# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 13:48:09 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (4R)-4-hydroxy-N-methyl-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H]1C[C@@H](O)CN1C(=O)Cc2onc(C)c2
#
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
 QD0  QD0  (4R)-4-hydroxy-N-methyl-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-L-prolinamide  ligand  36  19  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QD0
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
 QD0  C01   C  CH3   0  -0.734   5.9484   0.7920   0.5687
 QD0  C02   C  CR5   0   0.255   4.6280   0.2026   0.2242
 QD0  N03   N  N     0  -0.184   4.3500  -0.1701  -0.9921
 QD0  O04   O  O     0  -0.344   3.0769  -0.6632  -0.9644
 QD0  C05   C  CR5   0   0.500   2.5909  -0.5819   0.2764
 QD0  C06   C  CH2   0  -0.725   1.2138  -1.0730   0.5102
 QD0  C07   C  C     0   0.579   0.1762  -0.1445  -0.0992
 QD0  N08   N  NT    0  -0.469  -1.0750  -0.6184  -0.1602
 QD0  C09   C  CH1   0  -0.219  -2.1353   0.2059  -0.7075
 QD0  C10   C  C     0   0.566  -2.3900   1.4199   0.1824
 QD0  N11   N  NH1   0  -0.625  -2.8666   2.4887  -0.4618
 QD0  C12   C  CH3   0  -0.513  -3.2467   3.7049   0.2175
 QD0  O13   O  O     0  -0.494  -2.2189   1.3847   1.3921
 QD0  C14   C  CH2   0  -0.503  -3.3396  -0.7404  -0.7246
 QD0  C15   C  CH1   0   0.039  -3.0658  -1.7023   0.4234
 QD0  C17   C  CH2   0  -0.300  -1.5471  -1.8960   0.3473
 QD0  O18   O  O     0  -0.486   0.4687   0.9704  -0.5060
 QD0  C19   C  CR15  0  -0.526   3.5264  -0.0416   1.0879
 QD0  O16   O  OH1   0  -0.663  -3.7980  -2.8857   0.2596
 QD0  H011  H  HCH3  0   0.259   5.8283   1.8056   0.9511
 QD0  H012  H  HCH3  0   0.259   6.4369   0.2049   1.3461
 QD0  H013  H  HCH3  0   0.257   6.6017   0.8267  -0.3006
 QD0  H19   H  HCR5  0   0.277   3.4535   0.1560   2.1440
 QD0  H061  H  HCH2  0   0.310   1.0996  -2.0884   0.1207
 QD0  H062  H  HCH2  0   0.322   1.0424  -1.1384   1.5874
 QD0  H09   H  HCH1  0   0.290  -1.8832   0.5364  -1.7181
 QD0  H171  H  HCH2  0   0.248  -1.3127  -2.7094  -0.3466
 QD0  H172  H  HCH2  0   0.265  -1.1108  -2.1319   1.3184
 QD0  H141  H  HCH2  0   0.273  -4.2913  -0.2171  -0.6346
 QD0  H142  H  HCH2  0   0.265  -3.3486  -1.2936  -1.6670
 QD0  H11   H  HNH1  0   0.406  -2.9497   2.4597  -1.4642
 QD0  H121  H  HCH3  0   0.240  -3.9912   3.5144   0.9902
 QD0  H122  H  HCH3  0   0.239  -2.3896   4.1959   0.6799
 QD0  H123  H  HCH3  0   0.251  -3.6774   4.3844  -0.5119
 QD0  H15   H  HCH1  0   0.228  -3.3121  -1.2174   1.3746
 QD0  H16   H  HOH1  0   0.458  -3.7661  -3.3832   1.0825

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
 QD0  C01  C02   single    1.486  0.020  1.486
 QD0  C02  N03   aromatic  1.302  0.020  1.302
 QD0  C02  C19   aromatic  1.421  0.020  1.421
 QD0  N03  O04   aromatic  1.366  0.020  1.366
 QD0  O04  C05   aromatic  1.335  0.020  1.335
 QD0  C05  C06   single    1.481  0.020  1.481
 QD0  C05  C19   aromatic  1.351  0.020  1.351
 QD0  C06  C07   single    1.520  0.020  1.520
 QD0  C07  N08   single    1.339  0.020  1.339
 QD0  C07  O18   double    1.222  0.020  1.222
 QD0  N08  C09   single    1.450  0.020  1.450
 QD0  N08  C17   single    1.454  0.020  1.454
 QD0  C09  C10   single    1.527  0.020  1.527
 QD0  C09  C14   single    1.532  0.020  1.532
 QD0  C10  N11   single    1.336  0.020  1.336
 QD0  C10  O13   double    1.222  0.020  1.222
 QD0  N11  C12   single    1.444  0.020  1.444
 QD0  C14  C15   single    1.523  0.020  1.523
 QD0  C15  C17   single    1.533  0.020  1.533
 QD0  C15  O16   single    1.401  0.020  1.401
 QD0  C01  H011  single    0.970  0.020  1.090
 QD0  C01  H012  single    0.970  0.020  1.090
 QD0  C01  H013  single    0.970  0.020  1.090
 QD0  C19  H19   single    0.930  0.020  1.080
 QD0  C06  H061  single    0.970  0.020  1.090
 QD0  C06  H062  single    0.970  0.020  1.090
 QD0  C09  H09   single    0.970  0.020  1.090
 QD0  C17  H171  single    0.970  0.020  1.090
 QD0  C17  H172  single    0.970  0.020  1.090
 QD0  C14  H141  single    0.970  0.020  1.090
 QD0  C14  H142  single    0.970  0.020  1.090
 QD0  N11  H11   single    0.860  0.020  1.020
 QD0  C12  H121  single    0.970  0.020  1.090
 QD0  C12  H122  single    0.970  0.020  1.090
 QD0  C12  H123  single    0.970  0.020  1.090
 QD0  C15  H15   single    0.970  0.020  1.090
 QD0  O16  H16   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
 QD0  H013  C01  H012  108.54  3.000
 QD0  H013  C01  H011  108.47  3.000
 QD0  H012  C01  H011  107.46  3.000
 QD0  H013  C01  C02   111.15  3.000
 QD0  H012  C01  C02   110.48  3.000
 QD0  H011  C01  C02   110.62  3.000
 QD0  C19   C02  N03   110.68  3.000
 QD0  C19   C02  C01   128.02  3.000
 QD0  N03   C02  C01   121.31  3.000
 QD0  O04   N03  C02   106.47  3.000
 QD0  C05   O04  N03   109.65  3.000
 QD0  C19   C05  C06   132.98  3.000
 QD0  C19   C05  O04   109.30  3.000
 QD0  C06   C05  O04   117.72  3.000
 QD0  H062  C06  H061  106.21  3.000
 QD0  H062  C06  C07   108.94  3.000
 QD0  H061  C06  C07   110.68  3.000
 QD0  H062  C06  C05   108.75  3.000
 QD0  H061  C06  C05   110.42  3.000
 QD0  C07   C06  C05   111.66  3.000
 QD0  O18   C07  N08   122.08  3.000
 QD0  O18   C07  C06   121.82  3.000
 QD0  N08   C07  C06   116.10  3.000
 QD0  C17   N08  C09   113.19  3.000
 QD0  C17   N08  C07   126.77  3.000
 QD0  C09   N08  C07   119.94  3.000
 QD0  H09   C09  C14   110.97  3.000
 QD0  H09   C09  C10   109.70  3.000
 QD0  C14   C09  C10   111.51  3.000
 QD0  H09   C09  N08   110.62  3.000
 QD0  C14   C09  N08   103.18  3.000
 QD0  C10   C09  N08   110.73  3.000
 QD0  O13   C10  N11   123.38  3.000
 QD0  O13   C10  C09   122.05  3.000
 QD0  N11   C10  C09   114.50  3.000
 QD0  H11   N11  C12   118.11  3.000
 QD0  H11   N11  C10   119.13  3.000
 QD0  C12   N11  C10   122.75  3.000
 QD0  H123  C12  H122  108.34  3.000
 QD0  H123  C12  H121  108.34  3.000
 QD0  H122  C12  H121  108.36  3.000
 QD0  H123  C12  N11   108.39  3.000
 QD0  H122  C12  N11   111.82  3.000
 QD0  H121  C12  N11   111.48  3.000
 QD0  H142  C14  H141  107.88  3.000
 QD0  H142  C14  C15   109.38  3.000
 QD0  H141  C14  C15   113.46  3.000
 QD0  H142  C14  C09   109.20  3.000
 QD0  H141  C14  C09   112.90  3.000
 QD0  C15   C14  C09   103.92  3.000
 QD0  H15   C15  O16   110.97  3.000
 QD0  H15   C15  C17   108.76  3.000
 QD0  O16   C15  C17   113.90  3.000
 QD0  H15   C15  C14   109.54  3.000
 QD0  O16   C15  C14   110.58  3.000
 QD0  C17   C15  C14   102.74  3.000
 QD0  H172  C17  H171  108.55  3.000
 QD0  H172  C17  C15   112.31  3.000
 QD0  H171  C17  C15   109.72  3.000
 QD0  H172  C17  N08   111.79  3.000
 QD0  H171  C17  N08   111.24  3.000
 QD0  C15   C17  N08   103.18  3.000
 QD0  H19   C19  C05   127.99  3.000
 QD0  H19   C19  C02   128.10  3.000
 QD0  C05   C19  C02   103.91  3.000
 QD0  H16   O16  C15   108.62  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
 QD0  CONST_01  C05   O04  N03  C02    0.00   0.0  0
 QD0  CONST_02  O04   C05  C19  C02    0.00   0.0  0
 QD0  CONST_03  C05   C19  C02  N03    0.00   0.0  0
 QD0  CONST_04  C19   C05  O04  N03    0.00   0.0  0
 QD0  CONST_05  C19   C02  N03  O04    0.00   0.0  0
 QD0  CONST_06  O04   N03  C02  C01  180.00   0.0  0
 QD0  CONST_07  C05   C19  C02  C01  180.00   0.0  0
 QD0  CONST_08  C06   C05  C19  C02  180.00   0.0  0
 QD0  CONST_09  C06   C05  O04  N03  180.00   0.0  0
 QD0  CONST_10  H19   C19  C02  N03  180.00   0.0  0
 QD0  CONST_11  C09   N08  C07  C06  180.00   0.0  0
 QD0  CONST_12  C17   N08  C07  C06    0.00   0.0  0
 QD0  CONST_13  O18   C07  N08  C09    0.00   0.0  0
 QD0  CONST_14  O18   C07  N08  C17  180.00   0.0  0
 QD0  CONST_15  C12   N11  C10  C09  180.00   0.0  0
 QD0  CONST_16  H11   N11  C10  C09    0.00   0.0  0
 QD0  CONST_17  O13   C10  N11  C12    0.00   0.0  0
 QD0  Var_01    C15   C17  N08  C09  -14.28  30.0  1
 QD0  Var_02    C07   C06  C05  O04  -71.68  30.0  2
 QD0  Var_03    N08   C07  C06  C05  168.10  30.0  3
 QD0  Var_04    H011  C01  C02  N03  118.97  30.0  2
 QD0  Var_05    H121  C12  N11  C10  -56.13  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
 QD0  chir_01  C09  N08  C10  C14  positiv
 QD0  chir_02  C15  O16  C14  C17  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
 QD0  plan-1  C01  0.020
 QD0  plan-1  C02  0.020
 QD0  plan-1  N03  0.020
 QD0  plan-1  O04  0.020
 QD0  plan-1  C05  0.020
 QD0  plan-1  C06  0.020
 QD0  plan-1  C19  0.020
 QD0  plan-1  H19  0.020
 QD0  plan-2  C06  0.020
 QD0  plan-2  C07  0.020
 QD0  plan-2  N08  0.020
 QD0  plan-2  C09  0.020
 QD0  plan-2  C17  0.020
 QD0  plan-2  O18  0.020
 QD0  plan-3  C09  0.020
 QD0  plan-3  C10  0.020
 QD0  plan-3  N11  0.020
 QD0  plan-3  C12  0.020
 QD0  plan-3  O13  0.020
 QD0  plan-3  H11  0.020

