# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:09:47 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-({4-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]thiophen-2-yl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCCc3csc(c3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)cc2C(=O)N1
#
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
 3YB  3YB  'N-({4-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]thiophen-2-yl}carbonyl)-L-glutamic acid'  ligand  53  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3YB
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
 3YB  N1   N  N      0  -0.508   -8.0954  -1.1513  -1.2171
 3YB  C2   C  C      0   0.671   -9.3464  -0.8388  -1.0158
 3YB  N3   N  NH1    0  -0.720   -9.7616  -0.0687   0.0320
 3YB  C4   C  C      0   0.495   -8.9362   0.4688   1.0256
 3YB  N5   N  NR15   0  -0.704   -5.9166  -0.8402  -0.2825
 3YB  C6   C  CR5    0   0.372   -5.3535  -0.1995   0.8074
 3YB  C7   C  CR15   0  -0.467   -6.3545   0.4120   1.5039
 3YB  C8   C  CR5    0  -0.186   -7.5723   0.1320   0.8137
 3YB  C9   C  CR5    0   0.476   -7.2532  -0.6525  -0.2913
 3YB  O10  O  O      0  -0.488   -9.4228   1.1351   1.9295
 3YB  N11  N  NH2    0  -0.836  -10.3043  -1.3141  -1.8355
 3YB  C12  C  CR15   0  -0.228    1.4698   0.2384  -0.7492
 3YB  C13  C  CR5    0  -0.317    2.7863   0.4060  -0.4306
 3YB  S14  S  S2     0   0.225    3.0644   1.9847   0.2058
 3YB  C15  C  CR15   0  -0.543    1.4112   2.3950   0.0520
 3YB  C16  C  CR5    0   0.227    0.6659   1.3785  -0.4717
 3YB  O18  O  O      0  -0.497    3.6267  -1.5903  -1.3317
 3YB  N19  N  NH1    0  -0.644    5.0325  -0.3589  -0.0603
 3YB  C20  C  CH1    0  -0.193    6.1269  -1.3029  -0.1141
 3YB  C21  C  CH2    0  -0.446    7.4390  -0.5873   0.2086
 3YB  C22  C  CH2    0  -0.577    7.7793   0.5282  -0.7663
 3YB  C23  C  C      0   0.412    9.1337   1.2222  -0.5350
 3YB  O24  O  OC    -1  -0.633    9.3624   2.2215  -1.2495
 3YB  O25  O  O      0  -0.609    9.8980   0.7420   0.3252
 3YB  C26  C  C      0   0.414    5.9138  -2.5167   0.8273
 3YB  O27  O  O      0  -0.597    4.9889  -2.4559   1.6543
 3YB  O28  O  OC    -1  -0.619    6.7277  -3.4494   0.6710
 3YB  C29  C  CH2    0  -0.520   -3.8833  -0.2195   1.0382
 3YB  C30  C  CH2    0  -0.420   -3.0991   0.6396   0.0432
 3YB  C31  C  CH2    0  -0.420   -1.5971   0.5744   0.2828
 3YB  C32  C  CH2    0  -0.506   -0.8123   1.4385  -0.7043
 3YB  H1   H  HNH1   0   0.419  -10.7494   0.1258   0.1280
 3YB  H2   H  HNR5   0   0.406   -5.4113  -1.3859  -0.9631
 3YB  H3   H  HCR5   0   0.249   -6.2295   0.9982   2.4008
 3YB  H4   H  HNH2   0   0.406   -9.9991  -1.7342  -2.6972
 3YB  H5   H  HNH2   0   0.409  -11.2104  -0.8780  -1.8618
 3YB  H6   H  HCR5   0   0.263    1.0826  -0.6781  -1.1733
 3YB  H7   H  HCR5   0   0.296    1.0702   3.3758   0.3488
 3YB  H8   H  HNH1   0   0.387    5.0852   0.3414   0.6634
 3YB  H9   H  HCH1   0   0.231    6.1879  -1.6802  -1.1390
 3YB  H10  H  HCH2   0   0.210    7.3943  -0.1943   1.2308
 3YB  H11  H  HCH2   0   0.229    8.2325  -1.3336   0.2061
 3YB  H12  H  HCH2   0   0.221    7.7757   0.1272  -1.7878
 3YB  H13  H  HCH2   0   0.218    6.9989   1.2955  -0.7639
 3YB  H16  H  HCH2   0   0.250   -3.6914   0.1335   2.0535
 3YB  H17  H  HCH2   0   0.243   -3.5152  -1.2500   0.9946
 3YB  H18  H  HCH2   0   0.223   -3.3186   0.3175  -0.9794
 3YB  H19  H  HCH2   0   0.227   -3.4410   1.6761   0.1201
 3YB  H20  H  HCH2   0   0.227   -1.3713   0.8988   1.3029
 3YB  H21  H  HCH2   0   0.226   -1.2602  -0.4645   0.2076
 3YB  H22  H  HCH2   0   0.242   -1.1506   2.4748  -0.6313
 3YB  H23  H  HCH2   0   0.242   -1.0335   1.1102  -1.7241
 3YB  C17  C  C      0   0.560    3.8475  -0.6073  -0.6343

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
 3YB  O25  C23  deloc     1.247  0.020  1.247
 3YB  C23  O24  deloc     1.250  0.020  1.250
 3YB  C23  C22  single    1.539  0.020  1.539
 3YB  C22  C21  single    1.520  0.020  1.520
 3YB  C21  C20  single    1.529  0.020  1.529
 3YB  O18  C17  double    1.225  0.020  1.225
 3YB  C20  N19  single    1.446  0.020  1.446
 3YB  C20  C26  single    1.551  0.020  1.551
 3YB  C17  N19  single    1.340  0.020  1.340
 3YB  C17  C13  single    1.481  0.020  1.481
 3YB  C13  S14  aromatic  1.725  0.020  1.725
 3YB  C13  C12  aromatic  1.365  0.020  1.365
 3YB  S14  C15  aromatic  1.710  0.020  1.710
 3YB  O27  C26  deloc     1.242  0.020  1.242
 3YB  C26  O28  deloc     1.248  0.020  1.248
 3YB  C12  C16  aromatic  1.422  0.020  1.422
 3YB  C15  C16  aromatic  1.365  0.020  1.365
 3YB  C16  C32  single    1.498  0.020  1.498
 3YB  C32  C31  single    1.529  0.020  1.529
 3YB  C31  C30  single    1.522  0.020  1.522
 3YB  C30  C29  single    1.531  0.020  1.531
 3YB  C29  C6   single    1.488  0.020  1.488
 3YB  C6   N5   aromatic  1.384  0.020  1.384
 3YB  C6   C7   aromatic  1.364  0.020  1.364
 3YB  N5   C9   aromatic  1.350  0.020  1.350
 3YB  C7   C8   aromatic  1.428  0.020  1.428
 3YB  C9   C8   aromatic  1.392  0.020  1.392
 3YB  C9   N1   single    1.347  0.020  1.347
 3YB  C8   C4   single    1.421  0.020  1.421
 3YB  N1   C2   double    1.305  0.020  1.305
 3YB  C4   O10  double    1.224  0.020  1.224
 3YB  C4   N3   single    1.399  0.020  1.399
 3YB  C2   N3   single    1.365  0.020  1.365
 3YB  C2   N11  single    1.347  0.020  1.347
 3YB  N3   H1   single    0.860  0.020  1.020
 3YB  N5   H2   single    0.860  0.020  1.020
 3YB  C7   H3   single    0.930  0.020  1.080
 3YB  N11  H4   single    0.890  0.020  1.040
 3YB  N11  H5   single    0.890  0.020  1.040
 3YB  C12  H6   single    0.930  0.020  1.080
 3YB  C15  H7   single    0.930  0.020  1.080
 3YB  N19  H8   single    0.890  0.020  1.040
 3YB  C20  H9   single    0.970  0.020  1.090
 3YB  C21  H10  single    0.970  0.020  1.090
 3YB  C21  H11  single    0.970  0.020  1.090
 3YB  C22  H12  single    0.970  0.020  1.090
 3YB  C22  H13  single    0.970  0.020  1.090
 3YB  C29  H16  single    0.970  0.020  1.090
 3YB  C29  H17  single    0.970  0.020  1.090
 3YB  C30  H18  single    0.970  0.020  1.090
 3YB  C30  H19  single    0.970  0.020  1.090
 3YB  C31  H20  single    0.970  0.020  1.090
 3YB  C31  H21  single    0.970  0.020  1.090
 3YB  C32  H22  single    0.970  0.020  1.090
 3YB  C32  H23  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
 3YB  C9   N1   C2   113.86  3.000
 3YB  N11  C2   N3   116.73  3.000
 3YB  N11  C2   N1   120.21  3.000
 3YB  N3   C2   N1   123.03  3.000
 3YB  H1   N3   C4   115.78  3.000
 3YB  H1   N3   C2   118.58  3.000
 3YB  C4   N3   C2   125.62  3.000
 3YB  O10  C4   C8   128.38  3.000
 3YB  O10  C4   N3   119.94  3.000
 3YB  C8   C4   N3   111.68  3.000
 3YB  H2   N5   C9   124.55  3.000
 3YB  H2   N5   C6   125.33  3.000
 3YB  C9   N5   C6   110.10  3.000
 3YB  C29  C6   C7   130.67  3.000
 3YB  C7   C6   N5   108.12  3.000
 3YB  C29  C6   N5   121.18  3.000
 3YB  H3   C7   C8   127.40  3.000
 3YB  H3   C7   C6   125.66  3.000
 3YB  C8   C7   C6   106.93  3.000
 3YB  C9   C8   C7   107.38  3.000
 3YB  C9   C8   C4   118.16  3.000
 3YB  C7   C8   C4   134.46  3.000
 3YB  C8   C9   N5   107.47  3.000
 3YB  C8   C9   N1   127.65  3.000
 3YB  N5   C9   N1   124.89  3.000
 3YB  H5   N11  H4   115.59  3.000
 3YB  H5   N11  C2   120.22  3.000
 3YB  H4   N11  C2   116.92  3.000
 3YB  H6   C12  C16  123.59  3.000
 3YB  H6   C12  C13  122.75  3.000
 3YB  C16  C12  C13  113.66  3.000
 3YB  C17  C13  S14  124.15  3.000
 3YB  S14  C13  C12  110.74  3.000
 3YB  C17  C13  C12  125.10  3.000
 3YB  C15  S14  C13   91.75  3.000
 3YB  H7   C15  C16  127.54  3.000
 3YB  H7   C15  S14  119.89  3.000
 3YB  C16  C15  S14  112.56  3.000
 3YB  C32  C16  C15  124.66  3.000
 3YB  C32  C16  C12  124.04  3.000
 3YB  C15  C16  C12  111.29  3.000
 3YB  H8   N19  C20  116.13  3.000
 3YB  H8   N19  C17  118.84  3.000
 3YB  C20  N19  C17  122.15  3.000
 3YB  H9   C20  C26  107.84  3.000
 3YB  H9   C20  C21  108.14  3.000
 3YB  C26  C20  C21  110.86  3.000
 3YB  H9   C20  N19  107.59  3.000
 3YB  C26  C20  N19  112.60  3.000
 3YB  C21  C20  N19  109.63  3.000
 3YB  H11  C21  H10  106.11  3.000
 3YB  H11  C21  C22  109.77  3.000
 3YB  H10  C21  C22  110.13  3.000
 3YB  H11  C21  C20  107.69  3.000
 3YB  H10  C21  C20  109.25  3.000
 3YB  C22  C21  C20  113.59  3.000
 3YB  H13  C22  H12  104.83  3.000
 3YB  H13  C22  C23  108.12  3.000
 3YB  H12  C22  C23  107.91  3.000
 3YB  H13  C22  C21  110.70  3.000
 3YB  H12  C22  C21  109.15  3.000
 3YB  C23  C22  C21  115.56  3.000
 3YB  O25  C23  O24  126.17  3.000
 3YB  O24  C23  C22  115.83  3.000
 3YB  O25  C23  C22  118.00  3.000
 3YB  O28  C26  O27  127.27  3.000
 3YB  O28  C26  C20  114.80  3.000
 3YB  O27  C26  C20  117.91  3.000
 3YB  H17  C29  H16  106.39  3.000
 3YB  H17  C29  C30  109.27  3.000
 3YB  H16  C29  C30  109.45  3.000
 3YB  H17  C29  C6   109.78  3.000
 3YB  H16  C29  C6   108.27  3.000
 3YB  C30  C29  C6   113.43  3.000
 3YB  H19  C30  H18  106.37  3.000
 3YB  H19  C30  C31  109.75  3.000
 3YB  H18  C30  C31  109.41  3.000
 3YB  H19  C30  C29  109.03  3.000
 3YB  H18  C30  C29  109.84  3.000
 3YB  C31  C30  C29  112.28  3.000
 3YB  H21  C31  H20  106.38  3.000
 3YB  H21  C31  C32  109.52  3.000
 3YB  H20  C31  C32  109.18  3.000
 3YB  H21  C31  C30  109.48  3.000
 3YB  H20  C31  C30  109.73  3.000
 3YB  C32  C31  C30  112.37  3.000
 3YB  H23  C32  H22  106.52  3.000
 3YB  H23  C32  C31  109.18  3.000
 3YB  H22  C32  C31  109.51  3.000
 3YB  H23  C32  C16  109.41  3.000
 3YB  H22  C32  C16  109.47  3.000
 3YB  C31  C32  C16  112.57  3.000
 3YB  N19  C17  O18  123.50  3.000
 3YB  N19  C17  C13  116.60  3.000
 3YB  O18  C17  C13  119.86  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
 3YB  CONST_01  C8   C7   C6   N5      0.00   0.0  0
 3YB  CONST_02  C7   C8   C9   N5      0.00   0.0  0
 3YB  CONST_03  C8   C9   N5   C6      0.00   0.0  0
 3YB  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 3YB  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YB  CONST_06  C15  S14  C13  C12     0.00   0.0  0
 3YB  CONST_07  S14  C15  C16  C12     0.00   0.0  0
 3YB  CONST_08  C16  C15  S14  C13     0.00   0.0  0
 3YB  CONST_09  C15  C16  C12  C13     0.00   0.0  0
 3YB  CONST_10  C16  C12  C13  S14     0.00   0.0  0
 3YB  CONST_11  C4   N3   C2   N1      0.00   0.0  0
 3YB  CONST_12  C8   C4   N3   C2      0.00   0.0  0
 3YB  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 3YB  CONST_14  C29  C6   C7   C8    180.00   0.0  0
 3YB  CONST_15  C29  C6   N5   C9    180.00   0.0  0
 3YB  CONST_16  C32  C16  C12  C13   180.00   0.0  0
 3YB  CONST_17  C32  C16  C15  S14   180.00   0.0  0
 3YB  CONST_18  C17  C13  S14  C15   180.00   0.0  0
 3YB  CONST_19  C17  C13  C12  C16   180.00   0.0  0
 3YB  CONST_20  O10  C4   N3   C2    180.00   0.0  0
 3YB  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 3YB  CONST_22  N11  C2   N1   C9    180.00   0.0  0
 3YB  CONST_23  H2   N5   C9   N1      0.00   0.0  0
 3YB  CONST_24  H3   C7   C8   C4      0.00   0.0  0
 3YB  CONST_25  H7   C15  C16  C12   180.00   0.0  0
 3YB  CONST_26  H6   C12  C13  S14   180.00   0.0  0
 3YB  CONST_27  H1   N3   C2   N1    180.00   0.0  0
 3YB  CONST_28  H4   N11  C2   N1      0.00   0.0  0
 3YB  CONST_30  C20  N19  C17  C13   180.00   0.0  0
 3YB  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YB  Var_01    C30  C29  C6   N5     71.46  30.0  2
 3YB  Var_02    O18  C17  C13  C12    12.97  30.0  2
 3YB  Var_03    C31  C32  C16  C12    70.79  30.0  2
 3YB  Var_04    C31  C30  C29  C6   -178.66  30.0  1
 3YB  Var_05    C30  C31  C32  C16   179.94  30.0  3
 3YB  Var_06    C23  C22  C21  C20  -176.39  30.0  1
 3YB  Var_07    O25  C23  C22  C21     7.16  30.0  3
 3YB  Var_08    C32  C31  C30  C29  -179.64  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
 3YB  chir_01  C20  C21  N19  C26  positiv

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
 3YB  plan-1  C12  0.020
 3YB  plan-1  C13  0.020
 3YB  plan-1  S14  0.020
 3YB  plan-1  C15  0.020
 3YB  plan-1  C16  0.020
 3YB  plan-1  C32  0.020
 3YB  plan-1  H6   0.020
 3YB  plan-1  H7   0.020
 3YB  plan-1  C17  0.020
 3YB  plan-2  N1   0.020
 3YB  plan-2  C2   0.020
 3YB  plan-2  N3   0.020
 3YB  plan-2  C4   0.020
 3YB  plan-2  N5   0.020
 3YB  plan-2  C6   0.020
 3YB  plan-2  C7   0.020
 3YB  plan-2  C8   0.020
 3YB  plan-2  C9   0.020
 3YB  plan-2  O10  0.020
 3YB  plan-2  N11  0.020
 3YB  plan-2  C29  0.020
 3YB  plan-2  H1   0.020
 3YB  plan-2  H2   0.020
 3YB  plan-2  H3   0.020
 3YB  plan-2  H4   0.020
 3YB  plan-2  H5   0.020
 3YB  plan-3  C13  0.020
 3YB  plan-3  O18  0.020
 3YB  plan-3  N19  0.020
 3YB  plan-3  C20  0.020
 3YB  plan-3  H8   0.020
 3YB  plan-3  C17  0.020
 3YB  plan-4  C22  0.020
 3YB  plan-4  C23  0.020
 3YB  plan-4  O24  0.020
 3YB  plan-4  O25  0.020
 3YB  plan-5  C20  0.020
 3YB  plan-5  C26  0.020
 3YB  plan-5  O27  0.020
 3YB  plan-5  O28  0.020

