# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:07:29 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-[(2S)-2-aminopropyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CN(CC(O)=O)C(=O)CN1C=C(C)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
 40T  40T  N-[(2S)-2-aminopropyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine  peptide  39  21  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40T
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
 40T  C'    C  C     0   0.551  -2.9292  -2.0371   0.4251
 40T  N1    N  NR6   0  -0.511   1.5971  -0.5803   0.4415
 40T  C2    C  CR6   0   0.723   2.0725  -1.2116  -0.6815
 40T  O2    O  O     0  -0.479   1.4022  -1.9764  -1.3439
 40T  N3    N  NR16  0  -0.732   3.3777  -0.9216  -0.9817
 40T  C4    C  CR6   0   0.559   4.2268  -0.0493  -0.3233
 40T  O4    O  O     0  -0.456   5.3681   0.1172  -0.7137
 40T  C5    C  CR6   0  -0.180   3.6386   0.6110   0.8252
 40T  C6    C  CR16  0   0.059   2.3620   0.3207   1.1301
 40T  C7    C  CH3   0  -0.706   4.4679   1.5761   1.6069
 40T  N1'   N  NH2   0  -0.774  -2.1291   3.0540   0.3724
 40T  O1'   O  O     0  -0.427  -2.5798  -2.4184  -0.6600
 40T  C2'   C  CH1   0  -0.103  -3.2846   2.2942  -0.0736
 40T  C2M   C  CH3   0  -0.668  -4.2350   3.0662  -0.9863
 40T  C3'   C  CH2   0  -0.308  -2.8262   1.0212  -0.7841
 40T  N4'   N  NT    0  -0.439  -1.9661   0.1860   0.0353
 40T  C5'   C  CH2   0  -0.479  -2.6208  -0.6637   0.9900
 40T  C7'   C  C     0   0.577  -0.6316   0.2042  -0.1459
 40T  O7'   O  O     0  -0.477  -0.0713   0.9020  -0.9715
 40T  C8'   C  CH2   0  -0.467   0.1955  -0.7176   0.7526
 40T  HN3   H  HNR6  0   0.425   3.7512  -1.3933  -1.7963
 40T  H6    H  HCR6  0   0.311   1.8691   0.7850   1.9734
 40T  H22'  H  HCH1  0   0.225  -3.8406   2.0045   0.8256
 40T  H13'  H  HCH2  0   0.256  -3.7001   0.4351  -1.0798
 40T  H23'  H  HCH2  0   0.256  -2.2974   1.2805  -1.7010
 40T  H15'  H  HCH2  0   0.324  -3.5573  -0.1959   1.3010
 40T  H25'  H  HCH2  0   0.316  -2.0472  -0.7751   1.9123
 40T  H7    H  HCH3  0   0.247   3.9149   1.9584   2.4631
 40T  H7A   H  HCH3  0   0.247   5.3784   1.1048   1.9790
 40T  H7B   H  HCH3  0   0.247   4.7723   2.4279   0.9969
 40T  HXT'  H  HCH2  0   0.314  -0.1052  -1.7582   0.6350
 40T  H28'  H  HCH2  0   0.312   0.0596  -0.4625   1.8039
 40T  H2M   H  HCH3  0   0.223  -5.1231   2.4841  -1.2391
 40T  H2MA  H  HCH3  0   0.234  -4.5674   3.9845  -0.5008
 40T  H2MB  H  HCH3  0   0.219  -3.7373   3.3420  -1.9192
 40T  OXT   O  OH1   0  -0.587  -3.6266  -2.7585   1.2885
 40T  HNXT  H  HNH2  0   0.346  -2.4418   3.8798   0.8688
 40T  HXT   H  HOH1  0   0.488  -3.8083  -3.6385   0.9253
 40T  HN1'  H  HNH2  0   0.334  -1.6137   3.3922  -0.4324

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
 40T  C'    O1'   double  1.202  0.020  1.202
 40T  C'    C5'   single  1.517  0.020  1.517
 40T  C'    OXT   single  1.324  0.020  1.324
 40T  N1    C8'   single  1.442  0.020  1.442
 40T  N1    C6    single  1.368  0.020  1.368
 40T  C2    N1    single  1.373  0.020  1.373
 40T  O2    C2    double  1.214  0.020  1.214
 40T  N3    C2    single  1.370  0.020  1.370
 40T  N3    C4    single  1.384  0.020  1.384
 40T  C4    C5    single  1.449  0.020  1.449
 40T  O4    C4    double  1.218  0.020  1.218
 40T  C5    C6    double  1.344  0.020  1.344
 40T  C5    C7    single  1.493  0.020  1.493
 40T  C6    H6    single  0.930  0.020  1.080
 40T  C7    H7B   single  0.970  0.020  1.090
 40T  N1'   HNXT  single  0.890  0.020  1.040
 40T  C2'   N1'   single  1.453  0.020  1.453
 40T  C2'   C2M   single  1.527  0.020  1.527
 40T  C2'   H22'  single  0.970  0.020  1.090
 40T  C2M   H2MB  single  0.970  0.020  1.090
 40T  C3'   C2'   single  1.528  0.020  1.528
 40T  N4'   C3'   single  1.452  0.020  1.452
 40T  N4'   C5'   single  1.436  0.020  1.436
 40T  C5'   H15'  single  0.970  0.020  1.090
 40T  C5'   H25'  single  0.970  0.020  1.090
 40T  C7'   N4'   single  1.347  0.020  1.347
 40T  O7'   C7'   double  1.218  0.020  1.218
 40T  C8'   C7'   single  1.530  0.020  1.530
 40T  C8'   HXT'  single  0.970  0.020  1.090
 40T  HN3   N3    single  0.860  0.020  1.020
 40T  HN1'  N1'   single  0.890  0.020  1.040
 40T  H13'  C3'   single  0.970  0.020  1.090
 40T  H23'  C3'   single  0.970  0.020  1.090
 40T  H7    C7    single  0.970  0.020  1.090
 40T  H7A   C7    single  0.970  0.020  1.090
 40T  H28'  C8'   single  0.970  0.020  1.090
 40T  H2M   C2M   single  0.970  0.020  1.090
 40T  H2MA  C2M   single  0.970  0.020  1.090
 40T  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
 40T  OXT   C'   C5'   110.96  3.000
 40T  OXT   C'   O1'   124.69  3.000
 40T  C5'   C'   O1'   124.36  3.000
 40T  C8'   N1   C6    119.84  3.000
 40T  C6    N1   C2    121.40  3.000
 40T  C8'   N1   C2    117.97  3.000
 40T  N3    C2   O2    122.67  3.000
 40T  N3    C2   N1    114.30  3.000
 40T  O2    C2   N1    123.02  3.000
 40T  HN3   N3   C4    116.75  3.000
 40T  HN3   N3   C2    115.39  3.000
 40T  C4    N3   C2    127.85  3.000
 40T  C5    C4   O4    124.90  3.000
 40T  O4    C4   N3    120.58  3.000
 40T  C5    C4   N3    114.52  3.000
 40T  C7    C5   C6    123.25  3.000
 40T  C7    C5   C4    118.93  3.000
 40T  C6    C5   C4    117.82  3.000
 40T  H6    C6   C5    121.13  3.000
 40T  H6    C6   N1    114.86  3.000
 40T  C5    C6   N1    124.00  3.000
 40T  H7B   C7   H7A   107.17  3.000
 40T  H7A   C7   H7    107.90  3.000
 40T  H7B   C7   H7    107.89  3.000
 40T  H7A   C7   C5    111.28  3.000
 40T  H7    C7   C5    110.89  3.000
 40T  H7B   C7   C5    111.52  3.000
 40T  HNXT  N1'  HN1'  105.90  3.000
 40T  HN1'  N1'  C2'   109.58  3.000
 40T  HNXT  N1'  C2'   109.34  3.000
 40T  H22'  C2'  C3'   108.26  3.000
 40T  C3'   C2'  C2M   109.26  3.000
 40T  H22'  C2'  C2M   107.95  3.000
 40T  C3'   C2'  N1'   109.86  3.000
 40T  H22'  C2'  N1'   106.85  3.000
 40T  C2M   C2'  N1'   114.46  3.000
 40T  H2MB  C2M  H2MA  107.84  3.000
 40T  H2MA  C2M  H2M   107.71  3.000
 40T  H2MB  C2M  H2M   107.91  3.000
 40T  H2MA  C2M  C2'   110.44  3.000
 40T  H2M   C2M  C2'   112.03  3.000
 40T  H2MB  C2M  C2'   110.75  3.000
 40T  H23'  C3'  H13'  106.73  3.000
 40T  H23'  C3'  N4'   108.91  3.000
 40T  H13'  C3'  N4'   108.53  3.000
 40T  H23'  C3'  C2'   109.79  3.000
 40T  H13'  C3'  C2'   109.43  3.000
 40T  N4'   C3'  C2'   113.23  3.000
 40T  C7'   N4'  C5'   123.31  3.000
 40T  C7'   N4'  C3'   120.21  3.000
 40T  C5'   N4'  C3'   116.45  3.000
 40T  H25'  C5'  H15'  104.69  3.000
 40T  H25'  C5'  N4'   112.48  3.000
 40T  H15'  C5'  N4'   109.08  3.000
 40T  H25'  C5'  C'    109.21  3.000
 40T  H15'  C5'  C'    108.64  3.000
 40T  N4'   C5'  C'    112.39  3.000
 40T  C8'   C7'  O7'   119.65  3.000
 40T  C8'   C7'  N4'   116.64  3.000
 40T  O7'   C7'  N4'   123.70  3.000
 40T  H28'  C8'  HXT'  107.05  3.000
 40T  H28'  C8'  C7'   110.98  3.000
 40T  HXT'  C8'  C7'   111.27  3.000
 40T  H28'  C8'  N1    107.87  3.000
 40T  HXT'  C8'  N1    109.62  3.000
 40T  C7'   C8'  N1    109.96  3.000
 40T  HXT   OXT  C'    110.44  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
 40T  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 40T  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 40T  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 40T  CONST_04  O4   C4   N3   C2    180.00   0.0  0
 40T  CONST_05  C6   N1   C2   O2    180.00   0.0  0
 40T  CONST_06  C4   N3   C2   O2    180.00   0.0  0
 40T  CONST_07  C8'  N1   C2   N3    180.00   0.0  0
 40T  CONST_08  HN3  N3   C2   N1    180.00   0.0  0
 40T  CONST_09  C8'  N1   C2   O2      0.00   0.0  0
 40T  CONST_10  O7'  C7'  N4'  C3'     0.00   0.0  0
 40T  CONST_11  C8'  C7'  N4'  C3'   180.00   0.0  0
 40T  CONST_12  O7'  C7'  N4'  C5'   180.00   0.0  0
 40T  CONST_13  C8'  C7'  N4'  C5'     0.00   0.0  0
 40T  CONST_14  HXT  OXT  C'   O1'     0.00   0.0  0
 40T  Var_01    C7'  C8'  N1   C2    -77.74  30.0  3
 40T  Var_02    H7B  C7   C5   C4     62.34  30.0  3
 40T  Var_03    N4'  C7'  C8'  N1   -179.79  30.0  3
 40T  Var_04    C3'  N4'  C5'  C'     91.42  30.0  2
 40T  Var_05    N4'  C5'  C'   O1'     5.39  30.0  3
 40T  Var_06    C5'  N4'  C3'  C2'    81.01  30.0  2

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
 40T  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
 40T  plan-1  N1   0.020
 40T  plan-1  C2   0.020
 40T  plan-1  O2   0.020
 40T  plan-1  N3   0.020
 40T  plan-1  C4   0.020
 40T  plan-1  O4   0.020
 40T  plan-1  C5   0.020
 40T  plan-1  C6   0.020
 40T  plan-1  C7   0.020
 40T  plan-1  C8'  0.020
 40T  plan-1  HN3  0.020
 40T  plan-1  H6   0.020
 40T  plan-2  C3'  0.020
 40T  plan-2  N4'  0.020
 40T  plan-2  C5'  0.020
 40T  plan-2  C7'  0.020
 40T  plan-2  O7'  0.020
 40T  plan-2  C8'  0.020
 40T  plan-3  C'   0.020
 40T  plan-3  O1'  0.020
 40T  plan-3  C5'  0.020
 40T  plan-3  OXT  0.020
 40T  plan-3  HXT  0.020

