# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:45:34 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3R)-3-butylpiperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H]1CCCNC1
#
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
 DIY  DIY  '(3R)-3-butylpiperidine   '  ligand  29  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DIY
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
 DIY  N1    N  NH1   0  -0.598  -1.4482  -0.0972  -2.2204
 DIY  C2    C  CH2   0  -0.289  -0.4971   0.2793  -3.2511
 DIY  C6    C  CH2   0  -0.270  -1.0534   0.3854  -0.9088
 DIY  C3    C  CH2   0  -0.431   0.8630  -0.3291  -2.9432
 DIY  C4    C  CH2   0  -0.423   1.3320   0.0894  -1.5549
 DIY  C5    C  CH1   0  -0.227   0.2828  -0.2229  -0.4888
 DIY  C1'   C  CH2   0  -0.408   0.7329   0.2628   0.8871
 DIY  C2'   C  CH2   0  -0.416  -0.1198  -0.2353   2.0485
 DIY  C3'   C  CH2   0  -0.416   0.3796   0.2488   3.4042
 DIY  C4'   C  CH3   0  -0.662  -0.4493  -0.2821   4.5655
 DIY  HN1   H  HNH1  0   0.348  -2.3604   0.2739  -2.4518
 DIY  H21   H  HCH2  0   0.180  -0.3833   1.3734  -3.3403
 DIY  H22   H  HCH2  0   0.227  -0.8635  -0.0788  -4.2159
 DIY  H61   H  HCH2  0   0.228  -1.8359   0.1199  -0.1939
 DIY  H62   H  HCH2  0   0.174  -0.9541   1.4859  -0.8760
 DIY  H31   H  HCH2  0   0.225   1.5859  -0.0214  -3.7023
 DIY  H32   H  HCH2  0   0.210   0.7883  -1.4199  -2.9958
 DIY  H41   H  HCH2  0   0.203   1.5292   1.1685  -1.5500
 DIY  H42   H  HCH2  0   0.226   2.2773  -0.3993  -1.3029
 DIY  H5    H  HCH1  0   0.205   0.1530  -1.3124  -0.4470
 DIY  H1'1  H  HCH2  0   0.204   0.7575   1.3592   0.8930
 DIY  H1'2  H  HCH2  0   0.215   1.7675  -0.0604   1.0490
 DIY  H2'1  H  HCH2  0   0.206  -0.1341  -1.3310   2.0376
 DIY  H2'2  H  HCH2  0   0.213  -1.1599   0.0802   1.9184
 DIY  H3'1  H  HCH2  0   0.210   0.3751   1.3433   3.4216
 DIY  H3'2  H  HCH2  0   0.210   1.4244  -0.0507   3.5329
 DIY  H4'1  H  HCH3  0   0.226  -0.0842   0.0912   5.5230
 DIY  H4'2  H  HCH3  0   0.215  -1.4956   0.0157   4.4726
 DIY  H4'3  H  HCH3  0   0.216  -0.4218  -1.3728   4.6037

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
 DIY  N1   C2    single  1.452  0.020  1.452
 DIY  N1   C6    single  1.452  0.020  1.452
 DIY  N1   HN1   single  0.890  0.020  1.040
 DIY  C2   C3    single  1.521  0.020  1.521
 DIY  C2   H21   single  0.970  0.020  1.090
 DIY  C2   H22   single  0.970  0.020  1.090
 DIY  C6   C5    single  1.527  0.020  1.527
 DIY  C6   H61   single  0.970  0.020  1.090
 DIY  C6   H62   single  0.970  0.020  1.090
 DIY  C3   C4    single  1.524  0.020  1.524
 DIY  C3   H31   single  0.970  0.020  1.090
 DIY  C3   H32   single  0.970  0.020  1.090
 DIY  C4   C5    single  1.528  0.020  1.528
 DIY  C4   H41   single  0.970  0.020  1.090
 DIY  C4   H42   single  0.970  0.020  1.090
 DIY  C5   C1'   single  1.527  0.020  1.527
 DIY  C5   H5    single  0.970  0.020  1.090
 DIY  C1'  C2'   single  1.524  0.020  1.524
 DIY  C1'  H1'1  single  0.970  0.020  1.090
 DIY  C1'  H1'2  single  0.970  0.020  1.090
 DIY  C2'  C3'   single  1.524  0.020  1.524
 DIY  C2'  H2'1  single  0.970  0.020  1.090
 DIY  C2'  H2'2  single  0.970  0.020  1.090
 DIY  C3'  C4'   single  1.522  0.020  1.522
 DIY  C3'  H3'1  single  0.970  0.020  1.090
 DIY  C3'  H3'2  single  0.970  0.020  1.090
 DIY  C4'  H4'1  single  0.970  0.020  1.090
 DIY  C4'  H4'2  single  0.970  0.020  1.090
 DIY  C4'  H4'3  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
 DIY  HN1   N1   C6    109.26  3.000
 DIY  HN1   N1   C2    109.46  3.000
 DIY  C6    N1   C2    112.13  3.000
 DIY  H22   C2   H21   106.75  3.000
 DIY  H22   C2   C3    110.34  3.000
 DIY  H21   C2   C3    108.70  3.000
 DIY  H22   C2   N1    108.80  3.000
 DIY  H21   C2   N1    112.45  3.000
 DIY  C3    C2   N1    109.77  3.000
 DIY  H62   C6   H61   106.67  3.000
 DIY  H62   C6   C5    108.05  3.000
 DIY  H61   C6   C5    110.48  3.000
 DIY  H62   C6   N1    112.46  3.000
 DIY  H61   C6   N1    108.38  3.000
 DIY  C5    C6   N1    110.73  3.000
 DIY  H32   C3   H31   107.00  3.000
 DIY  H32   C3   C4    109.78  3.000
 DIY  H31   C3   C4    110.60  3.000
 DIY  H32   C3   C2    109.14  3.000
 DIY  H31   C3   C2    109.77  3.000
 DIY  C4    C3   C2    110.46  3.000
 DIY  H42   C4   H41   106.45  3.000
 DIY  H42   C4   C5    109.96  3.000
 DIY  H41   C4   C5    108.75  3.000
 DIY  H42   C4   C3    110.69  3.000
 DIY  H41   C4   C3    109.25  3.000
 DIY  C5    C4   C3    111.60  3.000
 DIY  H5    C5   C1'   108.44  3.000
 DIY  H5    C5   C4    108.09  3.000
 DIY  C1'   C5   C4    111.18  3.000
 DIY  H5    C5   C6    107.60  3.000
 DIY  C1'   C5   C6    112.28  3.000
 DIY  C4    C5   C6    109.11  3.000
 DIY  H1'2  C1'  H1'1  105.84  3.000
 DIY  H1'2  C1'  C2'   108.61  3.000
 DIY  H1'1  C1'  C2'   109.57  3.000
 DIY  H1'2  C1'  C5    108.52  3.000
 DIY  H1'1  C1'  C5    109.24  3.000
 DIY  C2'   C1'  C5    114.68  3.000
 DIY  H2'2  C2'  H2'1  105.94  3.000
 DIY  H2'2  C2'  C3'   109.00  3.000
 DIY  H2'1  C2'  C3'   109.31  3.000
 DIY  H2'2  C2'  C1'   110.29  3.000
 DIY  H2'1  C2'  C1'   109.05  3.000
 DIY  C3'   C2'  C1'   113.00  3.000
 DIY  H3'2  C3'  H3'1  106.00  3.000
 DIY  H3'2  C3'  C4'   109.55  3.000
 DIY  H3'1  C3'  C4'   109.53  3.000
 DIY  H3'2  C3'  C2'   109.30  3.000
 DIY  H3'1  C3'  C2'   109.30  3.000
 DIY  C4'   C3'  C2'   112.93  3.000
 DIY  H4'3  C4'  H4'2  107.44  3.000
 DIY  H4'3  C4'  H4'1  107.63  3.000
 DIY  H4'2  C4'  H4'1  107.59  3.000
 DIY  H4'3  C4'  C3'   111.18  3.000
 DIY  H4'2  C4'  C3'   111.21  3.000
 DIY  H4'1  C4'  C3'   111.60  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
 DIY  Var_01  C4    C3   C2   N1    -56.08  30.0  1
 DIY  Var_02  C5    C6   N1   C2    -61.91  30.0  1
 DIY  Var_03  C5    C4   C3   C2     53.39  30.0  1
 DIY  Var_04  C3    C2   N1   C6     61.17  30.0  1
 DIY  Var_05  C3'   C2'  C1'  C5    178.83  30.0  3
 DIY  Var_06  C4'   C3'  C2'  C1'  -178.35  30.0  3
 DIY  Var_07  H4'1  C4'  C3'  C2'  -179.01  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
 DIY  chir_01  C5  C6  C4  C1'  negativ

