# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:41:36 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N-({(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}carbamoyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(/C=C/C(=O)NC(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)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
 4D1  4D1  N-({(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}carbamoyl)-beta-D-glucopyranosylamine  ligand  54  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4D1
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
 4D1  C14  C  CR16  0  -0.285   5.8827   0.7058  -1.1752
 4D1  C5   C  C     0   0.585   1.0010   0.4294  -1.3321
 4D1  C11  C  CR16  0  -0.304   6.1838  -0.5713   1.2514
 4D1  C7   C  C1    0  -0.448   2.2510   0.1062  -0.6171
 4D1  C8   C  C1    0  -0.213   3.4359   0.5037  -1.0960
 4D1  C9   C  CR6   0   0.128   4.7421   0.2669  -0.4967
 4D1  C10  C  CR16  0  -0.294   4.9169  -0.3775   0.7312
 4D1  C12  C  CR6   0   0.164   7.3230  -0.1351   0.5742
 4D1  C13  C  CR16  0  -0.298   7.1486   0.5061  -0.6513
 4D1  N1   N  NH1   0  -0.735  -2.2990  -0.5388  -0.2186
 4D1  C16  C  CH3   0  -0.645   9.5036  -1.3321   0.2827
 4D1  C15  C  CH1   0  -0.328   8.6976  -0.3665   1.1522
 4D1  C17  C  CH3   0  -0.645   9.4563   0.9445   1.3586
 4D1  O6   O  O     0  -0.436   0.9567   1.0599  -2.3669
 4D1  N4   N  NH1   0  -0.772  -0.1141  -0.0656  -0.6852
 4D1  C2   C  C     0   0.764  -1.4385   0.0766  -1.0792
 4D1  O3   O  O     0  -0.473  -1.7880   0.6594  -2.0807
 4D1  C1'  C  CH1   0   0.205  -3.7118  -0.3884  -0.3220
 4D1  O5'  O  O2    0  -0.487  -4.1024   0.7308   0.4385
 4D1  C5'  C  CH1   0  -0.015  -5.4820   1.0212   0.3461
 4D1  C6'  C  CH2   0  -0.156  -5.7363   2.3055   1.1055
 4D1  O6'  O  OH1   0  -0.670  -5.0432   3.3528   0.4701
 4D1  C4'  C  CH1   0   0.036  -6.2886  -0.1484   0.9125
 4D1  O4'  O  OH1   0  -0.672  -7.6549   0.1474   0.7678
 4D1  C3'  C  CH1   0  -0.006  -5.9186  -1.4263   0.1690
 4D1  O3'  O  OH1   0  -0.672  -6.6179  -2.4862   0.7753
 4D1  C2'  C  CH1   0  -0.027  -4.4127  -1.6472   0.1960
 4D1  O2'  O  OH1   0  -0.663  -4.1331  -2.7613  -0.6109
 4D1  H1   H  HCR6  0   0.258   5.7738   1.2117  -2.1273
 4D1  H2   H  HCR6  0   0.254   6.2924  -1.0731   2.2057
 4D1  H3   H  H     0   0.277   2.1771  -0.4618   0.3034
 4D1  H4   H  H     0   0.266   3.4449   1.0621  -2.0275
 4D1  H5   H  HCR6  0   0.255   4.0617  -0.7307   1.2937
 4D1  H6   H  HCR6  0   0.252   8.0088   0.8589  -1.2082
 4D1  H7   H  HNH1  0   0.407  -1.9451  -0.8869   0.6612
 4D1  H8   H  HCH3  0   0.222   9.7074  -0.9034  -0.7002
 4D1  H9   H  HCH3  0   0.233  10.4633  -1.5560   0.7507
 4D1  H10  H  HCH3  0   0.233   8.9744  -2.2740   0.1343
 4D1  H11  H  HCH1  0   0.243   8.5645  -0.8327   2.1332
 4D1  H12  H  HCH3  0   0.233   8.8953   1.6387   1.9851
 4D1  H13  H  HCH3  0   0.233  10.4158   0.7549   1.8423
 4D1  H14  H  HCH3  0   0.220   9.6627   1.4406   0.4085
 4D1  H15  H  HNH1  0   0.424   0.0621  -0.5825   0.1635
 4D1  H16  H  HCH1  0   0.236  -3.9735  -0.2435  -1.3776
 4D1  H17  H  HCH1  0   0.224  -5.7678   1.1649  -0.7091
 4D1  H18  H  HCH2  0   0.213  -6.8156   2.4877   1.1261
 4D1  H19  H  HCH2  0   0.197  -5.4119   2.1712   2.1469
 4D1  H20  H  HOH1  0   0.457  -5.2422   4.1674   0.9398
 4D1  H21  H  HCH1  0   0.213  -6.0190  -0.2715   1.9739
 4D1  H22  H  HOH1  0   0.455  -8.1608  -0.5998   1.1041
 4D1  H23  H  HCH1  0   0.219  -6.2268  -1.3042  -0.8820
 4D1  H24  H  HOH1  0   0.458  -6.5402  -3.2661   0.2170
 4D1  H25  H  HCH1  0   0.225  -4.1009  -1.8146   1.2393
 4D1  H26  H  HOH1  0   0.457  -3.2049  -2.9953  -0.5091

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
 4D1  O3'  C3'  single    1.407  0.020  1.407
 4D1  O4'  C4'  single    1.405  0.020  1.405
 4D1  C3'  C4'  single    1.524  0.020  1.524
 4D1  C3'  C2'  single    1.522  0.020  1.522
 4D1  C4'  C5'  single    1.529  0.020  1.529
 4D1  O2'  C2'  single    1.404  0.020  1.404
 4D1  C2'  C1'  single    1.531  0.020  1.531
 4D1  O6'  C6'  single    1.407  0.020  1.407
 4D1  C5'  C6'  single    1.514  0.020  1.514
 4D1  C5'  O5'  single    1.413  0.020  1.413
 4D1  C1'  O5'  single    1.408  0.020  1.408
 4D1  C1'  N1   single    1.425  0.020  1.425
 4D1  N1   C2   single    1.364  0.020  1.364
 4D1  C2   O3   double    1.210  0.020  1.210
 4D1  C2   N4   single    1.389  0.020  1.389
 4D1  N4   C5   single    1.381  0.020  1.381
 4D1  C5   O6   double    1.213  0.020  1.213
 4D1  C5   C7   single    1.476  0.020  1.476
 4D1  C7   C8   double    1.338  0.020  1.338
 4D1  C8   C9   single    1.456  0.020  1.456
 4D1  C14  C9   aromatic  1.398  0.020  1.398
 4D1  C14  C13  aromatic  1.384  0.020  1.384
 4D1  C9   C10  aromatic  1.398  0.020  1.398
 4D1  C13  C12  aromatic  1.394  0.020  1.394
 4D1  C10  C11  aromatic  1.383  0.020  1.383
 4D1  C12  C11  aromatic  1.395  0.020  1.395
 4D1  C12  C15  single    1.509  0.020  1.509
 4D1  C16  C15  single    1.529  0.020  1.529
 4D1  C15  C17  single    1.529  0.020  1.529
 4D1  C14  H1   single    0.930  0.020  1.080
 4D1  C11  H2   single    0.930  0.020  1.080
 4D1  C7   H3   single    0.930  0.020  1.080
 4D1  C8   H4   single    0.930  0.020  1.080
 4D1  C10  H5   single    0.930  0.020  1.080
 4D1  C13  H6   single    0.930  0.020  1.080
 4D1  N1   H7   single    0.860  0.020  1.020
 4D1  C16  H8   single    0.970  0.020  1.090
 4D1  C16  H9   single    0.970  0.020  1.090
 4D1  C16  H10  single    0.970  0.020  1.090
 4D1  C15  H11  single    0.970  0.020  1.090
 4D1  C17  H12  single    0.970  0.020  1.090
 4D1  C17  H13  single    0.970  0.020  1.090
 4D1  C17  H14  single    0.970  0.020  1.090
 4D1  N4   H15  single    0.860  0.020  1.020
 4D1  C1'  H16  single    0.970  0.020  1.090
 4D1  C5'  H17  single    0.970  0.020  1.090
 4D1  C6'  H18  single    0.970  0.020  1.090
 4D1  C6'  H19  single    0.970  0.020  1.090
 4D1  O6'  H20  single    0.850  0.020  0.980
 4D1  C4'  H21  single    0.970  0.020  1.090
 4D1  O4'  H22  single    0.850  0.020  0.980
 4D1  C3'  H23  single    0.970  0.020  1.090
 4D1  O3'  H24  single    0.850  0.020  0.980
 4D1  C2'  H25  single    0.970  0.020  1.090
 4D1  O2'  H26  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
 4D1  H1   C14  C13  119.46  3.000
 4D1  H1   C14  C9   119.40  3.000
 4D1  C13  C14  C9   121.14  3.000
 4D1  N4   C5   O6   123.83  3.000
 4D1  O6   C5   C7   123.93  3.000
 4D1  N4   C5   C7   112.24  3.000
 4D1  H2   C11  C12  119.37  3.000
 4D1  H2   C11  C10  119.20  3.000
 4D1  C12  C11  C10  121.44  3.000
 4D1  H3   C7   C8   121.31  3.000
 4D1  H3   C7   C5   117.93  3.000
 4D1  C8   C7   C5   120.76  3.000
 4D1  H4   C8   C9   115.41  3.000
 4D1  H4   C8   C7   117.83  3.000
 4D1  C9   C8   C7   126.76  3.000
 4D1  C10  C9   C8   123.27  3.000
 4D1  C10  C9   C14  117.97  3.000
 4D1  C8   C9   C14  118.75  3.000
 4D1  H5   C10  C9   120.53  3.000
 4D1  H5   C10  C11  118.84  3.000
 4D1  C9   C10  C11  120.63  3.000
 4D1  C15  C12  C13  121.41  3.000
 4D1  C15  C12  C11  120.66  3.000
 4D1  C13  C12  C11  117.92  3.000
 4D1  H6   C13  C12  120.14  3.000
 4D1  H6   C13  C14  118.97  3.000
 4D1  C12  C13  C14  120.89  3.000
 4D1  H7   N1   C1'  116.55  3.000
 4D1  H7   N1   C2   118.95  3.000
 4D1  C1'  N1   C2   122.16  3.000
 4D1  H10  C16  H9   107.94  3.000
 4D1  H10  C16  H8   107.90  3.000
 4D1  H9   C16  H8   107.62  3.000
 4D1  H10  C16  C15  111.53  3.000
 4D1  H9   C16  C15  110.45  3.000
 4D1  H8   C16  C15  111.25  3.000
 4D1  H11  C15  C17  107.74  3.000
 4D1  H11  C15  C16  107.75  3.000
 4D1  C17  C15  C16  110.90  3.000
 4D1  H11  C15  C12  107.33  3.000
 4D1  C17  C15  C12  111.86  3.000
 4D1  C16  C15  C12  111.05  3.000
 4D1  H14  C17  H13  107.38  3.000
 4D1  H14  C17  H12  107.94  3.000
 4D1  H13  C17  H12  107.96  3.000
 4D1  H14  C17  C15  111.48  3.000
 4D1  H13  C17  C15  110.32  3.000
 4D1  H12  C17  C15  111.60  3.000
 4D1  H15  N4   C2   117.23  3.000
 4D1  H15  N4   C5   115.88  3.000
 4D1  C2   N4   C5   126.89  3.000
 4D1  O3   C2   N4   124.01  3.000
 4D1  N4   C2   N1   112.11  3.000
 4D1  O3   C2   N1   123.87  3.000
 4D1  H16  C1'  C2'  108.96  3.000
 4D1  H16  C1'  O5'  110.39  3.000
 4D1  C2'  C1'  O5'  110.10  3.000
 4D1  H16  C1'  N1   108.68  3.000
 4D1  O5'  C1'  N1   108.65  3.000
 4D1  C2'  C1'  N1   110.04  3.000
 4D1  C5'  O5'  C1'  113.51  3.000
 4D1  H17  C5'  C4'  108.51  3.000
 4D1  H17  C5'  C6'  109.03  3.000
 4D1  C4'  C5'  C6'  111.99  3.000
 4D1  H17  C5'  O5'  110.03  3.000
 4D1  C6'  C5'  O5'  107.79  3.000
 4D1  C4'  C5'  O5'  109.49  3.000
 4D1  H19  C6'  H18  107.07  3.000
 4D1  H19  C6'  O6'  111.93  3.000
 4D1  H18  C6'  O6'  111.73  3.000
 4D1  H19  C6'  C5'  108.79  3.000
 4D1  H18  C6'  C5'  108.43  3.000
 4D1  O6'  C6'  C5'  108.79  3.000
 4D1  H20  O6'  C6'  107.94  3.000
 4D1  H21  C4'  C3'  108.47  3.000
 4D1  H21  C4'  O4'  111.13  3.000
 4D1  C3'  C4'  O4'  111.24  3.000
 4D1  H21  C4'  C5'  108.25  3.000
 4D1  C3'  C4'  C5'  109.42  3.000
 4D1  O4'  C4'  C5'  108.28  3.000
 4D1  H22  O4'  C4'  108.15  3.000
 4D1  H23  C3'  C2'  108.04  3.000
 4D1  H23  C3'  O3'  110.81  3.000
 4D1  C2'  C3'  O3'  112.00  3.000
 4D1  H23  C3'  C4'  107.72  3.000
 4D1  C2'  C3'  C4'  110.68  3.000
 4D1  O3'  C3'  C4'  107.51  3.000
 4D1  H24  O3'  C3'  108.69  3.000
 4D1  H25  C2'  O2'  111.55  3.000
 4D1  H25  C2'  C3'  108.59  3.000
 4D1  O2'  C2'  C3'  107.58  3.000
 4D1  H25  C2'  C1'  108.41  3.000
 4D1  O2'  C2'  C1'  111.52  3.000
 4D1  C3'  C2'  C1'  109.12  3.000
 4D1  H26  O2'  C2'  108.92  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
 4D1  CONST_01  C11  C10  C9   C14    0.00   0.0  0
 4D1  CONST_02  C11  C12  C13  C14    0.00   0.0  0
 4D1  CONST_03  C12  C13  C14  C9     0.00   0.0  0
 4D1  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 4D1  CONST_05  C13  C14  C9   C10    0.00   0.0  0
 4D1  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 4D1  CONST_07  C15  C12  C13  C14  180.00   0.0  0
 4D1  CONST_08  C8   C9   C10  C11  180.00   0.0  0
 4D1  CONST_09  C13  C14  C9   C8   180.00   0.0  0
 4D1  CONST_10  C15  C12  C11  C10  180.00   0.0  0
 4D1  CONST_11  H5   C10  C9   C14  180.00   0.0  0
 4D1  CONST_12  H6   C13  C12  C11  180.00   0.0  0
 4D1  CONST_13  H2   C11  C10  C9   180.00   0.0  0
 4D1  CONST_14  H1   C14  C9   C10  180.00   0.0  0
 4D1  CONST_15  C1'  N1   C2   O3     0.00   0.0  0
 4D1  CONST_16  C1'  N1   C2   N4   180.00   0.0  0
 4D1  CONST_17  O3   C2   N4   C5     0.00   0.0  0
 4D1  CONST_18  C2   N4   C5   C7   180.00   0.0  0
 4D1  CONST_19  C2   N4   C5   O6     0.00   0.0  0
 4D1  CONST_20  N1   C2   N4   C5   180.00   0.0  0
 4D1  CONST_21  H15  N4   C5   C7     0.00   0.0  0
 4D1  CONST_22  H7   N1   C2   O3   180.00   0.0  0
 4D1  Var_01    C7   C8   C9   C14  177.05  30.0  2
 4D1  Var_02    C16  C15  C12  C11  113.94  30.0  2
 4D1  Var_03    C9   C8   C7   C5   179.54   0.0  2
 4D1  Var_04    H8   C16  C15  C12   65.17  30.0  3
 4D1  Var_05    H12  C17  C15  C12   55.94  30.0  3
 4D1  Var_06    N4   C5   C7   C8   179.94  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
 4D1  chir_01  C1'  C2'  O5'  N1   negativ
 4D1  chir_02  C5'  O5'  C6'  C4'  positiv
 4D1  chir_03  C4'  O4'  C5'  C3'  positiv
 4D1  chir_04  C3'  O3'  C4'  C2'  negativ
 4D1  chir_05  C2'  O2'  C3'  C1'  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
 4D1  plan-1  C14  0.020
 4D1  plan-1  C11  0.020
 4D1  plan-1  C8   0.020
 4D1  plan-1  C9   0.020
 4D1  plan-1  C10  0.020
 4D1  plan-1  C12  0.020
 4D1  plan-1  C13  0.020
 4D1  plan-1  C15  0.020
 4D1  plan-1  H1   0.020
 4D1  plan-1  H2   0.020
 4D1  plan-1  H5   0.020
 4D1  plan-1  H6   0.020
 4D1  plan-2  C5   0.020
 4D1  plan-2  C7   0.020
 4D1  plan-2  N1   0.020
 4D1  plan-2  O6   0.020
 4D1  plan-2  N4   0.020
 4D1  plan-2  C2   0.020
 4D1  plan-2  O3   0.020
 4D1  plan-2  C1'  0.020
 4D1  plan-2  H7   0.020
 4D1  plan-2  H15  0.020
 4D1  plan-3  C5   0.020
 4D1  plan-3  C7   0.020
 4D1  plan-3  C8   0.020
 4D1  plan-3  C9   0.020
 4D1  plan-3  H3   0.020
 4D1  plan-3  H4   0.020

