# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:43:16 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: N-({4-[2-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2c(CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c[nH]c2N1
#
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
 LYA  LYA  'N-({4-[2-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-glutamic acid'  ligand  50  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LYA
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
 LYA  C1    C  C      0   0.121  -1.1218   1.1193   0.9291
 LYA  C2    C  C1     0  -0.304  -2.2658   1.5027   0.2347
 LYA  C3    C  C1     0  -0.257  -2.3229   1.4191  -1.1475
 LYA  C4    C  C      0  -0.060  -1.2411   0.9317  -1.8763
 LYA  C5    C  C1     0  -0.282  -0.0900   0.5539  -1.1852
 LYA  C6    C  C1     0  -0.289  -0.0349   0.6470   0.1958
 LYA  C7    C  CH2    0  -0.504  -1.0586   1.1658   2.4271
 LYA  C8    C  CH2    0  -0.514  -1.3701  -0.2043   3.0478
 LYA  C9    C  CR5    0   0.010  -1.1934  -0.2095   4.5288
 LYA  C10   C  CR15   0  -0.103  -2.1802  -0.2239   5.4708
 LYA  N11   N  NR15   0  -0.664  -1.6100  -0.1895   6.7311
 LYA  C12   C  CR56   0   0.648  -0.2782  -0.1541   6.5875
 LYA  C13   C  CR56   0  -0.254   0.0458  -0.1618   5.2483
 LYA  C14   C  CR6    0   0.411   1.4409  -0.1437   4.8765
 LYA  O15   O  OC     0  -0.498   1.8353  -0.1625   3.7111
 LYA  N16   N  N      0  -0.538   2.3463  -0.1010   5.9125
 LYA  C17   C  CR6    0   0.661   1.9712  -0.0964   7.1626
 LYA  N18   N  NR16   0  -0.732   0.6697  -0.1212   7.5647
 LYA  N19   N  NH2    0  -0.827   2.8963  -0.1037   8.1380
 LYA  C20   C  C      0   0.540  -1.3594   0.8719  -3.3672
 LYA  O21   O  O      0  -0.505  -2.1914   1.5550  -3.9554
 LYA  N22   N  NH1    0  -0.631  -0.4981   0.0650  -4.0009
 LYA  C23   C  CH1    0  -0.200  -0.5732  -0.1928  -5.4213
 LYA  C24   C  CH2    0  -0.438   0.7873  -0.6681  -5.9327
 LYA  C25   C  CH2    0  -0.576   1.8842   0.3720  -5.7697
 LYA  C26   C  C      0   0.411   3.2630  -0.0128  -6.3340
 LYA  O27   O  O      0  -0.609   3.3615  -1.0869  -6.9596
 LYA  O28   O  OC    -1  -0.634   4.1859   0.8026  -6.1208
 LYA  C29   C  C      0   0.412  -1.6929  -1.2042  -5.7812
 LYA  O30   O  O      0  -0.619  -1.9242  -1.3189  -7.0021
 LYA  O31   O  OC    -1  -0.598  -2.2440  -1.8152  -4.8504
 LYA  HC2   H  H      0   0.248  -3.1228   1.8799   0.7800
 LYA  HC3   H  H      0   0.253  -3.2190   1.7352  -1.6647
 LYA  HC5   H  H      0   0.251   0.7894   0.2057  -1.7128
 LYA  HC6   H  H      0   0.252   0.8696   0.3546   0.7166
 LYA  HC71  H  HCH2   0   0.242  -1.7636   1.9047   2.8146
 LYA  HC72  H  HCH2   0   0.255  -0.0601   1.4746   2.7409
 LYA  HC81  H  HCH2   0   0.241  -0.7159  -0.9526   2.5944
 LYA  HC82  H  HCH2   0   0.242  -2.3947  -0.4903   2.7979
 LYA  H10   H  HCR5   0   0.281  -3.2514  -0.2565   5.3587
 LYA  H11   H  HNR5   0   0.419  -2.1192  -0.1983   7.5999
 LYA  H18   H  HNR6   0   0.431   0.4220  -0.1399   8.5430
 LYA  H191  H  HNH2   0   0.407   3.8488   0.0701   7.8680
 LYA  H192  H  HNH2   0   0.409   2.6521   0.1226   9.0872
 LYA  H22   H  HNH1   0   0.389   0.0035  -0.6145  -3.4517
 LYA  H23   H  HCH1   0   0.230  -0.8094   0.7528  -5.9171
 LYA  H241  H  HCH2   0   0.208   1.0660  -1.5959  -5.4204
 LYA  H242  H  HCH2   0   0.225   0.6741  -0.9258  -6.9852
 LYA  H251  H  HCH2   0   0.219   1.5683   1.3048  -6.2536
 LYA  H252  H  HCH2   0   0.220   2.0089   0.6326  -4.7139

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
 LYA  C1   C2    aromatic  1.392  0.020  1.392
 LYA  C1   C6    aromatic  1.394  0.020  1.394
 LYA  C1   C7    single    1.500  0.020  1.500
 LYA  C2   C3    aromatic  1.386  0.020  1.386
 LYA  C2   HC2   single    0.930  0.020  1.080
 LYA  C3   C4    aromatic  1.392  0.020  1.392
 LYA  C3   HC3   single    0.930  0.020  1.080
 LYA  C4   C5    aromatic  1.395  0.020  1.395
 LYA  C4   C20   single    1.497  0.020  1.497
 LYA  C5   C6    aromatic  1.385  0.020  1.385
 LYA  C5   HC5   single    0.930  0.020  1.080
 LYA  C6   HC6   single    0.930  0.020  1.080
 LYA  C7   C8    single    1.536  0.020  1.536
 LYA  C7   HC71  single    0.970  0.020  1.090
 LYA  C7   HC72  single    0.970  0.020  1.090
 LYA  C8   C9    single    1.491  0.020  1.491
 LYA  C8   HC81  single    0.970  0.020  1.090
 LYA  C8   HC82  single    0.970  0.020  1.090
 LYA  C9   C10   aromatic  1.364  0.020  1.364
 LYA  C9   C13   aromatic  1.434  0.020  1.434
 LYA  C10  N11   aromatic  1.384  0.020  1.384
 LYA  C10  H10   single    0.930  0.020  1.080
 LYA  N11  C12   aromatic  1.340  0.020  1.340
 LYA  N11  H11   single    0.860  0.020  1.020
 LYA  C12  C13   aromatic  1.378  0.020  1.378
 LYA  C12  N18   aromatic  1.362  0.020  1.362
 LYA  C13  C14   aromatic  1.444  0.020  1.444
 LYA  C14  O15   double    1.230  0.020  1.230
 LYA  C14  N16   aromatic  1.377  0.020  1.377
 LYA  N16  C17   aromatic  1.305  0.020  1.305
 LYA  C17  N18   aromatic  1.362  0.020  1.362
 LYA  C17  N19   single    1.344  0.020  1.344
 LYA  N18  H18   single    0.860  0.020  1.020
 LYA  N19  H191  single    0.890  0.020  1.040
 LYA  N19  H192  single    0.890  0.020  1.040
 LYA  C20  O21   double    1.227  0.020  1.227
 LYA  C20  N22   single    1.340  0.020  1.340
 LYA  N22  C23   single    1.446  0.020  1.446
 LYA  N22  H22   single    0.890  0.020  1.040
 LYA  C23  C24   single    1.529  0.020  1.529
 LYA  C23  C29   single    1.551  0.020  1.551
 LYA  C23  H23   single    0.970  0.020  1.090
 LYA  C24  C25   single    1.520  0.020  1.520
 LYA  C24  H241  single    0.970  0.020  1.090
 LYA  C24  H242  single    0.970  0.020  1.090
 LYA  C25  C26   single    1.539  0.020  1.539
 LYA  C25  H251  single    0.970  0.020  1.090
 LYA  C25  H252  single    0.970  0.020  1.090
 LYA  C26  O27   deloc     1.247  0.020  1.247
 LYA  C26  O28   deloc     1.250  0.020  1.250
 LYA  C29  O30   deloc     1.248  0.020  1.248
 LYA  C29  O31   deloc     1.242  0.020  1.242

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
 LYA  C7    C1   C6    120.21  3.000
 LYA  C7    C1   C2    121.62  3.000
 LYA  C6    C1   C2    118.15  3.000
 LYA  HC2   C2   C3    119.36  3.000
 LYA  HC2   C2   C1    119.66  3.000
 LYA  C3    C2   C1    120.98  3.000
 LYA  HC3   C3   C4    119.71  3.000
 LYA  HC3   C3   C2    119.56  3.000
 LYA  C4    C3   C2    120.74  3.000
 LYA  C20   C4   C5    123.23  3.000
 LYA  C20   C4   C3    118.29  3.000
 LYA  C5    C4   C3    118.47  3.000
 LYA  HC5   C5   C6    118.36  3.000
 LYA  HC5   C5   C4    121.05  3.000
 LYA  C6    C5   C4    120.57  3.000
 LYA  HC6   C6   C5    119.60  3.000
 LYA  HC6   C6   C1    119.30  3.000
 LYA  C5    C6   C1    121.09  3.000
 LYA  HC72  C7   HC71  107.28  3.000
 LYA  HC72  C7   C8    108.77  3.000
 LYA  HC71  C7   C8    109.22  3.000
 LYA  HC72  C7   C1    109.54  3.000
 LYA  HC71  C7   C1    110.37  3.000
 LYA  C8    C7   C1    111.55  3.000
 LYA  HC82  C8   HC81  106.70  3.000
 LYA  HC82  C8   C9    109.70  3.000
 LYA  HC81  C8   C9    109.80  3.000
 LYA  HC82  C8   C7    109.34  3.000
 LYA  HC81  C8   C7    108.77  3.000
 LYA  C9    C8   C7    112.36  3.000
 LYA  C13   C9   C10   106.20  3.000
 LYA  C13   C9   C8    126.91  3.000
 LYA  C10   C9   C8    126.87  3.000
 LYA  H10   C10  N11   120.34  3.000
 LYA  H10   C10  C9    130.36  3.000
 LYA  N11   C10  C9    109.30  3.000
 LYA  H11   N11  C12   126.52  3.000
 LYA  H11   N11  C10   125.26  3.000
 LYA  C12   N11  C10   108.22  3.000
 LYA  N18   C12  C13   122.27  3.000
 LYA  N18   C12  N11   127.99  3.000
 LYA  C13   C12  N11   109.74  3.000
 LYA  C14   C13  C12   118.52  3.000
 LYA  C14   C13  C9    134.93  3.000
 LYA  C12   C13  C9    106.54  3.000
 LYA  N16   C14  O15   120.16  3.000
 LYA  N16   C14  C13   116.24  3.000
 LYA  O15   C14  C13   123.60  3.000
 LYA  C17   N16  C14   122.13  3.000
 LYA  N19   C17  N18   116.30  3.000
 LYA  N19   C17  N16   119.81  3.000
 LYA  N18   C17  N16   123.86  3.000
 LYA  H18   N18  C17   121.39  3.000
 LYA  H18   N18  C12   121.62  3.000
 LYA  C17   N18  C12   116.97  3.000
 LYA  H192  N19  H191  116.40  3.000
 LYA  H192  N19  C17   121.09  3.000
 LYA  H191  N19  C17   117.14  3.000
 LYA  N22   C20  O21   123.00  3.000
 LYA  N22   C20  C4    116.39  3.000
 LYA  O21   C20  C4    120.59  3.000
 LYA  H22   N22  C23   116.18  3.000
 LYA  H22   N22  C20   117.94  3.000
 LYA  C23   N22  C20   122.60  3.000
 LYA  H23   C23  C29   107.62  3.000
 LYA  H23   C23  C24   108.02  3.000
 LYA  C29   C23  C24   111.22  3.000
 LYA  H23   C23  N22   107.61  3.000
 LYA  C29   C23  N22   112.44  3.000
 LYA  C24   C23  N22   109.74  3.000
 LYA  H242  C24  H241  106.12  3.000
 LYA  H242  C24  C25   109.90  3.000
 LYA  H241  C24  C25   110.22  3.000
 LYA  H242  C24  C23   107.71  3.000
 LYA  H241  C24  C23   109.46  3.000
 LYA  C25   C24  C23   113.17  3.000
 LYA  H252  C25  H251  104.82  3.000
 LYA  H252  C25  C26   108.13  3.000
 LYA  H251  C25  C26   107.99  3.000
 LYA  H252  C25  C24   110.39  3.000
 LYA  H251  C25  C24   109.06  3.000
 LYA  C26   C25  C24   115.85  3.000
 LYA  O28   C26  O27   126.10  3.000
 LYA  O28   C26  C25   115.85  3.000
 LYA  O27   C26  C25   118.05  3.000
 LYA  O31   C29  O30   127.27  3.000
 LYA  O31   C29  C23   117.84  3.000
 LYA  O30   C29  C23   114.88  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
 LYA  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 LYA  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 LYA  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 LYA  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 LYA  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 LYA  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 LYA  CONST_07  C12   N11  C10  C9      0.00   0.0  0
 LYA  CONST_08  N11   C12  C13  C9      0.00   0.0  0
 LYA  CONST_09  N18   C12  C13  C9    180.00   0.0  0
 LYA  CONST_10  N16   C14  C13  C9    180.00   0.0  0
 LYA  CONST_11  C12   C13  C9   C10     0.00   0.0  0
 LYA  CONST_12  C14   C13  C9   C10   180.00   0.0  0
 LYA  CONST_13  C13   C12  N11  C10     0.00   0.0  0
 LYA  CONST_14  N18   C12  N11  C10   180.00   0.0  0
 LYA  CONST_15  C13   C9   C10  N11     0.00   0.0  0
 LYA  CONST_16  C14   C13  C12  N11   180.00   0.0  0
 LYA  CONST_17  C17   N18  C12  N11   180.00   0.0  0
 LYA  CONST_18  N16   C14  C13  C12     0.00   0.0  0
 LYA  CONST_19  N16   C17  N18  C12     0.00   0.0  0
 LYA  CONST_20  C17   N18  C12  C13     0.00   0.0  0
 LYA  CONST_21  C17   N16  C14  C13     0.00   0.0  0
 LYA  CONST_22  N18   C12  C13  C14     0.00   0.0  0
 LYA  CONST_23  N18   C17  N16  C14     0.00   0.0  0
 LYA  CONST_24  C20   C4   C3   C2    180.00   0.0  0
 LYA  CONST_25  C7    C1   C2   C3    180.00   0.0  0
 LYA  CONST_26  C7    C1   C6   C5    180.00   0.0  0
 LYA  CONST_27  C20   C4   C5   C6    180.00   0.0  0
 LYA  CONST_28  N11   C10  C9   C8    180.00   0.0  0
 LYA  CONST_29  C12   C13  C9   C8    180.00   0.0  0
 LYA  CONST_30  C14   C13  C9   C8      0.00   0.0  0
 LYA  CONST_31  O15   C14  C13  C9      0.00   0.0  0
 LYA  CONST_32  O15   C14  C13  C12   180.00   0.0  0
 LYA  CONST_33  N19   C17  N18  C12   180.00   0.0  0
 LYA  CONST_34  N19   C17  N16  C14   180.00   0.0  0
 LYA  CONST_35  C17   N16  C14  O15   180.00   0.0  0
 LYA  CONST_36  HC3   C3   C2   C1    180.00   0.0  0
 LYA  CONST_37  HC5   C5   C6   C1    180.00   0.0  0
 LYA  CONST_38  HC6   C6   C1   C2    180.00   0.0  0
 LYA  CONST_39  HC2   C2   C3   C4    180.00   0.0  0
 LYA  CONST_40  H11   N11  C10  C9    180.00   0.0  0
 LYA  CONST_41  H18   N18  C12  N11     0.00   0.0  0
 LYA  CONST_42  H10   C10  N11  C12   180.00   0.0  0
 LYA  CONST_43  H191  N19  C17  N16     0.00   0.0  0
 LYA  CONST_45  C23   N22  C20  C4    180.00   0.0  0
 LYA  CONST_47  C23   N22  C20  O21     0.00   0.0  0
 LYA  Var_01    C9    C8   C7   C1    174.88  30.0  3
 LYA  Var_02    C8    C7   C1   C2     96.38  30.0  2
 LYA  Var_03    O21   C20  C4   C3     20.05  30.0  2
 LYA  Var_04    C10   C9   C8   C7    106.23  30.0  2
 LYA  Var_05    C26   C25  C24  C23  -176.80  30.0  3
 LYA  Var_06    O27   C26  C25  C24     5.03  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
 LYA  chir_01  C23  N22  C24  C29  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
 LYA  plan-1  C1    0.020
 LYA  plan-1  C2    0.020
 LYA  plan-1  C3    0.020
 LYA  plan-1  C4    0.020
 LYA  plan-1  C5    0.020
 LYA  plan-1  C6    0.020
 LYA  plan-1  C7    0.020
 LYA  plan-1  C20   0.020
 LYA  plan-1  HC2   0.020
 LYA  plan-1  HC3   0.020
 LYA  plan-1  HC5   0.020
 LYA  plan-1  HC6   0.020
 LYA  plan-2  C23   0.020
 LYA  plan-2  C29   0.020
 LYA  plan-2  O30   0.020
 LYA  plan-2  O31   0.020
 LYA  plan-3  C8    0.020
 LYA  plan-3  C9    0.020
 LYA  plan-3  C10   0.020
 LYA  plan-3  N11   0.020
 LYA  plan-3  C12   0.020
 LYA  plan-3  C13   0.020
 LYA  plan-3  C14   0.020
 LYA  plan-3  O15   0.020
 LYA  plan-3  N16   0.020
 LYA  plan-3  C17   0.020
 LYA  plan-3  N18   0.020
 LYA  plan-3  N19   0.020
 LYA  plan-3  H10   0.020
 LYA  plan-3  H11   0.020
 LYA  plan-3  H18   0.020
 LYA  plan-4  C4    0.020
 LYA  plan-4  C20   0.020
 LYA  plan-4  O21   0.020
 LYA  plan-4  N22   0.020
 LYA  plan-4  C23   0.020
 LYA  plan-4  H22   0.020
 LYA  plan-5  C17   0.020
 LYA  plan-5  N19   0.020
 LYA  plan-5  H191  0.020
 LYA  plan-5  H192  0.020
 LYA  plan-6  C25   0.020
 LYA  plan-6  C26   0.020
 LYA  plan-6  O27   0.020
 LYA  plan-6  O28   0.020

