# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 13:30:02 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(propoxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCO[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
 PRX  PRX  5'-O-[(R)-hydroxy(propoxy)phosphoryl]adenosine  ligand  45  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PRX
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
 PRX  O2'   O  OH1    0  -0.658  75.6297  125.0413  85.5823
 PRX  C2'   C  CH1    0  -0.045  75.9758  125.2268  84.2374
 PRX  C1'   C  CH1    0   0.177  75.9123  123.8539  83.5699
 PRX  O4'   O  O2     0  -0.490  74.6001  123.6698  83.1406
 PRX  C4'   C  CH1    0  -0.013  73.8393  124.8731  83.2777
 PRX  C5'   C  CH2    0  -0.155  72.9542  125.0752  82.0721
 PRX  O5'   O  O2     0  -0.626  72.0011  124.0387  82.0099
 PRX  P     P  P      0   1.363  71.3286  123.6297  80.5579
 PRX  O1P   O  O      0  -0.788  71.0287  124.8652  79.7715
 PRX  O2P   O  OP    -1  -0.785  70.2857  122.6129  80.8934
 PRX  O3P   O  O2     0  -0.623  72.5942  122.9230  79.7880
 PRX  C1P   C  CH2    0  -0.161  73.1186  121.6858  80.2459
 PRX  C2P   C  CH2    0  -0.450  73.7193  120.9196  79.0836
 PRX  C3P   C  CH3    0  -0.667  74.8733  121.6348  78.3961
 PRX  C3'   C  CH1    0  -0.015  74.8904  125.9732  83.4642
 PRX  O3'   O  OH1    0  -0.658  74.4565  127.0871  84.1859
 PRX  N9    N  NR5    0  -0.536  76.8124  123.7765  82.4235
 PRX  C8    C  CR15   0   0.105  76.5110  123.8232  81.0905
 PRX  N7    N  N      0  -0.451  77.5572  123.7281  80.3216
 PRX  C5    C  CR56   0  -0.003  78.6094  123.6110  81.1902
 PRX  C4    C  CR56   0   0.484  78.1671  123.6357  82.5032
 PRX  N3    N  N      0  -0.458  78.9206  123.5412  83.5979
 PRX  C2    C  CR16   0   0.038  80.2011  123.4127  83.2958
 PRX  N1    N  N      0  -0.471  80.7684  123.3765  82.0927
 PRX  C6    C  CR6    0   0.457  79.9975  123.4754  81.0039
 PRX  N6    N  NH2    0  -0.816  80.5637  123.4510  79.7963
 PRX  H2'   H  HOH1   0   0.456  75.4240  125.8997  85.9687
 PRX  H1    H  HCH1   0   0.262  76.9630  125.6912  84.1289
 PRX  H1'   H  HCH1   0   0.282  76.2070  123.0612  84.2636
 PRX  H4'   H  HCH1   0   0.240  73.2210  124.8061  84.1811
 PRX  H5'1  H  HCH2   0   0.219  72.4618  126.0502  82.1734
 PRX  H5'2  H  HCH2   0   0.211  73.5752  125.1272  81.1705
 PRX  H1P1  H  HCH2   0   0.198  73.8862  121.8666  81.0071
 PRX  H1P2  H  HCH2   0   0.211  72.3365  121.0800  80.7128
 PRX  H2P1  H  HCH2   0   0.219  74.0647  119.9575  79.4720
 PRX  H2P2  H  HCH2   0   0.218  72.9327  120.6921  78.3588
 PRX  H3P1  H  HCH3   0   0.226  75.2803  121.0289  77.5861
 PRX  H3P2  H  HCH3   0   0.220  74.5609  122.5874  77.9677
 PRX  H3P3  H  HCH3   0   0.218  75.6867  121.8360  79.0951
 PRX  H3'   H  HCH1   0   0.236  75.2973  126.2609  82.4840
 PRX  H2    H  HOH1   0   0.465  73.9149  127.6449  83.6190
 PRX  H8    H  HCR5   0   0.300  75.4979  123.9181  80.7334
 PRX  H3    H  HCR6   0   0.249  80.8838  123.3258  84.1346
 PRX  HN61  H  HNH2   0   0.402  81.5560  123.3177  79.7030
 PRX  HN62  H  HNH2   0   0.410  80.0057  123.4859  78.9613

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
 PRX  O2'  C2'   single    1.401  0.020  1.401
 PRX  O2'  H2'   single    0.850  0.020  0.980
 PRX  C2'  C1'   single    1.528  0.020  1.528
 PRX  C2'  C3'   single    1.527  0.020  1.527
 PRX  C2'  H1    single    0.970  0.020  1.090
 PRX  C1'  O4'   single    1.393  0.020  1.393
 PRX  C1'  N9    single    1.460  0.020  1.460
 PRX  C1'  H1'   single    0.970  0.020  1.090
 PRX  O4'  C4'   single    1.430  0.020  1.430
 PRX  C4'  C5'   single    1.509  0.020  1.509
 PRX  C4'  C3'   single    1.533  0.020  1.533
 PRX  C4'  H4'   single    0.970  0.020  1.090
 PRX  C5'  O5'   single    1.409  0.020  1.409
 PRX  C5'  H5'1  single    0.970  0.020  1.090
 PRX  C5'  H5'2  single    0.970  0.020  1.090
 PRX  O5'  P     single    1.652  0.020  1.652
 PRX  P    O1P   deloc     1.495  0.020  1.495
 PRX  P    O2P   deloc     1.495  0.020  1.495
 PRX  P    O3P   single    1.641  0.020  1.641
 PRX  O3P  C1P   single    1.420  0.020  1.420
 PRX  C1P  C2P   single    1.516  0.020  1.516
 PRX  C1P  H1P1  single    0.970  0.020  1.090
 PRX  C1P  H1P2  single    0.970  0.020  1.090
 PRX  C2P  C3P   single    1.522  0.020  1.522
 PRX  C2P  H2P1  single    0.970  0.020  1.090
 PRX  C2P  H2P2  single    0.970  0.020  1.090
 PRX  C3P  H3P1  single    0.970  0.020  1.090
 PRX  C3P  H3P2  single    0.970  0.020  1.090
 PRX  C3P  H3P3  single    0.970  0.020  1.090
 PRX  C3'  O3'   single    1.396  0.020  1.396
 PRX  C3'  H3'   single    0.970  0.020  1.090
 PRX  O3'  H2    single    0.850  0.020  0.980
 PRX  N9   C8    aromatic  1.367  0.020  1.367
 PRX  N9   C4    aromatic  1.364  0.020  1.364
 PRX  C8   N7    aromatic  1.302  0.020  1.302
 PRX  C8   H8    single    0.930  0.020  1.080
 PRX  N7   C5    aromatic  1.369  0.020  1.369
 PRX  C5   C4    aromatic  1.386  0.020  1.386
 PRX  C5   C6    aromatic  1.407  0.020  1.407
 PRX  C4   N3    aromatic  1.332  0.020  1.332
 PRX  N3   C2    aromatic  1.322  0.020  1.322
 PRX  C2   N1    aromatic  1.331  0.020  1.331
 PRX  C2   H3    single    0.930  0.020  1.080
 PRX  N1   C6    aromatic  1.338  0.020  1.338
 PRX  C6   N6    single    1.334  0.020  1.334
 PRX  N6   HN61  single    0.860  0.020  1.020
 PRX  N6   HN62  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
 PRX  H2'   O2'  C2'   108.65  3.000
 PRX  H1    C2'  C3'   112.51  3.000
 PRX  H1    C2'  C1'   112.02  3.000
 PRX  C3'   C2'  C1'   100.86  3.000
 PRX  H1    C2'  O2'   111.93  3.000
 PRX  C3'   C2'  O2'   112.03  3.000
 PRX  C1'   C2'  O2'   106.87  3.000
 PRX  H1'   C1'  N9    107.07  3.000
 PRX  H1'   C1'  O4'   110.70  3.000
 PRX  N9    C1'  O4'   109.39  3.000
 PRX  H1'   C1'  C2'   111.28  3.000
 PRX  N9    C1'  C2'   111.41  3.000
 PRX  O4'   C1'  C2'   107.02  3.000
 PRX  C4'   O4'  C1'   111.12  3.000
 PRX  H4'   C4'  C3'   109.27  3.000
 PRX  H4'   C4'  C5'   109.61  3.000
 PRX  C3'   C4'  C5'   113.78  3.000
 PRX  H4'   C4'  O4'   109.11  3.000
 PRX  C3'   C4'  O4'   104.52  3.000
 PRX  C5'   C4'  O4'   110.37  3.000
 PRX  H5'2  C5'  H5'1  106.74  3.000
 PRX  H5'2  C5'  O5'   112.44  3.000
 PRX  H5'1  C5'  O5'   110.74  3.000
 PRX  H5'2  C5'  C4'   109.34  3.000
 PRX  H5'1  C5'  C4'   107.97  3.000
 PRX  O5'   C5'  C4'   109.47  3.000
 PRX  P     O5'  C5'   119.76  3.000
 PRX  O3P   P    O2P   110.51  3.000
 PRX  O3P   P    O1P   105.30  3.000
 PRX  O2P   P    O1P   122.70  3.000
 PRX  O3P   P    O5'   101.83  3.000
 PRX  O2P   P    O5'   104.79  3.000
 PRX  O1P   P    O5'   109.85  3.000
 PRX  C1P   O3P  P     120.58  3.000
 PRX  H1P2  C1P  H1P1  107.19  3.000
 PRX  H1P2  C1P  C2P   109.30  3.000
 PRX  H1P1  C1P  C2P   109.78  3.000
 PRX  H1P2  C1P  O3P   110.87  3.000
 PRX  H1P1  C1P  O3P   109.81  3.000
 PRX  C2P   C1P  O3P   109.85  3.000
 PRX  H2P2  C2P  H2P1  106.23  3.000
 PRX  H2P2  C2P  C3P   110.10  3.000
 PRX  H2P1  C2P  C3P   109.54  3.000
 PRX  H2P2  C2P  C1P   109.17  3.000
 PRX  H2P1  C2P  C1P   107.31  3.000
 PRX  C3P   C2P  C1P   114.16  3.000
 PRX  H3P3  C3P  H3P2  107.71  3.000
 PRX  H3P3  C3P  H3P1  107.46  3.000
 PRX  H3P2  C3P  H3P1  107.49  3.000
 PRX  H3P3  C3P  C2P   111.26  3.000
 PRX  H3P2  C3P  C2P   111.77  3.000
 PRX  H3P1  C3P  C2P   110.95  3.000
 PRX  H3'   C3'  O3'   111.53  3.000
 PRX  H3'   C3'  C4'   109.45  3.000
 PRX  O3'   C3'  C4'   114.98  3.000
 PRX  H3'   C3'  C2'   108.43  3.000
 PRX  O3'   C3'  C2'   110.43  3.000
 PRX  C4'   C3'  C2'   101.43  3.000
 PRX  H2    O3'  C3'   109.44  3.000
 PRX  C4    N9   C8    106.22  3.000
 PRX  C4    N9   C1'   124.89  3.000
 PRX  C8    N9   C1'   128.89  3.000
 PRX  H8    C8   N7    124.46  3.000
 PRX  H8    C8   N9    122.20  3.000
 PRX  N7    C8   N9    113.34  3.000
 PRX  C5    N7   C8    104.43  3.000
 PRX  C6    C5   C4    116.24  3.000
 PRX  C6    C5   N7    133.02  3.000
 PRX  C4    C5   N7    110.74  3.000
 PRX  N3    C4   C5    126.63  3.000
 PRX  N3    C4   N9    128.09  3.000
 PRX  C5    C4   N9    105.27  3.000
 PRX  C2    N3   C4    111.53  3.000
 PRX  H3    C2   N1    115.37  3.000
 PRX  H3    C2   N3    116.15  3.000
 PRX  N1    C2   N3    128.48  3.000
 PRX  C6    N1   C2    119.22  3.000
 PRX  N6    C6   N1    119.40  3.000
 PRX  N6    C6   C5    122.71  3.000
 PRX  N1    C6   C5    117.90  3.000
 PRX  HN62  N6   HN61  118.39  3.000
 PRX  HN62  N6   C6    121.06  3.000
 PRX  HN61  N6   C6    120.35  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
 PRX  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 PRX  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 PRX  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 PRX  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 PRX  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 PRX  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 PRX  CONST_07  C4    C5   N7   C8     0.00   0.0  0
 PRX  CONST_08  C6    C5   N7   C8   180.00   0.0  0
 PRX  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 PRX  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 PRX  CONST_11  N1    C6   C5   N7   180.00   0.0  0
 PRX  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 PRX  CONST_13  C2    N1   C6   C5     0.00   0.0  0
 PRX  CONST_14  N1    C6   C5   C4     0.00   0.0  0
 PRX  CONST_15  N1    C2   N3   C4     0.00   0.0  0
 PRX  CONST_16  C6    C5   C4   N3     0.00   0.0  0
 PRX  CONST_17  C6    N1   C2   N3     0.00   0.0  0
 PRX  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 PRX  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 PRX  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 PRX  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 PRX  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 PRX  CONST_23  N6    C6   N1   C2   180.00   0.0  0
 PRX  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 PRX  CONST_25  H3    C2   N3   C4   180.00   0.0  0
 PRX  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 PRX  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 PRX  Var_01    O1P   P    O5'  C5'  -40.89  30.0  3
 PRX  Var_02    C2P   C1P  O3P  P    151.25  30.0  3
 PRX  Var_03    C3P   C2P  C1P  O3P   61.15  30.0  3
 PRX  Var_04    H5'1  C5'  O5'  P     85.96  30.0  1
 PRX  Var_05    H3P1  C3P  C2P  C1P  178.63  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
 PRX  chir_01  C2'  O2'  C1'  C3'  negativ
 PRX  chir_02  C1'  O4'  N9   C2'  negativ
 PRX  chir_03  C4'  O4'  C3'  C5'  negativ
 PRX  chir_05  C3'  C2'  C4'  O3'  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
 PRX  plan-1  C1'   0.020
 PRX  plan-1  N9    0.020
 PRX  plan-1  C8    0.020
 PRX  plan-1  N7    0.020
 PRX  plan-1  C5    0.020
 PRX  plan-1  C4    0.020
 PRX  plan-1  N3    0.020
 PRX  plan-1  C2    0.020
 PRX  plan-1  N1    0.020
 PRX  plan-1  C6    0.020
 PRX  plan-1  N6    0.020
 PRX  plan-1  H8    0.020
 PRX  plan-1  H3    0.020
 PRX  plan-2  C6    0.020
 PRX  plan-2  N6    0.020
 PRX  plan-2  HN61  0.020
 PRX  plan-2  HN62  0.020

