# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 05:28:31 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[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
 ND7  ND7  5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine  ligand  37  23  .  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_ND7
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
 ND7  O1A  O  OP    -1  -0.806  -4.9952   1.6651  -1.4872
 ND7  PA   P  P      0   1.303  -4.5198   1.1106  -0.1786
 ND7  O2A  O  O      0  -0.817  -4.2246   1.9838   1.0061
 ND7  N3A  N  NH2    0  -0.987  -5.6078  -0.0832   0.3315
 ND7  O5'  O  O2     0  -0.624  -3.1287   0.2951  -0.5907
 ND7  C5'  C  CH2    0  -0.154  -2.3799  -0.3256   0.4218
 ND7  C4'  C  CH1    0   0.003  -1.4001  -1.2866  -0.2071
 ND7  C3'  C  CH1    0  -0.043  -0.4957  -1.9846   0.8036
 ND7  O3'  O  OH1    0  -0.656  -1.1283  -3.1211   1.3202
 ND7  C2'  C  CH1    0  -0.041   0.7406  -2.2964  -0.0474
 ND7  O2'  O  OH1    0  -0.665   0.5166  -3.4062  -0.8726
 ND7  C1'  C  CH1    0   0.175   0.8001  -1.0570  -0.9394
 ND7  O4'  O  O2     0  -0.495  -0.5062  -0.5908  -1.0770
 ND7  N9   N  NR5    0  -0.535   1.6193  -0.0055  -0.3456
 ND7  C4   C  CR56   0   0.486   2.9821  -0.0003  -0.3156
 ND7  C5   C  CR56   0  -0.002   3.3292   1.1839   0.3151
 ND7  N7   N  N      0  -0.452   2.2110   1.8947   0.6614
 ND7  C8   C  CR15   0   0.102   1.2190   1.1581   0.2507
 ND7  N3   N  N      0  -0.459   3.8166  -0.9246  -0.7888
 ND7  C2   C  CR16   0   0.039   5.0787  -0.5857  -0.5916
 ND7  N1   N  N      0  -0.474   5.5597   0.5090  -0.0075
 ND7  C6   C  CR6    0   0.457   4.7078   1.4268   0.4633
 ND7  N6   N  NH2    0  -0.816   5.1880   2.5220   1.0536
 ND7  H2   H  HNH2   0   0.366  -5.7917  -0.8268  -0.3278
 ND7  H3   H  HNH2   0   0.367  -5.4403  -0.4760   1.2469
 ND7  H4   H  HCH2   0   0.204  -1.8464   0.4103   1.0371
 ND7  H5   H  HCH2   0   0.211  -3.0138  -0.9096   1.1032
 ND7  H6   H  HCH1   0   0.243  -1.9540  -2.0358  -0.7865
 ND7  H7   H  HCH1   0   0.246  -0.2159  -1.2833   1.6013
 ND7  H8   H  HOH1   0   0.469  -0.6857  -3.3805   2.1349
 ND7  H9   H  HCH1   0   0.260   1.6494  -2.4134   0.5549
 ND7  H10  H  HOH1   0   0.452  -0.0162  -4.0403  -0.3764
 ND7  H11  H  HCH1   0   0.283   1.2340  -1.2891  -1.9161
 ND7  H12  H  HCR5   0   0.296   0.1779   1.4210   0.3470
 ND7  H13  H  HCR6   0   0.252   5.8242  -1.2875  -0.9505
 ND7  H14  H  HNH2   0   0.411   4.5739   3.2496   1.3740
 ND7  H15  H  HNH2   0   0.403   6.1794   2.6836   1.0930

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
 ND7  O2A  PA   deloc     1.501  0.020  1.501
 ND7  N3A  PA   single    1.694  0.020  1.694
 ND7  PA   O5'  single    1.664  0.020  1.664
 ND7  PA   O1A  deloc     1.499  0.020  1.499
 ND7  O5'  C5'  single    1.404  0.020  1.404
 ND7  C5'  C4'  single    1.510  0.020  1.510
 ND7  O3'  C3'  single    1.399  0.020  1.399
 ND7  C4'  C3'  single    1.525  0.020  1.525
 ND7  C4'  O4'  single    1.428  0.020  1.428
 ND7  C3'  C2'  single    1.533  0.020  1.533
 ND7  O4'  C1'  single    1.394  0.020  1.394
 ND7  C1'  C2'  single    1.528  0.020  1.528
 ND7  C1'  N9   single    1.459  0.020  1.459
 ND7  C2'  O2'  single    1.401  0.020  1.401
 ND7  N9   C8   aromatic  1.367  0.020  1.367
 ND7  N9   C4   aromatic  1.363  0.020  1.363
 ND7  N3   C4   aromatic  1.332  0.020  1.332
 ND7  N3   C2   aromatic  1.322  0.020  1.322
 ND7  C8   N7   aromatic  1.302  0.020  1.302
 ND7  C4   C5   aromatic  1.386  0.020  1.386
 ND7  C2   N1   aromatic  1.331  0.020  1.331
 ND7  N7   C5   aromatic  1.370  0.020  1.370
 ND7  C5   C6   aromatic  1.408  0.020  1.408
 ND7  N1   C6   aromatic  1.338  0.020  1.338
 ND7  C6   N6   single    1.334  0.020  1.334
 ND7  N3A  H2   single    0.890  0.020  1.040
 ND7  N3A  H3   single    0.890  0.020  1.040
 ND7  C5'  H4   single    0.970  0.020  1.090
 ND7  C5'  H5   single    0.970  0.020  1.090
 ND7  C4'  H6   single    0.970  0.020  1.090
 ND7  C3'  H7   single    0.970  0.020  1.090
 ND7  O3'  H8   single    0.850  0.020  0.980
 ND7  C2'  H9   single    0.970  0.020  1.090
 ND7  O2'  H10  single    0.850  0.020  0.980
 ND7  C1'  H11  single    0.970  0.020  1.090
 ND7  C8   H12  single    0.930  0.020  1.080
 ND7  C2   H13  single    0.930  0.020  1.080
 ND7  N6   H14  single    0.860  0.020  1.020
 ND7  N6   H15  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
 ND7  O5'  PA   N3A  105.43  3.000
 ND7  O5'  PA   O2A  108.42  3.000
 ND7  N3A  PA   O2A  107.38  3.000
 ND7  O5'  PA   O1A  103.31  3.000
 ND7  N3A  PA   O1A  108.66  3.000
 ND7  O2A  PA   O1A  122.43  3.000
 ND7  H3   N3A  H2   109.59  3.000
 ND7  H3   N3A  PA   116.13  3.000
 ND7  H2   N3A  PA   116.04  3.000
 ND7  C5'  O5'  PA   118.94  3.000
 ND7  H5   C5'  H4   106.80  3.000
 ND7  H5   C5'  C4'  107.13  3.000
 ND7  H4   C5'  C4'  110.18  3.000
 ND7  H5   C5'  O5'  112.00  3.000
 ND7  H4   C5'  O5'  111.53  3.000
 ND7  C4'  C5'  O5'  109.10  3.000
 ND7  H6   C4'  O4'  109.08  3.000
 ND7  H6   C4'  C3'  109.69  3.000
 ND7  O4'  C4'  C3'  104.80  3.000
 ND7  H6   C4'  C5'  109.08  3.000
 ND7  O4'  C4'  C5'  110.47  3.000
 ND7  C3'  C4'  C5'  113.58  3.000
 ND7  H7   C3'  C2'  109.13  3.000
 ND7  H7   C3'  O3'  111.45  3.000
 ND7  C2'  C3'  O3'  113.85  3.000
 ND7  H7   C3'  C4'  109.88  3.000
 ND7  C2'  C3'  C4'  101.73  3.000
 ND7  O3'  C3'  C4'  110.37  3.000
 ND7  H8   O3'  C3'  108.87  3.000
 ND7  H9   C2'  C1'  112.02  3.000
 ND7  H9   C2'  O2'  111.81  3.000
 ND7  C1'  C2'  O2'  107.75  3.000
 ND7  H9   C2'  C3'  112.65  3.000
 ND7  O2'  C2'  C3'  111.05  3.000
 ND7  C1'  C2'  C3'  100.98  3.000
 ND7  H10  O2'  C2'  107.81  3.000
 ND7  H11  C1'  N9   107.07  3.000
 ND7  H11  C1'  O4'  110.77  3.000
 ND7  N9   C1'  O4'  108.98  3.000
 ND7  H11  C1'  C2'  111.38  3.000
 ND7  N9   C1'  C2'  111.64  3.000
 ND7  O4'  C1'  C2'  107.01  3.000
 ND7  C1'  O4'  C4'  111.31  3.000
 ND7  C8   N9   C4   106.25  3.000
 ND7  C4   N9   C1'  124.96  3.000
 ND7  C8   N9   C1'  128.78  3.000
 ND7  N3   C4   C5   126.70  3.000
 ND7  C5   C4   N9   105.29  3.000
 ND7  N3   C4   N9   128.01  3.000
 ND7  C6   C5   N7   133.11  3.000
 ND7  C6   C5   C4   116.15  3.000
 ND7  N7   C5   C4   110.73  3.000
 ND7  C8   N7   C5   104.40  3.000
 ND7  H12  C8   N7   124.72  3.000
 ND7  H12  C8   N9   121.94  3.000
 ND7  N7   C8   N9   113.33  3.000
 ND7  C2   N3   C4   111.55  3.000
 ND7  H13  C2   N1   115.40  3.000
 ND7  H13  C2   N3   116.17  3.000
 ND7  N1   C2   N3   128.43  3.000
 ND7  C6   N1   C2   119.25  3.000
 ND7  N6   C6   N1   119.33  3.000
 ND7  N6   C6   C5   122.75  3.000
 ND7  N1   C6   C5   117.92  3.000
 ND7  H15  N6   H14  118.29  3.000
 ND7  H15  N6   C6   120.30  3.000
 ND7  H14  N6   C6   121.05  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
 ND7  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 ND7  CONST_02  C2   N3   C4   N9   180.00   0.0  0
 ND7  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 ND7  CONST_04  C6   C5   C4   N9   180.00   0.0  0
 ND7  CONST_05  N7   C8   N9   C4     0.00   0.0  0
 ND7  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 ND7  CONST_07  C8   N7   C5   C4     0.00   0.0  0
 ND7  CONST_08  N1   C6   C5   C4     0.00   0.0  0
 ND7  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 ND7  CONST_10  C2   N3   C4   C5     0.00   0.0  0
 ND7  CONST_11  C2   N1   C6   C5     0.00   0.0  0
 ND7  CONST_12  N3   C4   C5   N7   180.00   0.0  0
 ND7  CONST_13  N1   C6   C5   N7   180.00   0.0  0
 ND7  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 ND7  CONST_15  C6   C5   N7   C8   180.00   0.0  0
 ND7  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 ND7  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 ND7  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 ND7  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 ND7  CONST_20  C5   C4   N9   C1'  180.00   0.0  0
 ND7  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 ND7  CONST_22  N6   C6   C5   N7     0.00   0.0  0
 ND7  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 ND7  CONST_24  H12  C8   N9   C1'    0.00   0.0  0
 ND7  CONST_25  H13  C2   N3   C4   180.00   0.0  0
 ND7  CONST_26  H14  N6   C6   C5     0.00   0.0  0
 ND7  CONST_27  H15  N6   C6   C5   180.00   0.0  0
 ND7  Var_01    C4'  C5'  O5'  PA   165.11  30.0  3
 ND7  Var_02    H2   N3A  PA   O1A   54.39  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
 ND7  chir_02  C4'  C5'  C3'  O4'  positiv
 ND7  chir_03  C3'  O3'  C2'  C4'  negativ
 ND7  chir_04  C2'  O2'  C1'  C3'  negativ
 ND7  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
 ND7  plan-1  C1'  0.020
 ND7  plan-1  N9   0.020
 ND7  plan-1  C4   0.020
 ND7  plan-1  C5   0.020
 ND7  plan-1  N7   0.020
 ND7  plan-1  C8   0.020
 ND7  plan-1  N3   0.020
 ND7  plan-1  C2   0.020
 ND7  plan-1  N1   0.020
 ND7  plan-1  C6   0.020
 ND7  plan-1  N6   0.020
 ND7  plan-1  H12  0.020
 ND7  plan-1  H13  0.020
 ND7  plan-2  C6   0.020
 ND7  plan-2  N6   0.020
 ND7  plan-2  H14  0.020
 ND7  plan-2  H15  0.020

