# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:12:11 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: (2S,3R,4R,6E)-2-amino-3,4-dihydroxy-2-(hydroxymethyl)-14-oxoicos-6-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC(=O)CCCCCC\C=C\C[C@@H](O)[C@H](O)[C@@](N)(CO)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
 VRP  VRP  '(2S,3R,4R,6E)-2-amino-3,4-dihydroxy-2-(hydroxymethyl)-14-oxoicos-6-enoic acid'  ligand  66  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VRP
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
 VRP  C10  C  CH2    0  -0.421  192.8775  181.7315  192.1059
 VRP  C11  C  CH2    0  -0.422  191.8081  181.7381  193.1925
 VRP  C12  C  CH2    0  -0.421  192.3492  181.5280  194.6039
 VRP  C13  C  CH2    0  -0.421  193.3291  182.6021  195.0616
 VRP  C14  C  CH2    0  -0.477  193.7136  182.4624  196.5349
 VRP  C01  C  CH3    0  -0.659  194.0360  182.5611  182.0072
 VRP  C02  C  CH2    0  -0.417  193.1249  182.1991  183.1716
 VRP  C03  C  CH2    0  -0.405  193.8084  182.3440  184.5255
 VRP  C04  C  CH2    0  -0.412  192.9000  181.9954  185.6968
 VRP  C05  C  CH2    0  -0.414  193.5879  182.1373  187.0488
 VRP  C06  C  CH2    0  -0.556  192.6528  181.8062  188.1997
 VRP  C07  C  C      0   0.407  193.2559  181.9091  189.5789
 VRP  C09  C  CH2    0  -0.554  192.2689  181.8531  190.7188
 VRP  C15  C  C1     0  -0.197  194.6713  183.5238  196.9734
 VRP  C16  C  C1     0  -0.230  195.8892  183.3063  197.4619
 VRP  C17  C  CH2    0  -0.498  196.8568  184.3715  197.8677
 VRP  C18  C  CH1    0   0.012  197.2553  184.3010  199.3431
 VRP  C19  C  CH1    0   0.080  196.0394  184.4817  200.2670
 VRP  C20  C  CT     0  -0.118  196.3773  184.4823  201.8105
 VRP  C21  C  CH2    0  -0.153  195.2204  183.8642  202.5951
 VRP  C23  C  C      0   0.458  197.6623  183.6461  202.0940
 VRP  N26  N  NH2    0  -0.827  196.5371  185.8835  202.2042
 VRP  O08  O  O      0  -0.407  194.4476  182.0285  189.7578
 VRP  O22  O  OH1    0  -0.668  194.0423  184.6227  202.4261
 VRP  O24  O  O      0  -0.554  197.5256  182.4479  202.3735
 VRP  O25  O  OC    -1  -0.609  198.7563  184.2619  201.9952
 VRP  O27  O  OH1    0  -0.686  195.3539  185.6629  199.9570
 VRP  O28  O  OH1    0  -0.710  198.2585  185.2674  199.5545
 VRP  H1   H  HCH2   0   0.218  193.4620  180.8089  192.1749
 VRP  H2   H  HCH2   0   0.226  193.5794  182.5522  192.2688
 VRP  H3   H  HCH2   0   0.210  191.2614  182.6867  193.1540
 VRP  H4   H  HCH2   0   0.219  191.0723  180.9570  192.9765
 VRP  H5   H  HCH2   0   0.218  191.5059  181.4964  195.3012
 VRP  H6   H  HCH2   0   0.210  192.8316  180.5467  194.6671
 VRP  H7   H  HCH2   0   0.221  194.2377  182.5692  194.4540
 VRP  H8   H  HCH2   0   0.211  192.8884  183.5916  194.8959
 VRP  H9   H  HCH2   0   0.223  192.8009  182.5167  197.1394
 VRP  H10  H  HCH2   0   0.225  194.1457  181.4732  196.7139
 VRP  H11  H  HCH3   0   0.224  193.5281  182.4474  181.0489
 VRP  H12  H  HCH3   0   0.215  194.3761  183.5957  182.0796
 VRP  H13  H  HCH3   0   0.215  194.9228  181.9248  181.9881
 VRP  H14  H  HCH2   0   0.209  192.2317  182.8310  183.1488
 VRP  H15  H  HCH2   0   0.209  192.7703  181.1705  183.0539
 VRP  H16  H  HCH2   0   0.206  194.6981  181.7051  184.5512
 VRP  H17  H  HCH2   0   0.206  194.1704  183.3716  184.6398
 VRP  H18  H  HCH2   0   0.209  192.0126  182.6372  185.6709
 VRP  H19  H  HCH2   0   0.209  192.5348  180.9691  185.5808
 VRP  H20  H  HCH2   0   0.219  194.4639  181.4841  187.0789
 VRP  H21  H  HCH2   0   0.219  193.9625  183.1592  187.1599
 VRP  H22  H  HCH2   0   0.256  191.7584  182.4378  188.1683
 VRP  H23  H  HCH2   0   0.266  192.2721  180.7820  188.0986
 VRP  H24  H  HCH2   0   0.265  191.6577  182.7617  190.6496
 VRP  H25  H  HCH2   0   0.257  191.5673  181.0337  190.5271
 VRP  H26  H  H      0   0.223  194.3302  184.5513  196.8570
 VRP  H27  H  H      0   0.223  196.2277  182.2778  197.5797
 VRP  H28  H  HCH2   0   0.232  197.7738  184.2638  197.2778
 VRP  H29  H  HCH2   0   0.226  196.4476  185.3590  197.6425
 VRP  H30  H  HCH1   0   0.178  197.6445  183.2837  199.5200
 VRP  H31  H  HCH1   0   0.199  195.3808  183.6231  200.0786
 VRP  H32  H  HCH2   0   0.203  195.0820  182.8328  202.2580
 VRP  H33  H  HCH2   0   0.196  195.5041  183.8192  203.6571
 VRP  H34  H  HNH2   0   0.359  196.1961  186.0419  203.1438
 VRP  H35  H  HNH2   0   0.351  197.5210  186.1226  202.2041
 VRP  H37  H  HOH1   0   0.449  193.3547  184.2107  202.9562
 VRP  H39  H  HOH1   0   0.434  195.6101  186.2538  200.6991
 VRP  H40  H  HOH1   0   0.442  198.6333  185.0654  200.4364

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
 VRP  C01  C02  single  1.522  0.020  1.522
 VRP  C02  C03  single  1.524  0.020  1.524
 VRP  C03  C04  single  1.523  0.020  1.523
 VRP  C04  C05  single  1.524  0.020  1.524
 VRP  C05  C06  single  1.519  0.020  1.519
 VRP  C06  C07  single  1.509  0.020  1.509
 VRP  C07  O08  double  1.211  0.020  1.211
 VRP  C07  C09  single  1.509  0.020  1.509
 VRP  C09  C10  single  1.520  0.020  1.520
 VRP  C10  C11  single  1.525  0.020  1.525
 VRP  C11  C12  single  1.526  0.020  1.526
 VRP  C12  C13  single  1.524  0.020  1.524
 VRP  C13  C14  single  1.529  0.020  1.529
 VRP  C14  C15  single  1.495  0.020  1.495
 VRP  C15  C16  double  1.330  0.020  1.330
 VRP  C16  C17  single  1.495  0.020  1.495
 VRP  C17  C18  single  1.530  0.020  1.530
 VRP  O28  C18  single  1.409  0.020  1.409
 VRP  C18  C19  single  1.538  0.020  1.538
 VRP  C19  O27  single  1.400  0.020  1.400
 VRP  C19  C20  single  1.580  0.020  1.580
 VRP  O24  C23  deloc   1.238  0.020  1.238
 VRP  C23  O25  deloc   1.259  0.020  1.259
 VRP  C23  C20  single  1.559  0.020  1.559
 VRP  C20  C21  single  1.528  0.020  1.528
 VRP  C20  N26  single  1.464  0.020  1.464
 VRP  C21  O22  single  1.411  0.020  1.411
 VRP  C10  H1   single  0.970  0.020  1.090
 VRP  C10  H2   single  0.970  0.020  1.090
 VRP  C11  H3   single  0.970  0.020  1.090
 VRP  C11  H4   single  0.970  0.020  1.090
 VRP  C12  H5   single  0.970  0.020  1.090
 VRP  C12  H6   single  0.970  0.020  1.090
 VRP  C13  H7   single  0.970  0.020  1.090
 VRP  C13  H8   single  0.970  0.020  1.090
 VRP  C14  H9   single  0.970  0.020  1.090
 VRP  C14  H10  single  0.970  0.020  1.090
 VRP  C01  H11  single  0.970  0.020  1.090
 VRP  C01  H12  single  0.970  0.020  1.090
 VRP  C01  H13  single  0.970  0.020  1.090
 VRP  C02  H14  single  0.970  0.020  1.090
 VRP  C02  H15  single  0.970  0.020  1.090
 VRP  C03  H16  single  0.970  0.020  1.090
 VRP  C03  H17  single  0.970  0.020  1.090
 VRP  C04  H18  single  0.970  0.020  1.090
 VRP  C04  H19  single  0.970  0.020  1.090
 VRP  C05  H20  single  0.970  0.020  1.090
 VRP  C05  H21  single  0.970  0.020  1.090
 VRP  C06  H22  single  0.970  0.020  1.090
 VRP  C06  H23  single  0.970  0.020  1.090
 VRP  C09  H24  single  0.970  0.020  1.090
 VRP  C09  H25  single  0.970  0.020  1.090
 VRP  C15  H26  single  0.930  0.020  1.080
 VRP  C16  H27  single  0.930  0.020  1.080
 VRP  C17  H28  single  0.970  0.020  1.090
 VRP  C17  H29  single  0.970  0.020  1.090
 VRP  C18  H30  single  0.970  0.020  1.090
 VRP  C19  H31  single  0.970  0.020  1.090
 VRP  C21  H32  single  0.970  0.020  1.090
 VRP  C21  H33  single  0.970  0.020  1.090
 VRP  N26  H34  single  0.890  0.020  1.040
 VRP  N26  H35  single  0.890  0.020  1.040
 VRP  O22  H37  single  0.850  0.020  0.980
 VRP  O27  H39  single  0.850  0.020  0.980
 VRP  O28  H40  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
 VRP  H2   C10  H1   106.31  3.000
 VRP  H2   C10  C09  109.48  3.000
 VRP  H1   C10  C09  109.81  3.000
 VRP  H2   C10  C11  109.95  3.000
 VRP  H1   C10  C11  109.47  3.000
 VRP  C09  C10  C11  111.67  3.000
 VRP  H4   C11  H3   105.99  3.000
 VRP  H4   C11  C12  108.82  3.000
 VRP  H3   C11  C12  109.19  3.000
 VRP  H4   C11  C10  109.13  3.000
 VRP  H3   C11  C10  109.19  3.000
 VRP  C12  C11  C10  114.20  3.000
 VRP  H6   C12  H5   106.06  3.000
 VRP  H6   C12  C13  109.32  3.000
 VRP  H5   C12  C13  108.92  3.000
 VRP  H6   C12  C11  109.45  3.000
 VRP  H5   C12  C11  108.66  3.000
 VRP  C13  C12  C11  114.12  3.000
 VRP  H8   C13  H7   106.10  3.000
 VRP  H8   C13  C14  109.23  3.000
 VRP  H7   C13  C14  108.88  3.000
 VRP  H8   C13  C12  109.42  3.000
 VRP  H7   C13  C12  110.25  3.000
 VRP  C14  C13  C12  112.75  3.000
 VRP  H10  C14  H9   106.46  3.000
 VRP  H10  C14  C15  109.93  3.000
 VRP  H9   C14  C15  109.66  3.000
 VRP  H10  C14  C13  109.85  3.000
 VRP  H9   C14  C13  108.51  3.000
 VRP  C15  C14  C13  112.26  3.000
 VRP  H13  C01  H12  107.49  3.000
 VRP  H13  C01  H11  107.59  3.000
 VRP  H12  C01  H11  107.59  3.000
 VRP  H13  C01  C02  111.16  3.000
 VRP  H12  C01  C02  111.18  3.000
 VRP  H11  C01  C02  111.63  3.000
 VRP  H15  C02  H14  106.02  3.000
 VRP  H15  C02  C03  109.29  3.000
 VRP  H14  C02  C03  109.25  3.000
 VRP  H15  C02  C01  109.59  3.000
 VRP  H14  C02  C01  109.59  3.000
 VRP  C03  C02  C01  112.87  3.000
 VRP  H17  C03  H16  106.03  3.000
 VRP  H17  C03  C04  109.36  3.000
 VRP  H16  C03  C04  109.44  3.000
 VRP  H17  C03  C02  109.28  3.000
 VRP  H16  C03  C02  109.25  3.000
 VRP  C04  C03  C02  113.21  3.000
 VRP  H19  C04  H18  106.04  3.000
 VRP  H19  C04  C05  109.37  3.000
 VRP  H18  C04  C05  109.40  3.000
 VRP  H19  C04  C03  109.38  3.000
 VRP  H18  C04  C03  109.33  3.000
 VRP  C05  C04  C03  113.08  3.000
 VRP  H21  C05  H20  106.32  3.000
 VRP  H21  C05  C06  109.72  3.000
 VRP  H20  C05  C06  110.01  3.000
 VRP  H21  C05  C04  109.37  3.000
 VRP  H20  C05  C04  109.30  3.000
 VRP  C06  C05  C04  111.96  3.000
 VRP  H23  C06  H22  104.61  3.000
 VRP  H23  C06  C07  106.65  3.000
 VRP  H22  C06  C07  108.26  3.000
 VRP  H23  C06  C05  110.31  3.000
 VRP  H22  C06  C05  110.80  3.000
 VRP  C07  C06  C05  115.56  3.000
 VRP  O08  C07  C09  122.40  3.000
 VRP  C09  C07  C06  115.25  3.000
 VRP  O08  C07  C06  122.35  3.000
 VRP  H25  C09  H24  104.57  3.000
 VRP  H25  C09  C07  108.33  3.000
 VRP  H24  C09  C07  106.62  3.000
 VRP  H25  C09  C10  110.88  3.000
 VRP  H24  C09  C10  110.29  3.000
 VRP  C07  C09  C10  115.50  3.000
 VRP  H26  C15  C16  118.71  3.000
 VRP  H26  C15  C14  115.97  3.000
 VRP  C16  C15  C14  125.31  3.000
 VRP  H27  C16  C17  116.25  3.000
 VRP  H27  C16  C15  118.60  3.000
 VRP  C17  C16  C15  125.15  3.000
 VRP  H29  C17  H28  106.93  3.000
 VRP  H29  C17  C18  109.76  3.000
 VRP  H28  C17  C18  107.26  3.000
 VRP  H29  C17  C16  110.23  3.000
 VRP  H28  C17  C16  108.99  3.000
 VRP  C18  C17  C16  113.42  3.000
 VRP  H30  C18  O28  110.92  3.000
 VRP  H30  C18  C19  106.91  3.000
 VRP  O28  C18  C19  113.09  3.000
 VRP  H30  C18  C17  106.80  3.000
 VRP  C19  C18  C17  111.60  3.000
 VRP  O28  C18  C17  107.38  3.000
 VRP  H31  C19  O27  109.14  3.000
 VRP  H31  C19  C20  107.22  3.000
 VRP  O27  C19  C20  108.70  3.000
 VRP  H31  C19  C18  106.21  3.000
 VRP  C20  C19  C18  114.70  3.000
 VRP  O27  C19  C18  110.68  3.000
 VRP  N26  C20  C23  111.99  3.000
 VRP  N26  C20  C21  109.36  3.000
 VRP  C23  C20  C21  108.27  3.000
 VRP  N26  C20  C19  106.64  3.000
 VRP  C21  C20  C19  109.85  3.000
 VRP  C23  C20  C19  110.71  3.000
 VRP  H33  C21  H32  106.96  3.000
 VRP  H33  C21  O22  110.66  3.000
 VRP  H32  C21  O22  111.36  3.000
 VRP  H33  C21  C20  108.47  3.000
 VRP  H32  C21  C20  108.59  3.000
 VRP  O22  C21  C20  110.67  3.000
 VRP  O25  C23  O24  125.94  3.000
 VRP  O25  C23  C20  116.07  3.000
 VRP  O24  C23  C20  117.98  3.000
 VRP  H35  N26  H34  106.89  3.000
 VRP  H35  N26  C20  109.39  3.000
 VRP  H34  N26  C20  111.27  3.000
 VRP  H37  O22  C21  107.51  3.000
 VRP  H39  O27  C19  102.26  3.000
 VRP  H40  O28  C18  105.44  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
 VRP  Var_01  C17  C16  C15  C14   178.40   0.0  2
 VRP  Var_02  C06  C07  C09  C10   170.60  30.0  1
 VRP  Var_03  C13  C12  C11  C10    61.18  30.0  3
 VRP  Var_04  C07  C09  C10  C11   177.73  30.0  2
 VRP  Var_05  C14  C13  C12  C11   172.69  30.0  3
 VRP  Var_06  C09  C10  C11  C12   176.24  30.0  1
 VRP  Var_07  C15  C14  C13  C12  -179.81  30.0  3
 VRP  Var_08  C16  C15  C14  C13  -120.22  30.0  3
 VRP  Var_09  C04  C03  C02  C01   179.49  30.0  3
 VRP  Var_10  C05  C04  C03  C02   179.82  30.0  3
 VRP  Var_11  C06  C05  C04  C03   179.04  30.0  3
 VRP  Var_12  C07  C06  C05  C04   179.49  30.0  3
 VRP  Var_13  C18  C17  C16  C15   119.67  30.0  3
 VRP  Var_14  H11  C01  C02  C03   179.83  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
 VRP  chir_01  C18  C17  O28  C19  negativ
 VRP  chir_02  C19  O27  C18  C20  negativ
 VRP  chir_03  C20  C21  C23  C19  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
 VRP  plan-1  C06  0.020
 VRP  plan-1  C07  0.020
 VRP  plan-1  C09  0.020
 VRP  plan-1  O08  0.020
 VRP  plan-2  C20  0.020
 VRP  plan-2  C23  0.020
 VRP  plan-2  O24  0.020
 VRP  plan-2  O25  0.020
 VRP  plan-3  C14  0.020
 VRP  plan-3  C15  0.020
 VRP  plan-3  C16  0.020
 VRP  plan-3  C17  0.020
 VRP  plan-3  H26  0.020
 VRP  plan-3  H27  0.020

