# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:20:38 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: di(piperidin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCCCC1)N2CCCCC2
#
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
 GOY  GOY  di(piperidin-1-yl)methanone  ligand  34  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GOY
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
 GOY  N1   N  NT    0  -0.480  -1.1497   0.0087   0.9023
 GOY  C4   C  CH2   0  -0.434   3.0258   0.3125  -1.1183
 GOY  C5   C  C     0   0.702  -0.1381   0.8889   0.6024
 GOY  C6   C  CH2   0  -0.311  -2.4253   0.5651   1.3300
 GOY  C7   C  CH2   0  -0.434  -3.3678   0.8108   0.1574
 GOY  C8   C  CH2   0  -0.442  -3.5634  -0.4735  -0.6416
 GOY  C10  C  CH2   0  -0.339  -1.3101  -1.2456   0.1714
 GOY  N    N  NT    0  -0.487   1.0908   0.3303   0.3589
 GOY  C    C  CH2   0  -0.443   3.6110  -0.8694  -0.3544
 GOY  O    O  O     0  -0.522  -0.3208   2.1008   0.5578
 GOY  C1   C  CH2   0  -0.434   2.5060  -1.6721   0.3230
 GOY  C2   C  CH2   0  -0.332   1.6263  -0.7606   1.1647
 GOY  C3   C  CH2   0  -0.287   2.1265   1.1616  -0.2289
 GOY  C9   C  CH2   0  -0.428  -2.2173  -1.0661  -1.0425
 GOY  H2   H  HCH2  0   0.219   2.4417  -0.0473  -1.9706
 GOY  H3   H  HCH2  0   0.232  -2.8820  -0.1575   2.0148
 GOY  H4   H  HCH2  0   0.250  -2.2545   1.4768   1.8982
 GOY  H5   H  HCH2  0   0.230  -4.3255   1.1813   0.5306
 GOY  H6   H  HCH2  0   0.222  -2.9480   1.5919  -0.4818
 GOY  H7   H  HCH2  0   0.214  -4.1056  -1.2006  -0.0270
 GOY  H8   H  HCH2  0   0.234  -4.1788  -0.2882  -1.5244
 GOY  H9   H  HCH2  0   0.269  -0.3463  -1.6326  -0.1462
 GOY  H10  H  HCH2  0   0.235  -1.7464  -1.9847   0.8507
 GOY  H11  H  HCH2  0   0.236   4.1957  -1.5067  -1.0207
 GOY  H12  H  HCH2  0   0.214   4.3020  -0.4965   0.4091
 GOY  H13  H  HCH2  0   0.223   1.8926  -2.1753  -0.4313
 GOY  H14  H  HCH2  0   0.236   2.9307  -2.4501   0.9609
 GOY  H15  H  HCH2  0   0.236   2.2277  -0.3356   1.9812
 GOY  H16  H  HCH2  0   0.271   0.8193  -1.3171   1.6349
 GOY  H17  H  HCH2  0   0.211   2.7275   1.6409   0.5565
 GOY  H18  H  HCH2  0   0.250   1.6670   1.9565  -0.8121
 GOY  H19  H  HCH2  0   0.235  -2.3514  -2.0343  -1.5312
 GOY  H20  H  HCH2  0   0.220  -1.7209  -0.4102  -1.7651
 GOY  H1   H  HCH2  0   0.234   3.8242   0.9397  -1.5213

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
 GOY  C1   C    single  1.525  0.020  1.525
 GOY  C1   C2   single  1.521  0.020  1.521
 GOY  C    C4   single  1.524  0.020  1.524
 GOY  C2   N    single  1.458  0.020  1.458
 GOY  C4   C3   single  1.523  0.020  1.523
 GOY  N    C3   single  1.452  0.020  1.452
 GOY  N    C5   single  1.372  0.020  1.372
 GOY  O    C5   double  1.226  0.020  1.226
 GOY  C5   N1   single  1.374  0.020  1.374
 GOY  C10  N1   single  1.461  0.020  1.461
 GOY  C10  C9   single  1.526  0.020  1.526
 GOY  N1   C6   single  1.456  0.020  1.456
 GOY  C9   C8   single  1.524  0.020  1.524
 GOY  C6   C7   single  1.524  0.020  1.524
 GOY  C8   C7   single  1.525  0.020  1.525
 GOY  C4   H1   single  0.970  0.020  1.090
 GOY  C4   H2   single  0.970  0.020  1.090
 GOY  C6   H3   single  0.970  0.020  1.090
 GOY  C6   H4   single  0.970  0.020  1.090
 GOY  C7   H5   single  0.970  0.020  1.090
 GOY  C7   H6   single  0.970  0.020  1.090
 GOY  C8   H7   single  0.970  0.020  1.090
 GOY  C8   H8   single  0.970  0.020  1.090
 GOY  C10  H9   single  0.970  0.020  1.090
 GOY  C10  H10  single  0.970  0.020  1.090
 GOY  C    H11  single  0.970  0.020  1.090
 GOY  C    H12  single  0.970  0.020  1.090
 GOY  C1   H13  single  0.970  0.020  1.090
 GOY  C1   H14  single  0.970  0.020  1.090
 GOY  C2   H15  single  0.970  0.020  1.090
 GOY  C2   H16  single  0.970  0.020  1.090
 GOY  C3   H17  single  0.970  0.020  1.090
 GOY  C3   H18  single  0.970  0.020  1.090
 GOY  C9   H19  single  0.970  0.020  1.090
 GOY  C9   H20  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
 GOY  C10  N1   C6   112.27  3.000
 GOY  C6   N1   C5   117.67  3.000
 GOY  C10  N1   C5   121.45  3.000
 GOY  H2   C4   H1   106.95  3.000
 GOY  H2   C4   C3   108.84  3.000
 GOY  H1   C4   C3   109.08  3.000
 GOY  H2   C4   C    109.90  3.000
 GOY  H1   C4   C    110.46  3.000
 GOY  C3   C4   C    111.49  3.000
 GOY  O    C5   N    121.96  3.000
 GOY  O    C5   N1   122.10  3.000
 GOY  N    C5   N1   115.94  3.000
 GOY  H4   C6   H3   106.97  3.000
 GOY  H4   C6   C7   111.33  3.000
 GOY  H3   C6   C7   109.23  3.000
 GOY  H4   C6   N1   109.65  3.000
 GOY  H3   C6   N1   107.27  3.000
 GOY  C7   C6   N1   112.17  3.000
 GOY  H6   C7   H5   107.10  3.000
 GOY  H6   C7   C8   110.16  3.000
 GOY  H5   C7   C8   110.61  3.000
 GOY  H6   C7   C6   109.12  3.000
 GOY  H5   C7   C6   109.50  3.000
 GOY  C8   C7   C6   110.28  3.000
 GOY  H8   C8   H7   106.69  3.000
 GOY  H8   C8   C9   110.55  3.000
 GOY  H7   C8   C9   109.06  3.000
 GOY  H8   C8   C7   110.66  3.000
 GOY  H7   C8   C7   109.18  3.000
 GOY  C9   C8   C7   110.60  3.000
 GOY  H10  C10  H9   107.13  3.000
 GOY  H10  C10  C9   109.64  3.000
 GOY  H9   C10  C9   109.69  3.000
 GOY  H10  C10  N1   108.25  3.000
 GOY  H9   C10  N1   110.78  3.000
 GOY  C9   C10  N1   111.24  3.000
 GOY  C3   N    C2   112.96  3.000
 GOY  C3   N    C5   118.53  3.000
 GOY  C2   N    C5   122.38  3.000
 GOY  H12  C    H11  106.64  3.000
 GOY  H12  C    C1   109.07  3.000
 GOY  H11  C    C1   110.61  3.000
 GOY  H12  C    C4   109.13  3.000
 GOY  H11  C    C4   110.63  3.000
 GOY  C1   C    C4   110.65  3.000
 GOY  H14  C1   H13  107.03  3.000
 GOY  H14  C1   C2   109.18  3.000
 GOY  H13  C1   C2   109.43  3.000
 GOY  H14  C1   C    110.66  3.000
 GOY  H13  C1   C    110.00  3.000
 GOY  C2   C1   C    110.46  3.000
 GOY  H16  C2   H15  106.42  3.000
 GOY  H16  C2   C1   111.22  3.000
 GOY  H15  C2   C1   109.04  3.000
 GOY  H16  C2   N    110.45  3.000
 GOY  H15  C2   N    108.78  3.000
 GOY  C1   C2   N    110.79  3.000
 GOY  H18  C3   H17  107.19  3.000
 GOY  H18  C3   N    109.52  3.000
 GOY  H17  C3   N    110.51  3.000
 GOY  H18  C3   C4   110.10  3.000
 GOY  H17  C3   C4   109.72  3.000
 GOY  N    C3   C4   109.77  3.000
 GOY  H20  C9   H19  106.93  3.000
 GOY  H20  C9   C10  109.03  3.000
 GOY  H19  C9   C10  108.93  3.000
 GOY  H20  C9   C8   109.94  3.000
 GOY  H19  C9   C8   110.71  3.000
 GOY  C10  C9   C8   111.19  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
 GOY  CONST_02  C3   N    C5   N1  180.00   0.0  0
 GOY  CONST_03  N    C5   N1   C6  180.00   0.0  0
 GOY  CONST_05  O    C5   N1   C6    0.00   0.0  0
 GOY  CONST_08  C3   N    C5   O     0.00   0.0  0
 GOY  Var_01    C8   C9   C10  N1  -54.92  30.0  1
 GOY  Var_02    C8   C7   C6   N1   55.34  30.0  1
 GOY  Var_03    C2   C1   C    C4  -52.58  30.0  1
 GOY  Var_04    C2   N    C3   C4   59.25  30.0  1
 GOY  Var_05    C9   C10  N1   C6   57.03  30.0  1
 GOY  Var_06    C9   C8   C7   C6  -53.02  30.0  1
 GOY  Var_07    C10  N1   C6   C7  -57.74  30.0  1
 GOY  Var_08    C10  C9   C8   C7   53.34  30.0  1
 GOY  Var_09    C    C1   C2   N    55.40  30.0  1
 GOY  Var_10    C    C4   C3   N   -55.43  30.0  1
 GOY  Var_11    C3   C4   C    C1   53.08  30.0  1
 GOY  Var_12    C3   N    C2   C1  -59.89  30.0  1

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
 GOY  plan-1  N1   0.020
 GOY  plan-1  C5   0.020
 GOY  plan-1  C6   0.020
 GOY  plan-1  C10  0.020
 GOY  plan-1  N    0.020
 GOY  plan-1  O    0.020
 GOY  plan-1  C2   0.020
 GOY  plan-1  C3   0.020

