# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:58:51 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-({[(2R)-2-{[hydroxy(hydroxymethyl)amino]methyl}heptanoyl]amino}methyl)-7-methoxy-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](CN(O)CO)C(=O)NCNC(=O)c1oc2c(OC)cccc2c1
#
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
 E7D  E7D  N-({[(2R)-2-{[hydroxy(hydroxymethyl)amino]methyl}heptanoyl]amino}methyl)-7-methoxy-1-benzofuran-2-carboxamide  ligand  58  29  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E7D
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
 E7D  C01  C  CH3   0  -0.662   8.4250  -2.7889   0.5641
 E7D  C02  C  CH2   0  -0.420   7.1583  -2.3900  -0.1804
 E7D  C03  C  CH2   0  -0.406   6.2426  -1.4976   0.6475
 E7D  C04  C  CH2   0  -0.421   4.9722  -1.0863  -0.0862
 E7D  C05  C  CH2   0  -0.404   4.0935  -0.1595   0.7446
 E7D  C06  C  CH1   0  -0.405   2.8559   0.3376   0.0008
 E7D  C07  C  CH2   0  -0.257   2.0877   1.4029   0.7904
 E7D  N08  N  NT    0  -0.223   2.8839   2.5905   1.0284
 E7D  O09  O  OH1   0  -0.581   3.0498   3.2510  -0.2070
 E7D  C10  C  CH2   0  -0.025   2.2107   3.5480   1.9051
 E7D  O11  O  OH1   0  -0.666   2.1556   3.0736   3.2146
 E7D  C12  C  C     0   0.571   1.8879  -0.7996  -0.2652
 E7D  O13  O  O     0  -0.490   1.4618  -1.5112   0.6333
 E7D  N14  N  NH1   0  -0.632   1.5000  -0.9560  -1.5452
 E7D  C15  C  CH2   0  -0.177   0.4702  -1.8926  -1.9131
 E7D  N16  N  NH1   0  -0.649  -0.8483  -1.4889  -1.4896
 E7D  C17  C  C     0   0.493  -1.5222  -0.5176  -2.1301
 E7D  O18  O  O     0  -0.472  -1.1351   0.0078  -3.1630
 E7D  C19  C  CR5   0   0.250  -2.7989  -0.0944  -1.5272
 E7D  C20  C  CR15  0  -0.359  -3.6855   0.8260  -1.9692
 E7D  C21  C  CR56  0   0.059  -4.7362   0.8635  -0.9969
 E7D  C22  C  CR16  0  -0.355  -5.9279   1.5848  -0.8500
 E7D  C23  C  CR16  0  -0.254  -6.6847   1.3295   0.2721
 E7D  C24  C  CR16  0  -0.407  -6.2977   0.3880   1.2424
 E7D  C25  C  CR6   0   0.295  -5.1237  -0.3381   1.1112
 E7D  O26  O  O2    0  -0.462  -4.6510  -1.2579   1.9625
 E7D  C27  C  CH3   0  -0.438  -5.4030  -1.5221   3.1335
 E7D  C28  C  CR56  0   0.327  -4.3677  -0.0677  -0.0308
 E7D  O29  O  O     0  -0.460  -3.1951  -0.6513  -0.3522
 E7D  H1   H  HCH3  0   0.226   9.0723  -3.4156  -0.0504
 E7D  H2   H  HCH3  0   0.215   9.0005  -1.9097   0.8612
 E7D  H3   H  HCH3  0   0.216   8.1892  -3.3468   1.4723
 E7D  H4   H  HCH2  0   0.211   7.4245  -1.8717  -1.1068
 E7D  H5   H  HCH2  0   0.211   6.6129  -3.2892  -0.4834
 E7D  H6   H  HCH2  0   0.209   5.9750  -2.0140   1.5759
 E7D  H7   H  HCH2  0   0.208   6.7908  -0.5983   0.9509
 E7D  H8   H  HCH2  0   0.212   5.2386  -0.5866  -1.0242
 E7D  H9   H  HCH2  0   0.219   3.7859  -0.6640   1.6652
 E7D  H10  H  HCH1  0   0.254   3.1694   0.7719  -0.9538
 E7D  H11  H  HCH2  0   0.224   1.1468   1.6522   0.2734
 E7D  H12  H  HCH2  0   0.236   1.8185   0.9842   1.7625
 E7D  H13  H  HOH1  0   0.466   4.0042   3.2953  -0.3248
 E7D  H14  H  HCH2  0   0.230   2.8154   4.4558   1.9009
 E7D  H15  H  HNH1  0   0.407   1.8188  -0.3018  -2.2411
 E7D  H16  H  HCH2  0   0.279   0.4923  -2.0059  -2.9936
 E7D  H17  H  HCH2  0   0.278   0.6734  -2.8636  -1.4685
 E7D  H18  H  HNH1  0   0.411  -1.1719  -1.8265  -0.5973
 E7D  H19  H  HCR5  0   0.278  -3.6060   1.4102  -2.8715
 E7D  H20  H  HCR6  0   0.259  -6.2403   2.3111  -1.5875
 E7D  H21  H  HCR6  0   0.264  -7.6126   1.8645   0.4253
 E7D  H22  H  HCR6  0   0.290  -6.9408   0.2422   2.0997
 E7D  H23  H  HCH3  0   0.263  -4.8563  -2.2824   3.6849
 E7D  H24  H  HCH3  0   0.234  -5.5021  -0.6319   3.7591
 E7D  H25  H  HCH3  0   0.233  -6.3995  -1.9031   2.8973
 E7D  H26  H  HCH2  0   0.215   4.4159  -1.9864  -0.3703
 E7D  H27  H  HCH2  0   0.232   4.6784   0.7097   1.0547
 E7D  H28  H  HCH2  0   0.194   1.2080   3.7994   1.5248
 E7D  H29  H  HOH1  0   0.460   1.3418   2.5781   3.3401

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
 E7D  C23  C24  aromatic  1.406  0.020  1.406
 E7D  C23  C22  aromatic  1.377  0.020  1.377
 E7D  C24  C25  aromatic  1.387  0.020  1.387
 E7D  C22  C21  aromatic  1.401  0.020  1.401
 E7D  C25  O26  single    1.339  0.020  1.339
 E7D  C25  C28  aromatic  1.396  0.020  1.396
 E7D  C21  C28  aromatic  1.392  0.020  1.392
 E7D  C21  C20  aromatic  1.432  0.020  1.432
 E7D  O26  C27  single    1.417  0.020  1.417
 E7D  C28  O29  aromatic  1.349  0.020  1.349
 E7D  C01  C02  single    1.522  0.020  1.522
 E7D  C20  C19  aromatic  1.352  0.020  1.352
 E7D  O29  C19  aromatic  1.359  0.020  1.359
 E7D  C02  C03  single    1.523  0.020  1.523
 E7D  C19  C17  single    1.474  0.020  1.474
 E7D  C03  C04  single    1.524  0.020  1.524
 E7D  C17  O18  double    1.222  0.020  1.222
 E7D  C17  N16  single    1.345  0.020  1.345
 E7D  C04  C05  single    1.524  0.020  1.524
 E7D  N16  C15  single    1.443  0.020  1.443
 E7D  C05  C06  single    1.527  0.020  1.527
 E7D  C15  N14  single    1.440  0.020  1.440
 E7D  O13  C12  double    1.223  0.020  1.223
 E7D  N14  C12  single    1.347  0.020  1.347
 E7D  C12  C06  single    1.517  0.020  1.517
 E7D  C06  C07  single    1.532  0.020  1.532
 E7D  C07  N08  single    1.449  0.020  1.449
 E7D  N08  C10  single    1.462  0.020  1.462
 E7D  N08  O09  single    1.411  0.020  1.411
 E7D  C10  O11  single    1.394  0.020  1.394
 E7D  C01  H1   single    0.970  0.020  1.090
 E7D  C01  H2   single    0.970  0.020  1.090
 E7D  C01  H3   single    0.970  0.020  1.090
 E7D  C02  H4   single    0.970  0.020  1.090
 E7D  C02  H5   single    0.970  0.020  1.090
 E7D  C03  H6   single    0.970  0.020  1.090
 E7D  C03  H7   single    0.970  0.020  1.090
 E7D  C04  H8   single    0.970  0.020  1.090
 E7D  C05  H9   single    0.970  0.020  1.090
 E7D  C06  H10  single    0.970  0.020  1.090
 E7D  C07  H11  single    0.970  0.020  1.090
 E7D  C07  H12  single    0.970  0.020  1.090
 E7D  O09  H13  single    0.850  0.020  0.980
 E7D  C10  H14  single    0.970  0.020  1.090
 E7D  N14  H15  single    0.860  0.020  1.020
 E7D  C15  H16  single    0.970  0.020  1.090
 E7D  C15  H17  single    0.970  0.020  1.090
 E7D  N16  H18  single    0.860  0.020  1.020
 E7D  C20  H19  single    0.930  0.020  1.080
 E7D  C22  H20  single    0.930  0.020  1.080
 E7D  C23  H21  single    0.930  0.020  1.080
 E7D  C24  H22  single    0.930  0.020  1.080
 E7D  C27  H23  single    0.970  0.020  1.090
 E7D  C27  H24  single    0.970  0.020  1.090
 E7D  C27  H25  single    0.970  0.020  1.090
 E7D  C04  H26  single    0.970  0.020  1.090
 E7D  C05  H27  single    0.970  0.020  1.090
 E7D  C10  H28  single    0.970  0.020  1.090
 E7D  O11  H29  single    0.850  0.020  0.980

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
 E7D  H3   C01  H2   107.40  3.000
 E7D  H3   C01  H1   107.65  3.000
 E7D  H2   C01  H1   107.65  3.000
 E7D  H3   C01  C02  111.16  3.000
 E7D  H2   C01  C02  111.14  3.000
 E7D  H1   C01  C02  111.64  3.000
 E7D  H5   C02  H4   106.02  3.000
 E7D  H5   C02  C03  109.40  3.000
 E7D  H4   C02  C03  109.20  3.000
 E7D  H5   C02  C01  109.56  3.000
 E7D  H4   C02  C01  109.61  3.000
 E7D  C03  C02  C01  112.82  3.000
 E7D  H7   C03  H6   105.93  3.000
 E7D  H7   C03  C04  109.20  3.000
 E7D  H6   C03  C04  109.37  3.000
 E7D  H7   C03  C02  109.30  3.000
 E7D  H6   C03  C02  109.35  3.000
 E7D  C04  C03  C02  113.43  3.000
 E7D  H26  C04  H8   106.03  3.000
 E7D  H26  C04  C05  110.38  3.000
 E7D  H8   C04  C05  109.24  3.000
 E7D  H26  C04  C03  109.06  3.000
 E7D  H8   C04  C03  109.43  3.000
 E7D  C05  C04  C03  112.49  3.000
 E7D  H27  C05  H9   106.17  3.000
 E7D  H27  C05  C06  108.25  3.000
 E7D  H9   C05  C06  109.40  3.000
 E7D  H27  C05  C04  109.27  3.000
 E7D  H9   C05  C04  109.91  3.000
 E7D  C06  C05  C04  113.57  3.000
 E7D  H10  C06  C12  109.10  3.000
 E7D  H10  C06  C07  108.49  3.000
 E7D  C12  C06  C07  106.96  3.000
 E7D  H10  C06  C05  108.77  3.000
 E7D  C07  C06  C05  112.44  3.000
 E7D  C12  C06  C05  111.01  3.000
 E7D  H12  C07  H11  107.08  3.000
 E7D  H12  C07  N08  107.66  3.000
 E7D  H11  C07  N08  111.14  3.000
 E7D  H12  C07  C06  108.41  3.000
 E7D  H11  C07  C06  110.09  3.000
 E7D  N08  C07  C06  112.26  3.000
 E7D  C10  N08  O09  105.82  3.000
 E7D  O09  N08  C07  107.72  3.000
 E7D  C10  N08  C07  112.46  3.000
 E7D  H13  O09  N08  104.20  3.000
 E7D  H28  C10  H14  108.26  3.000
 E7D  H28  C10  O11  111.47  3.000
 E7D  H14  C10  O11  107.99  3.000
 E7D  H28  C10  N08  111.19  3.000
 E7D  H14  C10  N08  106.70  3.000
 E7D  O11  C10  N08  111.01  3.000
 E7D  H29  O11  C10  109.37  3.000
 E7D  N14  C12  O13  122.04  3.000
 E7D  N14  C12  C06  115.95  3.000
 E7D  O13  C12  C06  121.99  3.000
 E7D  H15  N14  C15  118.20  3.000
 E7D  H15  N14  C12  119.36  3.000
 E7D  C15  N14  C12  121.63  3.000
 E7D  H17  C15  H16  108.04  3.000
 E7D  H17  C15  N16  107.51  3.000
 E7D  H16  C15  N16  109.86  3.000
 E7D  H17  C15  N14  110.05  3.000
 E7D  H16  C15  N14  107.90  3.000
 E7D  N16  C15  N14  113.37  3.000
 E7D  H18  N16  C17  120.20  3.000
 E7D  H18  N16  C15  117.38  3.000
 E7D  C17  N16  C15  121.36  3.000
 E7D  C19  C17  O18  119.78  3.000
 E7D  O18  C17  N16  123.68  3.000
 E7D  C19  C17  N16  116.53  3.000
 E7D  O29  C19  C20  111.73  3.000
 E7D  O29  C19  C17  119.24  3.000
 E7D  C20  C19  C17  129.02  3.000
 E7D  H19  C20  C21  127.47  3.000
 E7D  H19  C20  C19  126.45  3.000
 E7D  C21  C20  C19  106.08  3.000
 E7D  C28  C21  C22  119.81  3.000
 E7D  C28  C21  C20  105.05  3.000
 E7D  C22  C21  C20  135.15  3.000
 E7D  H20  C22  C23  121.43  3.000
 E7D  H20  C22  C21  121.34  3.000
 E7D  C23  C22  C21  117.22  3.000
 E7D  H21  C23  C24  117.99  3.000
 E7D  H21  C23  C22  119.66  3.000
 E7D  C24  C23  C22  122.34  3.000
 E7D  H22  C24  C25  120.52  3.000
 E7D  H22  C24  C23  118.26  3.000
 E7D  C25  C24  C23  121.22  3.000
 E7D  C28  C25  O26  117.50  3.000
 E7D  C28  C25  C24  115.75  3.000
 E7D  O26  C25  C24  126.75  3.000
 E7D  C27  O26  C25  117.78  3.000
 E7D  H25  C27  H24  108.97  3.000
 E7D  H25  C27  H23  108.94  3.000
 E7D  H24  C27  H23  108.97  3.000
 E7D  H25  C27  O26  111.75  3.000
 E7D  H24  C27  O26  111.69  3.000
 E7D  H23  C27  O26  106.43  3.000
 E7D  O29  C28  C25  125.59  3.000
 E7D  O29  C28  C21  110.75  3.000
 E7D  C25  C28  C21  123.65  3.000
 E7D  C28  O29  C19  106.39  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
 E7D  CONST_01  C22  C21  C20  C19   180.00   0.0  0
 E7D  CONST_02  C28  C21  C20  C19     0.00   0.0  0
 E7D  CONST_03  C25  C28  O29  C19   180.00   0.0  0
 E7D  CONST_04  C21  C28  O29  C19     0.00   0.0  0
 E7D  CONST_05  C23  C22  C21  C20   180.00   0.0  0
 E7D  CONST_06  C25  C28  C21  C20   180.00   0.0  0
 E7D  CONST_07  O29  C28  C21  C20     0.00   0.0  0
 E7D  CONST_08  C28  O29  C19  C20     0.00   0.0  0
 E7D  CONST_09  C24  C23  C22  C21     0.00   0.0  0
 E7D  CONST_10  C24  C25  C28  C21     0.00   0.0  0
 E7D  CONST_11  O29  C19  C20  C21     0.00   0.0  0
 E7D  CONST_12  C25  C24  C23  C22     0.00   0.0  0
 E7D  CONST_13  C25  C28  C21  C22     0.00   0.0  0
 E7D  CONST_14  O29  C28  C21  C22   180.00   0.0  0
 E7D  CONST_15  C28  C25  C24  C23     0.00   0.0  0
 E7D  CONST_16  C28  C21  C22  C23     0.00   0.0  0
 E7D  CONST_17  O29  C28  C25  C24   180.00   0.0  0
 E7D  CONST_18  C21  C20  C19  C17   180.00   0.0  0
 E7D  CONST_19  C28  O29  C19  C17   180.00   0.0  0
 E7D  CONST_20  O26  C25  C28  C21   180.00   0.0  0
 E7D  CONST_21  O26  C25  C24  C23   180.00   0.0  0
 E7D  CONST_22  O29  C28  C25  O26     0.00   0.0  0
 E7D  CONST_23  H20  C22  C21  C20     0.00   0.0  0
 E7D  CONST_24  H21  C23  C22  C21   180.00   0.0  0
 E7D  CONST_25  H22  C24  C23  C22   180.00   0.0  0
 E7D  CONST_26  H19  C20  C21  C22     0.00   0.0  0
 E7D  CONST_27  C19  C17  N16  C15   180.00   0.0  0
 E7D  CONST_28  H18  N16  C17  C19     0.00   0.0  0
 E7D  CONST_29  C15  N14  C12  C06   180.00   0.0  0
 E7D  CONST_30  C15  N14  C12  O13     0.00   0.0  0
 E7D  CONST_31  O18  C17  N16  C15     0.00   0.0  0
 E7D  CONST_32  H15  N14  C12  C06     0.00   0.0  0
 E7D  Var_01    C20  C19  C17  N16  -178.31  30.0  2
 E7D  Var_02    C28  C25  O26  C27   179.05  30.0  1
 E7D  Var_03    H23  C27  O26  C25  -179.72  30.0  3
 E7D  Var_04    C04  C03  C02  C01   179.82  30.0  3
 E7D  Var_05    C05  C04  C03  C02  -178.21  30.0  3
 E7D  Var_06    C06  C05  C04  C03   176.41  30.0  3
 E7D  Var_07    C10  N08  C07  C06  -173.68  30.0  3
 E7D  Var_08    O11  C10  N08  C07    70.83  30.0  3
 E7D  Var_09    N16  C15  N14  C12    70.85  30.0  2
 E7D  Var_10    C17  N16  C15  N14    75.50  30.0  2
 E7D  Var_11    H1   C01  C02  C03  -179.22  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
 E7D  chir_01  C06  C05  C12  C07  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
 E7D  plan-1  C17  0.020
 E7D  plan-1  C19  0.020
 E7D  plan-1  C20  0.020
 E7D  plan-1  C21  0.020
 E7D  plan-1  C22  0.020
 E7D  plan-1  C23  0.020
 E7D  plan-1  C24  0.020
 E7D  plan-1  C25  0.020
 E7D  plan-1  O26  0.020
 E7D  plan-1  C28  0.020
 E7D  plan-1  O29  0.020
 E7D  plan-1  H19  0.020
 E7D  plan-1  H20  0.020
 E7D  plan-1  H21  0.020
 E7D  plan-1  H22  0.020
 E7D  plan-2  C06  0.020
 E7D  plan-2  C12  0.020
 E7D  plan-2  O13  0.020
 E7D  plan-2  N14  0.020
 E7D  plan-2  C15  0.020
 E7D  plan-2  H15  0.020
 E7D  plan-3  C15  0.020
 E7D  plan-3  N16  0.020
 E7D  plan-3  C17  0.020
 E7D  plan-3  O18  0.020
 E7D  plan-3  C19  0.020
 E7D  plan-3  H18  0.020

