# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:05:54 2021
#   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  50  27  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.480  -2.5467  -47.0596  129.9204
 RFE  C05  C  CH1   0   0.035  -2.9881  -47.3651  132.2386
 RFE  C06  C  CH3   0  -0.726  -2.2658  -48.7018  132.3066
 RFE  C07  C  CH2   0  -0.308  -4.1687  -47.2896  133.1939
 RFE  C09  C  CR56  0   0.546  -5.2230  -49.4782  133.8197
 RFE  C11  C  CR16  0   0.071  -4.9317  -50.9137  135.4546
 RFE  C13  C  CR6   0   0.196  -6.5082  -51.4724  133.8744
 RFE  C15  C  CR56  0   0.195  -6.2007  -50.2625  133.2253
 RFE  C17  C  CR15  0   0.160  -5.9933  -48.5615  131.9975
 RFE  C19  C  CH1   0  -0.147  -3.9483  -43.3994  129.1605
 RFE  C20  C  C     0   0.464  -3.9305  -42.5285  127.9121
 RFE  C23  C  CH2   0  -0.490  -3.7648  -42.5454  130.4261
 RFE  C24  C  CH2   0  -0.503  -3.8201  -43.3555  131.7145
 RFE  C26  C  CH3   0  -0.854  -6.3591  -44.5902  131.2593
 RFE  N08  N  NR5   0  -0.566  -5.1056  -48.3802  133.0200
 RFE  N10  N  N     0  -0.500  -4.5562  -49.7583  134.9375
 RFE  N12  N  N     0  -0.504  -5.8453  -51.7677  134.9973
 RFE  N16  N  N     0  -0.396  -6.6697  -49.6699  132.0828
 RFE  N18  N  NH1   0  -0.746  -2.9390  -44.4205  129.1010
 RFE  O04  O  O2    0  -0.490  -3.4992  -47.0806  130.9499
 RFE  O21  O  OH1   0  -0.516  -4.9423  -41.6694  127.9072
 RFE  O22  O  O     0  -0.350  -3.1095  -42.6011  127.0364
 RFE  P02  P  P     0   1.293  -3.2064  -45.9761  128.6095
 RFE  S25  S  S2    0  -0.050  -5.4530  -43.5932  132.4675
 RFE  H1   H  HCH2  0   0.247  -2.3560  -48.0600  129.5117
 RFE  H2   H  HCH2  0   0.266  -1.5798  -46.6581  130.2505
 RFE  H3   H  HCH1  0   0.221  -2.2908  -46.5697  132.5381
 RFE  H4   H  HCH3  0   0.227  -2.0016  -48.9317  133.3391
 RFE  H5   H  HCH3  0   0.260  -2.8856  -49.5141  131.9245
 RFE  H6   H  HCH3  0   0.227  -1.3411  -48.6856  131.7278
 RFE  H7   H  HCH2  0   0.284  -3.8014  -47.3334  134.2185
 RFE  H8   H  HCH2  0   0.266  -4.6972  -46.3401  133.0786
 RFE  H9   H  HCR6  0   0.262  -4.4303  -51.2148  136.3684
 RFE  H10  H  HCR5  0   0.270  -6.0993  -47.8326  131.2091
 RFE  H11  H  HCH1  0   0.306  -4.9262  -43.8843  129.1859
 RFE  H12  H  HCH2  0   0.275  -2.7823  -42.0658  130.3658
 RFE  H13  H  HCH2  0   0.250  -4.5025  -41.7431  130.4566
 RFE  H14  H  HCH2  0   0.232  -3.3443  -44.3282  131.5828
 RFE  H15  H  HCH2  0   0.305  -3.2590  -42.8335  132.4904
 RFE  H16  H  HCH3  0   0.321  -7.0848  -45.1646  131.8262
 RFE  H17  H  HCH3  0   0.272  -6.8934  -43.9784  130.5362
 RFE  H18  H  HCH3  0   0.254  -5.6949  -45.2756  130.7353
 RFE  H19  H  HNH2  0   0.382  -7.5478  -53.2186  133.8550
 RFE  H20  H  HNH2  0   0.380  -7.8650  -52.1746  132.5243
 RFE  H21  H  HNH1  0   0.413  -1.9851  -44.1067  129.2131
 RFE  H22  H  HOH1  0   0.464  -4.9093  -41.1181  127.1109
 RFE  H23  H  HOH1  0   0.512  -2.0645  -47.0640  127.0843
 RFE  N14  N  NH2   0  -0.822  -7.4438  -52.3148  133.4261
 RFE  O01  O  O     0  -0.736  -4.6293  -46.2366  128.2691
 RFE  O27  O  OH1   0  -0.671  -2.1286  -46.1613  127.4226

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  double    1.486  0.020  1.486
 RFE  O27  P02  single    1.614  0.020  1.614
 RFE  O22  C20  double    1.203  0.020  1.203
 RFE  P02  N18  single    1.653  0.020  1.653
 RFE  P02  C03  single    1.824  0.020  1.824
 RFE  N18  C19  single    1.437  0.020  1.437
 RFE  C20  C19  single    1.522  0.020  1.522
 RFE  C20  O21  single    1.327  0.020  1.327
 RFE  C03  O04  single    1.403  0.020  1.403
 RFE  C19  C23  single    1.538  0.020  1.538
 RFE  C23  C24  single    1.523  0.020  1.523
 RFE  O04  C05  single    1.415  0.020  1.415
 RFE  C26  S25  single    1.810  0.020  1.810
 RFE  C24  S25  single    1.814  0.020  1.814
 RFE  C05  C06  single    1.521  0.020  1.521
 RFE  C05  C07  single    1.521  0.020  1.521
 RFE  N14  C13  single    1.336  0.020  1.336
 RFE  N12  C13  aromatic  1.337  0.020  1.337
 RFE  N12  C11  aromatic  1.332  0.020  1.332
 RFE  C13  C15  aromatic  1.407  0.020  1.407
 RFE  C11  N10  aromatic  1.320  0.020  1.320
 RFE  C15  C09  aromatic  1.387  0.020  1.387
 RFE  C15  N16  aromatic  1.370  0.020  1.370
 RFE  N10  C09  aromatic  1.331  0.020  1.331
 RFE  C09  N08  aromatic  1.363  0.020  1.363
 RFE  N16  C17  aromatic  1.301  0.020  1.301
 RFE  N08  C17  aromatic  1.366  0.020  1.366
 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    0.860  0.020  1.020
 RFE  O21  H22  single    0.850  0.020  0.980
 RFE  O27  H23  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
 RFE  H2   C03  H1   107.00  3.000
 RFE  H2   C03  P02  108.51  3.000
 RFE  H1   C03  P02  109.68  3.000
 RFE  H2   C03  O04  112.51  3.000
 RFE  H1   C03  O04  112.19  3.000
 RFE  P02  C03  O04  106.90  3.000
 RFE  H3   C05  O04  109.37  3.000
 RFE  H3   C05  C07  106.58  3.000
 RFE  O04  C05  C07  106.36  3.000
 RFE  H3   C05  C06  108.81  3.000
 RFE  C07  C05  C06  112.60  3.000
 RFE  O04  C05  C06  112.89  3.000
 RFE  H6   C06  H5   107.87  3.000
 RFE  H6   C06  H4   107.47  3.000
 RFE  H5   C06  H4   108.21  3.000
 RFE  H6   C06  C05  111.45  3.000
 RFE  H5   C06  C05  111.65  3.000
 RFE  H4   C06  C05  110.05  3.000
 RFE  H8   C07  H7   107.29  3.000
 RFE  H8   C07  N08  109.19  3.000
 RFE  H7   C07  N08  107.50  3.000
 RFE  H8   C07  C05  110.63  3.000
 RFE  H7   C07  C05  109.10  3.000
 RFE  N08  C07  C05  112.92  3.000
 RFE  N10  C09  N08  128.23  3.000
 RFE  N08  C09  C15  105.35  3.000
 RFE  N10  C09  C15  126.42  3.000
 RFE  H9   C11  N12  115.37  3.000
 RFE  H9   C11  N10  116.18  3.000
 RFE  N12  C11  N10  128.45  3.000
 RFE  N14  C13  N12  119.32  3.000
 RFE  N12  C13  C15  117.97  3.000
 RFE  N14  C13  C15  122.70  3.000
 RFE  N16  C15  C13  133.00  3.000
 RFE  N16  C15  C09  110.74  3.000
 RFE  C13  C15  C09  116.26  3.000
 RFE  H10  C17  N16  124.91  3.000
 RFE  H10  C17  N08  121.41  3.000
 RFE  N16  C17  N08  113.69  3.000
 RFE  H11  C19  N18  108.32  3.000
 RFE  H11  C19  C23  109.54  3.000
 RFE  N18  C19  C23  110.17  3.000
 RFE  H11  C19  C20  106.48  3.000
 RFE  C23  C19  C20  110.85  3.000
 RFE  N18  C19  C20  111.37  3.000
 RFE  O22  C20  O21  123.83  3.000
 RFE  O21  C20  C19  111.37  3.000
 RFE  O22  C20  C19  124.79  3.000
 RFE  H13  C23  H12  106.64  3.000
 RFE  H13  C23  C24  110.07  3.000
 RFE  H12  C23  C24  108.19  3.000
 RFE  H13  C23  C19  110.54  3.000
 RFE  H12  C23  C19  107.76  3.000
 RFE  C24  C23  C19  113.36  3.000
 RFE  H15  C24  H14  106.75  3.000
 RFE  H15  C24  S25  103.33  3.000
 RFE  H14  C24  S25  109.03  3.000
 RFE  H15  C24  C23  109.18  3.000
 RFE  H14  C24  C23  110.88  3.000
 RFE  S25  C24  C23  116.98  3.000
 RFE  H18  C26  H17  109.50  3.000
 RFE  H18  C26  H16  109.04  3.000
 RFE  H17  C26  H16  108.46  3.000
 RFE  H18  C26  S25  111.26  3.000
 RFE  H17  C26  S25  112.33  3.000
 RFE  H16  C26  S25  106.12  3.000
 RFE  C17  N08  C09  106.03  3.000
 RFE  C17  N08  C07  127.60  3.000
 RFE  C09  N08  C07  126.28  3.000
 RFE  C11  N10  C09  111.75  3.000
 RFE  C13  N12  C11  119.14  3.000
 RFE  C17  N16  C15  104.19  3.000
 RFE  H21  N18  P02  118.55  3.000
 RFE  H21  N18  C19  115.96  3.000
 RFE  P02  N18  C19  124.56  3.000
 RFE  C05  O04  C03  115.22  3.000
 RFE  H22  O21  C20  110.20  3.000
 RFE  O27  P02  O01  116.80  3.000
 RFE  O27  P02  N18  102.63  3.000
 RFE  O01  P02  N18  112.83  3.000
 RFE  N18  P02  C03  106.66  3.000
 RFE  O27  P02  C03  102.64  3.000
 RFE  O01  P02  C03  114.00  3.000
 RFE  C26  S25  C24  104.23  3.000
 RFE  H20  N14  H19  117.68  3.000
 RFE  H20  N14  C13  120.43  3.000
 RFE  H19  N14  C13  119.72  3.000
 RFE  H23  O27  P02  114.14  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  CONST_28  H22  O21  C20  C19   180.00   0.0  0
 RFE  Var_01    C09  N08  C07  C05   102.84  30.0  1
 RFE  Var_02    C19  N18  P02  C03  -127.81  30.0  3
 RFE  Var_03    P02  C03  O04  C05  -154.38  30.0  1
 RFE  Var_04    S25  C24  C23  C19   -88.71  30.0  3
 RFE  Var_05    O04  C03  P02  N18    78.82  30.0  3
 RFE  Var_06    H16  C26  S25  C24   151.70  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
 RFE  chir_03  P02  O27  N18  C03  both

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  O21  0.020
 RFE  plan-3  O22  0.020
 RFE  plan-3  H22  0.020

