# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 21:09:22 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[2-(2-hydroxyethoxy)ethyl]sulfanyl}methyl)pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCOCCO)C3)c[nH]c12
#
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
 2EL  2EL  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[2-(2-hydroxyethoxy)ethyl]sulfanyl}methyl)pyrrolidin-3-ol  ligand  50  25  .  2022-07-22  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_2EL
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
 2EL  OAY  O  OH1   0  -0.672   -9.2930  -0.4846  -1.6912
 2EL  CAX  C  CH2   0  -0.185   -9.3859  -0.7049  -0.3026
 2EL  CAW  C  CH2   0  -0.163   -8.0691  -1.2236   0.2152
 2EL  OAV  O  O2    0  -0.486   -7.0752  -0.2372   0.0753
 2EL  CAU  C  CH2   0  -0.120   -5.8152  -0.6732   0.5153
 2EL  CAI  C  CH2   0  -0.576   -4.8167   0.4458   0.2860
 2EL  SAH  S  S2    0  -0.043   -3.1870  -0.0972   0.8708
 2EL  CAG  C  CH2   0  -0.554   -2.1767   1.3063   0.3190
 2EL  CAF  C  CR15  0  -0.285   -0.7198   1.0536   0.6642
 2EL  CAE  C  CH2   0  -0.261   -0.1234  -0.1704  -0.0376
 2EL  CAB  C  CR15  0   0.051    0.2000   2.2220   0.2443
 2EL  OAA  O  OH1   0  -0.675    0.7692   2.7808   1.4084
 2EL  CAC  C  CH2   0  -0.297    1.2234   1.5610  -0.6797
 2EL  NAD  N  NR5   0  -0.415    1.2672   0.1866  -0.2271
 2EL  CAJ  C  CH2   0  -0.367    1.9775  -0.7179  -1.1057
 2EL  CAK  C  CR5   0  -0.038    3.4378  -0.4272  -1.1649
 2EL  CAN  C  CR15  0  -0.053    4.1305   0.1495  -2.1997
 2EL  NAO  N  NR15  0  -0.676    5.4485   0.2606  -1.8868
 2EL  C5   C  CR56  0   0.200    5.6422  -0.2499  -0.6345
 2EL  C6   C  CR56  0   0.158    4.4040  -0.6863  -0.1519
 2EL  N1   N  N     0  -0.449    4.2606  -1.2612   1.0603
 2EL  C2   C  CR16  0   0.006    5.3817  -1.3670   1.7330
 2EL  N3   N  N     0  -0.475    6.6093  -0.9796   1.3707
 2EL  C4   C  CR6   0   0.469    6.7768  -0.4109   0.1788
 2EL  NAR  N  NH2   0  -0.832    8.0082  -0.0229  -0.1840
 2EL  H1   H  HOH1  0   0.455  -10.1508  -0.1845  -2.0041
 2EL  H2   H  HCH2  0   0.201   -9.6544   0.2116   0.2395
 2EL  H3   H  HCH2  0   0.204  -10.1489  -1.4540  -0.0558
 2EL  H4   H  HCH2  0   0.206   -8.2009  -1.5023   1.2698
 2EL  H5   H  HCH2  0   0.204   -7.7874  -2.1397  -0.3238
 2EL  H6   H  HCH2  0   0.207   -5.8432  -0.9404   1.5812
 2EL  H7   H  HCH2  0   0.208   -5.4980  -1.5717  -0.0323
 2EL  H8   H  HCH2  0   0.267   -4.7519   0.6850  -0.7772
 2EL  H9   H  HCH2  0   0.267   -5.1180   1.3460   0.8250
 2EL  H10  H  HCH2  0   0.262   -2.2984   1.4297  -0.7604
 2EL  H11  H  HCH2  0   0.276   -2.5335   2.2164   0.8056
 2EL  H12  H  HCR5  0   0.262   -0.6285   0.9314   1.7473
 2EL  H13  H  HCH2  0   0.241   -0.2158  -1.0879   0.5479
 2EL  H14  H  HCH2  0   0.192   -0.6396  -0.3444  -1.0003
 2EL  H15  H  HCR5  0   0.218   -0.3608   2.9858  -0.3091
 2EL  H16  H  HOH1  0   0.449    1.2851   3.5503   1.1490
 2EL  H17  H  HCH2  0   0.189    0.8690   1.6352  -1.7246
 2EL  H18  H  HCH2  0   0.241    2.2037   2.0406  -0.6373
 2EL  H20  H  HCH2  0   0.239    1.8245  -1.7348  -0.7323
 2EL  H21  H  HCH2  0   0.205    1.5600  -0.6964  -2.1272
 2EL  H22  H  HCR5  0   0.289    3.7656   0.4951  -3.1543
 2EL  H23  H  HNR5  0   0.415    6.1495   0.6361  -2.5034
 2EL  H24  H  HCR6  0   0.236    5.3174  -1.8282   2.7142
 2EL  H25  H  HNH2  0   0.401    8.7854  -0.1978   0.4288
 2EL  H26  H  HNH2  0   0.406    8.2014   0.4037  -1.0715

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
 2EL  CAW  CAX  single    1.507  0.020  1.507
 2EL  CAW  OAV  single    1.407  0.020  1.407
 2EL  CAX  OAY  single    1.409  0.020  1.409
 2EL  SAH  CAI  single    1.815  0.020  1.815
 2EL  SAH  CAG  single    1.815  0.020  1.815
 2EL  CAU  OAV  single    1.404  0.020  1.404
 2EL  CAU  CAI  single    1.517  0.020  1.517
 2EL  C2   N3   aromatic  1.337  0.020  1.337
 2EL  C2   N1   aromatic  1.312  0.020  1.312
 2EL  N3   C4   aromatic  1.331  0.020  1.331
 2EL  CAG  CAF  single    1.518  0.020  1.518
 2EL  CAB  CAF  single    1.545  0.020  1.545
 2EL  CAB  CAC  single    1.529  0.020  1.529
 2EL  CAB  OAA  single    1.411  0.020  1.411
 2EL  N1   C6   aromatic  1.349  0.020  1.349
 2EL  C4   NAR  single    1.341  0.020  1.341
 2EL  C4   C5   aromatic  1.405  0.020  1.405
 2EL  CAF  CAE  single    1.532  0.020  1.532
 2EL  CAC  NAD  single    1.448  0.020  1.448
 2EL  C6   C5   aromatic  1.399  0.020  1.399
 2EL  C6   CAK  aromatic  1.424  0.020  1.424
 2EL  C5   NAO  aromatic  1.366  0.020  1.366
 2EL  CAE  NAD  single    1.448  0.020  1.448
 2EL  NAD  CAJ  single    1.447  0.020  1.447
 2EL  CAK  CAJ  single    1.490  0.020  1.490
 2EL  CAK  CAN  aromatic  1.372  0.020  1.372
 2EL  NAO  CAN  aromatic  1.359  0.020  1.359
 2EL  OAY  H1   single    0.850  0.020  0.980
 2EL  CAX  H2   single    0.970  0.020  1.090
 2EL  CAX  H3   single    0.970  0.020  1.090
 2EL  CAW  H4   single    0.970  0.020  1.090
 2EL  CAW  H5   single    0.970  0.020  1.090
 2EL  CAU  H6   single    0.970  0.020  1.090
 2EL  CAU  H7   single    0.970  0.020  1.090
 2EL  CAI  H8   single    0.970  0.020  1.090
 2EL  CAI  H9   single    0.970  0.020  1.090
 2EL  CAG  H10  single    0.970  0.020  1.090
 2EL  CAG  H11  single    0.970  0.020  1.090
 2EL  CAF  H12  single    0.970  0.020  1.090
 2EL  CAE  H13  single    0.970  0.020  1.090
 2EL  CAE  H14  single    0.970  0.020  1.090
 2EL  CAB  H15  single    0.970  0.020  1.090
 2EL  OAA  H16  single    0.850  0.020  0.980
 2EL  CAC  H17  single    0.970  0.020  1.090
 2EL  CAC  H18  single    0.970  0.020  1.090
 2EL  CAJ  H20  single    0.970  0.020  1.090
 2EL  CAJ  H21  single    0.970  0.020  1.090
 2EL  CAN  H22  single    0.930  0.020  1.080
 2EL  NAO  H23  single    0.860  0.020  1.020
 2EL  C2   H24  single    0.930  0.020  1.080
 2EL  NAR  H25  single    0.860  0.020  1.020
 2EL  NAR  H26  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
 2EL  H1   OAY  CAX  108.11  3.000
 2EL  H3   CAX  H2   106.78  3.000
 2EL  H3   CAX  CAW  107.18  3.000
 2EL  H2   CAX  CAW  109.35  3.000
 2EL  H3   CAX  OAY  111.97  3.000
 2EL  H2   CAX  OAY  111.85  3.000
 2EL  CAW  CAX  OAY  109.56  3.000
 2EL  H5   CAW  H4   106.85  3.000
 2EL  H5   CAW  OAV  110.75  3.000
 2EL  H4   CAW  OAV  110.97  3.000
 2EL  H5   CAW  CAX  110.01  3.000
 2EL  H4   CAW  CAX  108.20  3.000
 2EL  OAV  CAW  CAX  109.98  3.000
 2EL  CAU  OAV  CAW  112.64  3.000
 2EL  H7   CAU  H6   106.97  3.000
 2EL  H7   CAU  CAI  109.74  3.000
 2EL  H6   CAU  CAI  110.04  3.000
 2EL  H7   CAU  OAV  110.90  3.000
 2EL  H6   CAU  OAV  110.88  3.000
 2EL  CAI  CAU  OAV  108.31  3.000
 2EL  H9   CAI  H8   108.46  3.000
 2EL  H9   CAI  SAH  109.61  3.000
 2EL  H8   CAI  SAH  109.04  3.000
 2EL  H9   CAI  CAU  110.60  3.000
 2EL  H8   CAI  CAU  110.35  3.000
 2EL  SAH  CAI  CAU  108.76  3.000
 2EL  CAG  SAH  CAI   99.81  3.000
 2EL  H11  CAG  H10  108.03  3.000
 2EL  H11  CAG  CAF  110.54  3.000
 2EL  H10  CAG  CAF  110.49  3.000
 2EL  H11  CAG  SAH  109.09  3.000
 2EL  H10  CAG  SAH  109.00  3.000
 2EL  CAF  CAG  SAH  109.65  3.000
 2EL  H12  CAF  CAB  107.69  3.000
 2EL  H12  CAF  CAE  109.38  3.000
 2EL  CAB  CAF  CAE  104.36  3.000
 2EL  H12  CAF  CAG  108.89  3.000
 2EL  CAE  CAF  CAG  113.73  3.000
 2EL  CAB  CAF  CAG  112.55  3.000
 2EL  H14  CAE  H13  107.15  3.000
 2EL  H14  CAE  NAD  111.90  3.000
 2EL  H13  CAE  NAD  111.00  3.000
 2EL  H14  CAE  CAF  110.04  3.000
 2EL  H13  CAE  CAF  113.12  3.000
 2EL  NAD  CAE  CAF  103.71  3.000
 2EL  H15  CAB  CAC  109.77  3.000
 2EL  H15  CAB  OAA  110.27  3.000
 2EL  CAC  CAB  OAA  113.56  3.000
 2EL  H15  CAB  CAF  111.05  3.000
 2EL  OAA  CAB  CAF  108.39  3.000
 2EL  CAC  CAB  CAF  103.64  3.000
 2EL  H16  OAA  CAB  108.10  3.000
 2EL  H18  CAC  H17  107.15  3.000
 2EL  H18  CAC  NAD  112.19  3.000
 2EL  H17  CAC  NAD  111.64  3.000
 2EL  H18  CAC  CAB  112.80  3.000
 2EL  H17  CAC  CAB  109.12  3.000
 2EL  NAD  CAC  CAB  103.99  3.000
 2EL  CAJ  NAD  CAC  114.73  3.000
 2EL  CAJ  NAD  CAE  113.37  3.000
 2EL  CAC  NAD  CAE  104.23  3.000
 2EL  H21  CAJ  H20  106.33  3.000
 2EL  H21  CAJ  CAK  109.28  3.000
 2EL  H20  CAJ  CAK  109.39  3.000
 2EL  H21  CAJ  NAD  111.35  3.000
 2EL  H20  CAJ  NAD  107.76  3.000
 2EL  CAK  CAJ  NAD  112.53  3.000
 2EL  C6   CAK  CAN  105.69  3.000
 2EL  CAN  CAK  CAJ  127.34  3.000
 2EL  C6   CAK  CAJ  126.96  3.000
 2EL  H22  CAN  NAO  120.37  3.000
 2EL  H22  CAN  CAK  129.13  3.000
 2EL  NAO  CAN  CAK  110.50  3.000
 2EL  H23  NAO  C5   127.05  3.000
 2EL  H23  NAO  CAN  124.39  3.000
 2EL  C5   NAO  CAN  108.54  3.000
 2EL  C4   C5   C6   118.64  3.000
 2EL  C6   C5   NAO  107.90  3.000
 2EL  C4   C5   NAO  133.45  3.000
 2EL  N1   C6   C5   122.48  3.000
 2EL  C5   C6   CAK  107.36  3.000
 2EL  N1   C6   CAK  130.14  3.000
 2EL  C2   N1   C6   113.85  3.000
 2EL  H24  C2   N3   114.97  3.000
 2EL  H24  C2   N1   116.55  3.000
 2EL  N3   C2   N1   128.48  3.000
 2EL  C4   N3   C2   118.81  3.000
 2EL  NAR  C4   N3   118.78  3.000
 2EL  NAR  C4   C5   123.48  3.000
 2EL  N3   C4   C5   117.74  3.000
 2EL  H26  NAR  H25  117.67  3.000
 2EL  H26  NAR  C4   122.62  3.000
 2EL  H25  NAR  C4   119.65  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
 2EL  CONST_01  C2   N1   C6   CAK   180.00   0.0  0
 2EL  CONST_02  C4   C5   C6   CAK   180.00   0.0  0
 2EL  CONST_03  NAO  C5   C6   CAK     0.00   0.0  0
 2EL  CONST_04  C5   NAO  CAN  CAK     0.00   0.0  0
 2EL  CONST_05  N1   C6   CAK  CAN   180.00   0.0  0
 2EL  CONST_06  C5   C6   CAK  CAN     0.00   0.0  0
 2EL  CONST_07  C4   C5   NAO  CAN   180.00   0.0  0
 2EL  CONST_08  C6   C5   NAO  CAN     0.00   0.0  0
 2EL  CONST_09  N3   C4   C5   NAO   180.00   0.0  0
 2EL  CONST_10  N1   C6   C5   NAO   180.00   0.0  0
 2EL  CONST_11  C6   CAK  CAN  NAO     0.00   0.0  0
 2EL  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 2EL  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 2EL  CONST_14  N3   C2   N1   C6      0.00   0.0  0
 2EL  CONST_15  N3   C4   C5   C6      0.00   0.0  0
 2EL  CONST_16  C4   N3   C2   N1      0.00   0.0  0
 2EL  CONST_17  C4   C5   C6   N1      0.00   0.0  0
 2EL  CONST_18  N1   C6   CAK  CAJ     0.00   0.0  0
 2EL  CONST_19  C5   C6   CAK  CAJ   180.00   0.0  0
 2EL  CONST_20  NAO  CAN  CAK  CAJ   180.00   0.0  0
 2EL  CONST_21  NAR  C4   C5   NAO     0.00   0.0  0
 2EL  CONST_22  NAR  C4   C5   C6    180.00   0.0  0
 2EL  CONST_23  NAR  C4   N3   C2    180.00   0.0  0
 2EL  CONST_24  H23  NAO  CAN  CAK   180.00   0.0  0
 2EL  CONST_25  H22  CAN  NAO  C5    180.00   0.0  0
 2EL  CONST_26  H24  C2   N1   C6    180.00   0.0  0
 2EL  CONST_27  H25  NAR  C4   C5    180.00   0.0  0
 2EL  CONST_28  H26  NAR  C4   C5      0.00   0.0  0
 2EL  Var_01    CAC  NAD  CAE  CAF   -43.29  30.0  1
 2EL  Var_02    CAB  CAC  NAD  CAE    44.16  30.0  1
 2EL  Var_03    CAK  CAJ  NAD  CAE  -173.43  30.0  3
 2EL  Var_04    C6   CAK  CAJ  NAD    73.02  30.0  1
 2EL  Var_05    CAF  CAG  SAH  CAI  -178.06  30.0  3
 2EL  Var_06    OAV  CAW  CAX  OAY    65.41  30.0  1
 2EL  Var_07    CAI  CAU  OAV  CAW   178.47  30.0  1
 2EL  Var_08    SAH  CAI  CAU  OAV   179.27  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
 2EL  chir_01  CAF  CAG  CAB  CAE  positiv
 2EL  chir_02  CAB  OAA  CAC  CAF  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
 2EL  plan-1  CAJ  0.020
 2EL  plan-1  CAK  0.020
 2EL  plan-1  CAN  0.020
 2EL  plan-1  NAO  0.020
 2EL  plan-1  C5   0.020
 2EL  plan-1  C6   0.020
 2EL  plan-1  N1   0.020
 2EL  plan-1  C2   0.020
 2EL  plan-1  N3   0.020
 2EL  plan-1  C4   0.020
 2EL  plan-1  NAR  0.020
 2EL  plan-1  H22  0.020
 2EL  plan-1  H23  0.020
 2EL  plan-1  H24  0.020
 2EL  plan-2  C4   0.020
 2EL  plan-2  NAR  0.020
 2EL  plan-2  H25  0.020
 2EL  plan-2  H26  0.020

