# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:35:22 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[(4-{2-[(6S)-2-amino-4-hydroxy-5,6,7,8-tetrahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2C[C@H](CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CNc2n1
#
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
 L24  L24  'N-[(4-{2-[(6S)-2-amino-4-hydroxy-5,6,7,8-tetrahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}phenyl)carbonyl]-L-glutamic acid'  ligand  55  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L24
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
 L24  N2A   N  NH2    0  -0.822  -0.8153   0.5698  10.0955
 L24  N1    N  N      0  -0.527  -1.3673   0.2326   7.9028
 L24  C2    C  CR6    0   0.529  -0.4387   0.5623   8.7937
 L24  N3    N  N      0  -0.508   0.8348   0.8579   8.5350
 L24  C4    C  CR6    0   0.449   1.1950   0.7978   7.2616
 L24  O4A   O  OH1    0  -0.602   2.4789   1.1121   7.0590
 L24  C5    C  CR6    0  -0.244   0.3438   0.4500   6.2235
 L24  C6    C  CR6    0   0.515  -0.9756   0.1801   6.6269
 L24  N7    N  NH1    0  -0.666  -1.9032  -0.1616   5.7166
 L24  C8    C  CH2    0  -0.244  -1.6532  -0.1154   4.2956
 L24  C9    C  CH1    0  -0.281  -0.2192  -0.5324   3.9899
 L24  C10   C  CH2    0  -0.481   0.7441   0.3572   4.7772
 L24  C11   C  CH2    0  -0.418   0.0860  -0.4674   2.4967
 L24  C12   C  CH2    0  -0.524  -0.6685  -1.5058   1.6618
 L24  C1B   C  CR6    0   0.144  -0.2800  -1.4403   0.2126
 L24  C2B   C  CR16   0  -0.296   0.8926  -2.0466  -0.2357
 L24  C3B   C  CR16   0  -0.257   1.2746  -1.9694  -1.5637
 L24  C4B   C  CR6    0  -0.059   0.5009  -1.2673  -2.4859
 L24  C5B   C  CR16   0  -0.278  -0.6761  -0.6666  -2.0452
 L24  C6B   C  CR16   0  -0.304  -1.0581  -0.7532  -0.7145
 L24  C7B   C  C      0   0.538   0.9552  -1.2269  -3.9104
 L24  O7B   O  O      0  -0.505   1.7172  -2.0821  -4.3493
 L24  N     N  NH1    0  -0.634   0.4635  -0.2342  -4.6634
 L24  CA    C  CH1    0  -0.189   0.9095  -0.0028  -6.0183
 L24  CB    C  CH2    0  -0.447  -0.0740   0.9273  -6.7295
 L24  CG    C  CH2    0  -0.577  -1.4670   0.3359  -6.8744
 L24  CD    C  C      0   0.412  -2.4929   1.2140  -7.6122
 L24  OE1   O  O      0  -0.609  -2.0988   2.2936  -8.0959
 L24  OE2   O  OC    -1  -0.633  -3.6560   0.7609  -7.6694
 L24  C     C  C      0   0.410   2.3506   0.5665  -6.0830
 L24  O     O  O      0  -0.618   2.8709   0.5481  -7.2168
 L24  OXT   O  OC    -1  -0.600   2.8489   1.0072  -5.0332
 L24  HN21  H  HNH2   0   0.387  -1.8008   0.5846  10.2947
 L24  HN22  H  HNH2   0   0.387  -0.2202   1.0391  10.7559
 L24  HO4   H  HOH1   0   0.483   2.6996   1.0921   6.1208
 L24  HN7   H  HNH1   0   0.388  -2.8496  -0.2704   6.0422
 L24  H81   H  HCH2   0   0.224  -1.8325   0.8902   3.8929
 L24  H82   H  HCH2   0   0.256  -2.3651  -0.7841   3.8126
 L24  H9    H  HCH1   0   0.243  -0.0875  -1.5657   4.3327
 L24  H101  H  HCH2   0   0.246   0.7758   1.3502   4.3132
 L24  H102  H  HCH2   0   0.244   1.7514  -0.0599   4.6721
 L24  H111  H  HCH2   0   0.230  -0.1357   0.5375   2.1212
 L24  H112  H  HCH2   0   0.241   1.1602  -0.6179   2.3536
 L24  H121  H  HCH2   0   0.245  -0.4492  -2.5031   2.0535
 L24  H122  H  HCH2   0   0.251  -1.7467  -1.3599   1.7557
 L24  H2B   H  HCR6   0   0.249   1.5118  -2.5958   0.4642
 L24  H3B   H  HCR6   0   0.253   2.1846  -2.4570  -1.8876
 L24  H5B   H  HCR6   0   0.252  -1.3284  -0.1467  -2.7359
 L24  H6B   H  HCR6   0   0.252  -1.9845  -0.2884  -0.3985
 L24  HN    H  HNH1   0   0.390   0.0264   0.5431  -4.1946
 L24  HA    H  HCH1   0   0.227   0.9062  -0.9621  -6.5439
 L24  HB1   H  HCH2   0   0.210  -0.1204   1.8823  -6.1942
 L24  HB2   H  HCH2   0   0.227   0.3359   1.1533  -7.7141
 L24  HG1   H  HCH2   0   0.221  -1.3964  -0.6233  -7.4022
 L24  HG2   H  HCH2   0   0.219  -1.8812   0.0829  -5.8928

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
 L24  N2A  C2    single    1.355  0.020  1.355
 L24  N2A  HN21  single    0.890  0.020  1.040
 L24  N2A  HN22  single    0.890  0.020  1.040
 L24  N1   C2    aromatic  1.328  0.020  1.328
 L24  N1   C6    aromatic  1.336  0.020  1.336
 L24  C2   N3    aromatic  1.333  0.020  1.333
 L24  N3   C4    aromatic  1.325  0.020  1.325
 L24  C4   O4A   single    1.337  0.020  1.337
 L24  C4   C5    aromatic  1.387  0.020  1.387
 L24  O4A  HO4   single    0.850  0.020  0.980
 L24  C5   C6    aromatic  1.406  0.020  1.406
 L24  C5   C10   single    1.504  0.020  1.504
 L24  C6   N7    single    1.344  0.020  1.344
 L24  N7   C8    single    1.444  0.020  1.444
 L24  N7   HN7   single    0.860  0.020  1.020
 L24  C8   C9    single    1.524  0.020  1.524
 L24  C8   H81   single    0.970  0.020  1.090
 L24  C8   H82   single    0.970  0.020  1.090
 L24  C9   C10   single    1.529  0.020  1.529
 L24  C9   C11   single    1.525  0.020  1.525
 L24  C9   H9    single    0.970  0.020  1.090
 L24  C10  H101  single    0.970  0.020  1.090
 L24  C10  H102  single    0.970  0.020  1.090
 L24  C11  C12   single    1.531  0.020  1.531
 L24  C11  H111  single    0.970  0.020  1.090
 L24  C11  H112  single    0.970  0.020  1.090
 L24  C12  C1B   single    1.502  0.020  1.502
 L24  C12  H121  single    0.970  0.020  1.090
 L24  C12  H122  single    0.970  0.020  1.090
 L24  C1B  C2B   aromatic  1.394  0.020  1.394
 L24  C1B  C6B   aromatic  1.392  0.020  1.392
 L24  C2B  C3B   aromatic  1.384  0.020  1.384
 L24  C2B  H2B   single    0.930  0.020  1.080
 L24  C3B  C4B   aromatic  1.394  0.020  1.394
 L24  C3B  H3B   single    0.930  0.020  1.080
 L24  C4B  C5B   aromatic  1.393  0.020  1.393
 L24  C4B  C7B   single    1.496  0.020  1.496
 L24  C5B  C6B   aromatic  1.387  0.020  1.387
 L24  C5B  H5B   single    0.930  0.020  1.080
 L24  C6B  H6B   single    0.930  0.020  1.080
 L24  C7B  O7B   double    1.227  0.020  1.227
 L24  C7B  N     single    1.339  0.020  1.339
 L24  N    CA    single    1.445  0.020  1.445
 L24  N    HN    single    0.890  0.020  1.040
 L24  CA   CB    single    1.529  0.020  1.529
 L24  CA   C     single    1.551  0.020  1.551
 L24  CA   HA    single    0.970  0.020  1.090
 L24  CB   CG    single    1.520  0.020  1.520
 L24  CB   HB1   single    0.970  0.020  1.090
 L24  CB   HB2   single    0.970  0.020  1.090
 L24  CG   CD    single    1.539  0.020  1.539
 L24  CG   HG1   single    0.970  0.020  1.090
 L24  CG   HG2   single    0.970  0.020  1.090
 L24  CD   OE1   deloc     1.247  0.020  1.247
 L24  CD   OE2   deloc     1.250  0.020  1.250
 L24  C    O     deloc     1.248  0.020  1.248
 L24  C    OXT   deloc     1.243  0.020  1.243

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
 L24  HN22  N2A  HN21  116.31  3.000
 L24  HN22  N2A  C2    117.98  3.000
 L24  HN21  N2A  C2    117.56  3.000
 L24  C6    N1   C2    116.45  3.000
 L24  N3    C2   N1    126.36  3.000
 L24  N3    C2   N2A   116.79  3.000
 L24  N1    C2   N2A   116.83  3.000
 L24  C4    N3   C2    115.87  3.000
 L24  C5    C4   O4A   122.34  3.000
 L24  C5    C4   N3    124.33  3.000
 L24  O4A   C4   N3    113.33  3.000
 L24  HO4   O4A  C4    111.24  3.000
 L24  C10   C5   C6    120.93  3.000
 L24  C10   C5   C4    124.90  3.000
 L24  C6    C5   C4    114.17  3.000
 L24  N7    C6   C5    120.15  3.000
 L24  N7    C6   N1    117.04  3.000
 L24  C5    C6   N1    122.81  3.000
 L24  HN7   N7   C8    118.99  3.000
 L24  HN7   N7   C6    117.21  3.000
 L24  C8    N7   C6    122.62  3.000
 L24  H82   C8   H81   107.02  3.000
 L24  H82   C8   C9    110.97  3.000
 L24  H81   C8   C9    109.31  3.000
 L24  H82   C8   N7    107.67  3.000
 L24  H81   C8   N7    111.23  3.000
 L24  C9    C8   N7    110.59  3.000
 L24  H9    C9   C11   108.79  3.000
 L24  H9    C9   C10   108.15  3.000
 L24  C11   C9   C10   110.68  3.000
 L24  H9    C9   C8    107.94  3.000
 L24  C11   C9   C8    111.89  3.000
 L24  C10   C9   C8    109.28  3.000
 L24  H102  C10  H101  106.12  3.000
 L24  H102  C10  C9    107.96  3.000
 L24  H101  C10  C9    109.09  3.000
 L24  H102  C10  C5    111.14  3.000
 L24  H101  C10  C5    111.03  3.000
 L24  C9    C10  C5    111.31  3.000
 L24  H112  C11  H111  106.27  3.000
 L24  H112  C11  C12   108.61  3.000
 L24  H111  C11  C12   109.60  3.000
 L24  H112  C11  C9    108.58  3.000
 L24  H111  C11  C9    109.52  3.000
 L24  C12   C11  C9    113.97  3.000
 L24  H122  C12  H121  106.80  3.000
 L24  H122  C12  C1B   109.42  3.000
 L24  H121  C12  C1B   109.48  3.000
 L24  H122  C12  C11   110.42  3.000
 L24  H121  C12  C11   108.93  3.000
 L24  C1B   C12  C11   111.66  3.000
 L24  C6B   C1B  C2B   118.08  3.000
 L24  C6B   C1B  C12   121.32  3.000
 L24  C2B   C1B  C12   120.59  3.000
 L24  H2B   C2B  C3B   119.35  3.000
 L24  H2B   C2B  C1B   119.55  3.000
 L24  C3B   C2B  C1B   121.09  3.000
 L24  H3B   C3B  C4B   119.73  3.000
 L24  H3B   C3B  C2B   119.62  3.000
 L24  C4B   C3B  C2B   120.65  3.000
 L24  C7B   C4B  C5B   123.11  3.000
 L24  C7B   C4B  C3B   118.37  3.000
 L24  C5B   C4B  C3B   118.49  3.000
 L24  H5B   C5B  C6B   118.42  3.000
 L24  H5B   C5B  C4B   120.94  3.000
 L24  C6B   C5B  C4B   120.61  3.000
 L24  H6B   C6B  C5B   119.23  3.000
 L24  H6B   C6B  C1B   119.70  3.000
 L24  C5B   C6B  C1B   121.06  3.000
 L24  N     C7B  O7B   122.93  3.000
 L24  N     C7B  C4B   116.35  3.000
 L24  O7B   C7B  C4B   120.70  3.000
 L24  HN    N    CA    116.52  3.000
 L24  HN    N    C7B   118.00  3.000
 L24  CA    N    C7B   122.17  3.000
 L24  HA    CA   C     107.74  3.000
 L24  HA    CA   CB    107.94  3.000
 L24  C     CA   CB    110.79  3.000
 L24  HA    CA   N     108.01  3.000
 L24  C     CA   N     112.62  3.000
 L24  CB    CA   N     109.57  3.000
 L24  HB2   CB   HB1   106.05  3.000
 L24  HB2   CB   CG    109.82  3.000
 L24  HB1   CB   CG    110.30  3.000
 L24  HB2   CB   CA    107.71  3.000
 L24  HB1   CB   CA    109.27  3.000
 L24  CG    CB   CA    113.39  3.000
 L24  HG2   CG   HG1   104.69  3.000
 L24  HG2   CG   CD    108.03  3.000
 L24  HG1   CG   CD    108.13  3.000
 L24  HG2   CG   CB    110.55  3.000
 L24  HG1   CG   CB    109.09  3.000
 L24  CD    CG   CB    115.75  3.000
 L24  OE2   CD   OE1   126.19  3.000
 L24  OE2   CD   CG    115.82  3.000
 L24  OE1   CD   CG    117.99  3.000
 L24  OXT   C    O     127.27  3.000
 L24  OXT   C    CA    117.88  3.000
 L24  O     C    CA    114.84  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
 L24  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 L24  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 L24  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 L24  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 L24  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 L24  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 L24  CONST_07  C4B  C3B  C2B  C1B     0.00   0.0  0
 L24  CONST_08  C4B  C5B  C6B  C1B     0.00   0.0  0
 L24  CONST_09  C5B  C6B  C1B  C2B     0.00   0.0  0
 L24  CONST_10  C5B  C4B  C3B  C2B     0.00   0.0  0
 L24  CONST_11  C6B  C1B  C2B  C3B     0.00   0.0  0
 L24  CONST_12  C6B  C5B  C4B  C3B     0.00   0.0  0
 L24  CONST_13  C6   N1   C2   N2A   180.00   0.0  0
 L24  CONST_14  C4   N3   C2   N2A   180.00   0.0  0
 L24  CONST_15  O4A  C4   N3   C2    180.00   0.0  0
 L24  CONST_16  C6   C5   C4   O4A   180.00   0.0  0
 L24  CONST_17  C10  C5   C4   O4A     0.00   0.0  0
 L24  CONST_18  C3B  C2B  C1B  C12   180.00   0.0  0
 L24  CONST_19  C5B  C6B  C1B  C12   180.00   0.0  0
 L24  CONST_20  C7B  C4B  C3B  C2B   180.00   0.0  0
 L24  CONST_21  C7B  C4B  C5B  C6B   180.00   0.0  0
 L24  CONST_22  H3B  C3B  C2B  C1B   180.00   0.0  0
 L24  CONST_23  H5B  C5B  C6B  C1B   180.00   0.0  0
 L24  CONST_24  H6B  C6B  C1B  C2B   180.00   0.0  0
 L24  CONST_25  H2B  C2B  C3B  C4B   180.00   0.0  0
 L24  CONST_28  CA   N    C7B  C4B   180.00   0.0  0
 L24  CONST_30  CA   N    C7B  O7B     0.00   0.0  0
 L24  Var_01    C8   N7   C6   N1    173.10  30.0  1
 L24  Var_02    C9   C10  C5   C4    158.30  30.0  1
 L24  Var_03    C9   C8   N7   C6     36.54  30.0  1
 L24  Var_04    C1B  C12  C11  C9   -177.22  30.0  3
 L24  Var_05    C2B  C1B  C12  C11    80.51  30.0  2
 L24  Var_06    O7B  C7B  C4B  C3B    21.88  30.0  2
 L24  Var_07    CD   CG   CB   CA   -178.63  30.0  3
 L24  Var_08    OE1  CD   CG   CB      3.91  30.0  3

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
 L24  chir_01  C9  C8  C10  C11  positiv
 L24  chir_02  CA  N   CB   C    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
 L24  plan-1  C12   0.020
 L24  plan-1  C1B   0.020
 L24  plan-1  C2B   0.020
 L24  plan-1  C3B   0.020
 L24  plan-1  C4B   0.020
 L24  plan-1  C5B   0.020
 L24  plan-1  C6B   0.020
 L24  plan-1  C7B   0.020
 L24  plan-1  H2B   0.020
 L24  plan-1  H3B   0.020
 L24  plan-1  H5B   0.020
 L24  plan-1  H6B   0.020
 L24  plan-2  C4B   0.020
 L24  plan-2  C7B   0.020
 L24  plan-2  O7B   0.020
 L24  plan-2  N     0.020
 L24  plan-2  CA    0.020
 L24  plan-2  HN    0.020
 L24  plan-3  N2A   0.020
 L24  plan-3  C2    0.020
 L24  plan-3  HN21  0.020
 L24  plan-3  HN22  0.020
 L24  plan-4  N2A   0.020
 L24  plan-4  N1    0.020
 L24  plan-4  C2    0.020
 L24  plan-4  N3    0.020
 L24  plan-4  C4    0.020
 L24  plan-4  O4A   0.020
 L24  plan-4  C5    0.020
 L24  plan-4  C6    0.020
 L24  plan-4  N7    0.020
 L24  plan-4  C10   0.020
 L24  plan-5  CG    0.020
 L24  plan-5  CD    0.020
 L24  plan-5  OE1   0.020
 L24  plan-5  OE2   0.020
 L24  plan-6  CA    0.020
 L24  plan-6  C     0.020
 L24  plan-6  O     0.020
 L24  plan-6  OXT   0.020

