# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:24:49 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  55  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  -0.507   -8.1074  -1.2206  -1.1398
 3YB  C2   C  CR6   0   0.669   -9.3600  -0.9376  -0.9075
 3YB  N3   N  NR16  0  -0.720   -9.7664  -0.1671   0.1433
 3YB  C4   C  CR6   0   0.496   -8.9281   0.4064   1.1055
 3YB  N5   N  NR15  0  -0.704   -5.9135  -0.8499  -0.2650
 3YB  C6   C  CR5   0   0.374   -5.3376  -0.1853   0.8037
 3YB  C7   C  CR15  0  -0.468   -6.3343   0.4118   1.5188
 3YB  C8   C  CR56  0  -0.186   -7.5625   0.0973   0.8629
 3YB  C9   C  CR56  0   0.476   -7.2538  -0.6919  -0.2417
 3YB  O10  O  O     0  -0.488   -9.4052   1.0774   2.0110
 3YB  N11  N  NH2   0  -0.835  -10.3281  -1.4481  -1.6947
 3YB  C12  C  CR15  0  -0.220    1.4497   0.2384  -0.8425
 3YB  C13  C  CR5   0  -0.317    2.7667   0.4366  -0.5415
 3YB  S14  S  S2    0   0.239    3.0439   2.0577  -0.0253
 3YB  C15  C  CR15  0  -0.538    1.3889   2.4463  -0.1995
 3YB  C16  C  CR5   0   0.227    0.6435   1.3915  -0.6440
 3YB  O18  O  O     0  -0.473    3.6406  -1.6104  -1.2954
 3YB  N19  N  NH1   0  -0.665    5.0038  -0.3029  -0.0620
 3YB  C20  C  CH1   0  -0.198    6.0860  -1.2480  -0.0928
 3YB  C21  C  CH2   0  -0.463    7.4038  -0.5670   0.2878
 3YB  C22  C  CH2   0  -0.577    7.7749   0.5145  -0.7138
 3YB  C23  C  C     0   0.554    9.1002   1.1581  -0.4138
 3YB  O24  O  OH1   0  -0.595    9.4374   2.0433  -1.3453
 3YB  O25  O  O     0  -0.442    9.7873   0.9175   0.5473
 3YB  C26  C  C     0   0.551    5.7997  -2.4206   0.8361
 3YB  O27  O  O     0  -0.429    4.9550  -2.4205   1.6922
 3YB  O28  O  OH1   0  -0.590    6.6152  -3.4356   0.5941
 3YB  C29  C  CH2   0  -0.520   -3.8626  -0.1800   1.0026
 3YB  C30  C  CH2   0  -0.421   -3.1068   0.6454  -0.0418
 3YB  C31  C  CH2   0  -0.420   -1.6004   0.6050   0.1751
 3YB  C32  C  CH2   0  -0.506   -0.8373   1.4263  -0.8642
 3YB  H1   H  HNR6  0   0.419  -10.7566   0.0009   0.2637
 3YB  H2   H  HNR5  0   0.406   -5.4138  -1.3885  -0.9553
 3YB  H3   H  HCR5  0   0.249   -6.2005   1.0074   2.4083
 3YB  H4   H  HNH2  0   0.406  -10.0326  -1.8629  -2.5625
 3YB  H5   H  HNH2  0   0.408  -11.2403  -1.0237  -1.7088
 3YB  H6   H  HCR5  0   0.269    1.0650  -0.7093  -1.1942
 3YB  H7   H  HCR5  0   0.300    1.0458   3.4450   0.0269
 3YB  H8   H  HNH1  0   0.406    5.0383   0.4058   0.6557
 3YB  H9   H  HCH1  0   0.298    6.1799  -1.6418  -1.1083
 3YB  H10  H  HCH2  0   0.260    7.3240  -0.1500   1.2950
 3YB  H11  H  HCH2  0   0.275    8.1892  -1.3221   0.3207
 3YB  H12  H  HCH2  0   0.287    7.8135   0.0999  -1.7257
 3YB  H13  H  HCH2  0   0.288    7.0189   1.3042  -0.7494
 3YB  H14  H  HOH1  0   0.480   10.2944   2.4396  -1.1294
 3YB  H15  H  HOH1  0   0.487    6.4429  -4.1617   1.2127
 3YB  H16  H  HCH2  0   0.250   -3.6526   0.2139   1.9990
 3YB  H17  H  HCH2  0   0.243   -3.4850  -1.2079   0.9917
 3YB  H18  H  HCH2  0   0.223   -3.3395   0.2777  -1.0461
 3YB  H19  H  HCH2  0   0.228   -3.4587   1.6806  -0.0036
 3YB  H20  H  HCH2  0   0.228   -1.3607   0.9782   1.1753
 3YB  H21  H  HCH2  0   0.226   -1.2564  -0.4338   0.1444
 3YB  H22  H  HCH2  0   0.244   -1.1841   2.4619  -0.8404
 3YB  H23  H  HCH2  0   0.244   -1.0659   1.0446  -1.8637
 3YB  C17  C  C     0   0.569    3.8250  -0.5823  -0.6623

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  double    1.206  0.020  1.206
 3YB  C23  O24  single    1.328  0.020  1.328
 3YB  C23  C22  single    1.503  0.020  1.503
 3YB  C22  C21  single    1.520  0.020  1.520
 3YB  C21  C20  single    1.531  0.020  1.531
 3YB  O18  C17  double    1.221  0.020  1.221
 3YB  C20  N19  single    1.437  0.020  1.437
 3YB  C20  C26  single    1.523  0.020  1.523
 3YB  C17  N19  single    1.352  0.020  1.352
 3YB  C17  C13  single    1.474  0.020  1.474
 3YB  C13  S14  aromatic  1.724  0.020  1.724
 3YB  C13  C12  aromatic  1.365  0.020  1.365
 3YB  S14  C15  aromatic  1.709  0.020  1.709
 3YB  O27  C26  double    1.203  0.020  1.203
 3YB  C26  O28  single    1.324  0.020  1.324
 3YB  C12  C16  aromatic  1.421  0.020  1.421
 3YB  C15  C16  aromatic  1.366  0.020  1.366
 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    1.348  0.020  1.348
 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  O24  H14  single    0.850  0.020  0.980
 3YB  O28  H15  single    0.850  0.020  0.980
 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   116.71  3.000
 3YB  N11  C2   N1   120.21  3.000
 3YB  N3   C2   N1   123.04  3.000
 3YB  H1   N3   C4   115.89  3.000
 3YB  H1   N3   C2   118.48  3.000
 3YB  C4   N3   C2   125.62  3.000
 3YB  O10  C4   C8   128.34  3.000
 3YB  O10  C4   N3   119.99  3.000
 3YB  C8   C4   N3   111.67  3.000
 3YB  H2   N5   C9   124.51  3.000
 3YB  H2   N5   C6   125.38  3.000
 3YB  C9   N5   C6   110.10  3.000
 3YB  C29  C6   C7   130.72  3.000
 3YB  C7   C6   N5   108.12  3.000
 3YB  C29  C6   N5   121.15  3.000
 3YB  H3   C7   C8   127.39  3.000
 3YB  H3   C7   C6   125.67  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   107.48  3.000
 3YB  C8   C9   N1   127.65  3.000
 3YB  N5   C9   N1   124.87  3.000
 3YB  H5   N11  H4   115.34  3.000
 3YB  H5   N11  C2   119.97  3.000
 3YB  H4   N11  C2   116.67  3.000
 3YB  H6   C12  C16  123.69  3.000
 3YB  H6   C12  C13  122.82  3.000
 3YB  C16  C12  C13  113.49  3.000
 3YB  C17  C13  S14  124.00  3.000
 3YB  S14  C13  C12  110.96  3.000
 3YB  C17  C13  C12  125.03  3.000
 3YB  C15  S14  C13   91.58  3.000
 3YB  H7   C15  C16  127.51  3.000
 3YB  H7   C15  S14  119.77  3.000
 3YB  C16  C15  S14  112.71  3.000
 3YB  C32  C16  C15  124.72  3.000
 3YB  C32  C16  C12  124.01  3.000
 3YB  C15  C16  C12  111.26  3.000
 3YB  H8   N19  C20  116.82  3.000
 3YB  H8   N19  C17  119.39  3.000
 3YB  C20  N19  C17  120.74  3.000
 3YB  H9   C20  C26  107.77  3.000
 3YB  H9   C20  C21  108.49  3.000
 3YB  C26  C20  C21  110.64  3.000
 3YB  H9   C20  N19  108.76  3.000
 3YB  C26  C20  N19  110.59  3.000
 3YB  C21  C20  N19  110.50  3.000
 3YB  H11  C21  H10  106.81  3.000
 3YB  H11  C21  C22  109.68  3.000
 3YB  H10  C21  C22  110.71  3.000
 3YB  H11  C21  C20  108.63  3.000
 3YB  H10  C21  C20  109.62  3.000
 3YB  C22  C21  C20  111.26  3.000
 3YB  H13  C22  H12  105.54  3.000
 3YB  H13  C22  C23  107.86  3.000
 3YB  H12  C22  C23  108.40  3.000
 3YB  H13  C22  C21  111.49  3.000
 3YB  H12  C22  C21  110.39  3.000
 3YB  C23  C22  C21  112.84  3.000
 3YB  O25  C23  O24  123.18  3.000
 3YB  O24  C23  C22  111.65  3.000
 3YB  O25  C23  C22  125.17  3.000
 3YB  H14  O24  C23  109.93  3.000
 3YB  O28  C26  O27  124.24  3.000
 3YB  O28  C26  C20  111.28  3.000
 3YB  O27  C26  C20  124.47  3.000
 3YB  H15  O28  C26  110.36  3.000
 3YB  H17  C29  H16  106.34  3.000
 3YB  H17  C29  C30  109.21  3.000
 3YB  H16  C29  C30  109.46  3.000
 3YB  H17  C29  C6   109.69  3.000
 3YB  H16  C29  C6   108.29  3.000
 3YB  C30  C29  C6   113.58  3.000
 3YB  H19  C30  H18  106.36  3.000
 3YB  H19  C30  C31  109.78  3.000
 3YB  H18  C30  C31  109.40  3.000
 3YB  H19  C30  C29  109.12  3.000
 3YB  H18  C30  C29  109.87  3.000
 3YB  C31  C30  C29  112.15  3.000
 3YB  H21  C31  H20  106.29  3.000
 3YB  H21  C31  C32  109.50  3.000
 3YB  H20  C31  C32  109.20  3.000
 3YB  H21  C31  C30  109.40  3.000
 3YB  H20  C31  C30  109.75  3.000
 3YB  C32  C31  C30  112.51  3.000
 3YB  H23  C32  H22  106.52  3.000
 3YB  H23  C32  C31  109.23  3.000
 3YB  H22  C32  C31  109.64  3.000
 3YB  H23  C32  C16  109.44  3.000
 3YB  H22  C32  C16  109.43  3.000
 3YB  C31  C32  C16  112.41  3.000
 3YB  N19  C17  O18  122.39  3.000
 3YB  N19  C17  C13  116.53  3.000
 3YB  O18  C17  C13  121.06  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  CONST_33  H15  O28  C26  C20   180.00   0.0  0
 3YB  CONST_34  H14  O24  C23  C22   180.00   0.0  0
 3YB  Var_01    C30  C29  C6   N5     69.91  30.0  1
 3YB  Var_02    O18  C17  C13  C12    14.75  30.0  2
 3YB  Var_03    C31  C32  C16  C12    69.29  30.0  2
 3YB  Var_04    C31  C30  C29  C6   -178.82  30.0  1
 3YB  Var_05    C30  C31  C32  C16   179.66  30.0  3
 3YB  Var_06    C23  C22  C21  C20  -177.00  30.0  1
 3YB  Var_07    O25  C23  C22  C21    -3.76  30.0  1
 3YB  Var_08    C32  C31  C30  C29   179.97  30.0  2

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-4  H14  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
 3YB  plan-5  H15  0.020

