# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 07:20:42 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]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](C)(=O)=O
#
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
 VCD  VCD  4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]pyrimidin-2-yl}-1H-indole  ligand  53  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VCD
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
 VCD  C11   C  CH2   0  -0.184  15.5069  19.1579  64.2669
 VCD  C01   C  CR16  0  -0.480  18.9793  17.3334  65.9653
 VCD  C02   C  CR6   0   0.412  20.2336  16.9053  66.3388
 VCD  C04   C  CR6   0   0.334  20.8862  19.0428  66.7120
 VCD  C06   C  CR6   0   0.606  18.7553  18.7258  65.9507
 VCD  C08   C  CH1   0  -0.148  17.2935  20.6789  65.8575
 VCD  C09   C  CH2   0  -0.185  16.3379  21.2301  64.8100
 VCD  C12   C  CH2   0  -0.330  16.4294  18.4512  65.2444
 VCD  C13   C  CH3   0  -0.661  16.7667  20.8397  67.2796
 VCD  C14   C  CR6   0  -0.036  21.9347  19.9720  67.1777
 VCD  C15   C  CR16  0  -0.314  22.8948  19.5205  68.0733
 VCD  C16   C  CR16  0  -0.270  23.9068  20.3569  68.5561
 VCD  C17   C  CR16  0  -0.304  24.0014  21.6724  68.1458
 VCD  C18   C  CR56  0   0.351  23.0482  22.1303  67.2414
 VCD  C19   C  CR56  0   0.074  22.0004  21.3135  66.7490
 VCD  C20   C  CR15  0  -0.457  21.2500  22.1260  65.8435
 VCD  C21   C  CR15  0  -0.016  21.8475  23.3540  65.8247
 VCD  C23   C  CT    0  -0.373  20.6163  15.4644  66.3076
 VCD  C25   C  CH3   0  -0.784  23.4008  15.5746  66.9481
 VCD  C28   C  CH2   0  -0.462  19.6380  14.3875  65.9239
 VCD  C29   C  CH2   0  -0.449  20.7118  14.7610  64.9727
 VCD  N03   N  N     0  -0.492  21.1942  17.7517  66.7051
 VCD  N05   N  N     0  -0.496  19.7229  19.5571  66.3494
 VCD  N07   N  NT    0  -0.512  17.5863  19.2768  65.5472
 VCD  N22   N  NR15  0  -0.679  22.9204  23.3594  66.6640
 VCD  O10   O  O2    0  -0.472  15.1699  20.4529  64.6958
 VCD  O26   O  OS    0  -0.663  21.5007  15.5732  68.8108
 VCD  O27   O  OS    0  -0.671  21.9134  13.4974  67.4753
 VCD  S24   S  S     0   1.224  21.8344  14.9592  67.5278
 VCD  H111  H  HCH2  0   0.247  14.5844  18.5845  64.1682
 VCD  H112  H  HCH2  0   0.209  15.9898  19.1966  63.2803
 VCD  H011  H  HCR6  0   0.277  18.2071  16.6291  65.7074
 VCD  H081  H  HCH1  0   0.283  18.2201  21.2424  65.7637
 VCD  H091  H  HCH2  0   0.219  16.8555  21.2860  63.8415
 VCD  H092  H  HCH2  0   0.242  16.0391  22.2415  65.0897
 VCD  H121  H  HCH2  0   0.245  15.8890  18.1838  66.1599
 VCD  H122  H  HCH2  0   0.267  16.7413  17.5237  64.7678
 VCD  H133  H  HCH3  0   0.238  17.4877  20.4605  68.0036
 VCD  H131  H  HCH3  0   0.235  16.5993  21.8948  67.4990
 VCD  H132  H  HCH3  0   0.230  15.8232  20.3153  67.4325
 VCD  H151  H  HCR6  0   0.243  22.8455  18.4979  68.4232
 VCD  H161  H  HCR6  0   0.251  24.6250  19.9640  69.2637
 VCD  H171  H  HCR6  0   0.262  24.7870  22.3214  68.5118
 VCD  H201  H  HCR5  0   0.251  20.3803  21.8425  65.2781
 VCD  H211  H  HCR5  0   0.280  21.5813  24.2388  65.2687
 VCD  H252  H  HCH3  0   0.300  24.1538  15.2127  67.6478
 VCD  H253  H  HCH3  0   0.289  23.5948  15.1709  65.9570
 VCD  H251  H  HCH3  0   0.302  23.3817  16.6585  66.9249
 VCD  H281  H  HCH2  0   0.288  18.6223  14.6931  65.7176
 VCD  H282  H  HCH2  0   0.294  19.7124  13.4361  66.4308
 VCD  H291  H  HCH2  0   0.288  21.5278  14.0659  64.8169
 VCD  H292  H  HCH2  0   0.287  20.4628  15.3638  64.1092
 VCD  H221  H  HNR5  0   0.410  23.5306  24.1443  66.8210

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
 VCD  C11  O10   single    1.405  0.020  1.405
 VCD  C11  C12   single    1.519  0.020  1.519
 VCD  C09  O10   single    1.408  0.020  1.408
 VCD  C09  C08   single    1.521  0.020  1.521
 VCD  C29  C28   single    1.482  0.020  1.482
 VCD  C29  C23   single    1.512  0.020  1.512
 VCD  C12  N07   single    1.453  0.020  1.453
 VCD  N07  C06   single    1.354  0.020  1.354
 VCD  N07  C08   single    1.466  0.020  1.466
 VCD  C06  C01   aromatic  1.410  0.020  1.410
 VCD  C06  N05   aromatic  1.336  0.020  1.336
 VCD  C01  C02   aromatic  1.377  0.020  1.377
 VCD  C08  C13   single    1.525  0.020  1.525
 VCD  C20  C21   aromatic  1.366  0.020  1.366
 VCD  C20  C19   aromatic  1.429  0.020  1.429
 VCD  C21  N22   aromatic  1.362  0.020  1.362
 VCD  C28  C23   single    1.505  0.020  1.505
 VCD  N05  C04   aromatic  1.323  0.020  1.323
 VCD  C02  C23   single    1.491  0.020  1.491
 VCD  C02  N03   aromatic  1.332  0.020  1.332
 VCD  C23  S24   single    1.797  0.020  1.797
 VCD  C04  N03   aromatic  1.327  0.020  1.327
 VCD  C04  C14   single    1.476  0.020  1.476
 VCD  C19  C14   aromatic  1.410  0.020  1.410
 VCD  C19  C18   aromatic  1.417  0.020  1.417
 VCD  N22  C18   aromatic  1.364  0.020  1.364
 VCD  C25  S24   single    1.780  0.020  1.780
 VCD  C14  C15   aromatic  1.388  0.020  1.388
 VCD  C18  C17   aromatic  1.391  0.020  1.391
 VCD  S24  O27   double    1.465  0.020  1.465
 VCD  S24  O26   double    1.461  0.020  1.461
 VCD  C15  C16   aromatic  1.399  0.020  1.399
 VCD  C17  C16   aromatic  1.381  0.020  1.381
 VCD  C11  H111  single    0.970  0.020  1.090
 VCD  C11  H112  single    0.970  0.020  1.090
 VCD  C01  H011  single    0.930  0.020  1.080
 VCD  C08  H081  single    0.970  0.020  1.090
 VCD  C09  H091  single    0.970  0.020  1.090
 VCD  C09  H092  single    0.970  0.020  1.090
 VCD  C12  H121  single    0.970  0.020  1.090
 VCD  C12  H122  single    0.970  0.020  1.090
 VCD  C13  H133  single    0.970  0.020  1.090
 VCD  C13  H131  single    0.970  0.020  1.090
 VCD  C13  H132  single    0.970  0.020  1.090
 VCD  C15  H151  single    0.930  0.020  1.080
 VCD  C16  H161  single    0.930  0.020  1.080
 VCD  C17  H171  single    0.930  0.020  1.080
 VCD  C20  H201  single    0.930  0.020  1.080
 VCD  C21  H211  single    0.930  0.020  1.080
 VCD  C25  H252  single    0.970  0.020  1.090
 VCD  C25  H253  single    0.970  0.020  1.090
 VCD  C25  H251  single    0.970  0.020  1.090
 VCD  C28  H281  single    0.970  0.020  1.090
 VCD  C28  H282  single    0.970  0.020  1.090
 VCD  C29  H291  single    0.970  0.020  1.090
 VCD  C29  H292  single    0.970  0.020  1.090
 VCD  N22  H221  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
 VCD  H112  C11  H111  108.00  3.000
 VCD  H112  C11  O10   110.30  3.000
 VCD  H111  C11  O10   108.02  3.000
 VCD  H112  C11  C12   109.10  3.000
 VCD  H111  C11  C12   109.11  3.000
 VCD  O10   C11  C12   112.22  3.000
 VCD  H011  C01  C06   121.97  3.000
 VCD  H011  C01  C02   121.00  3.000
 VCD  C06   C01  C02   117.02  3.000
 VCD  N03   C02  C23   115.77  3.000
 VCD  N03   C02  C01   122.28  3.000
 VCD  C23   C02  C01   121.91  3.000
 VCD  N05   C04  N03   125.52  3.000
 VCD  N03   C04  C14   116.68  3.000
 VCD  N05   C04  C14   117.80  3.000
 VCD  N07   C06  N05   117.44  3.000
 VCD  N05   C06  C01   119.74  3.000
 VCD  N07   C06  C01   122.82  3.000
 VCD  H081  C08  N07   107.87  3.000
 VCD  H081  C08  C13   108.65  3.000
 VCD  N07   C08  C13   111.55  3.000
 VCD  H081  C08  C09   106.73  3.000
 VCD  C13   C08  C09   112.76  3.000
 VCD  N07   C08  C09   109.05  3.000
 VCD  H092  C09  H091  107.92  3.000
 VCD  H092  C09  O10   107.78  3.000
 VCD  H091  C09  O10   110.31  3.000
 VCD  H092  C09  C08   109.36  3.000
 VCD  H091  C09  C08   109.22  3.000
 VCD  O10   C09  C08   112.16  3.000
 VCD  H122  C12  H121  107.40  3.000
 VCD  H122  C12  N07   110.32  3.000
 VCD  H121  C12  N07   110.92  3.000
 VCD  H122  C12  C11   106.79  3.000
 VCD  H121  C12  C11   110.59  3.000
 VCD  N07   C12  C11   110.69  3.000
 VCD  H132  C13  H131  107.72  3.000
 VCD  H132  C13  H133  108.18  3.000
 VCD  H131  C13  H133  107.72  3.000
 VCD  H132  C13  C08   112.28  3.000
 VCD  H131  C13  C08   110.03  3.000
 VCD  H133  C13  C08   110.75  3.000
 VCD  C19   C14  C15   118.25  3.000
 VCD  C15   C14  C04   119.33  3.000
 VCD  C19   C14  C04   122.41  3.000
 VCD  H151  C15  C16   119.11  3.000
 VCD  H151  C15  C14   118.98  3.000
 VCD  C16   C15  C14   121.90  3.000
 VCD  H161  C16  C17   119.65  3.000
 VCD  H161  C16  C15   119.26  3.000
 VCD  C17   C16  C15   121.09  3.000
 VCD  H171  C17  C18   121.30  3.000
 VCD  H171  C17  C16   121.33  3.000
 VCD  C18   C17  C16   117.36  3.000
 VCD  N22   C18  C19   107.64  3.000
 VCD  N22   C18  C17   129.49  3.000
 VCD  C19   C18  C17   122.87  3.000
 VCD  C20   C19  C18   106.31  3.000
 VCD  C18   C19  C14   118.51  3.000
 VCD  C20   C19  C14   135.15  3.000
 VCD  H201  C20  C21   125.71  3.000
 VCD  H201  C20  C19   127.43  3.000
 VCD  C21   C20  C19   106.86  3.000
 VCD  H211  C21  N22   120.59  3.000
 VCD  H211  C21  C20   129.55  3.000
 VCD  N22   C21  C20   109.86  3.000
 VCD  S24   C23  C29   115.21  3.000
 VCD  S24   C23  C28   114.38  3.000
 VCD  C29   C23  C28    58.87  3.000
 VCD  S24   C23  C02   115.56  3.000
 VCD  C28   C23  C02   122.01  3.000
 VCD  C29   C23  C02   118.96  3.000
 VCD  H251  C25  H253  110.77  3.000
 VCD  H251  C25  H252  110.97  3.000
 VCD  H253  C25  H252  109.79  3.000
 VCD  H251  C25  S24   109.70  3.000
 VCD  H253  C25  S24   108.99  3.000
 VCD  H252  C25  S24   106.51  3.000
 VCD  H282  C28  H281  113.78  3.000
 VCD  H282  C28  C29   118.23  3.000
 VCD  H281  C28  C29   119.16  3.000
 VCD  H282  C28  C23   117.76  3.000
 VCD  H281  C28  C23   117.22  3.000
 VCD  C29   C28  C23    60.81  3.000
 VCD  H292  C29  H291  114.58  3.000
 VCD  H292  C29  C28   119.06  3.000
 VCD  H291  C29  C28   118.45  3.000
 VCD  H292  C29  C23   115.52  3.000
 VCD  H291  C29  C23   118.24  3.000
 VCD  C28   C29  C23    60.32  3.000
 VCD  C04   N03  C02   116.89  3.000
 VCD  C06   N05  C04   118.46  3.000
 VCD  C12   N07  C08   115.38  3.000
 VCD  C08   N07  C06   119.92  3.000
 VCD  C12   N07  C06   121.22  3.000
 VCD  H221  N22  C21   125.22  3.000
 VCD  H221  N22  C18   125.44  3.000
 VCD  C21   N22  C18   109.33  3.000
 VCD  C09   O10  C11   109.55  3.000
 VCD  O27   S24  O26   117.59  3.000
 VCD  O26   S24  C25   109.98  3.000
 VCD  O27   S24  C25   106.61  3.000
 VCD  O26   S24  C23   108.87  3.000
 VCD  O27   S24  C23   107.02  3.000
 VCD  C25   S24  C23   106.15  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
 VCD  CONST_01  C04   N05  C06  C01     0.00   0.0  0
 VCD  CONST_02  C04   N03  C02  C01     0.00   0.0  0
 VCD  CONST_03  N05   C06  C01  C02     0.00   0.0  0
 VCD  CONST_04  N05   C04  N03  C02     0.00   0.0  0
 VCD  CONST_05  C14   C04  N03  C02   180.00   0.0  0
 VCD  CONST_06  C20   C19  C14  C04     0.00   0.0  0
 VCD  CONST_07  C18   C19  C14  C04   180.00   0.0  0
 VCD  CONST_08  C16   C15  C14  C04   180.00   0.0  0
 VCD  CONST_09  N03   C02  C01  C06     0.00   0.0  0
 VCD  CONST_10  N03   C04  N05  C06     0.00   0.0  0
 VCD  CONST_11  C14   C04  N05  C06   180.00   0.0  0
 VCD  CONST_12  C21   C20  C19  C14   180.00   0.0  0
 VCD  CONST_13  N22   C18  C19  C14   180.00   0.0  0
 VCD  CONST_14  C17   C18  C19  C14     0.00   0.0  0
 VCD  CONST_15  C17   C16  C15  C14     0.00   0.0  0
 VCD  CONST_18  C20   C19  C14  C15   180.00   0.0  0
 VCD  CONST_19  C18   C19  C14  C15     0.00   0.0  0
 VCD  CONST_20  C18   C17  C16  C15     0.00   0.0  0
 VCD  CONST_21  C19   C14  C15  C16     0.00   0.0  0
 VCD  CONST_22  C19   C18  C17  C16     0.00   0.0  0
 VCD  CONST_23  N22   C18  C17  C16   180.00   0.0  0
 VCD  CONST_24  C20   C19  C18  C17   180.00   0.0  0
 VCD  CONST_25  C21   N22  C18  C17   180.00   0.0  0
 VCD  CONST_26  C21   C20  C19  C18     0.00   0.0  0
 VCD  CONST_27  C20   C21  N22  C18     0.00   0.0  0
 VCD  CONST_28  N22   C21  C20  C19     0.00   0.0  0
 VCD  CONST_31  C21   N22  C18  C19     0.00   0.0  0
 VCD  CONST_32  N22   C18  C19  C20     0.00   0.0  0
 VCD  CONST_33  N07   C06  C01  C02   180.00   0.0  0
 VCD  CONST_34  N07   C06  N05  C04   180.00   0.0  0
 VCD  CONST_35  C23   C02  N03  C04   180.00   0.0  0
 VCD  CONST_36  C23   C02  C01  C06   180.00   0.0  0
 VCD  CONST_37  H151  C15  C14  C04     0.00   0.0  0
 VCD  CONST_38  H201  C20  C19  C14     0.00   0.0  0
 VCD  CONST_39  H161  C16  C15  C14   180.00   0.0  0
 VCD  CONST_40  H171  C17  C16  C15   180.00   0.0  0
 VCD  CONST_41  H221  N22  C18  C17     0.00   0.0  0
 VCD  CONST_42  H211  C21  N22  C18   180.00   0.0  0
 VCD  CONST_43  H011  C01  C02  C23     0.00   0.0  0
 VCD  Var_01    C08   C09  O10  C11   -62.68  30.0  1
 VCD  Var_02    C06   N07  C12  C11  -154.59  30.0  1
 VCD  Var_03    C12   N07  C06  C01     7.08  30.0  2
 VCD  Var_04    C29   C23  C02  C01    66.75  30.0  2
 VCD  Var_05    C28   C29  C23  C02  -111.93  30.0  1
 VCD  Var_06    C12   C11  O10  C09    60.78  30.0  1
 VCD  Var_07    O10   C11  C12  N07   -52.28  30.0  1
 VCD  Var_08    C25   S24  C23  C02   -75.19  30.0  3
 VCD  Var_09    H252  C25  S24  C23  -176.18  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
 VCD  chir_01  C08  C09  N07  C13  positiv
 VCD  chir_02  C23  C28  C02  S24  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
 VCD  plan-1  C01   0.020
 VCD  plan-1  C02   0.020
 VCD  plan-1  C04   0.020
 VCD  plan-1  C06   0.020
 VCD  plan-1  C14   0.020
 VCD  plan-1  C23   0.020
 VCD  plan-1  N03   0.020
 VCD  plan-1  N05   0.020
 VCD  plan-1  N07   0.020
 VCD  plan-1  H011  0.020
 VCD  plan-2  C04   0.020
 VCD  plan-2  C14   0.020
 VCD  plan-2  C15   0.020
 VCD  plan-2  C16   0.020
 VCD  plan-2  C17   0.020
 VCD  plan-2  C18   0.020
 VCD  plan-2  C19   0.020
 VCD  plan-2  C20   0.020
 VCD  plan-2  C21   0.020
 VCD  plan-2  N22   0.020
 VCD  plan-2  H151  0.020
 VCD  plan-2  H161  0.020
 VCD  plan-2  H171  0.020
 VCD  plan-2  H201  0.020
 VCD  plan-2  H211  0.020
 VCD  plan-2  H221  0.020

