# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:49:59 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3S)-1-carbamimidoylpiperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N1CCC[C@@H](C1)C(O)=O
#
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
 01M  01M  '(3S)-1-carbamimidoylpiperidine-3-carboxylic acid'  peptide  25  12  .  2022-03-07  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_01M
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
 01M  C27   C  C     0   0.566  -2.3867  -0.4928  -0.0651
 01M  O28   O  O     0  -0.440  -3.3842   0.1606   0.1199
 01M  C29   C  CH1   0  -0.397  -1.0045   0.0675  -0.2809
 01M  C30   C  CH2   0  -0.292  -0.0431  -0.4069   0.8267
 01M  N31   N  NT    0  -0.454   1.2868   0.1308   0.6359
 01M  C32   C  CH2   0  -0.326   1.2922   1.5889   0.6386
 01M  C33   C  CH2   0  -0.438   0.4066   2.1379  -0.4735
 01M  C34   C  CH2   0  -0.426  -1.0128   1.5919  -0.3534
 01M  C35   C  C     0   0.553   2.1385  -0.5704  -0.1969
 01M  N37   N  N     0  -0.703   1.7590  -1.6693  -0.7368
 01M  N36   N  NH2   0  -0.837   3.3698   0.0208  -0.3879
 01M  H29   H  HCH1  0   0.281  -0.6306  -0.3470  -1.2252
 01M  H301  H  HCH2  0   0.248  -0.4100  -0.0593   1.7980
 01M  H302  H  HCH2  0   0.266   0.0129  -1.4911   0.8582
 01M  H321  H  HCH2  0   0.240   0.9154   1.9209   1.6104
 01M  H322  H  HCH2  0   0.254   2.3046   1.9751   0.5518
 01M  H331  H  HCH2  0   0.240   0.3942   3.2289  -0.4272
 01M  H332  H  HCH2  0   0.225   0.8357   1.8646  -1.4428
 01M  H341  H  HCH2  0   0.244  -1.6191   1.9311  -1.1956
 01M  H342  H  HCH2  0   0.225  -1.4751   1.9970   0.5520
 01M  HN7   H  H     0   0.317   2.5332  -2.1170  -1.2141
 01M  HN61  H  HNH2  0   0.386   3.7691   0.5031   0.4024
 01M  HN62  H  HNH2  0   0.386   4.0487  -0.5716  -0.8388
 01M  OXT   O  OH1   0  -0.596  -2.3948  -1.8225  -0.0927
 01M  HXT   H  HOH1  0   0.479  -3.2921  -2.1499   0.0698

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
 01M  C27  O28   double  1.207  0.020  1.207
 01M  C27  C29   single  1.507  0.020  1.507
 01M  C29  C30   single  1.541  0.020  1.541
 01M  C29  C34   single  1.526  0.020  1.526
 01M  C29  H29   single  0.970  0.020  1.090
 01M  C30  N31   single  1.447  0.020  1.447
 01M  C30  H301  single  0.970  0.020  1.090
 01M  C30  H302  single  0.970  0.020  1.090
 01M  N31  C32   single  1.458  0.020  1.458
 01M  N31  C35   single  1.382  0.020  1.382
 01M  C32  C33   single  1.524  0.020  1.524
 01M  C32  H321  single  0.970  0.020  1.090
 01M  C32  H322  single  0.970  0.020  1.090
 01M  C33  C34   single  1.525  0.020  1.525
 01M  C33  H331  single  0.970  0.020  1.090
 01M  C33  H332  single  0.970  0.020  1.090
 01M  C34  H341  single  0.970  0.020  1.090
 01M  C34  H342  single  0.970  0.020  1.090
 01M  C35  N37   double  1.282  0.020  1.282
 01M  C35  N36   single  1.379  0.020  1.379
 01M  N37  HN7   single  0.890  0.020  1.040
 01M  N36  HN61  single  0.890  0.020  1.040
 01M  N36  HN62  single  0.890  0.020  1.040
 01M  C27  OXT   single  1.330  0.020  1.330
 01M  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
 01M  OXT   C27  C29   111.98  3.000
 01M  OXT   C27  O28   122.65  3.000
 01M  C29   C27  O28   125.37  3.000
 01M  H29   C29  C34   109.78  3.000
 01M  H29   C29  C30   106.84  3.000
 01M  C34   C29  C30   110.18  3.000
 01M  H29   C29  C27   107.19  3.000
 01M  C34   C29  C27   111.91  3.000
 01M  C30   C29  C27   110.78  3.000
 01M  H302  C30  H301  107.96  3.000
 01M  H302  C30  N31   109.10  3.000
 01M  H301  C30  N31   107.87  3.000
 01M  H302  C30  C29   111.11  3.000
 01M  H301  C30  C29   109.32  3.000
 01M  N31   C30  C29   111.35  3.000
 01M  C35   N31  C32   120.40  3.000
 01M  C35   N31  C30   117.21  3.000
 01M  C32   N31  C30   112.01  3.000
 01M  H322  C32  H321  106.49  3.000
 01M  H322  C32  C33   110.79  3.000
 01M  H321  C32  C33   109.81  3.000
 01M  H322  C32  N31   111.01  3.000
 01M  H321  C32  N31   107.69  3.000
 01M  C33   C32  N31   110.90  3.000
 01M  H332  C33  H331  106.94  3.000
 01M  H332  C33  C34   110.19  3.000
 01M  H331  C33  C34   110.10  3.000
 01M  H332  C33  C32   109.17  3.000
 01M  H331  C33  C32   109.60  3.000
 01M  C34   C33  C32   110.75  3.000
 01M  H342  C34  H341  106.78  3.000
 01M  H342  C34  C33   109.01  3.000
 01M  H341  C34  C33   110.17  3.000
 01M  H342  C34  C29   109.44  3.000
 01M  H341  C34  C29   110.48  3.000
 01M  C33   C34  C29   110.86  3.000
 01M  N36   C35  N37   124.99  3.000
 01M  N36   C35  N31   114.59  3.000
 01M  N37   C35  N31   120.41  3.000
 01M  HN7   N37  C35   110.54  3.000
 01M  HN62  N36  HN61  111.42  3.000
 01M  HN62  N36  C35   114.30  3.000
 01M  HN61  N36  C35   116.75  3.000
 01M  HXT   OXT  C27   109.88  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
 01M  CONST_01  N37   C35  N31  C30    0.00   0.0  0
 01M  CONST_02  N36   C35  N31  C30  180.00   0.0  0
 01M  CONST_05  HXT   OXT  C27  C29  180.00   0.0  0
 01M  CONST_06  HN7   N37  C35  N31  180.00   0.0  0
 01M  CONST_08  HN62  N36  C35  N31  180.00   0.0  0
 01M  Var_01    C32   N31  C30  C29   59.33  30.0  1
 01M  Var_02    C32   C33  C34  C29  -53.17  30.0  1
 01M  Var_03    C33   C32  N31  C30  -59.65  30.0  1
 01M  Var_04    C34   C33  C32  N31   56.07  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
 01M  chir_01  C29  C27  C30  C34  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
 01M  plan-1  C30   0.020
 01M  plan-1  N31   0.020
 01M  plan-1  C32   0.020
 01M  plan-1  C35   0.020
 01M  plan-1  N37   0.020
 01M  plan-1  N36   0.020
 01M  plan-1  HN7   0.020
 01M  plan-1  HN61  0.020
 01M  plan-1  HN62  0.020
 01M  plan-2  C27   0.020
 01M  plan-2  O28   0.020
 01M  plan-2  C29   0.020
 01M  plan-2  OXT   0.020
 01M  plan-2  HXT   0.020

