# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 16:03:31 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{R},3~{S})-3-azanyl-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepiperidin-3-yl]butanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1CCCNC1=O)[C@@H](O)C#N
#
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
 4UG  4UG  (2~{R},3~{S})-3-azanyl-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepiperidin-3-yl]butanenitrile  ligand  29  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4UG
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
 4UG  C6   C  CH2   0  -0.468  -2.7850   1.8490  -0.2633
 4UG  C11  C  CH1   0  -0.149   1.4214   0.2711  -0.0265
 4UG  C13  C  CH2   0  -0.450  -1.3841   1.4292   0.1441
 4UG  C15  C  C     0   0.561  -2.2526  -0.9636  -0.0108
 4UG  C17  C  CH2   0  -0.426   0.1892  -0.5609   0.3208
 4UG  C19  C  CSP   0   0.091   3.8128   0.5727   0.4953
 4UG  C24  C  CH1   0  -0.034   2.6562  -0.3259   0.6908
 4UG  C25  C  CH1   0  -0.367  -1.1005  -0.0073  -0.2862
 4UG  C27  C  CH2   0  -0.261  -3.7994   0.9625   0.4260
 4UG  N3   N  NH2   0  -0.789   1.5596   0.3987  -1.4584
 4UG  N4   N  NH1   0  -0.630  -3.4588  -0.4373   0.2561
 4UG  O3   O  OH1   0  -0.634   2.9840  -1.6263   0.3022
 4UG  O4   O  O     0  -0.515  -2.0929  -2.1793  -0.0731
 4UG  H19  H  HCH2  0   0.250  -2.9767   2.8881   0.0074
 4UG  H20  H  HCH2  0   0.233  -2.8976   1.7730  -1.3486
 4UG  H21  H  HCH1  0   0.264   1.2999   1.2776   0.3859
 4UG  H22  H  HCH2  0   0.251  -0.6464   2.0949  -0.3061
 4UG  H23  H  HCH2  0   0.226  -1.2738   1.5234   1.2304
 4UG  H24  H  HCH2  0   0.246   0.3391  -1.5880  -0.0160
 4UG  H25  H  HCH2  0   0.240   0.0897  -0.5988   1.4100
 4UG  H26  H  HCH1  0   0.309   2.4587  -0.3524   1.7659
 4UG  H27  H  HCH1  0   0.273  -0.9845  -0.0104  -1.3767
 4UG  H28  H  HCH2  0   0.231  -3.8467   1.2100   1.4917
 4UG  H29  H  HCH2  0   0.252  -4.7979   1.1230   0.0179
 4UG  H30  H  HNH2  0   0.363   2.3387   0.9846  -1.7277
 4UG  H31  H  HNH1  0   0.390  -4.1922  -1.1078   0.4354
 4UG  H32  H  HOH1  0   0.451   3.0749  -1.6574  -0.6575
 4UG  H2   H  HNH2  0   0.348   1.6548  -0.4944  -1.9244
 4UG  N2   N  NS    0  -0.257   4.7094   1.2727   0.3250

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
 4UG  N2   C19  triple  1.150  0.020  1.150
 4UG  C19  C24  single  1.478  0.020  1.478
 4UG  O3   C24  single  1.396  0.020  1.396
 4UG  C24  C11  single  1.548  0.020  1.548
 4UG  C11  N3   single  1.444  0.020  1.444
 4UG  C11  C17  single  1.527  0.020  1.527
 4UG  C17  C25  single  1.529  0.020  1.529
 4UG  C25  C13  single  1.526  0.020  1.526
 4UG  C25  C15  single  1.522  0.020  1.522
 4UG  C13  C6   single  1.518  0.020  1.518
 4UG  O4   C15  double  1.228  0.020  1.228
 4UG  C15  N4   single  1.343  0.020  1.343
 4UG  C6   C27  single  1.513  0.020  1.513
 4UG  N4   C27  single  1.451  0.020  1.451
 4UG  C6   H19  single  0.970  0.020  1.090
 4UG  C6   H20  single  0.970  0.020  1.090
 4UG  C11  H21  single  0.970  0.020  1.090
 4UG  C13  H22  single  0.970  0.020  1.090
 4UG  C13  H23  single  0.970  0.020  1.090
 4UG  C17  H24  single  0.970  0.020  1.090
 4UG  C17  H25  single  0.970  0.020  1.090
 4UG  C24  H26  single  0.970  0.020  1.090
 4UG  C25  H27  single  0.970  0.020  1.090
 4UG  C27  H28  single  0.970  0.020  1.090
 4UG  C27  H29  single  0.970  0.020  1.090
 4UG  N3   H30  single  0.890  0.020  1.040
 4UG  N4   H31  single  0.860  0.020  1.020
 4UG  O3   H32  single  0.850  0.020  0.980
 4UG  N3   H2   single  0.890  0.020  1.040

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
 4UG  H20  C6   H19  107.11  3.000
 4UG  H20  C6   C27  110.02  3.000
 4UG  H19  C6   C27  109.10  3.000
 4UG  H20  C6   C13  110.00  3.000
 4UG  H19  C6   C13  111.04  3.000
 4UG  C27  C6   C13  109.54  3.000
 4UG  H21  C11  N3   107.64  3.000
 4UG  H21  C11  C24  105.59  3.000
 4UG  N3   C11  C24  114.66  3.000
 4UG  H21  C11  C17  109.02  3.000
 4UG  N3   C11  C17  110.54  3.000
 4UG  C24  C11  C17  109.16  3.000
 4UG  H23  C13  H22  106.77  3.000
 4UG  H23  C13  C25  109.98  3.000
 4UG  H22  C13  C25  109.41  3.000
 4UG  H23  C13  C6   109.58  3.000
 4UG  H22  C13  C6   110.16  3.000
 4UG  C25  C13  C6   110.86  3.000
 4UG  O4   C15  N4   121.00  3.000
 4UG  N4   C15  C25  118.00  3.000
 4UG  O4   C15  C25  120.96  3.000
 4UG  H25  C17  H24  106.68  3.000
 4UG  H25  C17  C25  109.32  3.000
 4UG  H24  C17  C25  109.52  3.000
 4UG  H25  C17  C11  108.58  3.000
 4UG  H24  C17  C11  109.39  3.000
 4UG  C25  C17  C11  113.15  3.000
 4UG  N2   C19  C24  180.00  3.000
 4UG  H26  C24  O3   107.06  3.000
 4UG  H26  C24  C19  106.63  3.000
 4UG  O3   C24  C19  110.23  3.000
 4UG  H26  C24  C11  108.72  3.000
 4UG  O3   C24  C11  114.68  3.000
 4UG  C19  C24  C11  109.18  3.000
 4UG  H27  C25  C17  107.73  3.000
 4UG  H27  C25  C15  104.95  3.000
 4UG  C17  C25  C15  109.82  3.000
 4UG  H27  C25  C13  107.62  3.000
 4UG  C15  C25  C13  113.56  3.000
 4UG  C17  C25  C13  112.68  3.000
 4UG  H29  C27  H28  106.95  3.000
 4UG  H29  C27  N4   108.25  3.000
 4UG  H28  C27  N4   110.01  3.000
 4UG  H29  C27  C6   110.92  3.000
 4UG  H28  C27  C6   109.87  3.000
 4UG  N4   C27  C6   110.76  3.000
 4UG  H2   N3   H30  108.44  3.000
 4UG  H2   N3   C11  112.81  3.000
 4UG  H30  N3   C11  112.89  3.000
 4UG  H31  N4   C27  116.70  3.000
 4UG  H31  N4   C15  115.30  3.000
 4UG  C27  N4   C15  127.77  3.000
 4UG  H32  O3   C24  109.21  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
 4UG  CONST_01  C27  N4   C15  C25    0.00   0.0  0
 4UG  CONST_02  O4   C15  N4   C27  180.00   0.0  0
 4UG  CONST_03  H31  N4   C15  C25  180.00   0.0  0
 4UG  Var_01    C15  N4   C27  C6    23.04  30.0  1
 4UG  Var_02    N4   C27  C6   C13  -49.65  30.0  1
 4UG  Var_03    C27  C6   C13  C25   61.71  30.0  1

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
 4UG  chir_01  C11  C24  N3   C17  negativ
 4UG  chir_02  C24  O3   C11  C19  positiv
 4UG  chir_03  C25  C15  C13  C17  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
 4UG  plan-1  C15  0.020
 4UG  plan-1  C25  0.020
 4UG  plan-1  C27  0.020
 4UG  plan-1  N4   0.020
 4UG  plan-1  O4   0.020
 4UG  plan-1  H31  0.020

