# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:14:55 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 5'-O-[(S)-{[(S)-amino(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](N)(O)=O)[C@@H](O)[C@H]3O
#
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
 AN2  AN2  5'-O-[(S)-{[(S)-amino(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine  ligand  43  27  .  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_AN2
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
 AN2  N3B   N  NH2   0  -0.944  -5.5987   2.3706  -0.5904
 AN2  PB    P  P     0   1.420  -5.3726   0.8904   0.0740
 AN2  O2B   O  OH1   0  -0.742  -4.5693   0.9401   1.4596
 AN2  O1B   O  O     0  -0.687  -6.5832   0.0651   0.2185
 AN2  O3A   O  O2    0  -0.691  -4.2674   0.2963  -0.9802
 AN2  PA    P  P     0   1.483  -3.1839  -0.8605  -0.6872
 AN2  O1A   O  O     0  -0.691  -3.6506  -2.0021   0.1128
 AN2  O2A   O  OH1   0  -0.717  -2.7384  -1.2970  -2.1440
 AN2  O5'   O  O2    0  -0.588  -1.9982   0.0070  -0.0682
 AN2  C5'   C  CH2   0  -0.191  -1.0487  -0.5604   0.8405
 AN2  C4'   C  CH1   0  -0.018  -0.0783  -1.4958   0.1578
 AN2  O4'   O  O2    0  -0.490   0.6285  -0.8195  -0.8765
 AN2  C3'   C  CH1   0  -0.032   0.9954  -2.0137   1.1131
 AN2  O3'   O  OH1   0  -0.653   0.5390  -3.1551   1.7773
 AN2  C2'   C  CH1   0  -0.043   2.1592  -2.2704   0.1494
 AN2  O2'   O  OH1   0  -0.661   1.9569  -3.4479  -0.5802
 AN2  C1'   C  CH1   0   0.173   1.9945  -1.1021  -0.8188
 AN2  N9    N  NR5   0  -0.539   2.7112   0.0804  -0.3495
 AN2  C8    C  CR15  0   0.101   2.2038   1.2685   0.1013
 AN2  N7    N  N     0  -0.449   3.1221   2.1344   0.4178
 AN2  C5    C  CR56  0  -0.002   4.3021   1.4910   0.1566
 AN2  C4    C  CR56  0   0.488   4.0688   0.2139  -0.3274
 AN2  N3    N  N     0  -0.459   4.9884  -0.6788  -0.6907
 AN2  C2    C  CR16  0   0.040   6.2128  -0.2056  -0.5357
 AN2  N1    N  N     0  -0.474   6.5877   0.9881  -0.0831
 AN2  C6    C  CR6   0   0.459   5.6516   1.8735   0.2768
 AN2  N6    N  NH2   0  -0.816   6.0233   3.0711   0.7288
 AN2  H3B1  H  HNH2  0   0.421  -6.3876   2.8980  -0.2437
 AN2  H3B2  H  HNH2  0   0.418  -4.7990   2.9606  -0.7742
 AN2  HO2B  H  HOH1  0   0.495  -3.9244   1.6534   1.5539
 AN2  HO2A  H  HOH1  0   0.505  -2.3187  -0.6243  -2.6981
 AN2  H5'1  H  HCH2  0   0.268  -1.5588  -1.0960   1.6443
 AN2  H5'2  H  HCH2  0   0.259  -0.5275   0.2882   1.2838
 AN2  H4'   H  HCH1  0   0.260  -0.6175  -2.3490  -0.2724
 AN2  H3'   H  HCH1  0   0.250   1.2790  -1.2223   1.8198
 AN2  HA    H  HOH1  0   0.471   1.0752  -3.2911   2.5650
 AN2  H2'   H  HCH1  0   0.267   3.1329  -2.2594   0.6528
 AN2  HB    H  HOH1  0   0.454   1.6387  -4.1247   0.0296
 AN2  H1'   H  HCH1  0   0.292   2.3724  -1.3427  -1.8157
 AN2  H8    H  HCR5  0   0.294   1.1436   1.4519   0.1653
 AN2  H2    H  HCR6  0   0.253   7.0217  -0.8737  -0.8118
 AN2  H6N1  H  HNH2  0   0.404   6.9975   3.3079   0.8020
 AN2  H6N2  H  HNH2  0   0.412   5.3431   3.7532   1.0142

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
 AN2  N3B  PB    single    1.638  0.020  1.638
 AN2  N3B  H3B1  single    0.890  0.020  1.040
 AN2  N3B  H3B2  single    0.890  0.020  1.040
 AN2  PB   O2B   single    1.602  0.020  1.602
 AN2  PB   O1B   double    1.472  0.020  1.472
 AN2  PB   O3A   single    1.639  0.020  1.639
 AN2  O2B  HO2B  single    0.850  0.020  0.980
 AN2  O3A  PA    single    1.612  0.020  1.612
 AN2  PA   O1A   double    1.470  0.020  1.470
 AN2  PA   O2A   single    1.585  0.020  1.585
 AN2  PA   O5'   single    1.594  0.020  1.594
 AN2  O2A  HO2A  single    0.850  0.020  0.980
 AN2  O5'  C5'   single    1.431  0.020  1.431
 AN2  C5'  C4'   single    1.511  0.020  1.511
 AN2  C5'  H5'1  single    0.970  0.020  1.090
 AN2  C5'  H5'2  single    0.970  0.020  1.090
 AN2  C4'  O4'   single    1.424  0.020  1.424
 AN2  C4'  C3'   single    1.528  0.020  1.528
 AN2  C4'  H4'   single    0.970  0.020  1.090
 AN2  O4'  C1'   single    1.396  0.020  1.396
 AN2  C3'  O3'   single    1.397  0.020  1.397
 AN2  C3'  C2'   single    1.533  0.020  1.533
 AN2  C3'  H3'   single    0.970  0.020  1.090
 AN2  O3'  HA    single    0.850  0.020  0.980
 AN2  C2'  O2'   single    1.400  0.020  1.400
 AN2  C2'  C1'   single    1.526  0.020  1.526
 AN2  C2'  H2'   single    0.970  0.020  1.090
 AN2  O2'  HB    single    0.850  0.020  0.980
 AN2  C1'  N9    single    1.460  0.020  1.460
 AN2  C1'  H1'   single    0.970  0.020  1.090
 AN2  N9   C8    aromatic  1.368  0.020  1.368
 AN2  N9   C4    aromatic  1.364  0.020  1.364
 AN2  C8   N7    aromatic  1.301  0.020  1.301
 AN2  C8   H8    single    0.930  0.020  1.080
 AN2  N7   C5    aromatic  1.369  0.020  1.369
 AN2  C5   C4    aromatic  1.386  0.020  1.386
 AN2  C5   C6    aromatic  1.408  0.020  1.408
 AN2  C4   N3    aromatic  1.332  0.020  1.332
 AN2  N3   C2    aromatic  1.322  0.020  1.322
 AN2  C2   N1    aromatic  1.331  0.020  1.331
 AN2  C2   H2    single    0.930  0.020  1.080
 AN2  N1   C6    aromatic  1.338  0.020  1.338
 AN2  C6   N6    single    1.333  0.020  1.333
 AN2  N6   H6N1  single    0.860  0.020  1.020
 AN2  N6   H6N2  single    0.860  0.020  1.020

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
 AN2  H3B2  N3B  H3B1  112.05  3.000
 AN2  H3B2  N3B  PB    119.48  3.000
 AN2  H3B1  N3B  PB    116.12  3.000
 AN2  O3A   PB   O1B   114.49  3.000
 AN2  O3A   PB   O2B   103.26  3.000
 AN2  O1B   PB   O2B   110.17  3.000
 AN2  O3A   PB   N3B    99.19  3.000
 AN2  O1B   PB   N3B   115.65  3.000
 AN2  O2B   PB   N3B   113.07  3.000
 AN2  HO2B  O2B  PB    116.22  3.000
 AN2  PA    O3A  PB    126.63  3.000
 AN2  O5'   PA   O2A   107.32  3.000
 AN2  O5'   PA   O1A   116.58  3.000
 AN2  O2A   PA   O1A   112.06  3.000
 AN2  O5'   PA   O3A   100.37  3.000
 AN2  O2A   PA   O3A   102.68  3.000
 AN2  O1A   PA   O3A   116.29  3.000
 AN2  HO2A  O2A  PA    117.20  3.000
 AN2  C5'   O5'  PA    121.61  3.000
 AN2  H5'2  C5'  H5'1  107.80  3.000
 AN2  H5'2  C5'  C4'   111.02  3.000
 AN2  H5'1  C5'  C4'   109.20  3.000
 AN2  H5'2  C5'  O5'   105.47  3.000
 AN2  H5'1  C5'  O5'   110.59  3.000
 AN2  C4'   C5'  O5'   112.62  3.000
 AN2  H4'   C4'  C3'   109.08  3.000
 AN2  H4'   C4'  O4'   109.18  3.000
 AN2  C3'   C4'  O4'   105.45  3.000
 AN2  H4'   C4'  C5'   110.06  3.000
 AN2  C3'   C4'  C5'   112.26  3.000
 AN2  O4'   C4'  C5'   110.68  3.000
 AN2  C1'   O4'  C4'   111.08  3.000
 AN2  H3'   C3'  C2'   109.22  3.000
 AN2  H3'   C3'  O3'   111.53  3.000
 AN2  C2'   C3'  O3'   114.22  3.000
 AN2  H3'   C3'  C4'   109.85  3.000
 AN2  C2'   C3'  C4'   101.38  3.000
 AN2  O3'   C3'  C4'   110.16  3.000
 AN2  HA    O3'  C3'   108.81  3.000
 AN2  H2'   C2'  C1'   112.30  3.000
 AN2  H2'   C2'  O2'   112.09  3.000
 AN2  C1'   C2'  O2'   107.32  3.000
 AN2  H2'   C2'  C3'   112.59  3.000
 AN2  C1'   C2'  C3'   100.88  3.000
 AN2  O2'   C2'  C3'   111.03  3.000
 AN2  HB    O2'  C2'   107.95  3.000
 AN2  H1'   C1'  N9    107.56  3.000
 AN2  H1'   C1'  C2'   111.88  3.000
 AN2  N9    C1'  C2'   111.29  3.000
 AN2  H1'   C1'  O4'   110.19  3.000
 AN2  N9    C1'  O4'   109.25  3.000
 AN2  C2'   C1'  O4'   106.66  3.000
 AN2  C4    N9   C8    106.18  3.000
 AN2  C4    N9   C1'   124.95  3.000
 AN2  C8    N9   C1'   128.83  3.000
 AN2  H8    C8   N7    124.50  3.000
 AN2  H8    C8   N9    122.15  3.000
 AN2  N7    C8   N9    113.35  3.000
 AN2  C5    N7   C8    104.42  3.000
 AN2  C6    C5   C4    116.21  3.000
 AN2  C6    C5   N7    133.01  3.000
 AN2  C4    C5   N7    110.77  3.000
 AN2  N3    C4   C5    126.63  3.000
 AN2  N3    C4   N9    128.09  3.000
 AN2  C5    C4   N9    105.28  3.000
 AN2  C2    N3   C4    111.57  3.000
 AN2  H2    C2   N1    115.40  3.000
 AN2  H2    C2   N3    116.13  3.000
 AN2  N1    C2   N3    128.46  3.000
 AN2  C6    N1   C2    119.22  3.000
 AN2  N6    C6   N1    119.39  3.000
 AN2  N6    C6   C5    122.71  3.000
 AN2  N1    C6   C5    117.90  3.000
 AN2  H6N2  N6   H6N1  118.39  3.000
 AN2  H6N2  N6   C6    121.17  3.000
 AN2  H6N1  N6   C6    120.44  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
 AN2  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 AN2  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 AN2  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 AN2  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 AN2  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 AN2  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 AN2  CONST_07  C4    C5   N7   C8     0.00   0.0  0
 AN2  CONST_08  C6    C5   N7   C8   180.00   0.0  0
 AN2  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 AN2  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 AN2  CONST_11  N1    C6   C5   N7   180.00   0.0  0
 AN2  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 AN2  CONST_13  C2    N1   C6   C5     0.00   0.0  0
 AN2  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 AN2  CONST_15  N1    C2   N3   C4     0.00   0.0  0
 AN2  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 AN2  CONST_17  C6    N1   C2   N3     0.00   0.0  0
 AN2  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 AN2  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 AN2  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 AN2  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 AN2  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 AN2  CONST_23  N6    C6   N1   C2   180.00   0.0  0
 AN2  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 AN2  CONST_25  H2    C2   N3   C4   180.00   0.0  0
 AN2  CONST_26  H6N1  N6   C6   C5   180.00   0.0  0
 AN2  CONST_27  H6N2  N6   C6   C5     0.00   0.0  0
 AN2  Var_01    C4'   C5'  O5'  PA    72.51  30.0  3
 AN2  Var_02    O1A   PA   O3A  PB    40.54  30.0  3
 AN2  Var_03    H3B1  N3B  PB   O2B  -83.47  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
 AN2  chir_03  C4'  C5'  O4'  C3'  negativ
 AN2  chir_04  C3'  O3'  C4'  C2'  positiv
 AN2  chir_05  C2'  O2'  C3'  C1'  positiv
 AN2  chir_06  C1'  O4'  N9   C2'  negativ
 AN2  chir_07  PB   O2B  O1B  O3A  both
 AN2  chir_08  PA   O1A  O2A  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
 AN2  plan-1  C1'   0.020
 AN2  plan-1  N9    0.020
 AN2  plan-1  C8    0.020
 AN2  plan-1  N7    0.020
 AN2  plan-1  C5    0.020
 AN2  plan-1  C4    0.020
 AN2  plan-1  N3    0.020
 AN2  plan-1  C2    0.020
 AN2  plan-1  N1    0.020
 AN2  plan-1  C6    0.020
 AN2  plan-1  N6    0.020
 AN2  plan-1  H8    0.020
 AN2  plan-1  H2    0.020
 AN2  plan-2  C6    0.020
 AN2  plan-2  N6    0.020
 AN2  plan-2  H6N1  0.020
 AN2  plan-2  H6N2  0.020

