# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:36:32 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSCCCCO)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
 GMD  GMD  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol  ligand  49  24  .  2022-07-25  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_GMD
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
 GMD  C    C  CH2   0  -0.137   -8.6825   1.3174   0.2386
 GMD  OXT  O  OH1   0  -0.675   -9.9123   0.8077   0.7084
 GMD  CA   C  CH2   0  -0.451   -7.6300   0.2299   0.3293
 GMD  CB   C  CH2   0  -0.432   -6.2722   0.7151  -0.1654
 GMD  CG   C  CH2   0  -0.538   -5.2128  -0.3711  -0.0603
 GMD  S5'  S  S2    0  -0.039   -3.6196   0.2472  -0.6716
 GMD  C5'  C  CH2   0  -0.554   -2.5741  -1.1985  -0.3369
 GMD  C4'  C  CH1   0  -0.284   -1.1294  -0.8922  -0.6898
 GMD  C1'  C  CH2   0  -0.260   -0.5187   0.2395   0.1434
 GMD  C3'  C  CH1   0   0.054   -0.1930  -2.0965  -0.4415
 GMD  O3'  O  OH1   0  -0.675    0.3434  -2.5081  -1.6798
 GMD  C2'  C  CH2   0  -0.296    0.8541  -1.5458   0.5277
 GMD  N1'  N  NT    0  -0.413    0.8777  -0.1272   0.2440
 GMD  C10  C  CH2   0  -0.362    1.6213   0.6722   1.1926
 GMD  C9   C  CR5   0  -0.042    3.0772   0.3525   1.1803
 GMD  C8   C  CR15  0  -0.052    3.7904  -0.3156   2.1435
 GMD  N7   N  NR15  0  -0.676    5.0927  -0.4388   1.7735
 GMD  C5   C  CR56  0   0.205    5.2546   0.1508   0.5523
 GMD  C4   C  CR56  0   0.161    4.0124   0.6553   0.1504
 GMD  N3   N  N     0  -0.444    3.8415   1.3076  -1.0171
 GMD  C2   C  CR16  0   0.005    4.9352   1.4136  -1.7333
 GMD  N1   N  N     0  -0.470    6.1622   0.9644  -1.4461
 GMD  C6   C  CR6   0   0.453    6.3577   0.3231  -0.2979
 GMD  N6   N  NH2   0  -0.826    7.5868  -0.1617  -0.0264
 GMD  H1   H  HCH2  0   0.189   -8.7624   1.6574  -0.8027
 GMD  H2   H  HCH2  0   0.189   -8.3565   2.1850   0.8285
 GMD  H3   H  HOH1  0   0.452  -10.5716   1.5036   0.6386
 GMD  H4   H  HCH2  0   0.224   -7.5441  -0.1066   1.3671
 GMD  H5   H  HCH2  0   0.225   -7.9478  -0.6356  -0.2603
 GMD  H6   H  HCH2  0   0.231   -6.3563   1.0446  -1.2051
 GMD  H7   H  HCH2  0   0.231   -5.9575   1.5873   0.4151
 GMD  H8   H  HCH2  0   0.258   -5.0923  -0.6854   0.9789
 GMD  H9   H  HCH2  0   0.257   -5.5050  -1.2485  -0.6417
 GMD  H10  H  HCH2  0   0.259   -2.6615  -1.4574   0.7219
 GMD  H11  H  HCH2  0   0.272   -2.9385  -2.0476  -0.9196
 GMD  H12  H  HCH1  0   0.260   -1.0693  -0.6361  -1.7516
 GMD  H13  H  HCH2  0   0.240   -0.6353   1.2237  -0.3155
 GMD  H14  H  HCH2  0   0.190   -1.0099   0.2818   1.1339
 GMD  H15  H  HCH1  0   0.215   -0.7358  -2.9248   0.0321
 GMD  H16  H  HOH1  0   0.448    0.8970  -3.2794  -1.5239
 GMD  H17  H  HCH2  0   0.189    0.5297  -1.7475   1.5647
 GMD  H18  H  HCH2  0   0.241    1.8351  -2.0083   0.3983
 GMD  H20  H  HCH2  0   0.238    1.4770   1.7239   0.9282
 GMD  H21  H  HCH2  0   0.204    1.2308   0.5515   2.2182
 GMD  H22  H  HCR5  0   0.290    3.4501  -0.7194   3.0842
 GMD  H23  H  HNR5  0   0.416    5.8004  -0.8914   2.3272
 GMD  H24  H  HCR6  0   0.237    4.8468   1.9331  -2.6826
 GMD  H25  H  HNH2  0   0.396    8.3469   0.1551  -0.6053
 GMD  H26  H  HNH2  0   0.400    7.8372  -0.4084   0.9154

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
 GMD  C2   N1   aromatic  1.338  0.020  1.338
 GMD  C2   N3   aromatic  1.312  0.020  1.312
 GMD  N1   C6   aromatic  1.330  0.020  1.330
 GMD  N3   C4   aromatic  1.348  0.020  1.348
 GMD  C6   N6   single    1.349  0.020  1.349
 GMD  C6   C5   aromatic  1.403  0.020  1.403
 GMD  C4   C5   aromatic  1.400  0.020  1.400
 GMD  C4   C9   aromatic  1.424  0.020  1.424
 GMD  C2'  N1'  single    1.447  0.020  1.447
 GMD  C2'  C3'  single    1.529  0.020  1.529
 GMD  C5   N7   aromatic  1.366  0.020  1.366
 GMD  C10  C9   single    1.491  0.020  1.491
 GMD  C10  N1'  single    1.446  0.020  1.446
 GMD  C9   C8   aromatic  1.372  0.020  1.372
 GMD  N1'  C1'  single    1.447  0.020  1.447
 GMD  C3'  O3'  single    1.411  0.020  1.411
 GMD  C3'  C4'  single    1.546  0.020  1.546
 GMD  N7   C8   aromatic  1.359  0.020  1.359
 GMD  C1'  C4'  single    1.532  0.020  1.532
 GMD  C4'  C5'  single    1.518  0.020  1.518
 GMD  C5'  S5'  single    1.815  0.020  1.815
 GMD  S5'  CG   single    1.815  0.020  1.815
 GMD  CG   CB   single    1.521  0.020  1.521
 GMD  CB   CA   single    1.524  0.020  1.524
 GMD  CA   C    single    1.516  0.020  1.516
 GMD  OXT  C    single    1.412  0.020  1.412
 GMD  C    H1   single    0.970  0.020  1.090
 GMD  C    H2   single    0.970  0.020  1.090
 GMD  OXT  H3   single    0.850  0.020  0.980
 GMD  CA   H4   single    0.970  0.020  1.090
 GMD  CA   H5   single    0.970  0.020  1.090
 GMD  CB   H6   single    0.970  0.020  1.090
 GMD  CB   H7   single    0.970  0.020  1.090
 GMD  CG   H8   single    0.970  0.020  1.090
 GMD  CG   H9   single    0.970  0.020  1.090
 GMD  C5'  H10  single    0.970  0.020  1.090
 GMD  C5'  H11  single    0.970  0.020  1.090
 GMD  C4'  H12  single    0.970  0.020  1.090
 GMD  C1'  H13  single    0.970  0.020  1.090
 GMD  C1'  H14  single    0.970  0.020  1.090
 GMD  C3'  H15  single    0.970  0.020  1.090
 GMD  O3'  H16  single    0.850  0.020  0.980
 GMD  C2'  H17  single    0.970  0.020  1.090
 GMD  C2'  H18  single    0.970  0.020  1.090
 GMD  C10  H20  single    0.970  0.020  1.090
 GMD  C10  H21  single    0.970  0.020  1.090
 GMD  C8   H22  single    0.930  0.020  1.080
 GMD  N7   H23  single    0.860  0.020  1.020
 GMD  C2   H24  single    0.930  0.020  1.080
 GMD  N6   H25  single    0.890  0.020  1.040
 GMD  N6   H26  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
 GMD  H2   C    H1   106.63  3.000
 GMD  H2   C    CA   109.17  3.000
 GMD  H1   C    CA   109.23  3.000
 GMD  H2   C    OXT  111.40  3.000
 GMD  H1   C    OXT  111.34  3.000
 GMD  CA   C    OXT  109.02  3.000
 GMD  H3   OXT  C    108.18  3.000
 GMD  H5   CA   H4   106.89  3.000
 GMD  H5   CA   CB   109.60  3.000
 GMD  H4   CA   CB   109.62  3.000
 GMD  H5   CA   C    109.48  3.000
 GMD  H4   CA   C    109.38  3.000
 GMD  CB   CA   C    111.75  3.000
 GMD  H7   CB   H6   106.64  3.000
 GMD  H7   CB   CG   109.41  3.000
 GMD  H6   CB   CG   109.53  3.000
 GMD  H7   CB   CA   109.74  3.000
 GMD  H6   CB   CA   109.63  3.000
 GMD  CG   CB   CA   111.76  3.000
 GMD  H9   CG   H8   107.74  3.000
 GMD  H9   CG   S5'  109.21  3.000
 GMD  H8   CG   S5'  108.76  3.000
 GMD  H9   CG   CB   110.52  3.000
 GMD  H8   CG   CB   110.37  3.000
 GMD  S5'  CG   CB   110.17  3.000
 GMD  C5'  S5'  CG    99.91  3.000
 GMD  H11  C5'  H10  107.80  3.000
 GMD  H11  C5'  C4'  110.50  3.000
 GMD  H10  C5'  C4'  110.42  3.000
 GMD  H11  C5'  S5'  109.18  3.000
 GMD  H10  C5'  S5'  108.73  3.000
 GMD  C4'  C5'  S5'  110.15  3.000
 GMD  H12  C4'  C3'  107.76  3.000
 GMD  H12  C4'  C1'  109.45  3.000
 GMD  C3'  C4'  C1'  104.28  3.000
 GMD  H12  C4'  C5'  108.97  3.000
 GMD  C1'  C4'  C5'  113.69  3.000
 GMD  C3'  C4'  C5'  112.45  3.000
 GMD  H14  C1'  H13  107.11  3.000
 GMD  H14  C1'  N1'  112.07  3.000
 GMD  H13  C1'  N1'  111.13  3.000
 GMD  H14  C1'  C4'  109.76  3.000
 GMD  H13  C1'  C4'  113.24  3.000
 GMD  N1'  C1'  C4'  103.61  3.000
 GMD  H15  C3'  C2'  109.69  3.000
 GMD  H15  C3'  O3'  110.27  3.000
 GMD  C2'  C3'  O3'  113.64  3.000
 GMD  H15  C3'  C4'  110.96  3.000
 GMD  O3'  C3'  C4'  108.46  3.000
 GMD  C2'  C3'  C4'  103.65  3.000
 GMD  H16  O3'  C3'  108.09  3.000
 GMD  H18  C2'  H17  107.30  3.000
 GMD  H18  C2'  N1'  112.16  3.000
 GMD  H17  C2'  N1'  111.58  3.000
 GMD  H18  C2'  C3'  112.79  3.000
 GMD  H17  C2'  C3'  109.15  3.000
 GMD  N1'  C2'  C3'  103.89  3.000
 GMD  C10  N1'  C2'  114.94  3.000
 GMD  C10  N1'  C1'  113.68  3.000
 GMD  C2'  N1'  C1'  104.26  3.000
 GMD  H21  C10  H20  106.44  3.000
 GMD  H21  C10  C9   109.25  3.000
 GMD  H20  C10  C9   109.45  3.000
 GMD  H21  C10  N1'  111.53  3.000
 GMD  H20  C10  N1'  107.76  3.000
 GMD  C9   C10  N1'  112.22  3.000
 GMD  C4   C9   C8   105.66  3.000
 GMD  C8   C9   C10  127.32  3.000
 GMD  C4   C9   C10  127.01  3.000
 GMD  H22  C8   N7   120.37  3.000
 GMD  H22  C8   C9   129.08  3.000
 GMD  N7   C8   C9   110.55  3.000
 GMD  H23  N7   C5   127.08  3.000
 GMD  H23  N7   C8   124.39  3.000
 GMD  C5   N7   C8   108.53  3.000
 GMD  C6   C5   C4   118.64  3.000
 GMD  C4   C5   N7   107.89  3.000
 GMD  C6   C5   N7   133.47  3.000
 GMD  N3   C4   C5   122.38  3.000
 GMD  C5   C4   C9   107.37  3.000
 GMD  N3   C4   C9   130.24  3.000
 GMD  C2   N3   C4   113.97  3.000
 GMD  H24  C2   N1   115.03  3.000
 GMD  H24  C2   N3   116.62  3.000
 GMD  N1   C2   N3   128.35  3.000
 GMD  C6   N1   C2   118.83  3.000
 GMD  N6   C6   N1   118.76  3.000
 GMD  N6   C6   C5   123.38  3.000
 GMD  N1   C6   C5   117.83  3.000
 GMD  H26  N6   H25  115.33  3.000
 GMD  H26  N6   C6   120.25  3.000
 GMD  H25  N6   C6   117.33  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
 GMD  CONST_01  C2   N3   C4   C9    180.00   0.0  0
 GMD  CONST_02  C6   C5   C4   C9    180.00   0.0  0
 GMD  CONST_03  N7   C5   C4   C9      0.00   0.0  0
 GMD  CONST_04  C5   N7   C8   C9      0.00   0.0  0
 GMD  CONST_05  N3   C4   C9   C8    180.00   0.0  0
 GMD  CONST_06  C5   C4   C9   C8      0.00   0.0  0
 GMD  CONST_07  C6   C5   N7   C8    180.00   0.0  0
 GMD  CONST_08  C4   C5   N7   C8      0.00   0.0  0
 GMD  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 GMD  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 GMD  CONST_11  C4   C9   C8   N7      0.00   0.0  0
 GMD  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 GMD  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 GMD  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 GMD  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 GMD  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 GMD  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 GMD  CONST_18  N3   C4   C9   C10     0.00   0.0  0
 GMD  CONST_19  C5   C4   C9   C10   180.00   0.0  0
 GMD  CONST_20  N7   C8   C9   C10   180.00   0.0  0
 GMD  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 GMD  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 GMD  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 GMD  CONST_24  H23  N7   C8   C9    180.00   0.0  0
 GMD  CONST_25  H22  C8   N7   C5    180.00   0.0  0
 GMD  CONST_26  H24  C2   N3   C4    180.00   0.0  0
 GMD  CONST_27  H25  N6   C6   C5    180.00   0.0  0
 GMD  Var_01    C2'  N1'  C1'  C4'   -43.62  30.0  1
 GMD  Var_02    C3'  C2'  N1'  C1'    44.38  30.0  1
 GMD  Var_03    C9   C10  N1'  C1'  -174.77  30.0  2
 GMD  Var_04    C4   C9   C10  N1'    70.49  30.0  2
 GMD  Var_05    C4'  C5'  S5'  CG   -176.33  30.0  1
 GMD  Var_06    CG   CB   CA   C     179.38  30.0  1
 GMD  Var_07    CB   CA   C    OXT   179.96  30.0  1
 GMD  Var_08    S5'  CG   CB   CA    179.55  30.0  2

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
 GMD  chir_01  C4'  C3'  C1'  C5'  positiv
 GMD  chir_02  C3'  O3'  C2'  C4'  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
 GMD  plan-1  C10  0.020
 GMD  plan-1  C9   0.020
 GMD  plan-1  C8   0.020
 GMD  plan-1  N7   0.020
 GMD  plan-1  C5   0.020
 GMD  plan-1  C4   0.020
 GMD  plan-1  N3   0.020
 GMD  plan-1  C2   0.020
 GMD  plan-1  N1   0.020
 GMD  plan-1  C6   0.020
 GMD  plan-1  N6   0.020
 GMD  plan-1  H22  0.020
 GMD  plan-1  H23  0.020
 GMD  plan-1  H24  0.020
 GMD  plan-2  C6   0.020
 GMD  plan-2  N6   0.020
 GMD  plan-2  H25  0.020
 GMD  plan-2  H26  0.020

