# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 00:40:22 2022
#   Inital geometry file: a 150 line input string
#   Ligand name: (2~{R})-~{N}-[(1~{R})-2-(~{tert}-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-~{N}-(4-~{tert}-butylphenyl)-2-oxidanyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C(=O)N([C@@H](C(=O)NC(C)(C)C)c1cccnc1)c2ccc(cc2)C(C)(C)C
#
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
 2XI  2XI  (2~{R})-~{N}-[(1~{R})-2-(~{tert}-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-~{N}-(4-~{tert}-butylphenyl)-2-oxidanyl-propanamide  ligand  63  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2XI
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
 2XI  C10  C  CR16  0  -0.318  -10.1887  -19.2431   3.7915
 2XI  N12  N  N     0  -0.402  -12.1567  -20.3414   4.5736
 2XI  C13  C  CR16  0  -0.088  -12.3837  -20.7624   3.3366
 2XI  C15  C  CR6   0   0.179  -13.6578  -22.5046   0.0870
 2XI  C17  C  CR16  0  -0.342  -16.0457  -22.7833   0.0494
 2XI  C20  C  CH3   0  -0.631  -17.5037  -21.8267  -3.0529
 2XI  C21  C  CH3   0  -0.632  -17.2388  -24.3188  -3.0193
 2XI  C22  C  CH3   0  -0.665  -18.5705  -23.1783  -1.2628
 2XI  C24  C  CR16  0  -0.218  -13.6401  -22.6244  -1.2966
 2XI  C26  C  CH1   0  -0.074  -12.1447  -24.7207   1.1019
 2XI  C01  C  CH3   0  -0.679  -12.5091  -18.3659  -3.0917
 2XI  C02  C  CT    0   0.096  -13.2889  -18.4981  -1.7852
 2XI  C03  C  CH3   0  -0.640  -13.3509  -17.1353  -1.0952
 2XI  C04  C  CH3   0  -0.646  -14.6954  -19.0141  -2.0890
 2XI  C06  C  C     0   0.553  -12.8736  -19.8974   0.2554
 2XI  C07  C  CH1   0  -0.269  -11.8785  -20.9128   0.8541
 2XI  C08  C  CR6   0   0.058  -11.5561  -20.4704   2.2584
 2XI  C09  C  CR16  0  -0.184  -10.4346  -19.6924   2.5034
 2XI  C11  C  CR16  0  -0.074  -11.0803  -19.5941   4.7924
 2XI  C16  C  CR16  0  -0.210  -14.8680  -22.5840   0.7562
 2XI  C18  C  CR6   0   0.201  -16.0519  -22.8927  -1.3400
 2XI  C19  C  CT    0  -0.171  -17.3322  -23.0570  -2.1511
 2XI  C23  C  CR16  0  -0.316  -14.8203  -22.8165  -1.9938
 2XI  C27  C  CH3   0  -0.685  -11.5684  -25.3547  -0.1600
 2XI  N05  N  NH1   0  -0.637  -12.5405  -19.4606  -0.9623
 2XI  N14  N  NT    0  -0.554  -12.4435  -22.2662   0.7977
 2XI  O28  O  OH1   0  -0.650  -11.7873  -25.4259   2.2614
 2XI  O29  O  O     0  -0.470  -10.5306  -23.0715   1.6746
 2XI  O30  O  O     0  -0.462  -13.8482  -19.5393   0.8943
 2XI  H1   H  HCR6  0   0.269   -9.3209  -18.6389   4.0176
 2XI  H2   H  HCR6  0   0.263  -13.2658  -21.3775   3.1979
 2XI  H3   H  HCR6  0   0.256  -16.9693  -22.8418   0.6083
 2XI  H4   H  HCH3  0   0.230  -17.5631  -20.9112  -2.4615
 2XI  H5   H  HCH3  0   0.229  -16.6776  -21.7156  -3.7573
 2XI  H6   H  HCH3  0   0.229  -18.4230  -21.9103  -3.6362
 2XI  H7   H  HCH3  0   0.228  -17.1222  -25.2123  -2.4037
 2XI  H8   H  HCH3  0   0.228  -18.1496  -24.4353  -3.6098
 2XI  H9   H  HCH3  0   0.230  -16.4002  -24.2772  -3.7146
 2XI  H10  H  HCH3  0   0.231  -18.5167  -24.0466  -0.6038
 2XI  H11  H  HCH3  0   0.230  -18.7240  -22.2908  -0.6466
 2XI  H12  H  HCH3  0   0.238  -19.4565  -23.2963  -1.8883
 2XI  H13  H  HCR6  0   0.266  -12.7011  -22.5605  -1.8327
 2XI  H14  H  HCH1  0   0.260  -13.2335  -24.7527   1.0545
 2XI  H15  H  HCH3  0   0.238  -11.4921  -18.0102  -2.9138
 2XI  H16  H  HCH3  0   0.239  -12.4523  -19.3205  -3.6188
 2XI  H17  H  HCH3  0   0.244  -13.0019  -17.6505  -3.7490
 2XI  H18  H  HCH3  0   0.238  -13.9058  -17.1783  -0.1598
 2XI  H19  H  HCH3  0   0.228  -12.3483  -16.7595  -0.8860
 2XI  H20  H  HCH3  0   0.228  -13.8494  -16.4165  -1.7471
 2XI  H21  H  HCH3  0   0.236  -15.3047  -19.0901  -1.1905
 2XI  H22  H  HCH3  0   0.228  -15.1947  -18.3286  -2.7752
 2XI  H23  H  HCH3  0   0.237  -14.6558  -19.9964  -2.5608
 2XI  H24  H  HCH1  0   0.290  -10.9505  -20.9001   0.2733
 2XI  H25  H  HCR6  0   0.268   -9.7549  -19.4441   1.6966
 2XI  H26  H  HCR6  0   0.261  -10.9185  -19.2625   5.8121
 2XI  H27  H  HCR6  0   0.266  -14.8956  -22.4944   1.8347
 2XI  H28  H  HCR6  0   0.256  -14.7697  -22.8954  -3.0727
 2XI  H29  H  HCH3  0   0.249  -11.8942  -26.3919  -0.2364
 2XI  H30  H  HCH3  0   0.238  -11.8976  -24.8343  -1.0591
 2XI  H31  H  HCH3  0   0.234  -10.4772  -25.3369  -0.1420
 2XI  H32  H  HNH1  0   0.409  -11.7097  -19.8505  -1.3799
 2XI  H33  H  HOH1  0   0.441  -10.8319  -25.3533   2.3729
 2XI  C25  C  C     0   0.517  -11.6417  -23.2797   1.2170

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
 2XI  C20  C19  single    1.535  0.020  1.535
 2XI  C21  C19  single    1.534  0.020  1.534
 2XI  C01  C02  single    1.527  0.020  1.527
 2XI  C19  C22  single    1.529  0.020  1.529
 2XI  C19  C18  single    1.525  0.020  1.525
 2XI  C23  C18  aromatic  1.396  0.020  1.396
 2XI  C23  C24  aromatic  1.384  0.020  1.384
 2XI  C18  C17  aromatic  1.394  0.020  1.394
 2XI  C02  C04  single    1.529  0.020  1.529
 2XI  C02  C03  single    1.529  0.020  1.529
 2XI  C02  N05  single    1.471  0.020  1.471
 2XI  C24  C15  aromatic  1.389  0.020  1.389
 2XI  N05  C06  single    1.336  0.020  1.336
 2XI  C17  C16  aromatic  1.388  0.020  1.388
 2XI  C15  C16  aromatic  1.385  0.020  1.385
 2XI  C15  N14  single    1.427  0.020  1.427
 2XI  C06  C07  single    1.543  0.020  1.543
 2XI  C06  O30  double    1.219  0.020  1.219
 2XI  C27  C26  single    1.525  0.020  1.525
 2XI  N14  C07  single    1.468  0.020  1.468
 2XI  N14  C25  single    1.359  0.020  1.359
 2XI  C07  C08  single    1.507  0.020  1.507
 2XI  C25  O29  double    1.219  0.020  1.219
 2XI  C25  C26  single    1.531  0.020  1.531
 2XI  C26  O28  single    1.403  0.020  1.403
 2XI  C08  C09  aromatic  1.387  0.020  1.387
 2XI  C08  C13  aromatic  1.390  0.020  1.390
 2XI  C09  C10  aromatic  1.386  0.020  1.386
 2XI  C13  N12  aromatic  1.326  0.020  1.326
 2XI  C10  C11  aromatic  1.386  0.020  1.386
 2XI  N12  C11  aromatic  1.328  0.020  1.328
 2XI  C10  H1   single    0.930  0.020  1.080
 2XI  C13  H2   single    0.930  0.020  1.080
 2XI  C17  H3   single    0.930  0.020  1.080
 2XI  C20  H4   single    0.970  0.020  1.090
 2XI  C20  H5   single    0.970  0.020  1.090
 2XI  C20  H6   single    0.970  0.020  1.090
 2XI  C21  H7   single    0.970  0.020  1.090
 2XI  C21  H8   single    0.970  0.020  1.090
 2XI  C21  H9   single    0.970  0.020  1.090
 2XI  C22  H10  single    0.970  0.020  1.090
 2XI  C22  H11  single    0.970  0.020  1.090
 2XI  C22  H12  single    0.970  0.020  1.090
 2XI  C24  H13  single    0.930  0.020  1.080
 2XI  C26  H14  single    0.970  0.020  1.090
 2XI  C01  H15  single    0.970  0.020  1.090
 2XI  C01  H16  single    0.970  0.020  1.090
 2XI  C01  H17  single    0.970  0.020  1.090
 2XI  C03  H18  single    0.970  0.020  1.090
 2XI  C03  H19  single    0.970  0.020  1.090
 2XI  C03  H20  single    0.970  0.020  1.090
 2XI  C04  H21  single    0.970  0.020  1.090
 2XI  C04  H22  single    0.970  0.020  1.090
 2XI  C04  H23  single    0.970  0.020  1.090
 2XI  C07  H24  single    0.970  0.020  1.090
 2XI  C09  H25  single    0.930  0.020  1.080
 2XI  C11  H26  single    0.930  0.020  1.080
 2XI  C16  H27  single    0.930  0.020  1.080
 2XI  C23  H28  single    0.930  0.020  1.080
 2XI  C27  H29  single    0.970  0.020  1.090
 2XI  C27  H30  single    0.970  0.020  1.090
 2XI  C27  H31  single    0.970  0.020  1.090
 2XI  N05  H32  single    0.860  0.020  1.020
 2XI  O28  H33  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
 2XI  H1   C10  C11  120.45  3.000
 2XI  H1   C10  C09  121.18  3.000
 2XI  C11  C10  C09  118.36  3.000
 2XI  C11  N12  C13  118.10  3.000
 2XI  H2   C13  C08  120.28  3.000
 2XI  H2   C13  N12  116.02  3.000
 2XI  C08  C13  N12  123.69  3.000
 2XI  N14  C15  C16  120.83  3.000
 2XI  N14  C15  C24  119.98  3.000
 2XI  C16  C15  C24  119.17  3.000
 2XI  H3   C17  C18  120.48  3.000
 2XI  H3   C17  C16  118.00  3.000
 2XI  C18  C17  C16  121.51  3.000
 2XI  H6   C20  H5   107.48  3.000
 2XI  H6   C20  H4   107.93  3.000
 2XI  H5   C20  H4   107.79  3.000
 2XI  H6   C20  C19  110.28  3.000
 2XI  H5   C20  C19  112.10  3.000
 2XI  H4   C20  C19  111.10  3.000
 2XI  H9   C21  H8   107.51  3.000
 2XI  H9   C21  H7   107.99  3.000
 2XI  H8   C21  H7   107.87  3.000
 2XI  H9   C21  C19  112.11  3.000
 2XI  H8   C21  C19  110.06  3.000
 2XI  H7   C21  C19  111.14  3.000
 2XI  H12  C22  H11  107.30  3.000
 2XI  H12  C22  H10  107.47  3.000
 2XI  H11  C22  H10  108.24  3.000
 2XI  H12  C22  C19  109.47  3.000
 2XI  H11  C22  C19  112.18  3.000
 2XI  H10  C22  C19  111.97  3.000
 2XI  H13  C24  C23  119.87  3.000
 2XI  H13  C24  C15  119.93  3.000
 2XI  C23  C24  C15  120.19  3.000
 2XI  H14  C26  O28  105.99  3.000
 2XI  H14  C26  C27  109.21  3.000
 2XI  O28  C26  C27  112.24  3.000
 2XI  H14  C26  C25  111.05  3.000
 2XI  O28  C26  C25  109.10  3.000
 2XI  C27  C26  C25  109.23  3.000
 2XI  H17  C01  H16  107.85  3.000
 2XI  H17  C01  H15  107.80  3.000
 2XI  H16  C01  H15  108.36  3.000
 2XI  H17  C01  C02  110.00  3.000
 2XI  H16  C01  C02  111.34  3.000
 2XI  H15  C01  C02  111.36  3.000
 2XI  N05  C02  C04  111.00  3.000
 2XI  N05  C02  C03  110.58  3.000
 2XI  C04  C02  C03  110.69  3.000
 2XI  N05  C02  C01  105.99  3.000
 2XI  C03  C02  C01  109.25  3.000
 2XI  C04  C02  C01  109.21  3.000
 2XI  H20  C03  H19  107.91  3.000
 2XI  H20  C03  H18  107.86  3.000
 2XI  H19  C03  H18  108.49  3.000
 2XI  H20  C03  C02  109.65  3.000
 2XI  H19  C03  C02  110.88  3.000
 2XI  H18  C03  C02  111.93  3.000
 2XI  H23  C04  H22  108.09  3.000
 2XI  H23  C04  H21  108.34  3.000
 2XI  H22  C04  H21  107.87  3.000
 2XI  H23  C04  C02  110.89  3.000
 2XI  H22  C04  C02  109.51  3.000
 2XI  H21  C04  C02  112.00  3.000
 2XI  O30  C06  N05  125.51  3.000
 2XI  O30  C06  C07  120.38  3.000
 2XI  N05  C06  C07  114.09  3.000
 2XI  H24  C07  N14  108.45  3.000
 2XI  H24  C07  C08  108.04  3.000
 2XI  N14  C07  C08  112.88  3.000
 2XI  H24  C07  C06  109.47  3.000
 2XI  C08  C07  C06  107.84  3.000
 2XI  N14  C07  C06  110.10  3.000
 2XI  C09  C08  C07  120.15  3.000
 2XI  C09  C08  C13  117.53  3.000
 2XI  C07  C08  C13  122.25  3.000
 2XI  H25  C09  C08  120.28  3.000
 2XI  H25  C09  C10  120.42  3.000
 2XI  C08  C09  C10  119.30  3.000
 2XI  H26  C11  N12  116.60  3.000
 2XI  H26  C11  C10  120.39  3.000
 2XI  N12  C11  C10  123.01  3.000
 2XI  H27  C16  C17  119.84  3.000
 2XI  H27  C16  C15  119.92  3.000
 2XI  C17  C16  C15  120.24  3.000
 2XI  C23  C18  C19  119.83  3.000
 2XI  C23  C18  C17  117.29  3.000
 2XI  C19  C18  C17  122.86  3.000
 2XI  C18  C19  C22  112.31  3.000
 2XI  C18  C19  C21  109.79  3.000
 2XI  C22  C19  C21  108.23  3.000
 2XI  C18  C19  C20  108.67  3.000
 2XI  C22  C19  C20  108.33  3.000
 2XI  C21  C19  C20  109.48  3.000
 2XI  H28  C23  C18  120.25  3.000
 2XI  H28  C23  C24  118.17  3.000
 2XI  C18  C23  C24  121.58  3.000
 2XI  H31  C27  H30  107.93  3.000
 2XI  H31  C27  H29  108.39  3.000
 2XI  H30  C27  H29  107.84  3.000
 2XI  H31  C27  C26  110.94  3.000
 2XI  H30  C27  C26  111.71  3.000
 2XI  H29  C27  C26  109.91  3.000
 2XI  H32  N05  C06  117.16  3.000
 2XI  H32  N05  C02  116.14  3.000
 2XI  C06  N05  C02  126.66  3.000
 2XI  C25  N14  C07  116.67  3.000
 2XI  C25  N14  C15  122.09  3.000
 2XI  C07  N14  C15  120.05  3.000
 2XI  H33  O28  C26  108.06  3.000
 2XI  O29  C25  N14  121.74  3.000
 2XI  O29  C25  C26  119.23  3.000
 2XI  N14  C25  C26  119.02  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
 2XI  CONST_01  C13  C08  C09  C10     0.00   0.0  0
 2XI  CONST_02  C13  N12  C11  C10     0.00   0.0  0
 2XI  CONST_03  C09  C08  C13  N12     0.00   0.0  0
 2XI  CONST_04  C09  C10  C11  N12     0.00   0.0  0
 2XI  CONST_05  C18  C23  C24  C15     0.00   0.0  0
 2XI  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 2XI  CONST_07  C24  C23  C18  C17     0.00   0.0  0
 2XI  CONST_08  C24  C15  C16  C17     0.00   0.0  0
 2XI  CONST_09  C11  C10  C09  C08     0.00   0.0  0
 2XI  CONST_10  C11  N12  C13  C08     0.00   0.0  0
 2XI  CONST_11  C23  C18  C17  C16     0.00   0.0  0
 2XI  CONST_12  C23  C24  C15  C16     0.00   0.0  0
 2XI  CONST_13  C07  C08  C09  C10   180.00   0.0  0
 2XI  CONST_14  C07  C08  C13  N12   180.00   0.0  0
 2XI  CONST_15  N14  C15  C16  C17   180.00   0.0  0
 2XI  CONST_16  C19  C18  C23  C24   180.00   0.0  0
 2XI  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 2XI  CONST_18  N14  C15  C24  C23   180.00   0.0  0
 2XI  CONST_19  H1   C10  C11  N12   180.00   0.0  0
 2XI  CONST_20  H25  C09  C08  C13   180.00   0.0  0
 2XI  CONST_21  H26  C11  N12  C13   180.00   0.0  0
 2XI  CONST_22  H28  C23  C24  C15   180.00   0.0  0
 2XI  CONST_23  H3   C17  C16  C15   180.00   0.0  0
 2XI  CONST_24  H27  C16  C15  C24   180.00   0.0  0
 2XI  CONST_25  H2   C13  C08  C09   180.00   0.0  0
 2XI  CONST_26  H13  C24  C15  C16   180.00   0.0  0
 2XI  CONST_31  O29  C25  N14  C15   180.00   0.0  0
 2XI  CONST_32  C26  C25  N14  C15     0.00   0.0  0
 2XI  CONST_33  C07  N14  C25  C26   180.00   0.0  0
 2XI  CONST_34  C07  C06  N05  C02   180.00   0.0  0
 2XI  CONST_35  O30  C06  N05  C02     0.00   0.0  0
 2XI  CONST_36  O29  C25  N14  C07     0.00   0.0  0
 2XI  CONST_37  H32  N05  C06  C07     0.00   0.0  0
 2XI  Var_01    C20  C19  C18  C17   116.06  30.0  3
 2XI  Var_02    H4   C20  C19  C18   -59.53  30.0  3
 2XI  Var_03    H7   C21  C19  C18    61.14  30.0  3
 2XI  Var_04    H10  C22  C19  C18   -60.77  30.0  3
 2XI  Var_05    C06  N05  C02  C01  -178.63  30.0  3
 2XI  Var_06    H21  C04  C02  C01  -177.86  30.0  3
 2XI  Var_07    H18  C03  C02  C01   179.56  30.0  3
 2XI  Var_08    H15  C01  C02  C03    59.50  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
 2XI  chir_01  C26  C27  C25  O28  positiv
 2XI  chir_02  C07  N14  C06  C08  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
 2XI  plan-1  C10  0.020
 2XI  plan-1  N12  0.020
 2XI  plan-1  C13  0.020
 2XI  plan-1  C07  0.020
 2XI  plan-1  C08  0.020
 2XI  plan-1  C09  0.020
 2XI  plan-1  C11  0.020
 2XI  plan-1  H1   0.020
 2XI  plan-1  H2   0.020
 2XI  plan-1  H25  0.020
 2XI  plan-1  H26  0.020
 2XI  plan-2  C15  0.020
 2XI  plan-2  C17  0.020
 2XI  plan-2  C24  0.020
 2XI  plan-2  C16  0.020
 2XI  plan-2  C18  0.020
 2XI  plan-2  C19  0.020
 2XI  plan-2  C23  0.020
 2XI  plan-2  N14  0.020
 2XI  plan-2  H3   0.020
 2XI  plan-2  H13  0.020
 2XI  plan-2  H27  0.020
 2XI  plan-2  H28  0.020
 2XI  plan-3  C02  0.020
 2XI  plan-3  C06  0.020
 2XI  plan-3  C07  0.020
 2XI  plan-3  N05  0.020
 2XI  plan-3  O30  0.020
 2XI  plan-3  H32  0.020
 2XI  plan-4  C15  0.020
 2XI  plan-4  C26  0.020
 2XI  plan-4  C07  0.020
 2XI  plan-4  N14  0.020
 2XI  plan-4  O29  0.020
 2XI  plan-4  C25  0.020

