# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:55:11 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: N-({5-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]thiophen-3-yl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(CCCCc3scc(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
 3YC  3YC  'N-({5-[4-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]thiophen-3-yl}carbonyl)-L-glutamic acid'  ligand  55  32  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3YC
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
 3YC  N1   N  N     0  -0.507  25.2960  -11.4402  26.3080
 3YC  C2   C  CR6   0   0.670  24.2463  -11.7155  25.5835
 3YC  N3   N  NR16  0  -0.720  23.7106  -12.9683  25.4950
 3YC  C4   C  CR6   0   0.496  24.1976  -14.1101  26.1394
 3YC  N5   N  NR15  0  -0.699  26.8945  -12.4779  27.7534
 3YC  C6   C  CR5   0   0.355  27.1558  -13.7428  28.2483
 3YC  C7   C  CR15  0  -0.454  26.2118  -14.5952  27.7524
 3YC  C8   C  CR56  0  -0.185  25.3449  -13.8195  26.9264
 3YC  C9   C  CR56  0   0.476  25.8079  -12.5068  26.9531
 3YC  O10  O  O     0  -0.488  23.6364  -15.1868  25.9850
 3YC  N11  N  NH2   0  -0.835  23.6639  -10.7532  24.8409
 3YC  C12  C  CR15  0  -0.262  26.6727  -10.4846  33.8710
 3YC  C13  C  CR5   0   0.044  25.7236   -9.4426  34.1060
 3YC  C14  C  CR15  0  -0.505  24.5278   -9.6871  33.4943
 3YC  S15  S  S2    0   0.248  24.5540  -11.1562  32.6336
 3YC  C16  C  CR5   0  -0.138  26.1863  -11.4899  33.0939
 3YC  O18  O  O     0  -0.483  24.9900   -7.5333  35.2962
 3YC  N19  N  NH1   0  -0.660  27.2061   -7.9136  35.2193
 3YC  C20  C  CH1   0  -0.188  27.5146   -6.7137  35.9479
 3YC  C21  C  CH2   0  -0.468  28.9769   -6.7229  36.4011
 3YC  C22  C  CH2   0  -0.577  29.2420   -7.8351  37.4032
 3YC  C23  C  C     0   0.555  30.6620   -7.8486  37.8977
 3YC  O24  O  O     0  -0.442  31.5260   -7.0843  37.5473
 3YC  O25  O  OH1   0  -0.595  30.8629   -8.8177  38.7838
 3YC  C26  C  C     0   0.547  27.2430   -5.4821  35.0946
 3YC  O27  O  OH1   0  -0.589  27.1051   -4.3987  35.8442
 3YC  O28  O  O     0  -0.431  27.1934   -5.4846  33.8931
 3YC  C29  C  CH2   0  -0.530  28.2770  -13.9951  29.1990
 3YC  C30  C  CH2   0  -0.418  27.8435  -14.0034  30.6682
 3YC  C31  C  CH2   0  -0.422  27.2447  -12.6874  31.1420
 3YC  C32  C  CH2   0  -0.496  26.8735  -12.7298  32.6259
 3YC  H1   H  HNR6  0   0.419  22.8960  -13.1037  24.9111
 3YC  H2   H  HNR5  0   0.405  27.4437  -11.6545  27.9459
 3YC  H3   H  HCR5  0   0.248  26.1453  -15.6515  27.9616
 3YC  H4   H  HNH2  0   0.406  23.9319   -9.8037  25.0381
 3YC  H5   H  HNH2  0   0.408  22.7274  -10.8775  24.4943
 3YC  H6   H  HCR5  0   0.262  27.6740  -10.5142  34.2803
 3YC  H7   H  HCR5  0   0.301  23.6424   -9.0704  33.5083
 3YC  H8   H  HNH1  0   0.410  27.9525   -8.3508  34.7017
 3YC  H9   H  HCH1  0   0.293  26.8748   -6.6623  36.8326
 3YC  H10  H  HCH2  0   0.261  29.6282   -6.8235  35.5288
 3YC  H11  H  HCH2  0   0.275  29.2074   -5.7588  36.8551
 3YC  H12  H  HCH2  0   0.289  28.5789   -7.7344  38.2682
 3YC  H13  H  HCH2  0   0.286  29.0212   -8.8190  36.9802
 3YC  H14  H  HOH1  0   0.481  31.7819   -8.8017  39.0900
 3YC  H15  H  HOH1  0   0.486  26.9893   -3.6153  35.2854
 3YC  H16  H  HCH2  0   0.259  28.7254  -14.9618  28.9629
 3YC  H17  H  HCH2  0   0.247  29.0623  -13.2480  29.0518
 3YC  H18  H  HCH2  0   0.225  27.1181  -14.8083  30.8187
 3YC  H19  H  HCH2  0   0.229  28.7141  -14.2530  31.2822
 3YC  H20  H  HCH2  0   0.230  27.9536  -11.8708  30.9747
 3YC  H21  H  HCH2  0   0.227  26.3535  -12.4511  30.5532
 3YC  H22  H  HCH2  0   0.253  26.2387  -13.6000  32.8167
 3YC  H23  H  HCH2  0   0.257  27.7751  -12.8680  33.2269
 3YC  C17  C  C     0   0.546  25.9267   -8.2197  34.9138

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
 3YC  N11  C2   single    1.348  0.020  1.348
 3YC  N3   C2   single    1.365  0.020  1.365
 3YC  N3   C4   single    1.399  0.020  1.399
 3YC  C2   N1   double    1.305  0.020  1.305
 3YC  O10  C4   double    1.224  0.020  1.224
 3YC  C4   C8   single    1.421  0.020  1.421
 3YC  N1   C9   single    1.348  0.020  1.348
 3YC  C8   C9   aromatic  1.392  0.020  1.392
 3YC  C8   C7   aromatic  1.427  0.020  1.427
 3YC  C9   N5   aromatic  1.350  0.020  1.350
 3YC  C7   C6   aromatic  1.365  0.020  1.365
 3YC  N5   C6   aromatic  1.383  0.020  1.383
 3YC  C6   C29  single    1.491  0.020  1.491
 3YC  C29  C30  single    1.532  0.020  1.532
 3YC  C30  C31  single    1.521  0.020  1.521
 3YC  C31  C32  single    1.530  0.020  1.530
 3YC  O28  C26  double    1.203  0.020  1.203
 3YC  C32  C16  single    1.493  0.020  1.493
 3YC  C16  S15  aromatic  1.728  0.020  1.728
 3YC  C16  C12  aromatic  1.361  0.020  1.361
 3YC  S15  C14  aromatic  1.703  0.020  1.703
 3YC  C26  O27  single    1.325  0.020  1.325
 3YC  C26  C20  single    1.523  0.020  1.523
 3YC  C12  C13  aromatic  1.429  0.020  1.429
 3YC  C14  C13  aromatic  1.365  0.020  1.365
 3YC  C13  C17  single    1.480  0.020  1.480
 3YC  N19  C17  single    1.351  0.020  1.351
 3YC  N19  C20  single    1.437  0.020  1.437
 3YC  C17  O18  double    1.223  0.020  1.223
 3YC  C20  C21  single    1.531  0.020  1.531
 3YC  C21  C22  single    1.520  0.020  1.520
 3YC  O24  C23  double    1.206  0.020  1.206
 3YC  C22  C23  single    1.504  0.020  1.504
 3YC  C23  O25  single    1.328  0.020  1.328
 3YC  N3   H1   single    0.860  0.020  1.020
 3YC  N5   H2   single    0.860  0.020  1.020
 3YC  C7   H3   single    0.930  0.020  1.080
 3YC  N11  H4   single    0.890  0.020  1.040
 3YC  N11  H5   single    0.890  0.020  1.040
 3YC  C12  H6   single    0.930  0.020  1.080
 3YC  C14  H7   single    0.930  0.020  1.080
 3YC  N19  H8   single    0.860  0.020  1.020
 3YC  C20  H9   single    0.970  0.020  1.090
 3YC  C21  H10  single    0.970  0.020  1.090
 3YC  C21  H11  single    0.970  0.020  1.090
 3YC  C22  H12  single    0.970  0.020  1.090
 3YC  C22  H13  single    0.970  0.020  1.090
 3YC  O25  H14  single    0.850  0.020  0.980
 3YC  O27  H15  single    0.850  0.020  0.980
 3YC  C29  H16  single    0.970  0.020  1.090
 3YC  C29  H17  single    0.970  0.020  1.090
 3YC  C30  H18  single    0.970  0.020  1.090
 3YC  C30  H19  single    0.970  0.020  1.090
 3YC  C31  H20  single    0.970  0.020  1.090
 3YC  C31  H21  single    0.970  0.020  1.090
 3YC  C32  H22  single    0.970  0.020  1.090
 3YC  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
 3YC  C9   N1   C2   113.86  3.000
 3YC  N11  C2   N3   116.73  3.000
 3YC  N3   C2   N1   123.03  3.000
 3YC  N11  C2   N1   120.20  3.000
 3YC  H1   N3   C4   115.92  3.000
 3YC  H1   N3   C2   118.44  3.000
 3YC  C4   N3   C2   125.63  3.000
 3YC  O10  C4   C8   128.31  3.000
 3YC  C8   C4   N3   111.67  3.000
 3YC  O10  C4   N3   120.02  3.000
 3YC  H2   N5   C9   124.69  3.000
 3YC  H2   N5   C6   125.15  3.000
 3YC  C9   N5   C6   110.16  3.000
 3YC  C29  C6   C7   130.22  3.000
 3YC  C29  C6   N5   121.65  3.000
 3YC  C7   C6   N5   108.08  3.000
 3YC  H3   C7   C8   127.38  3.000
 3YC  H3   C7   C6   125.70  3.000
 3YC  C8   C7   C6   106.92  3.000
 3YC  C9   C8   C7   107.42  3.000
 3YC  C7   C8   C4   134.42  3.000
 3YC  C9   C8   C4   118.16  3.000
 3YC  C8   C9   N5   107.42  3.000
 3YC  N5   C9   N1   124.94  3.000
 3YC  C8   C9   N1   127.64  3.000
 3YC  H5   N11  H4   115.59  3.000
 3YC  H5   N11  C2   120.25  3.000
 3YC  H4   N11  C2   116.79  3.000
 3YC  H6   C12  C16  121.78  3.000
 3YC  H6   C12  C13  124.92  3.000
 3YC  C16  C12  C13  113.28  3.000
 3YC  C17  C13  C14  120.85  3.000
 3YC  C17  C13  C12  126.97  3.000
 3YC  C14  C13  C12  112.18  3.000
 3YC  H7   C14  S15  120.81  3.000
 3YC  H7   C14  C13  127.63  3.000
 3YC  S15  C14  C13  111.56  3.000
 3YC  C16  S15  C14   92.66  3.000
 3YC  C32  C16  S15  120.77  3.000
 3YC  S15  C16  C12  110.31  3.000
 3YC  C32  C16  C12  128.91  3.000
 3YC  H8   N19  C20  117.61  3.000
 3YC  H8   N19  C17  119.14  3.000
 3YC  C20  N19  C17  120.48  3.000
 3YC  H9   C20  C26  108.13  3.000
 3YC  H9   C20  C21  108.65  3.000
 3YC  C26  C20  C21  109.94  3.000
 3YC  H9   C20  N19  108.90  3.000
 3YC  C21  C20  N19  110.49  3.000
 3YC  C26  C20  N19  110.66  3.000
 3YC  H11  C21  H10  106.72  3.000
 3YC  H11  C21  C22  109.61  3.000
 3YC  H10  C21  C22  110.78  3.000
 3YC  H11  C21  C20  108.66  3.000
 3YC  H10  C21  C20  109.48  3.000
 3YC  C22  C21  C20  111.47  3.000
 3YC  H13  C22  H12  105.44  3.000
 3YC  H13  C22  C23  108.04  3.000
 3YC  H12  C22  C23  108.24  3.000
 3YC  H13  C22  C21  111.60  3.000
 3YC  H12  C22  C21  110.36  3.000
 3YC  C23  C22  C21  112.83  3.000
 3YC  O25  C23  O24  123.23  3.000
 3YC  O25  C23  C22  111.64  3.000
 3YC  O24  C23  C22  125.14  3.000
 3YC  H14  O25  C23  110.01  3.000
 3YC  O28  C26  O27  124.25  3.000
 3YC  O27  C26  C20  111.28  3.000
 3YC  O28  C26  C20  124.44  3.000
 3YC  H15  O27  C26  110.32  3.000
 3YC  H17  C29  H16  106.31  3.000
 3YC  H17  C29  C30  109.63  3.000
 3YC  H16  C29  C30  108.59  3.000
 3YC  H17  C29  C6   109.78  3.000
 3YC  H16  C29  C6   108.71  3.000
 3YC  C30  C29  C6   113.55  3.000
 3YC  H19  C30  H18  106.41  3.000
 3YC  H19  C30  C31  109.62  3.000
 3YC  H18  C30  C31  109.42  3.000
 3YC  H19  C30  C29  108.32  3.000
 3YC  H18  C30  C29  108.88  3.000
 3YC  C31  C30  C29  113.91  3.000
 3YC  H21  C31  H20  106.52  3.000
 3YC  H21  C31  C32  109.29  3.000
 3YC  H20  C31  C32  109.03  3.000
 3YC  H21  C31  C30  109.87  3.000
 3YC  H20  C31  C30  110.06  3.000
 3YC  C32  C31  C30  111.93  3.000
 3YC  H23  C32  H22  106.40  3.000
 3YC  H23  C32  C31  109.68  3.000
 3YC  H22  C32  C31  109.39  3.000
 3YC  H23  C32  C16  108.22  3.000
 3YC  H22  C32  C16  109.81  3.000
 3YC  C31  C32  C16  113.12  3.000
 3YC  N19  C17  O18  121.85  3.000
 3YC  O18  C17  C13  121.98  3.000
 3YC  N19  C17  C13  116.16  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
 3YC  CONST_01  C7   C8   C9   N5      0.00   0.0  0
 3YC  CONST_02  C8   C7   C6   N5      0.00   0.0  0
 3YC  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 3YC  CONST_04  C8   C9   N5   C6      0.00   0.0  0
 3YC  CONST_05  C9   N5   C6   C7      0.00   0.0  0
 3YC  CONST_06  C14  S15  C16  C12     0.00   0.0  0
 3YC  CONST_07  S15  C14  C13  C12     0.00   0.0  0
 3YC  CONST_08  S15  C16  C12  C13     0.00   0.0  0
 3YC  CONST_09  C16  S15  C14  C13     0.00   0.0  0
 3YC  CONST_10  C16  C12  C13  C14     0.00   0.0  0
 3YC  CONST_11  C4   N3   C2   N1      0.00   0.0  0
 3YC  CONST_12  C8   C4   N3   C2      0.00   0.0  0
 3YC  CONST_13  C9   N1   C2   N3      0.00   0.0  0
 3YC  CONST_14  C29  C6   C7   C8    180.00   0.0  0
 3YC  CONST_15  C29  C6   N5   C9    180.00   0.0  0
 3YC  CONST_16  C32  C16  C12  C13   180.00   0.0  0
 3YC  CONST_17  C32  C16  S15  C14   180.00   0.0  0
 3YC  CONST_18  C17  C13  C14  S15   180.00   0.0  0
 3YC  CONST_19  C17  C13  C12  C16   180.00   0.0  0
 3YC  CONST_20  O10  C4   N3   C2    180.00   0.0  0
 3YC  CONST_21  N11  C2   N3   C4    180.00   0.0  0
 3YC  CONST_22  N11  C2   N1   C9    180.00   0.0  0
 3YC  CONST_23  H2   N5   C9   N1      0.00   0.0  0
 3YC  CONST_24  H3   C7   C8   C4      0.00   0.0  0
 3YC  CONST_25  H7   C14  C13  C12   180.00   0.0  0
 3YC  CONST_26  H6   C12  C13  C14   180.00   0.0  0
 3YC  CONST_27  H1   N3   C2   N1    180.00   0.0  0
 3YC  CONST_28  H4   N11  C2   N1      0.00   0.0  0
 3YC  CONST_30  C20  N19  C17  C13   180.00   0.0  0
 3YC  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YC  CONST_33  H15  O27  C26  C20   180.00   0.0  0
 3YC  CONST_34  H14  O25  C23  C22   180.00   0.0  0
 3YC  Var_01    C30  C29  C6   N5     96.25  30.0  2
 3YC  Var_02    C31  C32  C16  C12  -106.23  30.0  2
 3YC  Var_03    N19  C17  C13  C12    15.27  30.0  2
 3YC  Var_04    C31  C30  C29  C6    -61.05  30.0  3
 3YC  Var_05    C30  C31  C32  C16  -175.52  30.0  2
 3YC  Var_06    C23  C22  C21  C20  -178.43  30.0  3
 3YC  Var_07    O24  C23  C22  C21    -0.78  30.0  3
 3YC  Var_08    C32  C31  C30  C29  -177.99  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
 3YC  chir_01  C20  C26  N19  C21  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
 3YC  plan-1  C12  0.020
 3YC  plan-1  C13  0.020
 3YC  plan-1  C14  0.020
 3YC  plan-1  S15  0.020
 3YC  plan-1  C16  0.020
 3YC  plan-1  C32  0.020
 3YC  plan-1  H6   0.020
 3YC  plan-1  H7   0.020
 3YC  plan-1  C17  0.020
 3YC  plan-2  N1   0.020
 3YC  plan-2  C2   0.020
 3YC  plan-2  N3   0.020
 3YC  plan-2  C4   0.020
 3YC  plan-2  N5   0.020
 3YC  plan-2  C6   0.020
 3YC  plan-2  C7   0.020
 3YC  plan-2  C8   0.020
 3YC  plan-2  C9   0.020
 3YC  plan-2  O10  0.020
 3YC  plan-2  N11  0.020
 3YC  plan-2  C29  0.020
 3YC  plan-2  H1   0.020
 3YC  plan-2  H2   0.020
 3YC  plan-2  H3   0.020
 3YC  plan-2  H4   0.020
 3YC  plan-2  H5   0.020
 3YC  plan-3  C13  0.020
 3YC  plan-3  O18  0.020
 3YC  plan-3  N19  0.020
 3YC  plan-3  C20  0.020
 3YC  plan-3  H8   0.020
 3YC  plan-3  C17  0.020
 3YC  plan-4  C22  0.020
 3YC  plan-4  C23  0.020
 3YC  plan-4  O24  0.020
 3YC  plan-4  O25  0.020
 3YC  plan-4  H14  0.020
 3YC  plan-5  C20  0.020
 3YC  plan-5  C26  0.020
 3YC  plan-5  O27  0.020
 3YC  plan-5  O28  0.020
 3YC  plan-5  H15  0.020

