# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 01:12:15 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2R)-2-methyl-4-[2-oxo-2-(pyrrolidin-1-yl)ethyl]piperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CC[NH2+]1)CC(=O)N2CCCC2
#
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
 4YD  4YD  (2R)-2-methyl-4-[2-oxo-2-(pyrrolidin-1-yl)ethyl]piperazin-1-ium  ligand  37  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4YD
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
 4YD  C1   C  CH3   0  -0.673  -4.5737   1.6084   0.5370
 4YD  C2   C  CH1   0  -0.144  -3.5101   0.5323   0.5236
 4YD  C3   C  CH2   0  -0.268  -2.1611   1.0363   0.0430
 4YD  N4   N  NT    0  -0.424  -1.1830  -0.0323   0.0197
 4YD  C5   C  CH2   0  -0.408   0.1469   0.4652  -0.2321
 4YD  C6   C  C     0   0.544   1.2308  -0.5123   0.2016
 4YD  C10  C  CH2   0  -0.474   4.3881   1.1235  -0.6113
 4YD  C11  C  CH2   0  -0.484   4.7865   0.1132   0.4597
 4YD  C12  C  CH2   0  -0.259   3.6361  -0.8860   0.4434
 4YD  C13  C  CH2   0  -0.310  -1.5950  -1.0557  -0.9211
 4YD  C14  C  CH2   0  -0.325  -2.9087  -1.6612  -0.4855
 4YD  O7   O  O     0  -0.501   0.9742  -1.6205   0.6549
 4YD  N8   N  NT    0  -0.473   2.4882  -0.0733   0.0507
 4YD  C9   C  CH2   0  -0.276   2.8811   1.2518  -0.4216
 4YD  N15  N  NT2   1  -0.647  -3.9404  -0.5940  -0.3664
 4YD  H16  H  HCH3  0   0.263  -5.5310   1.2187   0.8820
 4YD  H18  H  HCH3  0   0.266  -4.2744   2.4013   1.2206
 4YD  H17  H  HCH3  0   0.247  -4.7116   2.0500  -0.4504
 4YD  H19  H  HCH1  0   0.303  -3.3996   0.0900   1.5147
 4YD  H20  H  HCH2  0   0.220  -2.2820   1.5181  -0.9432
 4YD  H21  H  HCH2  0   0.278  -1.8378   1.8125   0.7384
 4YD  H23  H  HCH2  0   0.248   0.3027   0.7321  -1.2906
 4YD  H22  H  HCH2  0   0.282   0.2835   1.3941   0.3306
 4YD  H26  H  HCH2  0   0.241   4.6088   0.7296  -1.6056
 4YD  H28  H  HCH2  0   0.253   5.7475  -0.3617   0.2672
 4YD  H29  H  HCH2  0   0.239   4.8446   0.6019   1.4347
 4YD  H30  H  HCH2  0   0.237   3.8064  -1.6805  -0.2889
 4YD  H31  H  HCH2  0   0.247   3.4717  -1.3571   1.4122
 4YD  H33  H  HCH2  0   0.227  -1.6891  -0.6588  -1.9464
 4YD  H32  H  HCH2  0   0.283  -0.8617  -1.8581  -0.9523
 4YD  H34  H  HCH2  0   0.306  -3.2728  -2.3919  -1.2034
 4YD  H35  H  HCH2  0   0.295  -2.8232  -2.1301   0.4927
 4YD  H25  H  HCH2  0   0.244   2.6455   2.0159   0.3262
 4YD  H24  H  HCH2  0   0.255   2.3688   1.5206  -1.3461
 4YD  H37  H  HNT2  0   0.476  -4.8105  -0.9972  -0.0162
 4YD  H36  H  HNT2  0   0.459  -4.1642  -0.2330  -1.2966
 4YD  H27  H  HCH2  0   0.254   4.8950   2.0823  -0.5117

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
 4YD  C10  C11  single  1.525  0.020  1.525
 4YD  C10  C9   single  1.524  0.020  1.524
 4YD  C11  C12  single  1.524  0.020  1.524
 4YD  C9   N8   single  1.461  0.020  1.461
 4YD  C12  N8   single  1.460  0.020  1.460
 4YD  N8   C6   single  1.340  0.020  1.340
 4YD  C6   O7   double  1.225  0.020  1.225
 4YD  C6   C5   single  1.523  0.020  1.523
 4YD  C5   N4   single  1.442  0.020  1.442
 4YD  N4   C3   single  1.449  0.020  1.449
 4YD  N4   C13  single  1.450  0.020  1.450
 4YD  C3   C2   single  1.518  0.020  1.518
 4YD  C13  C14  single  1.511  0.020  1.511
 4YD  C2   C1   single  1.513  0.020  1.513
 4YD  C2   N15  single  1.499  0.020  1.499
 4YD  C14  N15  single  1.489  0.020  1.489
 4YD  C1   H16  single  0.970  0.020  1.090
 4YD  C1   H18  single  0.970  0.020  1.090
 4YD  C1   H17  single  0.970  0.020  1.090
 4YD  C2   H19  single  0.970  0.020  1.090
 4YD  C3   H20  single  0.970  0.020  1.090
 4YD  C3   H21  single  0.970  0.020  1.090
 4YD  C5   H23  single  0.970  0.020  1.090
 4YD  C5   H22  single  0.970  0.020  1.090
 4YD  C10  H27  single  0.970  0.020  1.090
 4YD  C10  H26  single  0.970  0.020  1.090
 4YD  C11  H28  single  0.970  0.020  1.090
 4YD  C11  H29  single  0.970  0.020  1.090
 4YD  C12  H30  single  0.970  0.020  1.090
 4YD  C12  H31  single  0.970  0.020  1.090
 4YD  C13  H33  single  0.970  0.020  1.090
 4YD  C13  H32  single  0.970  0.020  1.090
 4YD  C14  H34  single  0.970  0.020  1.090
 4YD  C14  H35  single  0.970  0.020  1.090
 4YD  C9   H25  single  0.970  0.020  1.090
 4YD  C9   H24  single  0.970  0.020  1.090
 4YD  N15  H37  single  0.890  0.020  1.040
 4YD  N15  H36  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
 4YD  H17  C1   H18  107.96  3.000
 4YD  H17  C1   H16  108.69  3.000
 4YD  H18  C1   H16  107.65  3.000
 4YD  H17  C1   C2   111.65  3.000
 4YD  H18  C1   C2   109.29  3.000
 4YD  H16  C1   C2   111.47  3.000
 4YD  H19  C2   N15  105.30  3.000
 4YD  H19  C2   C3   109.40  3.000
 4YD  N15  C2   C3   108.46  3.000
 4YD  H19  C2   C1   110.58  3.000
 4YD  N15  C2   C1   109.75  3.000
 4YD  C3   C2   C1   113.04  3.000
 4YD  H21  C3   H20  106.94  3.000
 4YD  H21  C3   N4   109.57  3.000
 4YD  H20  C3   N4   112.42  3.000
 4YD  H21  C3   C2   107.32  3.000
 4YD  H20  C3   C2   109.28  3.000
 4YD  N4   C3   C2   111.10  3.000
 4YD  C13  N4   C5   113.10  3.000
 4YD  C13  N4   C3   109.83  3.000
 4YD  C5   N4   C3   111.77  3.000
 4YD  H22  C5   H23  105.69  3.000
 4YD  H22  C5   C6   108.03  3.000
 4YD  H23  C5   C6   109.16  3.000
 4YD  H22  C5   N4   108.55  3.000
 4YD  H23  C5   N4   112.42  3.000
 4YD  C6   C5   N4   112.66  3.000
 4YD  N8   C6   O7   122.32  3.000
 4YD  O7   C6   C5   122.49  3.000
 4YD  N8   C6   C5   115.18  3.000
 4YD  H26  C10  H27  107.87  3.000
 4YD  H26  C10  C9   110.09  3.000
 4YD  H27  C10  C9   112.01  3.000
 4YD  H26  C10  C11  110.34  3.000
 4YD  H27  C10  C11  113.41  3.000
 4YD  C9   C10  C11  103.09  3.000
 4YD  H29  C11  H28  107.81  3.000
 4YD  H29  C11  C12  110.07  3.000
 4YD  H28  C11  C12  112.23  3.000
 4YD  H29  C11  C10  110.15  3.000
 4YD  H28  C11  C10  113.28  3.000
 4YD  C12  C11  C10  103.28  3.000
 4YD  H31  C12  H30  107.74  3.000
 4YD  H31  C12  N8   111.16  3.000
 4YD  H30  C12  N8   110.27  3.000
 4YD  H31  C12  C11  112.82  3.000
 4YD  H30  C12  C11  111.47  3.000
 4YD  N8   C12  C11  103.38  3.000
 4YD  H32  C13  H33  107.23  3.000
 4YD  H32  C13  C14  107.40  3.000
 4YD  H33  C13  C14  109.75  3.000
 4YD  H32  C13  N4   110.35  3.000
 4YD  H33  C13  N4   111.92  3.000
 4YD  C14  C13  N4   110.05  3.000
 4YD  H35  C14  H34  109.29  3.000
 4YD  H35  C14  N15  106.94  3.000
 4YD  H34  C14  N15  107.61  3.000
 4YD  H35  C14  C13  111.32  3.000
 4YD  H34  C14  C13  111.73  3.000
 4YD  N15  C14  C13  109.78  3.000
 4YD  C9   N8   C12  112.35  3.000
 4YD  C12  N8   C6   121.66  3.000
 4YD  C9   N8   C6   125.87  3.000
 4YD  H24  C9   H25  107.81  3.000
 4YD  H24  C9   N8   111.79  3.000
 4YD  H25  C9   N8   110.76  3.000
 4YD  H24  C9   C10  112.31  3.000
 4YD  H25  C9   C10  110.89  3.000
 4YD  N8   C9   C10  103.29  3.000
 4YD  H36  N15  H37  105.36  3.000
 4YD  H36  N15  C14  109.39  3.000
 4YD  H37  N15  C14  109.57  3.000
 4YD  H36  N15  C2   109.74  3.000
 4YD  H37  N15  C2   109.74  3.000
 4YD  C14  N15  C2   112.78  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
 4YD  CONST_01  C9   N8   C6   C5      0.00   0.0  0
 4YD  CONST_02  C12  N8   C6   C5    180.00   0.0  0
 4YD  CONST_03  O7   C6   N8   C12     0.00   0.0  0
 4YD  CONST_04  C9   N8   C6   O7    180.00   0.0  0
 4YD  Var_01    C13  N4   C3   C2     62.62  30.0  1
 4YD  Var_02    C13  C14  N15  C2    -53.94  30.0  1
 4YD  Var_03    C14  C13  N4   C3    -62.18  30.0  1
 4YD  Var_04    N15  C14  C13  N4     57.35  30.0  1
 4YD  Var_05    N8   C12  C11  C10   -30.49  30.0  1
 4YD  Var_06    C12  N8   C9   C10    12.72  30.0  1
 4YD  Var_07    N8   C9   C10  C11   -31.32  30.0  1
 4YD  Var_08    C9   N8   C12  C11    11.21  30.0  1
 4YD  Var_09    C9   C10  C11  C12    38.50  30.0  1
 4YD  Var_10    C6   C5   N4   C3    160.25  30.0  1
 4YD  Var_11    N8   C6   C5   N4   -176.89  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
 4YD  chir_01  C2  C3  C1  N15  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
 4YD  plan-1  C5   0.020
 4YD  plan-1  C6   0.020
 4YD  plan-1  C12  0.020
 4YD  plan-1  O7   0.020
 4YD  plan-1  N8   0.020
 4YD  plan-1  C9   0.020

