# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:55:57 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: [(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC[C@H](NC(=O)OC[C@H]2CCCN2)C(=O)N1
#
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
 JP8  JP8  '[(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate'  ligand  35  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JP8
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
 JP8  C4   C  CH2   0  -0.593   4.4180   1.1692   0.5204
 JP8  C5   C  C     0   0.556   4.8810  -0.2227   0.1964
 JP8  C6   C  C     0   0.760  -0.2848   0.5437  -0.6091
 JP8  C11  C  CH2   0  -0.327  -5.3665  -0.7449   1.2765
 JP8  C7   C  CH2   0  -0.175  -2.6279   0.4136  -0.8573
 JP8  C8   C  CH1   0  -0.136  -3.8555   0.4330   0.0195
 JP8  C9   C  CH2   0  -0.465  -5.1558   0.4743  -0.8122
 JP8  C10  C  CH2   0  -0.463  -6.1693  -0.3223   0.0310
 JP8  N1   N  NH1   0  -0.686   3.8991  -1.1237  -0.1642
 JP8  N2   N  NH1   0  -0.658   0.7028   0.5814   0.3127
 JP8  C3   C  CH2   0  -0.472   2.9672   1.2338   0.9643
 JP8  N3   N  NH1   0  -0.576  -3.9595  -0.7285   0.8946
 JP8  C1   C  C     0   0.573   2.5437  -0.9054  -0.2635
 JP8  C2   C  CH1   0  -0.207   2.0847   0.5318  -0.0567
 JP8  O1   O  O     0  -0.417   1.7864  -1.8108  -0.5176
 JP8  O2   O  O     0  -0.433   6.0402  -0.5676   0.2242
 JP8  O3   O  O2    0  -0.481  -1.4739   0.4408  -0.0167
 JP8  O4   O  O     0  -0.514  -0.1218   0.6252  -1.8079
 JP8  H1   H  HCH2  0   0.298   5.0838   1.5788   1.2792
 JP8  H2   H  HCH2  0   0.294   4.5622   1.7743  -0.3809
 JP8  H4   H  HCH2  0   0.239  -5.6498  -1.7239   1.6630
 JP8  H5   H  HCH2  0   0.230  -2.6211  -0.4880  -1.4790
 JP8  H6   H  HCH2  0   0.245  -2.6390   1.2807  -1.5216
 JP8  H7   H  HCH1  0   0.239  -3.8198   1.3262   0.6549
 JP8  H8   H  HCH2  0   0.240  -5.4762   1.4983  -1.0041
 JP8  H9   H  HCH2  0   0.231  -5.0036  -0.0004  -1.7852
 JP8  H10  H  HCH2  0   0.231  -6.5188  -1.1997  -0.5150
 JP8  H11  H  HCH2  0   0.233  -7.0504   0.2644   0.2928
 JP8  H12  H  HNH1  0   0.417   4.2125  -2.0679  -0.3624
 JP8  H13  H  HNH1  0   0.404   0.4684   0.3848   1.2742
 JP8  H14  H  HCH2  0   0.262   2.8503   0.7681   1.9466
 JP8  H15  H  HCH2  0   0.282   2.6545   2.2729   1.0581
 JP8  H16  H  HNH1  0   0.337  -3.7715  -1.5621   0.3448
 JP8  H18  H  HCH1  0   0.310   2.2053   1.0372  -1.0209
 JP8  H3   H  HCH2  0   0.223  -5.5173  -0.0200   2.0813

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
 JP8  O2   C5   double  1.210  0.020  1.210
 JP8  C5   C4   single  1.502  0.020  1.502
 JP8  C5   N1   single  1.381  0.020  1.381
 JP8  C4   C3   single  1.519  0.020  1.519
 JP8  N1   C1   single  1.376  0.020  1.376
 JP8  C3   C2   single  1.521  0.020  1.521
 JP8  C1   C2   single  1.523  0.020  1.523
 JP8  C1   O1   double  1.207  0.020  1.207
 JP8  C2   N2   single  1.431  0.020  1.431
 JP8  N2   C6   single  1.351  0.020  1.351
 JP8  O4   C6   double  1.213  0.020  1.213
 JP8  C6   O3   single  1.332  0.020  1.332
 JP8  O3   C7   single  1.428  0.020  1.428
 JP8  C7   C8   single  1.509  0.020  1.509
 JP8  C8   C9   single  1.544  0.020  1.544
 JP8  C8   N3   single  1.458  0.020  1.458
 JP8  C9   C10  single  1.540  0.020  1.540
 JP8  N3   C11  single  1.458  0.020  1.458
 JP8  C10  C11  single  1.541  0.020  1.541
 JP8  C4   H1   single  0.970  0.020  1.090
 JP8  C4   H2   single  0.970  0.020  1.090
 JP8  C11  H3   single  0.970  0.020  1.090
 JP8  C11  H4   single  0.970  0.020  1.090
 JP8  C7   H5   single  0.970  0.020  1.090
 JP8  C7   H6   single  0.970  0.020  1.090
 JP8  C8   H7   single  0.970  0.020  1.090
 JP8  C9   H8   single  0.970  0.020  1.090
 JP8  C9   H9   single  0.970  0.020  1.090
 JP8  C10  H10  single  0.970  0.020  1.090
 JP8  C10  H11  single  0.970  0.020  1.090
 JP8  N1   H12  single  0.860  0.020  1.020
 JP8  N2   H13  single  0.860  0.020  1.020
 JP8  C3   H14  single  0.970  0.020  1.090
 JP8  C3   H15  single  0.970  0.020  1.090
 JP8  N3   H16  single  0.890  0.020  1.040
 JP8  C2   H18  single  0.970  0.020  1.090

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
 JP8  H2   C4   H1   106.57  3.000
 JP8  H2   C4   C3   110.05  3.000
 JP8  H1   C4   C3   111.36  3.000
 JP8  H2   C4   C5   107.09  3.000
 JP8  H1   C4   C5   108.07  3.000
 JP8  C3   C4   C5   113.38  3.000
 JP8  O2   C5   N1   120.10  3.000
 JP8  N1   C5   C4   116.22  3.000
 JP8  O2   C5   C4   123.68  3.000
 JP8  O4   C6   O3   124.38  3.000
 JP8  O3   C6   N2   110.55  3.000
 JP8  O4   C6   N2   125.04  3.000
 JP8  H4   C11  H3   107.37  3.000
 JP8  H4   C11  N3   110.72  3.000
 JP8  H3   C11  N3   108.57  3.000
 JP8  H4   C11  C10  113.42  3.000
 JP8  H3   C11  C10  109.95  3.000
 JP8  N3   C11  C10  106.74  3.000
 JP8  H6   C7   H5   107.96  3.000
 JP8  H6   C7   O3   110.56  3.000
 JP8  H5   C7   O3   110.18  3.000
 JP8  H6   C7   C8   109.57  3.000
 JP8  H5   C7   C8   110.21  3.000
 JP8  O3   C7   C8   108.37  3.000
 JP8  H7   C8   N3   107.66  3.000
 JP8  H7   C8   C9   108.52  3.000
 JP8  N3   C8   C9   106.53  3.000
 JP8  H7   C8   C7   108.71  3.000
 JP8  N3   C8   C7   113.37  3.000
 JP8  C9   C8   C7   111.87  3.000
 JP8  H9   C9   H8   106.99  3.000
 JP8  H9   C9   C10  110.75  3.000
 JP8  H8   C9   C10  112.88  3.000
 JP8  H9   C9   C8   110.52  3.000
 JP8  H8   C9   C8   111.55  3.000
 JP8  C10  C9   C8   104.20  3.000
 JP8  H11  C10  H10  107.10  3.000
 JP8  H11  C10  C9   112.63  3.000
 JP8  H10  C10  C9   110.65  3.000
 JP8  H11  C10  C11  111.99  3.000
 JP8  H10  C10  C11  110.54  3.000
 JP8  C9   C10  C11  103.98  3.000
 JP8  H12  N1   C1   115.96  3.000
 JP8  H12  N1   C5   116.02  3.000
 JP8  C1   N1   C5   128.01  3.000
 JP8  H13  N2   C2   117.61  3.000
 JP8  H13  N2   C6   118.34  3.000
 JP8  C2   N2   C6   121.91  3.000
 JP8  H15  C3   H14  107.35  3.000
 JP8  H15  C3   C2   109.36  3.000
 JP8  H14  C3   C2   110.14  3.000
 JP8  H15  C3   C4   109.88  3.000
 JP8  H14  C3   C4   110.28  3.000
 JP8  C2   C3   C4   109.79  3.000
 JP8  H16  N3   C8   108.40  3.000
 JP8  H16  N3   C11  108.13  3.000
 JP8  C8   N3   C11  103.59  3.000
 JP8  O1   C1   C2   123.18  3.000
 JP8  O1   C1   N1   120.93  3.000
 JP8  C2   C1   N1   115.89  3.000
 JP8  H18  C2   C1   106.42  3.000
 JP8  H18  C2   C3   108.30  3.000
 JP8  C1   C2   C3   110.60  3.000
 JP8  H18  C2   N2   108.52  3.000
 JP8  C1   C2   N2   111.03  3.000
 JP8  C3   C2   N2   111.77  3.000
 JP8  C7   O3   C6   117.45  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
 JP8  CONST_01  C1   N1   C5   C4      0.00   0.0  0
 JP8  CONST_02  O2   C5   N1   C1    180.00   0.0  0
 JP8  CONST_03  H12  N1   C5   C4    180.00   0.0  0
 JP8  Var_01    C2   C3   C4   C5    -52.32  30.0  1
 JP8  Var_02    C2   C1   N1   C5      5.26  30.0  1
 JP8  Var_03    C8   C9   C10  C11     0.31  30.0  1
 JP8  Var_04    C10  C11  N3   C8     37.94  30.0  1
 JP8  Var_05    N3   C11  C10  C9    -23.27  30.0  1
 JP8  Var_06    C3   C4   C5   N1     24.25  30.0  1
 JP8  Var_07    C8   C7   O3   C6   -174.43  30.0  3
 JP8  Var_08    O4   C6   N2   C2     -9.18  30.0  2
 JP8  Var_09    N2   C6   O3   C7    178.88  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
 JP8  chir_01  C8  C7  C9  N3  negativ
 JP8  chir_02  C2  N2  C1  C3  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
 JP8  plan-1  N1   0.020
 JP8  plan-1  C1   0.020
 JP8  plan-1  C2   0.020
 JP8  plan-1  O1   0.020
 JP8  plan-2  C4   0.020
 JP8  plan-2  C5   0.020
 JP8  plan-2  N1   0.020
 JP8  plan-2  C1   0.020
 JP8  plan-2  O2   0.020
 JP8  plan-2  H12  0.020
 JP8  plan-3  C6   0.020
 JP8  plan-3  N2   0.020
 JP8  plan-3  O3   0.020
 JP8  plan-3  O4   0.020

