# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:37:41 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-N-[(2S)-2-aminopropyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CN(CC(O)=O)C(=O)CN1C=CC(=NC1=O)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
 40C  40C  N-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-N-[(2S)-2-aminopropyl]glycine  peptide  36  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40C
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
 40C  C'    C  C      0   0.413   2.8970   2.1203   0.1163
 40C  N1    N  NR6    0  -0.493  -1.8828  -0.5196  -0.2581
 40C  C2    C  CR6    0   0.586  -2.4504   0.5419  -0.9744
 40C  O2    O  O      0  -0.519  -1.7872   1.0930  -1.8425
 40C  N3    N  N      0  -0.542  -3.7199   0.8970  -0.6852
 40C  C4    C  CR6    0   0.509  -4.3902   0.2950   0.2779
 40C  N4    N  NH2    0  -0.811  -5.6416   0.6898   0.5171
 40C  C5    C  CR16   0  -0.475  -3.8211  -0.7543   1.0616
 40C  C6    C  CR16   0   0.099  -2.5575  -1.1093   0.7514
 40C  N1'   N  NH2    0  -0.781   1.7382  -3.0674   0.5559
 40C  O1'   O  O      0  -0.591   2.4259   2.2182  -1.0275
 40C  C2'   C  CH1    0  -0.104   2.8708  -2.3053   0.0472
 40C  C2M   C  CH3    0  -0.672   3.7888  -3.1025  -0.8755
 40C  C3'   C  CH2    0  -0.303   2.3737  -1.0495  -0.6679
 40C  N4'   N  NT     0  -0.420   1.7306  -0.0984   0.2146
 40C  C5'   C  CH2    0  -0.468   2.6070   0.8223   0.9039
 40C  C7'   C  C      0   0.561   0.4078   0.0934   0.3059
 40C  O7'   O  O      0  -0.505  -0.0927   0.9508   1.0214
 40C  C8'   C  CH2    0  -0.465  -0.4977  -0.8508  -0.4827
 40C  H5    H  HCR6   0   0.285  -4.3641  -1.2407   1.8573
 40C  H6    H  HCR6   0   0.309  -2.0367  -1.8912   1.2872
 40C  H22'  H  HCH1   0   0.229   3.4538  -1.9866   0.9175
 40C  H13'  H  HCH2   0   0.256   3.2167  -0.5443  -1.1449
 40C  H23'  H  HCH2   0   0.249   1.7109  -1.3379  -1.4855
 40C  HN4   H  HNH2   0   0.401  -6.0512   1.4301  -0.0263
 40C  HN4A  H  HNH2   0   0.412  -6.1987   0.2681   1.2387
 40C  H15'  H  HCH2   0   0.250   3.5534   0.3127   1.1038
 40C  H25'  H  HCH2   0   0.254   2.1905   1.0751   1.8793
 40C  H18'  H  HCH2   0   0.297  -0.3242  -1.8744  -0.1518
 40C  H28'  H  HCH2   0   0.297  -0.2871  -0.8146  -1.5501
 40C  H2M   H  HCH3   0   0.233   4.1273  -4.0144  -0.3825
 40C  H2MA  H  HCH3   0   0.219   3.2665  -3.3929  -1.7907
 40C  H2MB  H  HCH3   0   0.225   4.6729  -2.5310  -1.1630
 40C  OXT   O  OC    -1  -0.625   3.6038   2.9479   0.7255
 40C  HN1'  H  HNH2   0   0.338   1.2922  -3.5566  -0.2128
 40C  HNXT  H  HNH2   0   0.352   2.0738  -3.7941   1.1765

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
 40C  C'    C5'   single  1.546  0.020  1.546
 40C  C'    O1'   deloc   1.241  0.020  1.241
 40C  C'    OXT   deloc   1.247  0.020  1.247
 40C  N1    C8'   single  1.442  0.020  1.442
 40C  C2    N1    single  1.401  0.020  1.401
 40C  O2    C2    double  1.224  0.020  1.224
 40C  N3    C2    single  1.350  0.020  1.350
 40C  N3    C4    double  1.319  0.020  1.319
 40C  C4    C5    single  1.428  0.020  1.428
 40C  N4    C4    single  1.334  0.020  1.334
 40C  C5    C6    double  1.349  0.020  1.349
 40C  C6    N1    single  1.350  0.020  1.350
 40C  C6    H6    single  0.930  0.020  1.080
 40C  N1'   C2'   single  1.457  0.020  1.457
 40C  N1'   HNXT  single  0.890  0.020  1.040
 40C  C2'   C2M   single  1.526  0.020  1.526
 40C  C2'   H22'  single  0.970  0.020  1.090
 40C  C2M   H2MA  single  0.970  0.020  1.090
 40C  C2M   H2M   single  0.970  0.020  1.090
 40C  C3'   C2'   single  1.528  0.020  1.528
 40C  C3'   H23'  single  0.970  0.020  1.090
 40C  N4'   C3'   single  1.448  0.020  1.448
 40C  N4'   C5'   single  1.446  0.020  1.446
 40C  C5'   H25'  single  0.970  0.020  1.090
 40C  C7'   N4'   single  1.340  0.020  1.340
 40C  O7'   C7'   double  1.224  0.020  1.224
 40C  C8'   C7'   single  1.528  0.020  1.528
 40C  C8'   H18'  single  0.970  0.020  1.090
 40C  H5    C5    single  0.930  0.020  1.080
 40C  HN1'  N1'   single  0.890  0.020  1.040
 40C  H13'  C3'   single  0.970  0.020  1.090
 40C  HN4   N4    single  0.860  0.020  1.020
 40C  HN4A  N4    single  0.860  0.020  1.020
 40C  H15'  C5'   single  0.970  0.020  1.090
 40C  H28'  C8'   single  0.970  0.020  1.090
 40C  H2MB  C2M   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
 40C  OXT   C'   C5'   114.50  3.000
 40C  OXT   C'   O1'   127.81  3.000
 40C  C5'   C'   O1'   117.69  3.000
 40C  C8'   N1   C6    119.76  3.000
 40C  C6    N1   C2    120.73  3.000
 40C  C8'   N1   C2    118.93  3.000
 40C  N3    C2   O2    122.91  3.000
 40C  N3    C2   N1    118.10  3.000
 40C  O2    C2   N1    118.98  3.000
 40C  C4    N3   C2    120.96  3.000
 40C  C5    C4   N4    119.54  3.000
 40C  N4    C4   N3    118.21  3.000
 40C  C5    C4   N3    122.25  3.000
 40C  HN4A  N4   HN4   118.12  3.000
 40C  HN4A  N4   C4    121.66  3.000
 40C  HN4   N4   C4    120.21  3.000
 40C  H5    C5   C6    121.49  3.000
 40C  H5    C5   C4    122.37  3.000
 40C  C6    C5   C4    116.14  3.000
 40C  H6    C6   C5    121.84  3.000
 40C  H6    C6   N1    116.46  3.000
 40C  C5    C6   N1    121.69  3.000
 40C  HNXT  N1'  HN1'  105.30  3.000
 40C  HN1'  N1'  C2'   109.24  3.000
 40C  HNXT  N1'  C2'   109.37  3.000
 40C  H22'  C2'  C3'   107.81  3.000
 40C  C3'   C2'  C2M   110.00  3.000
 40C  H22'  C2'  C2M   108.20  3.000
 40C  C3'   C2'  N1'   109.90  3.000
 40C  H22'  C2'  N1'   106.78  3.000
 40C  C2M   C2'  N1'   113.92  3.000
 40C  H2MB  C2M  H2MA  107.81  3.000
 40C  H2MB  C2M  H2M   107.79  3.000
 40C  H2MA  C2M  H2M   107.74  3.000
 40C  H2MB  C2M  C2'   111.90  3.000
 40C  H2M   C2M  C2'   110.49  3.000
 40C  H2MA  C2M  C2'   110.95  3.000
 40C  H23'  C3'  H13'  105.29  3.000
 40C  H13'  C3'  N4'   107.76  3.000
 40C  H23'  C3'  N4'   111.12  3.000
 40C  H13'  C3'  C2'   109.47  3.000
 40C  N4'   C3'  C2'   113.52  3.000
 40C  H23'  C3'  C2'   109.33  3.000
 40C  C7'   N4'  C5'   118.34  3.000
 40C  C7'   N4'  C3'   125.04  3.000
 40C  C5'   N4'  C3'   116.07  3.000
 40C  H25'  C5'  H15'  105.97  3.000
 40C  H15'  C5'  N4'   108.36  3.000
 40C  H25'  C5'  N4'   110.03  3.000
 40C  H15'  C5'  C'    108.80  3.000
 40C  H25'  C5'  C'    109.44  3.000
 40C  N4'   C5'  C'    113.92  3.000
 40C  C8'   C7'  O7'   119.50  3.000
 40C  C8'   C7'  N4'   117.49  3.000
 40C  O7'   C7'  N4'   122.96  3.000
 40C  H28'  C8'  H18'  107.35  3.000
 40C  H28'  C8'  C7'   111.77  3.000
 40C  H18'  C8'  C7'   109.24  3.000
 40C  H28'  C8'  N1    109.33  3.000
 40C  H18'  C8'  N1    108.75  3.000
 40C  C7'   C8'  N1    110.31  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
 40C  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 40C  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 40C  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 40C  CONST_04  N4    C4   N3   C2   180.00   0.0  0
 40C  CONST_05  C6    N1   C2   O2   180.00   0.0  0
 40C  CONST_06  C4    N3   C2   O2   180.00   0.0  0
 40C  CONST_07  C8'   N1   C2   N3   180.00   0.0  0
 40C  CONST_08  C8'   N1   C2   O2     0.00   0.0  0
 40C  CONST_09  HN4   N4   C4   N3     0.00   0.0  0
 40C  CONST_10  HN4A  N4   C4   N3   180.00   0.0  0
 40C  CONST_11  O7'   C7'  N4'  C3'  180.00   0.0  0
 40C  CONST_12  C8'   C7'  N4'  C3'    0.00   0.0  0
 40C  CONST_13  O7'   C7'  N4'  C5'    0.00   0.0  0
 40C  CONST_14  C8'   C7'  N4'  C5'  180.00   0.0  0
 40C  Var_01    C7'   C8'  N1   C2    80.73  30.0  3
 40C  Var_02    N4'   C7'  C8'  N1   179.14  30.0  3
 40C  Var_03    C3'   N4'  C5'  C'    88.57  30.0  2
 40C  Var_04    N4'   C5'  C'   O1'   -3.71  30.0  3
 40C  Var_05    C5'   N4'  C3'  C2'   84.96  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
 40C  chir_01  C2'  N1'  C2M  C3'  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
 40C  plan-1  N1    0.020
 40C  plan-1  C2    0.020
 40C  plan-1  O2    0.020
 40C  plan-1  N3    0.020
 40C  plan-1  C4    0.020
 40C  plan-1  N4    0.020
 40C  plan-1  C5    0.020
 40C  plan-1  C6    0.020
 40C  plan-1  C8'   0.020
 40C  plan-1  H5    0.020
 40C  plan-1  H6    0.020
 40C  plan-1  HN4   0.020
 40C  plan-1  HN4A  0.020
 40C  plan-2  C3'   0.020
 40C  plan-2  N4'   0.020
 40C  plan-2  C5'   0.020
 40C  plan-2  C7'   0.020
 40C  plan-2  O7'   0.020
 40C  plan-2  C8'   0.020
 40C  plan-3  C'    0.020
 40C  plan-3  O1'   0.020
 40C  plan-3  C5'   0.020
 40C  plan-3  OXT   0.020

