# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:25:37 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: [4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(COC(=O)N[C@H]2CC(=O)NC2=O)cc1
#
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
 JOQ  JOQ  '[4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate'  ligand  35  20  .  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_JOQ
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
 JOQ  C4   C  C     0   0.573  -3.8498  -0.1333  -0.9982
 JOQ  C5   C  C     0   0.766  -1.0367  -1.0396   0.5258
 JOQ  C6   C  CH2   0  -0.244   1.2403  -1.6601   0.4735
 JOQ  C11  C  CR16  0  -0.273   4.2682  -0.0270  -1.1143
 JOQ  C7   C  CR6   0   0.060   2.5631  -0.9787   0.3085
 JOQ  C8   C  CR16  0  -0.279   3.3167  -0.6135   1.4171
 JOQ  C9   C  CR16  0  -0.297   4.5356   0.0331   1.2616
 JOQ  C10  C  CR6   0   0.086   5.0314   0.3300  -0.0035
 JOQ  C12  C  CR16  0  -0.273   3.0527  -0.6740  -0.9597
 JOQ  C13  C  CH2   0  -0.342   6.3766   0.9915  -0.1634
 JOQ  N1   N  NH1   0  -0.678  -5.0273   0.5674  -0.9650
 JOQ  N2   N  NH1   0  -0.658  -1.8727   0.0213   0.4646
 JOQ  C3   C  CH1   0  -0.228  -3.2915  -0.1318   0.4230
 JOQ  N3   N  NH2   0  -0.792   6.3675   1.9925  -1.2161
 JOQ  C1   C  C     0   0.549  -5.2738   1.2051   0.2306
 JOQ  C2   C  CH2   0  -0.601  -4.0805   0.9713   1.1236
 JOQ  O1   O  O     0  -0.419  -6.2624   1.8488   0.4745
 JOQ  O2   O  O     0  -0.408  -3.3637  -0.6600  -1.9647
 JOQ  O3   O  O2    0  -0.478   0.2309  -0.6411   0.4202
 JOQ  O4   O  O     0  -0.511  -1.3819  -2.1915   0.6797
 JOQ  H1   H  HCH2  0   0.249   1.0753  -2.3881  -0.3233
 JOQ  H2   H  HCH2  0   0.250   1.1918  -2.1854   1.4296
 JOQ  H4   H  HCR6  0   0.253   2.9515  -0.8335   2.4132
 JOQ  H5   H  HCR6  0   0.249   5.1070   0.3101   2.1399
 JOQ  H6   H  HCR6  0   0.250   2.4810  -0.9511  -1.8380
 JOQ  H7   H  HCH2  0   0.215   6.6963   1.3729   0.8155
 JOQ  H8   H  HCH2  0   0.241   7.1084   0.2255  -0.4373
 JOQ  H9   H  HNH1  0   0.428  -5.6425   0.6518  -1.7650
 JOQ  H10  H  HNH1  0   0.409  -1.4869   0.9273   0.2435
 JOQ  H11  H  HCH1  0   0.332  -3.5525  -1.1001   0.8567
 JOQ  H12  H  HNH2  0   0.344   5.8174   2.7890  -0.9194
 JOQ  H13  H  HNH2  0   0.354   7.3077   2.3397  -1.3539
 JOQ  H15  H  HCH2  0   0.311  -4.3880   0.7160   2.1356
 JOQ  H16  H  HCH2  0   0.312  -3.5098   1.9027   1.1730
 JOQ  H3   H  HCR6  0   0.248   4.6318   0.2045  -2.1070

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
 JOQ  O1   C1   double    1.205  0.020  1.205
 JOQ  C1   N1   single    1.377  0.020  1.377
 JOQ  C1   C2   single    1.509  0.020  1.509
 JOQ  N1   C4   single    1.371  0.020  1.371
 JOQ  C4   O2   double    1.203  0.020  1.203
 JOQ  C4   C3   single    1.527  0.020  1.527
 JOQ  C2   C3   single    1.526  0.020  1.526
 JOQ  C3   N2   single    1.428  0.020  1.428
 JOQ  O4   C5   double    1.212  0.020  1.212
 JOQ  N2   C5   single    1.352  0.020  1.352
 JOQ  C5   O3   single    1.333  0.020  1.333
 JOQ  C12  C11  aromatic  1.386  0.020  1.386
 JOQ  C12  C7   aromatic  1.393  0.020  1.393
 JOQ  C11  C10  aromatic  1.394  0.020  1.394
 JOQ  O3   C6   single    1.435  0.020  1.435
 JOQ  C6   C7   single    1.497  0.020  1.497
 JOQ  C7   C8   aromatic  1.389  0.020  1.389
 JOQ  C10  C13  single    1.507  0.020  1.507
 JOQ  C10  C9   aromatic  1.391  0.020  1.391
 JOQ  C13  N3   single    1.453  0.020  1.453
 JOQ  C8   C9   aromatic  1.389  0.020  1.389
 JOQ  C6   H1   single    0.970  0.020  1.090
 JOQ  C6   H2   single    0.970  0.020  1.090
 JOQ  C11  H3   single    0.930  0.020  1.080
 JOQ  C8   H4   single    0.930  0.020  1.080
 JOQ  C9   H5   single    0.930  0.020  1.080
 JOQ  C12  H6   single    0.930  0.020  1.080
 JOQ  C13  H7   single    0.970  0.020  1.090
 JOQ  C13  H8   single    0.970  0.020  1.090
 JOQ  N1   H9   single    0.860  0.020  1.020
 JOQ  N2   H10  single    0.860  0.020  1.020
 JOQ  C3   H11  single    0.970  0.020  1.090
 JOQ  N3   H12  single    0.890  0.020  1.040
 JOQ  N3   H13  single    0.890  0.020  1.040
 JOQ  C2   H15  single    0.970  0.020  1.090
 JOQ  C2   H16  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
 JOQ  O2   C4   C3   126.89  3.000
 JOQ  C3   C4   N1   106.92  3.000
 JOQ  O2   C4   N1   126.18  3.000
 JOQ  O4   C5   O3   124.39  3.000
 JOQ  O3   C5   N2   110.48  3.000
 JOQ  O4   C5   N2   125.11  3.000
 JOQ  H2   C6   H1   108.15  3.000
 JOQ  H2   C6   O3   110.05  3.000
 JOQ  H1   C6   O3   109.88  3.000
 JOQ  H2   C6   C7   110.78  3.000
 JOQ  H1   C6   C7   110.88  3.000
 JOQ  O3   C6   C7   107.11  3.000
 JOQ  H3   C11  C12  119.80  3.000
 JOQ  H3   C11  C10  119.48  3.000
 JOQ  C12  C11  C10  120.72  3.000
 JOQ  C12  C7   C8   118.57  3.000
 JOQ  C8   C7   C6   120.73  3.000
 JOQ  C12  C7   C6   120.69  3.000
 JOQ  H4   C8   C9   119.56  3.000
 JOQ  H4   C8   C7   119.83  3.000
 JOQ  C9   C8   C7   120.61  3.000
 JOQ  H5   C9   C10  119.65  3.000
 JOQ  H5   C9   C8   119.41  3.000
 JOQ  C10  C9   C8   120.94  3.000
 JOQ  C13  C10  C9   120.54  3.000
 JOQ  C9   C10  C11  118.35  3.000
 JOQ  C13  C10  C11  121.09  3.000
 JOQ  H6   C12  C7   119.76  3.000
 JOQ  H6   C12  C11  119.44  3.000
 JOQ  C7   C12  C11  120.80  3.000
 JOQ  H8   C13  H7   105.76  3.000
 JOQ  H8   C13  N3   107.77  3.000
 JOQ  H7   C13  N3   114.11  3.000
 JOQ  H8   C13  C10  108.43  3.000
 JOQ  H7   C13  C10  108.52  3.000
 JOQ  N3   C13  C10  111.94  3.000
 JOQ  H9   N1   C1   122.57  3.000
 JOQ  H9   N1   C4   123.05  3.000
 JOQ  C1   N1   C4   114.30  3.000
 JOQ  H10  N2   C3   118.02  3.000
 JOQ  H10  N2   C5   118.54  3.000
 JOQ  C3   N2   C5   122.12  3.000
 JOQ  H11  C3   C2   109.56  3.000
 JOQ  H11  C3   N2   108.72  3.000
 JOQ  C2   C3   N2   115.01  3.000
 JOQ  H11  C3   C4   106.33  3.000
 JOQ  N2   C3   C4   112.99  3.000
 JOQ  C2   C3   C4   103.82  3.000
 JOQ  H13  N3   H12  105.95  3.000
 JOQ  H13  N3   C13  109.23  3.000
 JOQ  H12  N3   C13  109.45  3.000
 JOQ  O1   C1   C2   127.74  3.000
 JOQ  C2   C1   N1   107.49  3.000
 JOQ  O1   C1   N1   124.76  3.000
 JOQ  H16  C2   H15  107.78  3.000
 JOQ  H16  C2   C1   107.91  3.000
 JOQ  H15  C2   C1   111.31  3.000
 JOQ  H16  C2   C3   111.50  3.000
 JOQ  H15  C2   C3   113.79  3.000
 JOQ  C1   C2   C3   104.43  3.000
 JOQ  C6   O3   C5   116.98  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
 JOQ  CONST_01  C8   C7   C12  C11    0.00   0.0  0
 JOQ  CONST_02  C8   C9   C10  C11    0.00   0.0  0
 JOQ  CONST_03  C10  C11  C12  C7     0.00   0.0  0
 JOQ  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 JOQ  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 JOQ  CONST_06  C12  C7   C8   C9     0.00   0.0  0
 JOQ  CONST_07  C1   N1   C4   C3     0.00   0.0  0
 JOQ  CONST_08  C11  C12  C7   C6   180.00   0.0  0
 JOQ  CONST_09  C9   C8   C7   C6   180.00   0.0  0
 JOQ  CONST_10  C13  C10  C9   C8   180.00   0.0  0
 JOQ  CONST_11  C13  C10  C11  C12  180.00   0.0  0
 JOQ  CONST_12  O2   C4   N1   C1   180.00   0.0  0
 JOQ  CONST_13  H5   C9   C10  C11  180.00   0.0  0
 JOQ  CONST_14  H3   C11  C12  C7   180.00   0.0  0
 JOQ  CONST_15  H6   C12  C7   C8   180.00   0.0  0
 JOQ  CONST_16  H4   C8   C9   C10  180.00   0.0  0
 JOQ  CONST_17  H9   N1   C4   C3   180.00   0.0  0
 JOQ  Var_01    C2   C1   N1   C4     3.03  30.0  1
 JOQ  Var_02    C3   C2   C1   N1   -12.90  30.0  1
 JOQ  Var_03    N3   C13  C10  C11   41.24  30.0  2
 JOQ  Var_04    O3   C6   C7   C8    95.18  30.0  3
 JOQ  Var_05    C7   C6   O3   C5   178.91  30.0  3
 JOQ  Var_06    O4   C5   N2   C3    -7.43  30.0  2
 JOQ  Var_07    H12  N3   C13  C10   70.28  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
 JOQ  chir_01  C3  C4  C2  N2  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
 JOQ  plan-1  C6   0.020
 JOQ  plan-1  C11  0.020
 JOQ  plan-1  C7   0.020
 JOQ  plan-1  C8   0.020
 JOQ  plan-1  C9   0.020
 JOQ  plan-1  C10  0.020
 JOQ  plan-1  C12  0.020
 JOQ  plan-1  C13  0.020
 JOQ  plan-1  H4   0.020
 JOQ  plan-1  H5   0.020
 JOQ  plan-1  H6   0.020
 JOQ  plan-1  H3   0.020
 JOQ  plan-2  C4   0.020
 JOQ  plan-2  N1   0.020
 JOQ  plan-2  C3   0.020
 JOQ  plan-2  C1   0.020
 JOQ  plan-2  O2   0.020
 JOQ  plan-2  H9   0.020
 JOQ  plan-3  N1   0.020
 JOQ  plan-3  C1   0.020
 JOQ  plan-3  C2   0.020
 JOQ  plan-3  O1   0.020
 JOQ  plan-4  C5   0.020
 JOQ  plan-4  N2   0.020
 JOQ  plan-4  O3   0.020
 JOQ  plan-4  O4   0.020

