# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:18:05 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2R,3S)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)-3-[(thiophen-2-ylsulfanyl)methyl]butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(C)C)[C@H](CSc2sccc2)C(=O)NO
#
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
 BAT  BAT  (2R,3S)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)-3-[(thiophen-2-ylsulfanyl)methyl]butanediamide  ligand  63  32  .  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_BAT
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
 BAT  C1    C  CH1   0  -0.374   1.6905  -0.4255  -0.0487
 BAT  C2    C  C     0   0.557   3.0030  -1.1888   0.0011
 BAT  C3    C  CH2   0  -0.593   0.7776  -1.0968  -1.0709
 BAT  C4    C  CR5   0  -0.337   0.7432   0.3162  -3.4471
 BAT  C5    C  CR15  0  -0.171   0.3915   1.5060  -2.8775
 BAT  C6    C  CR15  0  -0.185  -0.2190   2.3931  -3.8056
 BAT  C7    C  CR15  0  -0.467  -0.3087   1.8739  -5.0593
 BAT  C8    C  CH1   0  -0.363   1.0201  -0.3931   1.3387
 BAT  C9    C  CH2   0  -0.430   1.8961   0.2457   2.4365
 BAT  C10   C  CH1   0  -0.255   2.7742  -0.7158   3.2450
 BAT  C11   C  CH3   0  -0.652   3.7036   0.0917   4.1457
 BAT  C12   C  CH3   0  -0.658   1.9299  -1.6797   4.0721
 BAT  C13   C  C     0   0.564  -0.2538   0.4271   1.2225
 BAT  C14   C  CH1   0  -0.185  -2.6938   0.3817   1.5217
 BAT  C15   C  C     0   0.561  -3.2857   0.8564   2.8495
 BAT  C16   C  CH3   0  -0.515  -2.9277   1.1997   5.2332
 BAT  C17   C  CH2   0  -0.539  -3.6504  -0.5949   0.8243
 BAT  C18   C  CR6   0   0.137  -3.1330  -1.0158  -0.5236
 BAT  C19   C  CR16  0  -0.328  -2.7002  -2.3186  -0.7508
 BAT  C20   C  CR16  0  -0.237  -2.2034  -2.6977  -1.9924
 BAT  C21   C  CR16  0  -0.261  -2.1205  -1.7722  -3.0220
 BAT  C22   C  CR16  0  -0.224  -2.5433  -0.4665  -2.8051
 BAT  C23   C  CR16  0  -0.296  -3.0493  -0.0956  -1.5681
 BAT  N1    N  NH1   0  -0.368   4.0859  -0.4051  -0.1068
 BAT  N2    N  NH1   0  -0.657  -1.3771  -0.1947   1.6389
 BAT  O1    O  O     0  -0.470   3.0515  -2.4016   0.1088
 BAT  O2    O  OH1   0  -0.538   5.3301  -0.9216   0.0728
 BAT  O3    O  O     0  -0.470  -0.2396   1.5782   0.8176
 BAT  O4    O  O     0  -0.502  -4.4216   1.3109   2.8847
 BAT  S1    S  S2    0   0.069   1.4779  -1.1084  -2.7482
 BAT  S2    S  S2    0   0.221   0.3200   0.2783  -5.1196
 BAT  H1    H  HCH1  0   0.281   1.8788   0.6097  -0.3477
 BAT  H31   H  HCH2  0   0.298   0.6120  -2.1410  -0.8045
 BAT  H32   H  HCH2  0   0.318  -0.1990  -0.6184  -1.1340
 BAT  H5    H  HCR5  0   0.268   0.5391   1.7465  -1.8341
 BAT  H6    H  HCR5  0   0.270  -0.5629   3.3842  -3.5462
 BAT  H7    H  HCR5  0   0.297  -0.6976   2.3398  -5.9514
 BAT  H8    H  HCH1  0   0.270   0.7669  -1.4207   1.6187
 BAT  H91   H  HCH2  0   0.243   2.5131   1.0287   1.9863
 BAT  H92   H  HCH2  0   0.240   1.2536   0.7670   3.1556
 BAT  H10   H  HCH1  0   0.236   3.3984  -1.3055   2.5686
 BAT  H111  H  HCH3  0   0.230   4.3406  -0.5630   4.7417
 BAT  H112  H  HCH3  0   0.227   4.3532   0.7473   3.5631
 BAT  H113  H  HCH3  0   0.216   3.1330   0.7177   4.8365
 BAT  H121  H  HCH3  0   0.215   1.2776  -1.1343   4.7597
 BAT  H122  H  HCH3  0   0.230   1.2989  -2.3157   3.4500
 BAT  H123  H  HCH3  0   0.234   2.5624  -2.3393   4.6674
 BAT  H14   H  HCH1  0   0.296  -2.6022   1.2781   0.9038
 BAT  H161  H  HCH3  0   0.252  -2.1006   1.0711   5.9248
 BAT  H162  H  HCH3  0   0.242  -3.2127   2.2515   5.2289
 BAT  H163  H  HCH3  0   0.241  -3.7745   0.6166   5.5962
 BAT  H171  H  HCH2  0   0.266  -3.8029  -1.4723   1.4587
 BAT  H172  H  HCH2  0   0.275  -4.6201  -0.1059   0.7242
 BAT  H19   H  HCR6  0   0.247  -2.7503  -3.0473   0.0499
 BAT  H20   H  HCR6  0   0.252  -1.8716  -3.7160  -2.1499
 BAT  H21   H  HCR6  0   0.247  -1.7207  -2.0615  -3.9847
 BAT  H22   H  HCR6  0   0.251  -2.4742   0.2667  -3.5984
 BAT  H23   H  HCR6  0   0.246  -3.3782   0.9260  -1.4125
 BAT  HN1   H  HNH1  0   0.417   4.0358   0.6031  -0.1340
 BAT  HN2   H  HNH1  0   0.407  -1.3175  -1.1754   1.8679
 BAT  HN3   H  HNH1  0   0.396  -1.5862   0.3591   3.8245
 BAT  HO2   H  HOH1  0   0.480   5.6653  -1.1385  -0.8073
 BAT  N3    N  NH1   0  -0.624  -2.5015   0.7636   3.9243

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
 BAT  C1   C2    single    1.519  0.020  1.519
 BAT  C1   C3    single    1.526  0.020  1.526
 BAT  C1   C8    single    1.541  0.020  1.541
 BAT  C1   H1    single    0.970  0.020  1.090
 BAT  C2   N1    single    1.341  0.020  1.341
 BAT  C2   O1    double    1.219  0.020  1.219
 BAT  C3   S1    single    1.818  0.020  1.818
 BAT  C3   H31   single    0.970  0.020  1.090
 BAT  C3   H32   single    0.970  0.020  1.090
 BAT  C4   C5    aromatic  1.365  0.020  1.365
 BAT  C4   S1    single    1.749  0.020  1.749
 BAT  C4   S2    aromatic  1.726  0.020  1.726
 BAT  C5   C6    aromatic  1.422  0.020  1.422
 BAT  C5   H5    single    0.930  0.020  1.080
 BAT  C6   C7    aromatic  1.360  0.020  1.360
 BAT  C6   H6    single    0.930  0.020  1.080
 BAT  C7   S2    aromatic  1.716  0.020  1.716
 BAT  C7   H7    single    0.930  0.020  1.080
 BAT  C8   C9    single    1.543  0.020  1.543
 BAT  C8   C13   single    1.520  0.020  1.520
 BAT  C8   H8    single    0.970  0.020  1.090
 BAT  C9   C10   single    1.533  0.020  1.533
 BAT  C9   H91   single    0.970  0.020  1.090
 BAT  C9   H92   single    0.970  0.020  1.090
 BAT  C10  C11   single    1.525  0.020  1.525
 BAT  C10  C12   single    1.525  0.020  1.525
 BAT  C10  H10   single    0.970  0.020  1.090
 BAT  C11  H111  single    0.970  0.020  1.090
 BAT  C11  H112  single    0.970  0.020  1.090
 BAT  C11  H113  single    0.970  0.020  1.090
 BAT  C12  H121  single    0.970  0.020  1.090
 BAT  C12  H122  single    0.970  0.020  1.090
 BAT  C12  H123  single    0.970  0.020  1.090
 BAT  C13  N2    single    1.350  0.020  1.350
 BAT  C13  O3    double    1.220  0.020  1.220
 BAT  C14  C15   single    1.529  0.020  1.529
 BAT  C14  C17   single    1.535  0.020  1.535
 BAT  C14  N2    single    1.442  0.020  1.442
 BAT  C14  H14   single    0.970  0.020  1.090
 BAT  C15  N3    single    1.334  0.020  1.334
 BAT  C15  O4    double    1.224  0.020  1.224
 BAT  C16  N3    single    1.444  0.020  1.444
 BAT  C16  H161  single    0.970  0.020  1.090
 BAT  C16  H162  single    0.970  0.020  1.090
 BAT  C16  H163  single    0.970  0.020  1.090
 BAT  C17  C18   single    1.504  0.020  1.504
 BAT  C17  H171  single    0.970  0.020  1.090
 BAT  C17  H172  single    0.970  0.020  1.090
 BAT  C18  C19   aromatic  1.391  0.020  1.391
 BAT  C18  C23   aromatic  1.394  0.020  1.394
 BAT  C19  C20   aromatic  1.390  0.020  1.390
 BAT  C19  H19   single    0.930  0.020  1.080
 BAT  C20  C21   aromatic  1.387  0.020  1.387
 BAT  C20  H20   single    0.930  0.020  1.080
 BAT  C21  C22   aromatic  1.390  0.020  1.390
 BAT  C21  H21   single    0.930  0.020  1.080
 BAT  C22  C23   aromatic  1.387  0.020  1.387
 BAT  C22  H22   single    0.930  0.020  1.080
 BAT  C23  H23   single    0.930  0.020  1.080
 BAT  N1   O2    single    1.359  0.020  1.359
 BAT  N1   HN1   single    0.860  0.020  1.020
 BAT  N2   HN2   single    0.860  0.020  1.020
 BAT  N3   HN3   single    0.860  0.020  1.020
 BAT  O2   HO2   single    0.850  0.020  0.980

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
 BAT  H1    C1   C8    107.52  3.000
 BAT  H1    C1   C3    109.65  3.000
 BAT  C8    C1   C3    110.61  3.000
 BAT  H1    C1   C2    109.61  3.000
 BAT  C8    C1   C2    110.91  3.000
 BAT  C3    C1   C2    108.53  3.000
 BAT  O1    C2   N1    123.82  3.000
 BAT  O1    C2   C1    122.51  3.000
 BAT  N1    C2   C1    113.67  3.000
 BAT  H32   C3   H31   107.37  3.000
 BAT  H32   C3   S1    107.14  3.000
 BAT  H31   C3   S1    106.13  3.000
 BAT  H32   C3   C1    112.46  3.000
 BAT  H31   C3   C1    110.39  3.000
 BAT  S1    C3   C1    112.98  3.000
 BAT  S2    C4   S1    118.20  3.000
 BAT  S2    C4   C5    111.13  3.000
 BAT  S1    C4   C5    130.65  3.000
 BAT  H5    C5   C6    123.36  3.000
 BAT  H5    C5   C4    124.16  3.000
 BAT  C6    C5   C4    112.46  3.000
 BAT  H6    C6   C7    123.40  3.000
 BAT  H6    C6   C5    123.52  3.000
 BAT  C7    C6   C5    113.08  3.000
 BAT  H7    C7   S2    120.30  3.000
 BAT  H7    C7   C6    128.40  3.000
 BAT  S2    C7   C6    111.30  3.000
 BAT  H8    C8   C13   109.41  3.000
 BAT  H8    C8   C9    109.75  3.000
 BAT  C13   C8   C9    107.87  3.000
 BAT  H8    C8   C1    108.13  3.000
 BAT  C13   C8   C1    107.89  3.000
 BAT  C9    C8   C1    113.72  3.000
 BAT  H92   C9   H91   105.08  3.000
 BAT  H92   C9   C10   106.74  3.000
 BAT  H91   C9   C10   110.06  3.000
 BAT  H92   C9   C8    109.32  3.000
 BAT  H91   C9   C8    108.89  3.000
 BAT  C10   C9   C8    116.16  3.000
 BAT  H10   C10  C12   108.10  3.000
 BAT  H10   C10  C11   107.64  3.000
 BAT  C12   C10  C11   110.58  3.000
 BAT  H10   C10  C9    109.83  3.000
 BAT  C12   C10  C9    111.43  3.000
 BAT  C11   C10  C9    109.17  3.000
 BAT  H113  C11  H112  107.70  3.000
 BAT  H113  C11  H111  107.65  3.000
 BAT  H112  C11  H111  107.73  3.000
 BAT  H113  C11  C10   111.00  3.000
 BAT  H112  C11  C10   111.43  3.000
 BAT  H111  C11  C10   111.15  3.000
 BAT  H123  C12  H122  107.11  3.000
 BAT  H123  C12  H121  107.72  3.000
 BAT  H122  C12  H121  107.71  3.000
 BAT  H123  C12  C10   110.93  3.000
 BAT  H122  C12  C10   112.30  3.000
 BAT  H121  C12  C10   110.86  3.000
 BAT  O3    C13  N2    123.13  3.000
 BAT  O3    C13  C8    121.66  3.000
 BAT  N2    C13  C8    115.18  3.000
 BAT  H14   C14  N2    107.30  3.000
 BAT  H14   C14  C17   108.50  3.000
 BAT  N2    C14  C17   110.59  3.000
 BAT  H14   C14  C15   105.60  3.000
 BAT  N2    C14  C15   114.01  3.000
 BAT  C17   C14  C15   110.54  3.000
 BAT  O4    C15  N3    123.26  3.000
 BAT  O4    C15  C14   119.96  3.000
 BAT  N3    C15  C14   116.78  3.000
 BAT  H163  C16  H162  108.32  3.000
 BAT  H163  C16  H161  108.43  3.000
 BAT  H162  C16  H161  108.43  3.000
 BAT  H163  C16  N3    111.68  3.000
 BAT  H162  C16  N3    111.41  3.000
 BAT  H161  C16  N3    108.47  3.000
 BAT  H172  C17  H171  106.80  3.000
 BAT  H172  C17  C18   110.43  3.000
 BAT  H171  C17  C18   110.08  3.000
 BAT  H172  C17  C14   108.10  3.000
 BAT  H171  C17  C14   109.51  3.000
 BAT  C18   C17  C14   111.77  3.000
 BAT  C23   C18  C19   118.48  3.000
 BAT  C23   C18  C17   120.48  3.000
 BAT  C19   C18  C17   121.02  3.000
 BAT  H19   C19  C20   119.54  3.000
 BAT  H19   C19  C18   119.64  3.000
 BAT  C20   C19  C18   120.82  3.000
 BAT  H20   C20  C21   120.08  3.000
 BAT  H20   C20  C19   119.74  3.000
 BAT  C21   C20  C19   120.17  3.000
 BAT  H21   C21  C22   120.18  3.000
 BAT  H21   C21  C20   120.29  3.000
 BAT  C22   C21  C20   119.53  3.000
 BAT  H22   C22  C23   119.73  3.000
 BAT  H22   C22  C21   120.17  3.000
 BAT  C23   C22  C21   120.10  3.000
 BAT  H23   C23  C22   119.37  3.000
 BAT  H23   C23  C18   119.73  3.000
 BAT  C22   C23  C18   120.89  3.000
 BAT  HN1   N1   O2    115.37  3.000
 BAT  HN1   N1   C2    123.06  3.000
 BAT  O2    N1   C2    120.44  3.000
 BAT  HN2   N2   C14   117.45  3.000
 BAT  HN2   N2   C13   117.95  3.000
 BAT  C14   N2   C13   123.41  3.000
 BAT  HO2   O2   N1    106.41  3.000
 BAT  C4    S1   C3    101.64  3.000
 BAT  C7    S2   C4     92.03  3.000
 BAT  HN3   N3   C16   118.69  3.000
 BAT  HN3   N3   C15   118.89  3.000
 BAT  C16   N3   C15   122.41  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
 BAT  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 BAT  CONST_02  C6    C7   S2   C4      0.00   0.0  0
 BAT  CONST_03  C7    S2   C4   C5      0.00   0.0  0
 BAT  CONST_04  S2    C7   C6   C5      0.00   0.0  0
 BAT  CONST_05  S2    C4   C5   C6      0.00   0.0  0
 BAT  CONST_06  C21   C20  C19  C18     0.00   0.0  0
 BAT  CONST_07  C21   C22  C23  C18     0.00   0.0  0
 BAT  CONST_08  C22   C23  C18  C19     0.00   0.0  0
 BAT  CONST_09  C22   C21  C20  C19     0.00   0.0  0
 BAT  CONST_10  C23   C18  C19  C20     0.00   0.0  0
 BAT  CONST_11  C23   C22  C21  C20     0.00   0.0  0
 BAT  CONST_12  S1    C4   C5   C6    180.00   0.0  0
 BAT  CONST_13  S1    C4   S2   C7    180.00   0.0  0
 BAT  CONST_14  C20   C19  C18  C17   180.00   0.0  0
 BAT  CONST_15  C22   C23  C18  C17   180.00   0.0  0
 BAT  CONST_16  H6    C6   C5   C4    180.00   0.0  0
 BAT  CONST_17  H7    C7   S2   C4    180.00   0.0  0
 BAT  CONST_18  H5    C5   C6   C7    180.00   0.0  0
 BAT  CONST_19  H20   C20  C19  C18   180.00   0.0  0
 BAT  CONST_20  H22   C22  C23  C18   180.00   0.0  0
 BAT  CONST_21  H23   C23  C18  C19   180.00   0.0  0
 BAT  CONST_22  H21   C21  C20  C19   180.00   0.0  0
 BAT  CONST_23  H19   C19  C20  C21   180.00   0.0  0
 BAT  CONST_24  O2    N1   C2   C1    180.00   0.0  0
 BAT  CONST_25  C14   N2   C13  C8    180.00   0.0  0
 BAT  CONST_26  C16   N3   C15  C14   180.00   0.0  0
 BAT  CONST_27  O3    C13  N2   C14     0.00   0.0  0
 BAT  CONST_28  O4    C15  N3   C16     0.00   0.0  0
 BAT  CONST_29  O2    N1   C2   O1      0.00   0.0  0
 BAT  CONST_30  HN1   N1   C2   C1      0.00   0.0  0
 BAT  CONST_31  HN2   N2   C13  C8      0.00   0.0  0
 BAT  CONST_32  HN3   N3   C15  C14     0.00   0.0  0
 BAT  Var_01    C5    C4   S1   C3     33.27  30.0  2
 BAT  Var_02    C19   C18  C17  C14   110.98  30.0  2
 BAT  Var_03    H31   C3   S1   C4    143.68  30.0  3
 BAT  Var_04    C11   C10  C9   C8    172.42  30.0  3
 BAT  Var_05    H111  C11  C10  C9    179.65  30.0  3
 BAT  Var_06    H121  C12  C10  C9    -58.61  30.0  3
 BAT  Var_07    H161  C16  N3   C15  -176.99  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
 BAT  chir_01  C1   C2  C3   C8   negativ
 BAT  chir_02  C8   C1  C9   C13  negativ
 BAT  chir_03  C14  N2  C15  C17  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
 BAT  plan-1  C4   0.020
 BAT  plan-1  C5   0.020
 BAT  plan-1  C6   0.020
 BAT  plan-1  C7   0.020
 BAT  plan-1  S1   0.020
 BAT  plan-1  S2   0.020
 BAT  plan-1  H5   0.020
 BAT  plan-1  H6   0.020
 BAT  plan-1  H7   0.020
 BAT  plan-2  C17  0.020
 BAT  plan-2  C18  0.020
 BAT  plan-2  C19  0.020
 BAT  plan-2  C20  0.020
 BAT  plan-2  C21  0.020
 BAT  plan-2  C22  0.020
 BAT  plan-2  C23  0.020
 BAT  plan-2  H19  0.020
 BAT  plan-2  H20  0.020
 BAT  plan-2  H21  0.020
 BAT  plan-2  H22  0.020
 BAT  plan-2  H23  0.020
 BAT  plan-3  C1   0.020
 BAT  plan-3  C2   0.020
 BAT  plan-3  N1   0.020
 BAT  plan-3  O1   0.020
 BAT  plan-3  O2   0.020
 BAT  plan-3  HN1  0.020
 BAT  plan-4  C8   0.020
 BAT  plan-4  C13  0.020
 BAT  plan-4  C14  0.020
 BAT  plan-4  N2   0.020
 BAT  plan-4  O3   0.020
 BAT  plan-4  HN2  0.020
 BAT  plan-5  C14  0.020
 BAT  plan-5  C15  0.020
 BAT  plan-5  C16  0.020
 BAT  plan-5  O4   0.020
 BAT  plan-5  HN3  0.020
 BAT  plan-5  N3   0.020

