# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 04:23:11 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-nitro-3-[(3~{S})-3-oxidanylpiperidin-1-yl]benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCN(C1)c2cc(C=O)ccc2[N](=O)=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
 U1B  U1B  4-nitro-3-[(3~{S})-3-oxidanylpiperidin-1-yl]benzaldehyde  ligand  32  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U1B
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
 U1B  C10  C  C1     0   0.123  -21.0182  -10.5311   -4.4052
 U1B  C13  C  CR16   0  -0.252  -20.6119   -6.8432   -4.9367
 U1B  C02  C  CH1    0   0.067  -22.7508   -9.6209   -9.6236
 U1B  C03  C  CH2    0  -0.468  -22.1192   -8.8621  -10.7766
 U1B  C04  C  CH2    0  -0.440  -21.0787   -7.8794  -10.2543
 U1B  C05  C  CH2    0  -0.331  -21.6606   -6.9336   -9.2066
 U1B  C07  C  CR6    0   0.440  -21.7643   -7.7957   -6.8887
 U1B  C08  C  CR16   0  -0.385  -21.6697   -9.0390   -6.2387
 U1B  C09  C  CR6    0   0.024  -21.0806   -9.1772   -4.9957
 U1B  C12  C  CR16   0  -0.305  -20.5265   -8.0784   -4.3376
 U1B  C14  C  CR6    0   0.150  -21.2556   -6.7013   -6.1636
 U1B  C18  C  CH2    0  -0.381  -23.3086   -8.6181   -8.6117
 U1B  N06  N  NT     0  -0.502  -22.3049   -7.6852   -8.1400
 U1B  N15  N  N      1   0.331  -21.4680   -5.3319   -6.6070
 U1B  O11  O  O      0  -0.361  -20.5065  -10.7802   -3.3420
 U1B  O16  O  O      0  -0.365  -22.5552   -5.0411   -7.0462
 U1B  O17  O  O     -1  -0.370  -20.5598   -4.5461   -6.4630
 U1B  H1   H  H      0   0.206  -21.4852  -11.3233   -5.0162
 U1B  H2   H  HCR6   0   0.294  -20.2223   -5.9706   -4.4308
 U1B  H3   H  HCH1   0   0.204  -21.9688  -10.2196   -9.1312
 U1B  H4   H  HCH2   0   0.224  -22.9022   -8.3177  -11.3164
 U1B  H5   H  HCH2   0   0.246  -21.6625   -9.5573  -11.4847
 U1B  H6   H  HCH2   0   0.230  -20.2409   -8.4257   -9.8117
 U1B  H7   H  HCH2   0   0.247  -20.6719   -7.2861  -11.0757
 U1B  H8   H  HCH2   0   0.260  -20.8521   -6.3229   -8.8104
 U1B  H9   H  HCH2   0   0.240  -22.3871   -6.2588   -9.6707
 U1B  H10  H  HCR6   0   0.292  -22.0341   -9.9276   -6.7397
 U1B  H11  H  HCR6   0   0.273  -20.0503   -8.1866   -3.3735
 U1B  H12  H  HCH2   0   0.258  -24.1028   -8.0409   -9.1016
 U1B  H13  H  HCH2   0   0.266  -23.7704   -9.1261   -7.7639
 U1B  O01  O  OH1    0  -0.663  -23.7734  -10.4465  -10.1296
 U1B  H14  H  HOH1   0   0.449  -24.0921  -11.0085   -9.4161

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
 U1B  C03  C04  single    1.524  0.020  1.524
 U1B  C03  C02  single    1.518  0.020  1.518
 U1B  C04  C05  single    1.527  0.020  1.527
 U1B  O01  C02  single    1.408  0.020  1.408
 U1B  C02  C18  single    1.530  0.020  1.530
 U1B  C05  N06  single    1.455  0.020  1.455
 U1B  C18  N06  single    1.449  0.020  1.449
 U1B  N06  C07  single    1.367  0.020  1.367
 U1B  O16  N15  double    1.208  0.020  1.208
 U1B  C07  C08  aromatic  1.406  0.020  1.406
 U1B  C07  C14  aromatic  1.408  0.020  1.408
 U1B  N15  O17  single    1.210  0.020  1.210
 U1B  N15  C14  single    1.455  0.020  1.455
 U1B  C08  C09  aromatic  1.382  0.020  1.382
 U1B  C14  C13  aromatic  1.393  0.020  1.393
 U1B  C09  C10  single    1.478  0.020  1.478
 U1B  C09  C12  aromatic  1.396  0.020  1.396
 U1B  C13  C12  aromatic  1.375  0.020  1.375
 U1B  C10  O11  double    1.206  0.020  1.206
 U1B  C10  H1   single    0.930  0.020  1.080
 U1B  C13  H2   single    0.930  0.020  1.080
 U1B  C02  H3   single    0.970  0.020  1.090
 U1B  C03  H4   single    0.970  0.020  1.090
 U1B  C03  H5   single    0.970  0.020  1.090
 U1B  C04  H6   single    0.970  0.020  1.090
 U1B  C04  H7   single    0.970  0.020  1.090
 U1B  C05  H8   single    0.970  0.020  1.090
 U1B  C05  H9   single    0.970  0.020  1.090
 U1B  C08  H10  single    0.930  0.020  1.080
 U1B  C12  H11  single    0.930  0.020  1.080
 U1B  C18  H12  single    0.970  0.020  1.090
 U1B  C18  H13  single    0.970  0.020  1.090
 U1B  O01  H14  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
 U1B  H1   C10  O11  121.28  3.000
 U1B  H1   C10  C09  114.72  3.000
 U1B  O11  C10  C09  124.00  3.000
 U1B  H2   C13  C14  119.77  3.000
 U1B  H2   C13  C12  119.90  3.000
 U1B  C14  C13  C12  120.26  3.000
 U1B  H3   C02  O01  110.95  3.000
 U1B  H3   C02  C18  108.63  3.000
 U1B  O01  C02  C18  110.93  3.000
 U1B  H3   C02  C03  108.42  3.000
 U1B  C18  C02  C03  109.06  3.000
 U1B  O01  C02  C03  108.80  3.000
 U1B  H5   C03  H4   107.19  3.000
 U1B  H5   C03  C04  110.32  3.000
 U1B  H4   C03  C04  109.66  3.000
 U1B  H5   C03  C02  110.38  3.000
 U1B  H4   C03  C02  108.98  3.000
 U1B  C04  C03  C02  110.25  3.000
 U1B  H7   C04  H6   106.88  3.000
 U1B  H7   C04  C05  108.76  3.000
 U1B  H6   C04  C05  108.88  3.000
 U1B  H7   C04  C03  110.31  3.000
 U1B  H6   C04  C03  109.86  3.000
 U1B  C05  C04  C03  112.00  3.000
 U1B  H9   C05  H8   107.55  3.000
 U1B  H9   C05  N06  109.59  3.000
 U1B  H8   C05  N06  110.61  3.000
 U1B  H9   C05  C04  110.11  3.000
 U1B  H8   C05  C04  108.33  3.000
 U1B  N06  C05  C04  110.60  3.000
 U1B  N06  C07  C14  123.45  3.000
 U1B  C14  C07  C08  115.14  3.000
 U1B  N06  C07  C08  121.40  3.000
 U1B  H10  C08  C09  118.51  3.000
 U1B  H10  C08  C07  119.26  3.000
 U1B  C09  C08  C07  122.19  3.000
 U1B  C12  C09  C08  120.96  3.000
 U1B  C12  C09  C10  121.06  3.000
 U1B  C08  C09  C10  117.95  3.000
 U1B  H11  C12  C09  121.12  3.000
 U1B  H11  C12  C13  120.39  3.000
 U1B  C09  C12  C13  118.49  3.000
 U1B  N15  C14  C07  121.46  3.000
 U1B  N15  C14  C13  115.58  3.000
 U1B  C07  C14  C13  122.79  3.000
 U1B  H13  C18  H12  106.59  3.000
 U1B  H13  C18  N06  109.88  3.000
 U1B  H12  C18  N06  107.94  3.000
 U1B  H13  C18  C02  111.29  3.000
 U1B  H12  C18  C02  108.26  3.000
 U1B  N06  C18  C02  112.63  3.000
 U1B  C18  N06  C07  121.30  3.000
 U1B  C07  N06  C05  122.50  3.000
 U1B  C18  N06  C05  113.61  3.000
 U1B  O17  N15  O16  124.23  3.000
 U1B  O17  N15  C14  117.75  3.000
 U1B  O16  N15  C14  117.95  3.000
 U1B  H14  O01  C02  108.44  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
 U1B  CONST_01  C08  C07  C14  C13     0.00   0.0  0
 U1B  CONST_02  C08  C09  C12  C13     0.00   0.0  0
 U1B  CONST_03  C12  C09  C08  C07     0.00   0.0  0
 U1B  CONST_04  C12  C13  C14  C07     0.00   0.0  0
 U1B  CONST_05  C14  C07  C08  C09     0.00   0.0  0
 U1B  CONST_06  C14  C13  C12  C09     0.00   0.0  0
 U1B  CONST_07  N06  C07  C14  C13   180.00   0.0  0
 U1B  CONST_08  N06  C07  C08  C09   180.00   0.0  0
 U1B  CONST_09  C07  C08  C09  C10   180.00   0.0  0
 U1B  CONST_10  C13  C12  C09  C10   180.00   0.0  0
 U1B  CONST_11  N15  C14  C07  C08   180.00   0.0  0
 U1B  CONST_12  N15  C14  C13  C12   180.00   0.0  0
 U1B  CONST_13  N15  C14  C07  N06     0.00   0.0  0
 U1B  CONST_14  H2   C13  C14  C07   180.00   0.0  0
 U1B  CONST_15  H11  C12  C09  C08   180.00   0.0  0
 U1B  CONST_16  H10  C08  C09  C12   180.00   0.0  0
 U1B  Var_01    C05  C04  C03  C02   -54.92  30.0  1
 U1B  Var_02    C05  N06  C18  C02    56.91  30.0  1
 U1B  Var_03    N06  C05  C04  C03    53.52  30.0  1
 U1B  Var_04    C18  N06  C05  C04   -54.41  30.0  1
 U1B  Var_05    C08  C07  N06  C05  -132.43  30.0  2
 U1B  Var_06    O11  C10  C09  C08   178.48  30.0  2

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
 U1B  chir_01  C02  C03  O01  C18  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
 U1B  plan-1  C10  0.020
 U1B  plan-1  C13  0.020
 U1B  plan-1  C07  0.020
 U1B  plan-1  C08  0.020
 U1B  plan-1  C09  0.020
 U1B  plan-1  C12  0.020
 U1B  plan-1  C14  0.020
 U1B  plan-1  N06  0.020
 U1B  plan-1  N15  0.020
 U1B  plan-1  H2   0.020
 U1B  plan-1  H10  0.020
 U1B  plan-1  H11  0.020
 U1B  plan-2  C14  0.020
 U1B  plan-2  N15  0.020
 U1B  plan-2  O16  0.020
 U1B  plan-2  O17  0.020
 U1B  plan-3  C10  0.020
 U1B  plan-3  C09  0.020
 U1B  plan-3  O11  0.020
 U1B  plan-3  H1   0.020

