# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:47:46 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-{[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl](carboxymethyl)amino}ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(CC(=O)N(CC[NH3+])CC(O)=O)C=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
 CPN  CPN  2-{[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl](carboxymethyl)amino}ethanaminium  peptide  35  19  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CPN
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
 CPN  C8'   C  CH2   0  -0.460   0.2949   0.4671   1.0015
 CPN  C7'   C  C     0   0.582  -0.5854  -0.4920   0.2072
 CPN  O7'   O  O     0  -0.469  -0.0939  -1.4199  -0.4068
 CPN  C5'   C  CH2   0  -0.484  -2.5330   0.8243   0.9360
 CPN  C'    C  C     0   0.552  -2.6656   2.0342   0.0303
 CPN  O1'   O  O     0  -0.422  -2.2721   2.0723  -1.1044
 CPN  OXT   O  OH1   0  -0.586  -3.2672   3.0314   0.6572
 CPN  N4'   N  NT    0  -0.452  -1.9225  -0.2880   0.2593
 CPN  C3'   C  CH2   0  -0.343  -2.7871  -1.1520  -0.5184
 CPN  C2'   C  CH2   0  -0.305  -3.1308  -2.4061   0.2719
 CPN  N1'   N  NT3   1  -0.778  -4.0221  -3.2866  -0.5223
 CPN  N1    N  NR6   0  -0.500   1.6812   0.2320   0.6968
 CPN  C2    C  CR6   0   0.590   2.1798   0.7214  -0.5193
 CPN  N3    N  N     0  -0.540   3.4610   0.4488  -0.8358
 CPN  C4    C  CR6   0   0.512   4.2055  -0.3086  -0.0530
 CPN  C5    C  CR16  0  -0.472   3.7055  -0.8768   1.1594
 CPN  C6    C  CR16  0   0.099   2.4312  -0.5759   1.4790
 CPN  O2    O  O     0  -0.514   1.4361   1.3809  -1.2327
 CPN  N4    N  NH2   0  -0.808   5.4658  -0.5430  -0.4165
 CPN  H8'1  H  HCH2  0   0.306   0.0503   1.5074   0.7960
 CPN  H8'2  H  HCH2  0   0.316   0.1400   0.3031   2.0701
 CPN  H5'1  H  HCH2  0   0.324  -1.9878   1.1032   1.8390
 CPN  H5'2  H  HCH2  0   0.330  -3.5258   0.5347   1.2882
 CPN  HXT   H  HOH1  0   0.489  -3.3459   3.8009   0.0730
 CPN  H3'1  H  HCH2  0   0.287  -3.6971  -0.6040  -0.7668
 CPN  H3'2  H  HCH2  0   0.287  -2.3040  -1.4148  -1.4595
 CPN  H2'1  H  HCH2  0   0.305  -2.2410  -2.9829   0.5099
 CPN  H2'2  H  HCH2  0   0.302  -3.6554  -2.1676   1.1940
 CPN  H1'1  H  HNT3  0   0.484  -4.2569  -4.1358  -0.0095
 CPN  H1'2  H  HNT3  0   0.473  -4.9037  -2.8311  -0.7579
 CPN  H1'3  H  HNT3  0   0.474  -3.5889  -3.5811  -1.3973
 CPN  H5    H  HCR6  0   0.289   4.3080  -1.5111   1.7914
 CPN  H6    H  HCR6  0   0.314   1.9599  -0.9521   2.3762
 CPN  HN41  H  HNH2  0   0.403   5.8268  -0.1524  -1.2701
 CPN  HN42  H  HNH2  0   0.414   6.0692  -1.1364   0.1247

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
 CPN  C8'  C7'   single  1.525  0.020  1.525
 CPN  C8'  N1    single  1.439  0.020  1.439
 CPN  C8'  H8'1  single  0.970  0.020  1.090
 CPN  C8'  H8'2  single  0.970  0.020  1.090
 CPN  C7'  O7'   double  1.216  0.020  1.216
 CPN  C7'  N4'   single  1.354  0.020  1.354
 CPN  C5'  C'    single  1.517  0.020  1.517
 CPN  C5'  N4'   single  1.438  0.020  1.438
 CPN  C5'  H5'1  single  0.970  0.020  1.090
 CPN  C5'  H5'2  single  0.970  0.020  1.090
 CPN  C'   O1'   double  1.202  0.020  1.202
 CPN  C'   OXT   single  1.323  0.020  1.323
 CPN  OXT  HXT   single  0.850  0.020  0.980
 CPN  N4'  C3'   single  1.449  0.020  1.449
 CPN  C3'  C2'   single  1.522  0.020  1.522
 CPN  C3'  H3'1  single  0.970  0.020  1.090
 CPN  C3'  H3'2  single  0.970  0.020  1.090
 CPN  C2'  N1'   single  1.483  0.020  1.483
 CPN  C2'  H2'1  single  0.970  0.020  1.090
 CPN  C2'  H2'2  single  0.970  0.020  1.090
 CPN  N1'  H1'1  single  0.890  0.020  1.040
 CPN  N1'  H1'2  single  0.890  0.020  1.040
 CPN  N1'  H1'3  single  0.890  0.020  1.040
 CPN  N1   C2    single  1.402  0.020  1.402
 CPN  N1   C6    single  1.352  0.020  1.352
 CPN  C2   N3    single  1.348  0.020  1.348
 CPN  C2   O2    double  1.224  0.020  1.224
 CPN  N3   C4    double  1.319  0.020  1.319
 CPN  C4   C5    single  1.429  0.020  1.429
 CPN  C4   N4    single  1.332  0.020  1.332
 CPN  C5   C6    double  1.348  0.020  1.348
 CPN  C5   H5    single  0.930  0.020  1.080
 CPN  C6   H6    single  0.930  0.020  1.080
 CPN  N4   HN41  single  0.860  0.020  1.020
 CPN  N4   HN42  single  0.860  0.020  1.020

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
 CPN  H8'2  C8'  H8'1  107.24  3.000
 CPN  H8'2  C8'  N1    108.62  3.000
 CPN  H8'1  C8'  N1    109.44  3.000
 CPN  H8'2  C8'  C7'   109.47  3.000
 CPN  H8'1  C8'  C7'   111.91  3.000
 CPN  N1    C8'  C7'   110.07  3.000
 CPN  N4'   C7'  O7'   122.25  3.000
 CPN  N4'   C7'  C8'   117.09  3.000
 CPN  O7'   C7'  C8'   120.62  3.000
 CPN  H5'2  C5'  H5'1  104.78  3.000
 CPN  H5'2  C5'  N4'   109.42  3.000
 CPN  H5'1  C5'  N4'   112.03  3.000
 CPN  H5'2  C5'  C'    108.93  3.000
 CPN  H5'1  C5'  C'    109.50  3.000
 CPN  N4'   C5'  C'    111.90  3.000
 CPN  OXT   C'   O1'   124.93  3.000
 CPN  OXT   C'   C5'   110.98  3.000
 CPN  O1'   C'   C5'   124.09  3.000
 CPN  HXT   OXT  C'    110.48  3.000
 CPN  C3'   N4'  C5'   117.42  3.000
 CPN  C3'   N4'  C7'   118.62  3.000
 CPN  C5'   N4'  C7'   123.65  3.000
 CPN  H3'2  C3'  H3'1  107.11  3.000
 CPN  H3'2  C3'  C2'   110.47  3.000
 CPN  H3'1  C3'  C2'   110.11  3.000
 CPN  H3'2  C3'  N4'   110.05  3.000
 CPN  H3'1  C3'  N4'   108.69  3.000
 CPN  C2'   C3'  N4'   110.33  3.000
 CPN  H2'2  C2'  H2'1  109.01  3.000
 CPN  H2'2  C2'  N1'   107.12  3.000
 CPN  H2'1  C2'  N1'   107.11  3.000
 CPN  H2'2  C2'  C3'   111.63  3.000
 CPN  H2'1  C2'  C3'   111.49  3.000
 CPN  N1'   C2'  C3'   110.29  3.000
 CPN  H1'3  N1'  H1'2  107.34  3.000
 CPN  H1'3  N1'  H1'1  106.79  3.000
 CPN  H1'2  N1'  H1'1  106.81  3.000
 CPN  H1'3  N1'  C2'   112.06  3.000
 CPN  H1'2  N1'  C2'   112.21  3.000
 CPN  H1'1  N1'  C2'   111.31  3.000
 CPN  C6    N1   C2    120.87  3.000
 CPN  C6    N1   C8'   120.65  3.000
 CPN  C2    N1   C8'   117.98  3.000
 CPN  O2    C2   N3    123.36  3.000
 CPN  O2    C2   N1    118.53  3.000
 CPN  N3    C2   N1    118.10  3.000
 CPN  C4    N3   C2    120.88  3.000
 CPN  N4    C4   C5    119.50  3.000
 CPN  N4    C4   N3    118.22  3.000
 CPN  C5    C4   N3    122.28  3.000
 CPN  H5    C5   C6    121.35  3.000
 CPN  H5    C5   C4    122.35  3.000
 CPN  C6    C5   C4    116.30  3.000
 CPN  H6    C6   C5    122.09  3.000
 CPN  H6    C6   N1    116.52  3.000
 CPN  C5    C6   N1    121.39  3.000
 CPN  HN42  N4   HN41  118.10  3.000
 CPN  HN42  N4   C4    121.67  3.000
 CPN  HN41  N4   C4    120.18  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
 CPN  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 CPN  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 CPN  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 CPN  CONST_04  N3    C2   N1   C8'  180.00   0.0  0
 CPN  CONST_05  N4    C4   N3   C2   180.00   0.0  0
 CPN  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 CPN  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 CPN  CONST_08  O2    C2   N1   C8'    0.00   0.0  0
 CPN  CONST_09  HN41  N4   C4   N3     0.00   0.0  0
 CPN  CONST_10  HN42  N4   C4   N3   180.00   0.0  0
 CPN  CONST_11  C5'   N4'  C7'  C8'    0.00   0.0  0
 CPN  CONST_12  C3'   N4'  C7'  C8'  180.00   0.0  0
 CPN  CONST_13  C5'   N4'  C7'  O7'  180.00   0.0  0
 CPN  CONST_14  C3'   N4'  C7'  O7'    0.00   0.0  0
 CPN  CONST_15  HXT   OXT  C'   C5'  180.00   0.0  0
 CPN  Var_01    C2    N1   C8'  C7'   76.90  30.0  3
 CPN  Var_02    N1    C8'  C7'  O7'   10.12  30.0  1
 CPN  Var_03    C'    C5'  N4'  C7'   88.28  30.0  2
 CPN  Var_04    C2'   C3'  N4'  C7'   86.68  30.0  3
 CPN  Var_05    N4'   C5'  C'   O1'   -2.05  30.0  1
 CPN  Var_06    N1'   C2'  C3'  N4'  179.69  30.0  3
 CPN  Var_07    H1'1  N1'  C2'  C3'  179.58  30.0  3

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
 CPN  plan-1  C8'   0.020
 CPN  plan-1  N1    0.020
 CPN  plan-1  C2    0.020
 CPN  plan-1  N3    0.020
 CPN  plan-1  C4    0.020
 CPN  plan-1  C5    0.020
 CPN  plan-1  C6    0.020
 CPN  plan-1  O2    0.020
 CPN  plan-1  N4    0.020
 CPN  plan-1  H5    0.020
 CPN  plan-1  H6    0.020
 CPN  plan-1  HN41  0.020
 CPN  plan-1  HN42  0.020
 CPN  plan-2  C8'   0.020
 CPN  plan-2  C7'   0.020
 CPN  plan-2  O7'   0.020
 CPN  plan-2  C5'   0.020
 CPN  plan-2  N4'   0.020
 CPN  plan-2  C3'   0.020
 CPN  plan-3  C5'   0.020
 CPN  plan-3  C'    0.020
 CPN  plan-3  O1'   0.020
 CPN  plan-3  OXT   0.020
 CPN  plan-3  HXT   0.020

