# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 15:11:08 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](CC[P](O)(O)=O)NCc1c[nH]c2C(=O)NC=Nc12
#
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
 SSI  SSI  '[(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid'  ligand  38  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SSI
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
 SSI  P     P  P     0   1.374  -3.6536  -1.5566  -0.0485
 SSI  N1    N  NR16  0  -0.662   3.3635  -2.3732   0.2623
 SSI  C2    C  CR16  0   0.128   2.0684  -2.1835  -0.1071
 SSI  N3    N  N     0  -0.452   1.5447  -1.0424  -0.3876
 SSI  C4    C  CR56  0   0.142   2.4022   0.0190  -0.2887
 SSI  C5    C  CR56  0   0.157   3.7339  -0.1083   0.0917
 SSI  C6    C  CR6   0   0.521   4.3172  -1.3718   0.3993
 SSI  O6    O  O     0  -0.481   5.4679  -1.6088   0.7358
 SSI  N7    N  NR15  0  -0.651   4.2885   1.1317   0.0943
 SSI  C8    C  CR15  0  -0.054   3.3446   2.0349  -0.2687
 SSI  C9    C  CR5   0  -0.042   2.1523   1.3949  -0.5224
 SSI  C1'   C  CH2   0  -0.353   0.8584   1.9910  -0.9676
 SSI  O1P   O  OH1   0  -0.745  -3.1586  -2.9235  -0.7361
 SSI  O2P   O  O     0  -0.719  -5.0604  -1.1676  -0.3125
 SSI  C3'   C  CH2   0  -0.148  -1.9148   3.4195  -0.1885
 SSI  O3'   O  OH1   0  -0.670  -2.0359   3.5607   1.2071
 SSI  O3P   O  OH1   0  -0.752  -3.4551  -1.7378   1.5401
 SSI  C4'   C  CH1   0  -0.071  -1.5411   1.9864  -0.5334
 SSI  N4'   N  NH1   0  -0.617  -0.2117   1.6639  -0.0382
 SSI  C5'   C  CH2   0  -0.463  -2.5678   0.9873   0.0004
 SSI  C6'   C  CH2   0  -0.769  -2.3960  -0.4026  -0.6192
 SSI  H2    H  HCR6  0   0.293   1.4711  -3.0847  -0.1572
 SSI  H8    H  HCR5  0   0.292   3.5812   3.0853  -0.3288
 SSI  H1'   H  HCH2  0   0.236   0.9683   3.0764  -1.0402
 SSI  H1'A  H  HCH2  0   0.206   0.6316   1.6402  -1.9878
 SSI  HO1P  H  HOH1  0   0.493  -3.7716  -3.6644  -0.6318
 SSI  H3'   H  HCH2  0   0.194  -2.8523   3.6653  -0.7054
 SSI  H3'A  H  HCH2  0   0.203  -1.1492   4.0944  -0.5952
 SSI  HO3'  H  HOH1  0   0.453  -2.2840   4.4700   1.3944
 SSI  HO3P  H  HOH1  0   0.488  -2.5796  -2.0301   1.8244
 SSI  H4'   H  HCH1  0   0.204  -1.5756   1.9293  -1.6361
 SSI  HN4'  H  HNH1  0   0.361  -0.1525   0.6760   0.1688
 SSI  H5'   H  HCH2  0   0.245  -2.4929   0.9315   1.0885
 SSI  H5'A  H  HCH2  0   0.247  -3.5695   1.3565  -0.2308
 SSI  H6'   H  HCH2  0   0.275  -1.4070  -0.8255  -0.4182
 SSI  H6'A  H  HCH2  0   0.289  -2.4890  -0.3396  -1.7067
 SSI  HN7   H  HNR5  0   0.420   5.2440   1.3500   0.3256
 SSI  HN1   H  HNR6  0   0.431   3.6627  -3.3204   0.4534

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
 SSI  O2P  P     double    1.483  0.020  1.483
 SSI  O3P  P     single    1.611  0.020  1.611
 SSI  P    O1P   single    1.608  0.020  1.608
 SSI  P    C6'   single    1.800  0.020  1.800
 SSI  C6   N1    single    1.390  0.020  1.390
 SSI  N1   C2    single    1.360  0.020  1.360
 SSI  N1   HN1   single    0.860  0.020  1.020
 SSI  C2   N3    double    1.286  0.020  1.286
 SSI  C2   H2    single    0.930  0.020  1.080
 SSI  C4   N3    single    1.368  0.020  1.368
 SSI  C5   C4    aromatic  1.391  0.020  1.391
 SSI  C4   C9    aromatic  1.418  0.020  1.418
 SSI  C6   C5    single    1.425  0.020  1.425
 SSI  N7   C5    aromatic  1.358  0.020  1.358
 SSI  O6   C6    double    1.222  0.020  1.222
 SSI  N7   C8    aromatic  1.356  0.020  1.356
 SSI  C8   C9    aromatic  1.377  0.020  1.377
 SSI  C8   H8    single    0.930  0.020  1.080
 SSI  C9   C1'   single    1.493  0.020  1.493
 SSI  C1'  N4'   single    1.455  0.020  1.455
 SSI  C1'  H1'   single    0.970  0.020  1.090
 SSI  C1'  H1'A  single    0.970  0.020  1.090
 SSI  O1P  HO1P  single    0.850  0.020  0.980
 SSI  C4'  C3'   single    1.521  0.020  1.521
 SSI  C3'  O3'   single    1.408  0.020  1.408
 SSI  C3'  H3'   single    0.970  0.020  1.090
 SSI  C3'  H3'A  single    0.970  0.020  1.090
 SSI  O3'  HO3'  single    0.850  0.020  0.980
 SSI  O3P  HO3P  single    0.850  0.020  0.980
 SSI  C5'  C4'   single    1.529  0.020  1.529
 SSI  N4'  C4'   single    1.455  0.020  1.455
 SSI  C4'  H4'   single    0.970  0.020  1.090
 SSI  N4'  HN4'  single    0.890  0.020  1.040
 SSI  C6'  C5'   single    1.531  0.020  1.531
 SSI  C5'  H5'   single    0.970  0.020  1.090
 SSI  C5'  H5'A  single    0.970  0.020  1.090
 SSI  C6'  H6'   single    0.970  0.020  1.090
 SSI  C6'  H6'A  single    0.970  0.020  1.090
 SSI  N7   HN7   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
 SSI  C6'   P    O3P  107.37  3.000
 SSI  C6'   P    O2P  115.98  3.000
 SSI  O3P   P    O2P  108.78  3.000
 SSI  C6'   P    O1P  101.20  3.000
 SSI  O3P   P    O1P  106.74  3.000
 SSI  O2P   P    O1P  116.02  3.000
 SSI  HN1   N1   C6   116.95  3.000
 SSI  HN1   N1   C2   117.62  3.000
 SSI  C6    N1   C2   125.44  3.000
 SSI  H2    C2   N3   120.25  3.000
 SSI  H2    C2   N1   114.96  3.000
 SSI  N3    C2   N1   124.79  3.000
 SSI  C4    N3   C2   114.66  3.000
 SSI  C9    C4   C5   107.62  3.000
 SSI  C9    C4   N3   129.09  3.000
 SSI  C5    C4   N3   123.29  3.000
 SSI  N7    C5   C6   129.92  3.000
 SSI  N7    C5   C4   107.93  3.000
 SSI  C6    C5   C4   122.14  3.000
 SSI  O6    C6   C5   128.08  3.000
 SSI  O6    C6   N1   122.25  3.000
 SSI  C5    C6   N1   109.67  3.000
 SSI  HN7   N7   C8   125.28  3.000
 SSI  HN7   N7   C5   125.85  3.000
 SSI  C8    N7   C5   108.87  3.000
 SSI  H8    C8   C9   129.24  3.000
 SSI  H8    C8   N7   120.73  3.000
 SSI  C9    C8   N7   110.03  3.000
 SSI  C1'   C9   C8   128.32  3.000
 SSI  C1'   C9   C4   126.12  3.000
 SSI  C8    C9   C4   105.55  3.000
 SSI  H1'A  C1'  H1'  105.97  3.000
 SSI  H1'A  C1'  N4'  111.62  3.000
 SSI  H1'   C1'  N4'  109.85  3.000
 SSI  H1'A  C1'  C9   109.11  3.000
 SSI  H1'   C1'  C9   109.21  3.000
 SSI  N4'   C1'  C9   110.94  3.000
 SSI  HO1P  O1P  P    114.20  3.000
 SSI  H3'A  C3'  H3'  106.45  3.000
 SSI  H3'A  C3'  C4'  108.89  3.000
 SSI  H3'   C3'  C4'  108.29  3.000
 SSI  H3'A  C3'  O3'  111.43  3.000
 SSI  H3'   C3'  O3'  111.75  3.000
 SSI  C4'   C3'  O3'  109.91  3.000
 SSI  HO3'  O3'  C3'  108.08  3.000
 SSI  HO3P  O3P  P    115.85  3.000
 SSI  H4'   C4'  C5'  107.09  3.000
 SSI  H4'   C4'  N4'  110.90  3.000
 SSI  C5'   C4'  N4'  110.48  3.000
 SSI  H4'   C4'  C3'  105.51  3.000
 SSI  N4'   C4'  C3'  110.87  3.000
 SSI  C5'   C4'  C3'  111.82  3.000
 SSI  HN4'  N4'  C4'  109.87  3.000
 SSI  HN4'  N4'  C1'  107.91  3.000
 SSI  C4'   N4'  C1'  113.89  3.000
 SSI  H5'A  C5'  H5'  106.93  3.000
 SSI  H5'A  C5'  C6'  108.90  3.000
 SSI  H5'   C5'  C6'  110.43  3.000
 SSI  H5'A  C5'  C4'  108.73  3.000
 SSI  H5'   C5'  C4'  109.59  3.000
 SSI  C6'   C5'  C4'  112.12  3.000
 SSI  H6'A  C6'  H6'  106.37  3.000
 SSI  H6'A  C6'  C5'  109.91  3.000
 SSI  H6'   C6'  C5'  112.20  3.000
 SSI  H6'A  C6'  P    107.04  3.000
 SSI  H6'   C6'  P    109.00  3.000
 SSI  C5'   C6'  P    112.04  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
 SSI  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 SSI  CONST_02  N7   C8   C9   C4      0.00   0.0  0
 SSI  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 SSI  CONST_04  C9   C8   N7   C5      0.00   0.0  0
 SSI  CONST_05  C9   C4   C5   N7      0.00   0.0  0
 SSI  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 SSI  CONST_07  C5   C6   N1   C2      0.00   0.0  0
 SSI  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 SSI  CONST_09  C1'  C9   C4   N3      0.00   0.0  0
 SSI  CONST_10  C1'  C9   C4   C5    180.00   0.0  0
 SSI  CONST_11  C1'  C9   C8   N7    180.00   0.0  0
 SSI  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 SSI  CONST_13  HN7  N7   C5   C4    180.00   0.0  0
 SSI  CONST_14  H8   C8   C9   C4    180.00   0.0  0
 SSI  CONST_15  HN1  N1   C2   N3    180.00   0.0  0
 SSI  CONST_16  H2   C2   N3   C4    180.00   0.0  0
 SSI  Var_01    N4'  C1'  C9   C4     57.57  30.0  2
 SSI  Var_02    C4'  N4'  C1'  C9   -168.74  30.0  3
 SSI  Var_03    C4'  C5'  C6'  P    -177.29  30.0  3
 SSI  Var_04    C5'  C6'  P    O1P  -175.17  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
 SSI  chir_01  C4'  C3'  C5'  N4'  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
 SSI  plan-1  N1   0.020
 SSI  plan-1  C2   0.020
 SSI  plan-1  N3   0.020
 SSI  plan-1  C4   0.020
 SSI  plan-1  C5   0.020
 SSI  plan-1  C6   0.020
 SSI  plan-1  O6   0.020
 SSI  plan-1  N7   0.020
 SSI  plan-1  C8   0.020
 SSI  plan-1  C9   0.020
 SSI  plan-1  C1'  0.020
 SSI  plan-1  H2   0.020
 SSI  plan-1  H8   0.020
 SSI  plan-1  HN7  0.020
 SSI  plan-1  HN1  0.020

