# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:51:29 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2S,3S)-3-amino-5-(ethylsulfanyl)-2-hydroxy-N-[(1S)-1-naphthalen-1-ylethyl]pentanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCSCC[C@H](N)[C@H](O)C(=O)N[C@@H](C)c1cccc2ccccc12
#
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
 AO1  AO1  '(2S,3S)-3-amino-5-(ethylsulfanyl)-2-hydroxy-N-[(1S)-1-naphthalen-1-ylethyl]pentanamide (non-preferred name)'  ligand  50  24  .  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_AO1
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
 AO1  C1    C  CH3   0  -0.662   8.0568  -2.3185  -0.2006
 AO1  C2    C  CH2   0  -0.534   6.5754  -2.1135  -0.4653
 AO1  S3    S  S2    0  -0.042   5.9794  -0.6618   0.4491
 AO1  C4    C  CH2   0  -0.553   4.2390  -0.6482  -0.0637
 AO1  C5    C  CH2   0  -0.418   3.5412   0.5693   0.5246
 AO1  C6    C  CH1   0  -0.140   2.0556   0.6093   0.1539
 AO1  C8    C  CH1   0  -0.010   1.3623   1.8474   0.7599
 AO1  C9    C  C     0   0.492  -0.1696   1.7452   0.7040
 AO1  N10   N  NH1   0  -0.643  -0.7036   1.4556  -0.4813
 AO1  C11   C  CH1   0  -0.148  -2.1235   1.2707  -0.6796
 AO1  C12   C  CR6   0   0.116  -2.6232  -0.0626  -0.1496
 AO1  O13   O  O     0  -0.501  -0.8181   1.9496   1.7260
 AO1  C14   C  CH3   0  -0.665  -2.4302   1.4099  -2.1690
 AO1  C15   C  CR16  0  -0.338  -1.7758  -1.1340  -0.0365
 AO1  C16   C  CR16  0  -0.242  -2.2281  -2.3935   0.4047
 AO1  C17   C  CR16  0  -0.334  -3.5404  -2.5772   0.7320
 AO1  C18   C  CR66  0   0.111  -4.4551  -1.5035   0.6296
 AO1  C19   C  CR66  0   0.095  -4.0003  -0.2312   0.1847
 AO1  C20   C  CR16  0  -0.311  -5.8189  -1.6789   0.9631
 AO1  C21   C  CR16  0  -0.261  -6.7070  -0.6445   0.8614
 AO1  C22   C  CR16  0  -0.249  -6.2634   0.6184   0.4225
 AO1  C23   C  CR16  0  -0.342  -4.9498   0.8183   0.0938
 AO1  O24   O  OH1   0  -0.676   1.7378   2.0453   2.0895
 AO1  N7    N  NH2   0  -0.809   1.8110   0.6214  -1.2852
 AO1  H11A  H  HCH3  0   0.233   8.2518  -2.4945   0.8572
 AO1  H12   H  HCH3  0   0.245   8.4174  -3.1848  -0.7554
 AO1  H13   H  HCH3  0   0.233   8.6423  -1.4542  -0.5148
 AO1  H21A  H  HCH2  0   0.258   6.3929  -1.9599  -1.5304
 AO1  H22A  H  HCH2  0   0.258   6.0060  -2.9903  -0.1523
 AO1  H41   H  HCH2  0   0.254   4.2003  -0.6365  -1.1545
 AO1  H42   H  HCH2  0   0.260   3.7557  -1.5662   0.2794
 AO1  H51   H  HCH2  0   0.247   3.6496   0.5561   1.6098
 AO1  H52   H  HCH2  0   0.230   4.0266   1.4832   0.1644
 AO1  H6    H  HCH1  0   0.247   1.5739  -0.2910   0.5536
 AO1  H8    H  HCH1  0   0.233   1.6569   2.7170   0.1496
 AO1  H10   H  HNH1  0   0.419  -0.0321   1.1746  -1.2014
 AO1  H11   H  HCH1  0   0.256  -2.6279   2.0770  -0.1429
 AO1  H141  H  HCH3  0   0.247  -3.4933   1.2741  -2.3597
 AO1  H142  H  HCH3  0   0.247  -2.1446   2.3979  -2.5308
 AO1  H143  H  HCH3  0   0.234  -1.8910   0.6586  -2.7484
 AO1  H15   H  HCR6  0   0.245  -0.7282  -1.0246  -0.2888
 AO1  H16   H  HCR6  0   0.256  -1.5238  -3.2113   0.4810
 AO1  H17   H  HCR6  0   0.255  -3.8970  -3.5421   1.0717
 AO1  H20   H  HCR6  0   0.256  -6.1502  -2.6535   1.3009
 AO1  H21   H  HCR6  0   0.259  -7.7483  -0.7912   1.1168
 AO1  H22   H  HCR6  0   0.260  -6.9676   1.4363   0.3449
 AO1  H23   H  HCR6  0   0.254  -4.6436   1.8002  -0.2396
 AO1  H24   H  HOH1  0   0.446   0.9112   2.1339   2.5900
 AO1  HN71  H  HNH2  0   0.360   2.4171   1.2921  -1.7443
 AO1  HN72  H  HNH2  0   0.375   2.0081  -0.2820  -1.6944

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
 AO1  C1   C2    single    1.519  0.020  1.519
 AO1  C1   H11A  single    0.970  0.020  1.090
 AO1  C1   H12   single    0.970  0.020  1.090
 AO1  C1   H13   single    0.970  0.020  1.090
 AO1  C2   S3    single    1.816  0.020  1.816
 AO1  C2   H21A  single    0.970  0.020  1.090
 AO1  C2   H22A  single    0.970  0.020  1.090
 AO1  S3   C4    single    1.814  0.020  1.814
 AO1  C4   C5    single    1.522  0.020  1.522
 AO1  C4   H41   single    0.970  0.020  1.090
 AO1  C4   H42   single    0.970  0.020  1.090
 AO1  C5   C6    single    1.532  0.020  1.532
 AO1  C5   H51   single    0.970  0.020  1.090
 AO1  C5   H52   single    0.970  0.020  1.090
 AO1  C6   C8    single    1.543  0.020  1.543
 AO1  C6   N7    single    1.460  0.020  1.460
 AO1  C6   H6    single    0.970  0.020  1.090
 AO1  C8   C9    single    1.536  0.020  1.536
 AO1  C8   O24   single    1.396  0.020  1.396
 AO1  C8   H8    single    0.970  0.020  1.090
 AO1  C9   N10   single    1.332  0.020  1.332
 AO1  C9   O13   double    1.227  0.020  1.227
 AO1  N10  C11   single    1.446  0.020  1.446
 AO1  N10  H10   single    0.860  0.020  1.020
 AO1  C11  C12   single    1.519  0.020  1.519
 AO1  C11  C14   single    1.527  0.020  1.527
 AO1  C11  H11   single    0.970  0.020  1.090
 AO1  C12  C15   aromatic  1.371  0.020  1.371
 AO1  C12  C19   aromatic  1.427  0.020  1.427
 AO1  C14  H141  single    0.970  0.020  1.090
 AO1  C14  H142  single    0.970  0.020  1.090
 AO1  C14  H143  single    0.970  0.020  1.090
 AO1  C15  C16   aromatic  1.409  0.020  1.409
 AO1  C15  H15   single    0.930  0.020  1.080
 AO1  C16  C17   aromatic  1.365  0.020  1.365
 AO1  C16  H16   single    0.930  0.020  1.080
 AO1  C17  C18   aromatic  1.414  0.020  1.414
 AO1  C17  H17   single    0.930  0.020  1.080
 AO1  C18  C19   aromatic  1.422  0.020  1.422
 AO1  C18  C20   aromatic  1.415  0.020  1.415
 AO1  C19  C23   aromatic  1.418  0.020  1.418
 AO1  C20  C21   aromatic  1.367  0.020  1.367
 AO1  C20  H20   single    0.930  0.020  1.080
 AO1  C21  C22   aromatic  1.409  0.020  1.409
 AO1  C21  H21   single    0.930  0.020  1.080
 AO1  C22  C23   aromatic  1.369  0.020  1.369
 AO1  C22  H22   single    0.930  0.020  1.080
 AO1  C23  H23   single    0.930  0.020  1.080
 AO1  O24  H24   single    0.850  0.020  0.980
 AO1  N7   HN71  single    0.890  0.020  1.040
 AO1  N7   HN72  single    0.890  0.020  1.040

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
 AO1  H13   C1   H12   107.80  3.000
 AO1  H13   C1   H11A  108.15  3.000
 AO1  H12   C1   H11A  107.84  3.000
 AO1  H13   C1   C2    111.51  3.000
 AO1  H12   C1   C2    109.95  3.000
 AO1  H11A  C1   C2    111.44  3.000
 AO1  H22A  C2   H21A  107.80  3.000
 AO1  H22A  C2   S3    109.06  3.000
 AO1  H21A  C2   S3    108.90  3.000
 AO1  H22A  C2   C1    110.51  3.000
 AO1  H21A  C2   C1    110.61  3.000
 AO1  S3    C2   C1    109.89  3.000
 AO1  C4    S3   C2    100.28  3.000
 AO1  H42   C4   H41   107.88  3.000
 AO1  H42   C4   C5    110.36  3.000
 AO1  H41   C4   C5    111.19  3.000
 AO1  H42   C4   S3    109.22  3.000
 AO1  H41   C4   S3    108.45  3.000
 AO1  C5    C4   S3    109.67  3.000
 AO1  H52   C5   H51   107.05  3.000
 AO1  H52   C5   C6    109.17  3.000
 AO1  H51   C5   C6    109.72  3.000
 AO1  H52   C5   C4    109.70  3.000
 AO1  H51   C5   C4    109.23  3.000
 AO1  C6    C5   C4    111.85  3.000
 AO1  H6    C6   N7    107.01  3.000
 AO1  H6    C6   C8    108.56  3.000
 AO1  N7    C6   C8    107.77  3.000
 AO1  H6    C6   C5    108.45  3.000
 AO1  N7    C6   C5    113.66  3.000
 AO1  C8    C6   C5    111.21  3.000
 AO1  H8    C8   O24   110.10  3.000
 AO1  H8    C8   C9    107.39  3.000
 AO1  O24   C8   C9    108.20  3.000
 AO1  H8    C8   C6    107.19  3.000
 AO1  O24   C8   C6    111.53  3.000
 AO1  C9    C8   C6    112.36  3.000
 AO1  O13   C9   N10   124.43  3.000
 AO1  O13   C9   C8    119.04  3.000
 AO1  N10   C9   C8    116.52  3.000
 AO1  H10   N10  C11   120.84  3.000
 AO1  H10   N10  C9    115.00  3.000
 AO1  C11   N10  C9    122.93  3.000
 AO1  H11   C11  C14   108.62  3.000
 AO1  H11   C11  C12   108.94  3.000
 AO1  C14   C11  C12   110.74  3.000
 AO1  H11   C11  N10   106.97  3.000
 AO1  C14   C11  N10   108.63  3.000
 AO1  C12   C11  N10   112.80  3.000
 AO1  C19   C12  C15   119.00  3.000
 AO1  C19   C12  C11   120.19  3.000
 AO1  C15   C12  C11   120.76  3.000
 AO1  H143  C14  H142  108.56  3.000
 AO1  H143  C14  H141  107.68  3.000
 AO1  H142  C14  H141  108.10  3.000
 AO1  H143  C14  C11   110.85  3.000
 AO1  H142  C14  C11   110.71  3.000
 AO1  H141  C14  C11   110.83  3.000
 AO1  H15   C15  C16   118.27  3.000
 AO1  H15   C15  C12   119.99  3.000
 AO1  C16   C15  C12   121.74  3.000
 AO1  H16   C16  C17   120.47  3.000
 AO1  H16   C16  C15   119.26  3.000
 AO1  C17   C16  C15   120.27  3.000
 AO1  H17   C17  C18   119.08  3.000
 AO1  H17   C17  C16   120.77  3.000
 AO1  C18   C17  C16   120.15  3.000
 AO1  C20   C18  C19   119.52  3.000
 AO1  C20   C18  C17   120.81  3.000
 AO1  C19   C18  C17   119.67  3.000
 AO1  C23   C19  C18   117.90  3.000
 AO1  C23   C19  C12   122.93  3.000
 AO1  C18   C19  C12   119.17  3.000
 AO1  H20   C20  C21   120.34  3.000
 AO1  H20   C20  C18   118.67  3.000
 AO1  C21   C20  C18   120.99  3.000
 AO1  H21   C21  C22   119.87  3.000
 AO1  H21   C21  C20   120.33  3.000
 AO1  C22   C21  C20   119.80  3.000
 AO1  H22   C22  C23   119.80  3.000
 AO1  H22   C22  C21   119.67  3.000
 AO1  C23   C22  C21   120.53  3.000
 AO1  H23   C23  C22   118.58  3.000
 AO1  H23   C23  C19   120.15  3.000
 AO1  C22   C23  C19   121.27  3.000
 AO1  H24   O24  C8    105.97  3.000
 AO1  HN72  N7   HN71  106.92  3.000
 AO1  HN72  N7   C6    111.04  3.000
 AO1  HN71  N7   C6    110.59  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
 AO1  CONST_01  C17   C16  C15  C12     0.00   0.0  0
 AO1  CONST_02  C17   C18  C19  C12     0.00   0.0  0
 AO1  CONST_03  C20   C18  C19  C12   180.00   0.0  0
 AO1  CONST_04  C22   C23  C19  C12   180.00   0.0  0
 AO1  CONST_05  C18   C19  C12  C15     0.00   0.0  0
 AO1  CONST_06  C23   C19  C12  C15   180.00   0.0  0
 AO1  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 AO1  CONST_08  C19   C12  C15  C16     0.00   0.0  0
 AO1  CONST_09  C19   C18  C17  C16     0.00   0.0  0
 AO1  CONST_10  C20   C18  C17  C16   180.00   0.0  0
 AO1  CONST_11  C23   C19  C18  C17   180.00   0.0  0
 AO1  CONST_12  C21   C20  C18  C17   180.00   0.0  0
 AO1  CONST_13  C22   C23  C19  C18     0.00   0.0  0
 AO1  CONST_14  C22   C21  C20  C18     0.00   0.0  0
 AO1  CONST_15  C21   C20  C18  C19     0.00   0.0  0
 AO1  CONST_16  C21   C22  C23  C19     0.00   0.0  0
 AO1  CONST_17  C23   C19  C18  C20     0.00   0.0  0
 AO1  CONST_18  C23   C22  C21  C20     0.00   0.0  0
 AO1  CONST_19  C16   C15  C12  C11   180.00   0.0  0
 AO1  CONST_20  C18   C19  C12  C11   180.00   0.0  0
 AO1  CONST_21  C23   C19  C12  C11     0.00   0.0  0
 AO1  CONST_22  H16   C16  C15  C12   180.00   0.0  0
 AO1  CONST_23  H23   C23  C19  C12     0.00   0.0  0
 AO1  CONST_24  H17   C17  C16  C15   180.00   0.0  0
 AO1  CONST_25  H15   C15  C16  C17   180.00   0.0  0
 AO1  CONST_26  H20   C20  C18  C17     0.00   0.0  0
 AO1  CONST_27  H21   C21  C20  C18   180.00   0.0  0
 AO1  CONST_28  H22   C22  C23  C19   180.00   0.0  0
 AO1  CONST_29  C11   N10  C9   C8    180.00   0.0  0
 AO1  CONST_30  O13   C9   N10  C11     0.00   0.0  0
 AO1  CONST_31  H10   N10  C9   C8      0.00   0.0  0
 AO1  Var_01    C5    C4   S3   C2   -176.29  30.0  3
 AO1  Var_02    C6    C5   C4   S3   -178.41  30.0  3
 AO1  Var_03    H11A  C1   C2   S3     60.94  30.0  3
 AO1  Var_04    H21A  C2   S3   C4     57.88  30.0  1

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
 AO1  chir_01  C6   C5   C8   N7   negativ
 AO1  chir_02  C8   O24  C6   C9   negativ
 AO1  chir_03  C11  N10  C12  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
 AO1  plan-1  C11  0.020
 AO1  plan-1  C12  0.020
 AO1  plan-1  C15  0.020
 AO1  plan-1  C16  0.020
 AO1  plan-1  C17  0.020
 AO1  plan-1  C18  0.020
 AO1  plan-1  C19  0.020
 AO1  plan-1  C20  0.020
 AO1  plan-1  C21  0.020
 AO1  plan-1  C22  0.020
 AO1  plan-1  C23  0.020
 AO1  plan-1  H15  0.020
 AO1  plan-1  H16  0.020
 AO1  plan-1  H17  0.020
 AO1  plan-1  H20  0.020
 AO1  plan-1  H21  0.020
 AO1  plan-1  H22  0.020
 AO1  plan-1  H23  0.020
 AO1  plan-2  C8   0.020
 AO1  plan-2  C9   0.020
 AO1  plan-2  N10  0.020
 AO1  plan-2  C11  0.020
 AO1  plan-2  O13  0.020
 AO1  plan-2  H10  0.020

