# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 20:12:51 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]-4-methylsulfanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N[P](O)(=O)CO[C@H](C)Cn1cnc2c(N)ncnc12)C(O)=O
#
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
 RFE  RFE  '(2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]-4-methylsulfanyl-butanoic acid'  ligand  48  27  .  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_RFE
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
 RFE  C03  C  CH2    0  -0.446  -1.8636  -46.8510  130.3307
 RFE  C05  C  CH1    0   0.067  -2.7475  -47.3782  132.4930
 RFE  C06  C  CH3    0  -0.692  -2.0095  -48.6798  132.7662
 RFE  C07  C  CH2    0  -0.355  -4.1103  -47.3016  133.1773
 RFE  C09  C  CR56   0   0.480  -5.3354  -49.5001  133.0710
 RFE  C11  C  CR16   0   0.032  -5.3220  -51.3537  134.2507
 RFE  C13  C  CR6    0   0.443  -6.7153  -51.3194  132.4219
 RFE  C15  C  CR56   0  -0.004  -6.2735  -50.0063  132.1828
 RFE  C17  C  CR15   0   0.084  -5.8506  -48.0462  131.5251
 RFE  C19  C  CH1    0  -0.151  -4.4635  -44.6660  129.5876
 RFE  C20  C  C      0   0.412  -5.6811  -44.9932  128.6913
 RFE  C23  C  CH2    0  -0.454  -4.6324  -43.2394  130.1213
 RFE  C24  C  CH2    0  -0.572  -3.6994  -42.9365  131.2858
 RFE  C26  C  CH3    0  -0.768  -5.5033  -41.3409  132.7034
 RFE  N08  N  NR5    0  -0.487  -5.0728  -48.2359  132.6330
 RFE  N10  N  N      0  -0.456  -4.8287  -50.1348  134.1279
 RFE  N12  N  N      0  -0.472  -6.2113  -51.9710  133.4755
 RFE  N16  N  N      0  -0.459  -6.5862  -49.0787  131.2243
 RFE  N18  N  NH1    0  -0.799  -3.1887  -44.7901  128.9024
 RFE  O04  O  O2     0  -0.481  -2.9865  -47.1686  131.1245
 RFE  O22  O  O      0  -0.603  -5.6748  -44.5717  127.5216
 RFE  P02  P  P      0   1.207  -2.4241  -46.2865  128.6555
 RFE  S25  S  S2     0  -0.042  -3.8617  -41.2562  131.9509
 RFE  H1   H  HCH2   0   0.203  -1.1993  -47.7184  130.2050
 RFE  H2   H  HCH2   0   0.198  -1.2592  -46.0620  130.8030
 RFE  H3   H  HCH1   0   0.211  -2.1541  -46.5488  132.9087
 RFE  H4   H  HCH3   0   0.232  -1.9053  -48.8418  133.8391
 RFE  H5   H  HCH3   0   0.229  -2.5357  -49.5361  132.3428
 RFE  H6   H  HCH3   0   0.241  -1.0064  -48.6578  132.3401
 RFE  H7   H  HCH2   0   0.272  -4.0041  -47.4987  134.2436
 RFE  H8   H  HCH2   0   0.280  -4.5187  -46.2962  133.0681
 RFE  H9   H  HCR6   0   0.245  -4.9571  -51.9344  135.0917
 RFE  H10  H  HCR5   0   0.301  -5.8617  -47.1070  130.9863
 RFE  H11  H  HCH1   0   0.212  -4.5072  -45.3287  130.4577
 RFE  H12  H  HCH2   0   0.222  -4.4675  -42.5197  129.3142
 RFE  H13  H  HCH2   0   0.239  -5.6657  -43.1144  130.4538
 RFE  H14  H  HCH2   0   0.261  -3.8571  -43.6520  132.0976
 RFE  H15  H  HCH2   0   0.268  -2.6511  -43.0185  130.9912
 RFE  H16  H  HCH3   0   0.272  -5.6730  -40.3974  133.2192
 RFE  H17  H  HCH3   0   0.260  -6.2876  -41.4714  131.9601
 RFE  H18  H  HCH3   0   0.258  -5.5573  -42.1490  133.4321
 RFE  H19  H  HNH2   0   0.399  -7.8478  -52.8939  131.8019
 RFE  H20  H  HNH2   0   0.407  -7.9439  -51.4938  130.8010
 RFE  H21  H  HNH1   0   0.351  -2.5458  -44.0298  129.0723
 RFE  N14  N  NH2    0  -0.818  -7.6221  -51.9261  131.6491
 RFE  O01  O  O      0  -0.807  -3.4520  -47.2754  128.1644
 RFE  O27  O  OP    -1  -0.809  -1.1601  -46.0124  127.8773
 RFE  O21  O  OC    -1  -0.615  -6.6146  -45.6090  129.2575

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
 RFE  O01  P02  deloc     1.509  0.020  1.509
 RFE  O27  P02  deloc     1.509  0.020  1.509
 RFE  O22  C20  deloc     1.243  0.020  1.243
 RFE  P02  N18  single    1.698  0.020  1.698
 RFE  P02  C03  single    1.855  0.020  1.855
 RFE  N18  C19  single    1.453  0.020  1.453
 RFE  C20  C19  single    1.547  0.020  1.547
 RFE  C20  O21  deloc     1.253  0.020  1.253
 RFE  C03  O04  single    1.411  0.020  1.411
 RFE  C19  C23  single    1.532  0.020  1.532
 RFE  C23  C24  single    1.523  0.020  1.523
 RFE  O04  C05  single    1.405  0.020  1.405
 RFE  C26  S25  single    1.808  0.020  1.808
 RFE  C24  S25  single    1.814  0.020  1.814
 RFE  C05  C06  single    1.521  0.020  1.521
 RFE  C05  C07  single    1.527  0.020  1.527
 RFE  N14  C13  single    1.337  0.020  1.337
 RFE  N12  C13  aromatic  1.337  0.020  1.337
 RFE  N12  C11  aromatic  1.332  0.020  1.332
 RFE  C13  C15  aromatic  1.406  0.020  1.406
 RFE  C11  N10  aromatic  1.321  0.020  1.321
 RFE  C15  C09  aromatic  1.388  0.020  1.388
 RFE  C15  N16  aromatic  1.370  0.020  1.370
 RFE  N10  C09  aromatic  1.333  0.020  1.333
 RFE  C09  N08  aromatic  1.363  0.020  1.363
 RFE  N16  C17  aromatic  1.303  0.020  1.303
 RFE  N08  C17  aromatic  1.367  0.020  1.367
 RFE  N08  C07  single    1.448  0.020  1.448
 RFE  C03  H1   single    0.970  0.020  1.090
 RFE  C03  H2   single    0.970  0.020  1.090
 RFE  C05  H3   single    0.970  0.020  1.090
 RFE  C06  H4   single    0.970  0.020  1.090
 RFE  C06  H5   single    0.970  0.020  1.090
 RFE  C06  H6   single    0.970  0.020  1.090
 RFE  C07  H7   single    0.970  0.020  1.090
 RFE  C07  H8   single    0.970  0.020  1.090
 RFE  C11  H9   single    0.930  0.020  1.080
 RFE  C17  H10  single    0.930  0.020  1.080
 RFE  C19  H11  single    0.970  0.020  1.090
 RFE  C23  H12  single    0.970  0.020  1.090
 RFE  C23  H13  single    0.970  0.020  1.090
 RFE  C24  H14  single    0.970  0.020  1.090
 RFE  C24  H15  single    0.970  0.020  1.090
 RFE  C26  H16  single    0.970  0.020  1.090
 RFE  C26  H17  single    0.970  0.020  1.090
 RFE  C26  H18  single    0.970  0.020  1.090
 RFE  N14  H19  single    0.860  0.020  1.020
 RFE  N14  H20  single    0.860  0.020  1.020
 RFE  N18  H21  single    0.890  0.020  1.040

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
 RFE  H2   C03  H1   106.43  3.000
 RFE  H2   C03  P02  109.60  3.000
 RFE  H1   C03  P02  108.63  3.000
 RFE  H2   C03  O04  110.91  3.000
 RFE  H1   C03  O04  111.56  3.000
 RFE  P02  C03  O04  109.63  3.000
 RFE  H3   C05  O04  110.30  3.000
 RFE  H3   C05  C07  105.90  3.000
 RFE  O04  C05  C07  106.10  3.000
 RFE  H3   C05  C06  108.38  3.000
 RFE  C07  C05  C06  113.29  3.000
 RFE  O04  C05  C06  112.65  3.000
 RFE  H6   C06  H5   107.94  3.000
 RFE  H6   C06  H4   107.44  3.000
 RFE  H5   C06  H4   108.16  3.000
 RFE  H6   C06  C05  111.04  3.000
 RFE  H5   C06  C05  111.60  3.000
 RFE  H4   C06  C05  110.51  3.000
 RFE  H8   C07  H7   107.53  3.000
 RFE  H8   C07  N08  107.96  3.000
 RFE  H7   C07  N08  108.42  3.000
 RFE  H8   C07  C05  109.61  3.000
 RFE  H7   C07  C05  110.03  3.000
 RFE  N08  C07  C05  113.11  3.000
 RFE  N10  C09  N08  128.54  3.000
 RFE  N08  C09  C15  105.24  3.000
 RFE  N10  C09  C15  126.22  3.000
 RFE  H9   C11  N12  115.32  3.000
 RFE  H9   C11  N10  116.13  3.000
 RFE  N12  C11  N10  128.55  3.000
 RFE  N14  C13  N12  119.33  3.000
 RFE  N12  C13  C15  118.07  3.000
 RFE  N14  C13  C15  122.59  3.000
 RFE  N16  C15  C13  132.82  3.000
 RFE  N16  C15  C09  110.80  3.000
 RFE  C13  C15  C09  116.38  3.000
 RFE  H10  C17  N16  124.52  3.000
 RFE  H10  C17  N08  121.97  3.000
 RFE  N16  C17  N08  113.47  3.000
 RFE  H11  C19  N18  110.99  3.000
 RFE  H11  C19  C23  106.40  3.000
 RFE  N18  C19  C23  109.91  3.000
 RFE  H11  C19  C20  107.52  3.000
 RFE  C23  C19  C20  108.18  3.000
 RFE  N18  C19  C20  113.54  3.000
 RFE  O22  C20  O21  126.53  3.000
 RFE  O21  C20  C19  115.36  3.000
 RFE  O22  C20  C19  118.00  3.000
 RFE  H13  C23  H12  106.96  3.000
 RFE  H13  C23  C24  108.91  3.000
 RFE  H12  C23  C24  109.94  3.000
 RFE  H13  C23  C19  108.46  3.000
 RFE  H12  C23  C19  109.81  3.000
 RFE  C24  C23  C19  112.58  3.000
 RFE  H15  C24  H14  106.84  3.000
 RFE  H15  C24  S25  104.73  3.000
 RFE  H14  C24  S25  108.72  3.000
 RFE  H15  C24  C23  111.53  3.000
 RFE  H14  C24  C23  110.44  3.000
 RFE  S25  C24  C23  114.19  3.000
 RFE  H18  C26  H17  109.40  3.000
 RFE  H18  C26  H16  108.55  3.000
 RFE  H17  C26  H16  108.37  3.000
 RFE  H18  C26  S25  110.99  3.000
 RFE  H17  C26  S25  112.07  3.000
 RFE  H16  C26  S25  107.35  3.000
 RFE  C17  N08  C09  106.23  3.000
 RFE  C17  N08  C07  126.41  3.000
 RFE  C09  N08  C07  127.28  3.000
 RFE  C11  N10  C09  111.79  3.000
 RFE  C13  N12  C11  118.98  3.000
 RFE  C17  N16  C15  104.26  3.000
 RFE  H21  N18  P02  113.64  3.000
 RFE  H21  N18  C19  114.52  3.000
 RFE  P02  N18  C19  122.61  3.000
 RFE  C05  O04  C03  116.49  3.000
 RFE  O27  P02  O01  121.45  3.000
 RFE  O27  P02  N18  106.97  3.000
 RFE  O01  P02  N18  108.55  3.000
 RFE  N18  P02  C03  105.84  3.000
 RFE  O27  P02  C03  105.54  3.000
 RFE  O01  P02  C03  107.49  3.000
 RFE  C26  S25  C24  100.98  3.000
 RFE  H20  N14  H19  118.07  3.000
 RFE  H20  N14  C13  120.65  3.000
 RFE  H19  N14  C13  120.08  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
 RFE  CONST_01  N12  C13  C15  C09     0.00   0.0  0
 RFE  CONST_02  C17  N16  C15  C09     0.00   0.0  0
 RFE  CONST_03  N12  C11  N10  C09     0.00   0.0  0
 RFE  CONST_04  N16  C17  N08  C09     0.00   0.0  0
 RFE  CONST_05  C15  C13  N12  C11     0.00   0.0  0
 RFE  CONST_06  C15  C09  N10  C11     0.00   0.0  0
 RFE  CONST_07  N08  C09  N10  C11   180.00   0.0  0
 RFE  CONST_08  N10  C11  N12  C13     0.00   0.0  0
 RFE  CONST_09  N10  C09  C15  C13     0.00   0.0  0
 RFE  CONST_10  N08  C09  C15  C13   180.00   0.0  0
 RFE  CONST_11  C17  N16  C15  C13   180.00   0.0  0
 RFE  CONST_12  C17  N08  C09  C15     0.00   0.0  0
 RFE  CONST_13  N08  C17  N16  C15     0.00   0.0  0
 RFE  CONST_14  N10  C09  N08  C17   180.00   0.0  0
 RFE  CONST_15  N16  C15  C09  N08     0.00   0.0  0
 RFE  CONST_16  N16  C15  C09  N10   180.00   0.0  0
 RFE  CONST_17  N16  C15  C13  N12   180.00   0.0  0
 RFE  CONST_18  C15  C09  N08  C07   180.00   0.0  0
 RFE  CONST_19  N10  C09  N08  C07     0.00   0.0  0
 RFE  CONST_20  N16  C17  N08  C07   180.00   0.0  0
 RFE  CONST_21  N14  C13  C15  C09   180.00   0.0  0
 RFE  CONST_22  N14  C13  N12  C11   180.00   0.0  0
 RFE  CONST_23  N16  C15  C13  N14     0.00   0.0  0
 RFE  CONST_24  H9   C11  N10  C09   180.00   0.0  0
 RFE  CONST_25  H10  C17  N08  C09   180.00   0.0  0
 RFE  CONST_26  H19  N14  C13  C15   180.00   0.0  0
 RFE  CONST_27  H20  N14  C13  C15     0.00   0.0  0
 RFE  Var_01    C09  N08  C07  C05    92.48  30.0  1
 RFE  Var_02    C19  N18  P02  C03   -69.64  30.0  3
 RFE  Var_03    P02  C03  O04  C05  -168.77  30.0  2
 RFE  Var_04    S25  C24  C23  C19   179.93  30.0  3
 RFE  Var_05    O04  C03  P02  N18    68.41  30.0  3
 RFE  Var_06    H16  C26  S25  C24   175.01  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
 RFE  chir_01  C05  O04  C06  C07  positiv
 RFE  chir_02  C19  N18  C20  C23  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
 RFE  plan-1  C07  0.020
 RFE  plan-1  C09  0.020
 RFE  plan-1  C11  0.020
 RFE  plan-1  C13  0.020
 RFE  plan-1  C15  0.020
 RFE  plan-1  C17  0.020
 RFE  plan-1  N08  0.020
 RFE  plan-1  N10  0.020
 RFE  plan-1  N12  0.020
 RFE  plan-1  N16  0.020
 RFE  plan-1  H9   0.020
 RFE  plan-1  H10  0.020
 RFE  plan-1  N14  0.020
 RFE  plan-2  C13  0.020
 RFE  plan-2  H19  0.020
 RFE  plan-2  H20  0.020
 RFE  plan-2  N14  0.020
 RFE  plan-3  C19  0.020
 RFE  plan-3  C20  0.020
 RFE  plan-3  O22  0.020
 RFE  plan-3  O21  0.020

