# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:41:46 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-cyclopropyl-N-[1-(methylsulfonyl)piperidin-4-yl]-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N1CCC(CC1)NC(=O)c2cc(on2)C3CC3
#
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
 O41  O41  5-cyclopropyl-N-[1-(methylsulfonyl)piperidin-4-yl]-1,2-oxazole-3-carboxamide  ligand  40  21  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O41
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
 O41  C10  C  CH2   0  -0.329  -3.0257   1.3087  -0.5970
 O41  C15  C  CR15  0  -0.497   4.0431   1.1031   0.0096
 O41  C20  C  CH2   0  -0.469   7.0642  -0.9796  -1.1208
 O41  C21  C  CH2   0  -0.468   7.2672  -0.9443   0.3528
 O41  C01  C  CH3   0  -0.804  -3.8574  -2.0318  -1.1062
 O41  C06  C  CH2   0  -0.328  -3.1816   0.1161   1.5418
 O41  C07  C  CH2   0  -0.454  -1.7308  -0.3348   1.4256
 O41  C08  C  CH1   0  -0.065  -0.9237   0.6618   0.6030
 O41  C09  C  CH2   0  -0.439  -1.5756   0.8738  -0.7616
 O41  C14  C  CR5   0   0.131   2.8176   0.4251   0.1877
 O41  C16  C  CR5   0   0.507   4.9461   0.0955  -0.1025
 O41  C19  C  CH1   0  -0.410   6.3912   0.0936  -0.3026
 O41  N05  N  N     0  -0.569  -3.7905   0.3900   0.2430
 O41  N11  N  NH1   0  -0.657   0.4496   0.2184   0.4832
 O41  N18  N  N     0  -0.171   2.9785  -0.8670   0.1841
 O41  O03  O  OS    0  -0.669  -5.4792  -0.0272  -1.5481
 O41  O04  O  OS    0  -0.669  -5.6384  -1.2403   0.6409
 O41  O13  O  O     0  -0.474   1.3952   2.2789   0.3901
 O41  O17  O  O     0  -0.337   4.3049  -1.0757   0.0039
 O41  S02  S  S     0   1.349  -4.8211  -0.6934  -0.4331
 O41  H1   H  HCH2  0   0.261  -3.0601   2.2889  -0.1124
 O41  H2   H  HCH2  0   0.282  -3.5103   1.4263  -1.5635
 O41  H4   H  HCH2  0   0.270   7.8742  -0.6587  -1.7619
 O41  H5   H  HCH2  0   0.265   6.4466  -1.7649  -1.5370
 O41  H6   H  HCH2  0   0.265   6.7880  -1.7042   0.9565
 O41  H7   H  HCH2  0   0.270   8.2179  -0.6004   0.7369
 O41  H8   H  HCH3  0   0.308  -4.5443  -2.7418  -1.5645
 O41  H9   H  HCH3  0   0.287  -3.1747  -1.6466  -1.8596
 O41  H10  H  HCH3  0   0.288  -3.3017  -2.5222  -0.3101
 O41  H11  H  HCH2  0   0.283  -3.7700  -0.6213   2.0827
 O41  H12  H  HCH2  0   0.262  -3.2321   1.0408   2.1234
 O41  H13  H  HCH2  0   0.266  -1.3103  -0.4263   2.4290
 O41  H14  H  HCH2  0   0.238  -1.6826  -1.3267   0.9658
 O41  H15  H  HCH1  0   0.254  -0.9138   1.6175   1.1347
 O41  H16  H  HCH2  0   0.234  -1.5150  -0.0491  -1.3463
 O41  H17  H  HCH2  0   0.261  -1.0390   1.6433  -1.3202
 O41  H18  H  HCH1  0   0.292   6.7996   1.0930  -0.3840
 O41  H19  H  HNH1  0   0.408   0.6213  -0.7713   0.3808
 O41  C12  C  C     0   0.545   1.4809   1.0612   0.3610
 O41  H3   H  HCR5  0   0.285   4.2220   2.1634  -0.0300

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
 O41  O04  S02  double    1.456  0.020  1.456
 O41  C01  S02  single    1.781  0.020  1.781
 O41  O17  N18  aromatic  1.355  0.020  1.355
 O41  O17  C16  aromatic  1.339  0.020  1.339
 O41  C10  N05  single    1.461  0.020  1.461
 O41  C10  C09  single    1.523  0.020  1.523
 O41  N18  C14  aromatic  1.302  0.020  1.302
 O41  S02  N05  single    1.641  0.020  1.641
 O41  S02  O03  double    1.456  0.020  1.456
 O41  C19  C21  single    1.508  0.020  1.508
 O41  C19  C16  single    1.459  0.020  1.459
 O41  C19  C20  single    1.508  0.020  1.508
 O41  C21  C20  single    1.488  0.020  1.488
 O41  C16  C15  aromatic  1.358  0.020  1.358
 O41  N05  C06  single    1.460  0.020  1.460
 O41  C09  C08  single    1.527  0.020  1.527
 O41  C14  C15  aromatic  1.412  0.020  1.412
 O41  C14  C12  single    1.490  0.020  1.490
 O41  N11  C12  single    1.338  0.020  1.338
 O41  N11  C08  single    1.448  0.020  1.448
 O41  C12  O13  double    1.221  0.020  1.221
 O41  C08  C07  single    1.524  0.020  1.524
 O41  C06  C07  single    1.524  0.020  1.524
 O41  C10  H1   single    0.970  0.020  1.090
 O41  C10  H2   single    0.970  0.020  1.090
 O41  C15  H3   single    0.930  0.020  1.080
 O41  C20  H4   single    0.970  0.020  1.090
 O41  C20  H5   single    0.970  0.020  1.090
 O41  C21  H6   single    0.970  0.020  1.090
 O41  C21  H7   single    0.970  0.020  1.090
 O41  C01  H8   single    0.970  0.020  1.090
 O41  C01  H9   single    0.970  0.020  1.090
 O41  C01  H10  single    0.970  0.020  1.090
 O41  C06  H11  single    0.970  0.020  1.090
 O41  C06  H12  single    0.970  0.020  1.090
 O41  C07  H13  single    0.970  0.020  1.090
 O41  C07  H14  single    0.970  0.020  1.090
 O41  C08  H15  single    0.970  0.020  1.090
 O41  C09  H16  single    0.970  0.020  1.090
 O41  C09  H17  single    0.970  0.020  1.090
 O41  C19  H18  single    0.970  0.020  1.090
 O41  N11  H19  single    0.860  0.020  1.020

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
 O41  H2   C10  H1   106.42  3.000
 O41  H2   C10  N05  110.22  3.000
 O41  H1   C10  N05  107.00  3.000
 O41  H2   C10  C09  111.05  3.000
 O41  H1   C10  C09  109.50  3.000
 O41  N05  C10  C09  112.40  3.000
 O41  H3   C15  C16  128.15  3.000
 O41  H3   C15  C14  128.48  3.000
 O41  C16  C15  C14  103.37  3.000
 O41  H5   C20  H4   114.50  3.000
 O41  H5   C20  C19  118.06  3.000
 O41  H4   C20  C19  116.39  3.000
 O41  H5   C20  C21  118.42  3.000
 O41  H4   C20  C21  118.54  3.000
 O41  C19  C20  C21   60.44  3.000
 O41  H7   C21  H6   114.47  3.000
 O41  H7   C21  C19  116.50  3.000
 O41  H6   C21  C19  117.94  3.000
 O41  H7   C21  C20  118.63  3.000
 O41  H6   C21  C20  118.38  3.000
 O41  C19  C21  C20   60.44  3.000
 O41  H10  C01  H9   110.25  3.000
 O41  H10  C01  H8   109.65  3.000
 O41  H9   C01  H8   109.60  3.000
 O41  H10  C01  S02  109.79  3.000
 O41  H9   C01  S02  109.59  3.000
 O41  H8   C01  S02  107.92  3.000
 O41  H12  C06  H11  106.48  3.000
 O41  H12  C06  N05  107.17  3.000
 O41  H11  C06  N05  110.12  3.000
 O41  H12  C06  C07  109.56  3.000
 O41  H11  C06  C07  110.64  3.000
 O41  N05  C06  C07  112.63  3.000
 O41  H14  C07  H13  107.05  3.000
 O41  H14  C07  C08  110.04  3.000
 O41  H13  C07  C08  110.30  3.000
 O41  H14  C07  C06  110.01  3.000
 O41  H13  C07  C06  108.75  3.000
 O41  C08  C07  C06  110.61  3.000
 O41  H15  C08  N11  107.41  3.000
 O41  H15  C08  C09  108.48  3.000
 O41  N11  C08  C09  111.93  3.000
 O41  H15  C08  C07  108.30  3.000
 O41  N11  C08  C07  110.29  3.000
 O41  C09  C08  C07  110.31  3.000
 O41  H17  C09  H16  107.08  3.000
 O41  H17  C09  C08  110.19  3.000
 O41  H16  C09  C08  109.68  3.000
 O41  H17  C09  C10  108.79  3.000
 O41  H16  C09  C10  110.57  3.000
 O41  C08  C09  C10  110.46  3.000
 O41  N18  C14  C12  122.32  3.000
 O41  C12  C14  C15  126.03  3.000
 O41  N18  C14  C15  111.65  3.000
 O41  O17  C16  C19  118.94  3.000
 O41  C19  C16  C15  132.15  3.000
 O41  O17  C16  C15  108.90  3.000
 O41  H18  C19  C16  112.50  3.000
 O41  H18  C19  C21  116.67  3.000
 O41  C16  C19  C21  121.11  3.000
 O41  H18  C19  C20  116.61  3.000
 O41  C16  C19  C20  121.16  3.000
 O41  C21  C19  C20   59.12  3.000
 O41  S02  N05  C06  120.29  3.000
 O41  C06  N05  C10  114.27  3.000
 O41  S02  N05  C10  120.47  3.000
 O41  H19  N11  C12  118.50  3.000
 O41  H19  N11  C08  118.03  3.000
 O41  C12  N11  C08  123.08  3.000
 O41  O17  N18  C14  105.91  3.000
 O41  N18  O17  C16  110.16  3.000
 O41  O04  S02  O03  118.88  3.000
 O41  O03  S02  N05  107.29  3.000
 O41  O04  S02  N05  107.25  3.000
 O41  O03  S02  C01  107.39  3.000
 O41  N05  S02  C01  108.18  3.000
 O41  O04  S02  C01  107.47  3.000
 O41  O13  C12  N11  124.90  3.000
 O41  O13  C12  C14  119.43  3.000
 O41  N11  C12  C14  115.67  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
 O41  CONST_01  N18  O17  C16  C15     0.00   0.0  0
 O41  CONST_02  O17  N18  C14  C15     0.00   0.0  0
 O41  CONST_03  C16  O17  N18  C14     0.00   0.0  0
 O41  CONST_04  O17  C16  C15  C14     0.00   0.0  0
 O41  CONST_05  N18  C14  C15  C16     0.00   0.0  0
 O41  CONST_06  C19  C16  C15  C14   180.00   0.0  0
 O41  CONST_07  N18  O17  C16  C19   180.00   0.0  0
 O41  CONST_08  O17  N18  C14  C12   180.00   0.0  0
 O41  CONST_09  C16  C15  C14  C12   180.00   0.0  0
 O41  CONST_10  H3   C15  C16  C19     0.00   0.0  0
 O41  CONST_11  C14  C12  N11  C08   180.00   0.0  0
 O41  CONST_12  O13  C12  N11  C08     0.00   0.0  0
 O41  CONST_13  H19  N11  C12  C14     0.00   0.0  0
 O41  Var_01    C07  C06  N05  C10   -52.32  30.0  1
 O41  Var_02    C21  C19  C16  C15   144.16  30.0  1
 O41  Var_03    C16  C19  C21  C20   110.07  30.0  1
 O41  Var_04    C09  C10  N05  C06    52.67  30.0  1
 O41  Var_05    N05  C10  C09  C08   -53.87  30.0  1
 O41  Var_06    N05  C06  C07  C08    53.21  30.0  1
 O41  Var_07    O04  S02  N05  C10  -167.50  30.0  2
 O41  Var_08    N11  C12  C14  C15   178.51  30.0  2
 O41  Var_09    H8   C01  S02  N05  -179.31  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
 O41  chir_01  C08  C09  N11  C07  positiv
 O41  chir_02  C19  C21  C16  C20  both

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
 O41  plan-1  C15  0.020
 O41  plan-1  C14  0.020
 O41  plan-1  C16  0.020
 O41  plan-1  C19  0.020
 O41  plan-1  N18  0.020
 O41  plan-1  O17  0.020
 O41  plan-1  C12  0.020
 O41  plan-1  H3   0.020
 O41  plan-2  C08  0.020
 O41  plan-2  C14  0.020
 O41  plan-2  N11  0.020
 O41  plan-2  O13  0.020
 O41  plan-2  H19  0.020
 O41  plan-2  C12  0.020

