# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:22:39 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N~2~-{3-[4-(5-methylthiophen-2-yl)phenyl]propanoyl}-L-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(cc1)c2ccc(CCC(=O)N[C@@H](CCC(O)=O)C(N)=O)cc2
#
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
 E1S  E1S  N~2~-{3-[4-(5-methylthiophen-2-yl)phenyl]propanoyl}-L-alpha-glutamine  ligand  47  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E1S
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
 E1S  C1    C  CH2    0  -0.582  -1.0344  -0.8408   0.2640
 E1S  N1    N  NH1    0  -0.643  -3.3759  -0.3089   0.0352
 E1S  C2    C  C      0   0.576  -2.4836  -1.1776   0.5412
 E1S  O2    O  O      0  -0.498  -2.8281  -2.1709   1.1658
 E1S  C3    C  CH2    0  -0.450  -5.5593   0.6157  -0.5278
 E1S  C4    C  CH2    0  -0.586  -5.4245   1.8823   0.3022
 E1S  C5    C  C      0   0.417  -6.2238   3.0915  -0.2202
 E1S  O6    O  OC    -1  -0.629  -6.0891   4.1500   0.4275
 E1S  O7    O  O      0  -0.606  -6.9343   2.9255  -1.2303
 E1S  C13   C  C      0   0.519  -5.1149  -1.8320  -0.7402
 E1S  C14   C  CH2    0  -0.505  -0.0672  -1.4754   1.2599
 E1S  C15   C  C      0   0.111   1.3568  -1.1520   0.9057
 E1S  C16   C  C1     0  -0.288   1.9734   0.0004   1.3853
 E1S  C17   C  C1     0  -0.309   3.2741   0.3205   1.0299
 E1S  C18   C  C1     0  -0.287   2.0870  -1.9722   0.0483
 E1S  C19   C  CR5    0  -0.217   5.3771  -0.1843  -0.2199
 E1S  C20   C  CR15   0  -0.236   6.3608  -1.0335  -0.6428
 E1S  C21   C  CR15   0  -0.204   7.5804  -0.3736  -0.9470
 E1S  S23   S  S2     0   0.201   5.9662   1.4439  -0.2033
 E1S  C27   C  CR5    0  -0.168   7.5309   0.9751  -0.7566
 E1S  C30   C  C      0   0.134   4.0037  -0.4999   0.1665
 E1S  C31   C  C1     0  -0.310   3.3825  -1.6524  -0.3213
 E1S  C35   C  CH1    0  -0.179  -4.7911  -0.5706   0.0625
 E1S  H1    H  HCH2   0   0.281  -0.8037  -1.1913  -0.7476
 E1S  H1A   H  HCH2   0   0.266  -0.8996   0.2436   0.2438
 E1S  HN1   H  HNH1   0   0.401  -3.0418   0.4454  -0.5436
 E1S  H3    H  HCH2   0   0.244  -6.6120   0.3375  -0.5998
 E1S  H3A   H  HCH2   0   0.232  -5.2175   0.7857  -1.5528
 E1S  HN3   H  HNH2   0   0.401  -6.5187  -3.3197  -0.7935
 E1S  HN3A  H  HNH2   0   0.407  -6.6545  -2.2611   0.5535
 E1S  H4    H  HCH2   0   0.229  -5.7451   1.6784   1.3304
 E1S  H4A   H  HCH2   0   0.228  -4.3752   2.1823   0.3877
 E1S  H14   H  HCH2   0   0.251  -0.2891  -1.1147   2.2665
 E1S  H14A  H  HCH2   0   0.252  -0.2106  -2.5567   1.2721
 E1S  H16   H  H      0   0.251   1.4332   0.6560   2.0586
 E1S  H17   H  H      0   0.250   3.7254   1.2133   1.4466
 E1S  H18   H  H      0   0.251   1.6333  -2.8742  -0.3456
 E1S  H20   H  HCR5   0   0.261   6.2280  -2.1040  -0.7194
 E1S  H21   H  HCR5   0   0.261   8.4700  -0.8833  -1.2913
 E1S  H24   H  HCH3   0   0.254   8.3005   2.7839  -1.6294
 E1S  H24A  H  HCH3   0   0.255   8.9136   2.4438  -0.0172
 E1S  H24B  H  HCH3   0   0.256   9.4864   1.5028  -1.3925
 E1S  H31   H  H      0   0.252   3.9113  -2.3011  -1.0079
 E1S  H35   H  HCH1   0   0.262  -5.1121  -0.7115   1.1003
 E1S  C24   C  CH3    0  -0.715   8.6106   1.9822  -0.9582
 E1S  N3    N  NH2    0  -0.801  -6.1761  -2.5159  -0.2932
 E1S  O5    O  O      0  -0.489  -4.4812  -2.1401  -1.7366

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
 E1S  C2   C1    single    1.513  0.020  1.513
 E1S  C14  C1    single    1.526  0.020  1.526
 E1S  C1   H1    single    0.970  0.020  1.090
 E1S  C1   H1A   single    0.970  0.020  1.090
 E1S  C35  N1    single    1.440  0.020  1.440
 E1S  N1   C2    single    1.344  0.020  1.344
 E1S  N1   HN1   single    0.860  0.020  1.020
 E1S  C2   O2    double    1.223  0.020  1.223
 E1S  C3   C4    single    1.520  0.020  1.520
 E1S  C3   C35   single    1.532  0.020  1.532
 E1S  C3   H3    single    0.970  0.020  1.090
 E1S  C3   H3A   single    0.970  0.020  1.090
 E1S  C13  N3    single    1.339  0.020  1.339
 E1S  N3   HN3   single    0.860  0.020  1.020
 E1S  N3   HN3A  single    0.860  0.020  1.020
 E1S  C5   C4    single    1.541  0.020  1.541
 E1S  C4   H4    single    0.970  0.020  1.090
 E1S  C4   H4A   single    0.970  0.020  1.090
 E1S  O7   C5    deloc     1.246  0.020  1.246
 E1S  C5   O6    deloc     1.248  0.020  1.248
 E1S  O5   C13   double    1.220  0.020  1.220
 E1S  C13  C35   single    1.530  0.020  1.530
 E1S  C14  C15   single    1.503  0.020  1.503
 E1S  C14  H14   single    0.970  0.020  1.090
 E1S  C14  H14A  single    0.970  0.020  1.090
 E1S  C18  C15   aromatic  1.393  0.020  1.393
 E1S  C15  C16   aromatic  1.392  0.020  1.392
 E1S  C16  C17   aromatic  1.386  0.020  1.386
 E1S  C16  H16   single    0.930  0.020  1.080
 E1S  C30  C17   aromatic  1.397  0.020  1.397
 E1S  C17  H17   single    0.930  0.020  1.080
 E1S  C18  C31   aromatic  1.385  0.020  1.385
 E1S  C18  H18   single    0.930  0.020  1.080
 E1S  C20  C19   aromatic  1.367  0.020  1.367
 E1S  C30  C19   single    1.461  0.020  1.461
 E1S  C19  S23   aromatic  1.732  0.020  1.732
 E1S  C20  C21   aromatic  1.420  0.020  1.420
 E1S  C20  H20   single    0.930  0.020  1.080
 E1S  C21  C27   aromatic  1.363  0.020  1.363
 E1S  C21  H21   single    0.930  0.020  1.080
 E1S  C27  S23   aromatic  1.725  0.020  1.725
 E1S  C27  C24   single    1.490  0.020  1.490
 E1S  C24  H24   single    0.970  0.020  1.090
 E1S  C24  H24A  single    0.970  0.020  1.090
 E1S  C24  H24B  single    0.970  0.020  1.090
 E1S  C31  C30   aromatic  1.397  0.020  1.397
 E1S  C31  H31   single    0.930  0.020  1.080
 E1S  C35  H35   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
 E1S  H1A   C1   H1    105.93  3.000
 E1S  H1A   C1   C14   110.27  3.000
 E1S  H1    C1   C14   109.64  3.000
 E1S  H1A   C1   C2    110.01  3.000
 E1S  H1    C1   C2    107.44  3.000
 E1S  C14   C1   C2    113.25  3.000
 E1S  HN1   N1   C35   118.22  3.000
 E1S  HN1   N1   C2    118.67  3.000
 E1S  C35   N1   C2    121.87  3.000
 E1S  O2    C2   N1    122.02  3.000
 E1S  O2    C2   C1    122.96  3.000
 E1S  N1    C2   C1    115.02  3.000
 E1S  H3A   C3   H3    106.22  3.000
 E1S  H3A   C3   C35   108.96  3.000
 E1S  H3    C3   C35   108.17  3.000
 E1S  H3A   C3   C4    110.76  3.000
 E1S  H3    C3   C4    109.51  3.000
 E1S  C35   C3   C4    112.98  3.000
 E1S  H4A   C4   H4    104.96  3.000
 E1S  H4A   C4   C5    107.98  3.000
 E1S  H4    C4   C5    108.20  3.000
 E1S  H4A   C4   C3    110.85  3.000
 E1S  H4    C4   C3    109.34  3.000
 E1S  C5    C4   C3    115.00  3.000
 E1S  O7    C5   O6    126.52  3.000
 E1S  O6    C5   C4    115.70  3.000
 E1S  O7    C5   C4    117.78  3.000
 E1S  C35   C13  O5    121.78  3.000
 E1S  C35   C13  N3    114.43  3.000
 E1S  O5    C13  N3    123.71  3.000
 E1S  H14A  C14  H14   106.89  3.000
 E1S  H14A  C14  C15   109.91  3.000
 E1S  H14   C14  C15   109.80  3.000
 E1S  H14A  C14  C1    109.64  3.000
 E1S  H14   C14  C1    109.59  3.000
 E1S  C15   C14  C1    110.93  3.000
 E1S  C18   C15  C16   117.85  3.000
 E1S  C16   C15  C14   121.11  3.000
 E1S  C18   C15  C14   121.00  3.000
 E1S  H16   C16  C17   119.16  3.000
 E1S  H16   C16  C15   119.60  3.000
 E1S  C17   C16  C15   121.24  3.000
 E1S  H17   C17  C30   120.27  3.000
 E1S  H17   C17  C16   118.85  3.000
 E1S  C30   C17  C16   120.87  3.000
 E1S  H18   C18  C31   119.14  3.000
 E1S  H18   C18  C15   119.62  3.000
 E1S  C31   C18  C15   121.25  3.000
 E1S  C30   C19  S23   121.35  3.000
 E1S  S23   C19  C20   110.02  3.000
 E1S  C30   C19  C20   128.62  3.000
 E1S  H20   C20  C21   123.40  3.000
 E1S  H20   C20  C19   123.27  3.000
 E1S  C21   C20  C19   113.32  3.000
 E1S  H21   C21  C27   122.73  3.000
 E1S  H21   C21  C20   123.76  3.000
 E1S  C27   C21  C20   113.51  3.000
 E1S  C27   S23  C19    92.87  3.000
 E1S  C24   C27  S23   121.13  3.000
 E1S  C24   C27  C21   128.58  3.000
 E1S  S23   C27  C21   110.29  3.000
 E1S  C31   C30  C19   120.25  3.000
 E1S  C31   C30  C17   117.91  3.000
 E1S  C19   C30  C17   121.84  3.000
 E1S  H31   C31  C30   119.90  3.000
 E1S  H31   C31  C18   119.21  3.000
 E1S  C30   C31  C18   120.88  3.000
 E1S  H35   C35  C13   109.21  3.000
 E1S  H35   C35  C3    108.53  3.000
 E1S  C13   C35  C3    109.28  3.000
 E1S  H35   C35  N1    109.23  3.000
 E1S  C13   C35  N1    110.37  3.000
 E1S  C3    C35  N1    110.18  3.000
 E1S  H24B  C24  H24A  107.87  3.000
 E1S  H24B  C24  H24   107.87  3.000
 E1S  H24A  C24  H24   107.39  3.000
 E1S  H24B  C24  C27   109.82  3.000
 E1S  H24A  C24  C27   111.75  3.000
 E1S  H24   C24  C27   111.96  3.000
 E1S  HN3A  N3   HN3   117.32  3.000
 E1S  HN3A  N3   C13   121.92  3.000
 E1S  HN3   N3   C13   120.76  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
 E1S  CONST_01  C30   C31  C18  C15     0.00   0.0  0
 E1S  CONST_02  C30   C17  C16  C15     0.00   0.0  0
 E1S  CONST_03  C31   C18  C15  C16     0.00   0.0  0
 E1S  CONST_04  C19   C30  C17  C16   180.00   0.0  0
 E1S  CONST_05  C31   C30  C17  C16     0.00   0.0  0
 E1S  CONST_06  C18   C15  C16  C17     0.00   0.0  0
 E1S  CONST_09  C18   C31  C30  C17     0.00   0.0  0
 E1S  CONST_10  C19   C30  C31  C18   180.00   0.0  0
 E1S  CONST_11  C27   C21  C20  C19     0.00   0.0  0
 E1S  CONST_12  C21   C27  S23  C19     0.00   0.0  0
 E1S  CONST_14  C27   S23  C19  C20     0.00   0.0  0
 E1S  CONST_15  S23   C27  C21  C20     0.00   0.0  0
 E1S  CONST_16  C30   C19  C20  C21   180.00   0.0  0
 E1S  CONST_17  S23   C19  C20  C21     0.00   0.0  0
 E1S  CONST_19  C30   C19  S23  C27   180.00   0.0  0
 E1S  CONST_20  C31   C18  C15  C14   180.00   0.0  0
 E1S  CONST_21  C17   C16  C15  C14   180.00   0.0  0
 E1S  CONST_22  C24   C27  S23  C19   180.00   0.0  0
 E1S  CONST_23  C24   C27  C21  C20   180.00   0.0  0
 E1S  CONST_24  H31   C31  C18  C15   180.00   0.0  0
 E1S  CONST_25  H17   C17  C16  C15   180.00   0.0  0
 E1S  CONST_26  H18   C18  C15  C16   180.00   0.0  0
 E1S  CONST_27  H16   C16  C15  C18   180.00   0.0  0
 E1S  CONST_28  H21   C21  C20  C19   180.00   0.0  0
 E1S  CONST_29  H20   C20  C19  S23   180.00   0.0  0
 E1S  CONST_30  C35   N1   C2   C1    180.00   0.0  0
 E1S  CONST_31  C35   N1   C2   O2      0.00   0.0  0
 E1S  CONST_32  HN1   N1   C2   C1      0.00   0.0  0
 E1S  CONST_33  HN3   N3   C13  O5      0.00   0.0  0
 E1S  CONST_34  HN3A  N3   C13  O5    180.00   0.0  0
 E1S  Var_01    C18   C15  C14  C1    -89.38  30.0  2
 E1S  Var_02    H24   C24  C27  C21   125.26  30.0  2
 E1S  Var_03    C15   C14  C1   C2    177.79  30.0  2
 E1S  Var_04    C14   C1   C2   N1    157.27  30.0  3
 E1S  Var_05    O7    C5   C4   C3      2.31  30.0  2
 E1S  Var_06    C35   C3   C4   C5   -177.74  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
 E1S  chir_01  C35  N1  C3  C13  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
 E1S  plan-1  C19   0.020
 E1S  plan-1  C20   0.020
 E1S  plan-1  C21   0.020
 E1S  plan-1  S23   0.020
 E1S  plan-1  C27   0.020
 E1S  plan-1  C30   0.020
 E1S  plan-1  H20   0.020
 E1S  plan-1  H21   0.020
 E1S  plan-1  C24   0.020
 E1S  plan-2  C14   0.020
 E1S  plan-2  C15   0.020
 E1S  plan-2  C16   0.020
 E1S  plan-2  C17   0.020
 E1S  plan-2  C18   0.020
 E1S  plan-2  C19   0.020
 E1S  plan-2  C30   0.020
 E1S  plan-2  C31   0.020
 E1S  plan-2  H16   0.020
 E1S  plan-2  H17   0.020
 E1S  plan-2  H18   0.020
 E1S  plan-2  H31   0.020
 E1S  plan-3  C1    0.020
 E1S  plan-3  N1    0.020
 E1S  plan-3  C2    0.020
 E1S  plan-3  O2    0.020
 E1S  plan-3  C35   0.020
 E1S  plan-3  HN1   0.020
 E1S  plan-4  C13   0.020
 E1S  plan-4  C35   0.020
 E1S  plan-4  HN3   0.020
 E1S  plan-4  HN3A  0.020
 E1S  plan-4  N3    0.020
 E1S  plan-4  O5    0.020
 E1S  plan-5  C4    0.020
 E1S  plan-5  C5    0.020
 E1S  plan-5  O6    0.020
 E1S  plan-5  O7    0.020

