# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:49:55 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC/C(C)=C/CN[C@@H](CCC(O)=O)C(O)=O
#
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
 R1V  R1V  'N-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-L-glutamic acid'  ligand  43  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R1V
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
 R1V  C01  C  CH3    0  -0.705   7.1669   1.0238  -1.0558
 R1V  C02  C  C      0   0.075   5.7049   1.0155  -0.7126
 R1V  C03  C  C1     0  -0.250   5.2220   0.1919   0.2212
 R1V  C04  C  CH2    0  -0.491   3.8082   0.0513   0.6906
 R1V  C05  C  CH2    0  -0.482   3.2461  -1.3500   0.4031
 R1V  C06  C  C      0   0.110   1.8638  -1.5578   0.9652
 R1V  C07  C  C1     0  -0.298   0.8125  -1.6630   0.1487
 R1V  C08  C  CH2    0  -0.312  -0.6307  -1.8444   0.5086
 R1V  C10  C  CH1    0  -0.186  -2.8520  -0.9116   0.2083
 R1V  C11  C  C      0   0.393  -3.5455  -2.1303  -0.4467
 R1V  C14  C  CH2    0  -0.418  -3.5861   0.3633  -0.2233
 R1V  C15  C  CH2    0  -0.575  -3.0867   1.6120   0.4835
 R1V  C16  C  C      0   0.407  -3.7502   2.9359   0.0729
 R1V  C19  C  CH3    0  -0.733   1.7912  -1.6293   2.4629
 R1V  C20  C  CH3    0  -0.720   4.8837   1.9994  -1.4927
 R1V  N09  N  NH1    0  -0.586  -1.4352  -0.7891  -0.0897
 R1V  O12  O  O      0  -0.614  -3.0525  -2.5601  -1.5106
 R1V  O13  O  OC    -1  -0.621  -4.5745  -2.5578   0.1170
 R1V  O17  O  O      0  -0.613  -4.5520   2.9210  -0.8828
 R1V  O18  O  OC    -1  -0.638  -3.4210   3.9423   0.7386
 R1V  H1   H  HCH3   0   0.230   7.6053   2.0090  -0.8750
 R1V  H2   H  HCH3   0   0.235   7.7304   0.2927  -0.4767
 R1V  H3   H  HCH3   0   0.230   7.3219   0.8066  -2.1158
 R1V  H4   H  H      0   0.220   5.9281  -0.4751   0.7125
 R1V  H5   H  HCH2   0   0.234   3.7788   0.2385   1.7689
 R1V  H6   H  HCH2   0   0.237   3.1545   0.7953   0.2321
 R1V  H7   H  HCH2   0   0.235   3.2401  -1.5095  -0.6781
 R1V  H8   H  HCH2   0   0.225   3.9275  -2.0965   0.8275
 R1V  H9   H  H      0   0.221   1.0043  -1.6114  -0.9220
 R1V  H10  H  HCH2   0   0.194  -0.9543  -2.8487   0.1926
 R1V  H11  H  HCH2   0   0.220  -0.7687  -1.8065   1.5914
 R1V  H12  H  HCH1   0   0.195  -2.9525  -1.0057   1.2972
 R1V  H13  H  HCH2   0   0.198  -3.4831   0.4798  -1.3072
 R1V  H14  H  HCH2   0   0.207  -4.6543   0.2304  -0.0346
 R1V  H15  H  HCH2   0   0.207  -3.2059   1.4911   1.5667
 R1V  H16  H  HCH2   0   0.223  -2.0069   1.7020   0.3298
 R1V  H17  H  HCH3   0   0.239   2.1158  -0.6929   2.9224
 R1V  H18  H  HCH3   0   0.244   0.7943  -1.8487   2.8384
 R1V  H19  H  HCH3   0   0.235   2.4641  -2.4049   2.8372
 R1V  H20  H  HCH3   0   0.233   5.0121   1.8394  -2.5662
 R1V  H21  H  HCH3   0   0.240   3.8191   1.9498  -1.2739
 R1V  H22  H  HCH3   0   0.234   5.2160   3.0213  -1.2922
 R1V  H23  H  HNH1   0   0.320  -1.3363  -0.8564  -1.0980

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
 R1V  O17  C16  deloc   1.248  0.020  1.248
 R1V  O18  C16  deloc   1.251  0.020  1.251
 R1V  C16  C15  single  1.537  0.020  1.537
 R1V  C14  C15  single  1.519  0.020  1.519
 R1V  C14  C10  single  1.533  0.020  1.533
 R1V  O12  C11  deloc   1.249  0.020  1.249
 R1V  C11  O13  deloc   1.249  0.020  1.249
 R1V  C11  C10  single  1.548  0.020  1.548
 R1V  C10  N09  single  1.453  0.020  1.453
 R1V  N09  C08  single  1.456  0.020  1.456
 R1V  C08  C07  single  1.498  0.020  1.498
 R1V  C07  C06  double  1.335  0.020  1.335
 R1V  C06  C19  single  1.501  0.020  1.501
 R1V  C06  C05  single  1.507  0.020  1.507
 R1V  C05  C04  single  1.537  0.020  1.537
 R1V  C04  C03  single  1.496  0.020  1.496
 R1V  C01  C02  single  1.502  0.020  1.502
 R1V  C03  C02  double  1.335  0.020  1.335
 R1V  C02  C20  single  1.500  0.020  1.500
 R1V  C01  H1   single  0.970  0.020  1.090
 R1V  C01  H2   single  0.970  0.020  1.090
 R1V  C01  H3   single  0.970  0.020  1.090
 R1V  C03  H4   single  0.930  0.020  1.080
 R1V  C04  H5   single  0.970  0.020  1.090
 R1V  C04  H6   single  0.970  0.020  1.090
 R1V  C05  H7   single  0.970  0.020  1.090
 R1V  C05  H8   single  0.970  0.020  1.090
 R1V  C07  H9   single  0.930  0.020  1.080
 R1V  C08  H10  single  0.970  0.020  1.090
 R1V  C08  H11  single  0.970  0.020  1.090
 R1V  C10  H12  single  0.970  0.020  1.090
 R1V  C14  H13  single  0.970  0.020  1.090
 R1V  C14  H14  single  0.970  0.020  1.090
 R1V  C15  H15  single  0.970  0.020  1.090
 R1V  C15  H16  single  0.970  0.020  1.090
 R1V  C19  H17  single  0.970  0.020  1.090
 R1V  C19  H18  single  0.970  0.020  1.090
 R1V  C19  H19  single  0.970  0.020  1.090
 R1V  C20  H20  single  0.970  0.020  1.090
 R1V  C20  H21  single  0.970  0.020  1.090
 R1V  C20  H22  single  0.970  0.020  1.090
 R1V  N09  H23  single  0.890  0.020  1.040

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
 R1V  H3   C01  H2   107.98  3.000
 R1V  H3   C01  H1   106.41  3.000
 R1V  H2   C01  H1   108.02  3.000
 R1V  H3   C01  C02  111.01  3.000
 R1V  H2   C01  C02  112.23  3.000
 R1V  H1   C01  C02  110.95  3.000
 R1V  C20  C02  C03  124.76  3.000
 R1V  C20  C02  C01  114.23  3.000
 R1V  C03  C02  C01  121.01  3.000
 R1V  H4   C03  C04  114.44  3.000
 R1V  H4   C03  C02  117.32  3.000
 R1V  C04  C03  C02  128.24  3.000
 R1V  H6   C04  H5   106.33  3.000
 R1V  H6   C04  C05  108.90  3.000
 R1V  H5   C04  C05  109.29  3.000
 R1V  H6   C04  C03  111.72  3.000
 R1V  H5   C04  C03  108.56  3.000
 R1V  C05  C04  C03  111.87  3.000
 R1V  H8   C05  H7   106.68  3.000
 R1V  H8   C05  C06  109.39  3.000
 R1V  H7   C05  C06  110.11  3.000
 R1V  H8   C05  C04  108.73  3.000
 R1V  H7   C05  C04  108.67  3.000
 R1V  C06  C05  C04  113.05  3.000
 R1V  C19  C06  C07  124.63  3.000
 R1V  C19  C06  C05  115.03  3.000
 R1V  C07  C06  C05  120.34  3.000
 R1V  H9   C07  C08  114.30  3.000
 R1V  H9   C07  C06  117.31  3.000
 R1V  C08  C07  C06  128.39  3.000
 R1V  H11  C08  H10  106.20  3.000
 R1V  H11  C08  N09  108.20  3.000
 R1V  H10  C08  N09  112.38  3.000
 R1V  H11  C08  C07  110.83  3.000
 R1V  H10  C08  C07  108.93  3.000
 R1V  N09  C08  C07  110.23  3.000
 R1V  H12  C10  N09  107.45  3.000
 R1V  H12  C10  C14  107.86  3.000
 R1V  N09  C10  C14  109.82  3.000
 R1V  H12  C10  C11  108.14  3.000
 R1V  N09  C10  C11  114.61  3.000
 R1V  C14  C10  C11  108.73  3.000
 R1V  O13  C11  O12  126.30  3.000
 R1V  O13  C11  C10  116.60  3.000
 R1V  O12  C11  C10  117.05  3.000
 R1V  H14  C14  H13  106.01  3.000
 R1V  H14  C14  C15  109.93  3.000
 R1V  H13  C14  C15  110.01  3.000
 R1V  H14  C14  C10  108.56  3.000
 R1V  H13  C14  C10  108.79  3.000
 R1V  C15  C14  C10  113.27  3.000
 R1V  H16  C15  H15  104.78  3.000
 R1V  H16  C15  C16  108.52  3.000
 R1V  H15  C15  C16  108.18  3.000
 R1V  H16  C15  C14  109.06  3.000
 R1V  H15  C15  C14  109.46  3.000
 R1V  C16  C15  C14  116.22  3.000
 R1V  O18  C16  O17  125.91  3.000
 R1V  O18  C16  C15  115.93  3.000
 R1V  O17  C16  C15  118.15  3.000
 R1V  H19  C19  H18  107.64  3.000
 R1V  H19  C19  H17  106.34  3.000
 R1V  H18  C19  H17  107.46  3.000
 R1V  H19  C19  C06  110.22  3.000
 R1V  H18  C19  C06  113.48  3.000
 R1V  H17  C19  C06  111.37  3.000
 R1V  H22  C20  H21  107.65  3.000
 R1V  H22  C20  H20  106.34  3.000
 R1V  H21  C20  H20  107.81  3.000
 R1V  H22  C20  C02  110.56  3.000
 R1V  H21  C20  C02  113.64  3.000
 R1V  H20  C20  C02  110.51  3.000
 R1V  H23  N09  C10  107.04  3.000
 R1V  H23  N09  C08  107.83  3.000
 R1V  C10  N09  C08  113.17  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
 R1V  Var_01  C04  C03  C02  C01   179.83   0.0  2
 R1V  Var_02  C08  C07  C06  C05  -178.75   0.0  2
 R1V  Var_03  C05  C04  C03  C02   117.20  30.0  1
 R1V  Var_04  C06  C05  C04  C03   175.29  30.0  1
 R1V  Var_05  C07  C06  C05  C04   110.37  30.0  2
 R1V  Var_06  N09  C08  C07  C06   124.31  30.0  1
 R1V  Var_07  C10  N09  C08  C07   179.41  30.0  1
 R1V  Var_08  C16  C15  C14  C10   178.37  30.0  3
 R1V  Var_09  O17  C16  C15  C14    -6.44  30.0  2
 R1V  Var_10  H20  C20  C02  C01    55.65  30.0  3
 R1V  Var_11  H1   C01  C02  C03  -120.05  30.0  3
 R1V  Var_12  H17  C19  C06  C05    62.61  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
 R1V  chir_01  C10  C14  C11  N09  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
 R1V  plan-1  C10  0.020
 R1V  plan-1  C11  0.020
 R1V  plan-1  O12  0.020
 R1V  plan-1  O13  0.020
 R1V  plan-2  C15  0.020
 R1V  plan-2  C16  0.020
 R1V  plan-2  O17  0.020
 R1V  plan-2  O18  0.020
 R1V  plan-3  C05  0.020
 R1V  plan-3  C06  0.020
 R1V  plan-3  C07  0.020
 R1V  plan-3  C08  0.020
 R1V  plan-3  C19  0.020
 R1V  plan-3  H9   0.020
 R1V  plan-4  C01  0.020
 R1V  plan-4  C02  0.020
 R1V  plan-4  C03  0.020
 R1V  plan-4  C04  0.020
 R1V  plan-4  C20  0.020
 R1V  plan-4  H4   0.020

