FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: VZRL1

Calculation Name: 6WRS-S-Other547

Preferred Name:

Target Type:

Ligand Name: tedizolid

Ligand 3-letter code: U7V

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6WRS

Chain ID: S

ChEMBL ID:

UniProt ID: Q2FW38

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1653964.976186
FMO2-HF: Nuclear repulsion 1581876.562386
FMO2-HF: Total energy -72088.4138
FMO2-MP2: Total energy -72302.206697


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:16:SER)


Summations of interaction energy for fragment #1(A:16:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-95.201-90.7640.371-2.127-2.681-0.015
Interaction energy analysis for fragmet #1(A:16:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.909
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A18GLU-1-0.866-0.9103.511-35.160-33.105-0.007-0.872-1.176-0.001
4A19LEU0-0.054-0.0292.695-17.880-15.7690.378-1.188-1.301-0.014
5A20SER00.0270.0025.0744.2774.322-0.001-0.007-0.0370.000
110A125VAL0-0.010-0.0083.8052.8863.1120.001-0.060-0.1670.000
6A21ASP-1-0.980-0.9896.974-27.607-27.6070.0000.0000.0000.000
7A22ALA00.0330.0249.6551.6601.6600.0000.0000.0000.000
8A23VAL0-0.054-0.03311.3961.4711.4710.0000.0000.0000.000
9A24PHE0-0.043-0.0408.5781.4601.4600.0000.0000.0000.000
10A25GLY00.0300.01711.195-0.691-0.6910.0000.0000.0000.000
11A26ILE0-0.053-0.00912.1890.9840.9840.0000.0000.0000.000
12A27GLU-1-0.869-0.91215.879-15.509-15.5090.0000.0000.0000.000
13A28PRO0-0.011-0.00417.1040.6390.6390.0000.0000.0000.000
14A29ASN00.0160.00819.6280.9330.9330.0000.0000.0000.000
15A30ASN00.0590.00922.983-0.183-0.1830.0000.0000.0000.000
16A31SER0-0.008-0.00824.9290.1850.1850.0000.0000.0000.000
17A32VAL0-0.025-0.00925.4650.3270.3270.0000.0000.0000.000
18A33LEU00.0260.01921.0380.2200.2200.0000.0000.0000.000
19A34PHE00.0040.00324.7820.1610.1610.0000.0000.0000.000
20A35GLU-1-0.917-0.96428.079-9.518-9.5180.0000.0000.0000.000
21A36ALA0-0.010-0.02025.5100.2310.2310.0000.0000.0000.000
22A37ILE00.0260.02323.8040.2050.2050.0000.0000.0000.000
23A38ASN0-0.035-0.01727.5120.3000.3000.0000.0000.0000.000
24A39LEU0-0.028-0.00330.3290.2500.2500.0000.0000.0000.000
25A40GLN00.0230.00825.7410.0080.0080.0000.0000.0000.000
26A41ARG10.9710.98229.8919.5179.5170.0000.0000.0000.000
27A42ALA0-0.041-0.01931.7530.2700.2700.0000.0000.0000.000
28A43SER0-0.051-0.06132.7960.3610.3610.0000.0000.0000.000
29A44LEU0-0.0030.02130.8970.1150.1150.0000.0000.0000.000
30A45ARG10.9180.97934.8377.7947.7940.0000.0000.0000.000
31A46GLN00.0280.00138.194-0.009-0.0090.0000.0000.0000.000
32A47GLY00.0450.01541.2480.0590.0590.0000.0000.0000.000
33A48THR0-0.0210.00444.866-0.034-0.0340.0000.0000.0000.000
34A49HIS0-0.023-0.01945.7290.0330.0330.0000.0000.0000.000
35A50ALA00.0090.00249.5280.0130.0130.0000.0000.0000.000
36A51VAL00.0150.01553.1540.0400.0400.0000.0000.0000.000
37A52LYS10.9270.96656.6665.4115.4110.0000.0000.0000.000
38A53ASN00.0760.03360.2100.0350.0350.0000.0000.0000.000
39A54ARG10.9400.94361.7934.6764.6760.0000.0000.0000.000
40A55SER00.0080.02164.0540.0500.0500.0000.0000.0000.000
41A56ALA00.0200.02862.1430.0230.0230.0000.0000.0000.000
42A57VAL0-0.040-0.01664.071-0.019-0.0190.0000.0000.0000.000
43A58SER00.0620.03765.8850.0800.0800.0000.0000.0000.000
44A59GLY00.0610.02768.9860.0220.0220.0000.0000.0000.000
45A60GLY00.007-0.01471.836-0.036-0.0360.0000.0000.0000.000
46A61GLY00.0070.00774.241-0.007-0.0070.0000.0000.0000.000
47A62ARG10.9660.99275.5543.9683.9680.0000.0000.0000.000
48A63LYS10.8930.94877.8873.9503.9500.0000.0000.0000.000
49A64PRO0-0.041-0.00878.0460.0390.0390.0000.0000.0000.000
50A65TRP00.020-0.00178.8890.0370.0370.0000.0000.0000.000
51A66LYS10.9950.99383.2533.5173.5170.0000.0000.0000.000
52A67GLN00.001-0.01681.257-0.041-0.0410.0000.0000.0000.000
53A68LYS10.9990.99384.9243.5933.5930.0000.0000.0000.000
54A69GLY00.0500.02387.8990.0160.0160.0000.0000.0000.000
55A70THR0-0.004-0.00585.9160.0220.0220.0000.0000.0000.000
56A71GLY00.0730.05987.059-0.023-0.0230.0000.0000.0000.000
57A72ARG10.9090.94879.9143.9093.9090.0000.0000.0000.000
58A73ALA00.0710.04378.5430.0130.0130.0000.0000.0000.000
59A74ARG10.9850.99378.2474.0394.0390.0000.0000.0000.000
60A75GLN00.0670.03675.024-0.105-0.1050.0000.0000.0000.000
61A76GLY00.002-0.00675.9220.0620.0620.0000.0000.0000.000
62A77THR00.0090.00071.5080.0010.0010.0000.0000.0000.000
63A78ILE00.0140.01772.988-0.020-0.0200.0000.0000.0000.000
64A79ARG10.8370.92568.5544.5664.5660.0000.0000.0000.000
65A80ALA0-0.016-0.00868.605-0.041-0.0410.0000.0000.0000.000
66A81PRO00.0680.02264.5700.0180.0180.0000.0000.0000.000
67A82GLN00.0150.02166.281-0.093-0.0930.0000.0000.0000.000
68A83TRP0-0.045-0.02568.8540.0850.0850.0000.0000.0000.000
69A84ARG11.0121.00167.9674.5324.5320.0000.0000.0000.000
70A85GLY0-0.010-0.02167.4270.0520.0520.0000.0000.0000.000
71A86GLY0-0.016-0.00565.3130.0130.0130.0000.0000.0000.000
72A87GLY00.0120.02064.3020.0530.0530.0000.0000.0000.000
73A88ILE0-0.0100.00057.7600.0100.0100.0000.0000.0000.000
74A89VAL0-0.010-0.02760.3950.0390.0390.0000.0000.0000.000
75A90PHE0-0.001-0.00555.949-0.032-0.0320.0000.0000.0000.000
76A91GLY00.0610.04754.747-0.061-0.0610.0000.0000.0000.000
77A92PRO0-0.019-0.00650.242-0.029-0.0290.0000.0000.0000.000
78A93THR00.025-0.00150.4710.1660.1660.0000.0000.0000.000
79A94PRO0-0.028-0.01348.500-0.144-0.1440.0000.0000.0000.000
80A95ARG10.9370.97845.3336.8996.8990.0000.0000.0000.000
81A96SER00.0350.01241.220-0.105-0.1050.0000.0000.0000.000
82A97TYR0-0.017-0.02839.2900.1800.1800.0000.0000.0000.000
83A98ALA00.0400.04536.329-0.128-0.1280.0000.0000.0000.000
84A99TYR00.0290.01433.6430.2620.2620.0000.0000.0000.000
85A100LYS10.9000.94233.8688.6218.6210.0000.0000.0000.000
86A101MET00.1260.09427.1480.1450.1450.0000.0000.0000.000
87A102PRO00.0470.00230.795-0.124-0.1240.0000.0000.0000.000
88A103LYS10.9550.96228.6149.5919.5910.0000.0000.0000.000
89A104LYS11.0021.00426.32110.09810.0980.0000.0000.0000.000
90A105MET00.0400.03525.409-0.299-0.2990.0000.0000.0000.000
91A106ARG10.9130.93425.38310.13110.1310.0000.0000.0000.000
92A107ARG10.8390.91920.93113.56213.5620.0000.0000.0000.000
93A108LEU00.0290.02520.832-0.518-0.5180.0000.0000.0000.000
94A109ALA0-0.0010.00620.740-0.484-0.4840.0000.0000.0000.000
95A110LEU00.0170.01318.274-0.223-0.2230.0000.0000.0000.000
96A111ARG10.9881.01215.99615.33415.3340.0000.0000.0000.000
97A112SER0-0.022-0.01215.939-0.606-0.6060.0000.0000.0000.000
98A113ALA0-0.019-0.01417.034-0.410-0.4100.0000.0000.0000.000
99A114LEU0-0.004-0.00712.599-0.358-0.3580.0000.0000.0000.000
100A115SER00.010-0.01612.290-1.882-1.8820.0000.0000.0000.000
101A116PHE0-0.028-0.01913.182-0.533-0.5330.0000.0000.0000.000
102A117LYS10.8240.92111.87018.25418.2540.0000.0000.0000.000
103A118VAL0-0.0020.0027.797-1.092-1.0920.0000.0000.0000.000
104A119GLN0-0.039-0.02710.1450.1160.1160.0000.0000.0000.000
105A120GLU-1-0.922-0.94912.628-16.689-16.6890.0000.0000.0000.000
106A121ASN0-0.095-0.0439.237-1.943-1.9430.0000.0000.0000.000
107A122GLY00.0450.03410.823-0.493-0.4930.0000.0000.0000.000
108A123LEU0-0.028-0.0236.0971.6911.6910.0000.0000.0000.000
109A124THR0-0.015-0.0056.700-3.443-3.4430.0000.0000.0000.000
111A126VAL0-0.055-0.0245.501-4.440-4.4400.0000.0000.0000.000
112A127ASP-1-0.826-0.9237.605-25.466-25.4660.0000.0000.0000.000
113A128ALA0-0.044-0.0189.5500.9700.9700.0000.0000.0000.000
114A129PHE0-0.014-0.01513.0310.1170.1170.0000.0000.0000.000
115A130ASN00.0190.01415.8240.0030.0030.0000.0000.0000.000
116A131PHE0-0.011-0.00117.7220.5430.5430.0000.0000.0000.000
117A132GLU-1-0.838-0.92321.571-13.526-13.5260.0000.0000.0000.000
118A133ALA0-0.051-0.02824.7110.5730.5730.0000.0000.0000.000
119A134PRO00.0040.00225.656-0.434-0.4340.0000.0000.0000.000
120A135LYS10.9200.97525.69411.05911.0590.0000.0000.0000.000
121A136THR00.0490.00424.959-0.501-0.5010.0000.0000.0000.000
122A137LYS10.9170.96524.77110.54810.5480.0000.0000.0000.000
123A138GLU-1-0.822-0.91422.183-12.258-12.2580.0000.0000.0000.000
124A139PHE00.0610.03017.816-0.475-0.4750.0000.0000.0000.000
125A140LYS10.9450.97419.98212.83312.8330.0000.0000.0000.000
126A141ASN0-0.054-0.02920.918-0.141-0.1410.0000.0000.0000.000
127A142VAL00.0570.03515.186-0.408-0.4080.0000.0000.0000.000
128A143LEU00.0290.00215.825-0.894-0.8940.0000.0000.0000.000
129A144SER0-0.079-0.03616.539-0.126-0.1260.0000.0000.0000.000
130A145THR0-0.070-0.04415.595-0.252-0.2520.0000.0000.0000.000
131A146LEU0-0.0030.00710.303-0.982-0.9820.0000.0000.0000.000
132A147GLU-1-0.945-0.95912.267-21.633-21.6330.0000.0000.0000.000
133A148GLN0-0.0090.01110.6000.4030.4030.0000.0000.0000.000
134A149PRO00.009-0.00414.9221.3671.3670.0000.0000.0000.000
135A150LYS10.9080.95318.13212.10512.1050.0000.0000.0000.000
136A151LYS10.7850.89320.59614.11214.1120.0000.0000.0000.000
137A152VAL00.0380.01816.287-0.649-0.6490.0000.0000.0000.000
138A153LEU0-0.034-0.00816.0770.9140.9140.0000.0000.0000.000
139A154VAL0-0.005-0.00114.826-1.396-1.3960.0000.0000.0000.000
140A155VAL0-0.025-0.00913.5571.1371.1370.0000.0000.0000.000
141A156THR00.017-0.00813.813-1.556-1.5560.0000.0000.0000.000
142A157GLU-1-0.895-0.96214.994-17.273-17.2730.0000.0000.0000.000
143A158ASN0-0.025-0.01616.4221.1471.1470.0000.0000.0000.000
144A159GLU-1-0.923-0.96519.775-12.704-12.7040.0000.0000.0000.000
145A160ASP-1-0.854-0.91618.459-15.452-15.4520.0000.0000.0000.000
146A161VAL00.023-0.01421.977-0.016-0.0160.0000.0000.0000.000
147A162ASN0-0.029-0.02323.3900.5890.5890.0000.0000.0000.000
148A163VAL0-0.024-0.00918.2360.0450.0450.0000.0000.0000.000
149A164GLU-1-0.839-0.89721.550-11.431-11.4310.0000.0000.0000.000
150A165LEU0-0.012-0.00724.0400.4080.4080.0000.0000.0000.000
151A166SER0-0.045-0.03123.0860.4810.4810.0000.0000.0000.000
152A167ALA0-0.013-0.00621.138-0.019-0.0190.0000.0000.0000.000
153A168ARG10.9070.95023.20410.66810.6680.0000.0000.0000.000
154A169ASN0-0.056-0.03025.9340.5380.5380.0000.0000.0000.000
155A170ILE0-0.032-0.01122.6840.3560.3560.0000.0000.0000.000
156A171PRO0-0.019-0.02625.369-0.223-0.2230.0000.0000.0000.000
157A172GLY0-0.0170.00023.708-0.175-0.1750.0000.0000.0000.000
158A173VAL0-0.0060.01019.811-0.637-0.6370.0000.0000.0000.000
159A174GLN0-0.043-0.01420.4641.0391.0390.0000.0000.0000.000
160A175VAL00.0150.00719.436-0.889-0.8890.0000.0000.0000.000
161A176THR0-0.042-0.01818.6470.5230.5230.0000.0000.0000.000
162A177THR00.0500.02418.355-0.433-0.4330.0000.0000.0000.000
163A178ALA00.0430.01916.0730.1050.1050.0000.0000.0000.000
164A179GLN0-0.047-0.01417.3660.2530.2530.0000.0000.0000.000
165A180GLY0-0.046-0.01420.5440.6000.6000.0000.0000.0000.000
166A181LEU00.0150.01115.2580.1220.1220.0000.0000.0000.000
167A182ASN0-0.017-0.00419.6250.8550.8550.0000.0000.0000.000
168A183VAL00.0410.00820.439-0.471-0.4710.0000.0000.0000.000
169A184LEU0-0.024-0.01721.662-0.199-0.1990.0000.0000.0000.000
170A185ASP-1-0.840-0.92020.639-14.340-14.3400.0000.0000.0000.000
171A186ILE00.0630.03515.561-0.179-0.1790.0000.0000.0000.000
172A187THR0-0.055-0.03717.823-0.483-0.4830.0000.0000.0000.000
173A188ASN0-0.049-0.02020.5220.2360.2360.0000.0000.0000.000
174A189ALA00.0040.02117.6370.3020.3020.0000.0000.0000.000
175A190ASP-1-0.849-0.93017.782-15.048-15.0480.0000.0000.0000.000
176A191SER0-0.033-0.02612.676-1.055-1.0550.0000.0000.0000.000
177A192LEU0-0.027-0.01611.1641.6011.6010.0000.0000.0000.000
178A193VAL00.0260.01010.454-2.314-2.3140.0000.0000.0000.000
179A194ILE00.0050.0027.7502.3122.3120.0000.0000.0000.000
180A195THR00.0220.0228.723-2.790-2.7900.0000.0000.0000.000
181A196GLU-1-0.826-0.9316.462-36.436-36.4360.0000.0000.0000.000
182A197ALA00.0030.0088.2280.7290.7290.0000.0000.0000.000
183A198ALA00.011-0.01011.8331.2821.2820.0000.0000.0000.000
184A199ALA0-0.0110.0048.0121.2171.2170.0000.0000.0000.000
185A200LYS10.9620.9838.91831.02431.0240.0000.0000.0000.000
186A201LYS10.8460.92511.73618.13118.1310.0000.0000.0000.000
187A202VAL0-0.016-0.02312.5791.4461.4460.0000.0000.0000.000
188A203GLU-1-0.873-0.93710.291-25.479-25.4790.0000.0000.0000.000
189A204GLU-1-0.858-0.92013.314-15.753-15.7530.0000.0000.0000.000
190A205VAL0-0.049-0.00816.3421.3171.3170.0000.0000.0000.000
191A206LEU0-0.095-0.06515.9631.4331.4330.0000.0000.0000.000
192A207GLY-1-0.887-0.93016.258-17.416-17.4160.0000.0000.0000.000