# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 21:05:33 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-{4-[1-(cyclopropylsulfonyl)cyclopropyl]-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl}-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COCCN1c2cc(nc(n2)c3cccc4[nH]ccc34)C5(CC5)[S](=O)(=O)C6CC6
#
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
 8DV  8DV  4-{4-[1-(cyclopropylsulfonyl)cyclopropyl]-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl}-1H-indole  ligand  57  31  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8DV
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
 8DV  C1   C  CH1   0  -0.145   2.0691  -3.0795  -0.2201
 8DV  C2   C  CH2   0  -0.183   2.2247  -4.4252   0.4733
 8DV  C3   C  CH2   0  -0.186   0.1457  -5.1603  -0.1819
 8DV  O1   O  OS    0  -0.673  -5.1426   1.2279  -0.3511
 8DV  O2   O  OS    0  -0.665  -3.8897  -0.6734   0.6967
 8DV  C11  C  CR16  0  -0.270   2.1030   4.0034   1.1800
 8DV  C12  C  CR16  0  -0.306   3.4660   3.7914   1.2500
 8DV  C13  C  CR56  0   0.349   3.9375   2.5410   0.8637
 8DV  C14  C  CR15  0  -0.018   5.2213   0.7975   0.3579
 8DV  C15  C  CR15  0  -0.463   3.9407   0.3946   0.1049
 8DV  C16  C  CR56  0   0.073   3.0865   1.4963   0.4223
 8DV  C17  C  CT    0  -0.308  -2.7070   0.7162  -1.2088
 8DV  C18  C  CH2   0  -0.457  -3.2757   0.4304  -2.5681
 8DV  C19  C  CH2   0  -0.458  -2.8551   1.8167  -2.2090
 8DV  C20  C  CH1   0  -0.432  -3.2070   1.7825   1.3254
 8DV  C21  C  CH2   0  -0.477  -3.6019   1.5804   2.7592
 8DV  C22  C  CH2   0  -0.457  -2.2096   1.2839   2.3197
 8DV  S    S  S     0   1.240  -3.8770   0.6763   0.1342
 8DV  C7   C  CR6   0   0.304  -1.3515   0.2315  -0.8182
 8DV  C6   C  CR16  0  -0.417  -1.0665  -1.1132  -0.8316
 8DV  N1   N  N     0  -0.444  -0.4742   1.1615  -0.4529
 8DV  C8   C  CR6   0   0.339   0.7239   0.7233  -0.0831
 8DV  C9   C  CR6   0  -0.052   1.6982   1.7428   0.3567
 8DV  N3   N  NR15  0  -0.678   5.2202   2.0793   0.8162
 8DV  C10  C  CR16  0  -0.320   1.2386   2.9985   0.7342
 8DV  N2   N  N     0  -0.496   1.1051  -0.5449  -0.0644
 8DV  C5   C  CR6   0   0.598   0.2316  -1.4888  -0.4268
 8DV  N    N  NT    0  -0.512   0.6436  -2.7771  -0.3653
 8DV  C    C  CH3   0  -0.677   2.7895  -3.0170  -1.5634
 8DV  C4   C  CH2   0  -0.328  -0.1662  -3.8593  -0.8995
 8DV  O    O  O2    0  -0.478   1.5223  -5.4513  -0.1875
 8DV  H1   H  HCH1  0   0.274   2.5012  -2.3363   0.4487
 8DV  H2   H  HCH2  0   0.243   3.2800  -4.7018   0.4927
 8DV  H3   H  HCH2  0   0.221   1.8789  -4.3368   1.5129
 8DV  H4   H  HCH2  0   0.211  -0.2262  -5.0998   0.8506
 8DV  H5   H  HCH2  0   0.249  -0.3736  -5.9792  -0.6806
 8DV  H6   H  HCR6  0   0.253   1.6946   4.9608   1.4754
 8DV  H7   H  HCR6  0   0.264   4.1407   4.5677   1.5883
 8DV  H8   H  HCR5  0   0.282   6.1468   0.2565   0.2430
 8DV  H9   H  HCR5  0   0.264   3.6487  -0.5707  -0.2657
 8DV  H10  H  HCH2  0   0.282  -2.6468  -0.1490  -3.2312
 8DV  H11  H  HCH2  0   0.283  -4.3338   0.2221  -2.6572
 8DV  H12  H  HCH2  0   0.281  -3.6274   2.5584  -2.0537
 8DV  H13  H  HCH2  0   0.280  -1.9328   2.2053  -2.6197
 8DV  H14  H  HCH1  0   0.329  -3.1127   2.7917   0.9414
 8DV  H15  H  HCH2  0   0.284  -3.7948   2.4800   3.3275
 8DV  H16  H  HCH2  0   0.277  -4.2451   0.7451   3.0044
 8DV  H17  H  HCH2  0   0.274  -1.9061   0.2466   2.2670
 8DV  H18  H  HCH2  0   0.279  -1.4167   1.9736   2.5743
 8DV  H19  H  HCR6  0   0.278  -1.8151  -1.8179  -1.1566
 8DV  H20  H  HNR5  0   0.411   6.0405   2.6064   1.0641
 8DV  H21  H  HCR6  0   0.251   0.1771   3.1995   0.6880
 8DV  H22  H  HCH3  0   0.239   2.4191  -3.7680  -2.2618
 8DV  H23  H  HCH3  0   0.238   2.6622  -2.0366  -2.0234
 8DV  H24  H  HCH3  0   0.237   3.8583  -3.1873  -1.4264
 8DV  H25  H  HCH2  0   0.245  -0.0090  -3.9686  -1.9790
 8DV  H26  H  HCH2  0   0.268  -1.2241  -3.6576  -0.7444

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
 8DV  C3   O    single    1.407  0.020  1.407
 8DV  C3   C4   single    1.518  0.020  1.518
 8DV  O    C2   single    1.408  0.020  1.408
 8DV  C4   N    single    1.453  0.020  1.453
 8DV  C2   C1   single    1.522  0.020  1.522
 8DV  N    C1   single    1.464  0.020  1.464
 8DV  N    C5   single    1.354  0.020  1.354
 8DV  C1   C    single    1.526  0.020  1.526
 8DV  C6   C5   aromatic  1.411  0.020  1.411
 8DV  C6   C7   aromatic  1.375  0.020  1.375
 8DV  C5   N2   aromatic  1.336  0.020  1.336
 8DV  C19  C17  single    1.494  0.020  1.494
 8DV  C19  C18  single    1.493  0.020  1.493
 8DV  O1   S    double    1.463  0.020  1.463
 8DV  N2   C8   aromatic  1.324  0.020  1.324
 8DV  C7   C17  single    1.492  0.020  1.492
 8DV  C7   N1   aromatic  1.330  0.020  1.330
 8DV  C17  S    single    1.782  0.020  1.782
 8DV  C17  C18  single    1.501  0.020  1.501
 8DV  O2   S    double    1.462  0.020  1.462
 8DV  S    C20  single    1.758  0.020  1.758
 8DV  C8   N1   aromatic  1.328  0.020  1.328
 8DV  C8   C9   single    1.477  0.020  1.477
 8DV  C15  C14  aromatic  1.366  0.020  1.366
 8DV  C15  C16  aromatic  1.430  0.020  1.430
 8DV  C14  N3   aromatic  1.361  0.020  1.361
 8DV  C20  C21  single    1.501  0.020  1.501
 8DV  C20  C22  single    1.494  0.020  1.494
 8DV  C16  C9   aromatic  1.411  0.020  1.411
 8DV  C16  C13  aromatic  1.418  0.020  1.418
 8DV  C9   C10  aromatic  1.389  0.020  1.389
 8DV  C21  C22  single    1.490  0.020  1.490
 8DV  N3   C13  aromatic  1.364  0.020  1.364
 8DV  C13  C12  aromatic  1.391  0.020  1.391
 8DV  C10  C11  aromatic  1.398  0.020  1.398
 8DV  C12  C11  aromatic  1.381  0.020  1.381
 8DV  C1   H1   single    0.970  0.020  1.090
 8DV  C2   H2   single    0.970  0.020  1.090
 8DV  C2   H3   single    0.970  0.020  1.090
 8DV  C3   H4   single    0.970  0.020  1.090
 8DV  C3   H5   single    0.970  0.020  1.090
 8DV  C11  H6   single    0.930  0.020  1.080
 8DV  C12  H7   single    0.930  0.020  1.080
 8DV  C14  H8   single    0.930  0.020  1.080
 8DV  C15  H9   single    0.930  0.020  1.080
 8DV  C18  H10  single    0.970  0.020  1.090
 8DV  C18  H11  single    0.970  0.020  1.090
 8DV  C19  H12  single    0.970  0.020  1.090
 8DV  C19  H13  single    0.970  0.020  1.090
 8DV  C20  H14  single    0.970  0.020  1.090
 8DV  C21  H15  single    0.970  0.020  1.090
 8DV  C21  H16  single    0.970  0.020  1.090
 8DV  C22  H17  single    0.970  0.020  1.090
 8DV  C22  H18  single    0.970  0.020  1.090
 8DV  C6   H19  single    0.930  0.020  1.080
 8DV  N3   H20  single    0.860  0.020  1.020
 8DV  C10  H21  single    0.930  0.020  1.080
 8DV  C    H22  single    0.970  0.020  1.090
 8DV  C    H23  single    0.970  0.020  1.090
 8DV  C    H24  single    0.970  0.020  1.090
 8DV  C4   H25  single    0.970  0.020  1.090
 8DV  C4   H26  single    0.970  0.020  1.090

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
 8DV  H1   C1   C    108.99  3.000
 8DV  H1   C1   N    107.82  3.000
 8DV  C    C1   N    111.34  3.000
 8DV  H1   C1   C2   106.44  3.000
 8DV  C    C1   C2   112.90  3.000
 8DV  N    C1   C2   109.10  3.000
 8DV  H3   C2   H2   107.93  3.000
 8DV  H3   C2   O    110.21  3.000
 8DV  H2   C2   O    107.83  3.000
 8DV  H3   C2   C1   109.12  3.000
 8DV  H2   C2   C1   109.34  3.000
 8DV  O    C2   C1   112.31  3.000
 8DV  H5   C3   H4   108.05  3.000
 8DV  H5   C3   O    107.98  3.000
 8DV  H4   C3   O    110.25  3.000
 8DV  H5   C3   C4   109.24  3.000
 8DV  H4   C3   C4   109.11  3.000
 8DV  O    C3   C4   112.11  3.000
 8DV  H6   C11  C10  119.31  3.000
 8DV  H6   C11  C12  119.63  3.000
 8DV  C10  C11  C12  121.05  3.000
 8DV  H7   C12  C13  121.33  3.000
 8DV  H7   C12  C11  121.38  3.000
 8DV  C13  C12  C11  117.28  3.000
 8DV  N3   C13  C16  107.71  3.000
 8DV  N3   C13  C12  129.25  3.000
 8DV  C16  C13  C12  123.04  3.000
 8DV  H8   C14  N3   120.60  3.000
 8DV  H8   C14  C15  129.56  3.000
 8DV  N3   C14  C15  109.84  3.000
 8DV  H9   C15  C16  127.33  3.000
 8DV  H9   C15  C14  125.71  3.000
 8DV  C16  C15  C14  106.96  3.000
 8DV  C9   C16  C15  135.39  3.000
 8DV  C9   C16  C13  118.43  3.000
 8DV  C15  C16  C13  106.15  3.000
 8DV  C7   C17  S    113.08  3.000
 8DV  S    C17  C19  117.12  3.000
 8DV  C7   C17  C19  120.31  3.000
 8DV  S    C17  C18  115.44  3.000
 8DV  C7   C17  C18  121.31  3.000
 8DV  C19  C17  C18   59.77  3.000
 8DV  H11  C18  H10  114.51  3.000
 8DV  H11  C18  C19  118.30  3.000
 8DV  H10  C18  C19  118.75  3.000
 8DV  H11  C18  C17  118.80  3.000
 8DV  H10  C18  C17  115.89  3.000
 8DV  C19  C18  C17   59.90  3.000
 8DV  H13  C19  H12  114.63  3.000
 8DV  H13  C19  C18  118.85  3.000
 8DV  H12  C19  C18  118.04  3.000
 8DV  H13  C19  C17  115.73  3.000
 8DV  H12  C19  C17  118.65  3.000
 8DV  C18  C19  C17   60.33  3.000
 8DV  H14  C20  S    112.27  3.000
 8DV  H14  C20  C22  119.24  3.000
 8DV  S    C20  C22  119.69  3.000
 8DV  H14  C20  C21  119.13  3.000
 8DV  C22  C20  C21   59.67  3.000
 8DV  S    C20  C21  117.53  3.000
 8DV  H16  C21  H15  114.64  3.000
 8DV  H16  C21  C22  117.94  3.000
 8DV  H15  C21  C22  119.16  3.000
 8DV  H16  C21  C20  118.47  3.000
 8DV  H15  C21  C20  115.91  3.000
 8DV  C22  C21  C20   59.94  3.000
 8DV  H18  C22  H17  114.66  3.000
 8DV  H18  C22  C21  119.27  3.000
 8DV  H17  C22  C21  117.86  3.000
 8DV  H18  C22  C20  115.68  3.000
 8DV  H17  C22  C20  118.35  3.000
 8DV  C21  C22  C20   60.40  3.000
 8DV  C20  S    C17  104.26  3.000
 8DV  C20  S    O2   108.87  3.000
 8DV  C17  S    O2   108.44  3.000
 8DV  C20  S    O1   108.49  3.000
 8DV  O2   S    O1   117.90  3.000
 8DV  C17  S    O1   108.03  3.000
 8DV  N1   C7   C6   123.37  3.000
 8DV  N1   C7   C17  116.38  3.000
 8DV  C6   C7   C17  120.25  3.000
 8DV  H19  C6   C5   123.46  3.000
 8DV  H19  C6   C7   119.88  3.000
 8DV  C5   C6   C7   116.65  3.000
 8DV  C8   N1   C7   116.16  3.000
 8DV  N2   C8   C9   117.83  3.000
 8DV  C9   C8   N1   116.75  3.000
 8DV  N2   C8   N1   125.41  3.000
 8DV  C10  C9   C8   119.11  3.000
 8DV  C10  C9   C16  118.07  3.000
 8DV  C8   C9   C16  122.82  3.000
 8DV  H20  N3   C14  125.14  3.000
 8DV  H20  N3   C13  125.51  3.000
 8DV  C14  N3   C13  109.34  3.000
 8DV  H21  C10  C9   118.76  3.000
 8DV  H21  C10  C11  119.13  3.000
 8DV  C9   C10  C11  122.11  3.000
 8DV  C5   N2   C8   118.98  3.000
 8DV  N    C5   N2   117.45  3.000
 8DV  N2   C5   C6   119.43  3.000
 8DV  N    C5   C6   123.12  3.000
 8DV  C4   N    C5   121.48  3.000
 8DV  C5   N    C1   119.81  3.000
 8DV  C4   N    C1   115.15  3.000
 8DV  H24  C    H23  107.92  3.000
 8DV  H24  C    H22  107.80  3.000
 8DV  H23  C    H22  108.03  3.000
 8DV  H24  C    C1   110.22  3.000
 8DV  H23  C    C1   110.68  3.000
 8DV  H22  C    C1   112.05  3.000
 8DV  H26  C4   H25  107.35  3.000
 8DV  H26  C4   N    110.57  3.000
 8DV  H25  C4   N    110.88  3.000
 8DV  H26  C4   C3   106.93  3.000
 8DV  H25  C4   C3   110.52  3.000
 8DV  N    C4   C3   110.48  3.000
 8DV  C3   O    C2   109.60  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
 8DV  CONST_01  C8   C9   C10  C11   180.00   0.0  0
 8DV  CONST_02  C16  C9   C10  C11     0.00   0.0  0
 8DV  CONST_03  C16  C13  C12  C11     0.00   0.0  0
 8DV  CONST_04  N3   C13  C12  C11   180.00   0.0  0
 8DV  CONST_05  C15  C16  C13  C12   180.00   0.0  0
 8DV  CONST_06  C9   C16  C13  C12     0.00   0.0  0
 8DV  CONST_07  C14  N3   C13  C12   180.00   0.0  0
 8DV  CONST_08  C9   C10  C11  C12     0.00   0.0  0
 8DV  CONST_09  C14  C15  C16  C13     0.00   0.0  0
 8DV  CONST_10  C8   C9   C16  C13   180.00   0.0  0
 8DV  CONST_11  C10  C9   C16  C13     0.00   0.0  0
 8DV  CONST_12  C15  C14  N3   C13     0.00   0.0  0
 8DV  CONST_13  C10  C11  C12  C13     0.00   0.0  0
 8DV  CONST_14  C9   C16  C15  C14   180.00   0.0  0
 8DV  CONST_15  C16  C13  N3   C14     0.00   0.0  0
 8DV  CONST_16  C8   C9   C16  C15     0.00   0.0  0
 8DV  CONST_17  C10  C9   C16  C15   180.00   0.0  0
 8DV  CONST_18  N3   C13  C16  C15     0.00   0.0  0
 8DV  CONST_19  N3   C14  C15  C16     0.00   0.0  0
 8DV  CONST_22  N2   C5   C6   C7      0.00   0.0  0
 8DV  CONST_23  N2   C8   N1   C7      0.00   0.0  0
 8DV  CONST_24  C9   C8   N1   C7    180.00   0.0  0
 8DV  CONST_25  C8   N2   C5   C6      0.00   0.0  0
 8DV  CONST_26  C8   N1   C7   C6      0.00   0.0  0
 8DV  CONST_27  C5   C6   C7   N1      0.00   0.0  0
 8DV  CONST_28  C5   N2   C8   N1      0.00   0.0  0
 8DV  CONST_30  C5   N2   C8   C9    180.00   0.0  0
 8DV  CONST_31  N3   C13  C16  C9    180.00   0.0  0
 8DV  CONST_33  C5   C6   C7   C17   180.00   0.0  0
 8DV  CONST_34  C8   N1   C7   C17   180.00   0.0  0
 8DV  CONST_35  N    C5   C6   C7    180.00   0.0  0
 8DV  CONST_36  N    C5   N2   C8    180.00   0.0  0
 8DV  CONST_37  H20  N3   C13  C12     0.00   0.0  0
 8DV  CONST_38  H21  C10  C11  C12   180.00   0.0  0
 8DV  CONST_39  H9   C15  C16  C13   180.00   0.0  0
 8DV  CONST_40  H8   C14  N3   C13   180.00   0.0  0
 8DV  CONST_41  H6   C11  C12  C13   180.00   0.0  0
 8DV  CONST_42  H7   C12  C13  C16   180.00   0.0  0
 8DV  CONST_43  H19  C6   C7   C17     0.00   0.0  0
 8DV  Var_01    C3   C4   N    C1     47.54  30.0  1
 8DV  Var_02    C6   C5   N    C1    166.81  30.0  2
 8DV  Var_03    C4   C3   O    C2     60.76  30.0  1
 8DV  Var_04    C7   C17  C19  C18   110.86  30.0  1
 8DV  Var_05    C6   C7   C17  C18   -59.17  30.0  3
 8DV  Var_06    O    C3   C4   N     -53.09  30.0  1
 8DV  Var_07    C21  C20  S    C17  -155.50  30.0  3
 8DV  Var_08    C20  S    C17  C18  -151.88  30.0  3
 8DV  Var_09    S    C20  C22  C21  -106.43  30.0  1
 8DV  Var_10    H2   C2   O    C3    177.42  30.0  1
 8DV  Var_11    H10  C18  C19  C17  -104.94  30.0  1
 8DV  Var_12    H17  C22  C21  C20  -108.50  30.0  1

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
 8DV  chir_01  C1   C2  N    C    positiv
 8DV  chir_02  C17  C7  S    C18  both
 8DV  chir_03  C20  S   C22  C21  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
 8DV  plan-1  C17  0.020
 8DV  plan-1  C7   0.020
 8DV  plan-1  C6   0.020
 8DV  plan-1  N1   0.020
 8DV  plan-1  C8   0.020
 8DV  plan-1  C9   0.020
 8DV  plan-1  N2   0.020
 8DV  plan-1  C5   0.020
 8DV  plan-1  N    0.020
 8DV  plan-1  H19  0.020
 8DV  plan-2  C11  0.020
 8DV  plan-2  C12  0.020
 8DV  plan-2  C13  0.020
 8DV  plan-2  C14  0.020
 8DV  plan-2  C15  0.020
 8DV  plan-2  C16  0.020
 8DV  plan-2  C8   0.020
 8DV  plan-2  C9   0.020
 8DV  plan-2  N3   0.020
 8DV  plan-2  C10  0.020
 8DV  plan-2  H6   0.020
 8DV  plan-2  H7   0.020
 8DV  plan-2  H8   0.020
 8DV  plan-2  H9   0.020
 8DV  plan-2  H20  0.020
 8DV  plan-2  H21  0.020

