# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:11:16 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (3S,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@@H]1CN(C[C@H]1O)Cc2c[nH]c3c(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
 4F0  4F0  (3S,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol  ligand  39  20  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4F0
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
 4F0  C2   C  CR16  0   0.005   3.2115  -2.1672   0.6487
 4F0  C4   C  CR56  0   0.159   2.4664  -0.3199  -0.3543
 4F0  C5   C  CR56  0   0.206   3.6767   0.3212  -0.0642
 4F0  C6   C  CR6   0   0.451   4.6690  -0.3933   0.6238
 4F0  CS5  C  CH3   0  -0.763  -6.1079  -2.0984   0.5032
 4F0  S    S  S2    0  -0.047  -5.1471  -0.9758  -0.5348
 4F0  C5'  C  CH2   0  -0.548  -3.9669  -0.3456   0.6921
 4F0  C4'  C  CH1   0  -0.299  -3.0165   0.6437   0.0402
 4F0  C1'  C  CH2   0  -0.249  -2.0518   0.0257  -0.9891
 4F0  N1'  N  NT    0  -0.424  -0.7148   0.3805  -0.5278
 4F0  C9   C  CR5   0  -0.046   1.6560   0.6065  -1.0696
 4F0  C8   C  CR15  0  -0.049   2.4041   1.7525  -1.1708
 4F0  N7   N  NR15  0  -0.676   3.6131   1.5870  -0.5726
 4F0  N6   N  NH2   0  -0.825   5.8573   0.1406   0.9788
 4F0  N1   N  N     0  -0.470   4.4011  -1.6480   0.9724
 4F0  N3   N  N     0  -0.445   2.2207  -1.5955   0.0067
 4F0  C2'  C  CH2   0  -0.294  -0.8471   1.6105   0.2182
 4F0  C3'  C  CH1   0   0.065  -2.0906   1.3266   1.0520
 4F0  O3'  O  OH1   0  -0.669  -2.7173   2.4531   1.6084
 4F0  H1   H  HCR6  0   0.237   3.0589  -3.1962   0.9597
 4F0  H2   H  HCH3  0   0.260  -6.6008  -1.5595   1.3112
 4F0  H3   H  HCH3  0   0.273  -6.8693  -2.5587  -0.1237
 4F0  H4   H  HCH3  0   0.260  -5.4805  -2.8841   0.9219
 4F0  H5   H  HCH2  0   0.269  -4.5213   0.1369   1.5007
 4F0  H6   H  HCH2  0   0.259  -3.4080  -1.1836   1.1172
 4F0  H7   H  HCH1  0   0.255  -3.6044   1.4303  -0.4451
 4F0  H8   H  HCH2  0   0.228  -2.1556  -1.0613  -1.0613
 4F0  H9   H  HCH2  0   0.206  -2.2611   0.4302  -1.9903
 4F0  H11  H  HCH2  0   0.238   0.2258  -0.5816  -2.0899
 4F0  H12  H  HCH2  0   0.204   0.0479   1.1475  -2.3492
 4F0  H13  H  HCR5  0   0.289   2.1500   2.6915  -1.6376
 4F0  H14  H  HNR5  0   0.416   4.3205   2.2996  -0.5128
 4F0  H15  H  HNH2  0   0.399   6.1970   0.9618   0.5078
 4F0  H16  H  HNH2  0   0.396   6.5716  -0.4986   1.2874
 4F0  H17  H  HCH2  0   0.238   0.0394   1.8069   0.8250
 4F0  H18  H  HCH2  0   0.186  -1.0178   2.4934  -0.4241
 4F0  H19  H  HCH1  0   0.207  -1.8173   0.6036   1.8337
 4F0  H20  H  HOH1  0   0.453  -2.1862   2.7601   2.3492
 4F0  C10  C  CH2   0  -0.358   0.2740   0.3866  -1.5823

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
 4F0  CS5  S    single    1.806  0.020  1.806
 4F0  S    C5'  single    1.815  0.020  1.815
 4F0  C5'  C4'  single    1.519  0.020  1.519
 4F0  C1'  C4'  single    1.540  0.020  1.540
 4F0  C1'  N1'  single    1.458  0.020  1.458
 4F0  C4'  C3'  single    1.532  0.020  1.532
 4F0  N1'  C2'  single    1.445  0.020  1.445
 4F0  N1'  C10  single    1.446  0.020  1.446
 4F0  C2'  C3'  single    1.524  0.020  1.524
 4F0  C3'  O3'  single    1.404  0.020  1.404
 4F0  C8   N7   aromatic  1.359  0.020  1.359
 4F0  C8   C9   aromatic  1.372  0.020  1.372
 4F0  N7   C5   aromatic  1.366  0.020  1.366
 4F0  C9   C10  single    1.490  0.020  1.490
 4F0  C9   C4   aromatic  1.424  0.020  1.424
 4F0  C5   C6   aromatic  1.403  0.020  1.403
 4F0  C5   C4   aromatic  1.400  0.020  1.400
 4F0  N6   C6   single    1.350  0.020  1.350
 4F0  C6   N1   aromatic  1.330  0.020  1.330
 4F0  C4   N3   aromatic  1.348  0.020  1.348
 4F0  N1   C2   aromatic  1.338  0.020  1.338
 4F0  N3   C2   aromatic  1.312  0.020  1.312
 4F0  C2   H1   single    0.930  0.020  1.080
 4F0  CS5  H2   single    0.970  0.020  1.090
 4F0  CS5  H3   single    0.970  0.020  1.090
 4F0  CS5  H4   single    0.970  0.020  1.090
 4F0  C5'  H5   single    0.970  0.020  1.090
 4F0  C5'  H6   single    0.970  0.020  1.090
 4F0  C4'  H7   single    0.970  0.020  1.090
 4F0  C1'  H8   single    0.970  0.020  1.090
 4F0  C1'  H9   single    0.970  0.020  1.090
 4F0  C10  H11  single    0.970  0.020  1.090
 4F0  C10  H12  single    0.970  0.020  1.090
 4F0  C8   H13  single    0.930  0.020  1.080
 4F0  N7   H14  single    0.860  0.020  1.020
 4F0  N6   H15  single    0.890  0.020  1.040
 4F0  N6   H16  single    0.890  0.020  1.040
 4F0  C2'  H17  single    0.970  0.020  1.090
 4F0  C2'  H18  single    0.970  0.020  1.090
 4F0  C3'  H19  single    0.970  0.020  1.090
 4F0  O3'  H20  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
 4F0  H1   C2   N3   116.56  3.000
 4F0  H1   C2   N1   115.05  3.000
 4F0  N3   C2   N1   128.39  3.000
 4F0  N3   C4   C9   130.28  3.000
 4F0  N3   C4   C5   122.36  3.000
 4F0  C9   C4   C5   107.35  3.000
 4F0  N7   C5   C6   133.43  3.000
 4F0  C6   C5   C4   118.68  3.000
 4F0  N7   C5   C4   107.89  3.000
 4F0  N1   C6   N6   118.79  3.000
 4F0  N1   C6   C5   117.81  3.000
 4F0  N6   C6   C5   123.37  3.000
 4F0  H4   CS5  H3   108.62  3.000
 4F0  H4   CS5  H2   109.41  3.000
 4F0  H3   CS5  H2   108.65  3.000
 4F0  H4   CS5  S    111.29  3.000
 4F0  H3   CS5  S    107.70  3.000
 4F0  H2   CS5  S    111.09  3.000
 4F0  C5'  S    CS5   99.97  3.000
 4F0  H6   C5'  H5   108.07  3.000
 4F0  H6   C5'  C4'  110.26  3.000
 4F0  H5   C5'  C4'  110.34  3.000
 4F0  H6   C5'  S    109.21  3.000
 4F0  H5   C5'  S    108.88  3.000
 4F0  C4'  C5'  S    110.05  3.000
 4F0  H7   C4'  C3'  107.27  3.000
 4F0  H7   C4'  C1'  109.16  3.000
 4F0  C3'  C4'  C1'  103.99  3.000
 4F0  H7   C4'  C5'  108.79  3.000
 4F0  C3'  C4'  C5'  112.64  3.000
 4F0  C1'  C4'  C5'  114.67  3.000
 4F0  H9   C1'  H8   106.69  3.000
 4F0  H9   C1'  N1'  111.90  3.000
 4F0  H8   C1'  N1'  110.46  3.000
 4F0  H9   C1'  C4'  109.97  3.000
 4F0  H8   C1'  C4'  112.53  3.000
 4F0  N1'  C1'  C4'  105.38  3.000
 4F0  C2'  N1'  C10  115.83  3.000
 4F0  C10  N1'  C1'  113.42  3.000
 4F0  C2'  N1'  C1'  106.65  3.000
 4F0  C8   C9   C10  127.11  3.000
 4F0  C10  C9   C4   127.21  3.000
 4F0  C8   C9   C4   105.67  3.000
 4F0  H13  C8   N7   120.39  3.000
 4F0  H13  C8   C9   129.07  3.000
 4F0  N7   C8   C9   110.54  3.000
 4F0  H14  N7   C8   124.45  3.000
 4F0  H14  N7   C5   127.00  3.000
 4F0  C8   N7   C5   108.55  3.000
 4F0  H16  N6   H15  114.97  3.000
 4F0  H16  N6   C6   116.99  3.000
 4F0  H15  N6   C6   119.80  3.000
 4F0  C6   N1   C2   118.82  3.000
 4F0  C4   N3   C2   113.94  3.000
 4F0  H18  C2'  H17  107.74  3.000
 4F0  H18  C2'  C3'  109.93  3.000
 4F0  H17  C2'  C3'  113.07  3.000
 4F0  H18  C2'  N1'  113.22  3.000
 4F0  H17  C2'  N1'  111.45  3.000
 4F0  C3'  C2'  N1'  101.46  3.000
 4F0  H19  C3'  O3'  110.91  3.000
 4F0  H19  C3'  C2'  107.98  3.000
 4F0  O3'  C3'  C2'  115.57  3.000
 4F0  H19  C3'  C4'  109.07  3.000
 4F0  O3'  C3'  C4'  110.46  3.000
 4F0  C2'  C3'  C4'  102.40  3.000
 4F0  H20  O3'  C3'  108.35  3.000
 4F0  H12  C10  H11  106.18  3.000
 4F0  H12  C10  C9   109.10  3.000
 4F0  H11  C10  C9   109.33  3.000
 4F0  H12  C10  N1'  111.70  3.000
 4F0  H11  C10  N1'  107.73  3.000
 4F0  C9   C10  N1'  112.58  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
 4F0  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 4F0  CONST_02  C9   C4   N3   C2    180.00   0.0  0
 4F0  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 4F0  CONST_04  N7   C8   C9   C4      0.00   0.0  0
 4F0  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 4F0  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 4F0  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 4F0  CONST_08  C9   C8   N7   C5      0.00   0.0  0
 4F0  CONST_09  C8   C9   C4   C5      0.00   0.0  0
 4F0  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 4F0  CONST_11  C9   C4   C5   C6    180.00   0.0  0
 4F0  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 4F0  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 4F0  CONST_14  N7   C5   C4   C9      0.00   0.0  0
 4F0  CONST_15  N3   C4   C9   C8    180.00   0.0  0
 4F0  CONST_16  N1   C6   C5   N7    180.00   0.0  0
 4F0  CONST_17  N3   C4   C5   N7    180.00   0.0  0
 4F0  CONST_18  N6   C6   N1   C2    180.00   0.0  0
 4F0  CONST_19  N6   C6   C5   C4    180.00   0.0  0
 4F0  CONST_20  C10  C9   C4   C5    180.00   0.0  0
 4F0  CONST_21  N7   C8   C9   C10   180.00   0.0  0
 4F0  CONST_22  N3   C4   C9   C10     0.00   0.0  0
 4F0  CONST_23  N6   C6   C5   N7      0.00   0.0  0
 4F0  CONST_24  H13  C8   C9   C4    180.00   0.0  0
 4F0  CONST_25  H14  N7   C5   C4    180.00   0.0  0
 4F0  CONST_26  H1   C2   N3   C4    180.00   0.0  0
 4F0  CONST_28  H16  N6   C6   C5    180.00   0.0  0
 4F0  Var_01    C2'  N1'  C1'  C4'   -27.40  30.0  1
 4F0  Var_02    C3'  C2'  N1'  C1'    43.83  30.0  1
 4F0  Var_03    N1'  C10  C9   C4     73.24  30.0  2
 4F0  Var_04    C9   C10  N1'  C1'  -173.83  30.0  3
 4F0  Var_05    C4'  C5'  S    CS5   179.73  30.0  3
 4F0  Var_06    H2   CS5  S    C5'    61.30  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
 4F0  chir_01  C4'  C5'  C1'  C3'  positiv
 4F0  chir_02  C3'  O3'  C4'  C2'  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
 4F0  plan-1  C2   0.020
 4F0  plan-1  C4   0.020
 4F0  plan-1  C5   0.020
 4F0  plan-1  C6   0.020
 4F0  plan-1  C9   0.020
 4F0  plan-1  C8   0.020
 4F0  plan-1  N7   0.020
 4F0  plan-1  N6   0.020
 4F0  plan-1  N1   0.020
 4F0  plan-1  N3   0.020
 4F0  plan-1  H1   0.020
 4F0  plan-1  H13  0.020
 4F0  plan-1  H14  0.020
 4F0  plan-1  C10  0.020
 4F0  plan-2  C6   0.020
 4F0  plan-2  N6   0.020
 4F0  plan-2  H15  0.020
 4F0  plan-2  H16  0.020

