# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 22:40:00 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-{(carboxymethyl)[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]amino}ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(CC(=O)N(CC[NH3+])CC(O)=O)C(=O)NC1=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
 TPN  TPN  2-{(carboxymethyl)[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]amino}ethanaminium  peptide  37  20  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TPN
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
 TPN  C8'   C  CH2   0  -0.471   0.0741   0.6309   0.7827
 TPN  C7'   C  C     0   0.581  -0.7879  -0.3255  -0.0364
 TPN  O7'   O  O     0  -0.464  -0.2720  -1.1499  -0.7663
 TPN  C5'   C  CH2   0  -0.484  -2.7683   0.8163   0.8738
 TPN  C'    C  C     0   0.555  -2.9357   2.1026   0.0862
 TPN  O1'   O  O     0  -0.428  -2.4589   2.2897  -1.0017
 TPN  OXT   O  OH1   0  -0.582  -3.6551   2.9823   0.7599
 TPN  N4'   N  NT    0  -0.453  -2.1296  -0.2104   0.0948
 TPN  C3'   C  CH2   0  -0.344  -2.9794  -1.0322  -0.7444
 TPN  C2'   C  CH2   0  -0.303  -3.2539  -2.3672  -0.0682
 TPN  N1'   N  NT3   1  -0.778  -4.1347  -3.2040  -0.9191
 TPN  N1    N  NR6   0  -0.512   1.4700   0.3560   0.5535
 TPN  C6    C  CR16  0   0.062   2.1438   1.0208  -0.4352
 TPN  C2    C  CR6   0   0.727   2.0319  -0.7116   1.2106
 TPN  O2    O  O     0  -0.481   1.4333  -1.3618   2.0425
 TPN  N3    N  NR16  0  -0.732   3.3301  -0.9690   0.8601
 TPN  C4    C  CR6   0   0.561   4.0940  -0.3249  -0.0985
 TPN  O4    O  O     0  -0.454   5.2410  -0.6723  -0.3111
 TPN  C5    C  CR6   0  -0.179   3.4115   0.7517  -0.7900
 TPN  C5M   C  CH3   0  -0.705   4.1381   1.5032  -1.8562
 TPN  H8'1  H  HCH2  0   0.314  -0.1191   1.6658   0.5001
 TPN  H8'2  H  HCH2  0   0.324  -0.1455   0.5488   1.8470
 TPN  H5'1  H  HCH2  0   0.326  -2.2210   1.0320   1.7935
 TPN  H5'2  H  HCH2  0   0.332  -3.7474   0.4645   1.2041
 TPN  HXT   H  HOH1  0   0.490  -3.7375   3.8087   0.2598
 TPN  H3'1  H  HCH2  0   0.290  -3.9149  -0.5002  -0.9229
 TPN  H3'2  H  HCH2  0   0.289  -2.5091  -1.1873  -1.7155
 TPN  H2'1  H  HCH2  0   0.305  -2.3367  -2.9279   0.0902
 TPN  H2'2  H  HCH2  0   0.302  -3.7598  -2.2383   0.8860
 TPN  H1'1  H  HNT3  0   0.474  -5.0314  -2.7553  -1.1057
 TPN  H1'2  H  HNT3  0   0.474  -3.7080  -3.4169  -1.8208
 TPN  H1'3  H  HNT3  0   0.484  -4.3403  -4.0971  -0.4725
 TPN  H6    H  HCR6  0   0.310   1.5840   1.8119  -0.9154
 TPN  HN3   H  HNR6  0   0.426   3.7693  -1.7384   1.3513
 TPN  HM51  H  HCH3  0   0.247   5.0313   1.9907  -1.4630
 TPN  HM52  H  HCH3  0   0.247   4.4592   0.8412  -2.6614
 TPN  HM53  H  HCH3  0   0.247   3.5011   2.2727  -2.2890

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
 TPN  C8'  C7'   single  1.526  0.020  1.526
 TPN  C8'  N1    single  1.441  0.020  1.441
 TPN  C8'  H8'1  single  0.970  0.020  1.090
 TPN  C8'  H8'2  single  0.970  0.020  1.090
 TPN  C7'  O7'   double  1.216  0.020  1.216
 TPN  C7'  N4'   single  1.353  0.020  1.353
 TPN  C5'  C'    single  1.518  0.020  1.518
 TPN  C5'  N4'   single  1.438  0.020  1.438
 TPN  C5'  H5'1  single  0.970  0.020  1.090
 TPN  C5'  H5'2  single  0.970  0.020  1.090
 TPN  C'   O1'   double  1.202  0.020  1.202
 TPN  C'   OXT   single  1.321  0.020  1.321
 TPN  OXT  HXT   single  0.850  0.020  0.980
 TPN  N4'  C3'   single  1.450  0.020  1.450
 TPN  C3'  C2'   single  1.521  0.020  1.521
 TPN  C3'  H3'1  single  0.970  0.020  1.090
 TPN  C3'  H3'2  single  0.970  0.020  1.090
 TPN  C2'  N1'   single  1.483  0.020  1.483
 TPN  C2'  H2'1  single  0.970  0.020  1.090
 TPN  C2'  H2'2  single  0.970  0.020  1.090
 TPN  N1'  H1'1  single  0.890  0.020  1.040
 TPN  N1'  H1'2  single  0.890  0.020  1.040
 TPN  N1'  H1'3  single  0.890  0.020  1.040
 TPN  N1   C6    single  1.369  0.020  1.369
 TPN  N1   C2    single  1.374  0.020  1.374
 TPN  C6   C5    double  1.344  0.020  1.344
 TPN  C6   H6    single  0.930  0.020  1.080
 TPN  C2   O2    double  1.214  0.020  1.214
 TPN  C2   N3    single  1.369  0.020  1.369
 TPN  N3   C4    single  1.385  0.020  1.385
 TPN  N3   HN3   single  0.860  0.020  1.020
 TPN  C4   O4    double  1.217  0.020  1.217
 TPN  C4   C5    single  1.450  0.020  1.450
 TPN  C5   C5M   single  1.493  0.020  1.493
 TPN  C5M  HM51  single  0.970  0.020  1.090
 TPN  C5M  HM52  single  0.970  0.020  1.090
 TPN  C5M  HM53  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
 TPN  H8'2  C8'  H8'1  106.80  3.000
 TPN  H8'2  C8'  N1    109.64  3.000
 TPN  H8'1  C8'  N1    108.15  3.000
 TPN  H8'2  C8'  C7'   111.29  3.000
 TPN  H8'1  C8'  C7'   110.84  3.000
 TPN  N1    C8'  C7'   110.01  3.000
 TPN  N4'   C7'  O7'   122.45  3.000
 TPN  N4'   C7'  C8'   117.05  3.000
 TPN  O7'   C7'  C8'   120.50  3.000
 TPN  H5'2  C5'  H5'1  104.98  3.000
 TPN  H5'2  C5'  N4'   109.39  3.000
 TPN  H5'1  C5'  N4'   112.01  3.000
 TPN  H5'2  C5'  C'    109.35  3.000
 TPN  H5'1  C5'  C'    108.97  3.000
 TPN  N4'   C5'  C'    111.90  3.000
 TPN  OXT   C'   O1'   125.01  3.000
 TPN  OXT   C'   C5'   111.09  3.000
 TPN  O1'   C'   C5'   123.89  3.000
 TPN  HXT   OXT  C'    110.53  3.000
 TPN  C3'   N4'  C5'   117.25  3.000
 TPN  C3'   N4'  C7'   118.48  3.000
 TPN  C5'   N4'  C7'   123.61  3.000
 TPN  H3'2  C3'  H3'1  107.07  3.000
 TPN  H3'2  C3'  C2'   110.43  3.000
 TPN  H3'1  C3'  C2'   110.24  3.000
 TPN  H3'2  C3'  N4'   110.09  3.000
 TPN  H3'1  C3'  N4'   108.71  3.000
 TPN  C2'   C3'  N4'   110.23  3.000
 TPN  H2'2  C2'  H2'1  109.02  3.000
 TPN  H2'2  C2'  N1'   107.10  3.000
 TPN  H2'1  C2'  N1'   107.08  3.000
 TPN  H2'2  C2'  C3'   111.71  3.000
 TPN  H2'1  C2'  C3'   111.42  3.000
 TPN  N1'   C2'  C3'   110.31  3.000
 TPN  H1'3  N1'  H1'2  106.79  3.000
 TPN  H1'3  N1'  H1'1  106.75  3.000
 TPN  H1'2  N1'  H1'1  107.33  3.000
 TPN  H1'3  N1'  C2'   111.26  3.000
 TPN  H1'2  N1'  C2'   112.11  3.000
 TPN  H1'1  N1'  C2'   112.26  3.000
 TPN  C2    N1   C6    121.44  3.000
 TPN  C2    N1   C8'   117.93  3.000
 TPN  C6    N1   C8'   119.94  3.000
 TPN  H6    C6   C5    121.18  3.000
 TPN  H6    C6   N1    114.90  3.000
 TPN  C5    C6   N1    123.91  3.000
 TPN  N3    C2   O2    122.85  3.000
 TPN  N3    C2   N1    114.30  3.000
 TPN  O2    C2   N1    122.85  3.000
 TPN  HN3   N3   C4    116.73  3.000
 TPN  HN3   N3   C2    115.45  3.000
 TPN  C4    N3   C2    127.79  3.000
 TPN  C5    C4   O4    124.89  3.000
 TPN  C5    C4   N3    114.57  3.000
 TPN  O4    C4   N3    120.53  3.000
 TPN  C5M   C5   C4    119.02  3.000
 TPN  C5M   C5   C6    123.15  3.000
 TPN  C4    C5   C6    117.83  3.000
 TPN  HM53  C5M  HM52  107.92  3.000
 TPN  HM53  C5M  HM51  107.85  3.000
 TPN  HM52  C5M  HM51  107.23  3.000
 TPN  HM53  C5M  C5    110.79  3.000
 TPN  HM52  C5M  C5    111.40  3.000
 TPN  HM51  C5M  C5    111.47  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
 TPN  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 TPN  CONST_02  N3    C2   N1   C6     0.00   0.0  0
 TPN  CONST_03  C5    C4   N3   C2     0.00   0.0  0
 TPN  CONST_04  N3    C2   N1   C8'  180.00   0.0  0
 TPN  CONST_05  O2    C2   N1   C6   180.00   0.0  0
 TPN  CONST_06  O4    C4   N3   C2   180.00   0.0  0
 TPN  CONST_07  C4    N3   C2   O2   180.00   0.0  0
 TPN  CONST_08  HN3   N3   C2   N1   180.00   0.0  0
 TPN  CONST_09  O2    C2   N1   C8'    0.00   0.0  0
 TPN  CONST_10  C5'   N4'  C7'  C8'    0.00   0.0  0
 TPN  CONST_11  C3'   N4'  C7'  C8'  180.00   0.0  0
 TPN  CONST_12  C5'   N4'  C7'  O7'  180.00   0.0  0
 TPN  CONST_13  C3'   N4'  C7'  O7'    0.00   0.0  0
 TPN  CONST_14  HXT   OXT  C'   C5'  180.00   0.0  0
 TPN  Var_01    C6    N1   C8'  C7'   91.69  30.0  3
 TPN  Var_02    HM51  C5M  C5   C6   119.84  30.0  3
 TPN  Var_03    N1    C8'  C7'  O7'   -1.19  30.0  1
 TPN  Var_04    C'    C5'  N4'  C7'   84.42  30.0  2
 TPN  Var_05    C2'   C3'  N4'  C7'   88.78  30.0  3
 TPN  Var_06    N4'   C5'  C'   O1'   -7.83  30.0  1
 TPN  Var_07    N1'   C2'  C3'  N4'  179.42  30.0  3
 TPN  Var_08    H1'1  N1'  C2'  C3'  -59.52  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
 TPN  plan-1  C8'  0.020
 TPN  plan-1  N1   0.020
 TPN  plan-1  C6   0.020
 TPN  plan-1  C2   0.020
 TPN  plan-1  O2   0.020
 TPN  plan-1  N3   0.020
 TPN  plan-1  C4   0.020
 TPN  plan-1  O4   0.020
 TPN  plan-1  C5   0.020
 TPN  plan-1  C5M  0.020
 TPN  plan-1  H6   0.020
 TPN  plan-1  HN3  0.020
 TPN  plan-2  C8'  0.020
 TPN  plan-2  C7'  0.020
 TPN  plan-2  O7'  0.020
 TPN  plan-2  C5'  0.020
 TPN  plan-2  N4'  0.020
 TPN  plan-2  C3'  0.020
 TPN  plan-3  C5'  0.020
 TPN  plan-3  C'   0.020
 TPN  plan-3  O1'  0.020
 TPN  plan-3  OXT  0.020
 TPN  plan-3  HXT  0.020

