# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:01:44 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: 3-({[5-(2-piperidin-4-ylethyl)thieno[2,3-b]thiophen-2-yl]carbonyl}amino)-N-(pyridin-3-ylsulfonyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](CNC(=O)c1sc2sc(CCC3CCNCC3)cc2c1)N[S](=O)(=O)c4cccnc4
#
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
 180  180  3-({[5-(2-piperidin-4-ylethyl)thieno[2,3-b]thiophen-2-yl]carbonyl}amino)-N-(pyridin-3-ylsulfonyl)-D-alanine  ligand  59  34  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_180
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
 180  O1    O  OC    -1  -0.588   0.9488  -0.6184    7.4032
 180  C1    C  C      0   0.437   1.6497   0.0286    6.6044
 180  O2    O  O      0  -0.596   2.6903   0.6655    6.8376
 180  C2    C  CH1    0  -0.254   1.2110   0.0054    5.1180
 180  C3    C  CH2    0  -0.286   2.2370  -0.7672    4.2867
 180  N1    N  NH1    0  -0.653   1.8699  -0.8595    2.8948
 180  C4    C  C      0   0.563   2.1269   0.1243    2.0138
 180  O3    O  O      0  -0.481   2.7386   1.1429    2.3048
 180  C5    C  CR5    0  -0.316   1.6325  -0.0811    0.6372
 180  C6    C  CR15   0  -0.217   1.5092   0.9053   -0.2933
 180  C7    C  CR5    0   0.272   0.9476   0.4347   -1.5086
 180  C8    C  C1     0  -0.271   0.5789   1.0003   -2.7676
 180  C9    C  C      0  -0.128   0.0414   0.0876   -3.6151
 180  C10   C  CH2    0  -0.515  -0.4412   0.2927   -5.0117
 180  C11   C  CH2    0  -0.408   0.3621  -0.4924   -6.0513
 180  C12   C  CH1    0  -0.241   0.0103  -0.1329   -7.4926
 180  C13   C  CH2    0  -0.411   0.9351  -0.8541   -8.4723
 180  C14   C  CH2    0  -0.293   0.5696  -0.5330   -9.9133
 180  N2    N  NH1    0  -0.595  -0.8148  -0.8924  -10.1662
 180  C15   C  CH2    0  -0.289  -1.7249  -0.1461   -9.3162
 180  C16   C  CH2    0  -0.423  -1.4428  -0.4448   -7.8498
 180  S1    S  S2     0   0.240  -0.0267  -1.5100   -2.9001
 180  C17   C  CR5    0  -0.464   0.6693  -0.9182   -1.4528
 180  S2    S  S2     0   0.250   1.0914  -1.6282    0.0422
 180  N3    N  NC1    0  -0.721  -0.1003  -0.6197    4.9530
 180  S3    S  S      0   1.363  -1.4085   0.3647    4.7910
 180  O4    O  OS     0  -0.661  -2.5751  -0.4634    5.0606
 180  O5    O  OS     0  -0.651  -1.2618   1.6215    5.5145
 180  C18   C  CR6    0  -0.274  -1.3928   0.7521    3.0634
 180  C19   C  CR16   0  -0.127  -1.7032  -0.2364    2.1380
 180  C20   C  CR16   0  -0.304  -1.7909   0.1288    0.8092
 180  C21   C  CR16   0  -0.035  -1.5611   1.4566    0.4699
 180  N4    N  N      0  -0.394  -1.2535   2.3970    1.3527
 180  C22   C  CR16   0  -0.039  -1.1720   2.0512    2.6313
 180  H2    H  HCH1   0   0.263   1.1820   1.0323    4.7465
 180  H31   H  HCH2   0   0.262   3.2093  -0.2876    4.3764
 180  H32   H  HCH2   0   0.261   2.3370  -1.7844    4.6688
 180  HN1   H  HNH1   0   0.401   1.2064  -1.5803    2.6593
 180  H6    H  HCR5   0   0.276   1.7821   1.9331   -0.1021
 180  H8    H  H      0   0.267   0.7071   2.0417   -3.0290
 180  H101  H  HCH2   0   0.261  -1.5009   0.0332   -5.0813
 180  H102  H  HCH2   0   0.255  -0.3725   1.3622   -5.2276
 180  H111  H  HCH2   0   0.235   1.4275  -0.3033   -5.8893
 180  H112  H  HCH2   0   0.218   0.2123  -1.5678   -5.9035
 180  H12   H  HCH1   0   0.210   0.1654   0.9483   -7.6171
 180  H131  H  HCH2   0   0.225   1.9756  -0.5743   -8.2866
 180  H132  H  HCH2   0   0.209   0.8605  -1.9358   -8.3138
 180  H141  H  HCH2   0   0.182   0.7672   0.5366  -10.0971
 180  H142  H  HCH2   0   0.228   1.2101  -1.0935  -10.5978
 180  HN2   H  HNH1   0   0.349  -1.0366  -0.7120  -11.1366
 180  H151  H  HCH2   0   0.182  -1.6490   0.9435   -9.4726
 180  H152  H  HCH2   0   0.228  -2.7505  -0.4283   -9.5634
 180  H161  H  HCH2   0   0.210  -1.6457  -1.5024   -7.6472
 180  H162  H  HCH2   0   0.232  -2.1317   0.1360   -7.2323
 180  HN3   H  HNC1   0   0.400  -0.2663  -1.2637    5.7286
 180  H19   H  HCR6   0   0.302  -1.8838  -1.2590    2.4428
 180  H20   H  HCR6   0   0.284  -2.0351  -0.5952    0.0449
 180  H21   H  HCR6   0   0.281  -1.6334   1.7691   -0.5654
 180  H22   H  HCR6   0   0.287  -0.9303   2.8387    3.3346

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
 180  O1   C1    deloc     1.244  0.020  1.244
 180  C1   O2    deloc     1.242  0.020  1.242
 180  C1   C2    single    1.550  0.020  1.550
 180  C2   C3    single    1.530  0.020  1.530
 180  C2   N3    single    1.462  0.020  1.462
 180  C2   H2    single    0.970  0.020  1.090
 180  C3   N1    single    1.442  0.020  1.442
 180  C3   H31   single    0.970  0.020  1.090
 180  C3   H32   single    0.970  0.020  1.090
 180  N1   C4    single    1.345  0.020  1.345
 180  N1   HN1   single    0.860  0.020  1.020
 180  C4   O3    double    1.223  0.020  1.223
 180  C4   C5    single    1.477  0.020  1.477
 180  C5   C6    aromatic  1.362  0.020  1.362
 180  C5   S2    aromatic  1.744  0.020  1.744
 180  C6   C7    aromatic  1.419  0.020  1.419
 180  C6   H6    single    0.930  0.020  1.080
 180  C7   C8    aromatic  1.429  0.020  1.429
 180  C7   C17   aromatic  1.382  0.020  1.382
 180  C8   C9    aromatic  1.357  0.020  1.357
 180  C8   H8    single    0.930  0.020  1.080
 180  C9   C10   single    1.492  0.020  1.492
 180  C9   S1    aromatic  1.752  0.020  1.752
 180  C10  C11   single    1.531  0.020  1.531
 180  C10  H101  single    0.970  0.020  1.090
 180  C10  H102  single    0.970  0.020  1.090
 180  C11  C12   single    1.527  0.020  1.527
 180  C11  H111  single    0.970  0.020  1.090
 180  C11  H112  single    0.970  0.020  1.090
 180  C12  C13   single    1.528  0.020  1.528
 180  C12  C16   single    1.529  0.020  1.529
 180  C12  H12   single    0.970  0.020  1.090
 180  C13  C14   single    1.521  0.020  1.521
 180  C13  H131  single    0.970  0.020  1.090
 180  C13  H132  single    0.970  0.020  1.090
 180  C14  N2    single    1.452  0.020  1.452
 180  C14  H141  single    0.970  0.020  1.090
 180  C14  H142  single    0.970  0.020  1.090
 180  N2   C15   single    1.452  0.020  1.452
 180  N2   HN2   single    0.890  0.020  1.040
 180  C15  C16   single    1.523  0.020  1.523
 180  C15  H151  single    0.970  0.020  1.090
 180  C15  H152  single    0.970  0.020  1.090
 180  C16  H161  single    0.970  0.020  1.090
 180  C16  H162  single    0.970  0.020  1.090
 180  S1   C17   aromatic  1.712  0.020  1.712
 180  C17  S2    aromatic  1.708  0.020  1.708
 180  N3   S3    single    1.645  0.020  1.645
 180  N3   HN3   single    0.890  0.020  1.040
 180  S3   O4    double    1.456  0.020  1.456
 180  S3   O5    double    1.458  0.020  1.458
 180  S3   C18   single    1.771  0.020  1.771
 180  C18  C19   aromatic  1.389  0.020  1.389
 180  C18  C22   aromatic  1.387  0.020  1.387
 180  C19  C20   aromatic  1.381  0.020  1.381
 180  C19  H19   single    0.930  0.020  1.080
 180  C20  C21   aromatic  1.390  0.020  1.390
 180  C20  H20   single    0.930  0.020  1.080
 180  C21  N4    aromatic  1.326  0.020  1.326
 180  C21  H21   single    0.930  0.020  1.080
 180  N4   C22   aromatic  1.327  0.020  1.327
 180  C22  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
 180  C2    C1   O2    115.14  3.000
 180  C2    C1   O1    116.65  3.000
 180  O2    C1   O1    128.17  3.000
 180  H2    C2   N3    109.86  3.000
 180  H2    C2   C3    107.92  3.000
 180  N3    C2   C3    108.92  3.000
 180  H2    C2   C1    108.63  3.000
 180  N3    C2   C1    111.62  3.000
 180  C3    C2   C1    109.81  3.000
 180  H32   C3   H31   107.46  3.000
 180  H32   C3   N1    107.55  3.000
 180  H31   C3   N1    109.59  3.000
 180  H32   C3   C2    109.99  3.000
 180  H31   C3   C2    109.39  3.000
 180  N1    C3   C2    112.70  3.000
 180  HN1   N1   C4    119.72  3.000
 180  HN1   N1   C3    116.04  3.000
 180  C4    N1   C3    122.44  3.000
 180  C5    C4   O3    120.32  3.000
 180  C5    C4   N1    116.40  3.000
 180  O3    C4   N1    123.27  3.000
 180  S2    C5   C6    112.42  3.000
 180  S2    C5   C4    123.05  3.000
 180  C6    C5   C4    124.50  3.000
 180  H6    C6   C7    124.54  3.000
 180  H6    C6   C5    123.05  3.000
 180  C7    C6   C5    112.38  3.000
 180  C17   C7   C8    111.79  3.000
 180  C17   C7   C6    111.70  3.000
 180  C8    C7   C6    136.51  3.000
 180  H8    C8   C9    122.95  3.000
 180  H8    C8   C7    124.31  3.000
 180  C9    C8   C7    112.73  3.000
 180  S1    C9   C10   119.67  3.000
 180  S1    C9   C8    111.97  3.000
 180  C10   C9   C8    128.36  3.000
 180  H102  C10  H101  106.29  3.000
 180  H102  C10  C11   109.55  3.000
 180  H101  C10  C11   110.11  3.000
 180  H102  C10  C9    107.40  3.000
 180  H101  C10  C9    109.91  3.000
 180  C11   C10  C9    113.30  3.000
 180  H112  C11  H111  106.43  3.000
 180  H112  C11  C12   109.09  3.000
 180  H111  C11  C12   108.87  3.000
 180  H112  C11  C10   109.88  3.000
 180  H111  C11  C10   108.77  3.000
 180  C12   C11  C10   113.55  3.000
 180  H12   C12  C16   107.96  3.000
 180  H12   C12  C13   107.83  3.000
 180  C16   C12  C13   109.22  3.000
 180  H12   C12  C11   107.82  3.000
 180  C16   C12  C11   113.06  3.000
 180  C13   C12  C11   110.77  3.000
 180  H132  C13  H131  107.04  3.000
 180  H132  C13  C14   109.21  3.000
 180  H131  C13  C14   109.61  3.000
 180  H132  C13  C12   109.39  3.000
 180  H131  C13  C12   110.26  3.000
 180  C14   C13  C12   111.24  3.000
 180  H142  C14  H141  106.75  3.000
 180  H142  C14  N2    108.83  3.000
 180  H141  C14  N2    112.44  3.000
 180  H142  C14  C13   110.15  3.000
 180  H141  C14  C13   108.63  3.000
 180  N2    C14  C13   109.99  3.000
 180  HN2   N2   C15   109.42  3.000
 180  HN2   N2   C14   109.38  3.000
 180  C15   N2   C14   111.61  3.000
 180  H152  C15  H151  106.72  3.000
 180  H152  C15  C16   109.96  3.000
 180  H151  C15  C16   108.51  3.000
 180  H152  C15  N2    108.87  3.000
 180  H151  C15  N2    112.43  3.000
 180  C16   C15  N2    110.29  3.000
 180  H162  C16  H161  106.97  3.000
 180  H162  C16  C15   108.86  3.000
 180  H161  C16  C15   109.46  3.000
 180  H162  C16  C12   111.03  3.000
 180  H161  C16  C12   109.25  3.000
 180  C15   C16  C12   111.17  3.000
 180  C17   S1   C9     90.80  3.000
 180  S2    C17  S1    134.18  3.000
 180  S2    C17  C7    113.11  3.000
 180  S1    C17  C7    112.71  3.000
 180  C17   S2   C5     90.38  3.000
 180  HN3   N3   S3    108.82  3.000
 180  HN3   N3   C2    109.24  3.000
 180  S3    N3   C2    117.94  3.000
 180  C18   S3   O5    107.14  3.000
 180  C18   S3   O4    108.19  3.000
 180  O5    S3   O4    118.64  3.000
 180  C18   S3   N3    102.70  3.000
 180  O5    S3   N3    112.77  3.000
 180  O4    S3   N3    106.18  3.000
 180  C22   C18  C19   119.64  3.000
 180  C22   C18  S3    120.69  3.000
 180  C19   C18  S3    119.50  3.000
 180  H19   C19  C20   120.69  3.000
 180  H19   C19  C18   121.46  3.000
 180  C20   C19  C18   117.85  3.000
 180  H20   C20  C21   120.32  3.000
 180  H20   C20  C19   121.18  3.000
 180  C21   C20  C19   118.50  3.000
 180  H21   C21  N4    116.55  3.000
 180  H21   C21  C20   119.84  3.000
 180  N4    C21  C20   123.61  3.000
 180  C22   N4   C21   118.09  3.000
 180  H22   C22  N4    116.74  3.000
 180  H22   C22  C18   120.95  3.000
 180  N4    C22  C18   122.31  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
 180  CONST_01  C8   C7   C6   C5    180.00   0.0  0
 180  CONST_02  C17  C7   C6   C5      0.00   0.0  0
 180  CONST_03  C7   C17  S2   C5      0.00   0.0  0
 180  CONST_04  S1   C17  S2   C5    180.00   0.0  0
 180  CONST_05  C17  S2   C5   C6      0.00   0.0  0
 180  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 180  CONST_07  S1   C17  C7   C6    180.00   0.0  0
 180  CONST_08  S2   C17  C7   C6      0.00   0.0  0
 180  CONST_09  S2   C5   C6   C7      0.00   0.0  0
 180  CONST_10  S1   C9   C8   C7      0.00   0.0  0
 180  CONST_11  C9   S1   C17  C7      0.00   0.0  0
 180  CONST_12  S1   C17  C7   C8      0.00   0.0  0
 180  CONST_13  S2   C17  C7   C8    180.00   0.0  0
 180  CONST_14  C17  S1   C9   C8      0.00   0.0  0
 180  CONST_15  C17  C7   C8   C9      0.00   0.0  0
 180  CONST_16  S2   C17  S1   C9    180.00   0.0  0
 180  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 180  CONST_18  C21  N4   C22  C18     0.00   0.0  0
 180  CONST_19  N4   C22  C18  C19     0.00   0.0  0
 180  CONST_20  N4   C21  C20  C19     0.00   0.0  0
 180  CONST_21  C22  C18  C19  C20     0.00   0.0  0
 180  CONST_22  C22  N4   C21  C20     0.00   0.0  0
 180  CONST_23  C7   C6   C5   C4    180.00   0.0  0
 180  CONST_24  C17  S2   C5   C4    180.00   0.0  0
 180  CONST_25  C10  C9   C8   C7    180.00   0.0  0
 180  CONST_26  C17  S1   C9   C10   180.00   0.0  0
 180  CONST_27  C20  C19  C18  S3    180.00   0.0  0
 180  CONST_28  N4   C22  C18  S3    180.00   0.0  0
 180  CONST_29  H8   C8   C7   C6      0.00   0.0  0
 180  CONST_30  H6   C6   C7   C8      0.00   0.0  0
 180  CONST_31  H20  C20  C19  C18   180.00   0.0  0
 180  CONST_32  H22  C22  C18  C19   180.00   0.0  0
 180  CONST_33  H21  C21  C20  C19   180.00   0.0  0
 180  CONST_34  H19  C19  C20  C21   180.00   0.0  0
 180  CONST_35  C5   C4   N1   C3    180.00   0.0  0
 180  CONST_36  HN1  N1   C4   C5      0.00   0.0  0
 180  CONST_37  O3   C4   N1   C3      0.00   0.0  0
 180  Var_01    N2   C14  C13  C12   -57.38  30.0  1
 180  Var_02    N2   C15  C16  C12    56.76  30.0  1
 180  Var_03    C15  N2   C14  C13    61.17  30.0  1
 180  Var_04    C16  C15  N2   C14   -60.95  30.0  1
 180  Var_05    C6   C5   C4   N1    163.59  30.0  2
 180  Var_06    C11  C10  C9   C8    116.03  30.0  2
 180  Var_07    C12  C11  C10  C9   -171.54  30.0  3
 180  Var_08    C19  C18  S3   N3     69.97  30.0  2
 180  Var_09    C18  S3   N3   C2     83.71  30.0  3
 180  Var_10    C4   N1   C3   C2     83.19  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
 180  chir_01  C2   C1   C3   N3   negativ
 180  chir_02  C12  C11  C13  C16  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
 180  plan-1  S3   0.020
 180  plan-1  C18  0.020
 180  plan-1  C19  0.020
 180  plan-1  C20  0.020
 180  plan-1  C21  0.020
 180  plan-1  N4   0.020
 180  plan-1  C22  0.020
 180  plan-1  H19  0.020
 180  plan-1  H20  0.020
 180  plan-1  H21  0.020
 180  plan-1  H22  0.020
 180  plan-2  C4   0.020
 180  plan-2  C5   0.020
 180  plan-2  C6   0.020
 180  plan-2  C7   0.020
 180  plan-2  C8   0.020
 180  plan-2  C9   0.020
 180  plan-2  C10  0.020
 180  plan-2  S1   0.020
 180  plan-2  C17  0.020
 180  plan-2  S2   0.020
 180  plan-2  H6   0.020
 180  plan-2  H8   0.020
 180  plan-3  C3   0.020
 180  plan-3  N1   0.020
 180  plan-3  C4   0.020
 180  plan-3  O3   0.020
 180  plan-3  C5   0.020
 180  plan-3  HN1  0.020
 180  plan-4  O1   0.020
 180  plan-4  C1   0.020
 180  plan-4  O2   0.020
 180  plan-4  C2   0.020

