# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 01:34:39 2022
#   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  53  32  .  2022-03-10  2022-03-10
;
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  -0.505  24.9828  -11.4899  26.4145
 3YC  C2   C  CR6    0   0.667  24.0259  -11.8671  25.6118
 3YC  N3   N  NR16   0  -0.720  23.7372  -13.1780  25.3616
 3YC  C4   C  CR6    0   0.493  24.4105  -14.2785  25.9054
 3YC  N5   N  NR15   0  -0.699  26.7020  -12.3748  27.8220
 3YC  C6   C  CR5    0   0.355  27.1751  -13.6190  28.1994
 3YC  C7   C  CR15   0  -0.455  26.4229  -14.5671  27.5675
 3YC  C8   C  CR56   0  -0.184  25.4551  -13.8742  26.7810
 3YC  C9   C  CR56   0   0.475  25.6652  -12.5114  26.9684
 3YC  O10  O  O      0  -0.478  24.0699  -15.4134  25.6038
 3YC  N11  N  NH2    0  -0.833  23.2984  -10.9443  24.9489
 3YC  C12  C  CR15   0  -0.269  26.6829  -10.3712  33.9034
 3YC  C13  C  CR5    0   0.045  25.7672   -9.3033  34.1577
 3YC  C14  C  CR15   0  -0.513  24.5678   -9.5045  33.5393
 3YC  S15  S  S2     0   0.232  24.5492  -10.9615  32.6526
 3YC  C16  C  CR5    0  -0.135  26.1709  -11.3489  33.1077
 3YC  O18  O  O      0  -0.501  25.0681   -7.3727  35.3275
 3YC  N19  N  NH1    0  -0.639  27.2736   -7.8578  35.3384
 3YC  C20  C  CH1    0  -0.186  27.6841   -6.6616  36.0400
 3YC  C21  C  CH2    0  -0.448  29.0557   -6.8816  36.6782
 3YC  C22  C  CH2    0  -0.561  29.0956   -8.0188  37.6888
 3YC  C23  C  C      0   0.404  30.4379   -8.1892  38.4311
 3YC  O24  O  O      0  -0.608  31.1428   -7.1700  38.5804
 3YC  O25  O  OC    -1  -0.620  30.6937   -9.3360  38.8535
 3YC  C26  C  C      0   0.407  27.7010   -5.4004  35.1306
 3YC  O27  O  OC    -1  -0.610  27.8245   -4.3217  35.7442
 3YC  O28  O  O      0  -0.594  27.6179   -5.5676  33.9017
 3YC  C29  C  CH2    0  -0.526  28.2923  -13.7716  29.1745
 3YC  C30  C  CH2    0  -0.417  27.8442  -13.8139  30.6392
 3YC  C31  C  CH2    0  -0.423  27.1763  -12.5340  31.1215
 3YC  C32  C  CH2    0  -0.494  26.8383  -12.5894  32.6125
 3YC  H1   H  HNR6   0   0.418  22.9829  -13.3959  24.7228
 3YC  H2   H  HNR5   0   0.405  27.0806  -11.4922  28.1295
 3YC  H3   H  HCR5   0   0.246  26.5506  -15.6344  27.6590
 3YC  H4   H  HNH2   0   0.404  23.3793   -9.9946  25.2717
 3YC  H5   H  HNH2   0   0.407  22.4039  -11.1908  24.5588
 3YC  H6   H  HCR5   0   0.261  27.6835  -10.4405  34.3102
 3YC  H7   H  HCR5   0   0.293  23.7000   -8.8637  33.5620
 3YC  H8   H  HNH1   0   0.393  28.0012   -8.3894  34.8881
 3YC  H9   H  HCH1   0   0.223  26.9613   -6.4824  36.8414
 3YC  H10  H  HCH2   0   0.207  29.7968   -7.0554  35.8884
 3YC  H11  H  HCH2   0   0.226  29.3460   -5.9534  37.1681
 3YC  H12  H  HCH2   0   0.215  28.3188   -7.8416  38.4446
 3YC  H13  H  HCH2   0   0.203  28.8289   -8.9676  37.2165
 3YC  H16  H  HCH2   0   0.256  28.8213  -14.6982  28.9451
 3YC  H17  H  HCH2   0   0.245  29.0165  -12.9625  29.0387
 3YC  H18  H  HCH2   0   0.224  27.1638  -14.6587  30.7799
 3YC  H19  H  HCH2   0   0.228  28.7237  -14.0185  31.2571
 3YC  H20  H  HCH2   0   0.228  27.8333  -11.6789  30.9339
 3YC  H21  H  HCH2   0   0.227  26.2599  -12.3518  30.5533
 3YC  H22  H  HCH2   0   0.250  26.2059  -13.4606  32.8072
 3YC  H23  H  HCH2   0   0.254  27.7535  -12.7366  33.1910
 3YC  C17  C  C      0   0.526  26.0028   -8.0895  34.9850

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    1.349  0.020  1.349
 3YC  N3   C2   single    1.365  0.020  1.365
 3YC  N3   C4   single    1.400  0.020  1.400
 3YC  C2   N1   double    1.305  0.020  1.305
 3YC  O10  C4   double    1.223  0.020  1.223
 3YC  C4   C8   single    1.422  0.020  1.422
 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  1.384  0.020  1.384
 3YC  C6   C29  single    1.491  0.020  1.491
 3YC  C29  C30  single    1.532  0.020  1.532
 3YC  C30  C31  single    1.522  0.020  1.522
 3YC  C31  C32  single    1.530  0.020  1.530
 3YC  O28  C26  deloc     1.243  0.020  1.243
 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  1.706  0.020  1.706
 3YC  C26  O27  deloc     1.247  0.020  1.247
 3YC  C26  C20  single    1.555  0.020  1.555
 3YC  C12  C13  aromatic  1.430  0.020  1.430
 3YC  C14  C13  aromatic  1.364  0.020  1.364
 3YC  C13  C17  single    1.488  0.020  1.488
 3YC  N19  C17  single    1.339  0.020  1.339
 3YC  N19  C20  single    1.446  0.020  1.446
 3YC  C17  O18  double    1.227  0.020  1.227
 3YC  C20  C21  single    1.529  0.020  1.529
 3YC  C21  C22  single    1.522  0.020  1.522
 3YC  O24  C23  deloc     1.248  0.020  1.248
 3YC  C22  C23  single    1.543  0.020  1.543
 3YC  C23  O25  deloc     1.249  0.020  1.249
 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  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   113.90  3.000
 3YC  N11  C2   N3   116.91  3.000
 3YC  N3   C2   N1   123.05  3.000
 3YC  N11  C2   N1   120.00  3.000
 3YC  H1   N3   C4   115.75  3.000
 3YC  H1   N3   C2   118.68  3.000
 3YC  C4   N3   C2   125.57  3.000
 3YC  O10  C4   C8   128.35  3.000
 3YC  C8   C4   N3   111.66  3.000
 3YC  O10  C4   N3   119.99  3.000
 3YC  H2   N5   C9   124.73  3.000
 3YC  H2   N5   C6   125.14  3.000
 3YC  C9   N5   C6   110.13  3.000
 3YC  C29  C6   C7   130.13  3.000
 3YC  C29  C6   N5   121.79  3.000
 3YC  C7   C6   N5   108.05  3.000
 3YC  H3   C7   C8   127.41  3.000
 3YC  H3   C7   C6   125.63  3.000
 3YC  C8   C7   C6   106.95  3.000
 3YC  C9   C8   C7   107.40  3.000
 3YC  C7   C8   C4   134.42  3.000
 3YC  C9   C8   C4   118.18  3.000
 3YC  C8   C9   N5   107.47  3.000
 3YC  N5   C9   N1   124.90  3.000
 3YC  C8   C9   N1   127.63  3.000
 3YC  H5   N11  H4   115.27  3.000
 3YC  H5   N11  C2   120.14  3.000
 3YC  H4   N11  C2   116.40  3.000
 3YC  H6   C12  C16  121.45  3.000
 3YC  H6   C12  C13  124.97  3.000
 3YC  C16  C12  C13  113.56  3.000
 3YC  C17  C13  C14  120.77  3.000
 3YC  C17  C13  C12  127.37  3.000
 3YC  C14  C13  C12  111.86  3.000
 3YC  H7   C14  S15  120.63  3.000
 3YC  H7   C14  C13  127.58  3.000
 3YC  S15  C14  C13  111.79  3.000
 3YC  C16  S15  C14   92.54  3.000
 3YC  C32  C16  S15  121.22  3.000
 3YC  S15  C16  C12  110.25  3.000
 3YC  C32  C16  C12  128.52  3.000
 3YC  H8   N19  C20  116.64  3.000
 3YC  H8   N19  C17  118.43  3.000
 3YC  C20  N19  C17  122.71  3.000
 3YC  H9   C20  C26  107.62  3.000
 3YC  H9   C20  C21  108.09  3.000
 3YC  C26  C20  C21  110.55  3.000
 3YC  H9   C20  N19  107.66  3.000
 3YC  C21  C20  N19  109.77  3.000
 3YC  C26  C20  N19  112.97  3.000
 3YC  H11  C21  H10  106.19  3.000
 3YC  H11  C21  C22  109.35  3.000
 3YC  H10  C21  C22  110.00  3.000
 3YC  H11  C21  C20  107.72  3.000
 3YC  H10  C21  C20  109.17  3.000
 3YC  C22  C21  C20  114.09  3.000
 3YC  H13  C22  H12  105.36  3.000
 3YC  H13  C22  C23  108.92  3.000
 3YC  H12  C22  C23  107.58  3.000
 3YC  H13  C22  C21  110.81  3.000
 3YC  H12  C22  C21  108.53  3.000
 3YC  C23  C22  C21  115.13  3.000
 3YC  O25  C23  O24  126.43  3.000
 3YC  O25  C23  C22  116.25  3.000
 3YC  O24  C23  C22  117.30  3.000
 3YC  O28  C26  O27  127.55  3.000
 3YC  O27  C26  C20  114.51  3.000
 3YC  O28  C26  C20  117.93  3.000
 3YC  H17  C29  H16  106.32  3.000
 3YC  H17  C29  C30  109.42  3.000
 3YC  H16  C29  C30  108.62  3.000
 3YC  H17  C29  C6   109.82  3.000
 3YC  H16  C29  C6   108.22  3.000
 3YC  C30  C29  C6   114.13  3.000
 3YC  H19  C30  H18  106.43  3.000
 3YC  H19  C30  C31  109.33  3.000
 3YC  H18  C30  C31  109.62  3.000
 3YC  H19  C30  C29  108.06  3.000
 3YC  H18  C30  C29  109.04  3.000
 3YC  C31  C30  C29  114.08  3.000
 3YC  H21  C31  H20  106.49  3.000
 3YC  H21  C31  C32  109.10  3.000
 3YC  H20  C31  C32  109.14  3.000
 3YC  H21  C31  C30  110.07  3.000
 3YC  H20  C31  C30  109.83  3.000
 3YC  C32  C31  C30  112.05  3.000
 3YC  H23  C32  H22  106.42  3.000
 3YC  H23  C32  C31  109.62  3.000
 3YC  H22  C32  C31  109.27  3.000
 3YC  H23  C32  C16  108.10  3.000
 3YC  H22  C32  C16  110.13  3.000
 3YC  C31  C32  C16  113.07  3.000
 3YC  N19  C17  O18  123.25  3.000
 3YC  O18  C17  C13  120.75  3.000
 3YC  N19  C17  C13  115.99  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_31  H8   N19  C17  C13     0.00   0.0  0
 3YC  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 3YC  Var_01    C30  C29  C6   N5     87.80  30.0  2
 3YC  Var_02    C31  C32  C16  C12  -107.52  30.0  2
 3YC  Var_03    N19  C17  C13  C12    12.43  30.0  2
 3YC  Var_04    C31  C30  C29  C6    -63.29  30.0  3
 3YC  Var_05    C30  C31  C32  C16  -179.50  30.0  1
 3YC  Var_06    C23  C22  C21  C20  -175.29  30.0  3
 3YC  Var_07    O24  C23  C22  C21    27.95  30.0  3
 3YC  Var_08    C32  C31  C30  C29  -175.93  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-5  C20  0.020
 3YC  plan-5  C26  0.020
 3YC  plan-5  O27  0.020
 3YC  plan-5  O28  0.020

