# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 02:46:46 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 5'-O-[(S)-{[(S)-{[(R)-[(2-amino-2-oxoethyl)sulfanyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CS[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[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
 112  112  5'-O-[(S)-{[(S)-{[(R)-[(2-amino-2-oxoethyl)sulfanyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine  ligand  54  35  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_112
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
 112  NS    N  NH2   0  -0.746  -22.4341  32.1923  12.2844
 112  C2S   C  C     0   0.516  -23.4735  31.6619  11.6677
 112  O2S   O  O     0  -0.550  -23.7075  31.8737  10.4706
 112  C1S   C  CH2   0  -0.730  -24.3780  30.7896  12.5121
 112  PG    P  P     0   1.205  -23.6821  28.1583  11.1036
 112  S1G   S  S2    0  -0.037  -23.6821  29.1510  12.9244
 112  O2G   O  OH1   0  -0.695  -22.7288  28.9665  10.1455
 112  O3G   O  O     0  -0.624  -23.4397  26.7178  11.2871
 112  PB    P  P     0   1.289  -25.8028  29.1673   9.2093
 112  O1B   O  O     0  -0.791  -27.2510  28.9309   9.1397
 112  O2B   O  OH1   0  -0.601  -25.3298  30.6369   9.1400
 112  O3B   O  O2    0  -0.584  -25.1676  28.5071  10.5443
 112  PA    P  P     0   1.423  -25.5310  27.1377   7.1694
 112  O1A   O  O     0  -0.757  -26.0674  26.0730   8.0278
 112  O2A   O  OH1   0  -0.626  -26.5426  27.7166   6.1132
 112  O3A   O  O2    0  -0.576  -24.9862  28.4269   8.0159
 112  O5'   O  O2    0  -0.552  -24.2437  26.8195   6.3016
 112  C5'   C  CH2   0  -0.221  -23.1572  25.9719   6.6673
 112  C4'   C  CH1   0   0.024  -21.8548  26.7071   6.4399
 112  O4'   O  O2    0  -0.538  -21.7541  27.2018   5.1054
 112  C3'   C  CH1   0   0.001  -21.6621  27.9356   7.3354
 112  O3'   O  OH1   0  -0.662  -21.1473  27.6330   8.6037
 112  C2'   C  CH1   0  -0.101  -20.8142  28.8438   6.4569
 112  O2'   O  OH1   0  -0.670  -19.5182  28.3152   6.4361
 112  C1'   C  CH1   0   0.131  -21.5056  28.5801   5.1127
 112  N9    N  NR5   0  -0.477  -22.7935  29.2829   4.9995
 112  C8    C  CR15  0   0.048  -23.8473  28.7843   4.2941
 112  N7    N  N     0  -0.400  -24.9511  29.4581   4.4565
 112  C5    C  CR56  0   0.039  -24.6059  30.4765   5.3122
 112  C6    C  CR6   0   0.417  -25.3466  31.5281   5.8780
 112  N6    N  NH2   0  -0.850  -26.6531  31.6903   5.6577
 112  N1    N  N     0  -0.392  -24.7058  32.3829   6.6789
 112  C2    C  CR16  0   0.025  -23.4159  32.1905   6.9232
 112  N3    N  N     0  -0.545  -22.6245  31.2383   6.4589
 112  C4    C  CR56  0   0.526  -23.2667  30.3969   5.6534
 112  HNS1  H  HNH2  0   0.412  -21.7742  32.7645  11.7803
 112  HNS2  H  HNH2  0   0.387  -22.2618  32.0385  13.2642
 112  H1S1  H  HCH2  0   0.328  -24.5399  31.2524  13.4864
 112  H1S2  H  HCH2  0   0.363  -25.3541  30.6764  12.0459
 112  HOG2  H  HOH1  0   0.504  -21.9524  28.4709   9.7432
 112  HOB2  H  HOH1  0   0.520  -24.5824  31.0514   9.7376
 112  HOA2  H  HOH1  0   0.521  -26.1689  28.3088   5.4128
 112  H5'1  H  HCH2  0   0.247  -23.2072  25.6591   7.7148
 112  H5'2  H  HCH2  0   0.320  -23.2060  25.0708   6.0545
 112  H4'   H  HCH1  0   0.304  -21.0562  25.9758   6.6061
 112  H3'   H  HCH1  0   0.290  -22.6211  28.4265   7.5087
 112  HO3'  H  HOH1  0   0.444  -20.1839  27.5552   8.5736
 112  H2'   H  HCH1  0   0.295  -20.8388  29.8891   6.7655
 112  HO2'  H  HOH1  0   0.456  -18.8974  29.0066   6.1881
 112  H1'   H  HCH1  0   0.306  -20.8845  28.8372   4.2540
 112  H8    H  HCR5  0   0.306  -23.7556  27.9073   3.6759
 112  HN61  H  HNH2  0   0.411  -27.1153  32.5098   6.0086
 112  HN62  H  HNH2  0   0.400  -27.1240  31.1598   4.9474
 112  H2    H  HCR6  0   0.269  -22.9513  32.9116   7.5860

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
 112  NS   C2S   single    1.320  0.020  1.320
 112  NS   HNS1  single    0.860  0.020  1.020
 112  NS   HNS2  single    0.860  0.020  1.020
 112  C2S  O2S   double    1.238  0.020  1.238
 112  C2S  C1S   single    1.514  0.020  1.514
 112  C1S  S1G   single    1.827  0.020  1.827
 112  C1S  H1S1  single    0.970  0.020  1.090
 112  C1S  H1S2  single    0.970  0.020  1.090
 112  PG   S1G   single    2.074  0.020  2.074
 112  PG   O2G   single    1.575  0.020  1.575
 112  PG   O3G   double    1.472  0.020  1.472
 112  PG   O3B   single    1.625  0.020  1.625
 112  O2G  HOG2  single    0.850  0.020  0.980
 112  PB   O1B   double    1.469  0.020  1.469
 112  PB   O2B   single    1.545  0.020  1.545
 112  PB   O3B   single    1.619  0.020  1.619
 112  PB   O3A   single    1.625  0.020  1.625
 112  O2B  HOB2  single    0.850  0.020  0.980
 112  PA   O1A   double    1.469  0.020  1.469
 112  PA   O2A   single    1.573  0.020  1.573
 112  PA   O3A   single    1.636  0.020  1.636
 112  PA   O5'   single    1.585  0.020  1.585
 112  O2A  HOA2  single    0.850  0.020  0.980
 112  O5'  C5'   single    1.426  0.020  1.426
 112  C5'  C4'   single    1.513  0.020  1.513
 112  C5'  H5'1  single    0.970  0.020  1.090
 112  C5'  H5'2  single    0.970  0.020  1.090
 112  C4'  O4'   single    1.427  0.020  1.427
 112  C4'  C3'   single    1.532  0.020  1.532
 112  C4'  H4'   single    0.970  0.020  1.090
 112  O4'  C1'   single    1.401  0.020  1.401
 112  C3'  O3'   single    1.402  0.020  1.402
 112  C3'  C2'   single    1.522  0.020  1.522
 112  C3'  H3'   single    0.970  0.020  1.090
 112  O3'  HO3'  single    0.850  0.020  0.980
 112  C2'  O2'   single    1.400  0.020  1.400
 112  C2'  C1'   single    1.534  0.020  1.534
 112  C2'  H2'   single    0.970  0.020  1.090
 112  O2'  HO2'  single    0.850  0.020  0.980
 112  C1'  N9    single    1.472  0.020  1.472
 112  C1'  H1'   single    0.970  0.020  1.090
 112  N9   C8    aromatic  1.363  0.020  1.363
 112  N9   C4    aromatic  1.376  0.020  1.376
 112  C8   N7    aromatic  1.303  0.020  1.303
 112  C8   H8    single    0.930  0.020  1.080
 112  N7   C5    aromatic  1.374  0.020  1.374
 112  C5   C6    aromatic  1.405  0.020  1.405
 112  C5   C4    aromatic  1.384  0.020  1.384
 112  C6   N6    single    1.335  0.020  1.335
 112  C6   N1    aromatic  1.335  0.020  1.335
 112  N6   HN61  single    0.860  0.020  1.020
 112  N6   HN62  single    0.860  0.020  1.020
 112  N1   C2    aromatic  1.327  0.020  1.327
 112  C2   N3    aromatic  1.322  0.020  1.322
 112  C2   H2    single    0.930  0.020  1.080
 112  N3   C4    aromatic  1.330  0.020  1.330

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
 112  HNS2  NS   HNS1  117.47  3.000
 112  HNS2  NS   C2S   121.89  3.000
 112  HNS1  NS   C2S   120.65  3.000
 112  C1S   C2S  O2S   121.67  3.000
 112  C1S   C2S  NS    116.19  3.000
 112  O2S   C2S  NS    122.13  3.000
 112  H1S2  C1S  H1S1  107.09  3.000
 112  H1S2  C1S  S1G   110.19  3.000
 112  H1S1  C1S  S1G   103.62  3.000
 112  H1S2  C1S  C2S   110.92  3.000
 112  H1S1  C1S  C2S   110.02  3.000
 112  S1G   C1S  C2S   114.52  3.000
 112  O3B   PG   O3G   113.80  3.000
 112  O3B   PG   O2G   103.52  3.000
 112  O3G   PG   O2G   118.58  3.000
 112  O3B   PG   S1G   101.50  3.000
 112  O3G   PG   S1G   111.03  3.000
 112  O2G   PG   S1G   106.77  3.000
 112  PG    S1G  C1S   103.36  3.000
 112  HOG2  O2G  PG    117.27  3.000
 112  O3A   PB   O3B   102.87  3.000
 112  O3A   PB   O2B   104.27  3.000
 112  O3B   PB   O2B   107.73  3.000
 112  O3A   PB   O1B   112.79  3.000
 112  O3B   PB   O1B   111.12  3.000
 112  O2B   PB   O1B   116.91  3.000
 112  HOB2  O2B  PB    124.86  3.000
 112  PB    O3B  PG    136.88  3.000
 112  O5'   PA   O3A    99.85  3.000
 112  O5'   PA   O2A   103.22  3.000
 112  O3A   PA   O2A   105.76  3.000
 112  O5'   PA   O1A   118.10  3.000
 112  O3A   PA   O1A   112.98  3.000
 112  O2A   PA   O1A   115.10  3.000
 112  HOA2  O2A  PA    116.89  3.000
 112  PA    O3A  PB    124.89  3.000
 112  C5'   O5'  PA    126.72  3.000
 112  H5'2  C5'  H5'1  107.43  3.000
 112  H5'2  C5'  C4'   110.83  3.000
 112  H5'1  C5'  C4'   108.79  3.000
 112  H5'2  C5'  O5'   108.24  3.000
 112  H5'1  C5'  O5'   112.37  3.000
 112  C4'   C5'  O5'   109.18  3.000
 112  H4'   C4'  C3'   110.78  3.000
 112  H4'   C4'  O4'   108.78  3.000
 112  C3'   C4'  O4'   105.05  3.000
 112  H4'   C4'  C5'   106.28  3.000
 112  C3'   C4'  C5'   114.21  3.000
 112  O4'   C4'  C5'   111.71  3.000
 112  C1'   O4'  C4'   110.42  3.000
 112  H3'   C3'  C2'   108.23  3.000
 112  H3'   C3'  O3'   106.03  3.000
 112  C2'   C3'  O3'   116.53  3.000
 112  H3'   C3'  C4'   110.05  3.000
 112  C2'   C3'  C4'   102.19  3.000
 112  O3'   C3'  C4'   113.69  3.000
 112  HO3'  O3'  C3'   110.80  3.000
 112  H2'   C2'  C1'   113.74  3.000
 112  H2'   C2'  O2'   112.78  3.000
 112  C1'   C2'  O2'   109.83  3.000
 112  H2'   C2'  C3'   113.35  3.000
 112  C1'   C2'  C3'    98.75  3.000
 112  O2'   C2'  C3'   107.40  3.000
 112  HO2'  O2'  C2'   109.26  3.000
 112  H1'   C1'  N9    108.99  3.000
 112  H1'   C1'  C2'   113.12  3.000
 112  N9    C1'  C2'   112.31  3.000
 112  H1'   C1'  O4'   109.21  3.000
 112  N9    C1'  O4'   108.32  3.000
 112  C2'   C1'  O4'   104.69  3.000
 112  C4    N9   C8    106.04  3.000
 112  C4    N9   C1'   130.64  3.000
 112  C8    N9   C1'   122.81  3.000
 112  H8    C8   N7    124.38  3.000
 112  H8    C8   N9    121.96  3.000
 112  N7    C8   N9    113.66  3.000
 112  C5    N7   C8    104.35  3.000
 112  C4    C5   C6    116.99  3.000
 112  C4    C5   N7    110.73  3.000
 112  C6    C5   N7    132.29  3.000
 112  N1    C6   N6    119.40  3.000
 112  N1    C6   C5    117.88  3.000
 112  N6    C6   C5    122.71  3.000
 112  HN62  N6   HN61  117.55  3.000
 112  HN62  N6   C6    120.78  3.000
 112  HN61  N6   C6    119.48  3.000
 112  C2    N1   C6    118.96  3.000
 112  H2    C2   N3    115.92  3.000
 112  H2    C2   N1    115.64  3.000
 112  N3    C2   N1    128.43  3.000
 112  C4    N3   C2    112.28  3.000
 112  N3    C4   C5    125.45  3.000
 112  N3    C4   N9    129.34  3.000
 112  C5    C4   N9    105.20  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
 112  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 112  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 112  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 112  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 112  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 112  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 112  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 112  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 112  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 112  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 112  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 112  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 112  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 112  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 112  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 112  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 112  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 112  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 112  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 112  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 112  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 112  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 112  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 112  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 112  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 112  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 112  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 112  CONST_28  HNS1  NS   C2S  O2S     0.00   0.0  0
 112  CONST_29  HNS2  NS   C2S  O2S   180.00   0.0  0
 112  Var_01    C4'   C5'  O5'  PA   -130.10  30.0  3
 112  Var_02    S1G   C1S  C2S  NS    -73.77  30.0  3
 112  Var_03    O2G   PG   S1G  C1S    62.26  30.0  1
 112  Var_04    O1B   PB   O3B  PG    166.45  30.0  1
 112  Var_05    O1A   PA   O3A  PB    -47.95  30.0  1

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
 112  chir_04  C4'  C5'  O4'  C3'  negativ
 112  chir_05  C3'  O3'  C4'  C2'  positiv
 112  chir_06  C2'  O2'  C3'  C1'  positiv
 112  chir_07  C1'  O4'  N9   C2'  negativ
 112  chir_08  PG   O2G  O3G  O3B  both
 112  chir_09  PB   O2B  O3B  O3A  both
 112  chir_10  PA   O2A  O3A  O5'  both

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
 112  plan-1  C1'   0.020
 112  plan-1  N9    0.020
 112  plan-1  C8    0.020
 112  plan-1  N7    0.020
 112  plan-1  C5    0.020
 112  plan-1  C6    0.020
 112  plan-1  N6    0.020
 112  plan-1  N1    0.020
 112  plan-1  C2    0.020
 112  plan-1  N3    0.020
 112  plan-1  C4    0.020
 112  plan-1  H8    0.020
 112  plan-1  H2    0.020
 112  plan-2  C6    0.020
 112  plan-2  N6    0.020
 112  plan-2  HN61  0.020
 112  plan-2  HN62  0.020
 112  plan-3  NS    0.020
 112  plan-3  C2S   0.020
 112  plan-3  O2S   0.020
 112  plan-3  C1S   0.020
 112  plan-3  HNS1  0.020
 112  plan-3  HNS2  0.020

