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FMO DATABASE | 6311Z
FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6311Z

Calculation Name: 7JJC-CG-Xray89

Preferred Name:
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Target Type:
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Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 7JJC

Chain ID: CG

ChEMBL ID:
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UniProt ID:
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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:


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 197
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1831243.860085
FMO2-HF: Nuclear repulsion 1762616.54634
FMO2-HF: Total energy -68627.313744
FMO2-MP2: Total energy -68826.315379


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(C:-3:GLY )


Summations of interaction energy for fragment #1(C:-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.
-1.7461.2010.084-1.506-1.5250
Interaction energy analysis for fragmet #1(C:-3:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.021
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].
3C-1HIS 0-0.052-0.0242.931-1.6021.3450.084-1.506-1.5250.000
4C0MET 0-0.006-0.0146.1020.2950.2950.0000.0000.0000.000
5C273PHE 0-0.008-0.0029.8160.1410.1410.0000.0000.0000.000
6C274LYS 10.8480.93212.7430.5950.5950.0000.0000.0000.000
7C424CYS 0-0.098-0.03815.2380.0230.0230.0000.0000.0000.000
8C276MET 00.0100.02018.7270.0150.0150.0000.0000.0000.000
9C277GLU -1-0.770-0.85716.419-0.389-0.3890.0000.0000.0000.000
10C278ALA 00.0060.00619.7210.0090.0090.0000.0000.0000.000
11C279LEU 0-0.027-0.03120.014-0.014-0.0140.0000.0000.0000.000
12C280GLY 00.0460.02221.7400.0040.0040.0000.0000.0000.000
13C281MET 0-0.047-0.00323.4810.0170.0170.0000.0000.0000.000
14C282GLU -1-0.890-0.91426.259-0.069-0.0690.0000.0000.0000.000
15C283SER 0-0.053-0.04521.6780.0150.0150.0000.0000.0000.000
16C284GLY 00.0020.00424.6250.0160.0160.0000.0000.0000.000
17C285GLU -1-0.808-0.83218.745-0.190-0.1900.0000.0000.0000.000
18C286ILE 0-0.065-0.00822.620-0.002-0.0020.0000.0000.0000.000
19C287HIS 00.0720.03923.9640.0140.0140.0000.0000.0000.000
20C288SER 00.037-0.00227.941-0.008-0.0080.0000.0000.0000.000
21C289ASP -1-0.857-0.86830.875-0.045-0.0450.0000.0000.0000.000
22C290GLN 00.0580.04425.1980.0050.0050.0000.0000.0000.000
23C291ILE 0-0.031-0.00630.106-0.009-0.0090.0000.0000.0000.000
24C292THR 00.0160.00232.9710.0050.0050.0000.0000.0000.000
25C293ALA 0-0.001-0.02036.466-0.005-0.0050.0000.0000.0000.000
26C294SER 0-0.027-0.02339.4040.0020.0020.0000.0000.0000.000
27C295SER 00.014-0.01442.6240.0040.0040.0000.0000.0000.000
28C296GLN 0-0.006-0.00942.425-0.001-0.0010.0000.0000.0000.000
29C297TYR 0-0.060-0.02944.9220.0020.0020.0000.0000.0000.000
30C298SER 0-0.013-0.02946.7440.0020.0020.0000.0000.0000.000
31C299THR 00.0870.03844.889-0.002-0.0020.0000.0000.0000.000
32C300ASN 0-0.098-0.04843.9230.0000.0000.0000.0000.0000.000
33C301TRP 0-0.042-0.03042.643-0.002-0.0020.0000.0000.0000.000
34C302SER 00.018-0.00739.488-0.003-0.0030.0000.0000.0000.000
35C303ALA 00.0600.01736.929-0.002-0.0020.0000.0000.0000.000
36C304GLU -1-0.775-0.83535.147-0.042-0.0420.0000.0000.0000.000
37C305ARG 10.7950.88734.9850.0250.0250.0000.0000.0000.000
38C306SER 0-0.031-0.03934.549-0.003-0.0030.0000.0000.0000.000
39C307ARG 10.8340.90627.7420.0490.0490.0000.0000.0000.000
40C308LEU 00.001-0.00128.8560.0060.0060.0000.0000.0000.000
41C309ASN 00.012-0.00229.6970.0070.0070.0000.0000.0000.000
42C310TYR 00.0000.02332.9670.0080.0080.0000.0000.0000.000
43C311PRO 00.0270.01734.879-0.001-0.0010.0000.0000.0000.000
44C312GLU -1-0.853-0.88837.444-0.015-0.0150.0000.0000.0000.000
45C313ASN 00.0020.00140.396-0.001-0.0010.0000.0000.0000.000
46C314GLY 00.0540.03338.856-0.002-0.0020.0000.0000.0000.000
47C315TRP 0-0.0140.00738.5680.0010.0010.0000.0000.0000.000
48C316THR 0-0.032-0.04740.225-0.002-0.0020.0000.0000.0000.000
49C317PRO 0-0.0230.01543.0960.0030.0030.0000.0000.0000.000
50C318GLY 00.0390.00645.1040.0020.0020.0000.0000.0000.000
51C319GLU -1-0.834-0.90148.198-0.033-0.0330.0000.0000.0000.000
52C320ASP -1-0.754-0.83047.910-0.045-0.0450.0000.0000.0000.000
53C321SER 00.012-0.00348.1230.0000.0000.0000.0000.0000.000
54C322TYR 00.0350.00146.053-0.001-0.0010.0000.0000.0000.000
55C323ARG 10.8690.94645.2350.0460.0460.0000.0000.0000.000
56C324GLU -1-0.817-0.83944.089-0.049-0.0490.0000.0000.0000.000
57C325TRP 0-0.004-0.01238.225-0.005-0.0050.0000.0000.0000.000
58C326ILE 0-0.0130.01035.4800.0050.0050.0000.0000.0000.000
59C327GLN 00.0050.00733.816-0.006-0.0060.0000.0000.0000.000
60C328VAL 00.0220.01328.1600.0060.0060.0000.0000.0000.000
61C329ASP -1-0.752-0.83128.767-0.115-0.1150.0000.0000.0000.000
62C330LEU 0-0.011-0.01423.9240.0030.0030.0000.0000.0000.000
63C331GLY 00.0190.01724.016-0.006-0.0060.0000.0000.0000.000
64C332LEU 0-0.057-0.03819.2680.0010.0010.0000.0000.0000.000
65C333LEU 0-0.035-0.01323.436-0.003-0.0030.0000.0000.0000.000
66C334ARG 10.9290.96718.0740.2560.2560.0000.0000.0000.000
67C335PHE 00.0130.00018.6660.0160.0160.0000.0000.0000.000
68C336VAL 0-0.008-0.00421.485-0.009-0.0090.0000.0000.0000.000
69C337THR 0-0.007-0.04622.386-0.007-0.0070.0000.0000.0000.000
70C338ALA 00.0080.01325.2150.0090.0090.0000.0000.0000.000
71C339VAL 0-0.0010.00527.220-0.002-0.0020.0000.0000.0000.000
72C340GLY 0-0.0060.01929.5060.0010.0010.0000.0000.0000.000
73C341THR 0-0.032-0.03230.7150.0030.0030.0000.0000.0000.000
74C342GLN 00.0050.00233.9350.0000.0000.0000.0000.0000.000
75C343GLY 00.0030.01836.3480.0000.0000.0000.0000.0000.000
76C344ALA 0-0.0150.00539.0560.0000.0000.0000.0000.0000.000
77C345ILE 0-0.044-0.03141.5180.0010.0010.0000.0000.0000.000
78C346SER 0-0.025-0.01144.0810.0020.0020.0000.0000.0000.000
79C347LYS 10.8730.91542.8390.0160.0160.0000.0000.0000.000
80C348GLU -1-0.810-0.89146.982-0.020-0.0200.0000.0000.0000.000
81C349THR 0-0.026-0.04450.1940.0010.0010.0000.0000.0000.000
82C350LYS 10.8350.91146.0180.0220.0220.0000.0000.0000.000
83C351LYS 10.9000.94949.3090.0300.0300.0000.0000.0000.000
84C352LYS 10.9380.96746.1420.0320.0320.0000.0000.0000.000
85C353TYR 0-0.033-0.02044.7170.0000.0000.0000.0000.0000.000
86C354TYR 00.0670.02541.464-0.001-0.0010.0000.0000.0000.000
87C355VAL 0-0.004-0.00140.2820.0020.0020.0000.0000.0000.000
88C356LYS 10.8590.93140.8430.0520.0520.0000.0000.0000.000
89C357THR 00.0160.02940.724-0.003-0.0030.0000.0000.0000.000
90C358TYR 00.0500.01734.5490.0030.0030.0000.0000.0000.000
91C359LYS 10.9200.97538.4570.0730.0730.0000.0000.0000.000
92C360ILE 00.0260.01832.3170.0030.0030.0000.0000.0000.000
93C361ASP -1-0.736-0.81335.840-0.095-0.0950.0000.0000.0000.000
94C362VAL 0-0.004-0.01030.512-0.002-0.0020.0000.0000.0000.000
95C363SER 00.0420.00331.4400.0060.0060.0000.0000.0000.000
96C364SER 00.0240.00829.598-0.004-0.0040.0000.0000.0000.000
97C365ASN 00.021-0.00730.203-0.005-0.0050.0000.0000.0000.000
98C366GLY 00.0220.02232.9010.0060.0060.0000.0000.0000.000
99C367GLU -1-0.999-0.99534.750-0.064-0.0640.0000.0000.0000.000
100C368ASP -1-0.869-0.92336.866-0.085-0.0850.0000.0000.0000.000
101C369TRP 0-0.077-0.03533.992-0.011-0.0110.0000.0000.0000.000
102C370ILE 0-0.0030.00435.0100.0040.0040.0000.0000.0000.000
103C371THR 0-0.075-0.06335.851-0.002-0.0020.0000.0000.0000.000
104C372ILE 00.0150.01931.818-0.002-0.0020.0000.0000.0000.000
105C373LYS 10.8750.92735.7320.1010.1010.0000.0000.0000.000
106C374GLU -1-0.824-0.91735.136-0.151-0.1510.0000.0000.0000.000
107C375GLY 00.0140.02538.8400.0070.0070.0000.0000.0000.000
108C376ASN 0-0.008-0.01641.6350.0050.0050.0000.0000.0000.000
109C377LYS 10.9310.96642.6780.0960.0960.0000.0000.0000.000
110C378PRO 0-0.034-0.01940.279-0.005-0.0050.0000.0000.0000.000
111C379VAL 00.0260.02435.9110.0040.0040.0000.0000.0000.000
112C380LEU 0-0.019-0.00538.9360.0020.0020.0000.0000.0000.000
113C381PHE 00.001-0.00333.1700.0000.0000.0000.0000.0000.000
114C382GLN 0-0.016-0.01637.1810.0110.0110.0000.0000.0000.000
115C383GLY 00.0490.01236.712-0.006-0.0060.0000.0000.0000.000
116C384ASN 0-0.046-0.00836.189-0.001-0.0010.0000.0000.0000.000
117C385THR 00.0650.00839.5170.0020.0020.0000.0000.0000.000
118C386ASN 0-0.015-0.02339.8770.0030.0030.0000.0000.0000.000
119C387PRO 0-0.033-0.00940.626-0.004-0.0040.0000.0000.0000.000
120C388THR 0-0.018-0.01538.5640.0020.0020.0000.0000.0000.000
121C389ASP -1-0.809-0.87335.799-0.062-0.0620.0000.0000.0000.000
122C390VAL 00.0420.03129.9770.0000.0000.0000.0000.0000.000
123C391VAL 0-0.034-0.00633.343-0.002-0.0020.0000.0000.0000.000
124C392VAL 00.0340.01327.708-0.002-0.0020.0000.0000.0000.000
125C393ALA 0-0.035-0.00131.0270.0010.0010.0000.0000.0000.000
126C394VAL 00.0120.00227.995-0.006-0.0060.0000.0000.0000.000
127C395PHE 0-0.015-0.02228.0710.0130.0130.0000.0000.0000.000
128C396PRO 00.0210.01229.971-0.007-0.0070.0000.0000.0000.000
129C397LYS 10.9610.98327.5840.2240.2240.0000.0000.0000.000
130C398PRO 00.005-0.00623.1280.0110.0110.0000.0000.0000.000
131C399LEU 0-0.037-0.00725.3030.0040.0040.0000.0000.0000.000
132C400ILE 00.0030.00922.880-0.011-0.0110.0000.0000.0000.000
133C401THR 0-0.015-0.01025.2130.0230.0230.0000.0000.0000.000
134C402ARG 10.8360.90125.4490.0970.0970.0000.0000.0000.000
135C403PHE 0-0.0130.00527.2720.0040.0040.0000.0000.0000.000
136C404VAL 00.000-0.00728.044-0.007-0.0070.0000.0000.0000.000
137C405ARG 10.8930.95031.1230.0880.0880.0000.0000.0000.000
138C406ILE 00.0070.00132.750-0.003-0.0030.0000.0000.0000.000
139C407LYS 10.8060.89536.3160.0930.0930.0000.0000.0000.000
140C408PRO 0-0.009-0.00640.005-0.003-0.0030.0000.0000.0000.000
141C409ALA 0-0.052-0.02841.9390.0020.0020.0000.0000.0000.000
142C410THR 0-0.022-0.02244.1580.0040.0040.0000.0000.0000.000
143C411TRP 00.0270.00944.349-0.004-0.0040.0000.0000.0000.000
144C412GLU -1-0.857-0.90946.143-0.045-0.0450.0000.0000.0000.000
145C413THR 0-0.050-0.02447.6240.0010.0010.0000.0000.0000.000
146C414GLY 0-0.028-0.03648.0450.0020.0020.0000.0000.0000.000
147C415ILE 0-0.014-0.00242.874-0.002-0.0020.0000.0000.0000.000
148C416SER 00.009-0.00942.3380.0030.0030.0000.0000.0000.000
149C417MET 0-0.059-0.01136.661-0.003-0.0030.0000.0000.0000.000
150C418ARG 10.8250.92534.3330.0550.0550.0000.0000.0000.000
151C419PHE 00.016-0.01330.547-0.004-0.0040.0000.0000.0000.000
152C420GLU -1-0.699-0.82425.640-0.124-0.1240.0000.0000.0000.000
153C421VAL 0-0.017-0.01125.369-0.002-0.0020.0000.0000.0000.000
154C422TYR 00.0160.01022.9790.0000.0000.0000.0000.0000.000
155C423GLY 00.0630.00321.2440.0100.0100.0000.0000.0000.000
156C425LYS 10.8440.89314.1040.3140.3140.0000.0000.0000.000
157C426ILE 00.0070.0077.940-0.032-0.0320.0000.0000.0000.000
158C427THR -1-0.852-0.9087.817-1.311-1.3110.0000.0000.0000.000
159G679ASN 00.020-0.00460.9870.0000.0000.0000.0000.0000.000
160G680SER 0-0.0030.00761.2260.0010.0010.0000.0000.0000.000
161G681PRO 00.005-0.00558.913-0.001-0.0010.0000.0000.0000.000
162G682ARG 10.8610.90552.8460.0310.0310.0000.0000.0000.000
163G683ARG 10.9630.99655.3260.0260.0260.0000.0000.0000.000
164G684ALA 00.0340.02253.531-0.001-0.0010.0000.0000.0000.000
165G685ARG 00.0910.10646.8330.0100.0100.0000.0000.0000.000
166C601HOH 0-0.021-0.03737.4510.0010.0010.0000.0000.0000.000
167C602HOH 0-0.007-0.01519.3780.0030.0030.0000.0000.0000.000
168C603HOH 0-0.048-0.05642.853-0.001-0.0010.0000.0000.0000.000
169C604HOH 0-0.049-0.04823.530-0.003-0.0030.0000.0000.0000.000
170C605HOH 0-0.034-0.02538.4620.0000.0000.0000.0000.0000.000
171C606HOH 00.0310.02937.327-0.001-0.0010.0000.0000.0000.000
172C607HOH 0-0.009-0.02938.8040.0010.0010.0000.0000.0000.000
173C608HOH 0-0.027-0.03823.8670.0000.0000.0000.0000.0000.000
174C609HOH 0-0.006-0.00931.934-0.003-0.0030.0000.0000.0000.000
175C610HOH 0-0.045-0.03715.260-0.024-0.0240.0000.0000.0000.000
176C611HOH 00.0000.00012.898-0.023-0.0230.0000.0000.0000.000
177C612HOH 0-0.016-0.01432.699-0.002-0.0020.0000.0000.0000.000
178C613HOH 0-0.031-0.03119.135-0.011-0.0110.0000.0000.0000.000
179C614HOH 0-0.037-0.04339.215-0.001-0.0010.0000.0000.0000.000
180C615HOH 0-0.044-0.04033.2670.0040.0040.0000.0000.0000.000
181C616HOH 0-0.014-0.01033.959-0.001-0.0010.0000.0000.0000.000
182C617HOH 0-0.025-0.02537.6090.0010.0010.0000.0000.0000.000
183C618HOH 0-0.036-0.02834.4900.0010.0010.0000.0000.0000.000
184C619HOH 00.0220.01433.325-0.003-0.0030.0000.0000.0000.000
185C620HOH 0-0.029-0.04631.236-0.001-0.0010.0000.0000.0000.000
186C621HOH 0-0.009-0.02040.135-0.001-0.0010.0000.0000.0000.000
187C622HOH 0-0.037-0.02832.964-0.001-0.0010.0000.0000.0000.000
188C623HOH 0-0.033-0.03740.6530.0020.0020.0000.0000.0000.000
189C624HOH 00.0130.00829.055-0.002-0.0020.0000.0000.0000.000
190C625HOH 0-0.045-0.03630.6370.0000.0000.0000.0000.0000.000
191C626HOH 0-0.014-0.02023.818-0.006-0.0060.0000.0000.0000.000
192C627HOH 0-0.039-0.03335.9050.0020.0020.0000.0000.0000.000
193C628HOH 00.0170.01435.0920.0010.0010.0000.0000.0000.000
194C629HOH 00.0020.00132.344-0.003-0.0030.0000.0000.0000.000
195C630HOH 00.0220.01935.147-0.001-0.0010.0000.0000.0000.000
196C631HOH 00.0000.00033.835-0.004-0.0040.0000.0000.0000.000
197G701HOH 0-0.011-0.00855.400-0.001-0.0010.0000.0000.0000.000