# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 09:14:55 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (2R,3R)-3-(glycyloxy)-2-methylnonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@@H](OC(=O)CN)[C@@H](C)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
 5BV  5BV  '(2R,3R)-3-(glycyloxy)-2-methylnonanoic acid'  ligand  39  17  .  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_5BV
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
 5BV  O34  O  O      0  -0.459   1.7943   1.2618  -1.4401
 5BV  O35  O  O2     0  -0.474   0.8469   0.5129   0.4516
 5BV  O46  O  O      0  -0.605   3.4394  -1.7657  -1.0663
 5BV  N31  N  NH2    0  -0.794   2.6059   3.5819  -0.2014
 5BV  C32  C  CH2    0  -0.416   1.8818   2.5935   0.5651
 5BV  C33  C  C      0   0.591   1.5285   1.3885  -0.2725
 5BV  C36  C  CH1    0   0.038   0.5570  -0.8010  -0.0602
 5BV  C37  C  CH2    0  -0.442  -0.8619  -1.1340   0.3738
 5BV  C38  C  CH2    0  -0.416  -1.9179  -0.1670  -0.1496
 5BV  C39  C  CH2    0  -0.411  -3.3279  -0.5714   0.2650
 5BV  C40  C  CH2    0  -0.407  -4.4034   0.3693  -0.2626
 5BV  C41  C  CH2    0  -0.418  -5.8110  -0.0248   0.1685
 5BV  C42  C  CH3    0  -0.663  -6.8820   0.9090  -0.3777
 5BV  C43  C  CH1    0  -0.333   1.6203  -1.7676   0.4777
 5BV  C44  C  CH3    0  -0.676   1.3232  -3.2002   0.0476
 5BV  C45  C  C      0   0.415   3.0240  -1.3066   0.0154
 5BV  H1   H  HNH2   0   0.346   1.9889   4.0131  -0.8774
 5BV  H2   H  HNH2   0   0.355   2.8943   4.3247   0.4212
 5BV  H4   H  HCH2   0   0.264   2.5131   2.2372   1.3831
 5BV  H5   H  HCH2   0   0.236   0.9577   2.9566   1.0370
 5BV  H6   H  HCH1   0   0.227   0.6049  -0.7862  -1.1537
 5BV  H7   H  HCH2   0   0.235  -1.0984  -2.1359   0.0082
 5BV  H8   H  HCH2   0   0.219  -0.9084  -1.1874   1.4675
 5BV  H9   H  HCH2   0   0.218  -1.7168   0.8463   0.2086
 5BV  H10  H  HCH2   0   0.210  -1.8576  -0.1236  -1.2428
 5BV  H11  H  HCH2   0   0.208  -3.5331  -1.5889  -0.0855
 5BV  H12  H  HCH2   0   0.208  -3.3860  -0.6109   1.3586
 5BV  H13  H  HCH2   0   0.206  -4.1942   1.3898   0.0768
 5BV  H14  H  HCH2   0   0.206  -4.3536   0.3987  -1.3569
 5BV  H15  H  HCH2   0   0.210  -6.0162  -1.0483  -0.1597
 5BV  H16  H  HCH2   0   0.210  -5.8627  -0.0416   1.2617
 5BV  H17  H  HCH3   0   0.215  -6.7158   1.9368  -0.0491
 5BV  H18  H  HCH3   0   0.216  -6.8840   0.9103  -1.4694
 5BV  H19  H  HCH3   0   0.226  -7.8784   0.6148  -0.0461
 5BV  H20  H  HCH1   0   0.207   1.5812  -1.7120   1.5716
 5BV  H21  H  HCH3   0   0.215   1.1871  -3.2775  -1.0321
 5BV  H22  H  HCH3   0   0.229   2.1436  -3.8642   0.3218
 5BV  H23  H  HCH3   0   0.220   0.4241  -3.5889   0.5260
 5BV  O1   O  OC    -1  -0.616   3.6225  -0.4992   0.7557

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
 5BV  N31  C32  single  1.445  0.020  1.445
 5BV  O34  C33  double  1.204  0.020  1.204
 5BV  O46  C45  deloc   1.246  0.020  1.246
 5BV  C33  C32  single  1.510  0.020  1.510
 5BV  C33  O35  single  1.325  0.020  1.325
 5BV  C45  C43  single  1.548  0.020  1.548
 5BV  O35  C36  single  1.440  0.020  1.440
 5BV  C36  C43  single  1.534  0.020  1.534
 5BV  C36  C37  single  1.521  0.020  1.521
 5BV  C38  C37  single  1.525  0.020  1.525
 5BV  C38  C39  single  1.524  0.020  1.524
 5BV  C43  C44  single  1.525  0.020  1.525
 5BV  C39  C40  single  1.523  0.020  1.523
 5BV  C40  C41  single  1.524  0.020  1.524
 5BV  C41  C42  single  1.522  0.020  1.522
 5BV  N31  H1   single  0.890  0.020  1.040
 5BV  N31  H2   single  0.890  0.020  1.040
 5BV  C32  H4   single  0.970  0.020  1.090
 5BV  C32  H5   single  0.970  0.020  1.090
 5BV  C36  H6   single  0.970  0.020  1.090
 5BV  C37  H7   single  0.970  0.020  1.090
 5BV  C37  H8   single  0.970  0.020  1.090
 5BV  C38  H9   single  0.970  0.020  1.090
 5BV  C38  H10  single  0.970  0.020  1.090
 5BV  C39  H11  single  0.970  0.020  1.090
 5BV  C39  H12  single  0.970  0.020  1.090
 5BV  C40  H13  single  0.970  0.020  1.090
 5BV  C40  H14  single  0.970  0.020  1.090
 5BV  C41  H15  single  0.970  0.020  1.090
 5BV  C41  H16  single  0.970  0.020  1.090
 5BV  C42  H17  single  0.970  0.020  1.090
 5BV  C42  H18  single  0.970  0.020  1.090
 5BV  C42  H19  single  0.970  0.020  1.090
 5BV  C43  H20  single  0.970  0.020  1.090
 5BV  C44  H21  single  0.970  0.020  1.090
 5BV  C44  H22  single  0.970  0.020  1.090
 5BV  C44  H23  single  0.970  0.020  1.090
 5BV  C45  O1   deloc   1.248  0.020  1.248

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
 5BV  C36  O35  C33  120.83  3.000
 5BV  H2   N31  H1   105.80  3.000
 5BV  H2   N31  C32  108.59  3.000
 5BV  H1   N31  C32  109.89  3.000
 5BV  H5   C32  H4   105.78  3.000
 5BV  H5   C32  C33  107.77  3.000
 5BV  H4   C32  C33  106.87  3.000
 5BV  H5   C32  N31  115.02  3.000
 5BV  H4   C32  N31  109.30  3.000
 5BV  C33  C32  N31  111.65  3.000
 5BV  C32  C33  O35  110.16  3.000
 5BV  O35  C33  O34  125.03  3.000
 5BV  C32  C33  O34  124.78  3.000
 5BV  H6   C36  C43  109.17  3.000
 5BV  H6   C36  C37  109.20  3.000
 5BV  C43  C36  C37  114.12  3.000
 5BV  H6   C36  O35  109.51  3.000
 5BV  C37  C36  O35  106.64  3.000
 5BV  C43  C36  O35  108.11  3.000
 5BV  H8   C37  H7   106.27  3.000
 5BV  H8   C37  C38  110.13  3.000
 5BV  H7   C37  C38  108.47  3.000
 5BV  H8   C37  C36  109.57  3.000
 5BV  H7   C37  C36  107.90  3.000
 5BV  C38  C37  C36  114.17  3.000
 5BV  H10  C38  H9   106.26  3.000
 5BV  H10  C38  C39  109.44  3.000
 5BV  H9   C38  C39  109.08  3.000
 5BV  H10  C38  C37  109.24  3.000
 5BV  H9   C38  C37  110.36  3.000
 5BV  C39  C38  C37  112.28  3.000
 5BV  H12  C39  H11  106.02  3.000
 5BV  H12  C39  C40  109.30  3.000
 5BV  H11  C39  C40  109.30  3.000
 5BV  H12  C39  C38  109.27  3.000
 5BV  H11  C39  C38  109.43  3.000
 5BV  C40  C39  C38  113.27  3.000
 5BV  H14  C40  H13  106.01  3.000
 5BV  H14  C40  C41  109.35  3.000
 5BV  H13  C40  C41  109.24  3.000
 5BV  H14  C40  C39  109.29  3.000
 5BV  H13  C40  C39  109.46  3.000
 5BV  C41  C40  C39  113.23  3.000
 5BV  H16  C41  H15  106.04  3.000
 5BV  H16  C41  C42  109.54  3.000
 5BV  H15  C41  C42  109.52  3.000
 5BV  H16  C41  C40  109.28  3.000
 5BV  H15  C41  C40  109.28  3.000
 5BV  C42  C41  C40  112.93  3.000
 5BV  H19  C42  H18  107.63  3.000
 5BV  H19  C42  H17  107.55  3.000
 5BV  H18  C42  H17  107.47  3.000
 5BV  H19  C42  C41  111.61  3.000
 5BV  H18  C42  C41  111.15  3.000
 5BV  H17  C42  C41  111.24  3.000
 5BV  H20  C43  C45  108.38  3.000
 5BV  H20  C43  C44  108.80  3.000
 5BV  C45  C43  C44  111.85  3.000
 5BV  H20  C43  C36  107.05  3.000
 5BV  C44  C43  C36  110.98  3.000
 5BV  C45  C43  C36  109.64  3.000
 5BV  H23  C44  H22  107.04  3.000
 5BV  H23  C44  H21  107.82  3.000
 5BV  H22  C44  H21  107.43  3.000
 5BV  H23  C44  C43  111.83  3.000
 5BV  H22  C44  C43  110.76  3.000
 5BV  H21  C44  C43  111.71  3.000
 5BV  O1   C45  C43  116.76  3.000
 5BV  O1   C45  O46  126.38  3.000
 5BV  C43  C45  O46  116.85  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
 5BV  Var_01  N31  C32  C33  O34    -0.98  30.0  3
 5BV  Var_02  C39  C38  C37  C36   177.76  30.0  1
 5BV  Var_03  C40  C39  C38  C37  -179.20  30.0  3
 5BV  Var_04  C41  C40  C39  C38  -179.20  30.0  3
 5BV  Var_05  C42  C41  C40  C39  -179.23  30.0  3
 5BV  Var_06  H1   N31  C32  C33    70.01  30.0  3
 5BV  Var_07  H17  C42  C41  C40   -59.15  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
 5BV  chir_01  C36  O35  C43  C37  negativ
 5BV  chir_02  C43  C44  C36  C45  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
 5BV  plan-1  O46  0.020
 5BV  plan-1  C43  0.020
 5BV  plan-1  C45  0.020
 5BV  plan-1  O1   0.020
 5BV  plan-2  O34  0.020
 5BV  plan-2  O35  0.020
 5BV  plan-2  C32  0.020
 5BV  plan-2  C33  0.020

