# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:01:01 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-[4-(phenylethynyl)phenyl]piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](NC(=O)N1CC[C@H](CC1)c2ccc(cc2)C#Cc3ccccc3)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
 P76  P76  N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-[4-(phenylethynyl)phenyl]piperidine-1-carboxamide  ligand  58  31  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P76
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
 P76  N1    N  NH1   0  -0.702    4.3672  -0.1454  -0.3198
 P76  C2    C  CH1   0  -0.237    5.3233  -1.0115   0.3331
 P76  C3    C  C     0   0.517    6.6352  -0.2715   0.5662
 P76  O4    O  O     0  -0.467    7.2030   0.3239  -0.3316
 P76  N5    N  NH1   0  -0.366    7.1077  -0.3857   1.8175
 P76  O6    O  OH1   0  -0.540    8.2028   0.3304   2.1952
 P76  C7    C  C     0   0.746    3.7485   0.8345   0.4290
 P76  O8    O  O     0  -0.526    3.9063   0.8919   1.6419
 P76  N9    N  NT    0  -0.484    2.9736   1.7152  -0.2601
 P76  C10   C  CH2   0  -0.338    2.3984   1.4454  -1.5693
 P76  C11   C  CH2   0  -0.409    0.9669   0.9380  -1.4354
 P76  C12   C  CH1   0  -0.357    0.1084   1.9259  -0.6378
 P76  C13   C  CH2   0  -0.413    0.7791   2.2460   0.7044
 P76  C14   C  CH2   0  -0.324    2.2142   2.7072   0.4830
 P76  C15   C  CR6   0   0.197   -1.3063   1.4419  -0.4640
 P76  C16   C  CR16  0  -0.330   -2.3782   2.2003  -0.9282
 P76  C17   C  CR16  0  -0.276   -3.6855   1.7700  -0.7731
 P76  C18   C  CR6   0  -0.127   -3.9551   0.5523  -0.1434
 P76  C19   C  CR16  0  -0.278   -2.8835  -0.2141   0.3283
 P76  C20   C  CR16  0  -0.309   -1.5832   0.2291   0.1684
 P76  C21   C  CSP   0   0.141   -5.2939   0.0986   0.0120
 P76  C22   C  CSP   0   0.127   -6.4316  -0.2878   0.1392
 P76  C23   C  CR6   0  -0.112   -7.7706  -0.7451   0.2890
 P76  C24   C  CR16  0  -0.296   -8.0281  -2.0146   0.8176
 P76  C25   C  CR16  0  -0.247   -9.3332  -2.4563   0.9623
 P76  C26   C  CR16  0  -0.254  -10.3942  -1.6426   0.5841
 P76  C27   C  CR16  0  -0.247  -10.1452  -0.3805   0.0584
 P76  C28   C  CR16  0  -0.296   -8.8433   0.0692  -0.0905
 P76  C29   C  CH1   0   0.057    5.5415  -2.2501  -0.5523
 P76  C30   C  CH3   0  -0.691    6.5062  -3.2365   0.0750
 P76  O31   O  OH1   0  -0.665    4.3135  -2.9097  -0.7524
 P76  HN1   H  HNH1  0   0.399    4.6192   0.1020  -1.2663
 P76  H2    H  HCH1  0   0.278    4.8929  -1.3496   1.2787
 P76  HN5   H  HNH1  0   0.417    6.5201  -0.6877   2.5815
 P76  HO6   H  HOH1  0   0.480    8.9505  -0.2791   2.1510
 P76  H10   H  HCH2  0   0.251    2.4118   2.3758  -2.1440
 P76  H10A  H  HCH2  0   0.260    2.9944   0.7328  -2.1331
 P76  H11   H  HCH2  0   0.250    0.5414   0.7878  -2.4303
 P76  H11A  H  HCH2  0   0.229    0.9829  -0.0393  -0.9440
 P76  H12   H  HCH1  0   0.247    0.0726   2.8601  -1.2109
 P76  H13   H  HCH2  0   0.246    0.2207   3.0283   1.2237
 P76  H13A  H  HCH2  0   0.231    0.7761   1.3644   1.3522
 P76  H14   H  HCH2  0   0.266    2.7085   2.9213   1.4266
 P76  H14A  H  HCH2  0   0.244    2.2152   3.6333  -0.1006
 P76  H16   H  HCR6  0   0.255   -2.1870   3.1449  -1.4234
 P76  H17   H  HCR6  0   0.258   -4.5027   2.3763  -1.1419
 P76  H19   H  HCR6  0   0.259   -3.0772  -1.1583   0.8203
 P76  H20   H  HCR6  0   0.253   -0.7724  -0.3851   0.5424
 P76  H24   H  HCR6  0   0.260   -7.2021  -2.6493   1.1111
 P76  H25   H  HCR6  0   0.264   -9.5235  -3.4393   1.3725
 P76  H26   H  HCR6  0   0.264  -11.4121  -1.9908   0.6991
 P76  H27   H  HCR6  0   0.263  -10.9689   0.2568  -0.2358
 P76  H28   H  HCR6  0   0.261   -8.6491   1.0518  -0.5001
 P76  H29   H  HCH1  0   0.209    5.9602  -1.9110  -1.5120
 P76  H30   H  HCH3  0   0.233    6.1717  -3.5396   1.0685
 P76  H30A  H  HCH3  0   0.250    6.5897  -4.1283  -0.5460
 P76  H30B  H  HCH3  0   0.239    7.5052  -2.8121   0.1664
 P76  HO31  H  HOH1  0   0.446    3.6624  -2.2471  -1.0117

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
 P76  N1   C7    single    1.380  0.020  1.380
 P76  N1   C2    single    1.446  0.020  1.446
 P76  N1   HN1   single    0.890  0.020  1.040
 P76  C29  C2    single    1.538  0.020  1.538
 P76  C2   C3    single    1.524  0.020  1.524
 P76  C2   H2    single    0.970  0.020  1.090
 P76  O4   C3    double    1.218  0.020  1.218
 P76  C3   N5    single    1.342  0.020  1.342
 P76  N5   O6    single    1.362  0.020  1.362
 P76  N5   HN5   single    0.890  0.020  1.040
 P76  O6   HO6   single    0.850  0.020  0.980
 P76  N9   C7    single    1.361  0.020  1.361
 P76  C7   O8    double    1.225  0.020  1.225
 P76  C10  N9    single    1.455  0.020  1.455
 P76  N9   C14   single    1.454  0.020  1.454
 P76  C11  C10   single    1.525  0.020  1.525
 P76  C10  H10   single    0.970  0.020  1.090
 P76  C10  H10A  single    0.970  0.020  1.090
 P76  C11  C12   single    1.533  0.020  1.533
 P76  C11  H11   single    0.970  0.020  1.090
 P76  C11  H11A  single    0.970  0.020  1.090
 P76  C15  C12   single    1.505  0.020  1.505
 P76  C12  C13   single    1.534  0.020  1.534
 P76  C12  H12   single    0.970  0.020  1.090
 P76  C13  C14   single    1.524  0.020  1.524
 P76  C13  H13   single    0.970  0.020  1.090
 P76  C13  H13A  single    0.970  0.020  1.090
 P76  C14  H14   single    0.970  0.020  1.090
 P76  C14  H14A  single    0.970  0.020  1.090
 P76  C20  C15   aromatic  1.396  0.020  1.396
 P76  C16  C15   aromatic  1.393  0.020  1.393
 P76  C17  C16   aromatic  1.385  0.020  1.385
 P76  C16  H16   single    0.930  0.020  1.080
 P76  C18  C17   aromatic  1.397  0.020  1.397
 P76  C17  H17   single    0.930  0.020  1.080
 P76  C21  C18   single    1.422  0.020  1.422
 P76  C19  C18   aromatic  1.399  0.020  1.399
 P76  C19  C20   aromatic  1.383  0.020  1.383
 P76  C19  H19   single    0.930  0.020  1.080
 P76  C20  H20   single    0.930  0.020  1.080
 P76  C22  C21   triple    1.208  0.020  1.208
 P76  C23  C22   single    1.423  0.020  1.423
 P76  C28  C23   aromatic  1.399  0.020  1.399
 P76  C24  C23   aromatic  1.399  0.020  1.399
 P76  C25  C24   aromatic  1.385  0.020  1.385
 P76  C24  H24   single    0.930  0.020  1.080
 P76  C26  C25   aromatic  1.390  0.020  1.390
 P76  C25  H25   single    0.930  0.020  1.080
 P76  C26  C27   aromatic  1.390  0.020  1.390
 P76  C26  H26   single    0.930  0.020  1.080
 P76  C27  C28   aromatic  1.385  0.020  1.385
 P76  C27  H27   single    0.930  0.020  1.080
 P76  C28  H28   single    0.930  0.020  1.080
 P76  C30  C29   single    1.516  0.020  1.516
 P76  C29  O31   single    1.408  0.020  1.408
 P76  C29  H29   single    0.970  0.020  1.090
 P76  C30  H30   single    0.970  0.020  1.090
 P76  C30  H30A  single    0.970  0.020  1.090
 P76  C30  H30B  single    0.970  0.020  1.090
 P76  O31  HO31  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
 P76  HN1   N1   C7    116.51  3.000
 P76  HN1   N1   C2    113.88  3.000
 P76  C7    N1   C2    118.48  3.000
 P76  H2    C2   C29   107.75  3.000
 P76  H2    C2   C3    110.92  3.000
 P76  C29   C2   C3    110.91  3.000
 P76  H2    C2   N1    108.40  3.000
 P76  C3    C2   N1    110.33  3.000
 P76  C29   C2   N1    108.44  3.000
 P76  N5    C3   O4    124.38  3.000
 P76  N5    C3   C2    113.84  3.000
 P76  O4    C3   C2    121.73  3.000
 P76  HN5   N5   O6    114.54  3.000
 P76  HN5   N5   C3    121.72  3.000
 P76  O6    N5   C3    119.79  3.000
 P76  HO6   O6   N5    106.14  3.000
 P76  N9    C7   O8    123.01  3.000
 P76  O8    C7   N1    120.87  3.000
 P76  N9    C7   N1    116.12  3.000
 P76  C14   N9   C10   112.33  3.000
 P76  C14   N9   C7    118.71  3.000
 P76  C10   N9   C7    124.11  3.000
 P76  H10A  C10  H10   106.17  3.000
 P76  H10A  C10  C11   110.02  3.000
 P76  H10   C10  C11   109.92  3.000
 P76  H10A  C10  N9    111.81  3.000
 P76  H10   C10  N9    108.07  3.000
 P76  C11   C10  N9    110.72  3.000
 P76  H11A  C11  H11   106.97  3.000
 P76  H11A  C11  C12   110.50  3.000
 P76  H11   C11  C12   110.14  3.000
 P76  H11A  C11  C10   108.85  3.000
 P76  H11   C11  C10   109.36  3.000
 P76  C12   C11  C10   110.93  3.000
 P76  H12   C12  C15   107.67  3.000
 P76  H12   C12  C13   107.08  3.000
 P76  C15   C12  C13   112.14  3.000
 P76  H12   C12  C11   107.18  3.000
 P76  C13   C12  C11   110.17  3.000
 P76  C15   C12  C11   112.29  3.000
 P76  H13A  C13  H13   107.11  3.000
 P76  H13A  C13  C14   109.43  3.000
 P76  H13   C13  C14   109.50  3.000
 P76  H13A  C13  C12   110.41  3.000
 P76  H13   C13  C12   109.99  3.000
 P76  C14   C13  C12   110.35  3.000
 P76  H14A  C14  H14   107.21  3.000
 P76  H14A  C14  C13   109.54  3.000
 P76  H14   C14  C13   111.22  3.000
 P76  H14A  C14  N9    107.72  3.000
 P76  H14   C14  N9    109.92  3.000
 P76  C13   C14  N9    111.09  3.000
 P76  C20   C15  C16   118.14  3.000
 P76  C16   C15  C12   120.65  3.000
 P76  C20   C15  C12   121.21  3.000
 P76  H16   C16  C17   119.24  3.000
 P76  H16   C16  C15   119.42  3.000
 P76  C17   C16  C15   121.33  3.000
 P76  H17   C17  C18   119.74  3.000
 P76  H17   C17  C16   120.03  3.000
 P76  C18   C17  C16   120.23  3.000
 P76  C21   C18  C19   120.62  3.000
 P76  C19   C18  C17   118.78  3.000
 P76  C21   C18  C17   120.60  3.000
 P76  H19   C19  C20   120.03  3.000
 P76  H19   C19  C18   119.60  3.000
 P76  C20   C19  C18   120.36  3.000
 P76  H20   C20  C19   118.81  3.000
 P76  H20   C20  C15   120.03  3.000
 P76  C19   C20  C15   121.16  3.000
 P76  C22   C21  C18   180.00  3.000
 P76  C23   C22  C21   180.00  3.000
 P76  C28   C23  C24   119.30  3.000
 P76  C24   C23  C22   120.31  3.000
 P76  C28   C23  C22   120.39  3.000
 P76  H24   C24  C25   120.24  3.000
 P76  H24   C24  C23   119.61  3.000
 P76  C25   C24  C23   120.15  3.000
 P76  H25   C25  C26   120.06  3.000
 P76  H25   C25  C24   119.67  3.000
 P76  C26   C25  C24   120.27  3.000
 P76  H26   C26  C27   120.07  3.000
 P76  H26   C26  C25   120.06  3.000
 P76  C27   C26  C25   119.87  3.000
 P76  H27   C27  C28   119.66  3.000
 P76  H27   C27  C26   120.09  3.000
 P76  C28   C27  C26   120.25  3.000
 P76  H28   C28  C27   120.27  3.000
 P76  H28   C28  C23   119.57  3.000
 P76  C27   C28  C23   120.16  3.000
 P76  H29   C29  O31   110.62  3.000
 P76  H29   C29  C30   108.62  3.000
 P76  O31   C29  C30   108.00  3.000
 P76  H29   C29  C2    107.93  3.000
 P76  O31   C29  C2    109.59  3.000
 P76  C30   C29  C2    112.09  3.000
 P76  H30B  C30  H30A  107.24  3.000
 P76  H30B  C30  H30   108.23  3.000
 P76  H30A  C30  H30   108.36  3.000
 P76  H30B  C30  C29   111.40  3.000
 P76  H30A  C30  C29   110.21  3.000
 P76  H30   C30  C29   111.25  3.000
 P76  HO31  O31  C29   107.77  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
 P76  CONST_01  C18  C19  C20  C15    0.00   0.0  0
 P76  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 P76  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 P76  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 P76  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 P76  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 P76  CONST_07  C26  C27  C28  C23    0.00   0.0  0
 P76  CONST_08  C26  C25  C24  C23    0.00   0.0  0
 P76  CONST_09  C27  C28  C23  C24    0.00   0.0  0
 P76  CONST_10  C27  C26  C25  C24    0.00   0.0  0
 P76  CONST_11  C28  C23  C24  C25    0.00   0.0  0
 P76  CONST_12  C28  C27  C26  C25    0.00   0.0  0
 P76  CONST_13  C19  C20  C15  C12  180.00   0.0  0
 P76  CONST_14  C17  C16  C15  C12  180.00   0.0  0
 P76  CONST_15  C21  C18  C17  C16  180.00   0.0  0
 P76  CONST_16  C21  C18  C19  C20  180.00   0.0  0
 P76  CONST_17  C27  C28  C23  C22  180.00   0.0  0
 P76  CONST_18  C25  C24  C23  C22  180.00   0.0  0
 P76  CONST_19  H20  C20  C15  C12    0.00   0.0  0
 P76  CONST_20  H16  C16  C15  C12    0.00   0.0  0
 P76  CONST_21  H19  C19  C20  C15  180.00   0.0  0
 P76  CONST_22  H17  C17  C16  C15  180.00   0.0  0
 P76  CONST_23  H27  C27  C28  C23  180.00   0.0  0
 P76  CONST_24  H25  C25  C24  C23  180.00   0.0  0
 P76  CONST_25  H28  C28  C23  C24  180.00   0.0  0
 P76  CONST_26  H26  C26  C25  C24  180.00   0.0  0
 P76  CONST_27  H24  C24  C25  C26  180.00   0.0  0
 P76  CONST_29  C14  N9   C7   O8     0.00   0.0  0
 P76  CONST_31  C14  N9   C7   N1   180.00   0.0  0
 P76  CONST_32  N9   C7   N1   C2   180.00   0.0  0
 P76  CONST_34  O8   C7   N1   C2     0.00   0.0  0
 P76  CONST_35  O6   N5   C3   C2   180.00   0.0  0
 P76  CONST_36  O6   N5   C3   O4     0.00   0.0  0
 P76  Var_01    C12  C11  C10  N9    55.67  30.0  1
 P76  Var_02    C12  C13  C14  N9   -56.22  30.0  1
 P76  Var_03    C13  C14  N9   C10   59.78  30.0  1
 P76  Var_04    C14  N9   C10  C11  -59.22  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
 P76  chir_01  C2   N1   C29  C3   negativ
 P76  chir_02  C12  C11  C15  C13  negativ
 P76  chir_03  C29  C2   C30  O31  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
 P76  plan-1  C12  0.020
 P76  plan-1  C15  0.020
 P76  plan-1  C16  0.020
 P76  plan-1  C17  0.020
 P76  plan-1  C18  0.020
 P76  plan-1  C19  0.020
 P76  plan-1  C20  0.020
 P76  plan-1  C21  0.020
 P76  plan-1  C22  0.020
 P76  plan-1  H16  0.020
 P76  plan-1  H17  0.020
 P76  plan-1  H19  0.020
 P76  plan-1  H20  0.020
 P76  plan-2  C21  0.020
 P76  plan-2  C22  0.020
 P76  plan-2  C23  0.020
 P76  plan-2  C24  0.020
 P76  plan-2  C25  0.020
 P76  plan-2  C26  0.020
 P76  plan-2  C27  0.020
 P76  plan-2  C28  0.020
 P76  plan-2  H24  0.020
 P76  plan-2  H25  0.020
 P76  plan-2  H26  0.020
 P76  plan-2  H27  0.020
 P76  plan-2  H28  0.020
 P76  plan-3  N1   0.020
 P76  plan-3  C2   0.020
 P76  plan-3  C7   0.020
 P76  plan-3  O8   0.020
 P76  plan-3  N9   0.020
 P76  plan-3  C10  0.020
 P76  plan-3  C14  0.020
 P76  plan-3  HN1  0.020
 P76  plan-4  C2   0.020
 P76  plan-4  C3   0.020
 P76  plan-4  O4   0.020
 P76  plan-4  N5   0.020
 P76  plan-4  O6   0.020
 P76  plan-4  HN5  0.020

