# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 09:13:53 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-O-(L-prolylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=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
 P5A  P5A  5'-O-(L-prolylsulfamoyl)adenosine  ligand  51  30  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P5A
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
 P5A  CB    C  CH2   0  -0.465   2.7854  -0.2624  -2.6770
 P5A  CG    C  CH2   0  -0.444   4.0081  -0.9634  -2.0559
 P5A  C     C  C     0   0.579   0.3324  -0.8283  -2.3891
 P5A  O     O  O     0  -0.406  -0.2073  -1.8998  -2.4665
 P5A  N     N  NR15  0  -0.609   2.1012  -1.6980  -0.9402
 P5A  CD    C  CH2   0  -0.304   3.5120  -1.4451  -0.6950
 P5A  CA    C  CR15  0  -0.201   1.6363  -0.5517  -1.6786
 P5A  N3S   N  NC1   0  -0.836  -0.1865   0.3063  -2.9945
 P5A  S     S  S     0   1.614  -1.6301   0.3519  -3.8080
 P5A  O1S   O  OS    0  -0.608  -1.7301  -0.7390  -4.7348
 P5A  O2S   O  OS    0  -0.631  -1.7657   1.7195  -4.2444
 P5A  O5'   O  OC2   0  -0.567  -2.7009   0.0205  -2.6880
 P5A  C5'   C  CH2   0  -0.209  -2.9051   0.9471  -1.5980
 P5A  C4'   C  CH1   0   0.027  -2.7627   0.2118  -0.2922
 P5A  O4'   O  O2    0  -0.495  -1.4099  -0.1578  -0.0925
 P5A  C1'   C  CH1   0   0.167  -1.0676  -0.1095   1.2721
 P5A  N9    N  NR5   0  -0.533   0.1074   0.7140   1.4288
 P5A  C4    C  CR56  0   0.487   1.3020   0.3096   1.9567
 P5A  N3    N  N     0  -0.462   1.6259  -0.8897   2.4335
 P5A  C2    C  CR16  0   0.044   2.8727  -0.9187   2.8751
 P5A  N1    N  N     0  -0.470   3.7665   0.0657   2.8904
 P5A  C6    C  CR6   0   0.462   3.4292   1.2631   2.3967
 P5A  N6    N  NH2   0  -0.813   4.3257   2.2477   2.3996
 P5A  C5    C  CR56  0   0.000   2.1253   1.4208   1.8879
 P5A  N7    N  N     0  -0.440   1.4649   2.4820   1.3244
 P5A  C8    C  CR15  0   0.103   0.2769   2.0250   1.0666
 P5A  C2'   C  CH1   0  -0.047  -2.3008   0.4051   2.0251
 P5A  O2'   O  OH1   0  -0.661  -2.9896  -0.7114   2.5146
 P5A  C3'   C  CH1   0  -0.039  -3.1034   1.0905   0.9091
 P5A  O3'   O  OH1   0  -0.653  -4.4823   1.1022   1.1298
 P5A  HB1   H  HCH2  0   0.258   2.5647  -0.6644  -3.6663
 P5A  HB2   H  HCH2  0   0.255   2.9323   0.8104  -2.7910
 P5A  HG1   H  HCH2  0   0.242   4.3145  -1.8096  -2.6708
 P5A  HG2   H  HCH2  0   0.244   4.8644  -0.2972  -1.9636
 P5A  HT1   H  HNR5  0   0.354   1.5864  -1.8429  -0.0808
 P5A  HD1   H  HCH2  0   0.241   4.0162  -2.3477  -0.3478
 P5A  HD2   H  HCH2  0   0.202   3.6773  -0.6625   0.0598
 P5A  HA    H  HCR5  0   0.256   1.4957   0.3396  -1.0440
 P5A  H3S   H  HNC1  0   0.450   0.2846   1.1977  -2.8936
 P5A  H1'1  H  HCH2  0   0.288  -3.9148   1.3442  -1.6978
 P5A  H1'2  H  HCH2  0   0.255  -2.2028   1.7830  -1.6435
 P5A  H4'   H  HCH1  0   0.265  -3.4104  -0.6742  -0.2929
 P5A  H1'   H  HCH1  0   0.284  -0.7895  -1.1003   1.6408
 P5A  H2    H  HCR6  0   0.257   3.2139  -1.8655   3.2791
 P5A  H61   H  HNH2  0   0.406   5.2309   2.1083   2.8150
 P5A  H62   H  HNH2  0   0.413   4.0896   3.1670   2.0695
 P5A  H8    H  HCR5  0   0.297  -0.5150   2.6009   0.6115
 P5A  H2'   H  HCH1  0   0.266  -2.0250   1.0974   2.8293
 P5A  HO'2  H  HOH1  0   0.454  -3.9266  -0.4827   2.5609
 P5A  H3'   H  HCH1  0   0.252  -2.7167   2.1062   0.7506
 P5A  H3T   H  HOH1  0   0.473  -4.7086   1.8777   1.6537

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
 P5A  CB   CG    single    1.540  0.020  1.540
 P5A  CB   CA    single    1.550  0.020  1.550
 P5A  CB   HB1   single    0.970  0.020  1.090
 P5A  CB   HB2   single    0.970  0.020  1.090
 P5A  CG   CD    single    1.526  0.020  1.526
 P5A  CG   HG1   single    0.970  0.020  1.090
 P5A  CG   HG2   single    0.970  0.020  1.090
 P5A  C    O     double    1.202  0.020  1.202
 P5A  C    CA    single    1.510  0.020  1.510
 P5A  C    N3S   single    1.387  0.020  1.387
 P5A  N    CD    single    1.454  0.020  1.454
 P5A  N    CA    single    1.441  0.020  1.441
 P5A  N    HT1   single    0.890  0.020  1.040
 P5A  CD   HD1   single    0.970  0.020  1.090
 P5A  CD   HD2   single    0.970  0.020  1.090
 P5A  CA   HA    single    0.970  0.020  1.090
 P5A  N3S  S     single    1.658  0.020  1.658
 P5A  N3S  H3S   single    0.860  0.020  1.020
 P5A  S    O1S   deloc     1.435  0.020  1.435
 P5A  S    O2S   deloc     1.442  0.020  1.442
 P5A  S    O5'   single    1.585  0.020  1.585
 P5A  O5'  C5'   single    1.445  0.020  1.445
 P5A  C5'  C4'   single    1.505  0.020  1.505
 P5A  C5'  H1'1  single    0.970  0.020  1.090
 P5A  C5'  H1'2  single    0.970  0.020  1.090
 P5A  C4'  O4'   single    1.416  0.020  1.416
 P5A  C4'  C3'   single    1.527  0.020  1.527
 P5A  C4'  H4'   single    0.970  0.020  1.090
 P5A  O4'  C1'   single    1.408  0.020  1.408
 P5A  C1'  N9    single    1.443  0.020  1.443
 P5A  C1'  C2'   single    1.534  0.020  1.534
 P5A  C1'  H1'   single    0.970  0.020  1.090
 P5A  N9   C4    aromatic  1.367  0.020  1.367
 P5A  N9   C8    aromatic  1.371  0.020  1.371
 P5A  C4   N3    aromatic  1.331  0.020  1.331
 P5A  C4   C5    aromatic  1.385  0.020  1.385
 P5A  N3   C2    aromatic  1.323  0.020  1.323
 P5A  C2   N1    aromatic  1.330  0.020  1.330
 P5A  C2   H2    single    0.930  0.020  1.080
 P5A  N1   C6    aromatic  1.338  0.020  1.338
 P5A  C6   N6    single    1.332  0.020  1.332
 P5A  C6   C5    aromatic  1.408  0.020  1.408
 P5A  N6   H61   single    0.860  0.020  1.020
 P5A  N6   H62   single    0.860  0.020  1.020
 P5A  C5   N7    aromatic  1.371  0.020  1.371
 P5A  N7   C8    aromatic  1.299  0.020  1.299
 P5A  C8   H8    single    0.930  0.020  1.080
 P5A  C2'  O2'   single    1.400  0.020  1.400
 P5A  C2'  C3'   single    1.536  0.020  1.536
 P5A  C2'  H2'   single    0.970  0.020  1.090
 P5A  O2'  HO'2  single    0.850  0.020  0.980
 P5A  C3'  O3'   single    1.396  0.020  1.396
 P5A  C3'  H3'   single    0.970  0.020  1.090
 P5A  O3'  H3T   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
 P5A  HB2   CB   HB1   107.19  3.000
 P5A  HB2   CB   CA    110.58  3.000
 P5A  HB1   CB   CA    111.45  3.000
 P5A  HB2   CB   CG    112.56  3.000
 P5A  HB1   CB   CG    111.03  3.000
 P5A  CA    CB   CG    104.12  3.000
 P5A  HG2   CG   HG1   107.56  3.000
 P5A  HG2   CG   CD    111.91  3.000
 P5A  HG1   CG   CD    110.45  3.000
 P5A  HG2   CG   CB    112.33  3.000
 P5A  HG1   CG   CB    110.42  3.000
 P5A  CD    CG   CB    104.19  3.000
 P5A  N3S   C    CA    112.24  3.000
 P5A  N3S   C    O     122.22  3.000
 P5A  CA    C    O     125.52  3.000
 P5A  HT1   N    CA    112.64  3.000
 P5A  HT1   N    CD    112.04  3.000
 P5A  CA    N    CD    105.14  3.000
 P5A  HD2   CD   HD1   107.51  3.000
 P5A  HD2   CD   N     112.66  3.000
 P5A  HD1   CD   N     111.00  3.000
 P5A  HD2   CD   CG    109.78  3.000
 P5A  HD1   CD   CG    113.25  3.000
 P5A  N     CD   CG    102.70  3.000
 P5A  HA    CA   N     112.90  3.000
 P5A  HA    CA   C     107.97  3.000
 P5A  N     CA   C     111.96  3.000
 P5A  HA    CA   CB    108.32  3.000
 P5A  N     CA   CB    103.85  3.000
 P5A  C     CA   CB    111.79  3.000
 P5A  H3S   N3S  S     115.44  3.000
 P5A  H3S   N3S  C     120.16  3.000
 P5A  S     N3S  C     124.24  3.000
 P5A  O5'   S    O2S   110.41  3.000
 P5A  O5'   S    O1S   104.50  3.000
 P5A  O2S   S    O1S   121.27  3.000
 P5A  O5'   S    N3S   103.64  3.000
 P5A  O2S   S    N3S   104.87  3.000
 P5A  O1S   S    N3S   110.90  3.000
 P5A  C5'   O5'  S     119.63  3.000
 P5A  H1'2  C5'  H1'1  108.23  3.000
 P5A  H1'2  C5'  C4'   110.43  3.000
 P5A  H1'1  C5'  C4'   110.19  3.000
 P5A  H1'2  C5'  O5'   111.61  3.000
 P5A  H1'1  C5'  O5'   107.19  3.000
 P5A  C4'   C5'  O5'   109.13  3.000
 P5A  H4'   C4'  C3'   109.47  3.000
 P5A  H4'   C4'  O4'   110.68  3.000
 P5A  C3'   C4'  O4'   104.62  3.000
 P5A  H4'   C4'  C5'   109.75  3.000
 P5A  C3'   C4'  C5'   112.35  3.000
 P5A  O4'   C4'  C5'   109.88  3.000
 P5A  C1'   O4'  C4'   111.10  3.000
 P5A  H1'   C1'  C2'   110.06  3.000
 P5A  H1'   C1'  N9    105.87  3.000
 P5A  C2'   C1'  N9    114.19  3.000
 P5A  H1'   C1'  O4'   110.96  3.000
 P5A  C2'   C1'  O4'   106.97  3.000
 P5A  N9    C1'  O4'   108.83  3.000
 P5A  C8    N9   C4    106.07  3.000
 P5A  C8    N9   C1'   128.15  3.000
 P5A  C4    N9   C1'   125.76  3.000
 P5A  C5    C4   N3    126.61  3.000
 P5A  C5    C4   N9    105.25  3.000
 P5A  N3    C4   N9    128.14  3.000
 P5A  C2    N3   C4    111.64  3.000
 P5A  H2    C2   N1    115.50  3.000
 P5A  H2    C2   N3    116.10  3.000
 P5A  N1    C2   N3    128.39  3.000
 P5A  C6    N1   C2    119.25  3.000
 P5A  C5    C6   N6    122.77  3.000
 P5A  C5    C6   N1    117.83  3.000
 P5A  N6    C6   N1    119.40  3.000
 P5A  H62   N6   H61   118.29  3.000
 P5A  H62   N6   C6    121.17  3.000
 P5A  H61   N6   C6    120.29  3.000
 P5A  N7    C5   C6    132.93  3.000
 P5A  N7    C5   C4    110.80  3.000
 P5A  C6    C5   C4    116.27  3.000
 P5A  C8    N7   C5    104.47  3.000
 P5A  H8    C8   N7    124.53  3.000
 P5A  H8    C8   N9    122.06  3.000
 P5A  N7    C8   N9    113.41  3.000
 P5A  H2'   C2'  C3'   112.50  3.000
 P5A  H2'   C2'  O2'   111.77  3.000
 P5A  C3'   C2'  O2'   110.66  3.000
 P5A  H2'   C2'  C1'   111.70  3.000
 P5A  C3'   C2'  C1'   102.30  3.000
 P5A  O2'   C2'  C1'   107.43  3.000
 P5A  HO'2  O2'  C2'   107.77  3.000
 P5A  H3'   C3'  O3'   111.26  3.000
 P5A  H3'   C3'  C2'   109.48  3.000
 P5A  O3'   C3'  C2'   113.88  3.000
 P5A  H3'   C3'  C4'   109.88  3.000
 P5A  O3'   C3'  C4'   110.46  3.000
 P5A  C2'   C3'  C4'   101.44  3.000
 P5A  H3T   O3'  C3'   108.96  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
 P5A  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 P5A  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 P5A  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 P5A  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 P5A  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 P5A  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 P5A  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 P5A  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 P5A  CONST_09  C8   N9   C4   N3    180.00   0.0  0
 P5A  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 P5A  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 P5A  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 P5A  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 P5A  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 P5A  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 P5A  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 P5A  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 P5A  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 P5A  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 P5A  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 P5A  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 P5A  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 P5A  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 P5A  CONST_24  H8   C8   N9   C1'     0.00   0.0  0
 P5A  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 P5A  CONST_26  H61  N6   C6   N1      0.00   0.0  0
 P5A  CONST_27  H62  N6   C6   N1    180.00   0.0  0
 P5A  CONST_28  S    N3S  C    CA    180.00   0.0  0
 P5A  CONST_29  H3S  N3S  C    CA      0.00   0.0  0
 P5A  CONST_30  S    N3S  C    O       0.00   0.0  0
 P5A  Var_01    N    CD   CG   CB     30.73  30.0  1
 P5A  Var_02    CA   N    CD   CG    -45.45  30.0  1
 P5A  Var_03    CA   CB   CG   CD     -6.50  30.0  1
 P5A  Var_04    C4'  C5'  O5'  S    -126.57  30.0  3
 P5A  Var_05    O1S  S    N3S  C     -48.20  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
 P5A  chir_01  CA   CB   C    N    negativ
 P5A  chir_02  C4'  O4'  C5'  C3'  positiv
 P5A  chir_03  C1'  O4'  N9   C2'  negativ
 P5A  chir_04  C2'  O2'  C1'  C3'  negativ
 P5A  chir_05  C3'  O3'  C4'  C2'  positiv

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
 P5A  plan-1  C    0.020
 P5A  plan-1  O    0.020
 P5A  plan-1  CA   0.020
 P5A  plan-1  N3S  0.020
 P5A  plan-1  S    0.020
 P5A  plan-1  H3S  0.020
 P5A  plan-2  C6   0.020
 P5A  plan-2  N6   0.020
 P5A  plan-2  H61  0.020
 P5A  plan-2  H62  0.020
 P5A  plan-3  C1'  0.020
 P5A  plan-3  N9   0.020
 P5A  plan-3  C4   0.020
 P5A  plan-3  N3   0.020
 P5A  plan-3  C2   0.020
 P5A  plan-3  N1   0.020
 P5A  plan-3  C6   0.020
 P5A  plan-3  N6   0.020
 P5A  plan-3  C5   0.020
 P5A  plan-3  N7   0.020
 P5A  plan-3  C8   0.020
 P5A  plan-3  H2   0.020
 P5A  plan-3  H8   0.020

