# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:02:52 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[(but-2-yn-1-yl)oxy]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CCOc1ccc(cc1)C(=O)N[C@H](C(=O)NO)C(C)(C)N
#
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
 7TD  7TD  N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[(but-2-yn-1-yl)oxy]benzamide  ligand  44  23  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7TD
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
 7TD  C1   C  CH1   0  -0.193   3.1637   0.2428  -0.1761
 7TD  C2   C  C     0   0.498   3.5719  -1.2422  -0.2581
 7TD  C3   C  CT    0   0.053   3.9071   1.0352   0.9417
 7TD  O1   O  O     0  -0.464   2.7536  -2.1425  -0.2054
 7TD  O2   O  O2    0  -0.465  -4.6195   0.1380  -0.2763
 7TD  O3   O  O     0  -0.487   1.3138   1.7289  -1.7347
 7TD  C11  C  CR6   0  -0.061  -0.5361   0.6864  -0.6846
 7TD  C12  C  CR16  0  -0.255  -1.4555   1.6825  -1.0189
 7TD  C13  C  CR16  0  -0.332  -2.8100   1.4764  -0.8666
 7TD  C15  C  CSP   0  -0.001  -7.7956  -0.8629   0.3578
 7TD  C16  C  CH3   0  -0.820  -9.2426  -0.7518   0.4368
 7TD  C4   C  CH3   0  -0.642   3.3119   2.4383   1.0614
 7TD  C5   C  CH3   0  -0.663   3.7924   0.3151   2.2825
 7TD  N1   N  NH2   0  -0.800   5.3204   1.0874   0.5576
 7TD  C6   C  CSP   0   0.132  -6.5983  -0.9472   0.2894
 7TD  C7   C  CH2   0  -0.394  -5.1521  -1.0821   0.2178
 7TD  C8   C  CR6   0   0.394  -3.2845   0.2490  -0.3943
 7TD  C9   C  CR16  0  -0.366  -2.3801  -0.7642  -0.0864
 7TD  C10  C  CR16  0  -0.275  -1.0189  -0.5355  -0.2304
 7TD  N2   N  NH1   0  -0.640   1.7380   0.2980  -0.0325
 7TD  N3   N  NH1   0  -0.387   4.8915  -1.4184  -0.4480
 7TD  O4   O  OH1   0  -0.553   5.3997  -2.6858  -0.3352
 7TD  H1   H  HCH1  0   0.296   3.4181   0.7138  -1.1299
 7TD  H2   H  HCR6  0   0.263  -1.1045   2.6357  -1.3913
 7TD  H3   H  HCR6  0   0.271  -3.5145   2.2609  -1.1127
 7TD  H4   H  HCH3  0   0.270  -9.6090  -1.0914   1.4054
 7TD  H5   H  HCH3  0   0.272  -9.5565   0.2840   0.3056
 7TD  H6   H  HCH3  0   0.269  -9.7264  -1.3485  -0.3364
 7TD  H7   H  HCH3  0   0.237   3.8828   3.0102   1.7953
 7TD  H8   H  HCH3  0   0.231   3.3584   2.9740   0.1113
 7TD  H9   H  HCH3  0   0.230   2.2735   2.4218   1.3904
 7TD  H10  H  HCH3  0   0.240   4.2640  -0.6683   2.2622
 7TD  H11  H  HCH3  0   0.246   4.2783   0.8962   3.0682
 7TD  H12  H  HCH3  0   0.236   2.7495   0.1891   2.5748
 7TD  H13  H  HNH2  0   0.363   5.4566   1.7631  -0.1866
 7TD  H14  H  HNH2  0   0.368   5.8820   1.4076   1.3380
 7TD  H16  H  HCH2  0   0.267  -4.8871  -1.9163  -0.4412
 7TD  H17  H  HCH2  0   0.267  -4.7479  -1.3083   1.2110
 7TD  H18  H  HCR6  0   0.294  -2.7073  -1.7350   0.2576
 7TD  H19  H  HCR6  0   0.261  -0.3405  -1.3514  -0.0109
 7TD  H20  H  HNH1  0   0.404   1.3261  -0.3016   0.6640
 7TD  H21  H  HNH1  0   0.423   5.5102  -0.6498  -0.1526
 7TD  H22  H  HOH1  0   0.475   5.5587  -2.9844  -1.2387
 7TD  C14  C  C     0   0.538   0.9167   0.9532  -0.8760

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
 7TD  C4   C3   single    1.529  0.020  1.529
 7TD  N1   C3   single    1.466  0.020  1.466
 7TD  C16  C15  single    1.453  0.020  1.453
 7TD  C15  C6   triple    1.202  0.020  1.202
 7TD  C3   C5   single    1.526  0.020  1.526
 7TD  C3   C1   single    1.559  0.020  1.559
 7TD  C6   C7   single    1.454  0.020  1.454
 7TD  C7   O2   single    1.420  0.020  1.420
 7TD  O2   C8   single    1.345  0.020  1.345
 7TD  C9   C8   aromatic  1.393  0.020  1.393
 7TD  C9   C10  aromatic  1.388  0.020  1.388
 7TD  C8   C13  aromatic  1.398  0.020  1.398
 7TD  C10  C11  aromatic  1.390  0.020  1.390
 7TD  C13  C12  aromatic  1.379  0.020  1.379
 7TD  C11  C12  aromatic  1.396  0.020  1.396
 7TD  C11  C14  single    1.490  0.020  1.490
 7TD  N2   C14  single    1.347  0.020  1.347
 7TD  N2   C1   single    1.434  0.020  1.434
 7TD  C14  O3   double    1.223  0.020  1.223
 7TD  C1   C2   single    1.542  0.020  1.542
 7TD  O1   C2   double    1.218  0.020  1.218
 7TD  C2   N3   single    1.345  0.020  1.345
 7TD  N3   O4   single    1.370  0.020  1.370
 7TD  C1   H1   single    0.970  0.020  1.090
 7TD  C12  H2   single    0.930  0.020  1.080
 7TD  C13  H3   single    0.930  0.020  1.080
 7TD  C16  H4   single    0.970  0.020  1.090
 7TD  C16  H5   single    0.970  0.020  1.090
 7TD  C16  H6   single    0.970  0.020  1.090
 7TD  C4   H7   single    0.970  0.020  1.090
 7TD  C4   H8   single    0.970  0.020  1.090
 7TD  C4   H9   single    0.970  0.020  1.090
 7TD  C5   H10  single    0.970  0.020  1.090
 7TD  C5   H11  single    0.970  0.020  1.090
 7TD  C5   H12  single    0.970  0.020  1.090
 7TD  N1   H13  single    0.890  0.020  1.040
 7TD  N1   H14  single    0.890  0.020  1.040
 7TD  C7   H16  single    0.970  0.020  1.090
 7TD  C7   H17  single    0.970  0.020  1.090
 7TD  C9   H18  single    0.930  0.020  1.080
 7TD  C10  H19  single    0.930  0.020  1.080
 7TD  N2   H20  single    0.860  0.020  1.020
 7TD  N3   H21  single    0.890  0.020  1.040
 7TD  O4   H22  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
 7TD  H1   C1   N2   107.57  3.000
 7TD  H1   C1   C3   107.19  3.000
 7TD  N2   C1   C3   112.50  3.000
 7TD  H1   C1   C2   107.86  3.000
 7TD  N2   C1   C2   107.79  3.000
 7TD  C3   C1   C2   113.66  3.000
 7TD  N3   C2   O1   124.65  3.000
 7TD  N3   C2   C1   113.17  3.000
 7TD  O1   C2   C1   122.12  3.000
 7TD  N1   C3   C5   108.63  3.000
 7TD  C5   C3   C4   109.57  3.000
 7TD  N1   C3   C4   111.30  3.000
 7TD  C5   C3   C1   110.75  3.000
 7TD  N1   C3   C1   106.86  3.000
 7TD  C4   C3   C1   109.70  3.000
 7TD  C8   O2   C7   118.28  3.000
 7TD  C10  C11  C14  122.56  3.000
 7TD  C14  C11  C12  118.93  3.000
 7TD  C10  C11  C12  118.47  3.000
 7TD  H2   C12  C13  119.24  3.000
 7TD  H2   C12  C11  119.83  3.000
 7TD  C13  C12  C11  120.93  3.000
 7TD  H3   C13  C8   119.48  3.000
 7TD  H3   C13  C12  120.39  3.000
 7TD  C8   C13  C12  120.13  3.000
 7TD  C6   C15  C16  180.00  3.000
 7TD  H6   C16  H5   107.87  3.000
 7TD  H6   C16  H4   108.10  3.000
 7TD  H5   C16  H4   107.83  3.000
 7TD  H6   C16  C15  111.20  3.000
 7TD  H5   C16  C15  110.65  3.000
 7TD  H4   C16  C15  111.05  3.000
 7TD  H9   C4   H8   108.11  3.000
 7TD  H9   C4   H7   107.66  3.000
 7TD  H8   C4   H7   107.81  3.000
 7TD  H9   C4   C3   112.38  3.000
 7TD  H8   C4   C3   111.45  3.000
 7TD  H7   C4   C3   109.26  3.000
 7TD  H12  C5   H11  107.12  3.000
 7TD  H12  C5   H10  108.32  3.000
 7TD  H11  C5   H10  107.51  3.000
 7TD  H12  C5   C3   111.22  3.000
 7TD  H11  C5   C3   110.36  3.000
 7TD  H10  C5   C3   112.12  3.000
 7TD  H14  N1   H13  106.27  3.000
 7TD  H14  N1   C3   110.11  3.000
 7TD  H13  N1   C3   110.22  3.000
 7TD  C7   C6   C15  180.00  3.000
 7TD  H17  C7   H16  107.37  3.000
 7TD  H17  C7   C6   109.96  3.000
 7TD  H16  C7   C6   109.92  3.000
 7TD  H17  C7   O2   110.76  3.000
 7TD  H16  C7   O2   110.74  3.000
 7TD  C6   C7   O2   108.09  3.000
 7TD  C9   C8   C13  119.54  3.000
 7TD  C13  C8   O2   116.04  3.000
 7TD  C9   C8   O2   124.42  3.000
 7TD  H18  C9   C10  118.56  3.000
 7TD  H18  C9   C8   121.82  3.000
 7TD  C10  C9   C8   119.62  3.000
 7TD  H19  C10  C9   117.97  3.000
 7TD  H19  C10  C11  120.70  3.000
 7TD  C9   C10  C11  121.29  3.000
 7TD  H20  N2   C14  118.24  3.000
 7TD  H20  N2   C1   116.94  3.000
 7TD  C14  N2   C1   124.20  3.000
 7TD  H21  N3   O4   116.35  3.000
 7TD  H21  N3   C2   116.82  3.000
 7TD  O4   N3   C2   118.27  3.000
 7TD  H22  O4   N3   105.68  3.000
 7TD  N2   C14  C11  115.28  3.000
 7TD  N2   C14  O3   123.36  3.000
 7TD  C11  C14  O3   121.36  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
 7TD  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 7TD  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 7TD  CONST_03  C9   C8   C13  C12     0.00   0.0  0
 7TD  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 7TD  CONST_05  C10  C9   C8   C13     0.00   0.0  0
 7TD  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 7TD  CONST_07  C10  C9   C8   O2    180.00   0.0  0
 7TD  CONST_08  C12  C13  C8   O2    180.00   0.0  0
 7TD  CONST_09  C14  C11  C12  C13   180.00   0.0  0
 7TD  CONST_10  C9   C10  C11  C14   180.00   0.0  0
 7TD  CONST_11  H18  C9   C10  C11   180.00   0.0  0
 7TD  CONST_12  H3   C13  C12  C11   180.00   0.0  0
 7TD  CONST_13  H19  C10  C11  C12   180.00   0.0  0
 7TD  CONST_14  H2   C12  C13  C8    180.00   0.0  0
 7TD  CONST_15  C11  C14  N2   C1    180.00   0.0  0
 7TD  CONST_16  H20  N2   C14  C11     0.00   0.0  0
 7TD  CONST_17  O3   C14  N2   C1      0.00   0.0  0
 7TD  CONST_18  O4   N3   C2   C1    180.00   0.0  0
 7TD  CONST_19  O4   N3   C2   O1      0.00   0.0  0
 7TD  Var_01    C10  C11  C14  O3    149.37  30.0  2
 7TD  Var_02    C9   C8   O2   C7      1.21  30.0  2
 7TD  Var_03    H16  C7   O2   C8    -61.11  30.0  1
 7TD  Var_04    H7   C4   C3   C1   -176.01  30.0  3
 7TD  Var_05    H13  N1   C3   C1     75.58  30.0  3
 7TD  Var_06    H10  C5   C3   C1     62.59  30.0  3
 7TD  Var_07    H4   C16  C15  C6   -133.87  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
 7TD  chir_01  C1  C3  N2  C2  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
 7TD  plan-1  O2   0.020
 7TD  plan-1  C11  0.020
 7TD  plan-1  C12  0.020
 7TD  plan-1  C13  0.020
 7TD  plan-1  C8   0.020
 7TD  plan-1  C9   0.020
 7TD  plan-1  C10  0.020
 7TD  plan-1  H2   0.020
 7TD  plan-1  H3   0.020
 7TD  plan-1  H18  0.020
 7TD  plan-1  H19  0.020
 7TD  plan-1  C14  0.020
 7TD  plan-2  C1   0.020
 7TD  plan-2  C2   0.020
 7TD  plan-2  O1   0.020
 7TD  plan-2  N3   0.020
 7TD  plan-2  O4   0.020
 7TD  plan-2  H21  0.020
 7TD  plan-3  C1   0.020
 7TD  plan-3  O3   0.020
 7TD  plan-3  C11  0.020
 7TD  plan-3  N2   0.020
 7TD  plan-3  H20  0.020
 7TD  plan-3  C14  0.020

