# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:38:40 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CNC(=O)CCC\C=C/NC(=O)c1ccc(Cc2ccc(I)cc2)cc1
#
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
 ICX  ICX  'methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate'  ligand  55  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ICX
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
 ICX  C5    C  CR16  0  -0.207    6.6681   1.1628   1.4772
 ICX  C4    C  CR16  0  -0.307    5.4961   1.2962   2.2107
 ICX  C3    C  CR6   0   0.160    4.4543   0.3848   2.0772
 ICX  C7    C  CH2   0  -0.628    3.1642   0.5629   2.8383
 ICX  C8    C  CR6   0   0.160    2.1361   1.2613   1.9859
 ICX  C9    C  CR16  0  -0.289    2.1184   2.6507   1.8851
 ICX  C10   C  CR16  0  -0.247    1.2119   3.2910   1.0588
 ICX  C11   C  CR6   0  -0.062    0.2841   2.5578   0.3202
 ICX  C12   C  CR16  0  -0.279    0.3013   1.1679   0.4166
 ICX  C13   C  CR16  0  -0.298    1.2167   0.5313   1.2396
 ICX  C23   C  C     0   0.547   -0.6564   3.3047  -0.5631
 ICX  O24   O  O     0  -0.473   -0.4113   4.4392  -0.9413
 ICX  N25   N  NH1   0  -0.688   -1.7943   2.6509  -0.9074
 ICX  C26   C  C1    0  -0.014   -2.7589   3.1753  -1.7618
 ICX  C27   C  C1    0  -0.303   -3.8939   2.5643  -2.1006
 ICX  C28   C  CH2   0  -0.488   -4.3814   1.2260  -1.6433
 ICX  C29   C  CH2   0  -0.414   -5.7853   1.3006  -1.0444
 ICX  C30   C  CH2   0  -0.580   -6.2852  -0.0725  -0.6176
 ICX  C31   C  C     0   0.572   -7.6488  -0.0340   0.0351
 ICX  O32   O  O     0  -0.502   -8.0152   0.8910   0.7473
 ICX  N33   N  NH1   0  -0.650   -8.4232  -1.1068  -0.1955
 ICX  C34   C  CH2   0  -0.370   -9.7116  -1.2601   0.4201
 ICX  C35   C  C     0   0.565  -10.2791  -2.6243   0.1156
 ICX  O36   O  O     0  -0.444   -9.7308  -3.4604  -0.5565
 ICX  O37   O  O2    0  -0.447  -11.4591  -2.7764   0.6845
 ICX  C38   C  CH3   0  -0.424  -12.1357  -4.0210   0.4878
 ICX  C2    C  CR16  0  -0.293    4.6109  -0.6755   1.1892
 ICX  C1    C  CR16  0  -0.207    5.7733  -0.8271   0.4471
 ICX  C6    C  CR6   0  -0.236    6.7953   0.0996   0.5965
 ICX  I1    I  I     0   0.048    8.5637  -0.1165  -0.5237
 ICX  H5    H  HCR6  0   0.279    7.4635   1.8845   1.6053
 ICX  H4    H  HCR6  0   0.261    5.4044   2.1255   2.9017
 ICX  H7    H  HCH2  0   0.280    2.7825  -0.4105   3.1504
 ICX  H7A   H  HCH2  0   0.280    3.3493   1.1401   3.7458
 ICX  H9    H  HCR6  0   0.255    2.8234   3.2417   2.4576
 ICX  H10   H  HCR6  0   0.261    1.2194   4.3708   0.9927
 ICX  H12   H  HCR6  0   0.256   -0.3767   0.5531  -0.1621
 ICX  H13   H  HCR6  0   0.258    1.2142  -0.5505   1.2957
 ICX  HN25  H  HNH1  0   0.416   -1.9793   1.7532  -0.4898
 ICX  H26   H  H     0   0.276   -2.5184   4.1505  -2.1599
 ICX  H27   H  H     0   0.249   -4.5402   3.1017  -2.7852
 ICX  H28   H  HCH2  0   0.245   -4.3930   0.5391  -2.4969
 ICX  H28A  H  HCH2  0   0.228   -3.7072   0.7742  -0.9097
 ICX  H29   H  HCH2  0   0.236   -5.7799   1.9769  -0.1881
 ICX  H29A  H  HCH2  0   0.233   -6.4692   1.7319  -1.7812
 ICX  H30   H  HCH2  0   0.254   -6.2872  -0.7556  -1.4704
 ICX  H30A  H  HCH2  0   0.271   -5.5914  -0.5036   0.1128
 ICX  HN33  H  HNH1  0   0.404   -8.0914  -1.8460  -0.7953
 ICX  H34   H  HCH2  0   0.287   -9.6471  -1.1436   1.5059
 ICX  H34A  H  HCH2  0   0.287  -10.4205  -0.5025   0.0702
 ICX  H38   H  HCH3  0   0.244  -11.5626  -4.8510   0.8994
 ICX  H38A  H  HCH3  0   0.257  -13.0776  -3.9331   1.0201
 ICX  H38B  H  HCH3  0   0.244  -12.3308  -4.2028  -0.5683
 ICX  H2    H  HCR6  0   0.260    3.8171  -1.4033   1.0692
 ICX  H1    H  HCR6  0   0.279    5.8684  -1.6619  -0.2340

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
 ICX  C4   C5    aromatic  1.389  0.020  1.389
 ICX  C5   C6    aromatic  1.386  0.020  1.386
 ICX  C5   H5    single    0.930  0.020  1.080
 ICX  C4   C3    aromatic  1.391  0.020  1.391
 ICX  C4   H4    single    0.930  0.020  1.080
 ICX  C7   C3    single    1.508  0.020  1.508
 ICX  C3   C2    aromatic  1.392  0.020  1.392
 ICX  C7   C8    single    1.507  0.020  1.507
 ICX  C7   H7    single    0.970  0.020  1.090
 ICX  C7   H7A   single    0.970  0.020  1.090
 ICX  C9   C8    aromatic  1.393  0.020  1.393
 ICX  C8   C13   aromatic  1.391  0.020  1.391
 ICX  C9   C10   aromatic  1.384  0.020  1.384
 ICX  C9   H9    single    0.930  0.020  1.080
 ICX  C10  C11   aromatic  1.394  0.020  1.394
 ICX  C10  H10   single    0.930  0.020  1.080
 ICX  C11  C23   single    1.491  0.020  1.491
 ICX  C11  C12   aromatic  1.393  0.020  1.393
 ICX  C13  C12   aromatic  1.386  0.020  1.386
 ICX  C12  H12   single    0.930  0.020  1.080
 ICX  C13  H13   single    0.930  0.020  1.080
 ICX  N25  C23   single    1.357  0.020  1.357
 ICX  C23  O24   double    1.221  0.020  1.221
 ICX  N25  C26   single    1.391  0.020  1.391
 ICX  N25  HN25  single    0.860  0.020  1.020
 ICX  C27  C26   double    1.333  0.020  1.333
 ICX  C26  H26   single    0.930  0.020  1.080
 ICX  C28  C27   single    1.496  0.020  1.496
 ICX  C27  H27   single    0.930  0.020  1.080
 ICX  C28  C29   single    1.528  0.020  1.528
 ICX  C28  H28   single    0.970  0.020  1.090
 ICX  C28  H28A  single    0.970  0.020  1.090
 ICX  C30  C29   single    1.522  0.020  1.522
 ICX  C29  H29   single    0.970  0.020  1.090
 ICX  C29  H29A  single    0.970  0.020  1.090
 ICX  C30  C31   single    1.512  0.020  1.512
 ICX  C30  H30   single    0.970  0.020  1.090
 ICX  C30  H30A  single    0.970  0.020  1.090
 ICX  N33  C31   single    1.343  0.020  1.343
 ICX  C31  O32   double    1.224  0.020  1.224
 ICX  N33  C34   single    1.436  0.020  1.436
 ICX  N33  HN33  single    0.860  0.020  1.020
 ICX  C35  C34   single    1.509  0.020  1.509
 ICX  C34  H34   single    0.970  0.020  1.090
 ICX  C34  H34A  single    0.970  0.020  1.090
 ICX  O36  C35   double    1.205  0.020  1.205
 ICX  C35  O37   single    1.319  0.020  1.319
 ICX  C38  O37   single    1.430  0.020  1.430
 ICX  C38  H38   single    0.970  0.020  1.090
 ICX  C38  H38A  single    0.970  0.020  1.090
 ICX  C38  H38B  single    0.970  0.020  1.090
 ICX  C2   C1    aromatic  1.387  0.020  1.387
 ICX  C2   H2    single    0.930  0.020  1.080
 ICX  C6   C1    aromatic  1.388  0.020  1.388
 ICX  C1   H1    single    0.930  0.020  1.080
 ICX  C6   I1    single    2.104  0.020  2.104

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
 ICX  H5    C5   C6    121.29  3.000
 ICX  H5    C5   C4    119.60  3.000
 ICX  C6    C5   C4    119.11  3.000
 ICX  H4    C4   C3    119.97  3.000
 ICX  H4    C4   C5    118.80  3.000
 ICX  C3    C4   C5    121.23  3.000
 ICX  C2    C3   C7    120.54  3.000
 ICX  C2    C3   C4    118.44  3.000
 ICX  C7    C3   C4    120.99  3.000
 ICX  H7A   C7   H7    107.05  3.000
 ICX  H7A   C7   C8    109.93  3.000
 ICX  H7    C7   C8    109.66  3.000
 ICX  H7A   C7   C3    109.70  3.000
 ICX  H7    C7   C3    109.77  3.000
 ICX  C8    C7   C3    110.66  3.000
 ICX  C13   C8   C9    118.43  3.000
 ICX  C13   C8   C7    120.74  3.000
 ICX  C9    C8   C7    120.78  3.000
 ICX  H9    C9   C10   119.30  3.000
 ICX  H9    C9   C8    119.83  3.000
 ICX  C10   C9   C8    120.87  3.000
 ICX  H10   C10  C11   119.81  3.000
 ICX  H10   C10  C9    119.60  3.000
 ICX  C11   C10  C9    120.59  3.000
 ICX  C23   C11  C12   123.27  3.000
 ICX  C12   C11  C10   118.67  3.000
 ICX  C23   C11  C10   118.04  3.000
 ICX  H12   C12  C13   118.04  3.000
 ICX  H12   C12  C11   121.45  3.000
 ICX  C13   C12  C11   120.49  3.000
 ICX  H13   C13  C12   119.21  3.000
 ICX  H13   C13  C8    119.86  3.000
 ICX  C12   C13  C8    120.93  3.000
 ICX  N25   C23  O24   122.52  3.000
 ICX  O24   C23  C11   121.50  3.000
 ICX  N25   C23  C11   115.98  3.000
 ICX  HN25  N25  C26   117.60  3.000
 ICX  HN25  N25  C23   118.57  3.000
 ICX  C26   N25  C23   123.76  3.000
 ICX  H26   C26  C27   120.64  3.000
 ICX  H26   C26  N25   114.34  3.000
 ICX  C27   C26  N25   125.02  3.000
 ICX  H27   C27  C28   116.25  3.000
 ICX  H27   C27  C26   116.17  3.000
 ICX  C28   C27  C26   127.58  3.000
 ICX  H28A  C28  H28   105.67  3.000
 ICX  H28A  C28  C29   108.88  3.000
 ICX  H28   C28  C29   109.03  3.000
 ICX  H28A  C28  C27   111.94  3.000
 ICX  H28   C28  C27   109.03  3.000
 ICX  C29   C28  C27   112.05  3.000
 ICX  H29A  C29  H29   106.70  3.000
 ICX  H29A  C29  C30   109.83  3.000
 ICX  H29   C29  C30   109.91  3.000
 ICX  H29A  C29  C28   109.25  3.000
 ICX  H29   C29  C28   109.47  3.000
 ICX  C30   C29  C28   111.56  3.000
 ICX  H30A  C30  H30   105.99  3.000
 ICX  H30A  C30  C31   107.05  3.000
 ICX  H30   C30  C31   110.56  3.000
 ICX  H30A  C30  C29   109.50  3.000
 ICX  H30   C30  C29   110.22  3.000
 ICX  C31   C30  C29   113.21  3.000
 ICX  N33   C31  O32   122.09  3.000
 ICX  O32   C31  C30   122.71  3.000
 ICX  N33   C31  C30   115.18  3.000
 ICX  HN33  N33  C34   118.17  3.000
 ICX  HN33  N33  C31   119.87  3.000
 ICX  C34   N33  C31   121.93  3.000
 ICX  H34A  C34  H34   106.36  3.000
 ICX  H34A  C34  C35   108.52  3.000
 ICX  H34   C34  C35   108.59  3.000
 ICX  H34A  C34  N33   111.72  3.000
 ICX  H34   C34  N33   111.18  3.000
 ICX  C35   C34  N33   110.33  3.000
 ICX  O37   C35  O36   124.60  3.000
 ICX  O37   C35  C34   110.72  3.000
 ICX  O36   C35  C34   124.68  3.000
 ICX  C38   O37  C35   117.67  3.000
 ICX  H38B  C38  H38A  109.48  3.000
 ICX  H38B  C38  H38   109.48  3.000
 ICX  H38A  C38  H38   109.45  3.000
 ICX  H38B  C38  O37   111.30  3.000
 ICX  H38A  C38  O37   105.82  3.000
 ICX  H38   C38  O37   111.24  3.000
 ICX  H2    C2   C1    118.76  3.000
 ICX  H2    C2   C3    119.98  3.000
 ICX  C1    C2   C3    121.25  3.000
 ICX  H1    C1   C6    121.23  3.000
 ICX  H1    C1   C2    119.66  3.000
 ICX  C6    C1   C2    119.11  3.000
 ICX  I1    C6   C1    119.54  3.000
 ICX  I1    C6   C5    119.60  3.000
 ICX  C1    C6   C5    120.86  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
 ICX  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 ICX  CONST_02  C2    C1   C6   C5      0.00   0.0  0
 ICX  CONST_03  C1    C6   C5   C4      0.00   0.0  0
 ICX  CONST_04  C1    C2   C3   C4      0.00   0.0  0
 ICX  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 ICX  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 ICX  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 ICX  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 ICX  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 ICX  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 ICX  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 ICX  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 ICX  CONST_13  C7    C3   C4   C5    180.00   0.0  0
 ICX  CONST_14  I1    C6   C5   C4    180.00   0.0  0
 ICX  CONST_15  C1    C2   C3   C7    180.00   0.0  0
 ICX  CONST_16  C10   C9   C8   C7    180.00   0.0  0
 ICX  CONST_17  C12   C13  C8   C7    180.00   0.0  0
 ICX  CONST_18  C23   C11  C10  C9    180.00   0.0  0
 ICX  CONST_19  C23   C11  C12  C13   180.00   0.0  0
 ICX  CONST_20  I1    C6   C1   C2    180.00   0.0  0
 ICX  CONST_21  H1    C1   C6   C5    180.00   0.0  0
 ICX  CONST_22  H2    C2   C3   C4    180.00   0.0  0
 ICX  CONST_23  H5    C5   C4   C3    180.00   0.0  0
 ICX  CONST_24  H10   C10  C9   C8    180.00   0.0  0
 ICX  CONST_25  H12   C12  C13  C8    180.00   0.0  0
 ICX  CONST_26  H13   C13  C8   C9    180.00   0.0  0
 ICX  CONST_27  H9    C9   C10  C11   180.00   0.0  0
 ICX  CONST_28  H4    C4   C3   C2    180.00   0.0  0
 ICX  CONST_29  C26   N25  C23  C11   180.00   0.0  0
 ICX  CONST_30  HN25  N25  C23  C11     0.00   0.0  0
 ICX  CONST_31  C26   N25  C23  O24     0.00   0.0  0
 ICX  CONST_32  C34   N33  C31  C30   180.00   0.0  0
 ICX  CONST_33  C34   N33  C31  O32     0.00   0.0  0
 ICX  CONST_34  HN33  N33  C31  C30     0.00   0.0  0
 ICX  Var_01    C8    C7   C3   C4     95.73  30.0  2
 ICX  Var_02    C9    C8   C7   C3    -83.68  30.0  2
 ICX  Var_03    N25   C23  C11  C10  -158.86  30.0  2
 ICX  Var_04    C28   C27  C26  N25     0.72   0.0  2
 ICX  Var_05    C27   C26  N25  C23  -178.93  30.0  2
 ICX  Var_06    C29   C28  C27  C26   125.96  30.0  2
 ICX  Var_07    C30   C29  C28  C27   178.45  30.0  3
 ICX  Var_08    C31   C30  C29  C28   177.54  30.0  1
 ICX  Var_09    N33   C31  C30  C29   146.55  30.0  3
 ICX  Var_10    C35   C34  N33  C31  -173.15  30.0  3
 ICX  Var_11    O36   C35  C34  N33    -0.48  30.0  1
 ICX  Var_12    H38   C38  O37  C35    61.96  30.0  3

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
 ICX  plan-1  C5    0.020
 ICX  plan-1  C4    0.020
 ICX  plan-1  C3    0.020
 ICX  plan-1  C7    0.020
 ICX  plan-1  C2    0.020
 ICX  plan-1  C1    0.020
 ICX  plan-1  C6    0.020
 ICX  plan-1  I1    0.020
 ICX  plan-1  H5    0.020
 ICX  plan-1  H4    0.020
 ICX  plan-1  H2    0.020
 ICX  plan-1  H1    0.020
 ICX  plan-2  C34   0.020
 ICX  plan-2  C35   0.020
 ICX  plan-2  O36   0.020
 ICX  plan-2  O37   0.020
 ICX  plan-3  C7    0.020
 ICX  plan-3  C8    0.020
 ICX  plan-3  C9    0.020
 ICX  plan-3  C10   0.020
 ICX  plan-3  C11   0.020
 ICX  plan-3  C12   0.020
 ICX  plan-3  C13   0.020
 ICX  plan-3  C23   0.020
 ICX  plan-3  H9    0.020
 ICX  plan-3  H10   0.020
 ICX  plan-3  H12   0.020
 ICX  plan-3  H13   0.020
 ICX  plan-4  C11   0.020
 ICX  plan-4  C23   0.020
 ICX  plan-4  O24   0.020
 ICX  plan-4  N25   0.020
 ICX  plan-4  C26   0.020
 ICX  plan-4  HN25  0.020
 ICX  plan-5  C30   0.020
 ICX  plan-5  C31   0.020
 ICX  plan-5  O32   0.020
 ICX  plan-5  N33   0.020
 ICX  plan-5  C34   0.020
 ICX  plan-5  HN33  0.020
 ICX  plan-6  N25   0.020
 ICX  plan-6  C26   0.020
 ICX  plan-6  C27   0.020
 ICX  plan-6  C28   0.020
 ICX  plan-6  H26   0.020
 ICX  plan-6  H27   0.020

