# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:51:09 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccccc1CC(=O)N2CCN(CC2)c3ncnc4sc5CCCc5c34
#
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
 2RY  2RY  1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone  ligand  52  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2RY
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
 2RY  F1   F  F     0  -0.299  -4.7881   2.3539   1.4931
 2RY  C22  C  CT    0   1.057  -4.2613   1.5054   0.6062
 2RY  F2   F  F     0  -0.317  -4.1222   2.1915  -0.5412
 2RY  F3   F  F     0  -0.313  -3.0199   1.2289   1.0347
 2RY  C21  C  CR6   0  -0.261  -5.0942   0.2715   0.4223
 2RY  C20  C  CR16  0  -0.281  -6.3555   0.2194   1.0066
 2RY  C19  C  CR16  0  -0.256  -7.1634  -0.8943   0.8374
 2RY  C18  C  CR16  0  -0.230  -6.7104  -1.9598   0.0769
 2RY  C17  C  CR16  0  -0.306  -5.4532  -1.9047  -0.5053
 2RY  C16  C  CR6   0   0.216  -4.6253  -0.7999  -0.3477
 2RY  C9   C  CH2   0  -0.761  -3.2729  -0.8249  -1.0013
 2RY  C8   C  C     0   0.582  -2.2031  -1.3488  -0.0504
 2RY  O1   O  O     0  -0.486  -2.5116  -1.8408   1.0235
 2RY  N4   N  NT    0  -0.464  -0.9230  -1.2702  -0.4712
 2RY  C15  C  CH2   0  -0.331  -0.4674  -0.7055  -1.7263
 2RY  C7   C  CH2   0  -0.285   0.4305   0.4963  -1.4782
 2RY  C6   C  CH2   0  -0.315   0.1778  -1.6660   0.3865
 2RY  C5   C  CH2   0  -0.326   1.0919  -0.4794   0.6305
 2RY  N3   N  NT    0  -0.505   1.5445   0.0894  -0.6372
 2RY  C1   C  CR6   0   0.483   2.6513   0.9000  -0.6038
 2RY  C3   C  CR56  0   0.017   3.8897   0.4459  -0.0943
 2RY  N1   N  N     0  -0.454   2.5494   2.1323  -1.0846
 2RY  C2   C  CR16  0   0.039   3.5897   2.9530  -0.9809
 2RY  N2   N  N     0  -0.420   4.7514   2.6910  -0.4171
 2RY  C4   C  CR56  0  -0.025   4.8796   1.4354  -0.0057
 2RY  S1   S  S2    0   0.216   6.3665   0.8168   0.6490
 2RY  C11  C  CR55  0  -0.214   5.6793  -0.7649   0.7304
 2RY  C10  C  CR55  0   0.158   4.3958  -0.8330   0.3096
 2RY  C12  C  CH2   0  -0.480   6.2964  -2.0878   1.0313
 2RY  C13  C  CH2   0  -0.461   5.0570  -3.0099   1.0029
 2RY  C14  C  CH2   0  -0.514   3.9626  -2.2680   0.2041
 2RY  H1   H  HCR6  0   0.272  -6.7235   1.0442   1.6001
 2RY  H2   H  HCR6  0   0.267  -8.1420  -0.9224   1.2968
 2RY  H3   H  HCR6  0   0.267  -7.3337  -2.8327  -0.0650
 2RY  H4   H  HCR6  0   0.261  -5.1048  -2.7388  -1.1023
 2RY  H5   H  HCH2  0   0.316  -3.3074  -1.4895  -1.8691
 2RY  H6   H  HCH2  0   0.288  -2.9980   0.1489  -1.4042
 2RY  H7   H  HCH2  0   0.258   0.0909  -1.4706  -2.2739
 2RY  H8   H  HCH2  0   0.284  -1.3003  -0.4085  -2.3568
 2RY  H9   H  HCH2  0   0.266   0.8074   0.8610  -2.4320
 2RY  H10  H  HCH2  0   0.227  -0.1532   1.3041  -1.0177
 2RY  H11  H  HCH2  0   0.276  -0.2025  -2.0381   1.3333
 2RY  H12  H  HCH2  0   0.250   0.7357  -2.4736  -0.0977
 2RY  H13  H  HCH2  0   0.252   0.5490   0.2830   1.2057
 2RY  H14  H  HCH2  0   0.274   1.9406  -0.7891   1.2359
 2RY  H15  H  HCR6  0   0.260   3.4576   3.9491  -1.3882
 2RY  H16  H  HCH2  0   0.257   7.0272  -2.3543   0.2625
 2RY  H17  H  HCH2  0   0.246   5.2844  -3.9877   0.5813
 2RY  H18  H  HCH2  0   0.251   2.9723  -2.4838   0.6023
 2RY  H19  H  HCH2  0   0.260   6.8163  -2.1167   1.9899
 2RY  H20  H  HCH2  0   0.248   4.7061  -3.1697   2.0230
 2RY  H21  H  HCH2  0   0.252   3.9474  -2.5717  -0.8465

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
 2RY  C2   N2   aromatic  1.318  0.020  1.318
 2RY  C2   N1   aromatic  1.329  0.020  1.329
 2RY  N2   C4   aromatic  1.328  0.020  1.328
 2RY  N1   C1   aromatic  1.327  0.020  1.327
 2RY  C4   S1   aromatic  1.738  0.020  1.738
 2RY  C4   C3   aromatic  1.402  0.020  1.402
 2RY  C1   C3   aromatic  1.414  0.020  1.414
 2RY  C1   N3   single    1.372  0.020  1.372
 2RY  S1   C11  aromatic  1.726  0.020  1.726
 2RY  C7   N3   single    1.454  0.020  1.454
 2RY  C7   C15  single    1.521  0.020  1.521
 2RY  C3   C10  aromatic  1.433  0.020  1.433
 2RY  F1   C22  single    1.336  0.020  1.336
 2RY  N3   C5   single    1.461  0.020  1.461
 2RY  C5   C6   single    1.518  0.020  1.518
 2RY  F2   C22  single    1.344  0.020  1.344
 2RY  C15  N4   single    1.450  0.020  1.450
 2RY  C11  C10  aromatic  1.352  0.020  1.352
 2RY  C11  C12  single    1.490  0.020  1.490
 2RY  C22  F3   single    1.342  0.020  1.342
 2RY  C22  C21  single    1.500  0.020  1.500
 2RY  C10  C14  single    1.503  0.020  1.503
 2RY  N4   C6   single    1.450  0.020  1.450
 2RY  N4   C8   single    1.350  0.020  1.350
 2RY  O1   C8   double    1.221  0.020  1.221
 2RY  C8   C9   single    1.524  0.020  1.524
 2RY  C12  C13  single    1.545  0.020  1.545
 2RY  C21  C20  aromatic  1.391  0.020  1.391
 2RY  C21  C16  aromatic  1.400  0.020  1.400
 2RY  C14  C13  single    1.545  0.020  1.545
 2RY  C9   C16  single    1.502  0.020  1.502
 2RY  C20  C19  aromatic  1.386  0.020  1.386
 2RY  C16  C17  aromatic  1.390  0.020  1.390
 2RY  C19  C18  aromatic  1.385  0.020  1.385
 2RY  C17  C18  aromatic  1.387  0.020  1.387
 2RY  C20  H1   single    0.930  0.020  1.080
 2RY  C19  H2   single    0.930  0.020  1.080
 2RY  C18  H3   single    0.930  0.020  1.080
 2RY  C17  H4   single    0.930  0.020  1.080
 2RY  C9   H5   single    0.970  0.020  1.090
 2RY  C9   H6   single    0.970  0.020  1.090
 2RY  C15  H7   single    0.970  0.020  1.090
 2RY  C15  H8   single    0.970  0.020  1.090
 2RY  C7   H9   single    0.970  0.020  1.090
 2RY  C7   H10  single    0.970  0.020  1.090
 2RY  C6   H11  single    0.970  0.020  1.090
 2RY  C6   H12  single    0.970  0.020  1.090
 2RY  C5   H13  single    0.970  0.020  1.090
 2RY  C5   H14  single    0.970  0.020  1.090
 2RY  C2   H15  single    0.930  0.020  1.080
 2RY  C12  H16  single    0.970  0.020  1.090
 2RY  C13  H17  single    0.970  0.020  1.090
 2RY  C14  H18  single    0.970  0.020  1.090
 2RY  C12  H19  single    0.970  0.020  1.090
 2RY  C13  H20  single    0.970  0.020  1.090
 2RY  C14  H21  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
 2RY  C21  C22  F3   112.54  3.000
 2RY  C21  C22  F2   111.88  3.000
 2RY  F3   C22  F2   106.38  3.000
 2RY  C21  C22  F1   112.64  3.000
 2RY  F3   C22  F1   106.48  3.000
 2RY  F2   C22  F1   106.46  3.000
 2RY  C16  C21  C20  120.39  3.000
 2RY  C16  C21  C22  120.73  3.000
 2RY  C20  C21  C22  118.87  3.000
 2RY  H1   C20  C19  118.79  3.000
 2RY  H1   C20  C21  120.72  3.000
 2RY  C19  C20  C21  120.49  3.000
 2RY  H2   C19  C18  120.60  3.000
 2RY  H2   C19  C20  119.77  3.000
 2RY  C18  C19  C20  119.63  3.000
 2RY  H3   C18  C17  119.95  3.000
 2RY  H3   C18  C19  120.28  3.000
 2RY  C17  C18  C19  119.77  3.000
 2RY  H4   C17  C16  118.89  3.000
 2RY  H4   C17  C18  119.50  3.000
 2RY  C16  C17  C18  121.61  3.000
 2RY  C9   C16  C17  118.28  3.000
 2RY  C17  C16  C21  118.11  3.000
 2RY  C9   C16  C21  123.60  3.000
 2RY  H6   C9   H5   104.94  3.000
 2RY  H6   C9   C8   111.16  3.000
 2RY  H5   C9   C8   107.96  3.000
 2RY  H6   C9   C16  111.92  3.000
 2RY  H5   C9   C16  109.08  3.000
 2RY  C8   C9   C16  111.48  3.000
 2RY  N4   C8   O1   122.50  3.000
 2RY  O1   C8   C9   120.66  3.000
 2RY  N4   C8   C9   116.82  3.000
 2RY  C6   N4   C15  112.31  3.000
 2RY  C6   N4   C8   121.30  3.000
 2RY  C15  N4   C8   126.20  3.000
 2RY  H8   C15  H7   106.98  3.000
 2RY  H8   C15  C7   109.35  3.000
 2RY  H7   C15  C7   109.46  3.000
 2RY  H8   C15  N4   111.60  3.000
 2RY  H7   C15  N4   108.74  3.000
 2RY  C7   C15  N4   110.62  3.000
 2RY  H10  C7   H9   107.77  3.000
 2RY  H10  C7   N3   111.76  3.000
 2RY  H9   C7   N3   109.59  3.000
 2RY  H10  C7   C15  109.63  3.000
 2RY  H9   C7   C15  109.05  3.000
 2RY  N3   C7   C15  109.00  3.000
 2RY  H12  C6   H11  108.14  3.000
 2RY  H12  C6   C5   109.94  3.000
 2RY  H11  C6   C5   109.79  3.000
 2RY  H12  C6   N4   109.06  3.000
 2RY  H11  C6   N4   110.07  3.000
 2RY  C5   C6   N4   109.81  3.000
 2RY  H14  C5   H13  106.97  3.000
 2RY  H14  C5   N3   110.61  3.000
 2RY  H13  C5   N3   109.70  3.000
 2RY  H14  C5   C6   109.69  3.000
 2RY  H13  C5   C6   109.22  3.000
 2RY  N3   C5   C6   110.57  3.000
 2RY  C1   N3   C5   117.30  3.000
 2RY  C5   N3   C7   111.92  3.000
 2RY  C1   N3   C7   117.82  3.000
 2RY  N1   C1   C3   119.75  3.000
 2RY  C3   C1   N3   121.69  3.000
 2RY  N1   C1   N3   118.55  3.000
 2RY  C10  C3   C4   111.25  3.000
 2RY  C10  C3   C1   134.21  3.000
 2RY  C4   C3   C1   114.48  3.000
 2RY  C2   N1   C1   119.02  3.000
 2RY  H15  C2   N2   116.80  3.000
 2RY  H15  C2   N1   116.27  3.000
 2RY  N2   C2   N1   126.92  3.000
 2RY  C4   N2   C2   113.94  3.000
 2RY  S1   C4   N2   122.40  3.000
 2RY  S1   C4   C3   112.11  3.000
 2RY  N2   C4   C3   125.42  3.000
 2RY  C11  S1   C4    90.19  3.000
 2RY  C12  C11  C10  114.27  3.000
 2RY  C12  C11  S1   131.14  3.000
 2RY  C10  C11  S1   114.16  3.000
 2RY  C14  C10  C11  110.09  3.000
 2RY  C14  C10  C3   136.92  3.000
 2RY  C11  C10  C3   112.20  3.000
 2RY  H19  C12  H16  107.03  3.000
 2RY  H19  C12  C13  112.50  3.000
 2RY  H16  C12  C13  112.19  3.000
 2RY  H19  C12  C11  113.46  3.000
 2RY  H16  C12  C11  110.55  3.000
 2RY  C13  C12  C11  101.18  3.000
 2RY  H20  C13  H17  107.33  3.000
 2RY  H20  C13  C14  109.03  3.000
 2RY  H17  C13  C14  112.27  3.000
 2RY  H20  C13  C12  109.17  3.000
 2RY  H17  C13  C12  112.05  3.000
 2RY  C14  C13  C12  106.93  3.000
 2RY  H21  C14  H18  106.48  3.000
 2RY  H21  C14  C13  111.91  3.000
 2RY  H18  C14  C13  111.10  3.000
 2RY  H21  C14  C10  109.67  3.000
 2RY  H18  C14  C10  115.20  3.000
 2RY  C13  C14  C10  102.60  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
 2RY  CONST_01  C18  C19  C20  C21     0.00   0.0  0
 2RY  CONST_02  C18  C17  C16  C21     0.00   0.0  0
 2RY  CONST_03  C17  C16  C21  C20     0.00   0.0  0
 2RY  CONST_04  C17  C18  C19  C20     0.00   0.0  0
 2RY  CONST_05  C16  C21  C20  C19     0.00   0.0  0
 2RY  CONST_06  C16  C17  C18  C19     0.00   0.0  0
 2RY  CONST_07  N2   C2   N1   C1      0.00   0.0  0
 2RY  CONST_08  N2   C4   C3   C1      0.00   0.0  0
 2RY  CONST_09  S1   C4   C3   C1    180.00   0.0  0
 2RY  CONST_10  C11  C10  C3   C1    180.00   0.0  0
 2RY  CONST_11  C2   N2   C4   C3      0.00   0.0  0
 2RY  CONST_12  C11  S1   C4   C3      0.00   0.0  0
 2RY  CONST_13  C2   N1   C1   C3      0.00   0.0  0
 2RY  CONST_14  S1   C11  C10  C3      0.00   0.0  0
 2RY  CONST_15  C4   N2   C2   N1      0.00   0.0  0
 2RY  CONST_16  C4   C3   C1   N1      0.00   0.0  0
 2RY  CONST_17  C10  C3   C1   N1    180.00   0.0  0
 2RY  CONST_18  S1   C4   N2   C2    180.00   0.0  0
 2RY  CONST_19  C11  S1   C4   N2    180.00   0.0  0
 2RY  CONST_20  C10  C3   C4   N2    180.00   0.0  0
 2RY  CONST_21  C10  C11  S1   C4      0.00   0.0  0
 2RY  CONST_22  C11  C10  C3   C4      0.00   0.0  0
 2RY  CONST_23  C10  C3   C4   S1      0.00   0.0  0
 2RY  CONST_24  C2   N1   C1   N3    180.00   0.0  0
 2RY  CONST_25  C4   C3   C1   N3    180.00   0.0  0
 2RY  CONST_26  C10  C3   C1   N3      0.00   0.0  0
 2RY  CONST_27  C19  C20  C21  C22   180.00   0.0  0
 2RY  CONST_28  C17  C16  C21  C22   180.00   0.0  0
 2RY  CONST_29  C9   C16  C21  C20   180.00   0.0  0
 2RY  CONST_30  C9   C16  C17  C18   180.00   0.0  0
 2RY  CONST_31  H2   C19  C20  C21   180.00   0.0  0
 2RY  CONST_32  H4   C17  C16  C21   180.00   0.0  0
 2RY  CONST_33  H3   C18  C19  C20   180.00   0.0  0
 2RY  CONST_34  H1   C20  C19  C18   180.00   0.0  0
 2RY  CONST_35  H15  C2   N1   C1    180.00   0.0  0
 2RY  CONST_36  C15  N4   C8   C9      0.00   0.0  0
 2RY  CONST_37  C6   N4   C8   C9    180.00   0.0  0
 2RY  CONST_38  C15  N4   C8   O1    180.00   0.0  0
 2RY  CONST_39  C6   N4   C8   O1      0.00   0.0  0
 2RY  Var_01    N3   C7   C15  N4     56.87  30.0  1
 2RY  Var_02    N3   C5   C6   N4    -55.17  30.0  1
 2RY  Var_03    C1   N3   C7   C15   161.97  30.0  1
 2RY  Var_04    C5   C6   N4   C15    56.27  30.0  1
 2RY  Var_05    N1   C1   N3   C7     14.68  30.0  2
 2RY  Var_06    C6   C5   N3   C7     57.48  30.0  1
 2RY  Var_07    C6   N4   C15  C7    -57.70  30.0  1
 2RY  Var_08    C13  C14  C10  C3   -176.11  30.0  1
 2RY  Var_09    C13  C12  C11  S1    176.76  30.0  1
 2RY  Var_10    C14  C13  C12  C11    20.26  30.0  1
 2RY  Var_11    C12  C13  C14  C10   -21.95  30.0  1
 2RY  Var_12    C20  C21  C22  F1      8.87  30.0  2
 2RY  Var_13    C8   C9   C16  C21    86.47  30.0  3
 2RY  Var_14    N4   C8   C9   C16  -172.44  30.0  1

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
 2RY  plan-1  C22  0.020
 2RY  plan-1  C21  0.020
 2RY  plan-1  C20  0.020
 2RY  plan-1  C19  0.020
 2RY  plan-1  C18  0.020
 2RY  plan-1  C17  0.020
 2RY  plan-1  C16  0.020
 2RY  plan-1  C9   0.020
 2RY  plan-1  H1   0.020
 2RY  plan-1  H2   0.020
 2RY  plan-1  H3   0.020
 2RY  plan-1  H4   0.020
 2RY  plan-2  N3   0.020
 2RY  plan-2  C1   0.020
 2RY  plan-2  C3   0.020
 2RY  plan-2  N1   0.020
 2RY  plan-2  C2   0.020
 2RY  plan-2  N2   0.020
 2RY  plan-2  C4   0.020
 2RY  plan-2  S1   0.020
 2RY  plan-2  C11  0.020
 2RY  plan-2  C10  0.020
 2RY  plan-2  C12  0.020
 2RY  plan-2  C14  0.020
 2RY  plan-2  H15  0.020
 2RY  plan-3  C9   0.020
 2RY  plan-3  C8   0.020
 2RY  plan-3  O1   0.020
 2RY  plan-3  N4   0.020
 2RY  plan-3  C15  0.020
 2RY  plan-3  C6   0.020

