# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 19:39:06 2020
#   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  56  32  .  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_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   0.020   5.0391   0.2571   1.5142
 6CX  C4    C  CR56   0   0.500   3.2373  -0.3185   0.4098
 6CX  C5    C  CR56   0  -0.013   3.2734  -1.6117   0.9061
 6CX  C6    C  CR6    0   0.409   4.3324  -1.9120   1.7833
 6CX  C8    C  CR15   0   0.090   1.5818  -1.5303  -0.3586
 6CX  N9    N  NR5    0  -0.527   2.1481  -0.2808  -0.4169
 6CX  C10   C  CH2    0  -0.365  -3.2068   2.4869  -0.4460
 6CX  CG    C  CH2    0  -0.300  -3.1408   0.0648  -0.4652
 6CX  CB    C  CH2    0  -0.423  -2.2111  -1.0986  -0.1483
 6CX  CA    C  CH1    0  -0.214  -2.8914  -2.4654  -0.1068
 6CX  C     C  C      0   0.416  -1.8262  -3.6153  -0.1327
 6CX  O     O  O      0  -0.590  -1.8761  -4.5179   0.7011
 6CX  OXT   O  OC    -1  -0.763  -0.9872  -3.5246  -1.0765
 6CX  N     N  NH2    0  -0.767  -3.8615  -2.5064   0.9749
 6CX  C5'   C  CH2    0  -0.305  -1.6409   1.3478  -1.8917
 6CX  C4'   C  CH1    0  -0.017  -0.2690   1.9680  -1.6834
 6CX  C3'   C  CH1    0   0.001   0.6009   1.8906  -2.9411
 6CX  C2'   C  CH1    0  -0.039   1.4816   0.6753  -2.6311
 6CX  O2'   O  OH1    0  -0.655   2.7063   0.6497  -3.3010
 6CX  C1'   C  CH1    0   0.182   1.6916   0.8746  -1.1369
 6CX  N3    N  N      0  -0.428   4.0933   0.6575   0.6869
 6CX  N1    N  N      0  -0.362   5.2038  -0.9435   2.0644
 6CX  N6    N  NH2    0  -0.785   4.4885  -3.1163   2.3427
 6CX  N7    N  N      0  -0.464   2.2275  -2.3495   0.4153
 6CX  O4'   O  O2     0  -0.453   0.4380   1.2609  -0.6560
 6CX  O3'   O  OH1    0  -0.655   1.3752   3.0544  -3.0433
 6CX  C51   C  CR5    0   0.116  -3.3848   2.7826   1.0057
 6CX  C52   C  CR15   0  -0.118  -2.6029   2.3685   2.0470
 6CX  N53   N  NR15   0  -0.446  -3.1573   2.9417   3.1558
 6CX  C54   C  CR15   0   0.014  -4.2229   3.6615   2.7528
 6CX  N55   N  N      0  -0.478  -4.3891   3.5883   1.4596
 6CX  H21   H  HCR6   0   0.238   5.7783   0.9997   1.7910
 6CX  H81   H  HCR5   0   0.311   0.6827  -1.7941  -0.8977
 6CX  H102  H  HCH2   0   0.238  -2.7062   3.3364  -0.9200
 6CX  H101  H  HCH2   0   0.218  -4.1953   2.4212  -0.9298
 6CX  HG2   H  HCH2   0   0.253  -3.8379   0.2109   0.3610
 6CX  HG3   H  HCH2   0   0.174  -3.7615  -0.1885  -1.3448
 6CX  HB2   H  HCH2   0   0.235  -1.4251  -1.1502  -0.8993
 6CX  HB3   H  HCH2   0   0.240  -1.7067  -0.8967   0.8039
 6CX  HA    H  HCH1   0   0.204  -3.4564  -2.5689  -1.0468
 6CX  H2    H  HNH2   0   0.338  -4.2351  -3.4435   1.0528
 6CX  H     H  HNH2   0   0.341  -3.3821  -2.3521   1.8541
 6CX  H5'2  H  HCH2   0   0.264  -1.5189   0.3378  -2.2911
 6CX  H5'1  H  HCH2   0   0.189  -2.1533   1.9131  -2.6851
 6CX  H4'1  H  HCH1   0   0.238  -0.3816   3.0141  -1.3782
 6CX  H3'1  H  HCH1   0   0.193  -0.0048   1.7343  -3.8444
 6CX  H2'1  H  HCH1   0   0.273   0.9008  -0.2410  -2.8044
 6CX  H2'2  H  HOH1   0   0.450   2.5935   0.1988  -4.1386
 6CX  H1'1  H  HCH1   0   0.301   2.4571   1.6446  -0.9730
 6CX  H61   H  HNH2   0   0.328   3.8815  -3.8812   2.1047
 6CX  H62   H  HNH2   0   0.372   5.2903  -3.3010   2.9216
 6CX  H3'2  H  HOH1   0   0.432   2.1362   2.8598  -3.6007
 6CX  H521  H  HCR5   0   0.280  -1.7313   1.7379   2.0829
 6CX  H531  H  HNR5   0   0.433  -2.8339   2.8395   4.1039
 6CX  H541  H  HCR5   0   0.274  -4.8431   4.2158   3.4402
 6CX  ND    N  NT     0  -0.397  -2.4058   1.3015  -0.6652

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    1.337  0.020  1.337
 6CX  C6   C5    aromatic  1.408  0.020  1.408
 6CX  C6   N1    aromatic  1.333  0.020  1.333
 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  1.331  0.020  1.331
 6CX  C8   N9    aromatic  1.373  0.020  1.373
 6CX  C2   N3    aromatic  1.319  0.020  1.319
 6CX  C4   N9    aromatic  1.368  0.020  1.368
 6CX  C4   N3    aromatic  1.327  0.020  1.327
 6CX  N9   C1'   single    1.436  0.020  1.436
 6CX  C54  N53   aromatic  1.348  0.020  1.348
 6CX  C54  N55   aromatic  1.306  0.020  1.306
 6CX  N53  C52   aromatic  1.366  0.020  1.366
 6CX  C1'  C2'   single    1.522  0.020  1.522
 6CX  C1'  O4'   single    1.397  0.020  1.397
 6CX  N55  C51   aromatic  1.365  0.020  1.365
 6CX  C2'  O2'   single    1.396  0.020  1.396
 6CX  C2'  C3'   single    1.533  0.020  1.533
 6CX  C52  C51   aromatic  1.366  0.020  1.366
 6CX  O4'  C4'   single    1.434  0.020  1.434
 6CX  C51  C10   single    1.492  0.020  1.492
 6CX  C5'  C4'   single    1.520  0.020  1.520
 6CX  C5'  ND    single    1.446  0.020  1.446
 6CX  C4'  C3'   single    1.531  0.020  1.531
 6CX  C3'  O3'   single    1.402  0.020  1.402
 6CX  C10  ND    single    1.447  0.020  1.447
 6CX  ND   CG    single    1.452  0.020  1.452
 6CX  CG   CB    single    1.523  0.020  1.523
 6CX  CB   CA    single    1.527  0.020  1.527
 6CX  N    CA    single    1.454  0.020  1.454
 6CX  CA   C     single    1.568  0.020  1.568
 6CX  O    C     deloc     1.230  0.020  1.230
 6CX  C    OXT   deloc     1.266  0.020  1.266
 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  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    115.35  3.000
 6CX  H21   C2   N3    116.19  3.000
 6CX  N1    C2   N3    128.46  3.000
 6CX  N3    C4   N9    128.27  3.000
 6CX  N3    C4   C5    126.49  3.000
 6CX  N9    C4   C5    105.24  3.000
 6CX  N7    C5   C6    133.03  3.000
 6CX  N7    C5   C4    110.75  3.000
 6CX  C6    C5   C4    116.23  3.000
 6CX  N6    C6   N1    119.34  3.000
 6CX  N1    C6   C5    117.93  3.000
 6CX  N6    C6   C5    122.74  3.000
 6CX  H81   C8   N7    123.83  3.000
 6CX  H81   C8   N9    122.95  3.000
 6CX  N7    C8   N9    113.22  3.000
 6CX  C1'   N9   C8    128.50  3.000
 6CX  C1'   N9   C4    125.33  3.000
 6CX  C8    N9   C4    106.12  3.000
 6CX  H101  C10  H102  105.45  3.000
 6CX  H101  C10  C51   109.38  3.000
 6CX  H102  C10  C51   108.80  3.000
 6CX  H101  C10  ND    112.39  3.000
 6CX  H102  C10  ND    108.49  3.000
 6CX  C51   C10  ND    112.07  3.000
 6CX  HG3   CG   HG2   105.92  3.000
 6CX  HG3   CG   CB    109.46  3.000
 6CX  HG2   CG   CB    109.56  3.000
 6CX  HG3   CG   ND    111.68  3.000
 6CX  HG2   CG   ND    108.28  3.000
 6CX  CB    CG   ND    111.74  3.000
 6CX  HB3   CB   HB2   106.01  3.000
 6CX  HB3   CB   CA    110.25  3.000
 6CX  HB2   CB   CA    107.33  3.000
 6CX  HB3   CB   CG    108.72  3.000
 6CX  HB2   CB   CG    109.48  3.000
 6CX  CA    CB   CG    114.68  3.000
 6CX  HA    CA   N     106.86  3.000
 6CX  HA    CA   C     105.39  3.000
 6CX  N     CA   C     116.42  3.000
 6CX  HA    CA   CB    106.82  3.000
 6CX  C     CA   CB    110.69  3.000
 6CX  N     CA   CB    110.04  3.000
 6CX  OXT   C    O     125.79  3.000
 6CX  OXT   C    CA    114.21  3.000
 6CX  O     C    CA    119.98  3.000
 6CX  H     N    H2    104.42  3.000
 6CX  H     N    CA    109.01  3.000
 6CX  H2    N    CA    109.26  3.000
 6CX  H5'1  C5'  H5'2  105.26  3.000
 6CX  H5'1  C5'  C4'   108.02  3.000
 6CX  H5'2  C5'  C4'   109.05  3.000
 6CX  H5'1  C5'  ND    112.43  3.000
 6CX  H5'2  C5'  ND    109.84  3.000
 6CX  C4'   C5'  ND    111.98  3.000
 6CX  H4'1  C4'  O4'   108.79  3.000
 6CX  H4'1  C4'  C3'   109.60  3.000
 6CX  O4'   C4'  C3'   106.47  3.000
 6CX  H4'1  C4'  C5'   109.57  3.000
 6CX  C3'   C4'  C5'   112.31  3.000
 6CX  O4'   C4'  C5'   110.01  3.000
 6CX  H3'1  C3'  O3'   111.27  3.000
 6CX  H3'1  C3'  C2'   111.73  3.000
 6CX  O3'   C3'  C2'   110.84  3.000
 6CX  H3'1  C3'  C4'   111.67  3.000
 6CX  O3'   C3'  C4'   109.37  3.000
 6CX  C2'   C3'  C4'   101.56  3.000
 6CX  H2'1  C2'  C1'   109.70  3.000
 6CX  H2'1  C2'  O2'   111.89  3.000
 6CX  C1'   C2'  O2'   110.63  3.000
 6CX  H2'1  C2'  C3'   109.00  3.000
 6CX  O2'   C2'  C3'   114.93  3.000
 6CX  C1'   C2'  C3'   100.02  3.000
 6CX  H2'2  O2'  C2'   108.96  3.000
 6CX  H1'1  C1'  O4'   112.35  3.000
 6CX  H1'1  C1'  C2'   109.54  3.000
 6CX  O4'   C1'  C2'   104.49  3.000
 6CX  H1'1  C1'  N9    105.53  3.000
 6CX  O4'   C1'  N9    109.58  3.000
 6CX  C2'   C1'  N9    115.51  3.000
 6CX  C4    N3   C2    111.72  3.000
 6CX  C6    N1   C2    119.17  3.000
 6CX  H62   N6   H61   118.55  3.000
 6CX  H62   N6   C6    119.94  3.000
 6CX  H61   N6   C6    121.06  3.000
 6CX  C8    N7   C5    104.66  3.000
 6CX  C1'   O4'  C4'   109.41  3.000
 6CX  H3'2  O3'  C3'   108.11  3.000
 6CX  N55   C51  C52   110.27  3.000
 6CX  C52   C51  C10   127.81  3.000
 6CX  N55   C51  C10   121.88  3.000
 6CX  H521  C52  N53   123.19  3.000
 6CX  H521  C52  C51   131.79  3.000
 6CX  N53   C52  C51   105.02  3.000
 6CX  H531  N53  C54   126.13  3.000
 6CX  H531  N53  C52   126.27  3.000
 6CX  C54   N53  C52   107.60  3.000
 6CX  H541  C54  N55   125.91  3.000
 6CX  H541  C54  N53   122.57  3.000
 6CX  N55   C54  N53   111.52  3.000
 6CX  C54   N55  C51   105.59  3.000
 6CX  C5'   ND   CG    114.31  3.000
 6CX  CG    ND   C10   113.36  3.000
 6CX  C5'   ND   C10   113.26  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      0.00   0.0  0
 6CX  CONST_37  H62   N6   C6   C5    180.00   0.0  0
 6CX  Var_01    N55   C51  C10  ND   -160.63  30.0  2
 6CX  Var_02    C4'   C5'  ND   C10    89.79  30.0  1
 6CX  Var_03    C51   C10  ND   CG     78.16  30.0  1
 6CX  Var_04    CB    CG   ND   C10  -157.07  30.0  3
 6CX  Var_05    CA    CB   CG   ND   -172.32  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

