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: 2KVVR

Calculation Name: 7JJC-DH-Xray89

Preferred Name:

Target Type:

Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 7JJC

Chain ID: DH

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1908964.017277
FMO2-HF: Nuclear repulsion 1838914.06528
FMO2-HF: Total energy -70049.951997
FMO2-MP2: Total energy -70253.10676


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(D:-10:GLY )


Summations of interaction energy for fragment #1(D:-10: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.
-23.719-27.65421.495-10.676-6.883-0.03
Interaction energy analysis for fragmet #1(D:-10:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.019
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].
3D-8GLU -1-0.742-0.8582.917-13.105-7.9970.187-2.994-2.301-0.020
4D-7ASN 0-0.034-0.0113.7821.3731.6630.007-0.060-0.2370.000
5D-6LEU 0-0.049-0.0244.9240.6480.6480.0000.0000.0000.000
6D-5TYR 00.0150.0057.868-0.086-0.0860.0000.0000.0000.000
7D-4GLN 00.0220.0159.2770.0710.0710.0000.0000.0000.000
8D-3GLY 00.0430.02312.1410.0390.0390.0000.0000.0000.000
9D-2GLY 00.0280.00215.0890.0330.0330.0000.0000.0000.000
10D-1HIS 0-0.055-0.01813.5980.0850.0850.0000.0000.0000.000
11D0MET 0-0.021-0.00216.1330.0010.0010.0000.0000.0000.000
12D273PHE 00.0310.01718.6720.0330.0330.0000.0000.0000.000
13D274LYS 10.8790.93222.0340.1640.1640.0000.0000.0000.000
14D424CYS 0-0.117-0.04319.9590.0110.0110.0000.0000.0000.000
15D276MET 00.0250.02720.436-0.008-0.0080.0000.0000.0000.000
16D277GLU -1-0.853-0.90722.930-0.124-0.1240.0000.0000.0000.000
17D278ALA 0-0.011-0.01226.0970.0020.0020.0000.0000.0000.000
18D279LEU 0-0.066-0.03024.7890.0040.0040.0000.0000.0000.000
19D280GLY 00.0770.02629.0480.0050.0050.0000.0000.0000.000
20D281MET 0-0.042-0.00330.4780.0070.0070.0000.0000.0000.000
21D282GLU -1-0.878-0.93332.864-0.062-0.0620.0000.0000.0000.000
22D283SER 0-0.021-0.01834.4720.0050.0050.0000.0000.0000.000
23D284GLY 00.0120.00936.2470.0020.0020.0000.0000.0000.000
24D285GLU -1-0.900-0.93632.908-0.063-0.0630.0000.0000.0000.000
25D286ILE 0-0.070-0.01430.7920.0020.0020.0000.0000.0000.000
26D287HIS 00.0380.01435.4340.0020.0020.0000.0000.0000.000
27D288SER 0-0.036-0.06637.5940.0010.0010.0000.0000.0000.000
28D289ASP -1-0.880-0.91539.023-0.018-0.0180.0000.0000.0000.000
29D290GLN 0-0.026-0.00933.9610.0020.0020.0000.0000.0000.000
30D291ILE 0-0.033-0.00434.1610.0010.0010.0000.0000.0000.000
31D292THR 00.0010.01134.6810.0040.0040.0000.0000.0000.000
32D293ALA 0-0.021-0.02734.420-0.001-0.0010.0000.0000.0000.000
33D294SER 00.003-0.01334.3600.0000.0000.0000.0000.0000.000
34D295SER 00.000-0.02036.1800.0000.0000.0000.0000.0000.000
35D296GLN 00.0180.00738.346-0.003-0.0030.0000.0000.0000.000
36D297TYR 00.0200.02440.8910.0010.0010.0000.0000.0000.000
37D298SER 00.005-0.02742.9680.0010.0010.0000.0000.0000.000
38D299THR 00.0670.03244.304-0.001-0.0010.0000.0000.0000.000
39D300ASN 0-0.012-0.00945.557-0.002-0.0020.0000.0000.0000.000
40D301TRP 0-0.026-0.02139.703-0.002-0.0020.0000.0000.0000.000
41D302SER 00.0770.03540.5000.0010.0010.0000.0000.0000.000
42D303ALA 00.0620.01136.846-0.002-0.0020.0000.0000.0000.000
43D304GLU -1-0.865-0.87437.126-0.022-0.0220.0000.0000.0000.000
44D305ARG 10.8110.90538.6890.0130.0130.0000.0000.0000.000
45D306SER 0-0.041-0.03733.644-0.003-0.0030.0000.0000.0000.000
46D307ARG 10.8570.92033.6270.0320.0320.0000.0000.0000.000
47D308LEU 0-0.015-0.00730.0050.0020.0020.0000.0000.0000.000
48D309ASN 0-0.050-0.03733.3980.0020.0020.0000.0000.0000.000
49D310TYR 00.0180.01936.2140.0020.0020.0000.0000.0000.000
50D311PRO 00.0040.00938.8620.0010.0010.0000.0000.0000.000
51D312GLU -1-0.843-0.90641.969-0.017-0.0170.0000.0000.0000.000
52D313ASN 0-0.024-0.01741.2940.0000.0000.0000.0000.0000.000
53D314GLY 00.0700.02937.610-0.003-0.0030.0000.0000.0000.000
54D315TRP 0-0.031-0.00432.3530.0020.0020.0000.0000.0000.000
55D316THR 0-0.008-0.03136.391-0.001-0.0010.0000.0000.0000.000
56D317PRO 0-0.0270.01735.4570.0000.0000.0000.0000.0000.000
57D318GLY 00.004-0.02438.210-0.001-0.0010.0000.0000.0000.000
58D319GLU -1-0.847-0.89938.5530.0270.0270.0000.0000.0000.000
59D320ASP -1-0.805-0.85836.8630.0090.0090.0000.0000.0000.000
60D321SER 0-0.001-0.02135.6080.0030.0030.0000.0000.0000.000
61D322TYR 0-0.005-0.01626.6600.0010.0010.0000.0000.0000.000
62D323ARG 10.8960.93131.062-0.055-0.0550.0000.0000.0000.000
63D324GLU -1-0.766-0.79332.1930.0190.0190.0000.0000.0000.000
64D325TRP 0-0.044-0.03930.0420.0020.0020.0000.0000.0000.000
65D326ILE 0-0.0110.00730.265-0.001-0.0010.0000.0000.0000.000
66D327GLN 00.0170.01129.7370.0050.0050.0000.0000.0000.000
67D328VAL 00.0370.01428.857-0.001-0.0010.0000.0000.0000.000
68D329ASP -1-0.772-0.83929.797-0.018-0.0180.0000.0000.0000.000
69D330LEU 0-0.001-0.00925.712-0.004-0.0040.0000.0000.0000.000
70D331GLY 00.0270.02330.264-0.005-0.0050.0000.0000.0000.000
71D332LEU 0-0.058-0.03029.7530.0030.0030.0000.0000.0000.000
72D333LEU 0-0.0080.00824.987-0.002-0.0020.0000.0000.0000.000
73D334ARG 10.8600.92124.9840.0590.0590.0000.0000.0000.000
74D335PHE 00.0500.02819.0860.0040.0040.0000.0000.0000.000
75D336VAL 0-0.023-0.01220.1510.0010.0010.0000.0000.0000.000
76D337THR 00.014-0.00717.1840.0040.0040.0000.0000.0000.000
77D338ALA 00.0360.01417.486-0.022-0.0220.0000.0000.0000.000
78D339VAL 00.0050.01620.0040.0150.0150.0000.0000.0000.000
79D340GLY 00.0140.02022.880-0.012-0.0120.0000.0000.0000.000
80D341THR 0-0.025-0.01525.5860.0070.0070.0000.0000.0000.000
81D342GLN 0-0.023-0.00428.106-0.004-0.0040.0000.0000.0000.000
82D343GLY 00.0070.00431.3200.0060.0060.0000.0000.0000.000
83D344ALA 0-0.0020.00333.734-0.003-0.0030.0000.0000.0000.000
84D345ILE 0-0.036-0.02237.4280.0030.0030.0000.0000.0000.000
85D346SER 0-0.002-0.00740.654-0.001-0.0010.0000.0000.0000.000
86D347LYS 10.8910.93643.6350.0150.0150.0000.0000.0000.000
87D348GLU -1-0.863-0.94146.656-0.012-0.0120.0000.0000.0000.000
88D349THR 0-0.041-0.05546.1360.0000.0000.0000.0000.0000.000
89D350LYS 10.7870.89845.0930.0180.0180.0000.0000.0000.000
90D351LYS 10.8800.94742.6870.0010.0010.0000.0000.0000.000
91D352LYS 10.9350.96638.2080.0200.0200.0000.0000.0000.000
92D353TYR 00.0230.02736.8470.0030.0030.0000.0000.0000.000
93D354TYR 00.0830.02330.744-0.005-0.0050.0000.0000.0000.000
94D355VAL 00.0070.01027.6450.0060.0060.0000.0000.0000.000
95D356LYS 10.8740.93427.341-0.015-0.0150.0000.0000.0000.000
96D357THR 0-0.013-0.00323.007-0.002-0.0020.0000.0000.0000.000
97D358TYR 0-0.001-0.02022.7510.0080.0080.0000.0000.0000.000
98D359LYS 10.8770.95420.992-0.070-0.0700.0000.0000.0000.000
99D360ILE 00.0360.02420.264-0.009-0.0090.0000.0000.0000.000
100D361ASP -1-0.762-0.82021.0350.0780.0780.0000.0000.0000.000
101D362VAL 0-0.024-0.01120.539-0.015-0.0150.0000.0000.0000.000
102D363SER 00.0430.00623.4660.0100.0100.0000.0000.0000.000
103D364SER 00.036-0.00424.609-0.012-0.0120.0000.0000.0000.000
104D365ASN 0-0.036-0.03926.918-0.006-0.0060.0000.0000.0000.000
105D366GLY 00.0140.02229.420-0.002-0.0020.0000.0000.0000.000
106D367GLU -1-0.946-0.95931.0040.0240.0240.0000.0000.0000.000
107D368ASP -1-0.837-0.88527.4850.0530.0530.0000.0000.0000.000
108D369TRP 0-0.080-0.02825.587-0.006-0.0060.0000.0000.0000.000
109D370ILE 00.0010.00319.2710.0150.0150.0000.0000.0000.000
110D371THR 0-0.079-0.05719.474-0.008-0.0080.0000.0000.0000.000
111D372ILE 00.0150.01715.5550.0250.0250.0000.0000.0000.000
112D373LYS 10.8790.93914.386-0.223-0.2230.0000.0000.0000.000
113D374GLU -1-0.843-0.9258.6940.4170.4170.0000.0000.0000.000
114D375GLY 00.0590.03310.0000.0330.0330.0000.0000.0000.000
115D376ASN 0-0.023-0.01910.524-0.065-0.0650.0000.0000.0000.000
116D377LYS 10.8920.95510.694-0.451-0.4510.0000.0000.0000.000
117D378PRO 0-0.027-0.02814.998-0.009-0.0090.0000.0000.0000.000
118D379VAL 00.0080.01913.7950.0110.0110.0000.0000.0000.000
119D380LEU 0-0.0020.00116.477-0.013-0.0130.0000.0000.0000.000
120D381PHE 00.0190.01116.680-0.005-0.0050.0000.0000.0000.000
121D382GLN 0-0.006-0.01119.2110.0160.0160.0000.0000.0000.000
122D383GLY 00.0360.00921.628-0.015-0.0150.0000.0000.0000.000
123D384ASN 0-0.057-0.02124.991-0.005-0.0050.0000.0000.0000.000
124D385THR 00.0440.00427.4200.0070.0070.0000.0000.0000.000
125D386ASN 0-0.029-0.02930.0260.0050.0050.0000.0000.0000.000
126D387PRO 0-0.016-0.00932.583-0.002-0.0020.0000.0000.0000.000
127D388THR 00.000-0.00634.5620.0020.0020.0000.0000.0000.000
128D389ASP -1-0.815-0.86630.571-0.065-0.0650.0000.0000.0000.000
129D390VAL 00.0240.01827.2720.0050.0050.0000.0000.0000.000
130D391VAL 0-0.0230.01323.537-0.010-0.0100.0000.0000.0000.000
131D392VAL 00.0230.01420.7500.0090.0090.0000.0000.0000.000
132D393ALA 0-0.0230.00919.658-0.012-0.0120.0000.0000.0000.000
133D394VAL 0-0.008-0.01014.6670.0090.0090.0000.0000.0000.000
134D395PHE 0-0.001-0.01115.5090.0210.0210.0000.0000.0000.000
135D396PRO 00.0410.01810.621-0.066-0.0660.0000.0000.0000.000
136D397LYS 10.8820.9316.923-0.209-0.2090.0000.0000.0000.000
137D398PRO 00.0510.03012.2080.0460.0460.0000.0000.0000.000
138D399LEU 0-0.052-0.01015.2290.0230.0230.0000.0000.0000.000
139D400ILE 00.0340.02417.749-0.013-0.0130.0000.0000.0000.000
140D401THR 0-0.012-0.02020.8280.0230.0230.0000.0000.0000.000
141D402ARG 10.8220.89523.3430.0090.0090.0000.0000.0000.000
142D403PHE 0-0.0010.01526.746-0.004-0.0040.0000.0000.0000.000
143D404VAL 0-0.001-0.00723.8750.0030.0030.0000.0000.0000.000
144D405ARG 10.8470.90425.583-0.027-0.0270.0000.0000.0000.000
145D406ILE 0-0.0020.00025.1840.0070.0070.0000.0000.0000.000
146D407LYS 10.8530.89724.364-0.059-0.0590.0000.0000.0000.000
147D408PRO 0-0.014-0.01326.2550.0050.0050.0000.0000.0000.000
148D409ALA 0-0.066-0.04025.2730.0080.0080.0000.0000.0000.000
149D410THR 00.0140.01126.8540.0030.0030.0000.0000.0000.000
150D411TRP 00.0000.00728.871-0.006-0.0060.0000.0000.0000.000
151D412GLU -1-0.839-0.90131.6040.0100.0100.0000.0000.0000.000
152D413THR 0-0.043-0.01234.386-0.003-0.0030.0000.0000.0000.000
153D414GLY 0-0.014-0.03336.5070.0020.0020.0000.0000.0000.000
154D415ILE 0-0.032-0.00332.787-0.004-0.0040.0000.0000.0000.000
155D416SER 00.012-0.01334.339-0.001-0.0010.0000.0000.0000.000
156D417MET 0-0.056-0.00927.5490.0010.0010.0000.0000.0000.000
157D418ARG 10.8130.91632.3370.0380.0380.0000.0000.0000.000
158D419PHE 0-0.011-0.02127.721-0.003-0.0030.0000.0000.0000.000
159D420GLU -1-0.698-0.82227.968-0.066-0.0660.0000.0000.0000.000
160D421VAL 0-0.025-0.01424.201-0.003-0.0030.0000.0000.0000.000
161D422TYR 00.0250.01322.480-0.001-0.0010.0000.0000.0000.000
162D423GLY 00.0480.01221.785-0.001-0.0010.0000.0000.0000.000
163D425LYS 10.9810.98724.5030.0870.0870.0000.0000.0000.000
164D426ILE 0-0.022-0.00923.618-0.009-0.0090.0000.0000.0000.000
165D427THR -1-0.949-0.96324.884-0.112-0.1120.0000.0000.0000.000
166H683ARG 10.9130.95945.904-0.006-0.0060.0000.0000.0000.000
167H684ALA 0-0.032-0.03148.0570.0000.0000.0000.0000.0000.000
168H685ARG 00.0720.08539.568-0.010-0.0100.0000.0000.0000.000
169D601HOH 00.0280.0146.755-0.089-0.0890.0000.0000.0000.000
170D602HOH 0-0.093-0.07337.3250.0020.0020.0000.0000.0000.000
171D603HOH 0-0.031-0.04231.6470.0020.0020.0000.0000.0000.000
172D604HOH 0-0.009-0.00823.3930.0030.0030.0000.0000.0000.000
173D605HOH 00.005-0.00321.3020.0090.0090.0000.0000.0000.000
174D606HOH 00.0080.00522.5310.0040.0040.0000.0000.0000.000
175D607HOH 00.001-0.01024.3370.0020.0020.0000.0000.0000.000
176D608HOH 0-0.027-0.03314.1730.0240.0240.0000.0000.0000.000
177D609HOH 0-0.022-0.02118.617-0.005-0.0050.0000.0000.0000.000
178D610HOH 0-0.021-0.02732.0790.0020.0020.0000.0000.0000.000
179D611HOH 0-0.023-0.02027.190-0.003-0.0030.0000.0000.0000.000
180D612HOH 00.003-0.00117.2500.0080.0080.0000.0000.0000.000
181D613HOH 0-0.044-0.03714.222-0.012-0.0120.0000.0000.0000.000
182D614HOH 0-0.013-0.02028.9020.0010.0010.0000.0000.0000.000
183D615HOH 0-0.009-0.0089.4330.0140.0140.0000.0000.0000.000
184D616HOH 00.0160.01525.643-0.001-0.0010.0000.0000.0000.000
185D617HOH 0-0.021-0.02428.4150.0030.0030.0000.0000.0000.000
186D618HOH 00.0440.02732.911-0.001-0.0010.0000.0000.0000.000
187D619HOH 0-0.052-0.0404.8410.4950.4950.0000.0000.0000.000
188D620HOH 0-0.019-0.01534.8070.0020.0020.0000.0000.0000.000
189D621HOH 00.0130.00324.653-0.002-0.0020.0000.0000.0000.000
190D622HOH 00.0350.01918.1530.0120.0120.0000.0000.0000.000
191D623HOH 0-0.026-0.04342.090-0.001-0.0010.0000.0000.0000.000
192D624HOH 0-0.005-0.00612.485-0.044-0.0440.0000.0000.0000.000
193D625HOH 0-0.021-0.0251.831-9.464-18.62716.131-4.609-2.3590.023
194D626HOH 00.0500.03236.8500.0000.0000.0000.0000.0000.000
195D627HOH 0-0.052-0.0452.129-3.156-3.3265.170-3.013-1.986-0.033
196D628HOH 0-0.033-0.04028.2400.0000.0000.0000.0000.0000.000
197D629HOH 0-0.008-0.00938.669-0.001-0.0010.0000.0000.0000.000
198D630HOH 0-0.027-0.02125.098-0.003-0.0030.0000.0000.0000.000
199D631HOH 0-0.017-0.01719.610-0.012-0.0120.0000.0000.0000.000
200D632HOH 0-0.013-0.01426.820-0.006-0.0060.0000.0000.0000.000
201D633HOH 0-0.014-0.01022.098-0.005-0.0050.0000.0000.0000.000
202D634HOH 00.0100.00328.784-0.001-0.0010.0000.0000.0000.000
203D635HOH 00.0000.00035.2530.0000.0000.0000.0000.0000.000