# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:19:40 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5'-S-(2-aminoethyl)-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCSC[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
 NEA  NEA  5'-S-(2-aminoethyl)-5'-thioadenosine  ligand  40  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NEA
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
 NEA  N     N  NH2   0  -0.796   2.8322  -0.5113   6.2923
 NEA  CB    C  CH2   0  -0.277   2.3209   0.2751   5.1810
 NEA  CG    C  CH2   0  -0.546   1.1043  -0.4134   4.5805
 NEA  SD    S  S2    0  -0.022   0.4814   0.5744   3.1913
 NEA  C5'   C  CH2   0  -0.580  -0.9327  -0.4490   2.6980
 NEA  C4'   C  CH1   0  -0.007  -1.8767   0.3691   1.8323
 NEA  O4'   O  O2    0  -0.493  -1.1668   1.0462   0.7896
 NEA  C3'   C  CH1   0  -0.013  -2.9044  -0.4973   1.1186
 NEA  O3'   O  OH1   0  -0.667  -4.0214   0.2938   0.8126
 NEA  C2'   C  CH1   0  -0.052  -2.1341  -0.8710  -0.1511
 NEA  O2'   O  OH1   0  -0.651  -2.9334  -1.2168  -1.2418
 NEA  C1'   C  CH1   0   0.224  -1.3825   0.4311  -0.4454
 NEA  N9    N  NR5   0  -0.540  -0.1105   0.2279  -1.1035
 NEA  C8    C  CR15  0   0.108   1.0788  -0.1295  -0.5261
 NEA  N7    N  N     0  -0.452   2.0416  -0.2835  -1.3870
 NEA  C5    C  CR56  0  -0.010   1.4614  -0.0196  -2.5998
 NEA  C6    C  CR6   0   0.457   1.9594  -0.0097  -3.9157
 NEA  N6    N  NH2   0  -0.817   3.2276  -0.3012  -4.2082
 NEA  N1    N  N     0  -0.474   1.1153   0.3108  -4.9026
 NEA  C2    C  CR16  0   0.041  -0.1476   0.6065  -4.6036
 NEA  N3    N  N     0  -0.453  -0.7296   0.6263  -3.4175
 NEA  C4    C  CR56  0   0.488   0.1221   0.3039  -2.4462
 NEA  HN1   H  HNH2  0   0.353   3.6988  -0.1022   6.6168
 NEA  HN2   H  HNH2  0   0.343   2.1912  -0.4469   7.0735
 NEA  HB1   H  HCH2  0   0.206   2.0522   1.3048   5.4536
 NEA  HB2   H  HCH2  0   0.230   3.1028   0.3459   4.4218
 NEA  HG1   H  HCH2  0   0.263   1.3701  -1.4130   4.2331
 NEA  HG2   H  HCH2  0   0.260   0.3136  -0.5089   5.3286
 NEA  H5'1  H  HCH2  0   0.268  -0.5819  -1.3489   2.1864
 NEA  H5'2  H  HCH2  0   0.292  -1.4706  -0.7696   3.5924
 NEA  H4'   H  HCH1  0   0.273  -2.3571   1.1291   2.4536
 NEA  H3'   H  HCH1  0   0.254  -3.1772  -1.3812   1.7102
 NEA  H3T   H  HOH1  0   0.451  -4.4979  -0.1304   0.0891
 NEA  H2'   H  HCH1  0   0.251  -1.4107  -1.6622   0.0820
 NEA  HO'2  H  HOH1  0   0.470  -3.1523  -2.1522  -1.1821
 NEA  H1'   H  HCH1  0   0.265  -1.9750   1.0681  -1.1107
 NEA  H8    H  HCR5  0   0.291   1.1883  -0.2301   0.5448
 NEA  H61   H  HNH2  0   0.403   3.5398  -0.3094  -5.1637
 NEA  H62   H  HNH2  0   0.411   3.8783  -0.5684  -3.4908
 NEA  H2    H  HCR6  0   0.251  -0.7774   0.8635  -5.4487

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
 NEA  N    CB    single    1.454  0.020  1.454
 NEA  N    HN1   single    0.890  0.020  1.040
 NEA  N    HN2   single    0.890  0.020  1.040
 NEA  CB   CG    single    1.521  0.020  1.521
 NEA  CB   HB1   single    0.970  0.020  1.090
 NEA  CB   HB2   single    0.970  0.020  1.090
 NEA  CG   SD    single    1.815  0.020  1.815
 NEA  CG   HG1   single    0.970  0.020  1.090
 NEA  CG   HG2   single    0.970  0.020  1.090
 NEA  SD   C5'   single    1.814  0.020  1.814
 NEA  C5'  C4'   single    1.520  0.020  1.520
 NEA  C5'  H5'1  single    0.970  0.020  1.090
 NEA  C5'  H5'2  single    0.970  0.020  1.090
 NEA  C4'  O4'   single    1.432  0.020  1.432
 NEA  C4'  C3'   single    1.522  0.020  1.522
 NEA  C4'  H4'   single    0.970  0.020  1.090
 NEA  O4'  C1'   single    1.396  0.020  1.396
 NEA  C3'  O3'   single    1.403  0.020  1.403
 NEA  C3'  C2'   single    1.531  0.020  1.531
 NEA  C3'  H3'   single    0.970  0.020  1.090
 NEA  O3'  H3T   single    0.850  0.020  0.980
 NEA  C2'  O2'   single    1.396  0.020  1.396
 NEA  C2'  C1'   single    1.532  0.020  1.532
 NEA  C2'  H2'   single    0.970  0.020  1.090
 NEA  O2'  HO'2  single    0.850  0.020  0.980
 NEA  C1'  N9    single    1.446  0.020  1.446
 NEA  C1'  H1'   single    0.970  0.020  1.090
 NEA  N9   C8    aromatic  1.370  0.020  1.370
 NEA  N9   C4    aromatic  1.365  0.020  1.365
 NEA  C8   N7    aromatic  1.301  0.020  1.301
 NEA  C8   H8    single    0.930  0.020  1.080
 NEA  N7   C5    aromatic  1.370  0.020  1.370
 NEA  C5   C6    aromatic  1.407  0.020  1.407
 NEA  C5   C4    aromatic  1.386  0.020  1.386
 NEA  C6   N6    single    1.334  0.020  1.334
 NEA  C6   N1    aromatic  1.338  0.020  1.338
 NEA  N6   H61   single    0.860  0.020  1.020
 NEA  N6   H62   single    0.860  0.020  1.020
 NEA  N1   C2    aromatic  1.331  0.020  1.331
 NEA  C2   N3    aromatic  1.321  0.020  1.321
 NEA  C2   H2    single    0.930  0.020  1.080
 NEA  N3   C4    aromatic  1.331  0.020  1.331

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
 NEA  HN2   N    HN1   105.61  3.000
 NEA  HN2   N    CB    109.42  3.000
 NEA  HN1   N    CB    109.12  3.000
 NEA  HB2   CB   HB1   106.66  3.000
 NEA  HB2   CB   CG    109.11  3.000
 NEA  HB1   CB   CG    109.06  3.000
 NEA  HB2   CB   N     108.33  3.000
 NEA  HB1   CB   N     113.79  3.000
 NEA  CG    CB   N     109.76  3.000
 NEA  HG2   CG   HG1   108.32  3.000
 NEA  HG2   CG   SD    108.86  3.000
 NEA  HG1   CG   SD    109.79  3.000
 NEA  HG2   CG   CB    110.36  3.000
 NEA  HG1   CG   CB    110.21  3.000
 NEA  SD    CG   CB    109.29  3.000
 NEA  C5'   SD   CG     99.71  3.000
 NEA  H5'2  C5'  H5'1  107.44  3.000
 NEA  H5'2  C5'  C4'   108.58  3.000
 NEA  H5'1  C5'  C4'   112.08  3.000
 NEA  H5'2  C5'  SD    109.09  3.000
 NEA  H5'1  C5'  SD    109.98  3.000
 NEA  C4'   C5'  SD    109.60  3.000
 NEA  H4'   C4'  C3'   111.44  3.000
 NEA  H4'   C4'  O4'   107.65  3.000
 NEA  C3'   C4'  O4'   105.22  3.000
 NEA  H4'   C4'  C5'   108.88  3.000
 NEA  C3'   C4'  C5'   112.34  3.000
 NEA  O4'   C4'  C5'   111.19  3.000
 NEA  C1'   O4'  C4'   111.05  3.000
 NEA  H3'   C3'  C2'   112.04  3.000
 NEA  H3'   C3'  O3'   111.95  3.000
 NEA  C2'   C3'  O3'   110.94  3.000
 NEA  H3'   C3'  C4'   111.92  3.000
 NEA  C2'   C3'  C4'   100.84  3.000
 NEA  O3'   C3'  C4'   108.60  3.000
 NEA  H3T   O3'  C3'   108.00  3.000
 NEA  H2'   C2'  C1'   109.29  3.000
 NEA  H2'   C2'  O2'   111.41  3.000
 NEA  C1'   C2'  O2'   109.96  3.000
 NEA  H2'   C2'  C3'   109.36  3.000
 NEA  C1'   C2'  C3'   101.46  3.000
 NEA  O2'   C2'  C3'   114.85  3.000
 NEA  HO'2  O2'  C2'   108.82  3.000
 NEA  H1'   C1'  N9    106.32  3.000
 NEA  H1'   C1'  C2'   110.22  3.000
 NEA  N9    C1'  C2'   113.54  3.000
 NEA  H1'   C1'  O4'   111.38  3.000
 NEA  N9    C1'  O4'   109.17  3.000
 NEA  C2'   C1'  O4'   106.28  3.000
 NEA  C4    N9   C8    106.34  3.000
 NEA  C4    N9   C1'   126.13  3.000
 NEA  C8    N9   C1'   127.48  3.000
 NEA  H8    C8   N7    124.73  3.000
 NEA  H8    C8   N9    121.99  3.000
 NEA  N7    C8   N9    113.24  3.000
 NEA  C5    N7   C8    104.45  3.000
 NEA  C4    C5   C6    116.36  3.000
 NEA  C4    C5   N7    110.86  3.000
 NEA  C6    C5   N7    132.79  3.000
 NEA  N1    C6   N6    119.38  3.000
 NEA  N1    C6   C5    117.93  3.000
 NEA  N6    C6   C5    122.69  3.000
 NEA  H62   N6   H61   118.38  3.000
 NEA  H62   N6   C6    121.16  3.000
 NEA  H61   N6   C6    120.37  3.000
 NEA  C2    N1   C6    119.09  3.000
 NEA  H2    C2   N3    116.10  3.000
 NEA  H2    C2   N1    115.37  3.000
 NEA  N3    C2   N1    128.53  3.000
 NEA  C4    N3   C2    111.68  3.000
 NEA  N3    C4   C5    126.41  3.000
 NEA  N3    C4   N9    128.48  3.000
 NEA  C5    C4   N9    105.11  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
 NEA  CONST_01  C5   N7   C8  N9      0.00   0.0  0
 NEA  CONST_02  N7   C5   C4  N9      0.00   0.0  0
 NEA  CONST_03  C6   C5   C4  N9    180.00   0.0  0
 NEA  CONST_04  C2   N3   C4  N9    180.00   0.0  0
 NEA  CONST_05  C5   C4   N9  C8      0.00   0.0  0
 NEA  CONST_06  N3   C4   N9  C8    180.00   0.0  0
 NEA  CONST_07  C6   C5   N7  C8    180.00   0.0  0
 NEA  CONST_08  C4   C5   N7  C8      0.00   0.0  0
 NEA  CONST_09  C4   N9   C8  N7      0.00   0.0  0
 NEA  CONST_10  N1   C6   C5  N7    180.00   0.0  0
 NEA  CONST_11  N3   C4   C5  N7    180.00   0.0  0
 NEA  CONST_12  C2   N1   C6  C5      0.00   0.0  0
 NEA  CONST_13  C2   N3   C4  C5      0.00   0.0  0
 NEA  CONST_14  N3   C4   C5  C6      0.00   0.0  0
 NEA  CONST_15  N3   C2   N1  C6      0.00   0.0  0
 NEA  CONST_16  C4   C5   C6  N1      0.00   0.0  0
 NEA  CONST_17  C4   N3   C2  N1      0.00   0.0  0
 NEA  CONST_18  N7   C8   N9  C1'   180.00   0.0  0
 NEA  CONST_19  C5   C4   N9  C1'   180.00   0.0  0
 NEA  CONST_20  N3   C4   N9  C1'     0.00   0.0  0
 NEA  CONST_21  N6   C6   C5  N7      0.00   0.0  0
 NEA  CONST_22  C4   C5   C6  N6    180.00   0.0  0
 NEA  CONST_23  C2   N1   C6  N6    180.00   0.0  0
 NEA  CONST_24  H8   C8   N9  C1'     0.00   0.0  0
 NEA  CONST_25  H2   C2   N1  C6    180.00   0.0  0
 NEA  CONST_26  H61  N6   C6  C5    180.00   0.0  0
 NEA  CONST_27  H62  N6   C6  C5      0.00   0.0  0
 NEA  Var_01    C4'  C5'  SD  CG    162.50  30.0  3
 NEA  Var_02    SD   CG   CB  N    -179.75  30.0  3
 NEA  Var_03    HN1  N    CB  CG    173.65  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
 NEA  chir_01  C4'  C5'  O4'  C3'  negativ
 NEA  chir_02  C3'  O3'  C4'  C2'  positiv
 NEA  chir_03  C2'  O2'  C3'  C1'  positiv
 NEA  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
 NEA  plan-1  C1'  0.020
 NEA  plan-1  N9   0.020
 NEA  plan-1  C8   0.020
 NEA  plan-1  N7   0.020
 NEA  plan-1  C5   0.020
 NEA  plan-1  C6   0.020
 NEA  plan-1  N6   0.020
 NEA  plan-1  N1   0.020
 NEA  plan-1  C2   0.020
 NEA  plan-1  N3   0.020
 NEA  plan-1  C4   0.020
 NEA  plan-1  H8   0.020
 NEA  plan-1  H2   0.020
 NEA  plan-2  C6   0.020
 NEA  plan-2  N6   0.020
 NEA  plan-2  H61  0.020
 NEA  plan-2  H62  0.020

