# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:53:07 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-[(2R)-2-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-5-oxo-1,3-oxazolidin-3-yl]-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c([C@H]2OC(=O)CN2CCCC[C@H](N)C(O)=O)c1O
#
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
 9EV  9EV  6-[(2R)-2-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-5-oxo-1,3-oxazolidin-3-yl]-L-norleucine  L-peptide  53  29  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_9EV
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
 9EV  C13  C  CR15  0   0.108  -0.4697   0.0864   0.2731
 9EV  C15  C  CR5   0   0.564  -0.2680   1.4405   2.0837
 9EV  C17  C  CH2   0  -0.484   0.8796   0.4609   2.0890
 9EV  C20  C  CH2   0  -0.445   3.3087   0.1249   0.1869
 9EV  C21  C  CH2   0  -0.433   4.3149   0.8123  -0.7285
 9EV  C22  C  CH2   0  -0.437   5.7480   0.3869  -0.4352
 9EV  C28  C  CR6   0   0.270  -0.8830  -2.3396   0.9545
 9EV  C02  C  CR6   0   0.135  -1.7843  -3.4011   1.1649
 9EV  C04  C  CR16  0  -0.133  -3.5507  -2.0919   0.5243
 9EV  C05  C  CR6   0  -0.064  -2.7512  -0.9890   0.2831
 9EV  C06  C  CH2   0  -0.204  -3.3592   0.2911  -0.2276
 9EV  C12  C  CR6   0   0.041  -1.3744  -1.1009   0.5349
 9EV  C23  C  CH1   0  -0.216   6.7767   1.1756  -1.2702
 9EV  C1   C  C     0   0.546   8.1694   0.6968  -0.9163
 9EV  N03  N  N     0  -0.400  -3.0779  -3.2564   0.9591
 9EV  N18  N  NR5   0  -0.539   0.8982  -0.0829   0.7354
 9EV  N24  N  NH2   0  -0.786   6.6052   1.1077  -2.7053
 9EV  O07  O  O2    0  -0.592  -4.5836  -0.0162  -0.8930
 9EV  O09  O  O     0  -0.709  -5.6266   2.3768  -0.7920
 9EV  O10  O  OH1   0  -0.740  -4.6110   1.5440  -2.9307
 9EV  O11  O  OH1   0  -0.729  -6.6683   0.2878  -2.0065
 9EV  O14  O  O     0  -0.436  -0.9801   1.2358   0.9723
 9EV  O16  O  O     0  -0.408  -0.5558   2.2744   2.8909
 9EV  O27  O  O     0  -0.440   8.8667   0.0251  -1.6335
 9EV  O29  O  OH1   0  -0.636   0.4091  -2.5994   1.1716
 9EV  P08  P  P     0   1.466  -5.4030   1.1625  -1.5970
 9EV  H1   H  HCR5  0   0.307  -0.4774   0.3258  -0.7924
 9EV  H2   H  HCH2  0   0.318   1.8146   0.9499   2.3562
 9EV  H3   H  HCH2  0   0.320   0.6933  -0.3108   2.8427
 9EV  H4   H  HCH2  0   0.236   3.3898  -0.9611   0.0841
 9EV  H5   H  HCH2  0   0.233   3.5519   0.3626   1.2266
 9EV  H6   H  HCH2  0   0.224   4.0652   0.5869  -1.7691
 9EV  H7   H  HCH2  0   0.228   4.2268   1.8982  -0.6140
 9EV  H8   H  HCH2  0   0.237   5.9531   0.5322   0.6285
 9EV  H9   H  HCH2  0   0.233   5.8612  -0.6838  -0.6372
 9EV  H10  H  HCH3  0   0.248  -0.7934  -4.6533   2.6101
 9EV  H11  H  HCH3  0   0.247  -2.1039  -5.4316   1.7172
 9EV  H12  H  HCH3  0   0.247  -0.5393  -5.1452   0.9468
 9EV  H13  H  HCR6  0   0.260  -4.6190  -2.0487   0.3573
 9EV  H14  H  HCH2  0   0.271  -3.5523   0.9823   0.5958
 9EV  H15  H  HCH2  0   0.251  -2.6823   0.7899  -0.9274
 9EV  H16  H  HCH2  0   0.238   1.8078   1.6492  -0.1007
 9EV  H17  H  HCH2  0   0.264   1.6578   0.2535  -1.1650
 9EV  H18  H  HCH1  0   0.269   6.7048   2.2285  -0.9775
 9EV  H21  H  HNH2  0   0.344   6.5454   0.1429  -3.0094
 9EV  H22  H  HNH2  0   0.359   5.7269   1.5406  -2.9590
 9EV  H24  H  HOH1  0   0.497  -4.4529   0.8195  -3.5511
 9EV  H25  H  HOH1  0   0.506  -7.3690   0.7898  -2.4448
 9EV  H26  H  HOH1  0   0.483   0.9147  -1.7738   0.9546
 9EV  OXT  O  OH1   0  -0.595   8.5294   1.0741   0.3054
 9EV  HXT  H  HOH1  0   0.481   9.4041   0.7167   0.5206
 9EV  C01  C  CH3   0  -0.719  -1.2775  -4.7292   1.6345
 9EV  C19  C  CH2   0  -0.284   1.8897   0.5552  -0.1430

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
 9EV  O09  P08  double    1.474  0.020  1.474
 9EV  P08  O11  single    1.592  0.020  1.592
 9EV  P08  O10  single    1.597  0.020  1.597
 9EV  P08  O07  single    1.599  0.020  1.599
 9EV  O07  C06  single    1.427  0.020  1.427
 9EV  C06  C05  single    1.506  0.020  1.506
 9EV  O16  C15  double    1.196  0.020  1.196
 9EV  O14  C15  single    1.336  0.020  1.336
 9EV  O14  C13  single    1.439  0.020  1.439
 9EV  C15  C17  single    1.509  0.020  1.509
 9EV  C05  C04  aromatic  1.383  0.020  1.383
 9EV  C05  C12  aromatic  1.404  0.020  1.404
 9EV  C13  C12  single    1.516  0.020  1.516
 9EV  C13  N18  single    1.454  0.020  1.454
 9EV  C04  N03  aromatic  1.330  0.020  1.330
 9EV  C17  N18  single    1.459  0.020  1.459
 9EV  C12  C28  aromatic  1.397  0.020  1.397
 9EV  N18  C19  single    1.470  0.020  1.470
 9EV  C19  C20  single    1.519  0.020  1.519
 9EV  N03  C02  aromatic  1.318  0.020  1.318
 9EV  N24  C23  single    1.447  0.020  1.447
 9EV  C28  C02  aromatic  1.408  0.020  1.408
 9EV  C28  O29  single    1.336  0.020  1.336
 9EV  C02  C01  single    1.497  0.020  1.497
 9EV  C21  C20  single    1.524  0.020  1.524
 9EV  C21  C22  single    1.523  0.020  1.523
 9EV  C23  C22  single    1.542  0.020  1.542
 9EV  C23  C1   single    1.515  0.020  1.515
 9EV  O27  C1   double    1.205  0.020  1.205
 9EV  C13  H1   single    0.970  0.020  1.090
 9EV  C17  H2   single    0.970  0.020  1.090
 9EV  C17  H3   single    0.970  0.020  1.090
 9EV  C20  H4   single    0.970  0.020  1.090
 9EV  C20  H5   single    0.970  0.020  1.090
 9EV  C21  H6   single    0.970  0.020  1.090
 9EV  C21  H7   single    0.970  0.020  1.090
 9EV  C22  H8   single    0.970  0.020  1.090
 9EV  C22  H9   single    0.970  0.020  1.090
 9EV  C01  H10  single    0.970  0.020  1.090
 9EV  C01  H11  single    0.970  0.020  1.090
 9EV  C01  H12  single    0.970  0.020  1.090
 9EV  C04  H13  single    0.930  0.020  1.080
 9EV  C06  H14  single    0.970  0.020  1.090
 9EV  C06  H15  single    0.970  0.020  1.090
 9EV  C19  H16  single    0.970  0.020  1.090
 9EV  C19  H17  single    0.970  0.020  1.090
 9EV  C23  H18  single    0.970  0.020  1.090
 9EV  N24  H21  single    0.890  0.020  1.040
 9EV  N24  H22  single    0.890  0.020  1.040
 9EV  O10  H24  single    0.850  0.020  0.980
 9EV  O11  H25  single    0.850  0.020  0.980
 9EV  O29  H26  single    0.850  0.020  0.980
 9EV  C1   OXT  single    1.328  0.020  1.328
 9EV  OXT  HXT  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
 9EV  H1   C13  O14  107.24  3.000
 9EV  H1   C13  N18  110.02  3.000
 9EV  O14  C13  N18  105.80  3.000
 9EV  H1   C13  C12  109.64  3.000
 9EV  N18  C13  C12  114.55  3.000
 9EV  O14  C13  C12  109.28  3.000
 9EV  O16  C15  O14  122.70  3.000
 9EV  O14  C15  C17  107.99  3.000
 9EV  O16  C15  C17  129.31  3.000
 9EV  H3   C17  H2   107.10  3.000
 9EV  H3   C17  N18  112.22  3.000
 9EV  H2   C17  N18  112.59  3.000
 9EV  H3   C17  C15  109.31  3.000
 9EV  H2   C17  C15  111.26  3.000
 9EV  N18  C17  C15  104.38  3.000
 9EV  H5   C20  H4   106.78  3.000
 9EV  H5   C20  C19  110.64  3.000
 9EV  H4   C20  C19  109.27  3.000
 9EV  H5   C20  C21  109.03  3.000
 9EV  H4   C20  C21  110.02  3.000
 9EV  C19  C20  C21  111.01  3.000
 9EV  H7   C21  H6   106.58  3.000
 9EV  H7   C21  C22  109.41  3.000
 9EV  H6   C21  C22  109.90  3.000
 9EV  H7   C21  C20  109.35  3.000
 9EV  H6   C21  C20  109.13  3.000
 9EV  C22  C21  C20  112.30  3.000
 9EV  H9   C22  H8   106.85  3.000
 9EV  H9   C22  C23  109.34  3.000
 9EV  H8   C22  C23  109.50  3.000
 9EV  H9   C22  C21  109.56  3.000
 9EV  H8   C22  C21  109.07  3.000
 9EV  C23  C22  C21  112.36  3.000
 9EV  O29  C28  C12  124.16  3.000
 9EV  O29  C28  C02  116.62  3.000
 9EV  C12  C28  C02  119.21  3.000
 9EV  N03  C02  C01  118.60  3.000
 9EV  C01  C02  C28  119.93  3.000
 9EV  N03  C02  C28  121.47  3.000
 9EV  H13  C04  N03  115.87  3.000
 9EV  H13  C04  C05  120.79  3.000
 9EV  N03  C04  C05  123.34  3.000
 9EV  C12  C05  C06  121.62  3.000
 9EV  C12  C05  C04  118.16  3.000
 9EV  C06  C05  C04  120.22  3.000
 9EV  H15  C06  H14  107.64  3.000
 9EV  H15  C06  O07  109.32  3.000
 9EV  H14  C06  O07  109.64  3.000
 9EV  H15  C06  C05  110.77  3.000
 9EV  H14  C06  C05  110.70  3.000
 9EV  O07  C06  C05  108.75  3.000
 9EV  C05  C12  C28  118.00  3.000
 9EV  C28  C12  C13  122.44  3.000
 9EV  C05  C12  C13  119.47  3.000
 9EV  H18  C23  N24  107.60  3.000
 9EV  H18  C23  C1   107.57  3.000
 9EV  N24  C23  C1   109.02  3.000
 9EV  H18  C23  C22  107.65  3.000
 9EV  C1   C23  C22  108.98  3.000
 9EV  N24  C23  C22  115.72  3.000
 9EV  OXT  C1   O27  123.29  3.000
 9EV  OXT  C1   C23  111.99  3.000
 9EV  O27  C1   C23  124.70  3.000
 9EV  C04  N03  C02  119.75  3.000
 9EV  C19  N18  C17  113.65  3.000
 9EV  C19  N18  C13  113.20  3.000
 9EV  C17  N18  C13  103.86  3.000
 9EV  H22  N24  H21  106.32  3.000
 9EV  H22  N24  C23  109.37  3.000
 9EV  H21  N24  C23  110.45  3.000
 9EV  P08  O07  C06  119.10  3.000
 9EV  H24  O10  P08  115.97  3.000
 9EV  H25  O11  P08  114.04  3.000
 9EV  C15  O14  C13  109.73  3.000
 9EV  H26  O29  C28  107.19  3.000
 9EV  O11  P08  O10  108.10  3.000
 9EV  O10  P08  O09  109.54  3.000
 9EV  O11  P08  O09  118.20  3.000
 9EV  O10  P08  O07  106.83  3.000
 9EV  O11  P08  O07   96.63  3.000
 9EV  O09  P08  O07  116.40  3.000
 9EV  HXT  OXT  C1   110.13  3.000
 9EV  H12  C01  H11  108.40  3.000
 9EV  H12  C01  H10  106.84  3.000
 9EV  H11  C01  H10  108.30  3.000
 9EV  H12  C01  C02  111.68  3.000
 9EV  H11  C01  C02  109.84  3.000
 9EV  H10  C01  C02  111.64  3.000
 9EV  H17  C19  H16  107.22  3.000
 9EV  H17  C19  N18  107.25  3.000
 9EV  H16  C19  N18  111.05  3.000
 9EV  H17  C19  C20  108.89  3.000
 9EV  H16  C19  C20  110.09  3.000
 9EV  N18  C19  C20  112.16  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
 9EV  CONST_01  C04  C05  C12  C28     0.00   0.0  0
 9EV  CONST_02  C04  N03  C02  C28     0.00   0.0  0
 9EV  CONST_03  C05  C04  N03  C02     0.00   0.0  0
 9EV  CONST_04  C05  C12  C28  C02     0.00   0.0  0
 9EV  CONST_05  N03  C04  C05  C12     0.00   0.0  0
 9EV  CONST_06  N03  C02  C28  C12     0.00   0.0  0
 9EV  CONST_07  C04  C05  C12  C13   180.00   0.0  0
 9EV  CONST_08  C02  C28  C12  C13   180.00   0.0  0
 9EV  CONST_09  C06  C05  C12  C13     0.00   0.0  0
 9EV  CONST_10  O29  C28  C12  C13     0.00   0.0  0
 9EV  CONST_11  C06  C05  C12  C28   180.00   0.0  0
 9EV  CONST_12  C04  N03  C02  C01   180.00   0.0  0
 9EV  CONST_13  C12  C28  C02  C01   180.00   0.0  0
 9EV  CONST_14  O29  C28  C12  C05   180.00   0.0  0
 9EV  CONST_15  N03  C04  C05  C06   180.00   0.0  0
 9EV  CONST_16  O29  C28  C02  N03   180.00   0.0  0
 9EV  CONST_17  H13  C04  N03  C02   180.00   0.0  0
 9EV  CONST_18  HXT  OXT  C1   C23   180.00   0.0  0
 9EV  Var_01    C17  C15  O14  C13     5.60  30.0  1
 9EV  Var_02    C15  C17  N18  C13   -25.06  30.0  1
 9EV  Var_03    O14  C15  C17  N18    12.60  30.0  1
 9EV  Var_04    C20  C19  N18  C13  -167.92  30.0  3
 9EV  Var_05    O07  C06  C05  C04   -23.91  30.0  1
 9EV  Var_06    H10  C01  C02  C28    61.32  30.0  2
 9EV  Var_07    N18  C19  C20  C21  -179.40  30.0  1
 9EV  Var_08    C23  C22  C21  C20  -174.74  30.0  3
 9EV  Var_09    C19  C20  C21  C22  -179.22  30.0  3
 9EV  Var_10    O09  P08  O07  C06   -48.55  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
 9EV  chir_01  C13  O14  C12  N18  positiv
 9EV  chir_02  C23  N24  C22  C1   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
 9EV  plan-1  C13  0.020
 9EV  plan-1  C28  0.020
 9EV  plan-1  C02  0.020
 9EV  plan-1  C04  0.020
 9EV  plan-1  C05  0.020
 9EV  plan-1  C06  0.020
 9EV  plan-1  C12  0.020
 9EV  plan-1  N03  0.020
 9EV  plan-1  O29  0.020
 9EV  plan-1  H13  0.020
 9EV  plan-1  C01  0.020
 9EV  plan-2  C15  0.020
 9EV  plan-2  C17  0.020
 9EV  plan-2  O14  0.020
 9EV  plan-2  O16  0.020
 9EV  plan-3  C23  0.020
 9EV  plan-3  C1   0.020
 9EV  plan-3  O27  0.020
 9EV  plan-3  OXT  0.020
 9EV  plan-3  HXT  0.020

