# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:02:58 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCSC[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
 BIG  BIG  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol  ligand  48  23  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BIG
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
 BIG  C2    C  CR16  0   0.005    4.5918  -1.5839   1.5446
 BIG  C5    C  CR56  0   0.204    4.8460  -0.0040  -0.5426
 BIG  C4    C  CR56  0   0.161    3.6256  -0.6036  -0.2105
 BIG  C8    C  CR15  0  -0.050    3.3588   0.6123  -2.0589
 BIG  O3'   O  OH1   0  -0.676   -0.2394   2.1792   1.9830
 BIG  C3'   C  CH1   0   0.053   -0.6897   1.9246   0.6700
 BIG  C4'   C  CH1   0  -0.285   -1.6142   0.6878   0.7032
 BIG  C5'   C  CH2   0  -0.553   -3.0503   1.0207   0.3368
 BIG  S5'   S  S2    0  -0.041   -4.0835  -0.4648   0.4760
 BIG  C20   C  CH2   0  -0.540   -5.6702   0.1850  -0.1197
 BIG  C21   C  CH2   0  -0.415   -6.7333  -0.9017  -0.0640
 BIG  C22   C  CH2   0  -0.418   -8.0847  -0.4106  -0.5715
 BIG  C23   C  CH3   0  -0.661   -9.1541  -1.4927  -0.5177
 BIG  C1'   C  CH2   0  -0.259   -0.9494  -0.3062  -0.2522
 BIG  N1'   N  NT    0  -0.414    0.4493   0.0718  -0.2208
 BIG  C2'   C  CH2   0  -0.298    0.4263   1.5184  -0.2947
 BIG  N7    N  NR15  0  -0.676    4.6566   0.7350  -1.6754
 BIG  C6    C  CR6   0   0.455    5.9621  -0.2526   0.2709
 BIG  N6    N  NH2   0  -0.827    7.1888   0.2458   0.0191
 BIG  N3    N  N     0  -0.445    3.4874  -1.4164   0.8567
 BIG  C9    C  CR5   0  -0.046    2.6752  -0.2024  -1.1917
 BIG  N1    N  N     0  -0.471    5.7994  -1.0547   1.3191
 BIG  H2    H  HCR6  0   0.237    4.5293  -2.2313   2.4138
 BIG  H8    H  HCR5  0   0.289    3.0000   1.1190  -2.9411
 BIG  HO3'  H  HOH1  0   0.449    0.2820   2.9878   1.9705
 BIG  H3'   H  HCH1  0   0.217   -1.2184   2.8009   0.2740
 BIG  H4'   H  HCH1  0   0.259   -1.5918   0.2860   1.7205
 BIG  H5'   H  HCH2  0   0.272   -3.4444   1.7953   0.9985
 BIG  H5'A  H  HCH2  0   0.258   -3.1032   1.3972  -0.6881
 BIG  H20   H  HCH2  0   0.255   -5.9622   1.0375   0.4980
 BIG  H20A  H  HCH2  0   0.255   -5.5445   0.5438  -1.1440
 BIG  H21   H  HCH2  0   0.225   -6.4110  -1.7600  -0.6614
 BIG  H21A  H  HCH2  0   0.225   -6.8374  -1.2593   0.9647
 BIG  H22   H  HCH2  0   0.217   -8.4035   0.4529   0.0197
 BIG  H22A  H  HCH2  0   0.217   -7.9774  -0.0534  -1.5998
 BIG  H23   H  HCH3  0   0.229  -10.1079  -1.1297  -0.9013
 BIG  H23A  H  HCH3  0   0.218   -8.8662  -2.3603  -1.1141
 BIG  H23B  H  HCH3  0   0.218   -9.3188  -1.8366   0.5049
 BIG  H1'   H  HCH2  0   0.240   -1.0841  -1.3481   0.0460
 BIG  H1'A  H  HCH2  0   0.190   -1.3783  -0.1975  -1.2661
 BIG  H2'   H  HCH2  0   0.189    0.1728   1.8689  -1.3119
 BIG  H2'A  H  HCH2  0   0.242    1.3915   1.9577  -0.0334
 BIG  H10   H  HCH2  0   0.238    1.1212  -1.6510  -1.1406
 BIG  H10A  H  HCH2  0   0.203    0.8436  -0.3204  -2.2604
 BIG  HN7   H  HNR5  0   0.415    5.3469   1.2743  -2.1697
 BIG  HN6   H  HNH2  0   0.401    7.3046   1.0321  -0.5963
 BIG  HN6A  H  HNH2  0   0.397    7.8901   0.1440   0.7338
 BIG  C10   C  CH2   0  -0.362    1.2320  -0.5689  -1.2569

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
 BIG  C2   N3    aromatic  1.312  0.020  1.312
 BIG  C2   N1    aromatic  1.338  0.020  1.338
 BIG  C5   C4    aromatic  1.400  0.020  1.400
 BIG  C5   N7    aromatic  1.366  0.020  1.366
 BIG  C5   C6    aromatic  1.403  0.020  1.403
 BIG  C4   N3    aromatic  1.349  0.020  1.349
 BIG  C4   C9    aromatic  1.424  0.020  1.424
 BIG  C8   N7    aromatic  1.359  0.020  1.359
 BIG  C8   C9    aromatic  1.372  0.020  1.372
 BIG  O3'  C3'   single    1.411  0.020  1.411
 BIG  C3'  C4'   single    1.544  0.020  1.544
 BIG  C3'  C2'   single    1.530  0.020  1.530
 BIG  C4'  C5'   single    1.519  0.020  1.519
 BIG  C4'  C1'   single    1.531  0.020  1.531
 BIG  C5'  S5'   single    1.815  0.020  1.815
 BIG  S5'  C20   single    1.815  0.020  1.815
 BIG  C20  C21   single    1.521  0.020  1.521
 BIG  C21  C22   single    1.525  0.020  1.525
 BIG  C22  C23   single    1.522  0.020  1.522
 BIG  C1'  N1'   single    1.449  0.020  1.449
 BIG  N1'  C2'   single    1.449  0.020  1.449
 BIG  N1'  C10   single    1.448  0.020  1.448
 BIG  C10  C9    single    1.490  0.020  1.490
 BIG  C6   N6    single    1.348  0.020  1.348
 BIG  C6   N1    aromatic  1.330  0.020  1.330
 BIG  C2   H2    single    0.930  0.020  1.080
 BIG  C8   H8    single    0.930  0.020  1.080
 BIG  O3'  HO3'  single    0.850  0.020  0.980
 BIG  C3'  H3'   single    0.970  0.020  1.090
 BIG  C4'  H4'   single    0.970  0.020  1.090
 BIG  C5'  H5'   single    0.970  0.020  1.090
 BIG  C5'  H5'A  single    0.970  0.020  1.090
 BIG  C20  H20   single    0.970  0.020  1.090
 BIG  C20  H20A  single    0.970  0.020  1.090
 BIG  C21  H21   single    0.970  0.020  1.090
 BIG  C21  H21A  single    0.970  0.020  1.090
 BIG  C22  H22   single    0.970  0.020  1.090
 BIG  C22  H22A  single    0.970  0.020  1.090
 BIG  C23  H23   single    0.970  0.020  1.090
 BIG  C23  H23A  single    0.970  0.020  1.090
 BIG  C23  H23B  single    0.970  0.020  1.090
 BIG  C1'  H1'   single    0.970  0.020  1.090
 BIG  C1'  H1'A  single    0.970  0.020  1.090
 BIG  C2'  H2'   single    0.970  0.020  1.090
 BIG  C2'  H2'A  single    0.970  0.020  1.090
 BIG  C10  H10   single    0.970  0.020  1.090
 BIG  C10  H10A  single    0.970  0.020  1.090
 BIG  N7   HN7   single    0.860  0.020  1.020
 BIG  N6   HN6   single    0.890  0.020  1.040
 BIG  N6   HN6A  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
 BIG  H2    C2   N1    115.02  3.000
 BIG  H2    C2   N3    116.59  3.000
 BIG  N1    C2   N3    128.39  3.000
 BIG  C6    C5   N7    133.39  3.000
 BIG  C6    C5   C4    118.69  3.000
 BIG  N7    C5   C4    107.92  3.000
 BIG  C9    C4   N3    130.30  3.000
 BIG  C9    C4   C5    107.33  3.000
 BIG  N3    C4   C5    122.37  3.000
 BIG  H8    C8   C9    129.04  3.000
 BIG  H8    C8   N7    120.40  3.000
 BIG  C9    C8   N7    110.55  3.000
 BIG  HO3'  O3'  C3'   108.20  3.000
 BIG  H3'   C3'  C2'   109.62  3.000
 BIG  H3'   C3'  C4'   111.03  3.000
 BIG  C2'   C3'  C4'   103.74  3.000
 BIG  H3'   C3'  O3'   110.21  3.000
 BIG  C2'   C3'  O3'   113.69  3.000
 BIG  C4'   C3'  O3'   108.39  3.000
 BIG  H4'   C4'  C1'   109.45  3.000
 BIG  H4'   C4'  C5'   108.91  3.000
 BIG  C1'   C4'  C5'   113.73  3.000
 BIG  H4'   C4'  C3'   107.57  3.000
 BIG  C1'   C4'  C3'   104.28  3.000
 BIG  C5'   C4'  C3'   112.66  3.000
 BIG  H5'A  C5'  H5'   107.83  3.000
 BIG  H5'A  C5'  S5'   109.04  3.000
 BIG  H5'   C5'  S5'   109.18  3.000
 BIG  H5'A  C5'  C4'   110.33  3.000
 BIG  H5'   C5'  C4'   110.51  3.000
 BIG  S5'   C5'  C4'   109.90  3.000
 BIG  C20   S5'  C5'   100.34  3.000
 BIG  H20A  C20  H20   107.73  3.000
 BIG  H20A  C20  C21   110.44  3.000
 BIG  H20   C20  C21   110.48  3.000
 BIG  H20A  C20  S5'   108.94  3.000
 BIG  H20   C20  S5'   109.12  3.000
 BIG  C21   C20  S5'   110.07  3.000
 BIG  H21A  C21  H21   106.55  3.000
 BIG  H21A  C21  C22   109.50  3.000
 BIG  H21   C21  C22   109.39  3.000
 BIG  H21A  C21  C20   109.54  3.000
 BIG  H21   C21  C20   109.54  3.000
 BIG  C22   C21  C20   112.16  3.000
 BIG  H22A  C22  H22   106.19  3.000
 BIG  H22A  C22  C23   109.53  3.000
 BIG  H22   C22  C23   109.71  3.000
 BIG  H22A  C22  C21   109.34  3.000
 BIG  H22   C22  C21   109.43  3.000
 BIG  C23   C22  C21   112.46  3.000
 BIG  H23B  C23  H23A  107.54  3.000
 BIG  H23B  C23  H23   107.62  3.000
 BIG  H23A  C23  H23   107.65  3.000
 BIG  H23B  C23  C22   111.29  3.000
 BIG  H23A  C23  C22   111.12  3.000
 BIG  H23   C23  C22   111.44  3.000
 BIG  H1'A  C1'  H1'   107.23  3.000
 BIG  H1'A  C1'  N1'   111.62  3.000
 BIG  H1'   C1'  N1'   111.22  3.000
 BIG  H1'A  C1'  C4'   109.87  3.000
 BIG  H1'   C1'  C4'   113.30  3.000
 BIG  N1'   C1'  C4'   103.67  3.000
 BIG  C10   N1'  C2'   114.45  3.000
 BIG  C10   N1'  C1'   113.01  3.000
 BIG  C2'   N1'  C1'   104.12  3.000
 BIG  H2'A  C2'  H2'   107.18  3.000
 BIG  H2'A  C2'  N1'   112.05  3.000
 BIG  H2'   C2'  N1'   111.54  3.000
 BIG  H2'A  C2'  C3'   112.76  3.000
 BIG  H2'   C2'  C3'   109.20  3.000
 BIG  N1'   C2'  C3'   104.15  3.000
 BIG  HN7   N7   C8    124.42  3.000
 BIG  HN7   N7   C5    127.05  3.000
 BIG  C8    N7   C5    108.52  3.000
 BIG  N1    C6   N6    118.79  3.000
 BIG  N1    C6   C5    117.81  3.000
 BIG  N6    C6   C5    123.37  3.000
 BIG  HN6A  N6   HN6   115.70  3.000
 BIG  HN6A  N6   C6    117.66  3.000
 BIG  HN6   N6   C6    120.56  3.000
 BIG  C4    N3   C2    113.93  3.000
 BIG  C10   C9   C8    126.92  3.000
 BIG  C10   C9   C4    127.39  3.000
 BIG  C8    C9   C4    105.68  3.000
 BIG  C6    N1   C2    118.81  3.000
 BIG  H10A  C10  H10   106.47  3.000
 BIG  H10A  C10  C9    108.97  3.000
 BIG  H10   C10  C9    109.67  3.000
 BIG  H10A  C10  N1'   111.13  3.000
 BIG  H10   C10  N1'   107.86  3.000
 BIG  C9    C10  N1'   112.54  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
 BIG  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 BIG  CONST_02  C9    C4   N3   C2    180.00   0.0  0
 BIG  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 BIG  CONST_04  C8    C9   C4   C5      0.00   0.0  0
 BIG  CONST_05  C9    C8   N7   C5      0.00   0.0  0
 BIG  CONST_06  C8    N7   C5   C4      0.00   0.0  0
 BIG  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 BIG  CONST_08  N1    C2   N3   C4      0.00   0.0  0
 BIG  CONST_09  N7    C8   C9   C4      0.00   0.0  0
 BIG  CONST_10  C6    C5   N7   C8    180.00   0.0  0
 BIG  CONST_11  N3    C4   C9   C8    180.00   0.0  0
 BIG  CONST_12  N3    C4   C5   N7    180.00   0.0  0
 BIG  CONST_13  C9    C4   C5   N7      0.00   0.0  0
 BIG  CONST_14  N1    C6   C5   N7    180.00   0.0  0
 BIG  CONST_15  N3    C4   C5   C6      0.00   0.0  0
 BIG  CONST_16  C9    C4   C5   C6    180.00   0.0  0
 BIG  CONST_17  N3    C2   N1   C6      0.00   0.0  0
 BIG  CONST_18  N6    C6   N1   C2    180.00   0.0  0
 BIG  CONST_19  C10   C9   C4   C5    180.00   0.0  0
 BIG  CONST_20  N6    C6   C5   C4    180.00   0.0  0
 BIG  CONST_21  N3    C4   C9   C10     0.00   0.0  0
 BIG  CONST_22  N7    C8   C9   C10   180.00   0.0  0
 BIG  CONST_23  N6    C6   C5   N7      0.00   0.0  0
 BIG  CONST_24  H8    C8   N7   C5    180.00   0.0  0
 BIG  CONST_25  HN7   N7   C5   C4    180.00   0.0  0
 BIG  CONST_26  H2    C2   N3   C4    180.00   0.0  0
 BIG  CONST_28  HN6A  N6   C6   C5    180.00   0.0  0
 BIG  Var_01    C1'   N1'  C2'  C3'    43.62  30.0  1
 BIG  Var_02    C2'   N1'  C1'  C4'   -43.71  30.0  1
 BIG  Var_03    N1'   C10  C9   C4     70.88  30.0  1
 BIG  Var_04    C9    C10  N1'  C1'  -178.41  30.0  3
 BIG  Var_05    C21   C20  S5'  C5'  -178.71  30.0  3
 BIG  Var_06    C22   C21  C20  S5'  -179.29  30.0  3
 BIG  Var_07    C23   C22  C21  C20  -179.95  30.0  3
 BIG  Var_08    H5'   C5'  S5'  C20    62.47  30.0  2
 BIG  Var_09    H23   C23  C22  C21  -178.93  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
 BIG  chir_01  C3'  O3'  C4'  C2'  positiv
 BIG  chir_02  C4'  C1'  C5'  C3'  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
 BIG  plan-1  C2    0.020
 BIG  plan-1  C5    0.020
 BIG  plan-1  C4    0.020
 BIG  plan-1  C8    0.020
 BIG  plan-1  N7    0.020
 BIG  plan-1  C6    0.020
 BIG  plan-1  N6    0.020
 BIG  plan-1  N3    0.020
 BIG  plan-1  C9    0.020
 BIG  plan-1  N1    0.020
 BIG  plan-1  H2    0.020
 BIG  plan-1  H8    0.020
 BIG  plan-1  HN7   0.020
 BIG  plan-1  C10   0.020
 BIG  plan-2  C6    0.020
 BIG  plan-2  N6    0.020
 BIG  plan-2  HN6   0.020
 BIG  plan-2  HN6A  0.020

