# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:02:25 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-propylpyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 C1Y  C1Y  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-propylpyrrolidin-3-ol  ligand  41  20  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C1Y
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
 C1Y  C4   C  CR56  0   0.161   2.1835  -0.3582  -0.2412
 C1Y  C5   C  CR56  0   0.205   3.3371   0.4336  -0.2842
 C1Y  C6   C  CR6   0   0.453   4.4221   0.0888   0.5365
 C1Y  C20  C  CH2   0  -0.428  -4.6590   0.0035   0.1787
 C1Y  C21  C  CH2   0  -0.427  -5.3448  -1.2934  -0.2357
 C1Y  C8   C  CR15  0  -0.054   1.8855   1.2807  -1.7217
 C1Y  C22  C  CH3   0  -0.661  -6.8226  -1.1000  -0.5456
 C1Y  C3'  C  CR15  0   0.051  -2.4886   1.1362   0.9509
 C1Y  C2'  C  CH2   0  -0.297  -1.3181   1.2430  -0.0273
 C1Y  N1'  N  NR5   0  -0.413  -1.0295  -0.1329  -0.3724
 C1Y  C1'  C  CH2   0  -0.267  -2.3353  -0.7130  -0.6094
 C1Y  C4'  C  CR15  0  -0.270  -3.1918  -0.1760   0.5416
 C1Y  C9   C  CR5   0  -0.040   1.2558   0.1937  -1.1702
 C1Y  N3   N  N     0  -0.444   2.0821  -1.4423   0.5545
 C1Y  N7   N  NR15  0  -0.677   3.1297   1.4299  -1.1950
 C1Y  N6   N  NH2   0  -0.826   5.5904   0.7624   0.5415
 C1Y  N1   N  N     0  -0.470   4.2961  -0.9821   1.3143
 C1Y  C2   C  CR16  0   0.004   3.1531  -1.6759   1.2750
 C1Y  H3   H  HCH2  0   0.211  -4.7463   0.7343  -0.6337
 C1Y  H4   H  HCH2  0   0.223  -5.1916   0.4339   1.0335
 C1Y  H5   H  HCH2  0   0.221  -4.8408  -1.7117  -1.1123
 C1Y  H6   H  HCH2  0   0.213  -5.2293  -2.0323   0.5632
 C1Y  H7   H  HCR5  0   0.289   1.5219   1.9681  -2.4695
 C1Y  H8   H  HCH3  0   0.217  -7.3627  -0.7247   0.3258
 C1Y  H9   H  HCH3  0   0.216  -6.9656  -0.3817  -1.3552
 C1Y  H10  H  HCH3  0   0.227  -7.2954  -2.0351  -0.8478
 C1Y  H12  H  HCR5  0   0.209  -3.1599   1.9951   0.8234
 C1Y  H13  H  HCH2  0   0.184  -1.6404   1.8218  -0.9124
 C1Y  H14  H  HCH2  0   0.238  -0.4508   1.7544   0.3957
 C1Y  H16  H  HCH2  0   0.184  -2.7577  -0.3823  -1.5783
 C1Y  H17  H  HCH2  0   0.235  -2.2824  -1.8038  -0.6354
 C1Y  H18  H  HCR5  0   0.240  -3.1231  -0.8664   1.3885
 C1Y  H19  H  HNR5  0   0.416   3.7821   2.1440  -1.4718
 C1Y  H20  H  HNH2  0   0.400   5.6355   1.6999   0.1822
 C1Y  H21  H  HNH2  0   0.396   6.2490   0.5464   1.2714
 C1Y  H22  H  HCR6  0   0.237   3.1191  -2.5405   1.9308
 C1Y  C10  C  CH2   0  -0.362  -0.1146  -0.3045  -1.4789
 C1Y  O3'  O  OH1   0  -0.679  -2.0837   1.0323   2.3008
 C1Y  H1   H  HCH2  0   0.237  -0.0711  -1.3726  -1.7118
 C1Y  H2   H  HCH2  0   0.202  -0.4847   0.1974  -2.3907
 C1Y  H11  H  HOH1  0   0.446  -1.7126   1.8788   2.5673

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
 C1Y  C8   N7   aromatic  1.359  0.020  1.359
 C1Y  C8   C9   aromatic  1.372  0.020  1.372
 C1Y  N7   C5   aromatic  1.366  0.020  1.366
 C1Y  C9   C10  single    1.491  0.020  1.491
 C1Y  C9   C4   aromatic  1.424  0.020  1.424
 C1Y  C10  N1'  single    1.446  0.020  1.446
 C1Y  C5   C4   aromatic  1.400  0.020  1.400
 C1Y  C5   C6   aromatic  1.403  0.020  1.403
 C1Y  N6   C6   single    1.349  0.020  1.349
 C1Y  C4   N3   aromatic  1.349  0.020  1.349
 C1Y  C6   N1   aromatic  1.330  0.020  1.330
 C1Y  N1'  C1'  single    1.448  0.020  1.448
 C1Y  N1'  C2'  single    1.448  0.020  1.448
 C1Y  C1'  C4'  single    1.532  0.020  1.532
 C1Y  N3   C2   aromatic  1.312  0.020  1.312
 C1Y  N1   C2   aromatic  1.338  0.020  1.338
 C1Y  C2'  C3'  single    1.529  0.020  1.529
 C1Y  C4'  C20  single    1.522  0.020  1.522
 C1Y  C4'  C3'  single    1.544  0.020  1.544
 C1Y  C21  C20  single    1.524  0.020  1.524
 C1Y  C21  C22  single    1.522  0.020  1.522
 C1Y  O3'  C3'  single    1.413  0.020  1.413
 C1Y  C10  H1   single    0.970  0.020  1.090
 C1Y  C10  H2   single    0.970  0.020  1.090
 C1Y  C20  H3   single    0.970  0.020  1.090
 C1Y  C20  H4   single    0.970  0.020  1.090
 C1Y  C21  H5   single    0.970  0.020  1.090
 C1Y  C21  H6   single    0.970  0.020  1.090
 C1Y  C8   H7   single    0.930  0.020  1.080
 C1Y  C22  H8   single    0.970  0.020  1.090
 C1Y  C22  H9   single    0.970  0.020  1.090
 C1Y  C22  H10  single    0.970  0.020  1.090
 C1Y  O3'  H11  single    0.850  0.020  0.980
 C1Y  C3'  H12  single    0.970  0.020  1.090
 C1Y  C2'  H13  single    0.970  0.020  1.090
 C1Y  C2'  H14  single    0.970  0.020  1.090
 C1Y  C1'  H16  single    0.970  0.020  1.090
 C1Y  C1'  H17  single    0.970  0.020  1.090
 C1Y  C4'  H18  single    0.970  0.020  1.090
 C1Y  N7   H19  single    0.860  0.020  1.020
 C1Y  N6   H20  single    0.890  0.020  1.040
 C1Y  N6   H21  single    0.890  0.020  1.040
 C1Y  C2   H22  single    0.930  0.020  1.080

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
 C1Y  N3   C4   C9   130.35  3.000
 C1Y  N3   C4   C5   122.33  3.000
 C1Y  C9   C4   C5   107.31  3.000
 C1Y  N7   C5   C6   133.37  3.000
 C1Y  C6   C5   C4   118.69  3.000
 C1Y  N7   C5   C4   107.94  3.000
 C1Y  N1   C6   N6   118.83  3.000
 C1Y  N1   C6   C5   117.82  3.000
 C1Y  N6   C6   C5   123.31  3.000
 C1Y  H4   C20  H3   106.13  3.000
 C1Y  H4   C20  C4'  109.21  3.000
 C1Y  H3   C20  C4'  109.39  3.000
 C1Y  H4   C20  C21  109.13  3.000
 C1Y  H3   C20  C21  109.26  3.000
 C1Y  C4'  C20  C21  113.46  3.000
 C1Y  H6   C21  H5   106.14  3.000
 C1Y  H6   C21  C22  109.69  3.000
 C1Y  H5   C21  C22  109.43  3.000
 C1Y  H6   C21  C20  109.18  3.000
 C1Y  H5   C21  C20  109.62  3.000
 C1Y  C22  C21  C20  112.58  3.000
 C1Y  H7   C8   N7   120.47  3.000
 C1Y  H7   C8   C9   128.96  3.000
 C1Y  N7   C8   C9   110.57  3.000
 C1Y  H10  C22  H9   107.57  3.000
 C1Y  H10  C22  H8   107.55  3.000
 C1Y  H9   C22  H8   107.51  3.000
 C1Y  H10  C22  C21  111.62  3.000
 C1Y  H9   C22  C21  111.21  3.000
 C1Y  H8   C22  C21  111.19  3.000
 C1Y  H12  C3'  C4'  110.84  3.000
 C1Y  H12  C3'  C2'  109.83  3.000
 C1Y  C4'  C3'  C2'  103.79  3.000
 C1Y  H12  C3'  O3'  110.11  3.000
 C1Y  C4'  C3'  O3'  108.74  3.000
 C1Y  C2'  C3'  O3'  113.38  3.000
 C1Y  H14  C2'  H13  107.24  3.000
 C1Y  H14  C2'  N1'  112.28  3.000
 C1Y  H13  C2'  N1'  111.40  3.000
 C1Y  H14  C2'  C3'  113.13  3.000
 C1Y  H13  C2'  C3'  109.00  3.000
 C1Y  N1'  C2'  C3'  103.81  3.000
 C1Y  C1'  N1'  C2'  103.89  3.000
 C1Y  C2'  N1'  C10  114.92  3.000
 C1Y  C1'  N1'  C10  113.43  3.000
 C1Y  H17  C1'  H16  107.20  3.000
 C1Y  H17  C1'  C4'  113.27  3.000
 C1Y  H16  C1'  C4'  109.83  3.000
 C1Y  H17  C1'  N1'  111.12  3.000
 C1Y  H16  C1'  N1'  111.56  3.000
 C1Y  C4'  C1'  N1'  103.93  3.000
 C1Y  H18  C4'  C1'  108.97  3.000
 C1Y  H18  C4'  C3'  107.59  3.000
 C1Y  C1'  C4'  C3'  104.03  3.000
 C1Y  H18  C4'  C20  108.62  3.000
 C1Y  C3'  C4'  C20  113.71  3.000
 C1Y  C1'  C4'  C20  113.66  3.000
 C1Y  C8   C9   C10  127.13  3.000
 C1Y  C10  C9   C4   127.19  3.000
 C1Y  C8   C9   C4   105.68  3.000
 C1Y  C2   N3   C4   113.95  3.000
 C1Y  H19  N7   C8   124.39  3.000
 C1Y  H19  N7   C5   127.07  3.000
 C1Y  C8   N7   C5   108.50  3.000
 C1Y  H21  N6   H20  115.48  3.000
 C1Y  H21  N6   C6   117.54  3.000
 C1Y  H20  N6   C6   120.23  3.000
 C1Y  C2   N1   C6   118.79  3.000
 C1Y  H22  C2   N1   114.96  3.000
 C1Y  H22  C2   N3   116.62  3.000
 C1Y  N1   C2   N3   128.42  3.000
 C1Y  H2   C10  H1   106.33  3.000
 C1Y  H2   C10  C9   109.09  3.000
 C1Y  H1   C10  C9   109.50  3.000
 C1Y  H2   C10  N1'  111.46  3.000
 C1Y  H1   C10  N1'  107.69  3.000
 C1Y  C9   C10  N1'  112.56  3.000
 C1Y  H11  O3'  C3'  108.09  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
 C1Y  CONST_01  N7   C8   C9   C4     0.00   0.0  0
 C1Y  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 C1Y  CONST_03  N1   C6   C5   C4     0.00   0.0  0
 C1Y  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 C1Y  CONST_05  C9   C8   N7   C5     0.00   0.0  0
 C1Y  CONST_06  C8   C9   C4   C5     0.00   0.0  0
 C1Y  CONST_07  C2   N3   C4   C5     0.00   0.0  0
 C1Y  CONST_08  C2   N1   C6   C5     0.00   0.0  0
 C1Y  CONST_09  C8   N7   C5   C6   180.00   0.0  0
 C1Y  CONST_10  C9   C4   C5   C6   180.00   0.0  0
 C1Y  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 C1Y  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 C1Y  CONST_13  N3   C4   C9   C8   180.00   0.0  0
 C1Y  CONST_14  N7   C5   C4   C9     0.00   0.0  0
 C1Y  CONST_15  C2   N3   C4   C9   180.00   0.0  0
 C1Y  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 C1Y  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 C1Y  CONST_18  N6   C6   C5   C4   180.00   0.0  0
 C1Y  CONST_19  C10  C9   C4   C5   180.00   0.0  0
 C1Y  CONST_20  N7   C8   C9   C10  180.00   0.0  0
 C1Y  CONST_21  N3   C4   C9   C10    0.00   0.0  0
 C1Y  CONST_22  N6   C6   C5   N7     0.00   0.0  0
 C1Y  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 C1Y  CONST_24  H7   C8   C9   C4   180.00   0.0  0
 C1Y  CONST_25  H19  N7   C5   C4   180.00   0.0  0
 C1Y  CONST_26  H22  C2   N3   C4   180.00   0.0  0
 C1Y  CONST_28  H21  N6   C6   C5   180.00   0.0  0
 C1Y  Var_01    C1'  N1'  C2'  C3'   44.65  30.0  1
 C1Y  Var_02    C4'  C1'  N1'  C2'  -43.67  30.0  1
 C1Y  Var_03    N1'  C10  C9   C4    68.23  30.0  2
 C1Y  Var_04    C9   C10  N1'  C2'   65.64  30.0  1
 C1Y  Var_05    C4'  C20  C21  C22  177.93  30.0  3
 C1Y  Var_06    H8   C22  C21  C20  -60.37  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
 C1Y  chir_01  C3'  C2'  C4'  O3'  negativ
 C1Y  chir_02  C4'  C3'  C20  C1'  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
 C1Y  plan-1  C4   0.020
 C1Y  plan-1  C5   0.020
 C1Y  plan-1  C6   0.020
 C1Y  plan-1  C8   0.020
 C1Y  plan-1  C9   0.020
 C1Y  plan-1  N3   0.020
 C1Y  plan-1  N7   0.020
 C1Y  plan-1  N6   0.020
 C1Y  plan-1  N1   0.020
 C1Y  plan-1  C2   0.020
 C1Y  plan-1  H7   0.020
 C1Y  plan-1  H19  0.020
 C1Y  plan-1  H22  0.020
 C1Y  plan-1  C10  0.020
 C1Y  plan-2  C6   0.020
 C1Y  plan-2  N6   0.020
 C1Y  plan-2  H20  0.020
 C1Y  plan-2  H21  0.020

