# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 22:11:34 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(L-prolylamino)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)NC(=O)[C@@H]4CCCN4)[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
 PSD  PSD  5'-O-[(R)-hydroxy(L-prolylamino)phosphoryl]adenosine  ligand  52  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PSD
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
 PSD  CB    C  CH2   0  -0.459  21.9634  105.4581  100.2024
 PSD  CG    C  CH2   0  -0.501  21.1598  106.7016   99.8273
 PSD  C     C  C     0   0.565  22.3363  106.2026  102.5667
 PSD  O     O  O     0  -0.439  21.8250  107.1374  103.1463
 PSD  N     N  NR15  0  -0.598  20.1439  105.5149  101.6391
 PSD  CD    C  CH2   0  -0.269  19.8722  106.5719  100.6548
 PSD  CA    C  CR15  0  -0.232  21.5585  105.2479  101.6675
 PSD  N10   N  NH1   0  -0.843  23.6797  105.9514  102.6642
 PSD  P     P  P     0   1.489  24.7302  107.0227  103.4424
 PSD  O1P   O  O     0  -0.677  24.4039  107.4082  104.8243
 PSD  O2P   O  OH1   0  -0.747  26.0717  106.1953  103.1952
 PSD  O5'   O  O2    0  -0.586  24.7967  108.3181  102.5036
 PSD  C5'   C  CH2   0  -0.215  25.2644  108.2391  101.1559
 PSD  C4'   C  CH1   0  -0.001  25.0396  109.5499  100.4442
 PSD  O4'   O  O2    0  -0.490  23.6456  109.7636  100.2227
 PSD  C1'   C  CH1   0   0.195  23.2805  111.0420  100.6638
 PSD  N9    N  NR5   0  -0.545  21.9099  111.0071  101.0932
 PSD  C4    C  CR56  0   0.485  20.9043  111.8389  100.6888
 PSD  N3    N  N     0  -0.456  20.9685  112.8624   99.8412
 PSD  C2    C  CR16  0   0.045  19.7925  113.4478   99.6924
 PSD  N1    N  N     0  -0.474  18.6345  113.1355  100.2678
 PSD  C6    C  CR6   0   0.457  18.5864  112.1026  101.1170
 PSD  N6    N  NH2   0  -0.817  17.4297  111.7937  101.7063
 PSD  C5    C  CR56  0  -0.010  19.7768  111.3939  101.3605
 PSD  N7    N  N     0  -0.454  20.0742  110.3132  102.1511
 PSD  C8    C  CR15  0   0.108  21.3455  110.1161  101.9671
 PSD  C2'   C  CH1   0  -0.016  24.2874  111.3792  101.7672
 PSD  O2'   O  OH1   0  -0.658  24.4131  112.7460  102.0144
 PSD  C3'   C  CH1   0  -0.053  25.5661  110.7902  101.1755
 PSD  O3'   O  OH1   0  -0.667  26.1263  111.6481  100.2126
 PSD  HCB1  H  HCH2  0   0.249  23.0372  105.5705  100.0530
 PSD  HCB2  H  HCH2  0   0.259  21.6411  104.5917   99.6232
 PSD  HCG1  H  HCH2  0   0.252  20.9636  106.7632   98.7575
 PSD  HCG2  H  HCH2  0   0.240  21.7083  107.6038  100.1061
 PSD  HN    H  HNR5  0   0.353  19.7725  105.7380  102.5518
 PSD  HCD1  H  HCH2  0   0.215  19.0247  106.2853  100.0262
 PSD  HCD2  H  HCH2  0   0.225  19.6156  107.5253  101.1235
 PSD  HCA   H  HCR5  0   0.285  21.7704  104.2243  101.9984
 PSD  HN01  H  HNH1  0   0.436  24.0509  105.1248  102.2135
 PSD  HOP2  H  HOH1  0   0.507  26.8387  106.5150  103.6911
 PSD  H5'1  H  HCH2  0   0.252  24.7505  107.4397  100.6126
 PSD  H5'2  H  HCH2  0   0.258  26.3344  108.0210  101.1404
 PSD  HC'4  H  HCH1  0   0.270  25.5501  109.4570   99.4792
 PSD  HC'1  H  HCH1  0   0.258  23.3367  111.7892   99.8637
 PSD  HC2   H  HCR6  0   0.252  19.7628  114.2939   99.0145
 PSD  HN61  H  HNH2  0   0.403  16.5897  112.2871  101.4579
 PSD  HN62  H  HNH2  0   0.411  17.3458  110.9728  102.2798
 PSD  HC8   H  HCR5  0   0.301  21.9235  109.3295  102.4260
 PSD  HC'2  H  HCH1  0   0.252  24.0258  110.8219  102.6747
 PSD  HO'2  H  HOH1  0   0.468  23.7848  113.0031  102.6949
 PSD  HC'3  H  HCH1  0   0.260  26.2942  110.5350  101.9545
 PSD  HO'3  H  HOH1  0   0.456  26.3638  112.4763  100.6434

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
 PSD  CB   CG    single    1.527  0.020  1.527
 PSD  CB   CA    single    1.535  0.020  1.535
 PSD  CB   HCB1  single    0.970  0.020  1.090
 PSD  CB   HCB2  single    0.970  0.020  1.090
 PSD  CG   CD    single    1.536  0.020  1.536
 PSD  CG   HCG1  single    0.970  0.020  1.090
 PSD  CG   HCG2  single    0.970  0.020  1.090
 PSD  C    O     double    1.213  0.020  1.213
 PSD  C    CA    single    1.525  0.020  1.525
 PSD  C    N10   single    1.370  0.020  1.370
 PSD  N    CD    single    1.470  0.020  1.470
 PSD  N    CA    single    1.440  0.020  1.440
 PSD  N    HN    single    0.890  0.020  1.040
 PSD  CD   HCD1  single    0.970  0.020  1.090
 PSD  CD   HCD2  single    0.970  0.020  1.090
 PSD  CA   HCA   single    0.970  0.020  1.090
 PSD  N10  P     single    1.690  0.020  1.690
 PSD  N10  HN01  single    0.860  0.020  1.020
 PSD  P    O1P   double    1.471  0.020  1.471
 PSD  P    O2P   single    1.595  0.020  1.595
 PSD  P    O5'   single    1.601  0.020  1.601
 PSD  O2P  HOP2  single    0.850  0.020  0.980
 PSD  O5'  C5'   single    1.429  0.020  1.429
 PSD  C5'  C4'   single    1.508  0.020  1.508
 PSD  C5'  H5'1  single    0.970  0.020  1.090
 PSD  C5'  H5'2  single    0.970  0.020  1.090
 PSD  C4'  O4'   single    1.428  0.020  1.428
 PSD  C4'  C3'   single    1.533  0.020  1.533
 PSD  C4'  HC'4  single    0.970  0.020  1.090
 PSD  O4'  C1'   single    1.401  0.020  1.401
 PSD  C1'  N9    single    1.437  0.020  1.437
 PSD  C1'  C2'   single    1.531  0.020  1.531
 PSD  C1'  HC'1  single    0.970  0.020  1.090
 PSD  N9   C4    aromatic  1.366  0.020  1.366
 PSD  N9   C8    aromatic  1.370  0.020  1.370
 PSD  C4   N3    aromatic  1.330  0.020  1.330
 PSD  C4   C5    aromatic  1.386  0.020  1.386
 PSD  N3   C2    aromatic  1.322  0.020  1.322
 PSD  C2   N1    aromatic  1.330  0.020  1.330
 PSD  C2   HC2   single    0.930  0.020  1.080
 PSD  N1   C6    aromatic  1.338  0.020  1.338
 PSD  C6   N6    single    1.334  0.020  1.334
 PSD  C6   C5    aromatic  1.407  0.020  1.407
 PSD  N6   HN61  single    0.860  0.020  1.020
 PSD  N6   HN62  single    0.860  0.020  1.020
 PSD  C5   N7    aromatic  1.372  0.020  1.372
 PSD  N7   C8    aromatic  1.300  0.020  1.300
 PSD  C8   HC8   single    0.930  0.020  1.080
 PSD  C2'  O2'   single    1.395  0.020  1.395
 PSD  C2'  C3'   single    1.527  0.020  1.527
 PSD  C2'  HC'2  single    0.970  0.020  1.090
 PSD  O2'  HO'2  single    0.850  0.020  0.980
 PSD  C3'  O3'   single    1.406  0.020  1.406
 PSD  C3'  HC'3  single    0.970  0.020  1.090
 PSD  O3'  HO'3  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
 PSD  HCB2  CB   HCB1  107.47  3.000
 PSD  HCB2  CB   CA    108.67  3.000
 PSD  HCB1  CB   CA    113.88  3.000
 PSD  HCB2  CB   CG    111.15  3.000
 PSD  HCB1  CB   CG    113.62  3.000
 PSD  CA    CB   CG    101.96  3.000
 PSD  HCG2  CG   HCG1  107.12  3.000
 PSD  HCG2  CG   CD    110.68  3.000
 PSD  HCG1  CG   CD    112.51  3.000
 PSD  HCG2  CG   CB    110.23  3.000
 PSD  HCG1  CG   CB    112.46  3.000
 PSD  CD    CG   CB    103.89  3.000
 PSD  N10   C    CA    115.29  3.000
 PSD  N10   C    O     121.37  3.000
 PSD  CA    C    O     123.32  3.000
 PSD  HN    N    CA    112.60  3.000
 PSD  HN    N    CD    112.22  3.000
 PSD  CA    N    CD    109.16  3.000
 PSD  HCD2  CD   HCD1  107.05  3.000
 PSD  HCD2  CD   N     112.56  3.000
 PSD  HCD1  CD   N     109.86  3.000
 PSD  HCD2  CD   CG    110.75  3.000
 PSD  HCD1  CD   CG    111.23  3.000
 PSD  N     CD   CG    105.46  3.000
 PSD  HCA   CA   N     111.65  3.000
 PSD  HCA   CA   C     107.94  3.000
 PSD  N     CA   C     113.37  3.000
 PSD  HCA   CA   CB    111.41  3.000
 PSD  N     CA   CB    102.41  3.000
 PSD  C     CA   CB    110.04  3.000
 PSD  HN01  N10  P     119.66  3.000
 PSD  HN01  N10  C     118.54  3.000
 PSD  P     N10  C     121.73  3.000
 PSD  O5'   P    O2P   107.09  3.000
 PSD  O5'   P    O1P   110.36  3.000
 PSD  O2P   P    O1P   117.90  3.000
 PSD  O5'   P    N10   105.58  3.000
 PSD  O2P   P    N10    97.04  3.000
 PSD  O1P   P    N10   117.43  3.000
 PSD  HOP2  O2P  P     114.56  3.000
 PSD  C5'   O5'  P     121.46  3.000
 PSD  H5'2  C5'  H5'1  107.88  3.000
 PSD  H5'2  C5'  C4'   108.23  3.000
 PSD  H5'1  C5'  C4'   109.30  3.000
 PSD  H5'2  C5'  O5'   110.19  3.000
 PSD  H5'1  C5'  O5'   110.78  3.000
 PSD  C4'   C5'  O5'   110.38  3.000
 PSD  HC'4  C4'  C3'   109.20  3.000
 PSD  HC'4  C4'  O4'   109.33  3.000
 PSD  C3'   C4'  O4'   106.75  3.000
 PSD  HC'4  C4'  C5'   105.81  3.000
 PSD  C3'   C4'  C5'   115.27  3.000
 PSD  O4'   C4'  C5'   110.41  3.000
 PSD  C1'   O4'  C4'   110.02  3.000
 PSD  HC'1  C1'  C2'   110.00  3.000
 PSD  HC'1  C1'  N9    106.48  3.000
 PSD  C2'   C1'  N9    114.66  3.000
 PSD  HC'1  C1'  O4'   112.27  3.000
 PSD  C2'   C1'  O4'   104.86  3.000
 PSD  N9    C1'  O4'   108.70  3.000
 PSD  C8    N9   C4    106.36  3.000
 PSD  C8    N9   C1'   126.84  3.000
 PSD  C4    N9   C1'   126.79  3.000
 PSD  C5    C4   N3    126.51  3.000
 PSD  C5    C4   N9    105.06  3.000
 PSD  N3    C4   N9    128.42  3.000
 PSD  C2    N3   C4    111.68  3.000
 PSD  HC2   C2   N1    115.44  3.000
 PSD  HC2   C2   N3    116.12  3.000
 PSD  N1    C2   N3    128.44  3.000
 PSD  C6    N1   C2    119.15  3.000
 PSD  C5    C6   N6    122.72  3.000
 PSD  C5    C6   N1    117.93  3.000
 PSD  N6    C6   N1    119.35  3.000
 PSD  HN62  N6   HN61  118.17  3.000
 PSD  HN62  N6   C6    120.90  3.000
 PSD  HN61  N6   C6    120.10  3.000
 PSD  N7    C5   C6    132.86  3.000
 PSD  N7    C5   C4    110.85  3.000
 PSD  C6    C5   C4    116.29  3.000
 PSD  C8    N7   C5    104.48  3.000
 PSD  HC8   C8   N7    125.07  3.000
 PSD  HC8   C8   N9    121.67  3.000
 PSD  N7    C8   N9    113.25  3.000
 PSD  HC'2  C2'  C3'   108.93  3.000
 PSD  HC'2  C2'  O2'   111.90  3.000
 PSD  C3'   C2'  O2'   111.79  3.000
 PSD  HC'2  C2'  C1'   109.12  3.000
 PSD  C3'   C2'  C1'   100.75  3.000
 PSD  O2'   C2'  C1'   113.75  3.000
 PSD  HO'2  O2'  C2'   109.19  3.000
 PSD  HC'3  C3'  O3'   111.35  3.000
 PSD  HC'3  C3'  C2'   111.75  3.000
 PSD  O3'   C3'  C2'   111.32  3.000
 PSD  HC'3  C3'  C4'   112.25  3.000
 PSD  O3'   C3'  C4'   107.68  3.000
 PSD  C2'   C3'  C4'   102.08  3.000
 PSD  HO'3  O3'  C3'   108.45  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
 PSD  CONST_01  C2    N3   C4   N9   180.00   0.0  0
 PSD  CONST_02  C6    C5   C4   N9   180.00   0.0  0
 PSD  CONST_03  N7    C5   C4   N9     0.00   0.0  0
 PSD  CONST_04  C5    N7   C8   N9     0.00   0.0  0
 PSD  CONST_05  N7    C8   N9   C4     0.00   0.0  0
 PSD  CONST_06  N1    C2   N3   C4     0.00   0.0  0
 PSD  CONST_07  N1    C6   C5   C4     0.00   0.0  0
 PSD  CONST_08  C8    N7   C5   C4     0.00   0.0  0
 PSD  CONST_09  C8    N9   C4   N3   180.00   0.0  0
 PSD  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 PSD  CONST_11  N7    C5   C4   N3   180.00   0.0  0
 PSD  CONST_12  C6    N1   C2   N3     0.00   0.0  0
 PSD  CONST_13  C5    C4   N3   C2     0.00   0.0  0
 PSD  CONST_14  C5    C6   N1   C2     0.00   0.0  0
 PSD  CONST_15  N7    C5   C6   N1   180.00   0.0  0
 PSD  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 PSD  CONST_17  C8    N9   C4   C5     0.00   0.0  0
 PSD  CONST_18  N3    C4   N9   C1'    0.00   0.0  0
 PSD  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 PSD  CONST_20  N7    C8   N9   C1'  180.00   0.0  0
 PSD  CONST_21  N6    C6   C5   C4   180.00   0.0  0
 PSD  CONST_22  N6    C6   N1   C2   180.00   0.0  0
 PSD  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 PSD  CONST_24  HC8   C8   N9   C1'    0.00   0.0  0
 PSD  CONST_25  HC2   C2   N3   C4   180.00   0.0  0
 PSD  CONST_26  HN61  N6   C6   N1     0.00   0.0  0
 PSD  CONST_27  HN62  N6   C6   N1   180.00   0.0  0
 PSD  CONST_28  P     N10  C    CA   180.00   0.0  0
 PSD  CONST_29  HN01  N10  C    CA     0.00   0.0  0
 PSD  CONST_30  P     N10  C    O      0.00   0.0  0
 PSD  Var_01    N     CD   CG   CB    13.11  30.0  1
 PSD  Var_02    CA    N    CD   CG    13.64  30.0  1
 PSD  Var_03    CA    CB   CG   CD   -32.96  30.0  1
 PSD  Var_04    C4'   C5'  O5'  P    171.96  30.0  3
 PSD  Var_05    O1P   P    N10  C     54.26  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
 PSD  chir_01  CA   CB   C    N    negativ
 PSD  chir_03  C4'  C5'  O4'  C3'  negativ
 PSD  chir_04  C1'  O4'  N9   C2'  negativ
 PSD  chir_05  C2'  O2'  C1'  C3'  negativ
 PSD  chir_06  C3'  O3'  C4'  C2'  positiv
 PSD  chir_07  P    O1P  O2P  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
 PSD  plan-1  C     0.020
 PSD  plan-1  O     0.020
 PSD  plan-1  CA    0.020
 PSD  plan-1  N10   0.020
 PSD  plan-1  P     0.020
 PSD  plan-1  HN01  0.020
 PSD  plan-2  C6    0.020
 PSD  plan-2  N6    0.020
 PSD  plan-2  HN61  0.020
 PSD  plan-2  HN62  0.020
 PSD  plan-3  C1'   0.020
 PSD  plan-3  N9    0.020
 PSD  plan-3  C4    0.020
 PSD  plan-3  N3    0.020
 PSD  plan-3  C2    0.020
 PSD  plan-3  N1    0.020
 PSD  plan-3  C6    0.020
 PSD  plan-3  N6    0.020
 PSD  plan-3  C5    0.020
 PSD  plan-3  N7    0.020
 PSD  plan-3  C8    0.020
 PSD  plan-3  HC2   0.020
 PSD  plan-3  HC8   0.020

