# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:08:00 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (3R)-3-(hydroxymethyl)piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N1CCC[C@@H](CO)C1
#
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
 04P  04P  (3R)-3-(hydroxymethyl)piperidine-1-carboximidamide  ligand  26  11  .  2021-08-03  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_04P
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
 04P  C20   C  CH2   0  -0.130   2.7520  -0.2824   0.0988
 04P  C27   C  CH1   0  -0.281   1.3227   0.1392  -0.1892
 04P  C32   C  CH2   0  -0.275   0.3514  -0.3923   0.8668
 04P  C33   C  CH2   0  -0.435   1.2350   1.6646  -0.2582
 04P  N37   N  NT    0  -0.457  -1.0056   0.0769   0.6519
 04P  C38   C  CH2   0  -0.428  -0.2048   2.1416  -0.4125
 04P  C40   C  CH2   0  -0.324  -1.0882   1.5303   0.6691
 04P  C41   C  C     0   0.550  -1.8264  -0.6727  -0.1618
 04P  N42   N  N     0  -0.710  -1.4182  -1.7844  -0.6562
 04P  N43   N  NH2   0  -0.839  -3.0728  -0.1232  -0.3953
 04P  H201  H  HCH2  0   0.198   3.4147   0.1705  -0.6518
 04P  H202  H  HCH2  0   0.184   3.0537   0.1285   1.0732
 04P  H27   H  HCH1  0   0.227   1.0248  -0.2732  -1.1609
 04P  H321  H  HCH2  0   0.254   0.3518  -1.4785   0.8828
 04P  H322  H  HCH2  0   0.221   0.6711  -0.0452   1.8570
 04P  H331  H  HCH2  0   0.211   1.6530   2.0922   0.6617
 04P  H332  H  HCH2  0   0.234   1.8499   2.0387  -1.0813
 04P  H381  H  HCH2  0   0.234  -0.2546   3.2315  -0.3536
 04P  H382  H  HCH2  0   0.221  -0.5937   1.8568  -1.3955
 04P  H401  H  HCH2  0   0.249  -2.1153   1.8703   0.5624
 04P  H402  H  HCH2  0   0.235  -0.7526   1.8714   1.6534
 04P  H42   H  H     0   0.313  -2.1785  -2.2618  -1.1267
 04P  H431  H  HNH2  0   0.384  -3.4974   0.3770   0.3703
 04P  H432  H  HNH2  0   0.384  -3.7280  -0.7619  -0.8174
 04P  OXT   O  OH1   0  -0.674   2.8486  -1.6902   0.0834
 04P  HXT   H  HOH1  0   0.452   3.7448  -1.9318   0.3325

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
 04P  C20  C27   single  1.518  0.020  1.518
 04P  C27  C32   single  1.530  0.020  1.530
 04P  C27  C33   single  1.529  0.020  1.529
 04P  C32  N37   single  1.452  0.020  1.452
 04P  C33  C38   single  1.525  0.020  1.525
 04P  N37  C40   single  1.456  0.020  1.456
 04P  N37  C41   single  1.377  0.020  1.377
 04P  C38  C40   single  1.524  0.020  1.524
 04P  C41  N42   double  1.283  0.020  1.283
 04P  C41  N43   single  1.382  0.020  1.382
 04P  C20  H201  single  0.970  0.020  1.090
 04P  C20  H202  single  0.970  0.020  1.090
 04P  C27  H27   single  0.970  0.020  1.090
 04P  C32  H321  single  0.970  0.020  1.090
 04P  C32  H322  single  0.970  0.020  1.090
 04P  C33  H331  single  0.970  0.020  1.090
 04P  C33  H332  single  0.970  0.020  1.090
 04P  C38  H381  single  0.970  0.020  1.090
 04P  C38  H382  single  0.970  0.020  1.090
 04P  C40  H401  single  0.970  0.020  1.090
 04P  C40  H402  single  0.970  0.020  1.090
 04P  N42  H42   single  0.890  0.020  1.040
 04P  N43  H431  single  0.890  0.020  1.040
 04P  N43  H432  single  0.890  0.020  1.040
 04P  C20  OXT   single  1.411  0.020  1.411
 04P  OXT  HXT   single  0.850  0.020  0.980

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
 04P  OXT   C20  H202  111.32  3.000
 04P  OXT   C20  H201  111.25  3.000
 04P  H202  C20  H201  106.60  3.000
 04P  OXT   C20  C27   109.85  3.000
 04P  H202  C20  C27   108.83  3.000
 04P  H201  C20  C27   108.89  3.000
 04P  H27   C27  C33   108.63  3.000
 04P  H27   C27  C32   107.96  3.000
 04P  C33   C27  C32   109.95  3.000
 04P  H27   C27  C20   108.63  3.000
 04P  C33   C27  C20   109.85  3.000
 04P  C32   C27  C20   111.74  3.000
 04P  H322  C32  H321  107.64  3.000
 04P  H322  C32  N37   107.68  3.000
 04P  H321  C32  N37   109.00  3.000
 04P  H322  C32  C27   109.16  3.000
 04P  H321  C32  C27   110.94  3.000
 04P  N37   C32  C27   112.27  3.000
 04P  H332  C33  H331  106.47  3.000
 04P  H332  C33  C38   110.36  3.000
 04P  H331  C33  C38   108.82  3.000
 04P  H332  C33  C27   110.06  3.000
 04P  H331  C33  C27   109.21  3.000
 04P  C38   C33  C27   111.76  3.000
 04P  C41   N37  C40   121.09  3.000
 04P  C41   N37  C32   117.94  3.000
 04P  C40   N37  C32   111.95  3.000
 04P  H382  C38  H381  106.96  3.000
 04P  H382  C38  C40   109.08  3.000
 04P  H381  C38  C40   109.60  3.000
 04P  H382  C38  C33   110.18  3.000
 04P  H381  C38  C33   110.47  3.000
 04P  C40   C38  C33   110.49  3.000
 04P  H402  C40  H401  106.28  3.000
 04P  H402  C40  C38   109.60  3.000
 04P  H401  C40  C38   110.64  3.000
 04P  H402  C40  N37   107.72  3.000
 04P  H401  C40  N37   111.38  3.000
 04P  C38   C40  N37   111.05  3.000
 04P  N43   C41  N42   124.48  3.000
 04P  N43   C41  N37   114.89  3.000
 04P  N42   C41  N37   120.63  3.000
 04P  H42   N42  C41   110.38  3.000
 04P  H432  N43  H431  111.02  3.000
 04P  H432  N43  C41   113.90  3.000
 04P  H431  N43  C41   116.66  3.000
 04P  HXT   OXT  C20   108.17  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
 04P  CONST_01  N42   C41  N37  C32    0.00   0.0  0
 04P  CONST_02  N43   C41  N37  C32  180.00   0.0  0
 04P  CONST_05  H42   N42  C41  N37  180.00   0.0  0
 04P  CONST_07  H432  N43  C41  N37  180.00   0.0  0
 04P  Var_01    C40   N37  C32  C27  -58.82  30.0  1
 04P  Var_02    C40   C38  C33  C27   52.59  30.0  1
 04P  Var_03    N37   C40  C38  C33  -55.88  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
 04P  chir_01  C27  C20  C32  C33  negativ

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
 04P  plan-1  C32   0.020
 04P  plan-1  N37   0.020
 04P  plan-1  C40   0.020
 04P  plan-1  C41   0.020
 04P  plan-1  N42   0.020
 04P  plan-1  N43   0.020
 04P  plan-1  H42   0.020
 04P  plan-1  H431  0.020
 04P  plan-1  H432  0.020

