# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:55:48 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3S)-3-(aminomethyl)piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CCCN(C1)C(N)=N
#
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
 04H  04H  (3S)-3-(aminomethyl)piperidine-1-carboximidamide  ligand  27  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_04H
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
 04H  N19   N  NH2   0  -0.797  -2.9866   1.7012  -0.1986
 04H  C23   C  CH2   0  -0.268  -2.8430   0.2834   0.0984
 04H  C26   C  CH1   0  -0.255  -1.4745  -0.2479  -0.3088
 04H  C28   C  CH2   0  -0.240  -0.3574   0.4836   0.4295
 04H  C29   C  CH2   0  -0.430  -1.3811  -1.7510  -0.0661
 04H  N30   N  NT    0  -0.472   0.9437  -0.0529   0.0788
 04H  C31   C  CH2   0  -0.432   0.0132  -2.2652  -0.3941
 04H  C32   C  CH2   0  -0.298   1.0722  -1.4757   0.3586
 04H  C33   C  C     0   0.554   2.0289   0.7918   0.1109
 04H  N34   N  NH2   0  -0.840   3.2368   0.2027  -0.2118
 04H  N35   N  N     0  -0.717   1.8894   2.0246   0.4421
 04H  H19   H  HNH2  0   0.337  -2.9999   1.8307  -1.2032
 04H  H231  H  HCH2  0   0.210  -2.9661   0.1462   1.1775
 04H  H232  H  HCH2  0   0.201  -3.6118  -0.3412  -0.3799
 04H  H26   H  HCH1  0   0.215  -1.3382  -0.0694  -1.3841
 04H  H281  H  HCH2  0   0.251  -0.3808   1.5419   0.1900
 04H  H282  H  HCH2  0   0.194  -0.5263   0.3998   1.5154
 04H  H291  H  HCH2  0   0.209  -1.6073  -1.9608   0.9862
 04H  H292  H  HCH2  0   0.232  -2.1341  -2.2777  -0.6585
 04H  H311  H  HCH2  0   0.234   0.1063  -3.3221  -0.1345
 04H  H312  H  HCH2  0   0.219   0.1982  -2.1810  -1.4692
 04H  H321  H  HCH2  0   0.250   2.0608  -1.8373   0.0893
 04H  H322  H  HCH2  0   0.215   0.9586  -1.6538   1.4382
 04H  H341  H  HNH2  0   0.385   3.2183  -0.5051  -0.9293
 04H  H342  H  HNH2  0   0.384   3.9859   0.8587  -0.3665
 04H  H35   H  H     0   0.314   2.7564   2.5287   0.2964
 04H  H2    H  HNH2  0   0.347  -3.8878   2.0238   0.1294

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
 04H  N19  C23   single  1.456  0.020  1.456
 04H  C23  C26   single  1.523  0.020  1.523
 04H  C26  C28   single  1.526  0.020  1.526
 04H  C26  C29   single  1.525  0.020  1.525
 04H  C28  N30   single  1.450  0.020  1.450
 04H  C29  C31   single  1.522  0.020  1.522
 04H  N30  C32   single  1.456  0.020  1.456
 04H  N30  C33   single  1.376  0.020  1.376
 04H  C31  C32   single  1.520  0.020  1.520
 04H  C33  N34   single  1.382  0.020  1.382
 04H  C33  N35   double  1.284  0.020  1.284
 04H  N19  H19   single  0.890  0.020  1.040
 04H  C23  H231  single  0.970  0.020  1.090
 04H  C23  H232  single  0.970  0.020  1.090
 04H  C26  H26   single  0.970  0.020  1.090
 04H  C28  H281  single  0.970  0.020  1.090
 04H  C28  H282  single  0.970  0.020  1.090
 04H  C29  H291  single  0.970  0.020  1.090
 04H  C29  H292  single  0.970  0.020  1.090
 04H  C31  H311  single  0.970  0.020  1.090
 04H  C31  H312  single  0.970  0.020  1.090
 04H  C32  H321  single  0.970  0.020  1.090
 04H  C32  H322  single  0.970  0.020  1.090
 04H  N34  H341  single  0.890  0.020  1.040
 04H  N34  H342  single  0.890  0.020  1.040
 04H  N35  H35   single  0.890  0.020  1.040
 04H  N19  H2    single  0.890  0.020  1.040

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
 04H  H2    N19  H19   105.61  3.000
 04H  H2    N19  C23   109.40  3.000
 04H  H19   N19  C23   109.16  3.000
 04H  H232  C23  H231  106.20  3.000
 04H  H232  C23  C26   108.28  3.000
 04H  H231  C23  C26   108.71  3.000
 04H  H232  C23  N19   113.29  3.000
 04H  H231  C23  N19   108.19  3.000
 04H  C26   C23  N19   111.94  3.000
 04H  H26   C26  C29   107.96  3.000
 04H  H26   C26  C28   107.75  3.000
 04H  C29   C26  C28   110.52  3.000
 04H  H26   C26  C23   108.45  3.000
 04H  C29   C26  C23   110.86  3.000
 04H  C28   C26  C23   111.17  3.000
 04H  H282  C28  H281  106.76  3.000
 04H  H282  C28  N30   110.34  3.000
 04H  H281  C28  N30   109.07  3.000
 04H  H282  C28  C26   109.15  3.000
 04H  H281  C28  C26   110.18  3.000
 04H  N30   C28  C26   111.25  3.000
 04H  H292  C29  H291  106.60  3.000
 04H  H292  C29  C31   110.57  3.000
 04H  H291  C29  C31   109.34  3.000
 04H  H292  C29  C26   110.26  3.000
 04H  H291  C29  C26   109.19  3.000
 04H  C31   C29  C26   110.78  3.000
 04H  C33   N30  C32   121.74  3.000
 04H  C33   N30  C28   118.35  3.000
 04H  C32   N30  C28   113.22  3.000
 04H  H312  C31  H311  107.07  3.000
 04H  H312  C31  C32   109.19  3.000
 04H  H311  C31  C32   109.00  3.000
 04H  H312  C31  C29   109.92  3.000
 04H  H311  C31  C29   110.72  3.000
 04H  C32   C31  C29   110.86  3.000
 04H  H322  C32  H321  106.46  3.000
 04H  H322  C32  C31   109.26  3.000
 04H  H321  C32  C31   109.77  3.000
 04H  H322  C32  N30   109.74  3.000
 04H  H321  C32  N30   110.98  3.000
 04H  C31   C32  N30   110.54  3.000
 04H  N35   C33  N34   124.36  3.000
 04H  N35   C33  N30   120.65  3.000
 04H  N34   C33  N30   114.98  3.000
 04H  H342  N34  H341  111.19  3.000
 04H  H342  N34  C33   114.08  3.000
 04H  H341  N34  C33   116.71  3.000
 04H  H35   N35  C33   110.33  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
 04H  CONST_01  N34   C33  N30  C28  180.00   0.0  0
 04H  CONST_02  N35   C33  N30  C28    0.00   0.0  0
 04H  CONST_06  H342  N34  C33  N30  180.00   0.0  0
 04H  CONST_07  H35   N35  C33  N30  180.00   0.0  0
 04H  Var_01    C32   N30  C28  C26  -58.01  30.0  1
 04H  Var_02    C32   C31  C29  C26   53.76  30.0  1
 04H  Var_03    N30   C32  C31  C29  -55.58  30.0  1
 04H  Var_04    H19   N19  C23  C26   67.78  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
 04H  chir_01  C26  C23  C28  C29  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
 04H  plan-1  C28   0.020
 04H  plan-1  N30   0.020
 04H  plan-1  C32   0.020
 04H  plan-1  C33   0.020
 04H  plan-1  N34   0.020
 04H  plan-1  N35   0.020
 04H  plan-1  H341  0.020
 04H  plan-1  H342  0.020
 04H  plan-1  H35   0.020

