# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 08:09:14 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-[(3-butyl-6-methoxy-2-methylquinolin-4-yl)sulfanyl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1c(C)nc2ccc(OC)cc2c1SCCC#N
#
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
 9MT  9MT  3-[(3-butyl-6-methoxy-2-methylquinolin-4-yl)sulfanyl]propanenitrile  ligand  44  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9MT
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
 9MT  N1    N  NS    0  -0.269   1.0272  -4.8934  -2.1777
 9MT  C17   C  CSP   0   0.130   0.9921  -4.0102  -1.4412
 9MT  C16   C  CH2   0  -0.516   0.9284  -2.8983  -0.5039
 9MT  C15   C  CH2   0  -0.566  -0.4834  -2.7390   0.0564
 9MT  S     S  S2    0   0.021  -0.6139  -1.3752   1.2484
 9MT  C14   C  CR6   0  -0.156  -0.3894   0.0246   0.1712
 9MT  C13   C  CR66  0   0.165   0.8895   0.6526   0.1054
 9MT  C12   C  CR16  0  -0.444   2.0173   0.2314   0.8314
 9MT  C10   C  CR6   0   0.417   3.2220   0.8892   0.7090
 9MT  O     O  O2    0  -0.471   4.2443   0.4166   1.4438
 9MT  C11   C  CH3   0  -0.439   5.5091   1.0431   1.3454
 9MT  C9    C  CR16  0  -0.385   3.3343   2.0028  -0.1538
 9MT  C8    C  CR16  0  -0.278   2.2431   2.4262  -0.8632
 9MT  C7    C  CR66  0   0.158   1.0002   1.7712  -0.7552
 9MT  N     N  N     0  -0.451  -0.0385   2.2381  -1.4824
 9MT  C5    C  CR6   0   0.175  -1.2037   1.6584  -1.3963
 9MT  C6    C  CH3   0  -0.752  -2.3067   2.2345  -2.2337
 9MT  C4    C  CR6   0   0.091  -1.4451   0.5219  -0.5568
 9MT  C3    C  CH2   0  -0.532  -2.8344  -0.0373  -0.4471
 9MT  C2    C  CH2   0  -0.404  -3.6368   0.6562   0.6583
 9MT  C1    C  CH2   0  -0.425  -5.0105   0.0308   0.8600
 9MT  C     C  CH3   0  -0.671  -5.8256   0.7458   1.9286
 9MT  H161  H  HCH2  0   0.316   1.6452  -3.0835   0.2972
 9MT  H162  H  HCH2  0   0.315   1.2491  -1.9978  -1.0308
 9MT  H151  H  HCH2  0   0.296  -1.2068  -2.5950  -0.7457
 9MT  H152  H  HCH2  0   0.308  -0.7745  -3.6310   0.6115
 9MT  H12   H  HCR6  0   0.264   1.9418  -0.6139   1.5026
 9MT  H9    H  HCR6  0   0.287   4.2709   2.5321  -0.2634
 9MT  H111  H  HCH3  0   0.231   5.4741   2.0895   1.6586
 9MT  H112  H  HCH3  0   0.262   6.1722   0.5014   2.0154
 9MT  H113  H  HCH3  0   0.231   5.9136   0.9893   0.3317
 9MT  H8    H  HCR6  0   0.267   2.3190   3.2799  -1.5242
 9MT  H61C  H  HCH3  0   0.255  -2.6652   1.5183  -2.9756
 9MT  H62C  H  HCH3  0   0.250  -3.1688   2.5246  -1.6309
 9MT  H63C  H  HCH3  0   0.259  -1.9480   3.1167  -2.7590
 9MT  H31C  H  HCH2  0   0.252  -3.3606   0.0613  -1.3982
 9MT  H32C  H  HCH2  0   0.256  -2.7993  -1.1045  -0.2292
 9MT  H21C  H  HCH2  0   0.225  -3.0696   0.6038   1.5926
 9MT  H22C  H  HCH2  0   0.220  -3.7494   1.7206   0.4274
 9MT  H11C  H  HCH2  0   0.214  -5.5596   0.0398  -0.0867
 9MT  H12C  H  HCH2  0   0.222  -4.8881  -1.0222   1.1308
 9MT  HC1   H  HCH3  0   0.221  -5.3021   0.7509   2.8866
 9MT  HC2   H  HCH3  0   0.222  -6.0143   1.7841   1.6501
 9MT  HC3   H  HCH3  0   0.230  -6.7918   0.2640   2.0826

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
 9MT  N1   C17   triple    1.150  0.020  1.150
 9MT  C17  C16   single    1.456  0.020  1.456
 9MT  C16  C15   single    1.527  0.020  1.527
 9MT  C15  S     single    1.816  0.020  1.816
 9MT  S    C14   single    1.781  0.020  1.781
 9MT  C14  C13   aromatic  1.426  0.020  1.426
 9MT  C14  C4    aromatic  1.375  0.020  1.375
 9MT  C13  C12   aromatic  1.406  0.020  1.406
 9MT  C13  C7    aromatic  1.416  0.020  1.416
 9MT  C12  C10   aromatic  1.378  0.020  1.378
 9MT  C10  O     single    1.345  0.020  1.345
 9MT  C10  C9    aromatic  1.413  0.020  1.413
 9MT  O    C11   single    1.415  0.020  1.415
 9MT  C9   C8    aromatic  1.369  0.020  1.369
 9MT  C8   C7    aromatic  1.409  0.020  1.409
 9MT  C7   N     aromatic  1.351  0.020  1.351
 9MT  N    C5    aromatic  1.304  0.020  1.304
 9MT  C5   C6    single    1.500  0.020  1.500
 9MT  C5   C4    aromatic  1.433  0.020  1.433
 9MT  C4   C3    single    1.502  0.020  1.502
 9MT  C3   C2    single    1.532  0.020  1.532
 9MT  C2   C1    single    1.523  0.020  1.523
 9MT  C1   C     single    1.522  0.020  1.522
 9MT  C16  H161  single    0.970  0.020  1.090
 9MT  C16  H162  single    0.970  0.020  1.090
 9MT  C15  H151  single    0.970  0.020  1.090
 9MT  C15  H152  single    0.970  0.020  1.090
 9MT  C12  H12   single    0.930  0.020  1.080
 9MT  C9   H9    single    0.930  0.020  1.080
 9MT  C11  H111  single    0.970  0.020  1.090
 9MT  C11  H112  single    0.970  0.020  1.090
 9MT  C11  H113  single    0.970  0.020  1.090
 9MT  C8   H8    single    0.930  0.020  1.080
 9MT  C6   H61C  single    0.970  0.020  1.090
 9MT  C6   H62C  single    0.970  0.020  1.090
 9MT  C6   H63C  single    0.970  0.020  1.090
 9MT  C3   H31C  single    0.970  0.020  1.090
 9MT  C3   H32C  single    0.970  0.020  1.090
 9MT  C2   H21C  single    0.970  0.020  1.090
 9MT  C2   H22C  single    0.970  0.020  1.090
 9MT  C1   H11C  single    0.970  0.020  1.090
 9MT  C1   H12C  single    0.970  0.020  1.090
 9MT  C    HC1   single    0.970  0.020  1.090
 9MT  C    HC2   single    0.970  0.020  1.090
 9MT  C    HC3   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
 9MT  C16   C17  N1    180.00  3.000
 9MT  H162  C16  H161  107.55  3.000
 9MT  H162  C16  C15   111.26  3.000
 9MT  H161  C16  C15   110.84  3.000
 9MT  H162  C16  C17   107.85  3.000
 9MT  H161  C16  C17   108.33  3.000
 9MT  C15   C16  C17   110.88  3.000
 9MT  H152  C15  H151  107.80  3.000
 9MT  H152  C15  S     105.13  3.000
 9MT  H151  C15  S     109.64  3.000
 9MT  H152  C15  C16   110.38  3.000
 9MT  H151  C15  C16   110.94  3.000
 9MT  S     C15  C16   112.68  3.000
 9MT  C14   S    C15   100.61  3.000
 9MT  C4    C14  C13   120.30  3.000
 9MT  C4    C14  S     120.51  3.000
 9MT  C13   C14  S     119.15  3.000
 9MT  C7    C13  C12   119.20  3.000
 9MT  C7    C13  C14   116.50  3.000
 9MT  C12   C13  C14   124.30  3.000
 9MT  H12   C12  C10   119.28  3.000
 9MT  H12   C12  C13   119.90  3.000
 9MT  C10   C12  C13   120.82  3.000
 9MT  C9    C10  O     123.37  3.000
 9MT  C9    C10  C12   119.99  3.000
 9MT  O     C10  C12   116.64  3.000
 9MT  C11   O    C10   119.08  3.000
 9MT  H113  C11  H112  108.75  3.000
 9MT  H113  C11  H111  108.96  3.000
 9MT  H112  C11  H111  108.67  3.000
 9MT  H113  C11  O     111.94  3.000
 9MT  H112  C11  O     106.37  3.000
 9MT  H111  C11  O     112.04  3.000
 9MT  H9    C9   C8    119.12  3.000
 9MT  H9    C9   C10   121.09  3.000
 9MT  C8    C9   C10   119.79  3.000
 9MT  H8    C8   C7    118.38  3.000
 9MT  H8    C8   C9    120.31  3.000
 9MT  C7    C8   C9    121.31  3.000
 9MT  N     C7   C8    118.44  3.000
 9MT  N     C7   C13   122.69  3.000
 9MT  C8    C7   C13   118.88  3.000
 9MT  C5    N    C7    119.84  3.000
 9MT  C4    C5   C6    120.51  3.000
 9MT  C4    C5   N     122.79  3.000
 9MT  C6    C5   N     116.70  3.000
 9MT  H63C  C6   H62C  108.17  3.000
 9MT  H63C  C6   H61C  108.20  3.000
 9MT  H62C  C6   H61C  106.88  3.000
 9MT  H63C  C6   C5    109.79  3.000
 9MT  H62C  C6   C5    112.00  3.000
 9MT  H61C  C6   C5    111.65  3.000
 9MT  C3    C4   C5    119.59  3.000
 9MT  C3    C4   C14   122.47  3.000
 9MT  C5    C4   C14   117.87  3.000
 9MT  H32C  C3   H31C  106.16  3.000
 9MT  H32C  C3   C2    108.42  3.000
 9MT  H31C  C3   C2    109.60  3.000
 9MT  H32C  C3   C4    110.46  3.000
 9MT  H31C  C3   C4    110.41  3.000
 9MT  C2    C3   C4    111.64  3.000
 9MT  H22C  C2   H21C  106.25  3.000
 9MT  H22C  C2   C1    109.54  3.000
 9MT  H21C  C2   C1    109.56  3.000
 9MT  H22C  C2   C3    109.99  3.000
 9MT  H21C  C2   C3    108.84  3.000
 9MT  C1    C2   C3    112.47  3.000
 9MT  H12C  C1   H11C  106.15  3.000
 9MT  H12C  C1   C     109.76  3.000
 9MT  H11C  C1   C     109.55  3.000
 9MT  H12C  C1   C2    109.10  3.000
 9MT  H11C  C1   C2    109.55  3.000
 9MT  C     C1   C2    112.53  3.000
 9MT  HC3   C    HC2   107.64  3.000
 9MT  HC3   C    HC1   107.64  3.000
 9MT  HC2   C    HC1   107.60  3.000
 9MT  HC3   C    C1    111.47  3.000
 9MT  HC2   C    C1    111.12  3.000
 9MT  HC1   C    C1    111.19  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
 9MT  CONST_01  C10   C12  C13  C14   180.00   0.0  0
 9MT  CONST_02  C8    C7   C13  C14   180.00   0.0  0
 9MT  CONST_03  N     C7   C13  C14     0.00   0.0  0
 9MT  CONST_04  N     C5   C4   C14     0.00   0.0  0
 9MT  CONST_05  C5    C4   C14  C13     0.00   0.0  0
 9MT  CONST_06  C9    C10  C12  C13     0.00   0.0  0
 9MT  CONST_07  C9    C8   C7   C13     0.00   0.0  0
 9MT  CONST_08  C5    N    C7   C13     0.00   0.0  0
 9MT  CONST_09  C4    C14  C13  C12   180.00   0.0  0
 9MT  CONST_10  C8    C7   C13  C12     0.00   0.0  0
 9MT  CONST_11  N     C7   C13  C12   180.00   0.0  0
 9MT  CONST_12  C8    C9   C10  C12     0.00   0.0  0
 9MT  CONST_13  C7    C13  C12  C10     0.00   0.0  0
 9MT  CONST_14  C7    C8   C9   C10     0.00   0.0  0
 9MT  CONST_15  N     C7   C8   C9    180.00   0.0  0
 9MT  CONST_16  C5    N    C7   C8    180.00   0.0  0
 9MT  CONST_17  C4    C14  C13  C7      0.00   0.0  0
 9MT  CONST_18  C4    C5   N    C7      0.00   0.0  0
 9MT  CONST_19  C12   C13  C14  S       0.00   0.0  0
 9MT  CONST_20  C7    C13  C14  S     180.00   0.0  0
 9MT  CONST_21  C5    C4   C14  S     180.00   0.0  0
 9MT  CONST_22  C6    C5   C4   C14   180.00   0.0  0
 9MT  CONST_23  C3    C4   C14  C13   180.00   0.0  0
 9MT  CONST_24  O     C10  C12  C13   180.00   0.0  0
 9MT  CONST_25  C8    C9   C10  O     180.00   0.0  0
 9MT  CONST_26  C6    C5   N    C7    180.00   0.0  0
 9MT  CONST_27  C3    C4   C5   N     180.00   0.0  0
 9MT  CONST_28  H12   C12  C13  C14     0.00   0.0  0
 9MT  CONST_29  H8    C8   C7   C13   180.00   0.0  0
 9MT  CONST_30  H9    C9   C10  C12   180.00   0.0  0
 9MT  Var_01    C13   C14  S    C15   -99.81  30.0  2
 9MT  Var_02    C2    C3   C4   C14    88.97  30.0  2
 9MT  Var_03    C9    C10  O    C11    -0.94  30.0  2
 9MT  Var_04    H61C  C6   C5   N     116.79  30.0  2
 9MT  Var_05    C1    C2   C3   C4   -175.49  30.0  3
 9MT  Var_06    H151  C15  S    C14   -55.26  30.0  2
 9MT  Var_07    H111  C11  O    C10    61.49  30.0  3
 9MT  Var_08    C15   C16  C17  N1     -8.65  30.0  3
 9MT  Var_09    S     C15  C16  C17   179.32  30.0  3
 9MT  Var_10    C     C1   C2   C3   -178.24  30.0  3
 9MT  Var_11    HC1   C    C1   C2    -57.98  30.0  3

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
 9MT  plan-1  S    0.020
 9MT  plan-1  C14  0.020
 9MT  plan-1  C13  0.020
 9MT  plan-1  C12  0.020
 9MT  plan-1  C10  0.020
 9MT  plan-1  O    0.020
 9MT  plan-1  C9   0.020
 9MT  plan-1  C8   0.020
 9MT  plan-1  C7   0.020
 9MT  plan-1  N    0.020
 9MT  plan-1  C5   0.020
 9MT  plan-1  C6   0.020
 9MT  plan-1  C4   0.020
 9MT  plan-1  C3   0.020
 9MT  plan-1  H12  0.020
 9MT  plan-1  H9   0.020
 9MT  plan-1  H8   0.020

