# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:16:31 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S)-2-amino-3-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N1CC[C@H](CC1)c2onc(n2)c3sccc3
#
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
 LL5  LL5  (2S)-2-amino-3-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}butan-1-one  ligand  45  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LL5
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
 LL5  C22   C  CH3   0  -0.671  -5.6260  -1.9770  -0.5817
 LL5  C20   C  CH1   0  -0.227  -5.9981  -0.7838   0.2947
 LL5  C21   C  CH3   0  -0.648  -6.8032  -1.2467   1.5034
 LL5  C19   C  CH1   0  -0.193  -4.7605   0.0152   0.7426
 LL5  N33   N  NH2   0  -0.775  -5.1623   1.1761   1.5155
 LL5  C7    C  C     0   0.540  -3.9512   0.4286  -0.4938
 LL5  O32   O  O     0  -0.509  -4.3901   1.3381  -1.1915
 LL5  N1    N  NT    0  -0.447  -2.7995  -0.2053  -0.8015
 LL5  C2    C  CH2   0  -0.328  -2.0004   0.2302  -1.9357
 LL5  C3    C  CH2   0  -0.423  -0.6590   0.7762  -1.4662
 LL5  C6    C  CH2   0  -0.331  -2.1490  -1.2619  -0.0489
 LL5  C5    C  CH2   0  -0.415  -0.8145  -0.7831   0.5079
 LL5  C4    C  CH1   0  -0.408   0.0789  -0.2798  -0.6348
 LL5  C14   C  CR5   0   0.569   1.3821   0.2184  -0.1287
 LL5  N23   N  N     0  -0.461   2.5578  -0.2865  -0.3014
 LL5  O26   O  O     0  -0.328   1.4127   1.3198   0.6100
 LL5  N25   N  N     0  -0.157   2.7171   1.5573   0.9499
 LL5  C24   C  CR5   0   0.340   3.3609   0.5779   0.3864
 LL5  C27   C  CR5   0  -0.278   4.7924   0.4052   0.4665
 LL5  C31   C  CR15  0  -0.210   5.7208   1.2095   1.0687
 LL5  C30   C  CR15  0  -0.168   7.0370   0.7073   0.9345
 LL5  C29   C  CR15  0  -0.460   7.0795  -0.4641   0.2363
 LL5  S28   S  S2    0   0.264   5.5272  -0.9679  -0.2659
 LL5  H22   H  HCH3  0   0.218  -4.9631  -2.6671  -0.0536
 LL5  H22A  H  HCH3  0   0.237  -6.5208  -2.5345  -0.8618
 LL5  H22B  H  HCH3  0   0.234  -5.1305  -1.6828  -1.5077
 LL5  H20   H  HCH1  0   0.222  -6.6229  -0.1072  -0.3006
 LL5  H21   H  HCH3  0   0.211  -6.2121  -1.9201   2.1296
 LL5  H21A  H  HCH3  0   0.233  -7.1177  -0.4069   2.1196
 LL5  H21B  H  HCH3  0   0.224  -7.6959  -1.7890   1.1873
 LL5  H19   H  HCH1  0   0.240  -4.1818  -0.6205   1.4147
 LL5  HN33  H  HNH2  0   0.349  -4.3466   1.6458   1.8883
 LL5  HN3A  H  HNH2  0   0.339  -5.6166   1.8443   0.9043
 LL5  H2    H  HCH2  0   0.248  -1.8443  -0.6249  -2.6020
 LL5  H2A   H  HCH2  0   0.275  -2.5415   0.9853  -2.4975
 LL5  H3    H  HCH2  0   0.264  -0.0617   1.0596  -2.3351
 LL5  H3A   H  HCH2  0   0.247  -0.8268   1.6805  -0.8759
 LL5  H6    H  HCH2  0   0.275  -2.7778  -1.6283   0.7552
 LL5  H6A   H  HCH2  0   0.254  -1.9845  -2.1093  -0.7222
 LL5  H5    H  HCH2  0   0.248  -0.9901   0.0127   1.2363
 LL5  H5A   H  HCH2  0   0.265  -0.3276  -1.6075   1.0319
 LL5  H4    H  HCH1  0   0.289   0.3179  -1.1293  -1.2816
 LL5  H31   H  HCR5  0   0.273   5.4707   2.1254   1.5851
 LL5  H30   H  HCR5  0   0.276   7.9134   1.1949   1.3352
 LL5  H29   H  HCR5  0   0.305   7.9470  -1.0572  -0.0091

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
 LL5  C22  C20   single    1.527  0.020  1.527
 LL5  C22  H22   single    0.970  0.020  1.090
 LL5  C22  H22A  single    0.970  0.020  1.090
 LL5  C22  H22B  single    0.970  0.020  1.090
 LL5  C20  C19   single    1.540  0.020  1.540
 LL5  C20  C21   single    1.524  0.020  1.524
 LL5  C20  H20   single    0.970  0.020  1.090
 LL5  C21  H21   single    0.970  0.020  1.090
 LL5  C21  H21A  single    0.970  0.020  1.090
 LL5  C21  H21B  single    0.970  0.020  1.090
 LL5  C7   C19   single    1.534  0.020  1.534
 LL5  N33  C19   single    1.451  0.020  1.451
 LL5  C19  H19   single    0.970  0.020  1.090
 LL5  N33  HN33  single    0.890  0.020  1.040
 LL5  N33  HN3A  single    0.890  0.020  1.040
 LL5  O32  C7    double    1.227  0.020  1.227
 LL5  C7   N1    single    1.350  0.020  1.350
 LL5  C6   N1    single    1.451  0.020  1.451
 LL5  N1   C2    single    1.454  0.020  1.454
 LL5  C3   C2    single    1.523  0.020  1.523
 LL5  C2   H2    single    0.970  0.020  1.090
 LL5  C2   H2A   single    0.970  0.020  1.090
 LL5  C4   C3    single    1.533  0.020  1.533
 LL5  C3   H3    single    0.970  0.020  1.090
 LL5  C3   H3A   single    0.970  0.020  1.090
 LL5  C5   C6    single    1.523  0.020  1.523
 LL5  C6   H6    single    0.970  0.020  1.090
 LL5  C6   H6A   single    0.970  0.020  1.090
 LL5  C5   C4    single    1.535  0.020  1.535
 LL5  C5   H5    single    0.970  0.020  1.090
 LL5  C5   H5A   single    0.970  0.020  1.090
 LL5  C14  C4    single    1.484  0.020  1.484
 LL5  C4   H4    single    0.970  0.020  1.090
 LL5  O26  C14   aromatic  1.327  0.020  1.327
 LL5  C14  N23   aromatic  1.291  0.020  1.291
 LL5  C24  N23   aromatic  1.366  0.020  1.366
 LL5  N25  O26   aromatic  1.369  0.020  1.369
 LL5  N25  C24   aromatic  1.300  0.020  1.300
 LL5  C24  C27   single    1.444  0.020  1.444
 LL5  S28  C27   aromatic  1.721  0.020  1.721
 LL5  C27  C31   aromatic  1.368  0.020  1.368
 LL5  C30  C31   aromatic  1.415  0.020  1.415
 LL5  C31  H31   single    0.930  0.020  1.080
 LL5  C29  C30   aromatic  1.364  0.020  1.364
 LL5  C30  H30   single    0.930  0.020  1.080
 LL5  S28  C29   aromatic  1.708  0.020  1.708
 LL5  C29  H29   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
 LL5  H22B  C22  H22A  107.01  3.000
 LL5  H22B  C22  H22   107.76  3.000
 LL5  H22A  C22  H22   107.39  3.000
 LL5  H22B  C22  C20   112.79  3.000
 LL5  H22A  C22  C20   110.30  3.000
 LL5  H22   C22  C20   111.34  3.000
 LL5  H20   C20  C19   107.20  3.000
 LL5  H20   C20  C21   108.48  3.000
 LL5  C19   C20  C21   110.58  3.000
 LL5  H20   C20  C22   108.03  3.000
 LL5  C21   C20  C22   110.28  3.000
 LL5  C19   C20  C22   112.13  3.000
 LL5  H21B  C21  H21A  108.13  3.000
 LL5  H21B  C21  H21   107.59  3.000
 LL5  H21A  C21  H21   107.90  3.000
 LL5  H21B  C21  C20   110.69  3.000
 LL5  H21A  C21  C20   111.55  3.000
 LL5  H21   C21  C20   110.84  3.000
 LL5  H19   C19  C7    111.94  3.000
 LL5  H19   C19  N33   106.54  3.000
 LL5  C7    C19  N33   111.08  3.000
 LL5  H19   C19  C20   107.65  3.000
 LL5  N33   C19  C20   110.33  3.000
 LL5  C7    C19  C20   109.23  3.000
 LL5  HN3A  N33  HN33  106.10  3.000
 LL5  HN3A  N33  C19   109.29  3.000
 LL5  HN33  N33  C19   110.13  3.000
 LL5  N1    C7   O32   121.56  3.000
 LL5  N1    C7   C19   120.47  3.000
 LL5  O32   C7   C19   117.97  3.000
 LL5  C6    N1   C2    112.10  3.000
 LL5  C2    N1   C7    120.39  3.000
 LL5  C6    N1   C7    127.30  3.000
 LL5  H2A   C2   H2    107.41  3.000
 LL5  H2A   C2   C3    110.44  3.000
 LL5  H2    C2   C3    110.00  3.000
 LL5  H2A   C2   N1    109.76  3.000
 LL5  H2    C2   N1    108.60  3.000
 LL5  C3    C2   N1    110.55  3.000
 LL5  H3A   C3   H3    107.40  3.000
 LL5  H3A   C3   C4    110.54  3.000
 LL5  H3    C3   C4    110.31  3.000
 LL5  H3A   C3   C2    109.15  3.000
 LL5  H3    C3   C2    109.25  3.000
 LL5  C4    C3   C2    110.13  3.000
 LL5  H6A   C6   H6    106.36  3.000
 LL5  H6A   C6   C5    109.66  3.000
 LL5  H6    C6   C5    110.07  3.000
 LL5  H6A   C6   N1    108.18  3.000
 LL5  H6    C6   N1    111.75  3.000
 LL5  C5    C6   N1    110.70  3.000
 LL5  H5A   C5   H5    107.56  3.000
 LL5  H5A   C5   C4    110.20  3.000
 LL5  H5    C5   C4    110.54  3.000
 LL5  H5A   C5   C6    109.20  3.000
 LL5  H5    C5   C6    109.37  3.000
 LL5  C4    C5   C6    109.93  3.000
 LL5  H4    C4   C14   105.69  3.000
 LL5  H4    C4   C5    108.22  3.000
 LL5  C14   C4   C5    111.55  3.000
 LL5  H4    C4   C3    108.62  3.000
 LL5  C14   C4   C3    112.10  3.000
 LL5  C5    C4   C3    110.45  3.000
 LL5  O26   C14  N23   112.22  3.000
 LL5  N23   C14  C4    128.51  3.000
 LL5  O26   C14  C4    119.27  3.000
 LL5  C24   N23  C14   102.74  3.000
 LL5  N25   O26  C14   107.72  3.000
 LL5  C24   N25  O26   103.50  3.000
 LL5  C27   C24  N25   123.83  3.000
 LL5  C27   C24  N23   122.35  3.000
 LL5  N25   C24  N23   113.82  3.000
 LL5  S28   C27  C31   111.51  3.000
 LL5  C31   C27  C24   128.82  3.000
 LL5  S28   C27  C24   119.67  3.000
 LL5  H31   C31  C30   124.14  3.000
 LL5  H31   C31  C27   123.47  3.000
 LL5  C30   C31  C27   112.39  3.000
 LL5  H30   C30  C29   123.52  3.000
 LL5  H30   C30  C31   124.01  3.000
 LL5  C29   C30  C31   112.47  3.000
 LL5  H29   C29  S28   120.11  3.000
 LL5  H29   C29  C30   127.83  3.000
 LL5  S28   C29  C30   112.06  3.000
 LL5  C29   S28  C27    91.58  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
 LL5  CONST_01  C24  N25  O26  C14    0.00   0.0  0
 LL5  CONST_02  N25  C24  N23  C14    0.00   0.0  0
 LL5  CONST_03  C27  C24  N23  C14  180.00   0.0  0
 LL5  CONST_04  N25  O26  C14  N23    0.00   0.0  0
 LL5  CONST_05  O26  N25  C24  N23    0.00   0.0  0
 LL5  CONST_06  S28  C27  C24  N23    0.00   0.0  0
 LL5  CONST_07  C31  C27  C24  N23  180.00   0.0  0
 LL5  CONST_08  C24  N23  C14  O26    0.00   0.0  0
 LL5  CONST_09  C27  C24  N25  O26  180.00   0.0  0
 LL5  CONST_10  S28  C27  C24  N25  180.00   0.0  0
 LL5  CONST_11  C31  C27  C24  N25    0.00   0.0  0
 LL5  CONST_12  C29  S28  C27  C24  180.00   0.0  0
 LL5  CONST_13  C30  C31  C27  C24  180.00   0.0  0
 LL5  CONST_14  C30  C29  S28  C27    0.00   0.0  0
 LL5  CONST_15  C29  C30  C31  C27    0.00   0.0  0
 LL5  CONST_16  C29  S28  C27  C31    0.00   0.0  0
 LL5  CONST_17  S28  C29  C30  C31    0.00   0.0  0
 LL5  CONST_18  S28  C27  C31  C30    0.00   0.0  0
 LL5  CONST_19  N25  O26  C14  C4   180.00   0.0  0
 LL5  CONST_20  C24  N23  C14  C4   180.00   0.0  0
 LL5  CONST_21  H31  C31  C27  C24    0.00   0.0  0
 LL5  CONST_22  H29  C29  S28  C27  180.00   0.0  0
 LL5  CONST_23  H30  C30  C31  C27  180.00   0.0  0
 LL5  CONST_24  C6   N1   C7   C19    0.00   0.0  0
 LL5  CONST_25  C2   N1   C7   C19  180.00   0.0  0
 LL5  CONST_26  C6   N1   C7   O32  180.00   0.0  0
 LL5  CONST_27  C2   N1   C7   O32    0.00   0.0  0
 LL5  Var_01    C4   C5   C6   N1   -56.59  30.0  1
 LL5  Var_02    C4   C3   C2   N1    56.47  30.0  1
 LL5  Var_03    C5   C6   N1   C2    60.75  30.0  1
 LL5  Var_04    C6   N1   C2   C3   -60.60  30.0  1
 LL5  Var_05    H21  C21  C20  C22   62.28  30.0  3
 LL5  Var_06    H22  C22  C20  C21  -64.16  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
 LL5  chir_01  C19  C20  C7  N33  negativ
 LL5  chir_02  C4   C3   C5  C14  positiv

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
 LL5  plan-1  C4   0.020
 LL5  plan-1  C14  0.020
 LL5  plan-1  N23  0.020
 LL5  plan-1  O26  0.020
 LL5  plan-1  N25  0.020
 LL5  plan-1  C24  0.020
 LL5  plan-1  C27  0.020
 LL5  plan-2  C24  0.020
 LL5  plan-2  C27  0.020
 LL5  plan-2  C31  0.020
 LL5  plan-2  C30  0.020
 LL5  plan-2  C29  0.020
 LL5  plan-2  S28  0.020
 LL5  plan-2  H31  0.020
 LL5  plan-2  H30  0.020
 LL5  plan-2  H29  0.020
 LL5  plan-3  C19  0.020
 LL5  plan-3  C7   0.020
 LL5  plan-3  O32  0.020
 LL5  plan-3  N1   0.020
 LL5  plan-3  C2   0.020
 LL5  plan-3  C6   0.020

