# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 17:55:34 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl][(1H-imidazol-4-yl)methyl]amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4c[nH]cn4)C(O)=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
 6CX  6CX  5'-{[(3S)-3-amino-3-carboxypropyl][(1H-imidazol-4-yl)methyl]amino}-5'-deoxyadenosine  ligand  57  32  .  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_6CX
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
 6CX  C2    C  CR16  0   0.046  48.6947  41.2319  126.5478
 6CX  C4    C  CR56  0   0.491  49.7750  39.4351  127.1969
 6CX  C5    C  CR56  0  -0.012  50.3603  39.2651  125.9523
 6CX  C6    C  CR6   0   0.460  50.0204  40.2118  124.9681
 6CX  C8    C  CR15  0   0.110  51.0847  37.6845  127.1483
 6CX  N9    N  NR5   0  -0.539  50.2500  38.4060  127.9590
 6CX  C10   C  CH2   0  -0.358  52.5013  33.4789  130.7896
 6CX  CG    C  CH2   0  -0.329  51.9916  34.7431  132.7995
 6CX  CB    C  CH2   0  -0.463  53.3963  35.1914  133.2115
 6CX  CA    C  CH1   0  -0.194  53.5345  35.5426  134.6976
 6CX  C     C  C     0   0.521  53.2377  34.3124  135.5442
 6CX  O     O  O     0  -0.443  54.0503  33.4573  135.7967
 6CX  OXT   O  OH1   0  -0.589  51.9799  34.2691  135.9661
 6CX  N     N  NH2   0  -0.778  54.8516  36.0914  134.9418
 6CX  C5'   C  CH2   0  -0.302  51.9117  35.7965  130.5870
 6CX  C4'   C  CR15  0  -0.037  50.9529  36.9050  131.0117
 6CX  C3'   C  CR15  0  -0.036  49.4757  36.5040  130.9793
 6CX  C2'   C  CR15  0  -0.013  49.1268  36.8389  129.5314
 6CX  O2'   O  OH1   0  -0.651  47.7858  37.0555  129.2366
 6CX  C1'   C  CR15  0   0.206  49.9107  38.1364  129.3336
 6CX  N3    N  N     0  -0.456  48.9335  40.4037  127.5496
 6CX  N1    N  N     0  -0.475  49.1753  41.1918  125.3080
 6CX  N6    N  NH2   0  -0.817  50.5018  40.1660  123.7258
 6CX  N7    N  N     0  -0.448  51.1789  38.1648  125.9451
 6CX  O4'   O  O     0  -0.496  51.0799  37.9972  130.0906
 6CX  O3'   O  OH1   0  -0.669  48.6827  37.3147  131.8077
 6CX  C51   C  CR5   0   0.121  51.8288  32.9583  129.5595
 6CX  C52   C  CR15  0  -0.113  50.4952  32.9772  129.2531
 6CX  N53   N  NR15  0  -0.560  50.3942  32.3515  128.0439
 6CX  C54   C  CR15  0   0.083  51.6326  31.9852  127.6692
 6CX  N55   N  N     0  -0.462  52.5257  32.3385  128.5606
 6CX  H21   H  HCR6  0   0.252  48.0188  42.0540  126.7584
 6CX  H81   H  HCR5  0   0.293  51.6124  36.8119  127.5035
 6CX  H102  H  HCH2  0   0.252  52.5560  32.6838  131.5399
 6CX  H101  H  HCH2  0   0.217  53.5441  33.7319  130.5434
 6CX  HG2   H  HCH2  0   0.238  51.2599  35.4518  133.1985
 6CX  HG3   H  HCH2  0   0.249  51.7474  33.7832  133.2608
 6CX  HB2   H  HCH2  0   0.241  54.1321  34.4222  132.9559
 6CX  HB3   H  HCH2  0   0.252  53.6803  36.0919  132.6617
 6CX  HA    H  HCH1  0   0.263  52.7962  36.3127  134.9372
 6CX  H3    H  HOH1  0   0.479  51.8226  33.4530  136.4657
 6CX  H2    H  HNH2  0   0.355  54.9372  36.3856  135.9066
 6CX  H     H  HNH2  0   0.346  55.5573  35.3792  134.7972
 6CX  H5'2  H  HCH2  0   0.238  51.7074  35.5308  129.5457
 6CX  H5'1  H  HCH2  0   0.230  52.9372  36.1984  130.5980
 6CX  H4'1  H  HCR5  0   0.257  51.2263  37.2821  132.0020
 6CX  H3'1  H  HCR5  0   0.260  49.3478  35.4397  131.2068
 6CX  H2'1  H  HCR5  0   0.232  49.5584  36.0550  128.8920
 6CX  H2'2  H  HOH1  0   0.464  47.3371  36.2064  129.1776
 6CX  H1'1  H  HCR5  0   0.263  49.3131  38.9911  129.6696
 6CX  H61   H  HNH2  0   0.404  50.2329  40.8613  123.0514
 6CX  H62   H  HNH2  0   0.412  51.1456  39.4486  123.4428
 6CX  H3'2  H  HOH1  0   0.456  48.9035  37.1221  132.7244
 6CX  H521  H  HCR5  0   0.278  49.6388  33.3667  129.7758
 6CX  H531  H  HNR5  0   0.419  49.5463  32.2040  127.5203
 6CX  H541  H  HCR5  0   0.276  51.8294  31.4711  126.7412
 6CX  ND    N  NT    0  -0.422  51.7690  34.5886  131.3723

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
 6CX  N6   C6    single    1.333  0.020  1.333
 6CX  C6   C5    aromatic  1.407  0.020  1.407
 6CX  C6   N1    aromatic  1.338  0.020  1.338
 6CX  N7   C5    aromatic  1.371  0.020  1.371
 6CX  N7   C8    aromatic  1.299  0.020  1.299
 6CX  C5   C4    aromatic  1.386  0.020  1.386
 6CX  N1   C2    aromatic  1.330  0.020  1.330
 6CX  C8   N9    aromatic  1.369  0.020  1.369
 6CX  C2   N3    aromatic  1.322  0.020  1.322
 6CX  C4   N9    aromatic  1.366  0.020  1.366
 6CX  C4   N3    aromatic  1.331  0.020  1.331
 6CX  N9   C1'   single    1.441  0.020  1.441
 6CX  C54  N53   aromatic  1.345  0.020  1.345
 6CX  C54  N55   aromatic  1.310  0.020  1.310
 6CX  N53  C52   aromatic  1.365  0.020  1.365
 6CX  C1'  C2'   single    1.529  0.020  1.529
 6CX  C1'  O4'   single    1.400  0.020  1.400
 6CX  N55  C51   aromatic  1.367  0.020  1.367
 6CX  C2'  O2'   single    1.390  0.020  1.390
 6CX  C2'  C3'   single    1.526  0.020  1.526
 6CX  C52  C51   aromatic  1.368  0.020  1.368
 6CX  O4'  C4'   single    1.434  0.020  1.434
 6CX  C51  C10   single    1.496  0.020  1.496
 6CX  C5'  C4'   single    1.526  0.020  1.526
 6CX  C5'  ND    single    1.448  0.020  1.448
 6CX  C4'  C3'   single    1.531  0.020  1.531
 6CX  C3'  O3'   single    1.404  0.020  1.404
 6CX  C10  ND    single    1.452  0.020  1.452
 6CX  ND   CG    single    1.453  0.020  1.453
 6CX  CG   CB    single    1.531  0.020  1.531
 6CX  CB   CA    single    1.533  0.020  1.533
 6CX  N    CA    single    1.448  0.020  1.448
 6CX  CA   C     single    1.523  0.020  1.523
 6CX  O    C     double    1.206  0.020  1.206
 6CX  C    OXT   single    1.327  0.020  1.327
 6CX  C2   H21   single    0.930  0.020  1.080
 6CX  C8   H81   single    0.930  0.020  1.080
 6CX  C10  H102  single    0.970  0.020  1.090
 6CX  C10  H101  single    0.970  0.020  1.090
 6CX  CG   HG2   single    0.970  0.020  1.090
 6CX  CG   HG3   single    0.970  0.020  1.090
 6CX  CB   HB2   single    0.970  0.020  1.090
 6CX  CB   HB3   single    0.970  0.020  1.090
 6CX  CA   HA    single    0.970  0.020  1.090
 6CX  OXT  H3    single    0.850  0.020  0.980
 6CX  N    H2    single    0.890  0.020  1.040
 6CX  N    H     single    0.860  0.020  1.020
 6CX  C5'  H5'2  single    0.970  0.020  1.090
 6CX  C5'  H5'1  single    0.970  0.020  1.090
 6CX  C4'  H4'1  single    0.970  0.020  1.090
 6CX  C3'  H3'1  single    0.970  0.020  1.090
 6CX  C2'  H2'1  single    0.970  0.020  1.090
 6CX  O2'  H2'2  single    0.850  0.020  0.980
 6CX  C1'  H1'1  single    0.970  0.020  1.090
 6CX  N6   H61   single    0.860  0.020  1.020
 6CX  N6   H62   single    0.860  0.020  1.020
 6CX  O3'  H3'2  single    0.850  0.020  0.980
 6CX  C52  H521  single    0.930  0.020  1.080
 6CX  N53  H531  single    0.860  0.020  1.020
 6CX  C54  H541  single    0.930  0.020  1.080

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
 6CX  H21   C2   N1    115.40  3.000
 6CX  H21   C2   N3    116.12  3.000
 6CX  N1    C2   N3    128.48  3.000
 6CX  N3    C4   N9    128.35  3.000
 6CX  N3    C4   C5    126.48  3.000
 6CX  N9    C4   C5    105.17  3.000
 6CX  N7    C5   C6    132.86  3.000
 6CX  N7    C5   C4    110.81  3.000
 6CX  C6    C5   C4    116.33  3.000
 6CX  N6    C6   N1    119.34  3.000
 6CX  N1    C6   C5    117.88  3.000
 6CX  N6    C6   C5    122.78  3.000
 6CX  H81   C8   N7    124.62  3.000
 6CX  H81   C8   N9    121.93  3.000
 6CX  N7    C8   N9    113.44  3.000
 6CX  C1'   N9   C8    127.57  3.000
 6CX  C1'   N9   C4    126.24  3.000
 6CX  C8    N9   C4    106.18  3.000
 6CX  H101  C10  H102  105.84  3.000
 6CX  H101  C10  C51   108.78  3.000
 6CX  H102  C10  C51   109.47  3.000
 6CX  H101  C10  ND    113.08  3.000
 6CX  H102  C10  ND    107.78  3.000
 6CX  C51   C10  ND    111.68  3.000
 6CX  HG3   CG   HG2   105.40  3.000
 6CX  HG3   CG   CB    110.41  3.000
 6CX  HG2   CG   CB    109.02  3.000
 6CX  HG3   CG   ND    106.69  3.000
 6CX  HG2   CG   ND    108.95  3.000
 6CX  CB    CG   ND    115.86  3.000
 6CX  HB3   CB   HB2   106.67  3.000
 6CX  HB3   CB   CA    105.99  3.000
 6CX  HB2   CB   CA    109.06  3.000
 6CX  HB3   CB   CG    110.15  3.000
 6CX  HB2   CB   CG    110.37  3.000
 6CX  CA    CB   CG    114.25  3.000
 6CX  HA    CA   N     108.08  3.000
 6CX  HA    CA   C     108.39  3.000
 6CX  N     CA   C     112.95  3.000
 6CX  HA    CA   CB    108.23  3.000
 6CX  C     CA   CB    109.65  3.000
 6CX  N     CA   CB    109.41  3.000
 6CX  OXT   C    O     123.27  3.000
 6CX  OXT   C    CA    112.82  3.000
 6CX  O     C    CA    123.90  3.000
 6CX  H3    OXT  C     110.17  3.000
 6CX  H     N    H2    106.35  3.000
 6CX  H     N    CA    110.07  3.000
 6CX  H2    N    CA    110.36  3.000
 6CX  H5'1  C5'  H5'2  105.78  3.000
 6CX  H5'1  C5'  C4'   108.49  3.000
 6CX  H5'2  C5'  C4'   108.91  3.000
 6CX  H5'1  C5'  ND    113.00  3.000
 6CX  H5'2  C5'  ND    107.18  3.000
 6CX  C4'   C5'  ND    113.15  3.000
 6CX  H4'1  C4'  O4'   107.25  3.000
 6CX  H4'1  C4'  C3'   110.51  3.000
 6CX  O4'   C4'  C3'   105.74  3.000
 6CX  H4'1  C4'  C5'   110.20  3.000
 6CX  C3'   C4'  C5'   114.21  3.000
 6CX  O4'   C4'  C5'   108.59  3.000
 6CX  H3'1  C3'  O3'   111.86  3.000
 6CX  H3'1  C3'  C2'   112.54  3.000
 6CX  O3'   C3'  C2'   107.69  3.000
 6CX  H3'1  C3'  C4'   111.26  3.000
 6CX  O3'   C3'  C4'   112.40  3.000
 6CX  C2'   C3'  C4'   100.55  3.000
 6CX  H2'1  C2'  C1'   109.18  3.000
 6CX  H2'1  C2'  O2'   111.49  3.000
 6CX  C1'   C2'  O2'   109.57  3.000
 6CX  H2'1  C2'  C3'   107.78  3.000
 6CX  O2'   C2'  C3'   117.12  3.000
 6CX  C1'   C2'  C3'   101.05  3.000
 6CX  H2'2  O2'  C2'   108.98  3.000
 6CX  H1'1  C1'  O4'   111.55  3.000
 6CX  H1'1  C1'  C2'   110.04  3.000
 6CX  O4'   C1'  C2'   105.90  3.000
 6CX  H1'1  C1'  N9    105.96  3.000
 6CX  O4'   C1'  N9    109.74  3.000
 6CX  C2'   C1'  N9    113.76  3.000
 6CX  C4    N3   C2    111.68  3.000
 6CX  C6    N1   C2    119.15  3.000
 6CX  H62   N6   H61   118.44  3.000
 6CX  H62   N6   C6    121.23  3.000
 6CX  H61   N6   C6    120.32  3.000
 6CX  C8    N7   C5    104.39  3.000
 6CX  C1'   O4'  C4'   110.43  3.000
 6CX  H3'2  O3'  C3'   108.47  3.000
 6CX  N55   C51  C52   109.85  3.000
 6CX  C52   C51  C10   128.14  3.000
 6CX  N55   C51  C10   121.99  3.000
 6CX  H521  C52  N53   122.49  3.000
 6CX  H521  C52  C51   132.20  3.000
 6CX  N53   C52  C51   105.31  3.000
 6CX  H531  N53  C54   126.19  3.000
 6CX  H531  N53  C52   126.14  3.000
 6CX  C54   N53  C52   107.67  3.000
 6CX  H541  C54  N55   126.10  3.000
 6CX  H541  C54  N53   122.51  3.000
 6CX  N55   C54  N53   111.39  3.000
 6CX  C54   N55  C51   105.78  3.000
 6CX  C5'   ND   CG    115.41  3.000
 6CX  CG    ND   C10   113.47  3.000
 6CX  C5'   ND   C10   111.73  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
 6CX  CONST_01  C5    C6   N1   C2     0.00   0.0  0
 6CX  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 6CX  CONST_03  N9    C4   N3   C2   180.00   0.0  0
 6CX  CONST_04  N1    C6   C5   C4     0.00   0.0  0
 6CX  CONST_05  C8    N7   C5   C4     0.00   0.0  0
 6CX  CONST_06  N7    C8   N9   C4     0.00   0.0  0
 6CX  CONST_07  N1    C2   N3   C4     0.00   0.0  0
 6CX  CONST_08  N9    C8   N7   C5     0.00   0.0  0
 6CX  CONST_09  C8    N9   C4   C5     0.00   0.0  0
 6CX  CONST_10  C8    N7   C5   C6   180.00   0.0  0
 6CX  CONST_11  N9    C4   C5   C6   180.00   0.0  0
 6CX  CONST_12  N3    C4   C5   C6     0.00   0.0  0
 6CX  CONST_13  N3    C2   N1   C6     0.00   0.0  0
 6CX  CONST_14  N3    C4   N9   C8   180.00   0.0  0
 6CX  CONST_15  N7    C5   C4   N9     0.00   0.0  0
 6CX  CONST_16  N7    C5   C4   N3   180.00   0.0  0
 6CX  CONST_17  N7    C5   C6   N1   180.00   0.0  0
 6CX  CONST_18  N53   C54  N55  C51    0.00   0.0  0
 6CX  CONST_19  C54   N53  C52  C51    0.00   0.0  0
 6CX  CONST_20  N55   C54  N53  C52    0.00   0.0  0
 6CX  CONST_21  C54   N55  C51  C52    0.00   0.0  0
 6CX  CONST_22  N55   C51  C52  N53    0.00   0.0  0
 6CX  CONST_23  C1'   N9   C4   C5   180.00   0.0  0
 6CX  CONST_24  N7    C8   N9   C1'  180.00   0.0  0
 6CX  CONST_25  N3    C4   N9   C1'    0.00   0.0  0
 6CX  CONST_26  N6    C6   N1   C2   180.00   0.0  0
 6CX  CONST_27  N6    C6   C5   C4   180.00   0.0  0
 6CX  CONST_28  C54   N55  C51  C10  180.00   0.0  0
 6CX  CONST_29  N53   C52  C51  C10  180.00   0.0  0
 6CX  CONST_30  N7    C5   C6   N6     0.00   0.0  0
 6CX  CONST_31  H81   C8   N9   C4   180.00   0.0  0
 6CX  CONST_32  H21   C2   N3   C4   180.00   0.0  0
 6CX  CONST_33  H541  C54  N55  C51  180.00   0.0  0
 6CX  CONST_34  H531  N53  C52  C51  180.00   0.0  0
 6CX  CONST_35  H521  C52  N53  C54  180.00   0.0  0
 6CX  CONST_36  H61   N6   C6   C5   180.00   0.0  0
 6CX  CONST_37  H62   N6   C6   C5     0.00   0.0  0
 6CX  CONST_38  H3    OXT  C    CA   180.00   0.0  0
 6CX  Var_01    N55   C51  C10  ND   152.91  30.0  2
 6CX  Var_02    C4'   C5'  ND   C10  169.01  30.0  2
 6CX  Var_03    C51   C10  ND   CG   154.12  30.0  1
 6CX  Var_04    CB    CG   ND   C10   68.33  30.0  3
 6CX  Var_05    CA    CB   CG   ND   171.41  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
 6CX  chir_01  CA   CB   N    C    positiv
 6CX  chir_02  C4'  O4'  C5'  C3'  positiv
 6CX  chir_03  C3'  O3'  C4'  C2'  positiv
 6CX  chir_04  C2'  O2'  C3'  C1'  positiv
 6CX  chir_05  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
 6CX  plan-1  C10   0.020
 6CX  plan-1  C51   0.020
 6CX  plan-1  C52   0.020
 6CX  plan-1  N53   0.020
 6CX  plan-1  C54   0.020
 6CX  plan-1  N55   0.020
 6CX  plan-1  H521  0.020
 6CX  plan-1  H531  0.020
 6CX  plan-1  H541  0.020
 6CX  plan-2  C2    0.020
 6CX  plan-2  C4    0.020
 6CX  plan-2  C5    0.020
 6CX  plan-2  C6    0.020
 6CX  plan-2  C8    0.020
 6CX  plan-2  N9    0.020
 6CX  plan-2  C1'   0.020
 6CX  plan-2  N3    0.020
 6CX  plan-2  N1    0.020
 6CX  plan-2  N6    0.020
 6CX  plan-2  N7    0.020
 6CX  plan-2  H21   0.020
 6CX  plan-2  H81   0.020
 6CX  plan-3  C6    0.020
 6CX  plan-3  N6    0.020
 6CX  plan-3  H61   0.020
 6CX  plan-3  H62   0.020
 6CX  plan-4  CA    0.020
 6CX  plan-4  C     0.020
 6CX  plan-4  O     0.020
 6CX  plan-4  OXT   0.020
 6CX  plan-4  H3    0.020

