# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:52:20 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: N~2~-{[(5-ethyl-1,3-dioxan-5-yl)oxy]carbonyl}-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1(COCOC1)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
#
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
 QZD  QZD  N~2~-{[(5-ethyl-1,3-dioxan-5-yl)oxy]carbonyl}-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide  ligand  65  30  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QZD
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
 QZD  C12  C  CH2   0  -0.422  -16.3627   -7.8852  -10.0326
 QZD  C14  C  CR5   0   0.569  -18.2813   -9.5137   -9.7963
 QZD  N15  N  NR15  0  -0.627  -18.7424  -10.4723  -10.6163
 QZD  C16  C  CH2   0  -0.263  -17.7348  -11.0836  -11.4544
 QZD  C02  C  C     0   0.766  -13.4639  -12.2252   -8.6685
 QZD  C04  C  CH1   0  -0.208  -12.5089  -10.0278   -8.4200
 QZD  C05  C  CH2   0  -0.441  -11.1385   -9.3617   -8.3058
 QZD  C06  C  CH1   0  -0.234  -10.2616   -9.8680   -7.1575
 QZD  C07  C  CH3   0  -0.651   -8.9431   -9.1010   -7.1546
 QZD  C08  C  CH3   0  -0.665  -10.9576   -9.7529   -5.8062
 QZD  C09  C  C     0   0.571  -13.2515   -9.4369   -9.6228
 QZD  C11  C  CH1   0  -0.138  -14.8696   -7.6964  -10.2993
 QZD  C13  C  CR15  0  -0.422  -16.7971   -9.3412  -10.0776
 QZD  C17  C  CH2   0  -0.474  -16.6084  -10.0479  -11.4207
 QZD  C19  C  CH2   0  -0.128  -14.4508   -6.2298  -10.2715
 QZD  C23  C  CT    0   0.185  -14.0976  -14.4720   -9.4018
 QZD  C24  C  CH2   0  -0.432  -13.2388  -15.6568   -9.8547
 QZD  C25  C  CH3   0  -0.685  -12.4112  -16.3236   -8.7637
 QZD  C26  C  CH2   0  -0.229  -15.0197  -14.8399   -8.2307
 QZD  C28  C  CH2   0   0.043  -16.7386  -15.2530   -9.7240
 QZD  C30  C  CH2   0  -0.230  -14.9791  -13.9952  -10.5691
 QZD  N03  N  NH1   0  -0.655  -12.3628  -11.4515   -8.5807
 QZD  N10  N  NH1   0  -0.635  -14.0773   -8.4217   -9.3281
 QZD  O01  O  O     0  -0.501  -14.5837  -11.8312   -8.4165
 QZD  O20  O  OH1   0  -0.668  -15.1537   -5.5396  -11.2759
 QZD  O21  O  O     0  -0.488  -13.0489   -9.8568  -10.7508
 QZD  O22  O  O2    0  -0.506  -13.1376  -13.4675   -9.0391
 QZD  O27  O  O2    0  -0.481  -15.9719  -15.7825   -8.6855
 QZD  O29  O  O2    0  -0.479  -15.9625  -14.9711  -10.8500
 QZD  H1   H  HCH2  0   0.233  -16.6117   -7.4594   -9.0554
 QZD  H2   H  HCH2  0   0.245  -16.9255   -7.3152  -10.7756
 QZD  H3   H  HNR5  0   0.396  -19.6780  -10.8395  -10.5369
 QZD  H4   H  HCH2  0   0.253  -18.1132  -11.2633  -12.4601
 QZD  H5   H  HCH2  0   0.225  -17.4150  -12.0473  -11.0448
 QZD  H6   H  HCH1  0   0.271  -13.0771   -9.8286   -7.5077
 QZD  H7   H  HCH2  0   0.246  -10.6008   -9.4849   -9.2516
 QZD  H8   H  HCH2  0   0.245  -11.3005   -8.2864   -8.1808
 QZD  H9   H  HCH1  0   0.223  -10.0315  -10.9245   -7.3331
 QZD  H10  H  HCH3  0   0.229   -8.2709   -9.4809   -6.3838
 QZD  H11  H  HCH3  0   0.227   -8.4275   -9.1831   -8.1131
 QZD  H12  H  HCH3  0   0.216   -9.1079   -8.0393   -6.9556
 QZD  H13  H  HCH3  0   0.233  -10.2829  -10.0419   -4.9989
 QZD  H14  H  HCH3  0   0.217  -11.2793   -8.7257   -5.6175
 QZD  H15  H  HCH3  0   0.231  -11.8354  -10.3969   -5.7386
 QZD  H16  H  HCH1  0   0.264  -14.6208   -8.1076  -11.2791
 QZD  H17  H  HCR5  0   0.290  -16.2682   -9.9043   -9.2984
 QZD  H18  H  HCH2  0   0.258  -15.6248  -10.4999  -11.5294
 QZD  H19  H  HCH2  0   0.245  -16.7404   -9.3346  -12.2388
 QZD  H20  H  HCH2  0   0.210  -13.3655   -6.1756  -10.4248
 QZD  H21  H  HCH2  0   0.193  -14.6571   -5.8178   -9.2735
 QZD  H22  H  HCH2  0   0.244  -13.8821  -16.4006  -10.3250
 QZD  H23  H  HCH2  0   0.241  -12.5766  -15.2949  -10.6462
 QZD  H24  H  HCH3  0   0.240  -11.7227  -17.0409   -9.2106
 QZD  H25  H  HCH3  0   0.229  -11.8144  -15.6060   -8.2006
 QZD  H26  H  HCH3  0   0.227  -13.0309  -16.8745   -8.0562
 QZD  H27  H  HCH2  0   0.245  -15.5290  -13.9531   -7.8415
 QZD  H28  H  HCH2  0   0.258  -14.4624  -15.2961   -7.4120
 QZD  H29  H  HCH2  0   0.192  -17.2562  -14.3397   -9.3828
 QZD  H30  H  HCH2  0   0.244  -17.4736  -16.0041  -10.0109
 QZD  H31  H  HCH2  0   0.256  -14.3795  -13.8608  -11.4715
 QZD  H32  H  HCH2  0   0.238  -15.4559  -13.0385  -10.3282
 QZD  H33  H  HNH1  0   0.401  -11.5020  -11.7992   -8.9744
 QZD  H34  H  HNH1  0   0.397  -14.2095   -8.1845   -8.3564
 QZD  H35  H  HOH1  0   0.459  -14.9337   -4.6063  -11.2109
 QZD  O18  O  O     0  -0.498  -18.9351   -8.9017   -8.9663

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
 QZD  O29  C28  single  1.396  0.020  1.396
 QZD  O29  C30  single  1.414  0.020  1.414
 QZD  C16  C17  single  1.531  0.020  1.531
 QZD  C16  N15  single  1.446  0.020  1.446
 QZD  C28  O27  single  1.395  0.020  1.395
 QZD  C17  C13  single  1.529  0.020  1.529
 QZD  O20  C19  single  1.407  0.020  1.407
 QZD  O21  C09  double  1.221  0.020  1.221
 QZD  C30  C23  single  1.539  0.020  1.539
 QZD  N15  C14  single  1.343  0.020  1.343
 QZD  C19  C11  single  1.525  0.020  1.525
 QZD  C11  C12  single  1.529  0.020  1.529
 QZD  C11  N10  single  1.448  0.020  1.448
 QZD  O27  C26  single  1.415  0.020  1.415
 QZD  C13  C12  single  1.520  0.020  1.520
 QZD  C13  C14  single  1.520  0.020  1.520
 QZD  C09  N10  single  1.341  0.020  1.341
 QZD  C09  C04  single  1.532  0.020  1.532
 QZD  C14  O18  double  1.221  0.020  1.221
 QZD  C23  C26  single  1.535  0.020  1.535
 QZD  C23  C24  single  1.532  0.020  1.532
 QZD  C23  O22  single  1.436  0.020  1.436
 QZD  C24  C25  single  1.523  0.020  1.523
 QZD  N03  C04  single  1.440  0.020  1.440
 QZD  N03  C02  single  1.349  0.020  1.349
 QZD  C05  C04  single  1.528  0.020  1.528
 QZD  C05  C06  single  1.531  0.020  1.531
 QZD  C02  O22  single  1.337  0.020  1.337
 QZD  C02  O01  double  1.214  0.020  1.214
 QZD  C07  C06  single  1.525  0.020  1.525
 QZD  C06  C08  single  1.524  0.020  1.524
 QZD  C12  H1   single  0.970  0.020  1.090
 QZD  C12  H2   single  0.970  0.020  1.090
 QZD  N15  H3   single  0.860  0.020  1.020
 QZD  C16  H4   single  0.970  0.020  1.090
 QZD  C16  H5   single  0.970  0.020  1.090
 QZD  C04  H6   single  0.970  0.020  1.090
 QZD  C05  H7   single  0.970  0.020  1.090
 QZD  C05  H8   single  0.970  0.020  1.090
 QZD  C06  H9   single  0.970  0.020  1.090
 QZD  C07  H10  single  0.970  0.020  1.090
 QZD  C07  H11  single  0.970  0.020  1.090
 QZD  C07  H12  single  0.970  0.020  1.090
 QZD  C08  H13  single  0.970  0.020  1.090
 QZD  C08  H14  single  0.970  0.020  1.090
 QZD  C08  H15  single  0.970  0.020  1.090
 QZD  C11  H16  single  0.970  0.020  1.090
 QZD  C13  H17  single  0.970  0.020  1.090
 QZD  C17  H18  single  0.970  0.020  1.090
 QZD  C17  H19  single  0.970  0.020  1.090
 QZD  C19  H20  single  0.970  0.020  1.090
 QZD  C19  H21  single  0.970  0.020  1.090
 QZD  C24  H22  single  0.970  0.020  1.090
 QZD  C24  H23  single  0.970  0.020  1.090
 QZD  C25  H24  single  0.970  0.020  1.090
 QZD  C25  H25  single  0.970  0.020  1.090
 QZD  C25  H26  single  0.970  0.020  1.090
 QZD  C26  H27  single  0.970  0.020  1.090
 QZD  C26  H28  single  0.970  0.020  1.090
 QZD  C28  H29  single  0.970  0.020  1.090
 QZD  C28  H30  single  0.970  0.020  1.090
 QZD  C30  H31  single  0.970  0.020  1.090
 QZD  C30  H32  single  0.970  0.020  1.090
 QZD  N03  H33  single  0.890  0.020  1.040
 QZD  N10  H34  single  0.860  0.020  1.020
 QZD  O20  H35  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
 QZD  H2   C12  H1   106.68  3.000
 QZD  H2   C12  C13  109.42  3.000
 QZD  H1   C12  C13  109.51  3.000
 QZD  H2   C12  C11  108.67  3.000
 QZD  H1   C12  C11  109.26  3.000
 QZD  C13  C12  C11  113.09  3.000
 QZD  O18  C14  C13  126.27  3.000
 QZD  O18  C14  N15  126.08  3.000
 QZD  C13  C14  N15  107.65  3.000
 QZD  H3   N15  C16  122.56  3.000
 QZD  H3   N15  C14  122.03  3.000
 QZD  C16  N15  C14  114.61  3.000
 QZD  H5   C16  H4   107.56  3.000
 QZD  H5   C16  C17  111.87  3.000
 QZD  H4   C16  C17  112.80  3.000
 QZD  H5   C16  N15  111.02  3.000
 QZD  H4   C16  N15  111.27  3.000
 QZD  C17  C16  N15  102.35  3.000
 QZD  O22  C02  O01  125.77  3.000
 QZD  O01  C02  N03  123.62  3.000
 QZD  O22  C02  N03  110.60  3.000
 QZD  H6   C04  N03  109.03  3.000
 QZD  H6   C04  C09  109.45  3.000
 QZD  N03  C04  C09  110.05  3.000
 QZD  H6   C04  C05  108.93  3.000
 QZD  N03  C04  C05  110.38  3.000
 QZD  C09  C04  C05  108.98  3.000
 QZD  H8   C05  H7   106.37  3.000
 QZD  H8   C05  C06  108.91  3.000
 QZD  H7   C05  C06  109.23  3.000
 QZD  H8   C05  C04  107.70  3.000
 QZD  H7   C05  C04  109.08  3.000
 QZD  C06  C05  C04  115.19  3.000
 QZD  H9   C06  C08  108.11  3.000
 QZD  H9   C06  C07  107.67  3.000
 QZD  C08  C06  C07  110.79  3.000
 QZD  H9   C06  C05  108.61  3.000
 QZD  C08  C06  C05  112.24  3.000
 QZD  C07  C06  C05  109.29  3.000
 QZD  H12  C07  H11  107.71  3.000
 QZD  H12  C07  H10  107.62  3.000
 QZD  H11  C07  H10  107.65  3.000
 QZD  H12  C07  C06  111.01  3.000
 QZD  H11  C07  C06  111.64  3.000
 QZD  H10  C07  C06  111.03  3.000
 QZD  H15  C08  H14  107.89  3.000
 QZD  H15  C08  H13  107.18  3.000
 QZD  H14  C08  H13  107.65  3.000
 QZD  H15  C08  C06  112.20  3.000
 QZD  H14  C08  C06  111.01  3.000
 QZD  H13  C08  C06  110.71  3.000
 QZD  O21  C09  N10  124.44  3.000
 QZD  N10  C09  C04  114.70  3.000
 QZD  O21  C09  C04  120.82  3.000
 QZD  H16  C11  N10  106.78  3.000
 QZD  H16  C11  C19  108.42  3.000
 QZD  N10  C11  C19  108.61  3.000
 QZD  H16  C11  C12  109.44  3.000
 QZD  N10  C11  C12  110.83  3.000
 QZD  C19  C11  C12  112.56  3.000
 QZD  H17  C13  C17  109.09  3.000
 QZD  H17  C13  C14  106.32  3.000
 QZD  C17  C13  C14  103.32  3.000
 QZD  H17  C13  C12  109.44  3.000
 QZD  C14  C13  C12  112.46  3.000
 QZD  C17  C13  C12  115.68  3.000
 QZD  H19  C17  H18  107.78  3.000
 QZD  H19  C17  C13  109.93  3.000
 QZD  H18  C17  C13  113.03  3.000
 QZD  H19  C17  C16  109.64  3.000
 QZD  H18  C17  C16  112.46  3.000
 QZD  C13  C17  C16  103.96  3.000
 QZD  H21  C19  H20  107.09  3.000
 QZD  H21  C19  O20  111.75  3.000
 QZD  H20  C19  O20  111.72  3.000
 QZD  H21  C19  C11  108.99  3.000
 QZD  H20  C19  C11  108.44  3.000
 QZD  O20  C19  C11  108.76  3.000
 QZD  O22  C23  C30  110.97  3.000
 QZD  O22  C23  C26  112.12  3.000
 QZD  C30  C23  C26  107.99  3.000
 QZD  O22  C23  C24  103.94  3.000
 QZD  C26  C23  C24  112.14  3.000
 QZD  C30  C23  C24  109.67  3.000
 QZD  H23  C24  H22  105.72  3.000
 QZD  H23  C24  C25  109.52  3.000
 QZD  H22  C24  C25  109.33  3.000
 QZD  H23  C24  C23  107.31  3.000
 QZD  H22  C24  C23  108.93  3.000
 QZD  C25  C24  C23  115.56  3.000
 QZD  H26  C25  H25  107.98  3.000
 QZD  H26  C25  H24  107.02  3.000
 QZD  H25  C25  H24  107.41  3.000
 QZD  H26  C25  C24  112.16  3.000
 QZD  H25  C25  C24  112.29  3.000
 QZD  H24  C25  C24  109.73  3.000
 QZD  H28  C26  H27  108.06  3.000
 QZD  H28  C26  O27  107.86  3.000
 QZD  H27  C26  O27  109.94  3.000
 QZD  H28  C26  C23  111.47  3.000
 QZD  H27  C26  C23  110.89  3.000
 QZD  O27  C26  C23  108.58  3.000
 QZD  H30  C28  H29  109.60  3.000
 QZD  H30  C28  O29  107.57  3.000
 QZD  H29  C28  O29  110.04  3.000
 QZD  H30  C28  O27  107.77  3.000
 QZD  H29  C28  O27  109.98  3.000
 QZD  O29  C28  O27  111.80  3.000
 QZD  H32  C30  H31  108.25  3.000
 QZD  H32  C30  O29  110.10  3.000
 QZD  H31  C30  O29  107.63  3.000
 QZD  H32  C30  C23  110.67  3.000
 QZD  H31  C30  C23  110.53  3.000
 QZD  O29  C30  C23  109.60  3.000
 QZD  H33  N03  C04  118.10  3.000
 QZD  H33  N03  C02  118.28  3.000
 QZD  C04  N03  C02  119.44  3.000
 QZD  H34  N10  C11  117.16  3.000
 QZD  H34  N10  C09  118.05  3.000
 QZD  C11  N10  C09  124.65  3.000
 QZD  H35  O20  C19  108.29  3.000
 QZD  C23  O22  C02  123.84  3.000
 QZD  C28  O27  C26  110.87  3.000
 QZD  C30  O29  C28  111.46  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
 QZD  CONST_01  C13  C14  N15  C16     0.00   0.0  0
 QZD  CONST_02  O18  C14  N15  C16   180.00   0.0  0
 QZD  CONST_03  H3   N15  C14  C13   180.00   0.0  0
 QZD  CONST_04  C11  N10  C09  C04   180.00   0.0  0
 QZD  CONST_05  O21  C09  N10  C11     0.00   0.0  0
 QZD  CONST_06  H34  N10  C09  C04     0.00   0.0  0
 QZD  Var_01    C17  C16  N15  C14   -19.32  30.0  1
 QZD  Var_02    C13  C17  C16  N15    27.37  30.0  1
 QZD  Var_03    O29  C28  O27  C26    63.90  30.0  1
 QZD  Var_04    O27  C28  O29  C30   -62.12  30.0  1
 QZD  Var_05    H31  C30  O29  C28   177.15  30.0  1
 QZD  Var_06    H27  C26  O27  C28    61.42  30.0  1
 QZD  Var_07    N03  C02  O22  C23  -170.87  30.0  1
 QZD  Var_08    H24  C25  C24  C23  -170.96  30.0  3
 QZD  Var_09    O22  C02  N03  C04   169.45  30.0  2
 QZD  Var_10    C07  C06  C05  C04  -179.08  30.0  3
 QZD  Var_11    H10  C07  C06  C05  -176.57  30.0  3
 QZD  Var_12    H13  C08  C06  C05  -175.31  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
 QZD  chir_01  C04  C09  N03  C05  negativ
 QZD  chir_02  C11  N10  C12  C19  negativ
 QZD  chir_03  C13  C14  C12  C17  positiv
 QZD  chir_04  C23  C30  C26  C24  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
 QZD  plan-1  C04  0.020
 QZD  plan-1  C09  0.020
 QZD  plan-1  C11  0.020
 QZD  plan-1  N10  0.020
 QZD  plan-1  O21  0.020
 QZD  plan-1  H34  0.020
 QZD  plan-2  C14  0.020
 QZD  plan-2  N15  0.020
 QZD  plan-2  C16  0.020
 QZD  plan-2  C13  0.020
 QZD  plan-2  H3   0.020
 QZD  plan-2  O18  0.020
 QZD  plan-3  C02  0.020
 QZD  plan-3  N03  0.020
 QZD  plan-3  O01  0.020
 QZD  plan-3  O22  0.020

