# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:58:48 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5'-S-[(1E)-6-amino-1-(2-aminoethylidene)hexyl]-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCC(\SC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)=C/CN
#
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
 AAT  AAT  5'-S-[(1E)-6-amino-1-(2-aminoethylidene)hexyl]-5'-thioadenosine  ligand  58  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AAT
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
 AAT  N     N  NH2   0  -0.798  -3.7753  -1.5297   5.3925
 AAT  CA    C  CH2   0  -0.333  -2.4101  -1.4682   4.8845
 AAT  CB    C  C1    0  -0.235  -2.3982  -0.8212   3.5330
 AAT  CG    C  C     0  -0.077  -1.5841   0.1647   3.1484
 AAT  SD    S  S2    0   0.051  -1.5646   0.8948   1.5431
 AAT  C5'   C  CH2   0  -0.622  -2.7619  -0.0712   0.5956
 AAT  C4'   C  CH1   0   0.001  -3.0240   0.6317  -0.7313
 AAT  O4'   O  O2    0  -0.487  -1.8190   1.1373  -1.3048
 AAT  C3'   C  CH1   0  -0.011  -3.5970  -0.3191  -1.7740
 AAT  O3'   O  OH1   0  -0.666  -4.3110   0.4299  -2.7197
 AAT  C2'   C  CH1   0  -0.062  -2.3102  -0.8867  -2.3833
 AAT  O2'   O  OH1   0  -0.652  -2.4413  -1.3721  -3.6854
 AAT  C1'   C  CH1   0   0.214  -1.4033   0.3466  -2.3825
 AAT  N9    N  NR5   0  -0.542  -0.0004   0.0432  -2.2510
 AAT  C8    C  CR15  0   0.118   0.6305  -0.5610  -1.1950
 AAT  N7    N  N     0  -0.449   1.9167  -0.6552  -1.3488
 AAT  C5    C  CR56  0  -0.012   2.1587  -0.0794  -2.5701
 AAT  C6    C  CR6   0   0.460   3.3358   0.1419  -3.3089
 AAT  N6    N  NH2   0  -0.817   4.5396  -0.2376  -2.8797
 AAT  N1    N  N     0  -0.475   3.2264   0.7614  -4.4899
 AAT  C2    C  CR16  0   0.046   2.0241   1.1396  -4.9146
 AAT  N3    N  N     0  -0.457   0.8552   0.9845  -4.3172
 AAT  C4    C  CR56  0   0.493   0.9803   0.3676  -3.1452
 AAT  C11   C  CH2   0  -0.518  -0.4937   0.7615   4.0017
 AAT  C12   C  CH2   0  -0.400   0.7826  -0.0799   3.9826
 AAT  C13   C  CH2   0  -0.422   1.9213   0.5698   4.7577
 AAT  C14   C  CH2   0  -0.427   3.1633  -0.3079   4.8351
 AAT  C15   C  CH2   0  -0.271   4.3002   0.3502   5.6016
 AAT  N16   N  NH2   0  -0.801   5.4611  -0.5265   5.6706
 AAT  HN1   H  HNH2  0   0.348  -3.7849  -2.0413   6.2659
 AAT  HN2   H  HNH2  0   0.340  -4.0908  -0.5939   5.6153
 AAT  HCA1  H  HCH2  0   0.232  -2.0501  -2.4973   4.7834
 AAT  HCA2  H  HCH2  0   0.208  -1.7089  -0.9697   5.5646
 AAT  HCB   H  H     0   0.242  -3.1314  -1.2277   2.8451
 AAT  H5'1  H  HCH2  0   0.277  -2.3879  -1.0903   0.4667
 AAT  H5'2  H  HCH2  0   0.297  -3.7082  -0.1344   1.1352
 AAT  H4'C  H  HCH1  0   0.277  -3.6906   1.4790  -0.5557
 AAT  H3'C  H  HCH1  0   0.256  -4.2153  -1.1016  -1.3152
 AAT  H3'O  H  HOH1  0   0.451  -4.3385  -0.0748  -3.5413
 AAT  H2'C  H  HCH1  0   0.255  -1.9004  -1.6521  -1.7124
 AAT  H2'O  H  HOH1  0   0.471  -2.7548  -2.2814  -3.6478
 AAT  H1'C  H  HCH1  0   0.268  -1.5034   0.8905  -3.3272
 AAT  HC8   H  HCR5  0   0.290   0.0898  -0.9012  -0.3242
 AAT  HN61  H  HNH2  0   0.404   5.3579  -0.0497  -3.4325
 AAT  HN62  H  HNH2  0   0.412   4.6554  -0.6998  -1.9954
 AAT  HC2   H  HCR6  0   0.252   2.0061   1.6399  -5.8770
 AAT  H111  H  HCH2  0   0.251  -0.8457   0.8713   5.0303
 AAT  H112  H  HCH2  0   0.248  -0.2625   1.7749   3.6578
 AAT  H121  H  HCH2  0   0.220   1.0906  -0.2505   2.9463
 AAT  H122  H  HCH2  0   0.223   0.5682  -1.0668   4.4047
 AAT  H131  H  HCH2  0   0.213   1.5794   0.8061   5.7713
 AAT  H132  H  HCH2  0   0.215   2.1758   1.5279   4.2916
 AAT  H141  H  HCH2  0   0.213   3.5082  -0.5590   3.8271
 AAT  H142  H  HCH2  0   0.211   2.9036  -1.2568   5.3182
 AAT  H151  H  HCH2  0   0.186   3.9271   0.6617   6.5886
 AAT  H152  H  HCH2  0   0.211   4.5923   1.2683   5.0843
 AAT  H161  H  HNH2  0   0.345   6.2071  -0.0601   6.1708
 AAT  H162  H  HNH2  0   0.336   5.2283  -1.3376   6.2311

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
 AAT  N    CA    single    1.458  0.020  1.458
 AAT  N    HN1   single    0.890  0.020  1.040
 AAT  N    HN2   single    0.890  0.020  1.040
 AAT  CA   CB    single    1.498  0.020  1.498
 AAT  CA   HCA1  single    0.970  0.020  1.090
 AAT  CA   HCA2  single    0.970  0.020  1.090
 AAT  CB   CG    double    1.335  0.020  1.335
 AAT  CB   HCB   single    0.930  0.020  1.080
 AAT  CG   SD    single    1.764  0.020  1.764
 AAT  CG   C11   single    1.508  0.020  1.508
 AAT  SD   C5'   single    1.807  0.020  1.807
 AAT  C5'  C4'   single    1.524  0.020  1.524
 AAT  C5'  H5'1  single    0.970  0.020  1.090
 AAT  C5'  H5'2  single    0.970  0.020  1.090
 AAT  C4'  O4'   single    1.427  0.020  1.427
 AAT  C4'  C3'   single    1.523  0.020  1.523
 AAT  C4'  H4'C  single    0.970  0.020  1.090
 AAT  O4'  C1'   single    1.400  0.020  1.400
 AAT  C3'  O3'   single    1.402  0.020  1.402
 AAT  C3'  C2'   single    1.533  0.020  1.533
 AAT  C3'  H3'C  single    0.970  0.020  1.090
 AAT  O3'  H3'O  single    0.850  0.020  0.980
 AAT  C2'  O2'   single    1.396  0.020  1.396
 AAT  C2'  C1'   single    1.531  0.020  1.531
 AAT  C2'  H2'C  single    0.970  0.020  1.090
 AAT  O2'  H2'O  single    0.850  0.020  0.980
 AAT  C1'  N9    single    1.441  0.020  1.441
 AAT  C1'  H1'C  single    0.970  0.020  1.090
 AAT  N9   C8    aromatic  1.370  0.020  1.370
 AAT  N9   C4    aromatic  1.366  0.020  1.366
 AAT  C8   N7    aromatic  1.299  0.020  1.299
 AAT  C8   HC8   single    0.930  0.020  1.080
 AAT  N7   C5    aromatic  1.372  0.020  1.372
 AAT  C5   C6    aromatic  1.407  0.020  1.407
 AAT  C5   C4    aromatic  1.385  0.020  1.385
 AAT  C6   N6    single    1.333  0.020  1.333
 AAT  C6   N1    aromatic  1.338  0.020  1.338
 AAT  N6   HN61  single    0.860  0.020  1.020
 AAT  N6   HN62  single    0.860  0.020  1.020
 AAT  N1   C2    aromatic  1.330  0.020  1.330
 AAT  C2   N3    aromatic  1.322  0.020  1.322
 AAT  C2   HC2   single    0.930  0.020  1.080
 AAT  N3   C4    aromatic  1.330  0.020  1.330
 AAT  C11  C12   single    1.529  0.020  1.529
 AAT  C11  H111  single    0.970  0.020  1.090
 AAT  C11  H112  single    0.970  0.020  1.090
 AAT  C12  C13   single    1.523  0.020  1.523
 AAT  C12  H121  single    0.970  0.020  1.090
 AAT  C12  H122  single    0.970  0.020  1.090
 AAT  C13  C14   single    1.523  0.020  1.523
 AAT  C13  H131  single    0.970  0.020  1.090
 AAT  C13  H132  single    0.970  0.020  1.090
 AAT  C14  C15   single    1.521  0.020  1.521
 AAT  C14  H141  single    0.970  0.020  1.090
 AAT  C14  H142  single    0.970  0.020  1.090
 AAT  C15  N16   single    1.456  0.020  1.456
 AAT  C15  H151  single    0.970  0.020  1.090
 AAT  C15  H152  single    0.970  0.020  1.090
 AAT  N16  H161  single    0.890  0.020  1.040
 AAT  N16  H162  single    0.890  0.020  1.040

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
 AAT  HN2   N    HN1   105.93  3.000
 AAT  HN2   N    CA    109.24  3.000
 AAT  HN1   N    CA    109.32  3.000
 AAT  HCA2  CA   HCA1  105.92  3.000
 AAT  HCA2  CA   CB    110.97  3.000
 AAT  HCA1  CA   CB    108.66  3.000
 AAT  HCA2  CA   N     113.69  3.000
 AAT  HCA1  CA   N     107.48  3.000
 AAT  CB    CA   N     109.87  3.000
 AAT  HCB   CB   CG    120.42  3.000
 AAT  HCB   CB   CA    113.89  3.000
 AAT  CG    CB   CA    125.70  3.000
 AAT  C11   CG   SD    110.08  3.000
 AAT  C11   CG   CB    124.76  3.000
 AAT  SD    CG   CB    125.07  3.000
 AAT  C5'   SD   CG    104.40  3.000
 AAT  H5'2  C5'  H5'1  107.52  3.000
 AAT  H5'2  C5'  C4'   107.94  3.000
 AAT  H5'1  C5'  C4'   112.70  3.000
 AAT  H5'2  C5'  SD    110.27  3.000
 AAT  H5'1  C5'  SD    109.48  3.000
 AAT  C4'   C5'  SD    108.90  3.000
 AAT  H4'C  C4'  C3'   111.39  3.000
 AAT  H4'C  C4'  O4'   107.76  3.000
 AAT  C3'   C4'  O4'   105.29  3.000
 AAT  H4'C  C4'  C5'   108.82  3.000
 AAT  C3'   C4'  C5'   111.89  3.000
 AAT  O4'   C4'  C5'   111.59  3.000
 AAT  C1'   O4'  C4'   111.10  3.000
 AAT  H3'C  C3'  C2'   112.03  3.000
 AAT  H3'C  C3'  O3'   112.08  3.000
 AAT  C2'   C3'  O3'   110.93  3.000
 AAT  H3'C  C3'  C4'   111.76  3.000
 AAT  C2'   C3'  C4'   100.81  3.000
 AAT  O3'   C3'  C4'   108.66  3.000
 AAT  H3'O  O3'  C3'   108.03  3.000
 AAT  H2'C  C2'  C1'   109.90  3.000
 AAT  H2'C  C2'  O2'   111.27  3.000
 AAT  C1'   C2'  O2'   109.65  3.000
 AAT  H2'C  C2'  C3'   109.20  3.000
 AAT  C1'   C2'  C3'   101.47  3.000
 AAT  O2'   C2'  C3'   114.89  3.000
 AAT  H2'O  O2'  C2'   108.82  3.000
 AAT  H1'C  C1'  N9    105.80  3.000
 AAT  H1'C  C1'  C2'   110.22  3.000
 AAT  N9    C1'  C2'   114.02  3.000
 AAT  H1'C  C1'  O4'   110.90  3.000
 AAT  N9    C1'  O4'   109.74  3.000
 AAT  C2'   C1'  O4'   106.24  3.000
 AAT  C4    N9   C8    106.17  3.000
 AAT  C4    N9   C1'   126.09  3.000
 AAT  C8    N9   C1'   127.68  3.000
 AAT  HC8   C8   N7    124.63  3.000
 AAT  HC8   C8   N9    121.98  3.000
 AAT  N7    C8   N9    113.37  3.000
 AAT  C5    N7   C8    104.46  3.000
 AAT  C4    C5   C6    116.29  3.000
 AAT  C4    C5   N7    110.79  3.000
 AAT  C6    C5   N7    132.92  3.000
 AAT  N1    C6   N6    119.32  3.000
 AAT  N1    C6   C5    117.89  3.000
 AAT  N6    C6   C5    122.79  3.000
 AAT  HN62  N6   HN61  118.44  3.000
 AAT  HN62  N6   C6    121.22  3.000
 AAT  HN61  N6   C6    120.32  3.000
 AAT  C2    N1   C6    119.17  3.000
 AAT  HC2   C2   N3    116.13  3.000
 AAT  HC2   C2   N1    115.43  3.000
 AAT  N3    C2   N1    128.44  3.000
 AAT  C4    N3   C2    111.68  3.000
 AAT  N3    C4   C5    126.54  3.000
 AAT  N3    C4   N9    128.25  3.000
 AAT  C5    C4   N9    105.21  3.000
 AAT  H112  C11  H111  105.70  3.000
 AAT  H112  C11  C12   109.23  3.000
 AAT  H111  C11  C12   109.64  3.000
 AAT  H112  C11  CG    109.95  3.000
 AAT  H111  C11  CG    109.84  3.000
 AAT  C12   C11  CG    112.26  3.000
 AAT  H122  C12  H121  106.24  3.000
 AAT  H122  C12  C13   109.56  3.000
 AAT  H121  C12  C13   109.75  3.000
 AAT  H122  C12  C11   109.14  3.000
 AAT  H121  C12  C11   109.42  3.000
 AAT  C13   C12  C11   112.52  3.000
 AAT  H132  C13  H131  106.11  3.000
 AAT  H132  C13  C14   109.65  3.000
 AAT  H131  C13  C14   109.38  3.000
 AAT  H132  C13  C12   109.29  3.000
 AAT  H131  C13  C12   109.24  3.000
 AAT  C14   C13  C12   112.94  3.000
 AAT  H142  C14  H141  106.37  3.000
 AAT  H142  C14  C15   109.25  3.000
 AAT  H141  C14  C15   109.14  3.000
 AAT  H142  C14  C13   109.15  3.000
 AAT  H141  C14  C13   110.02  3.000
 AAT  C15   C14  C13   112.70  3.000
 AAT  H152  C15  H151  106.10  3.000
 AAT  H152  C15  N16   108.35  3.000
 AAT  H151  C15  N16   113.47  3.000
 AAT  H152  C15  C14   108.93  3.000
 AAT  H151  C15  C14   108.73  3.000
 AAT  N16   C15  C14   111.05  3.000
 AAT  H162  N16  H161  105.36  3.000
 AAT  H162  N16  C15   108.96  3.000
 AAT  H161  N16  C15   109.49  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
 AAT  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 AAT  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 AAT  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 AAT  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 AAT  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 AAT  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 AAT  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 AAT  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 AAT  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 AAT  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 AAT  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 AAT  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 AAT  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 AAT  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 AAT  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 AAT  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 AAT  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 AAT  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 AAT  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 AAT  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 AAT  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 AAT  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 AAT  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 AAT  CONST_24  HC8   C8   N9   C1'    0.00   0.0  0
 AAT  CONST_25  HC2   C2   N1   C6   180.00   0.0  0
 AAT  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 AAT  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 AAT  Var_01    C4'   C5'  SD   CG   169.43  30.0  3
 AAT  Var_02    SD    CG   CB   CA   178.83   0.0  2
 AAT  Var_03    CG    CB   CA   N    131.30  30.0  3
 AAT  Var_04    C12   C11  CG   CB    81.69  30.0  3
 AAT  Var_05    C13   C12  C11  CG   175.71  30.0  3
 AAT  Var_06    C14   C13  C12  C11  175.61  30.0  3
 AAT  Var_07    C15   C14  C13  C12  179.59  30.0  3
 AAT  Var_08    N16   C15  C14  C13  179.16  30.0  3
 AAT  Var_09    HN1   N    CA   CB   174.96  30.0  3
 AAT  Var_10    H161  N16  C15  C14  179.04  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
 AAT  chir_01  C4'  C5'  O4'  C3'  negativ
 AAT  chir_02  C3'  O3'  C4'  C2'  positiv
 AAT  chir_03  C2'  O2'  C3'  C1'  positiv
 AAT  chir_04  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
 AAT  plan-1  C1'   0.020
 AAT  plan-1  N9    0.020
 AAT  plan-1  C8    0.020
 AAT  plan-1  N7    0.020
 AAT  plan-1  C5    0.020
 AAT  plan-1  C6    0.020
 AAT  plan-1  N6    0.020
 AAT  plan-1  N1    0.020
 AAT  plan-1  C2    0.020
 AAT  plan-1  N3    0.020
 AAT  plan-1  C4    0.020
 AAT  plan-1  HC8   0.020
 AAT  plan-1  HC2   0.020
 AAT  plan-2  C6    0.020
 AAT  plan-2  N6    0.020
 AAT  plan-2  HN61  0.020
 AAT  plan-2  HN62  0.020
 AAT  plan-3  CA    0.020
 AAT  plan-3  CB    0.020
 AAT  plan-3  CG    0.020
 AAT  plan-3  SD    0.020
 AAT  plan-3  C11   0.020
 AAT  plan-3  HCB   0.020

