FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: R1778

Calculation Name: 7JJC-AE-Xray89

Preferred Name:

Target Type:

Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 7JJC

Chain ID: AE

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1795229.283419
FMO2-HF: Nuclear repulsion 1727805.709284
FMO2-HF: Total energy -67423.574135
FMO2-MP2: Total energy -67618.88604


3D Structure
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:-3:GLY )


Summations of interaction energy for fragment #1(A:-3:GLY )
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.
-5.658-3.1290.182-1.324-1.3870.006
Interaction energy analysis for fragmet #1(A:-3:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.014
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].
3A-1HIS 10.8600.9083.219-5.839-3.3100.182-1.324-1.3870.006
4A0MET 00.0270.0125.790-0.174-0.1740.0000.0000.0000.000
5A273PHE 0-0.0050.0069.2600.0820.0820.0000.0000.0000.000
6A274LYS 10.9110.96412.549-0.110-0.1100.0000.0000.0000.000
7A424CYS 0-0.095-0.04215.2120.0320.0320.0000.0000.0000.000
8A276MET 00.0190.01718.731-0.019-0.0190.0000.0000.0000.000
9A277GLU -1-0.831-0.89116.6510.0810.0810.0000.0000.0000.000
10A278ALA 0-0.009-0.00120.2230.0110.0110.0000.0000.0000.000
11A279LEU 0-0.028-0.03020.5460.0230.0230.0000.0000.0000.000
12A280GLY 00.0640.01922.3360.0170.0170.0000.0000.0000.000
13A281MET 0-0.044-0.00223.999-0.003-0.0030.0000.0000.0000.000
14A282GLU -1-0.874-0.92226.2400.0400.0400.0000.0000.0000.000
15A283SER 0-0.021-0.03222.8540.0010.0010.0000.0000.0000.000
16A284GLY 00.0240.02124.886-0.005-0.0050.0000.0000.0000.000
17A285GLU -1-0.863-0.87819.5580.2670.2670.0000.0000.0000.000
18A286ILE 0-0.047-0.00323.1740.0150.0150.0000.0000.0000.000
19A287HIS 00.0800.03824.437-0.029-0.0290.0000.0000.0000.000
20A288SER 00.019-0.01728.723-0.002-0.0020.0000.0000.0000.000
21A289ASP -1-0.893-0.90631.5690.1140.1140.0000.0000.0000.000
22A290GLN 0-0.0010.00025.9470.0000.0000.0000.0000.0000.000
23A291ILE 0-0.040-0.00630.8230.0000.0000.0000.0000.0000.000
24A292THR 0-0.010-0.01233.741-0.006-0.0060.0000.0000.0000.000
25A293ALA 0-0.001-0.02337.2250.0000.0000.0000.0000.0000.000
26A294SER 0-0.023-0.02440.1220.0010.0010.0000.0000.0000.000
27A295SER 00.005-0.00843.427-0.002-0.0020.0000.0000.0000.000
28A296GLN 00.0150.00442.2740.0030.0030.0000.0000.0000.000
29A297TYR 0-0.017-0.00645.187-0.001-0.0010.0000.0000.0000.000
30A298SER 00.024-0.01246.511-0.001-0.0010.0000.0000.0000.000
31A299THR 00.0600.02544.2560.0010.0010.0000.0000.0000.000
32A300ASN 0-0.0210.00143.2400.0030.0030.0000.0000.0000.000
33A301TRP 0-0.093-0.05942.801-0.002-0.0020.0000.0000.0000.000
34A302SER 00.030-0.01940.2570.0000.0000.0000.0000.0000.000
35A303ALA 00.0600.01937.7710.0000.0000.0000.0000.0000.000
36A304GLU -1-0.817-0.85835.2590.0600.0600.0000.0000.0000.000
37A305ARG 10.8310.91934.974-0.038-0.0380.0000.0000.0000.000
38A306SER 0-0.056-0.04035.015-0.003-0.0030.0000.0000.0000.000
39A307ARG 10.8470.91428.339-0.093-0.0930.0000.0000.0000.000
40A308LEU 0-0.001-0.00129.075-0.007-0.0070.0000.0000.0000.000
41A309ASN 0-0.052-0.04329.996-0.003-0.0030.0000.0000.0000.000
42A310TYR 00.0340.03033.175-0.004-0.0040.0000.0000.0000.000
43A311PRO 00.0410.03034.778-0.004-0.0040.0000.0000.0000.000
44A312GLU -1-0.951-0.98537.4070.0240.0240.0000.0000.0000.000
45A313ASN 0-0.015-0.01440.4390.0010.0010.0000.0000.0000.000
46A314GLY 00.0790.03939.0930.0000.0000.0000.0000.0000.000
47A315TRP 0-0.0070.01138.9790.0000.0000.0000.0000.0000.000
48A316THR 0-0.014-0.03540.572-0.003-0.0030.0000.0000.0000.000
49A317PRO 0-0.0360.00943.8930.0010.0010.0000.0000.0000.000
50A318GLY 00.017-0.00345.635-0.002-0.0020.0000.0000.0000.000
51A319GLU -1-0.842-0.92549.0600.0260.0260.0000.0000.0000.000
52A320ASP -1-0.797-0.86648.7460.0310.0310.0000.0000.0000.000
53A321SER 00.016-0.00348.912-0.001-0.0010.0000.0000.0000.000
54A322TYR 00.0500.01145.8330.0020.0020.0000.0000.0000.000
55A323ARG 10.8630.92145.120-0.044-0.0440.0000.0000.0000.000
56A324GLU -1-0.799-0.82944.7360.0460.0460.0000.0000.0000.000
57A325TRP 0-0.046-0.03838.5460.0010.0010.0000.0000.0000.000
58A326ILE 0-0.0120.00836.115-0.001-0.0010.0000.0000.0000.000
59A327GLN 0-0.0050.00434.660-0.004-0.0040.0000.0000.0000.000
60A328VAL 00.0310.01229.011-0.002-0.0020.0000.0000.0000.000
61A329ASP -1-0.777-0.84029.5100.1490.1490.0000.0000.0000.000
62A330LEU 00.002-0.00424.6880.0040.0040.0000.0000.0000.000
63A331GLY 00.0280.02324.7600.0210.0210.0000.0000.0000.000
64A332LEU 0-0.035-0.02420.1170.0090.0090.0000.0000.0000.000
65A333LEU 0-0.032-0.01223.563-0.013-0.0130.0000.0000.0000.000
66A334ARG 10.8890.94918.381-0.254-0.2540.0000.0000.0000.000
67A335PHE 00.0230.00118.671-0.024-0.0240.0000.0000.0000.000
68A336VAL 0-0.010-0.01221.7840.0040.0040.0000.0000.0000.000
69A337THR 0-0.009-0.04922.349-0.002-0.0020.0000.0000.0000.000
70A338ALA 00.0160.01725.295-0.014-0.0140.0000.0000.0000.000
71A339VAL 0-0.0040.01527.6480.0110.0110.0000.0000.0000.000
72A340GLY 00.0060.01730.070-0.008-0.0080.0000.0000.0000.000
73A341THR 0-0.014-0.00831.1490.0050.0050.0000.0000.0000.000
74A342GLN 00.014-0.00734.253-0.001-0.0010.0000.0000.0000.000
75A343GLY 00.0270.03836.8040.0030.0030.0000.0000.0000.000
76A344ALA 0-0.0050.00739.1950.0020.0020.0000.0000.0000.000
77A345ILE 0-0.053-0.02841.590-0.002-0.0020.0000.0000.0000.000
78A346SER 0-0.034-0.04344.0090.0010.0010.0000.0000.0000.000
79A347LYS 10.9160.95741.174-0.024-0.0240.0000.0000.0000.000
80A348GLU -1-0.768-0.86846.6110.0230.0230.0000.0000.0000.000
81A349THR 0-0.046-0.03549.728-0.001-0.0010.0000.0000.0000.000
82A350LYS 10.8230.91347.861-0.014-0.0140.0000.0000.0000.000
83A351LYS 10.8760.94749.215-0.020-0.0200.0000.0000.0000.000
84A352LYS 10.9290.96646.325-0.009-0.0090.0000.0000.0000.000
85A353TYR 0-0.052-0.04144.8310.0000.0000.0000.0000.0000.000
86A354TYR 00.0630.01341.9580.0000.0000.0000.0000.0000.000
87A355VAL 0-0.0030.00340.840-0.001-0.0010.0000.0000.0000.000
88A356LYS 10.8360.91741.310-0.019-0.0190.0000.0000.0000.000
89A357THR 0-0.037-0.01941.1580.0000.0000.0000.0000.0000.000
90A358TYR 00.014-0.01734.9200.0020.0020.0000.0000.0000.000
91A359LYS 10.8770.94638.922-0.041-0.0410.0000.0000.0000.000
92A360ILE 00.0280.01532.7240.0010.0010.0000.0000.0000.000
93A361ASP -1-0.790-0.86036.1380.0620.0620.0000.0000.0000.000
94A362VAL 0-0.023-0.01430.6710.0040.0040.0000.0000.0000.000
95A363SER 00.0420.00531.914-0.003-0.0030.0000.0000.0000.000
96A364SER 00.0440.02330.1070.0060.0060.0000.0000.0000.000
97A365ASN 00.016-0.00630.9010.0120.0120.0000.0000.0000.000
98A366GLY 00.0330.03833.653-0.001-0.0010.0000.0000.0000.000
99A367GLU -1-0.946-0.96935.4040.0880.0880.0000.0000.0000.000
100A368ASP -1-0.857-0.91637.4470.0770.0770.0000.0000.0000.000
101A369TRP 0-0.080-0.03734.5590.0060.0060.0000.0000.0000.000
102A370ILE 00.0120.00734.248-0.005-0.0050.0000.0000.0000.000
103A371THR 0-0.078-0.06235.9060.0010.0010.0000.0000.0000.000
104A372ILE 00.0160.02431.768-0.001-0.0010.0000.0000.0000.000
105A373LYS 10.8220.90635.637-0.054-0.0540.0000.0000.0000.000
106A374GLU -1-0.912-0.94836.3060.0430.0430.0000.0000.0000.000
107A375GLY 00.0420.01637.949-0.002-0.0020.0000.0000.0000.000
108A376ASN 00.027-0.00439.8360.0000.0000.0000.0000.0000.000
109A377LYS 10.9801.00041.718-0.034-0.0340.0000.0000.0000.000
110A378PRO 0-0.031-0.01840.0810.0010.0010.0000.0000.0000.000
111A379VAL 00.0060.01535.718-0.004-0.0040.0000.0000.0000.000
112A380LEU 0-0.020-0.00638.8060.0020.0020.0000.0000.0000.000
113A381PHE 00.0170.00633.202-0.003-0.0030.0000.0000.0000.000
114A382GLN 0-0.027-0.03037.608-0.003-0.0030.0000.0000.0000.000
115A383GLY 00.0470.03137.3860.0010.0010.0000.0000.0000.000
116A384ASN 0-0.0230.02136.8650.0010.0010.0000.0000.0000.000
117A385THR 00.0280.00140.091-0.001-0.0010.0000.0000.0000.000
118A386ASN 0-0.059-0.03140.3860.0010.0010.0000.0000.0000.000
119A387PRO 0-0.006-0.02141.3410.0020.0020.0000.0000.0000.000
120A388THR 0-0.024-0.01138.8220.0030.0030.0000.0000.0000.000
121A389ASP -1-0.829-0.89236.3870.0070.0070.0000.0000.0000.000
122A390VAL 00.005-0.00330.4290.0040.0040.0000.0000.0000.000
123A391VAL 0-0.0270.00033.757-0.004-0.0040.0000.0000.0000.000
124A392VAL 00.0190.01528.4520.0070.0070.0000.0000.0000.000
125A393ALA 0-0.0060.00731.722-0.007-0.0070.0000.0000.0000.000
126A394VAL 00.017-0.00428.0990.0080.0080.0000.0000.0000.000
127A395PHE 0-0.027-0.03428.120-0.003-0.0030.0000.0000.0000.000
128A396PRO 00.0190.00529.632-0.002-0.0020.0000.0000.0000.000
129A397LYS 10.9230.95926.903-0.089-0.0890.0000.0000.0000.000
130A398PRO 00.0150.00222.8860.0030.0030.0000.0000.0000.000
131A399LEU 0-0.052-0.01525.056-0.003-0.0030.0000.0000.0000.000
132A400ILE 00.0150.01922.7300.0090.0090.0000.0000.0000.000
133A401THR 0-0.023-0.01425.217-0.014-0.0140.0000.0000.0000.000
134A402ARG 10.8040.87525.855-0.138-0.1380.0000.0000.0000.000
135A403PHE 0-0.0030.01827.8520.0000.0000.0000.0000.0000.000
136A404VAL 00.004-0.00428.642-0.003-0.0030.0000.0000.0000.000
137A405ARG 10.8840.94331.738-0.078-0.0780.0000.0000.0000.000
138A406ILE 00.0110.00733.502-0.003-0.0030.0000.0000.0000.000
139A407LYS 10.8100.88737.050-0.060-0.0600.0000.0000.0000.000
140A408PRO 00.0050.00240.704-0.002-0.0020.0000.0000.0000.000
141A409ALA 0-0.053-0.02742.6510.0000.0000.0000.0000.0000.000
142A410THR 00.0190.01744.839-0.001-0.0010.0000.0000.0000.000
143A411TRP 00.0430.01944.9760.0020.0020.0000.0000.0000.000
144A412GLU -1-0.861-0.90746.5530.0150.0150.0000.0000.0000.000
145A413THR 0-0.0230.01147.8960.0010.0010.0000.0000.0000.000
146A414GLY 0-0.034-0.05148.3180.0000.0000.0000.0000.0000.000
147A415ILE 0-0.027-0.00343.5480.0000.0000.0000.0000.0000.000
148A416SER 00.024-0.00542.7430.0000.0000.0000.0000.0000.000
149A417MET 0-0.068-0.01737.153-0.001-0.0010.0000.0000.0000.000
150A418ARG 10.8090.92534.637-0.030-0.0300.0000.0000.0000.000
151A419PHE 0-0.016-0.02631.193-0.004-0.0040.0000.0000.0000.000
152A420GLU -1-0.696-0.82125.8680.1080.1080.0000.0000.0000.000
153A421VAL 0-0.006-0.01125.897-0.006-0.0060.0000.0000.0000.000
154A422TYR 0-0.001-0.00223.4310.0080.0080.0000.0000.0000.000
155A423GLY 00.0670.01721.644-0.005-0.0050.0000.0000.0000.000
156A425LYS 10.8580.92514.696-0.226-0.2260.0000.0000.0000.000
157A426ILE 00.0110.0128.585-0.035-0.0350.0000.0000.0000.000
158A427THR -1-0.831-0.8858.2450.4660.4660.0000.0000.0000.000
159E683ARG 10.9580.99152.370-0.025-0.0250.0000.0000.0000.000
160E684ALA 00.0070.00852.6210.0010.0010.0000.0000.0000.000
161E685ARG 00.0910.09748.230-0.008-0.0080.0000.0000.0000.000
162A601HOH 0-0.020-0.02412.744-0.027-0.0270.0000.0000.0000.000
163A602HOH 00.0300.01949.8560.0000.0000.0000.0000.0000.000
164A603HOH 00.0080.00433.619-0.003-0.0030.0000.0000.0000.000
165A604HOH 0-0.002-0.01434.5310.0010.0010.0000.0000.0000.000
166A605HOH 0-0.037-0.02938.467-0.002-0.0020.0000.0000.0000.000
167A606HOH 00.0080.00242.821-0.001-0.0010.0000.0000.0000.000
168A607HOH 0-0.034-0.03920.008-0.011-0.0110.0000.0000.0000.000
169A608HOH 0-0.018-0.01122.5180.0080.0080.0000.0000.0000.000
170A609HOH 0-0.008-0.01029.542-0.003-0.0030.0000.0000.0000.000
171A610HOH 0-0.007-0.02240.395-0.001-0.0010.0000.0000.0000.000
172A611HOH 0-0.012-0.03139.2610.0000.0000.0000.0000.0000.000
173A612HOH 00.0560.02239.2780.0010.0010.0000.0000.0000.000
174A613HOH 0-0.024-0.02121.869-0.005-0.0050.0000.0000.0000.000
175A614HOH 0-0.008-0.02131.765-0.001-0.0010.0000.0000.0000.000
176A615HOH 0-0.026-0.01139.672-0.002-0.0020.0000.0000.0000.000
177A616HOH 0-0.018-0.02037.7610.0010.0010.0000.0000.0000.000
178A617HOH 0-0.031-0.02750.3000.0000.0000.0000.0000.0000.000
179A618HOH 0-0.027-0.02037.4970.0000.0000.0000.0000.0000.000
180A619HOH 00.001-0.00623.8290.0050.0050.0000.0000.0000.000
181A620HOH 0-0.017-0.01518.1530.0130.0130.0000.0000.0000.000
182A621HOH 0-0.005-0.00225.9040.0010.0010.0000.0000.0000.000
183A622HOH 0-0.009-0.00532.3300.0020.0020.0000.0000.0000.000
184A623HOH 0-0.014-0.01333.255-0.001-0.0010.0000.0000.0000.000
185A624HOH 0-0.024-0.02122.480-0.004-0.0040.0000.0000.0000.000
186A625HOH 00.0430.02335.7500.0000.0000.0000.0000.0000.000
187A626HOH 0-0.018-0.02439.622-0.001-0.0010.0000.0000.0000.000
188A627HOH 0-0.048-0.02927.161-0.001-0.0010.0000.0000.0000.000
189A628HOH 0-0.012-0.01247.5240.0010.0010.0000.0000.0000.000
190A629HOH 00.0380.02631.1380.0030.0030.0000.0000.0000.000
191A630HOH 0-0.013-0.00941.3660.0000.0000.0000.0000.0000.000
192A631HOH 0-0.011-0.02030.5740.0050.0050.0000.0000.0000.000
193A632HOH 00.0360.02331.7160.0020.0020.0000.0000.0000.000
194A633HOH 0-0.005-0.00329.0000.0000.0000.0000.0000.0000.000
195A634HOH 00.0000.00045.6670.0000.0000.0000.0000.0000.000
196A635HOH 0-0.0010.00056.3190.0000.0000.0000.0000.0000.000
197A636HOH 00.0060.00235.2200.0030.0030.0000.0000.0000.000
198A637HOH 00.0000.00044.944-0.001-0.0010.0000.0000.0000.000