# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 03:45:05 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  45  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 PERFECT
;

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  -0.747   7.1392   1.0438  -0.8946
 R1V  C02  C  C     0   0.192   5.6423   0.9227  -0.8862
 R1V  C03  C  C1    0  -0.268   4.9862   0.6132   0.2352
 R1V  C04  C  CH2   0  -0.483   3.5125   0.4337   0.4211
 R1V  C05  C  CH2   0  -0.499   3.1533  -1.0313   0.7179
 R1V  C06  C  C     0   0.188   1.6817  -1.2359   0.9413
 R1V  C07  C  C1    0  -0.324   0.9583  -1.9829   0.1035
 R1V  C08  C  CH2   0  -0.342  -0.5267  -2.1850   0.2051
 R1V  C10  C  CH1   0  -0.173  -2.6684  -1.0351  -0.0398
 R1V  C11  C  C     0   0.506  -3.2869  -1.8525  -1.1681
 R1V  C14  C  CH2   0  -0.421  -3.2814   0.3738  -0.0655
 R1V  C15  C  CH2   0  -0.573  -2.8428   1.1746   1.1481
 R1V  C16  C  C     0   0.545  -3.3142   2.5997   1.1249
 R1V  C19  C  CH3   0  -0.741   1.0881  -0.5285   2.1251
 R1V  C20  C  CH3   0  -0.748   4.9963   1.1771  -2.2157
 R1V  N09  N  NH1   0  -0.540  -1.2353  -0.9522  -0.1082
 R1V  O12  O  O     0  -0.337  -2.7592  -2.0424  -2.2355
 R1V  O13  O  OH1   0  -0.717  -4.4962  -2.3037  -0.8584
 R1V  O17  O  O     0  -0.407  -3.8896   3.1299   0.2066
 R1V  O18  O  OH1   0  -0.610  -3.0125   3.2371   2.2527
 R1V  H1   H  HCH3  0   0.212   7.4498   2.0478  -1.1952
 R1V  H2   H  HCH3  0   0.219   7.5738   0.8330   0.0823
 R1V  H3   H  HCH3  0   0.235   7.5823   0.3548  -1.6185
 R1V  H4   H  H     0   0.216   5.5819   0.4430   1.1301
 R1V  H5   H  HCH2  0   0.174   3.1797   1.0589   1.2555
 R1V  H6   H  HCH2  0   0.264   2.9504   0.7666  -0.4536
 R1V  H7   H  HCH2  0   0.266   3.4969  -1.6543  -0.1113
 R1V  H8   H  HCH2  0   0.221   3.7072  -1.3541   1.6070
 R1V  H9   H  H     0   0.251   1.4600  -2.4468  -0.7404
 R1V  H10  H  HCH2  0   0.176  -0.8286  -3.0266  -0.4366
 R1V  H11  H  HCH2  0   0.233  -0.8013  -2.4723   1.2260
 R1V  H12  H  HCH1  0   0.284  -2.9417  -1.5110   0.9085
 R1V  H13  H  HCH2  0   0.224  -2.9733   0.8759  -0.9862
 R1V  H14  H  HCH2  0   0.263  -4.3702   0.3045  -0.0923
 R1V  H15  H  HCH2  0   0.256  -3.2030   0.7030   2.0671
 R1V  H16  H  HCH2  0   0.279  -1.7518   1.1712   1.2250
 R1V  H17  H  HCH3  0   0.288   0.8652   0.5148   1.8904
 R1V  H18  H  HCH3  0   0.209   0.1548  -0.9822   2.4546
 R1V  H19  H  HCH3  0   0.243   1.7851  -0.5253   2.9655
 R1V  H20  H  HCH3  0   0.271   5.4050   0.5022  -2.9722
 R1V  H21  H  HCH3  0   0.241   3.9157   1.0523  -2.2087
 R1V  H22  H  HCH3  0   0.193   5.2137   2.1916  -2.5610
 R1V  H23  H  HNH1  0   0.352  -0.9492  -0.6080  -1.0173
 R1V  H25  H  HOH1  0   0.462  -4.8828  -2.7738  -1.6130
 R1V  H26  H  HOH1  0   0.470  -3.3137   4.1562   2.2024

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  double  1.206  0.020  1.206
 R1V  O18  C16  single  1.330  0.020  1.330
 R1V  C16  C15  single  1.501  0.020  1.501
 R1V  C14  C15  single  1.519  0.020  1.519
 R1V  C14  C10  single  1.537  0.020  1.537
 R1V  O12  C11  double  1.206  0.020  1.206
 R1V  C11  O13  single  1.327  0.020  1.327
 R1V  C11  C10  single  1.524  0.020  1.524
 R1V  C10  N09  single  1.437  0.020  1.437
 R1V  N09  C08  single  1.456  0.020  1.456
 R1V  C08  C07  single  1.502  0.020  1.502
 R1V  C07  C06  double  1.335  0.020  1.335
 R1V  C06  C19  single  1.501  0.020  1.501
 R1V  C06  C05  single  1.503  0.020  1.503
 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  1.336  0.020  1.336
 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
 R1V  O13  H25  single  0.850  0.020  0.980
 R1V  O18  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
 R1V  H3   C01  H2   108.06  3.000
 R1V  H3   C01  H1   106.36  3.000
 R1V  H2   C01  H1   108.11  3.000
 R1V  H3   C01  C02  110.91  3.000
 R1V  H2   C01  C02  112.14  3.000
 R1V  H1   C01  C02  111.03  3.000
 R1V  C20  C02  C03  124.89  3.000
 R1V  C20  C02  C01  114.24  3.000
 R1V  C03  C02  C01  120.87  3.000
 R1V  H4   C03  C04  114.72  3.000
 R1V  H4   C03  C02  117.23  3.000
 R1V  C04  C03  C02  128.03  3.000
 R1V  H6   C04  H5   106.26  3.000
 R1V  H6   C04  C05  108.96  3.000
 R1V  H5   C04  C05  109.03  3.000
 R1V  H6   C04  C03  111.78  3.000
 R1V  H5   C04  C03  109.01  3.000
 R1V  C05  C04  C03  111.62  3.000
 R1V  H8   C05  H7   106.78  3.000
 R1V  H8   C05  C06  109.53  3.000
 R1V  H7   C05  C06  110.07  3.000
 R1V  H8   C05  C04  108.62  3.000
 R1V  H7   C05  C04  108.87  3.000
 R1V  C06  C05  C04  112.79  3.000
 R1V  C19  C06  C07  122.96  3.000
 R1V  C19  C06  C05  116.12  3.000
 R1V  C07  C06  C05  120.90  3.000
 R1V  H9   C07  C08  116.86  3.000
 R1V  H9   C07  C06  118.45  3.000
 R1V  C08  C07  C06  124.63  3.000
 R1V  H11  C08  H10  105.91  3.000
 R1V  H11  C08  N09  107.49  3.000
 R1V  H10  C08  N09  112.86  3.000
 R1V  H11  C08  C07  110.25  3.000
 R1V  H10  C08  C07  109.55  3.000
 R1V  N09  C08  C07  110.65  3.000
 R1V  H12  C10  N09  108.36  3.000
 R1V  H12  C10  C14  108.25  3.000
 R1V  N09  C10  C14  110.13  3.000
 R1V  H12  C10  C11  107.84  3.000
 R1V  N09  C10  C11  113.60  3.000
 R1V  C14  C10  C11  108.51  3.000
 R1V  O13  C11  O12  123.48  3.000
 R1V  O13  C11  C10  112.29  3.000
 R1V  O12  C11  C10  124.20  3.000
 R1V  H14  C14  H13  106.84  3.000
 R1V  H14  C14  C15  109.95  3.000
 R1V  H13  C14  C15  110.46  3.000
 R1V  H14  C14  C10  109.89  3.000
 R1V  H13  C14  C10  108.83  3.000
 R1V  C15  C14  C10  110.79  3.000
 R1V  H16  C15  H15  105.55  3.000
 R1V  H16  C15  C16  108.50  3.000
 R1V  H15  C15  C16  108.59  3.000
 R1V  H16  C15  C14  110.04  3.000
 R1V  H15  C15  C14  110.42  3.000
 R1V  C16  C15  C14  113.42  3.000
 R1V  O18  C16  O17  122.89  3.000
 R1V  O18  C16  C15  111.75  3.000
 R1V  O17  C16  C15  125.36  3.000
 R1V  H19  C19  H18  108.39  3.000
 R1V  H19  C19  H17  107.03  3.000
 R1V  H18  C19  H17  106.75  3.000
 R1V  H19  C19  C06  110.85  3.000
 R1V  H18  C19  C06  112.41  3.000
 R1V  H17  C19  C06  111.18  3.000
 R1V  H22  C20  H21  107.81  3.000
 R1V  H22  C20  H20  106.26  3.000
 R1V  H21  C20  H20  107.76  3.000
 R1V  H22  C20  C02  110.59  3.000
 R1V  H21  C20  C02  113.74  3.000
 R1V  H20  C20  C02  110.35  3.000
 R1V  H23  N09  C10  110.11  3.000
 R1V  H23  N09  C08  110.07  3.000
 R1V  C10  N09  C08  115.23  3.000
 R1V  H25  O13  C11  110.27  3.000
 R1V  H26  O18  C16  109.89  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  CONST_01  H25  O13  C11  C10   180.00   0.0  0
 R1V  CONST_02  H26  O18  C16  C15   180.00   0.0  0
 R1V  Var_01    C04  C03  C02  C01  -179.08   0.0  2
 R1V  Var_02    C08  C07  C06  C05  -176.67   0.0  2
 R1V  Var_03    C05  C04  C03  C02   111.70  30.0  1
 R1V  Var_04    C06  C05  C04  C03   178.66  30.0  1
 R1V  Var_05    C07  C06  C05  C04   115.42  30.0  2
 R1V  Var_06    N09  C08  C07  C06    69.04  30.0  1
 R1V  Var_07    C10  N09  C08  C07  -179.97  30.0  1
 R1V  Var_08    C16  C15  C14  C10   175.15  30.0  3
 R1V  Var_09    O17  C16  C15  C14    -5.93  30.0  2
 R1V  Var_10    H20  C20  C02  C01    56.69  30.0  3
 R1V  Var_11    H1   C01  C02  C03  -119.89  30.0  3
 R1V  Var_12    H17  C19  C06  C05    81.68  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-1  H25  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-2  H26  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

