# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:49:06 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2~{S})-2-methyl-4-(oxetan-3-yl)-~{N}-(phenylmethyl)piperazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CN(CCN1)C2COC2)C(=O)NCc3ccccc3
#
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
 LO8  LO8  (2~{S})-2-methyl-4-(oxetan-3-yl)-~{N}-(phenylmethyl)piperazine-2-carboxamide  ligand  44  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LO8
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
 LO8  N1   N  NH1   0  -0.602   0.3579  -1.7337  -1.2912
 LO8  C4   C  CH2   0  -0.326   0.5123  -0.4400  -1.9449
 LO8  C5   C  C     0  -0.181   3.6763   0.7560  -0.3943
 LO8  C6   C  C     0  -0.138   4.0802   1.1385   1.0342
 LO8  C7   C  C     0  -0.137   3.7115   2.2666  -0.6451
 LO8  C8   C  C     0   0.582   0.1033  -1.0563   1.0542
 LO8  C10  C  CR6   0   0.077  -3.2676   0.2848   0.7041
 LO8  C13  C  CR16  0  -0.267  -5.2352   1.4392  -0.9073
 LO8  C15  C  CR16  0  -0.285  -2.9606   1.3632  -0.1238
 LO8  N    N  NT    0  -0.430   2.3812   0.1378  -0.5216
 LO8  C    C  CH3   0  -0.655   1.0369  -3.2628   0.4660
 LO8  O    O  O     0  -0.512   4.1038   2.5326   0.7062
 LO8  C1   C  CT    0  -0.089   0.9771  -1.7990   0.0292
 LO8  C11  C  CR16  0  -0.304  -4.5682  -0.2060   0.7157
 LO8  C12  C  CR16  0  -0.241  -5.5506   0.3696  -0.0821
 LO8  C14  C  CR16  0  -0.240  -3.9374   1.9388  -0.9223
 LO8  C2   C  CH2   0  -0.244   2.3840  -1.2017   0.0347
 LO8  C3   C  CH2   0  -0.293   1.9317   0.0967  -1.9023
 LO8  C9   C  CH2   0  -0.326  -2.1991  -0.3493   1.5523
 LO8  N2   N  NH1   0  -0.624  -1.1873  -0.9575   0.7181
 LO8  O1   O  O     0  -0.501   0.5590  -0.6513   2.1157
 LO8  H1   H  HNH1  0   0.358   0.7681  -2.4533  -1.8761
 LO8  H3   H  HCH2  0   0.247   0.1740  -0.5368  -2.9771
 LO8  H4   H  HCH2  0   0.224  -0.1492   0.2830  -1.4598
 LO8  H5   H  H     0   0.236   4.4589   0.2013  -0.9350
 LO8  H6   H  H     0   0.213   3.3331   0.9018   1.7987
 LO8  H7   H  H     0   0.219   5.0565   0.7696   1.3583
 LO8  H8   H  H     0   0.219   4.4552   2.6047  -1.3715
 LO8  H9   H  H     0   0.212   2.7436   2.7142  -0.8919
 LO8  H10  H  HCR6  0   0.257  -5.9968   1.8858  -1.5333
 LO8  H11  H  HCR6  0   0.250  -1.9509   1.7576  -0.1463
 LO8  H13  H  HCH3  0   0.245   0.0417  -3.7079   0.4625
 LO8  H14  H  HCH3  0   0.242   1.6690  -3.8339  -0.2163
 LO8  H15  H  HCH3  0   0.244   1.4532  -3.3582   1.4684
 LO8  H16  H  HCR6  0   0.253  -4.8141  -1.0458   1.3553
 LO8  H17  H  HCR6  0   0.256  -6.5587  -0.0238  -0.0605
 LO8  H18  H  HCR6  0   0.257  -3.6891   2.7780  -1.5591
 LO8  H19  H  HCH2  0   0.207   3.0466  -1.8730  -0.5408
 LO8  H20  H  HCH2  0   0.246   2.7638  -1.1714   1.0560
 LO8  H21  H  HCH2  0   0.196   2.5930  -0.5306  -2.5256
 LO8  H22  H  HCH2  0   0.241   1.9462   1.1034  -2.3268
 LO8  H23  H  HCH2  0   0.259  -1.7165   0.4005   2.1811
 LO8  H24  H  HCH2  0   0.252  -2.6461  -1.0860   2.2262
 LO8  H25  H  HNH1  0   0.402  -1.4557  -1.3647  -0.1671

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
 LO8  C14  C13  aromatic  1.391  0.020  1.391
 LO8  C14  C15  aromatic  1.387  0.020  1.387
 LO8  O    C7   single    1.432  0.020  1.432
 LO8  O    C6   single    1.432  0.020  1.432
 LO8  C7   C5   single    1.532  0.020  1.532
 LO8  C13  C12  aromatic  1.387  0.020  1.387
 LO8  C15  C10  aromatic  1.394  0.020  1.394
 LO8  C6   C5   single    1.533  0.020  1.533
 LO8  C    C1   single    1.529  0.020  1.529
 LO8  C12  C11  aromatic  1.390  0.020  1.390
 LO8  C5   N    single    1.441  0.020  1.441
 LO8  C10  C11  aromatic  1.390  0.020  1.390
 LO8  C10  C9   single    1.504  0.020  1.504
 LO8  C2   N    single    1.450  0.020  1.450
 LO8  C2   C1   single    1.528  0.020  1.528
 LO8  N2   C9   single    1.446  0.020  1.446
 LO8  N2   C8   single    1.337  0.020  1.337
 LO8  N    C3   single    1.453  0.020  1.453
 LO8  C1   C8   single    1.538  0.020  1.538
 LO8  C1   N1   single    1.460  0.020  1.460
 LO8  C3   C4   single    1.518  0.020  1.518
 LO8  C8   O1   double    1.224  0.020  1.224
 LO8  C4   N1   single    1.458  0.020  1.458
 LO8  N1   H1   single    0.890  0.020  1.040
 LO8  C4   H3   single    0.970  0.020  1.090
 LO8  C4   H4   single    0.970  0.020  1.090
 LO8  C5   H5   single    0.970  0.020  1.090
 LO8  C6   H6   single    0.970  0.020  1.090
 LO8  C6   H7   single    0.970  0.020  1.090
 LO8  C7   H8   single    0.970  0.020  1.090
 LO8  C7   H9   single    0.970  0.020  1.090
 LO8  C13  H10  single    0.930  0.020  1.080
 LO8  C15  H11  single    0.930  0.020  1.080
 LO8  C    H13  single    0.970  0.020  1.090
 LO8  C    H14  single    0.970  0.020  1.090
 LO8  C    H15  single    0.970  0.020  1.090
 LO8  C11  H16  single    0.930  0.020  1.080
 LO8  C12  H17  single    0.930  0.020  1.080
 LO8  C14  H18  single    0.930  0.020  1.080
 LO8  C2   H19  single    0.970  0.020  1.090
 LO8  C2   H20  single    0.970  0.020  1.090
 LO8  C3   H21  single    0.970  0.020  1.090
 LO8  C3   H22  single    0.970  0.020  1.090
 LO8  C9   H23  single    0.970  0.020  1.090
 LO8  C9   H24  single    0.970  0.020  1.090
 LO8  N2   H25  single    0.860  0.020  1.020

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
 LO8  H1   N1   C1   108.57  3.000
 LO8  H1   N1   C4   109.17  3.000
 LO8  C1   N1   C4   113.60  3.000
 LO8  H4   C4   H3   106.91  3.000
 LO8  H4   C4   C3   108.63  3.000
 LO8  H3   C4   C3   110.37  3.000
 LO8  H4   C4   N1   108.89  3.000
 LO8  H3   C4   N1   108.23  3.000
 LO8  C3   C4   N1   113.59  3.000
 LO8  H5   C5   N    112.29  3.000
 LO8  H5   C5   C7   113.58  3.000
 LO8  N    C5   C7   115.43  3.000
 LO8  H5   C5   C6   113.33  3.000
 LO8  N    C5   C6   115.23  3.000
 LO8  C7   C5   C6    84.28  3.000
 LO8  H7   C6   H6   109.24  3.000
 LO8  H7   C6   O    112.44  3.000
 LO8  H6   C6   O    112.43  3.000
 LO8  H7   C6   C5   115.31  3.000
 LO8  H6   C6   C5   114.64  3.000
 LO8  O    C6   C5    91.94  3.000
 LO8  H9   C7   H8   108.98  3.000
 LO8  H9   C7   O    112.27  3.000
 LO8  H8   C7   O    112.53  3.000
 LO8  H9   C7   C5   114.83  3.000
 LO8  H8   C7   C5   115.43  3.000
 LO8  O    C7   C5    92.01  3.000
 LO8  O1   C8   N2   123.56  3.000
 LO8  O1   C8   C1   121.75  3.000
 LO8  N2   C8   C1   114.61  3.000
 LO8  C9   C10  C11  120.73  3.000
 LO8  C9   C10  C15  120.30  3.000
 LO8  C11  C10  C15  118.96  3.000
 LO8  H10  C13  C14  120.15  3.000
 LO8  H10  C13  C12  120.14  3.000
 LO8  C14  C13  C12  119.71  3.000
 LO8  H11  C15  C14  119.55  3.000
 LO8  H11  C15  C10  119.92  3.000
 LO8  C14  C15  C10  120.53  3.000
 LO8  C3   N    C2   109.82  3.000
 LO8  C3   N    C5   111.98  3.000
 LO8  C2   N    C5   111.14  3.000
 LO8  H15  C    H14  107.94  3.000
 LO8  H15  C    H13  108.42  3.000
 LO8  H14  C    H13  108.24  3.000
 LO8  H15  C    C1   111.20  3.000
 LO8  H14  C    C1   110.19  3.000
 LO8  H13  C    C1   110.75  3.000
 LO8  C7   O    C6    91.76  3.000
 LO8  C2   C1   C    109.70  3.000
 LO8  C2   C1   C8   109.38  3.000
 LO8  C    C1   C8   107.11  3.000
 LO8  C8   C1   N1   109.89  3.000
 LO8  C2   C1   N1   112.09  3.000
 LO8  C    C1   N1   108.53  3.000
 LO8  H16  C11  C12  119.94  3.000
 LO8  H16  C11  C10  119.39  3.000
 LO8  C12  C11  C10  120.67  3.000
 LO8  H17  C12  C11  119.75  3.000
 LO8  H17  C12  C13  120.26  3.000
 LO8  C11  C12  C13  119.99  3.000
 LO8  H18  C14  C15  119.93  3.000
 LO8  H18  C14  C13  119.93  3.000
 LO8  C15  C14  C13  120.14  3.000
 LO8  H20  C2   H19  107.21  3.000
 LO8  H20  C2   C1   109.57  3.000
 LO8  H19  C2   C1   108.23  3.000
 LO8  H20  C2   N    109.54  3.000
 LO8  H19  C2   N    111.25  3.000
 LO8  C1   C2   N    110.96  3.000
 LO8  H22  C3   H21  107.23  3.000
 LO8  H22  C3   N    109.83  3.000
 LO8  H21  C3   N    111.55  3.000
 LO8  H22  C3   C4   109.10  3.000
 LO8  H21  C3   C4   110.07  3.000
 LO8  N    C3   C4   109.03  3.000
 LO8  H24  C9   H23  106.77  3.000
 LO8  H24  C9   N2   110.99  3.000
 LO8  H23  C9   N2   108.19  3.000
 LO8  H24  C9   C10  109.93  3.000
 LO8  H23  C9   C10  110.45  3.000
 LO8  N2   C9   C10  110.43  3.000
 LO8  H25  N2   C9   119.29  3.000
 LO8  H25  N2   C8   116.53  3.000
 LO8  C9   N2   C8   124.16  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
 LO8  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 LO8  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 LO8  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 LO8  CONST_04  C12  C11  C10  C15     0.00   0.0  0
 LO8  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 LO8  CONST_06  C14  C15  C10  C11     0.00   0.0  0
 LO8  CONST_07  C9   C10  C11  C12   180.00   0.0  0
 LO8  CONST_08  C9   C10  C15  C14   180.00   0.0  0
 LO8  CONST_09  H18  C14  C15  C10   180.00   0.0  0
 LO8  CONST_10  H17  C12  C11  C10   180.00   0.0  0
 LO8  CONST_11  H11  C15  C14  C13   180.00   0.0  0
 LO8  CONST_12  H16  C11  C12  C13   180.00   0.0  0
 LO8  CONST_13  H10  C13  C14  C15   180.00   0.0  0
 LO8  CONST_14  C9   N2   C8   C1    180.00   0.0  0
 LO8  CONST_15  H25  N2   C8   C1      0.00   0.0  0
 LO8  CONST_16  O1   C8   N2   C9      0.00   0.0  0
 LO8  Var_01    N    C3   C4   N1    -54.84  30.0  1
 LO8  Var_02    C5   N    C3   C4   -174.53  30.0  1
 LO8  Var_03    C1   C2   N    C5    174.14  30.0  1
 LO8  Var_04    C3   C4   N1   C1     47.59  30.0  1
 LO8  Var_05    H8   C7   O    C6   -119.36  30.0  1
 LO8  Var_06    H6   C6   O    C7   -117.05  30.0  1
 LO8  Var_07    N2   C9   C10  C15   -64.56  30.0  2
 LO8  Var_08    C10  C9   N2   C8    148.66  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
 LO8  chir_01  C5  C7  C6  N  negativ
 LO8  chir_02  C1  N1  C2  C  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
 LO8  plan-1  C10  0.020
 LO8  plan-1  C13  0.020
 LO8  plan-1  C15  0.020
 LO8  plan-1  C11  0.020
 LO8  plan-1  C12  0.020
 LO8  plan-1  C14  0.020
 LO8  plan-1  C9   0.020
 LO8  plan-1  H10  0.020
 LO8  plan-1  H11  0.020
 LO8  plan-1  H16  0.020
 LO8  plan-1  H17  0.020
 LO8  plan-1  H18  0.020
 LO8  plan-2  C8   0.020
 LO8  plan-2  C1   0.020
 LO8  plan-2  C9   0.020
 LO8  plan-2  N2   0.020
 LO8  plan-2  O1   0.020
 LO8  plan-2  H25  0.020

