# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 02:15:02 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N-({4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)c1ccc(CCc2c[nH]c3N=C(N)NC(=O)c23)cc1)C(O)=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
 LYD  LYD  N-({4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]phenyl}carbonyl)-L-valine  ligand  52  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LYD
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
 LYD  C5'   C  CR16  0  -0.289  -0.0985  -0.9021   0.2083
 LYD  C4'   C  CR6   0   0.125  -1.3090  -0.6014  -0.4142
 LYD  C3'   C  CR16  0  -0.303  -2.4231  -0.3635   0.3871
 LYD  C2'   C  CR16  0  -0.252  -2.3351  -0.4281   1.7680
 LYD  C1'   C  CR6   0  -0.055  -1.1189  -0.7106   2.3841
 LYD  C6'   C  CR16  0  -0.273   0.0001  -0.9538   1.5888
 LYD  C9    C  C     0   0.546  -1.0731  -0.7700   3.8705
 LYD  O9    O  O     0  -0.483  -2.0603  -1.0440   4.5399
 LYD  N     N  NH1   0  -0.666   0.1155  -0.5035   4.4461
 LYD  CA    C  CH1   0  -0.119   0.2580  -0.5095   5.8819
 LYD  CB    C  CH1   0  -0.298   1.7230  -0.2119   6.2581
 LYD  CG1   C  CH3   0  -0.664   1.9068  -0.0660   7.7651
 LYD  CG2   C  CH3   0  -0.651   2.6342  -1.3149   5.7237
 LYD  C8    C  CH2   0  -0.506  -1.3835  -0.4994  -1.9089
 LYD  C7    C  CH2   0  -0.519  -0.8689   0.8602  -2.4063
 LYD  C5    C  CR5   0   0.025  -0.8074   0.9407  -3.8944
 LYD  C     C  C     0   0.530  -0.6950   0.4758   6.5417
 LYD  OX1   O  O     0  -0.439  -1.2866   0.2538   7.5678
 LYD  OX2   O  OH1   0  -0.587  -0.7578   1.6271   5.8890
 LYD  C6    C  CR15  0  -0.104  -1.6216   1.6656  -4.7133
 LYD  N7    N  NR15  0  -0.662  -1.2558   1.4561  -6.0278
 LYD  C7A   C  CR56  0   0.501  -0.2149   0.6033  -6.0746
 LYD  C4A   C  CR56  0  -0.240   0.0997   0.2503  -4.7622
 LYD  C4    C  CR6   0   0.497   1.1888  -0.6399  -4.5525
 LYD  O4    O  OC    0  -0.482   1.6359  -1.0634  -3.4942
 LYD  N3    N  NR16  0  -0.722   1.7725  -1.0386  -5.7600
 LYD  C2    C  CR6   0   0.671   1.3833  -0.6319  -7.0038
 LYD  N1    N  N     0  -0.507   0.3936   0.1941  -7.2051
 LYD  N2    N  NH2   0  -0.834   2.0481  -1.1594  -8.0501
 LYD  H5'   H  HCR6  0   0.254   0.7764  -1.1038  -0.3990
 LYD  H3'   H  HCR6  0   0.252  -3.3742  -0.1278  -0.0751
 LYD  H2'   H  HCR6  0   0.258  -3.2152  -0.2469   2.3711
 LYD  H6'   H  HCR6  0   0.255   0.9517  -1.2160   2.0347
 LYD  HN    H  HNH1  0   0.410   0.8364  -0.0559   3.9020
 LYD  HCA   H  HCH1  0   0.279  -0.0016  -1.4971   6.2735
 LYD  HCB   H  HCH1  0   0.248   2.0035   0.7356   5.7841
 LYD  HG11  H  HCH3  0   0.242   2.9636   0.0697   7.9942
 LYD  HG12  H  HCH3  0   0.239   1.3776   0.7942   8.1745
 LYD  HG13  H  HCH3  0   0.228   1.5639  -0.9573   8.2941
 LYD  HG21  H  HCH3  0   0.227   2.3616  -2.2817   6.1521
 LYD  HG22  H  HCH3  0   0.233   2.5942  -1.4099   4.6387
 LYD  HG23  H  HCH3  0   0.241   3.6700  -1.1108   5.9954
 LYD  HC81  H  HCH2  0   0.257  -0.7843  -1.2925  -2.3595
 LYD  HC82  H  HCH2  0   0.245  -2.4125  -0.6410  -2.2463
 LYD  HC71  H  HCH2  0   0.245  -1.5145   1.6530  -2.0203
 LYD  HC72  H  HCH2  0   0.242   0.1241   1.0373  -1.9853
 LYD  HX2   H  HOH1  0   0.484  -1.3529   2.2376   6.3496
 LYD  HC6   H  HCR5  0   0.279  -2.4427   2.3203  -4.4699
 LYD  HN7   H  HNR5  0   0.408  -1.6953   1.8783  -6.8295
 LYD  HN3   H  HNR6  0   0.418   2.5489  -1.6824  -5.6826
 LYD  HN21  H  HNH2  0   0.407   1.9017  -0.7239  -8.9455
 LYD  HN22  H  HNH2  0   0.409   2.9528  -1.5783  -7.9146

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
 LYD  C5'  C4'   aromatic  1.394  0.020  1.394
 LYD  C5'  C6'   aromatic  1.385  0.020  1.385
 LYD  C5'  H5'   single    0.930  0.020  1.080
 LYD  C4'  C3'   aromatic  1.393  0.020  1.393
 LYD  C4'  C8    single    1.500  0.020  1.500
 LYD  C3'  C2'   aromatic  1.385  0.020  1.385
 LYD  C3'  H3'   single    0.930  0.020  1.080
 LYD  C2'  C1'   aromatic  1.392  0.020  1.392
 LYD  C2'  H2'   single    0.930  0.020  1.080
 LYD  C1'  C6'   aromatic  1.394  0.020  1.394
 LYD  C1'  C9    single    1.488  0.020  1.488
 LYD  C6'  H6'   single    0.930  0.020  1.080
 LYD  C9   O9    double    1.224  0.020  1.224
 LYD  C9   N     single    1.347  0.020  1.347
 LYD  N    CA    single    1.443  0.020  1.443
 LYD  N    HN    single    0.860  0.020  1.020
 LYD  CA   CB    single    1.541  0.020  1.541
 LYD  CA   C     single    1.521  0.020  1.521
 LYD  CA   HCA   single    0.970  0.020  1.090
 LYD  CB   CG1   single    1.525  0.020  1.525
 LYD  CB   CG2   single    1.527  0.020  1.527
 LYD  CB   HCB   single    0.970  0.020  1.090
 LYD  CG1  HG11  single    0.970  0.020  1.090
 LYD  CG1  HG12  single    0.970  0.020  1.090
 LYD  CG1  HG13  single    0.970  0.020  1.090
 LYD  CG2  HG21  single    0.970  0.020  1.090
 LYD  CG2  HG22  single    0.970  0.020  1.090
 LYD  CG2  HG23  single    0.970  0.020  1.090
 LYD  C8   C7    single    1.536  0.020  1.536
 LYD  C8   HC81  single    0.970  0.020  1.090
 LYD  C8   HC82  single    0.970  0.020  1.090
 LYD  C7   C5    single    1.492  0.020  1.492
 LYD  C7   HC71  single    0.970  0.020  1.090
 LYD  C7   HC72  single    0.970  0.020  1.090
 LYD  C5   C6    aromatic  1.363  0.020  1.363
 LYD  C5   C4A   aromatic  1.433  0.020  1.433
 LYD  C    OX1   double    1.205  0.020  1.205
 LYD  C    OX2   single    1.325  0.020  1.325
 LYD  OX2  HX2   single    0.850  0.020  0.980
 LYD  C6   N7    aromatic  1.380  0.020  1.380
 LYD  C6   HC6   single    0.930  0.020  1.080
 LYD  N7   C7A   aromatic  1.347  0.020  1.347
 LYD  N7   HN7   single    0.860  0.020  1.020
 LYD  C7A  C4A   aromatic  1.395  0.020  1.395
 LYD  C7A  N1    aromatic  1.347  0.020  1.347
 LYD  C4A  C4    aromatic  1.422  0.020  1.422
 LYD  C4   O4    double    1.224  0.020  1.224
 LYD  C4   N3    aromatic  1.399  0.020  1.399
 LYD  N3   C2    aromatic  1.365  0.020  1.365
 LYD  N3   HN3   single    0.860  0.020  1.020
 LYD  C2   N1    aromatic  1.305  0.020  1.305
 LYD  C2   N2    single    1.347  0.020  1.347
 LYD  N2   HN21  single    0.890  0.020  1.040
 LYD  N2   HN22  single    0.890  0.020  1.040

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
 LYD  H5'   C5'  C6'   119.61  3.000
 LYD  H5'   C5'  C4'   119.39  3.000
 LYD  C6'   C5'  C4'   121.00  3.000
 LYD  C8    C4'  C3'   121.46  3.000
 LYD  C8    C4'  C5'   120.18  3.000
 LYD  C3'   C4'  C5'   118.33  3.000
 LYD  H3'   C3'  C2'   119.42  3.000
 LYD  H3'   C3'  C4'   119.60  3.000
 LYD  C2'   C3'  C4'   120.98  3.000
 LYD  H2'   C2'  C1'   119.85  3.000
 LYD  H2'   C2'  C3'   119.74  3.000
 LYD  C1'   C2'  C3'   120.40  3.000
 LYD  C9    C1'  C6'   122.55  3.000
 LYD  C9    C1'  C2'   118.49  3.000
 LYD  C6'   C1'  C2'   118.95  3.000
 LYD  H6'   C6'  C1'   120.83  3.000
 LYD  H6'   C6'  C5'   118.81  3.000
 LYD  C1'   C6'  C5'   120.32  3.000
 LYD  N     C9   O9    121.49  3.000
 LYD  N     C9   C1'   116.49  3.000
 LYD  O9    C9   C1'   122.03  3.000
 LYD  HN    N    CA    117.93  3.000
 LYD  HN    N    C9    119.22  3.000
 LYD  CA    N    C9    120.76  3.000
 LYD  HCA   CA   C     106.32  3.000
 LYD  HCA   CA   CB    108.21  3.000
 LYD  C     CA   CB    111.38  3.000
 LYD  HCA   CA   N     109.67  3.000
 LYD  C     CA   N     111.53  3.000
 LYD  CB    CA   N     109.62  3.000
 LYD  HCB   CB   CG2   108.68  3.000
 LYD  HCB   CB   CG1   108.28  3.000
 LYD  CG2   CB   CG1   110.06  3.000
 LYD  HCB   CB   CA    107.74  3.000
 LYD  CG2   CB   CA    110.01  3.000
 LYD  CG1   CB   CA    111.97  3.000
 LYD  HG13  CG1  HG12  108.06  3.000
 LYD  HG13  CG1  HG11  107.72  3.000
 LYD  HG12  CG1  HG11  107.08  3.000
 LYD  HG13  CG1  CB    111.27  3.000
 LYD  HG12  CG1  CB    112.84  3.000
 LYD  HG11  CG1  CB    109.66  3.000
 LYD  HG23  CG2  HG22  107.41  3.000
 LYD  HG23  CG2  HG21  107.76  3.000
 LYD  HG22  CG2  HG21  107.71  3.000
 LYD  HG23  CG2  CB    110.15  3.000
 LYD  HG22  CG2  CB    112.92  3.000
 LYD  HG21  CG2  CB    110.69  3.000
 LYD  HC82  C8   HC81  107.19  3.000
 LYD  HC82  C8   C7    109.29  3.000
 LYD  HC81  C8   C7    109.00  3.000
 LYD  HC82  C8   C4'   110.23  3.000
 LYD  HC81  C8   C4'   109.56  3.000
 LYD  C7    C8   C4'   111.47  3.000
 LYD  HC72  C7   HC71  106.44  3.000
 LYD  HC72  C7   C5    109.76  3.000
 LYD  HC71  C7   C5    109.72  3.000
 LYD  HC72  C7   C8    108.85  3.000
 LYD  HC71  C7   C8    109.25  3.000
 LYD  C5    C7   C8    112.61  3.000
 LYD  C4A   C5   C6    105.69  3.000
 LYD  C4A   C5   C7    127.19  3.000
 LYD  C6    C5   C7    127.11  3.000
 LYD  OX2   C    OX1   123.80  3.000
 LYD  OX2   C    CA    112.27  3.000
 LYD  OX1   C    CA    123.88  3.000
 LYD  HX2   OX2  C     110.03  3.000
 LYD  HC6   C6   N7    120.60  3.000
 LYD  HC6   C6   C5    129.94  3.000
 LYD  N7    C6   C5    109.45  3.000
 LYD  HN7   N7   C7A   125.11  3.000
 LYD  HN7   N7   C6    125.37  3.000
 LYD  C7A   N7   C6    109.52  3.000
 LYD  N1    C7A  C4A   127.64  3.000
 LYD  N1    C7A  N7    124.79  3.000
 LYD  C4A   C7A  N7    107.57  3.000
 LYD  C4    C4A  C7A   118.02  3.000
 LYD  C4    C4A  C5    134.20  3.000
 LYD  C7A   C4A  C5    107.77  3.000
 LYD  N3    C4   O4    119.67  3.000
 LYD  N3    C4   C4A   111.75  3.000
 LYD  O4    C4   C4A   128.58  3.000
 LYD  HN3   N3   C2    118.56  3.000
 LYD  HN3   N3   C4    115.82  3.000
 LYD  C2    N3   C4    125.62  3.000
 LYD  N2    C2   N1    120.16  3.000
 LYD  N2    C2   N3    116.76  3.000
 LYD  N1    C2   N3    123.05  3.000
 LYD  C2    N1   C7A   113.92  3.000
 LYD  HN22  N2   HN21  115.52  3.000
 LYD  HN22  N2   C2    120.14  3.000
 LYD  HN21  N2   C2    116.73  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
 LYD  CONST_01  C2'   C3'  C4'  C5'    0.00   0.0  0
 LYD  CONST_02  C2'   C1'  C6'  C5'    0.00   0.0  0
 LYD  CONST_03  C1'   C6'  C5'  C4'    0.00   0.0  0
 LYD  CONST_04  C1'   C2'  C3'  C4'    0.00   0.0  0
 LYD  CONST_05  C6'   C5'  C4'  C3'    0.00   0.0  0
 LYD  CONST_06  C6'   C1'  C2'  C3'    0.00   0.0  0
 LYD  CONST_07  C7A   N7   C6   C5     0.00   0.0  0
 LYD  CONST_08  N7    C7A  C4A  C5     0.00   0.0  0
 LYD  CONST_09  N1    C7A  C4A  C5   180.00   0.0  0
 LYD  CONST_10  N3    C4   C4A  C5   180.00   0.0  0
 LYD  CONST_11  C7A   C4A  C5   C6     0.00   0.0  0
 LYD  CONST_12  C4    C4A  C5   C6   180.00   0.0  0
 LYD  CONST_13  C4A   C7A  N7   C6     0.00   0.0  0
 LYD  CONST_14  N1    C7A  N7   C6   180.00   0.0  0
 LYD  CONST_15  C4A   C5   C6   N7     0.00   0.0  0
 LYD  CONST_16  C4    C4A  C7A  N7   180.00   0.0  0
 LYD  CONST_17  C2    N1   C7A  N7   180.00   0.0  0
 LYD  CONST_18  N3    C4   C4A  C7A    0.00   0.0  0
 LYD  CONST_19  N3    C2   N1   C7A    0.00   0.0  0
 LYD  CONST_20  C2    N1   C7A  C4A    0.00   0.0  0
 LYD  CONST_21  C2    N3   C4   C4A    0.00   0.0  0
 LYD  CONST_22  N1    C7A  C4A  C4     0.00   0.0  0
 LYD  CONST_23  N1    C2   N3   C4     0.00   0.0  0
 LYD  CONST_24  C9    C1'  C6'  C5'  180.00   0.0  0
 LYD  CONST_25  C9    C1'  C2'  C3'  180.00   0.0  0
 LYD  CONST_26  C8    C4'  C3'  C2'  180.00   0.0  0
 LYD  CONST_27  C8    C4'  C5'  C6'  180.00   0.0  0
 LYD  CONST_28  N7    C6   C5   C7   180.00   0.0  0
 LYD  CONST_29  C7A   C4A  C5   C7   180.00   0.0  0
 LYD  CONST_30  C4    C4A  C5   C7     0.00   0.0  0
 LYD  CONST_31  O4    C4   C4A  C5     0.00   0.0  0
 LYD  CONST_32  O4    C4   C4A  C7A  180.00   0.0  0
 LYD  CONST_33  N2    C2   N1   C7A  180.00   0.0  0
 LYD  CONST_34  N2    C2   N3   C4   180.00   0.0  0
 LYD  CONST_35  C2    N3   C4   O4   180.00   0.0  0
 LYD  CONST_36  H3'   C3'  C4'  C5'  180.00   0.0  0
 LYD  CONST_37  H6'   C6'  C5'  C4'  180.00   0.0  0
 LYD  CONST_38  H2'   C2'  C3'  C4'  180.00   0.0  0
 LYD  CONST_39  H5'   C5'  C4'  C3'  180.00   0.0  0
 LYD  CONST_40  HN7   N7   C6   C5   180.00   0.0  0
 LYD  CONST_41  HC6   C6   N7   C7A  180.00   0.0  0
 LYD  CONST_42  HN3   N3   C4   C4A  180.00   0.0  0
 LYD  CONST_43  HN21  N2   C2   N3   180.00   0.0  0
 LYD  CONST_45  CA    N    C9   C1'  180.00   0.0  0
 LYD  CONST_47  CA    N    C9   O9     0.00   0.0  0
 LYD  CONST_48  HX2   OX2  C    CA   180.00   0.0  0
 LYD  Var_01    C7    C8   C4'  C5'  -80.02  30.0  2
 LYD  Var_02    C5    C7   C8   C4'  174.45  30.0  3
 LYD  Var_03    O9    C9   C1'  C2'   25.93  30.0  2
 LYD  Var_04    C6    C5   C7   C8   108.44  30.0  2
 LYD  Var_05    HG11  CG1  CB   CA   175.84  30.0  3
 LYD  Var_06    HG21  CG2  CB   CA   -60.47  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
 LYD  chir_01  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
 LYD  plan-1  C5'   0.020
 LYD  plan-1  C4'   0.020
 LYD  plan-1  C3'   0.020
 LYD  plan-1  C2'   0.020
 LYD  plan-1  C1'   0.020
 LYD  plan-1  C6'   0.020
 LYD  plan-1  C9    0.020
 LYD  plan-1  C8    0.020
 LYD  plan-1  H5'   0.020
 LYD  plan-1  H3'   0.020
 LYD  plan-1  H2'   0.020
 LYD  plan-1  H6'   0.020
 LYD  plan-2  CA    0.020
 LYD  plan-2  C     0.020
 LYD  plan-2  OX1   0.020
 LYD  plan-2  OX2   0.020
 LYD  plan-2  HX2   0.020
 LYD  plan-3  C7    0.020
 LYD  plan-3  C5    0.020
 LYD  plan-3  C6    0.020
 LYD  plan-3  N7    0.020
 LYD  plan-3  C7A   0.020
 LYD  plan-3  C4A   0.020
 LYD  plan-3  C4    0.020
 LYD  plan-3  O4    0.020
 LYD  plan-3  N3    0.020
 LYD  plan-3  C2    0.020
 LYD  plan-3  N1    0.020
 LYD  plan-3  N2    0.020
 LYD  plan-3  HC6   0.020
 LYD  plan-3  HN7   0.020
 LYD  plan-3  HN3   0.020
 LYD  plan-4  C1'   0.020
 LYD  plan-4  C9    0.020
 LYD  plan-4  O9    0.020
 LYD  plan-4  N     0.020
 LYD  plan-4  CA    0.020
 LYD  plan-4  HN    0.020
 LYD  plan-5  C2    0.020
 LYD  plan-5  N2    0.020
 LYD  plan-5  HN21  0.020
 LYD  plan-5  HN22  0.020

