# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 10:52:17 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 5'-O-[(S)-{[(2S)-2-amino-3-hydroxypropanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=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
 SRP  SRP  5'-O-[(S)-{[(2S)-2-amino-3-hydroxypropanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  48  29  .  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_SRP
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
 SRP  PA    P  P     0   1.477  72.1444  33.5154  66.8828
 SRP  O1A   O  O     0  -0.667  71.4228  34.7180  66.4488
 SRP  O2A   O  OH1   0  -0.770  73.3508  33.0389  65.9908
 SRP  O3A   O  O2    0  -0.588  72.9723  33.6838  68.2907
 SRP  O5'   O  O2    0  -0.587  71.1592  32.2845  67.1288
 SRP  C5'   C  CH2   0  -0.261  71.6291  30.9666  67.4355
 SRP  C4'   C  CR15  0   0.037  71.4101  30.0100  66.2867
 SRP  O4'   O  O     0  -0.494  70.0558  29.5791  66.2168
 SRP  C3'   C  CR15  0  -0.018  71.6704  30.5534  64.8876
 SRP  O3'   O  OH1   0  -0.672  73.0485  30.7491  64.6877
 SRP  C2'   C  CR15  0  -0.065  70.9688  29.5078  64.0335
 SRP  O2'   O  OH1   0  -0.652  71.7584  28.3580  63.9901
 SRP  C1'   C  CR15  0   0.161  69.7013  29.2990  64.8926
 SRP  N9    N  NR5   0  -0.533  68.6243  30.1946  64.5035
 SRP  C8    C  CR15  0   0.101  68.2213  31.3626  65.0947
 SRP  N7    N  N     0  -0.449  67.2195  31.9262  64.4854
 SRP  C5    C  CR56  0  -0.001  66.9420  31.0906  63.4359
 SRP  C6    C  CR6   0   0.457  65.9875  31.1277  62.4025
 SRP  N6    N  NH2   0  -0.815  65.0857  32.1040  62.2865
 SRP  N1    N  N     0  -0.473  65.9880  30.1276  61.5137
 SRP  C2    C  CR16  0   0.041  66.8787  29.1472  61.6368
 SRP  N3    N  N     0  -0.459  67.8204  29.0045  62.5538
 SRP  C4    C  CR56  0   0.488  67.8046  30.0067  63.4303
 SRP  O     O  O     0  -0.396  71.1866  34.1764  69.5445
 SRP  C     C  C     0   0.612  72.3551  33.9427  69.4697
 SRP  CA    C  CH1   0  -0.265  73.3361  33.8646  70.6209
 SRP  N     N  NH2   0  -0.782  72.6607  34.2278  71.8447
 SRP  CB    C  CH2   0  -0.167  73.9980  32.4851  70.6146
 SRP  OG    O  OH1   0  -0.666  72.9672  31.5237  70.6089
 SRP  H2A   H  HOH1  0   0.510  73.3154  32.1785  65.4867
 SRP  H5'1  H  HCH2  0   0.264  72.6909  30.9632  67.6892
 SRP  H5'2  H  HCH2  0   0.292  71.0932  30.6234  68.3200
 SRP  H4'   H  HCR5  0   0.272  72.0633  29.1495  66.4772
 SRP  H3'   H  HCR5  0   0.258  71.1280  31.4957  64.7392
 SRP  H2    H  HOH1  0   0.490  73.2203  30.9427  63.7567
 SRP  H2'   H  HCR5  0   0.284  70.7154  29.8776  63.0335
 SRP  H1    H  HOH1  0   0.468  71.3490  27.7221  63.3947
 SRP  H1'   H  HCR5  0   0.290  69.3246  28.2765  64.7970
 SRP  H8    H  HCR5  0   0.295  68.7011  31.7500  65.9792
 SRP  HN61  H  HNH2  0   0.403  64.4825  32.1379  61.4826
 SRP  HN62  H  HNH2  0   0.411  65.1199  32.9111  62.8844
 SRP  H3    H  HCR6  0   0.253  66.8219  28.3684  60.8843
 SRP  HA    H  HCH1  0   0.298  74.1211  34.6038  70.4289
 SRP  HN1   H  HNH2  0   0.361  73.3486  34.3500  72.5764
 SRP  HN2   H  HNH2  0   0.349  72.0496  33.4790  72.1464
 SRP  HB1   H  HCH2  0   0.216  74.6593  32.3831  69.7478
 SRP  HB2   H  HCH2  0   0.227  74.6261  32.4115  71.5106
 SRP  HOG   H  HOH1  0   0.465  73.3618  30.6469  70.5962

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
 SRP  PA   O1A   double    1.468  0.020  1.468
 SRP  PA   O2A   single    1.574  0.020  1.574
 SRP  PA   O3A   single    1.642  0.020  1.642
 SRP  PA   O5'   single    1.596  0.020  1.596
 SRP  O2A  H2A   single    0.850  0.020  0.980
 SRP  O3A  C     single    1.356  0.020  1.356
 SRP  O5'  C5'   single    1.432  0.020  1.432
 SRP  C5'  C4'   single    1.511  0.020  1.511
 SRP  C5'  H5'1  single    0.970  0.020  1.090
 SRP  C5'  H5'2  single    0.970  0.020  1.090
 SRP  C4'  O4'   single    1.423  0.020  1.423
 SRP  C4'  C3'   single    1.523  0.020  1.523
 SRP  C4'  H4'   single    0.970  0.020  1.090
 SRP  O4'  C1'   single    1.399  0.020  1.399
 SRP  C3'  O3'   single    1.406  0.020  1.406
 SRP  C3'  C2'   single    1.522  0.020  1.522
 SRP  C3'  H3'   single    0.970  0.020  1.090
 SRP  O3'  H2    single    0.850  0.020  0.980
 SRP  C2'  O2'   single    1.395  0.020  1.395
 SRP  C2'  C1'   single    1.545  0.020  1.545
 SRP  C2'  H2'   single    0.970  0.020  1.090
 SRP  O2'  H1    single    0.850  0.020  0.980
 SRP  C1'  N9    single    1.454  0.020  1.454
 SRP  C1'  H1'   single    0.970  0.020  1.090
 SRP  N9   C8    aromatic  1.370  0.020  1.370
 SRP  N9   C4    aromatic  1.363  0.020  1.363
 SRP  C8   N7    aromatic  1.301  0.020  1.301
 SRP  C8   H8    single    0.930  0.020  1.080
 SRP  N7   C5    aromatic  1.370  0.020  1.370
 SRP  C5   C6    aromatic  1.407  0.020  1.407
 SRP  C5   C4    aromatic  1.385  0.020  1.385
 SRP  C6   N6    single    1.334  0.020  1.334
 SRP  C6   N1    aromatic  1.338  0.020  1.338
 SRP  N6   HN61  single    0.860  0.020  1.020
 SRP  N6   HN62  single    0.860  0.020  1.020
 SRP  N1   C2    aromatic  1.330  0.020  1.330
 SRP  C2   N3    aromatic  1.322  0.020  1.322
 SRP  C2   H3    single    0.930  0.020  1.080
 SRP  N3   C4    aromatic  1.332  0.020  1.332
 SRP  O    C     double    1.194  0.020  1.194
 SRP  C    CA    single    1.514  0.020  1.514
 SRP  CA   N     single    1.444  0.020  1.444
 SRP  CA   CB    single    1.530  0.020  1.530
 SRP  CA   HA    single    0.970  0.020  1.090
 SRP  N    HN1   single    0.890  0.020  1.040
 SRP  N    HN2   single    0.890  0.020  1.040
 SRP  CB   OG    single    1.410  0.020  1.410
 SRP  CB   HB1   single    0.970  0.020  1.090
 SRP  CB   HB2   single    0.970  0.020  1.090
 SRP  OG   HOG   single    0.850  0.020  0.980

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
 SRP  O5'   PA   O3A   104.97  3.000
 SRP  O5'   PA   O2A   109.09  3.000
 SRP  O3A   PA   O2A    97.50  3.000
 SRP  O5'   PA   O1A   111.96  3.000
 SRP  O3A   PA   O1A   114.66  3.000
 SRP  O2A   PA   O1A   117.20  3.000
 SRP  H2A   O2A  PA    121.34  3.000
 SRP  C     O3A  PA    122.39  3.000
 SRP  C5'   O5'  PA    122.70  3.000
 SRP  H5'2  C5'  H5'1  106.79  3.000
 SRP  H5'2  C5'  C4'   110.27  3.000
 SRP  H5'1  C5'  C4'   108.40  3.000
 SRP  H5'2  C5'  O5'   107.59  3.000
 SRP  H5'1  C5'  O5'   111.82  3.000
 SRP  C4'   C5'  O5'   111.85  3.000
 SRP  H4'   C4'  C3'   109.73  3.000
 SRP  H4'   C4'  O4'   109.74  3.000
 SRP  C3'   C4'  O4'   103.03  3.000
 SRP  H4'   C4'  C5'   106.16  3.000
 SRP  C3'   C4'  C5'   116.60  3.000
 SRP  O4'   C4'  C5'   111.53  3.000
 SRP  C1'   O4'  C4'   110.38  3.000
 SRP  H3'   C3'  C2'   106.64  3.000
 SRP  H3'   C3'  O3'   110.22  3.000
 SRP  C2'   C3'  O3'   117.89  3.000
 SRP  H3'   C3'  C4'   110.25  3.000
 SRP  C2'   C3'  C4'   101.05  3.000
 SRP  O3'   C3'  C4'   110.34  3.000
 SRP  H2    O3'  C3'   109.82  3.000
 SRP  H2'   C2'  C1'   111.30  3.000
 SRP  H2'   C2'  O2'   112.37  3.000
 SRP  C1'   C2'  O2'   111.72  3.000
 SRP  H2'   C2'  C3'   112.76  3.000
 SRP  C1'   C2'  C3'    99.15  3.000
 SRP  O2'   C2'  C3'   108.83  3.000
 SRP  H1    O2'  C2'   108.84  3.000
 SRP  H1'   C1'  N9    107.30  3.000
 SRP  H1'   C1'  C2'   111.11  3.000
 SRP  N9    C1'  C2'   112.06  3.000
 SRP  H1'   C1'  O4'   110.92  3.000
 SRP  N9    C1'  O4'   108.52  3.000
 SRP  C2'   C1'  O4'   106.94  3.000
 SRP  C4    N9   C8    106.28  3.000
 SRP  C4    N9   C1'   124.83  3.000
 SRP  C8    N9   C1'   128.89  3.000
 SRP  H8    C8   N7    124.83  3.000
 SRP  H8    C8   N9    121.97  3.000
 SRP  N7    C8   N9    113.20  3.000
 SRP  C5    N7   C8    104.51  3.000
 SRP  C4    C5   C6    116.11  3.000
 SRP  C4    C5   N7    110.74  3.000
 SRP  C6    C5   N7    133.15  3.000
 SRP  N1    C6   N6    119.31  3.000
 SRP  N1    C6   C5    117.90  3.000
 SRP  N6    C6   C5    122.79  3.000
 SRP  HN62  N6   HN61  117.97  3.000
 SRP  HN62  N6   C6    120.86  3.000
 SRP  HN61  N6   C6    119.98  3.000
 SRP  C2    N1   C6    119.32  3.000
 SRP  H3    C2   N3    116.17  3.000
 SRP  H3    C2   N1    115.47  3.000
 SRP  N3    C2   N1    128.36  3.000
 SRP  C4    N3   C2    111.52  3.000
 SRP  N3    C4   C5    126.80  3.000
 SRP  N3    C4   N9    127.93  3.000
 SRP  C5    C4   N9    105.27  3.000
 SRP  CA    C    O     126.61  3.000
 SRP  CA    C    O3A   110.87  3.000
 SRP  O     C    O3A   122.50  3.000
 SRP  HA    CA   CB    107.32  3.000
 SRP  HA    CA   N     108.30  3.000
 SRP  CB    CA   N     115.62  3.000
 SRP  HA    CA   C     107.23  3.000
 SRP  CB    CA   C     108.88  3.000
 SRP  N     CA   C     109.16  3.000
 SRP  HN2   N    HN1   106.51  3.000
 SRP  HN2   N    CA    110.42  3.000
 SRP  HN1   N    CA    108.98  3.000
 SRP  HB2   CB   HB1   107.13  3.000
 SRP  HB2   CB   OG    112.10  3.000
 SRP  HB1   CB   OG    112.01  3.000
 SRP  HB2   CB   CA    107.76  3.000
 SRP  HB1   CB   CA    110.39  3.000
 SRP  OG    CB   CA    107.38  3.000
 SRP  HOG   OG   CB    108.78  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
 SRP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 SRP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 SRP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 SRP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 SRP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 SRP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 SRP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 SRP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 SRP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 SRP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 SRP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 SRP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 SRP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 SRP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 SRP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 SRP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 SRP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 SRP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 SRP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 SRP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 SRP  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 SRP  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 SRP  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 SRP  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 SRP  CONST_25  H3    C2   N1   C6    180.00   0.0  0
 SRP  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 SRP  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 SRP  Var_01    C4'   C5'  O5'  PA   -109.42  30.0  3
 SRP  Var_02    O     C    O3A  PA     -6.48  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
 SRP  chir_02  C4'  C5'  O4'  C3'  negativ
 SRP  chir_03  C3'  O3'  C4'  C2'  positiv
 SRP  chir_04  C2'  O2'  C3'  C1'  positiv
 SRP  chir_05  C1'  O4'  N9   C2'  negativ
 SRP  chir_06  CA   C    N    CB   negativ
 SRP  chir_07  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
 SRP  plan-1  C1'   0.020
 SRP  plan-1  N9    0.020
 SRP  plan-1  C8    0.020
 SRP  plan-1  N7    0.020
 SRP  plan-1  C5    0.020
 SRP  plan-1  C6    0.020
 SRP  plan-1  N6    0.020
 SRP  plan-1  N1    0.020
 SRP  plan-1  C2    0.020
 SRP  plan-1  N3    0.020
 SRP  plan-1  C4    0.020
 SRP  plan-1  H8    0.020
 SRP  plan-1  H3    0.020
 SRP  plan-2  C6    0.020
 SRP  plan-2  N6    0.020
 SRP  plan-2  HN61  0.020
 SRP  plan-2  HN62  0.020
 SRP  plan-3  O3A   0.020
 SRP  plan-3  O     0.020
 SRP  plan-3  C     0.020
 SRP  plan-3  CA    0.020

