IK  CONST_09  N7   C5  C4  N3  180.00   0.0  0
 4IK  CONST_10  C6   C5  C4  N3    0.00   0.0  0
 4IK  CONST_11  N7   C8  N9  C4    0.00   0.0  0
 4IK  CONST_12  C8   N7  C5  C4    0.00   0.0  0
 4IK  CONST_13  C8   N9  C4  C5    0.00   0.0  0
 4IK  CONST_14  N9   C8  N7  C5    0.00   0.0  0
 4IK  CONST_15  N9   C4  C5  C6  180.00   0.0  0
 4IK  CONST_16  C8   N7  C5  C6  180.00   0.0  0
 4IK  CONST_17  N9   C4  C5  N7    0.00   0.0  0
 4IK  CONST_18  C1'  N9  C4  N3    0.00   0.0  0
 4IK  CONST_19  C1'  N9  C4  C5  180.00   0.0  0
 4IK  CONST_20  C1'  N9  C8  N7  180.00   0.0  0
 4IK  CONST_21  N6   C6  N1  C2  180.00   0.0  0
 4IK  CONST_22  N6   C6  C5  C4  180.00   0.0  0
 4IK  CONST_23  N7   C5  C6  N6    0.00   0.0  0
 4IK  CONST_24  H2A  C2  N3  C4  180.00   0.0  0
 4IK  CONST_25  H8   C8  N9  C4  180.00   0.0  0
 4IK  CONST_26  H62  N6  C6  N1    0.00   0.0  0
 4IK  CONST_27  H61  N6  C6  N1  180.00   0.0  0
 4IK  Var_01    CD   CG  CB  CA  175.87  30.0  1
 4IK  Var_02    HZ2  NZ  CE  CD  175.86  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
 4IK  chir_01  CA   C    N    CB   negativ
 4IK  chir_02  CD   CE   CG   C5'  negativ
 4IK  chir_03  C3'  O3'  C4'  C2'  positiv
 4IK  chir_04  C2'  O2'  C3'  C1'  positiv
 4IK  chir_05  C4'  O4'  C5'  C3'  positiv
 4IK  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
 4IK  plan-1  N1   0.020
 4IK  plan-1  C2   0.020
 4IK  plan-1  N3   0.020
 4IK  plan-1  C4   0.020
 4IK  plan-1  C5   0.020
 4IK  plan-1  C6   0.020
 4IK  plan-1  N6   0.020
 4IK  plan-1  N7   0.020
 4IK  plan-1  C8   0.020
 4IK  plan-1  N9   0.020
 4IK  plan-1  C1'  0.020
 4IK  plan-1  H8   0.020
 4IK  plan-1  H2A  0.020
 4IK  plan-2  C6   0.020
 4IK  plan-2  N6   0.020
 4IK  plan-2  H62  0.020
 4IK  plan-2  H61  0.020
 4IK  plan-3  C    0.020
 4IK  plan-3  O    0.020
 4IK  plan-3  CA   0.020
 4IK  plan-3  OXT  0.020

