FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 98322

Calculation Name: 2VK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VK9

Chain ID: A

ChEMBL ID:

UniProt ID: Q46149

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 540
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11470820.762535
FMO2-HF: Nuclear repulsion 11251919.735092
FMO2-HF: Total energy -218901.027443
FMO2-MP2: Total energy -219543.212744


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-14.63-8.58711.425-6.226-11.243-0.05
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.017
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].
3A4THR0-0.015-0.0172.807-1.0690.8120.455-0.604-1.732-0.002
4A5ARG11.0141.0055.2350.0820.0820.0000.0000.0000.000
5A6GLU-1-0.809-0.9157.042-0.162-0.1620.0000.0000.0000.000
6A7GLN0-0.041-0.0579.630-0.023-0.0230.0000.0000.0000.000
7A8LEU0-0.066-0.0337.5760.0070.0070.0000.0000.0000.000
8A9MET00.0730.0669.706-0.038-0.0380.0000.0000.0000.000
9A10LYS10.8590.94611.4760.1050.1050.0000.0000.0000.000
10A11ILE00.0280.02513.3830.0360.0360.0000.0000.0000.000
11A12ALA0-0.001-0.00615.3890.0040.0040.0000.0000.0000.000
12A13SER0-0.099-0.04117.0730.0280.0280.0000.0000.0000.000
13A14ILE00.0460.02019.8360.0000.0000.0000.0000.0000.000
14A15PRO00.0420.00323.4760.0070.0070.0000.0000.0000.000
15A16LEU00.0130.01526.0300.0000.0000.0000.0000.0000.000
16A17LYS10.9140.98123.6740.1400.1400.0000.0000.0000.000
17A18ARG10.9600.96624.0220.0570.0570.0000.0000.0000.000
18A19LYS10.9430.97618.1170.0810.0810.0000.0000.0000.000
19A20GLU-1-0.730-0.83221.666-0.144-0.1440.0000.0000.0000.000
20A21PRO00.0270.00820.629-0.007-0.0070.0000.0000.0000.000
21A22GLU-1-0.767-0.88719.588-0.145-0.1450.0000.0000.0000.000
22A23TYR0-0.027-0.01215.100-0.001-0.0010.0000.0000.0000.000
23A24ASN00.025-0.02015.779-0.017-0.0170.0000.0000.0000.000
24A25LEU00.0330.04115.358-0.003-0.0030.0000.0000.0000.000
25A26ILE0-0.0120.00911.715-0.013-0.0130.0000.0000.0000.000
26A27LEU0-0.070-0.04411.194-0.036-0.0360.0000.0000.0000.000
27A28ASP-1-0.843-0.91411.334-0.109-0.1090.0000.0000.0000.000
28A29ALA0-0.053-0.03310.6990.0050.0050.0000.0000.0000.000
29A30LEU0-0.058-0.0355.342-0.049-0.0490.0000.0000.0000.000
30A31GLU-1-0.952-0.9636.4950.0720.0720.0000.0000.0000.000
31A32ASN0-0.021-0.0287.9150.0970.0970.0000.0000.0000.000
32A33PHE0-0.029-0.0022.1030.719-1.9466.235-1.123-2.4470.002
33A34ASN00.013-0.0062.762-2.383-0.6980.649-0.766-1.567-0.006
34A35ARG10.8670.9643.488-0.2870.2870.032-0.168-0.438-0.001
35A36ASP-1-0.925-0.9796.201-0.034-0.0340.0000.0000.0000.000
36A37ILE0-0.017-0.0162.408-0.629-0.4331.409-0.280-1.326-0.001
37A38GLU-1-0.922-0.9596.1930.4500.4500.0000.0000.0000.000
38A39GLY0-0.054-0.0249.000-0.035-0.0350.0000.0000.0000.000
39A40THR0-0.0060.0118.768-0.017-0.0170.0000.0000.0000.000
40A41SER00.0290.00111.8050.0380.0380.0000.0000.0000.000
41A42VAL00.0250.00011.216-0.047-0.0470.0000.0000.0000.000
42A43LYS10.9070.94711.5800.1180.1180.0000.0000.0000.000
43A44GLU-1-0.909-0.94812.255-0.271-0.2710.0000.0000.0000.000
44A45ILE00.0010.0186.191-0.023-0.0230.0000.0000.0000.000
45A46TYR0-0.044-0.0738.785-0.065-0.0650.0000.0000.0000.000
46A47SER00.010-0.00211.108-0.022-0.0220.0000.0000.0000.000
47A48LYS10.9520.9688.2170.3860.3860.0000.0000.0000.000
48A49LEU0-0.0040.0065.1830.0290.0290.0000.0000.0000.000
49A50SER00.0120.0099.0810.0320.0320.0000.0000.0000.000
50A51LYS10.9480.97312.1310.3130.3130.0000.0000.0000.000
51A52LEU00.0030.0067.1370.0410.0410.0000.0000.0000.000
52A53ASN00.0480.02511.453-0.012-0.0120.0000.0000.0000.000
53A54GLU-1-0.928-0.95313.411-0.227-0.2270.0000.0000.0000.000
54A55LEU0-0.051-0.02913.1350.0340.0340.0000.0000.0000.000
55A56VAL0-0.007-0.00313.0490.0330.0330.0000.0000.0000.000
56A57ASP-1-0.813-0.90615.905-0.293-0.2930.0000.0000.0000.000
57A58ASN0-0.016-0.01819.0890.0290.0290.0000.0000.0000.000
58A59TYR0-0.093-0.03018.4600.0270.0270.0000.0000.0000.000
59A60GLN0-0.057-0.04518.9070.0220.0220.0000.0000.0000.000
60A61THR0-0.0290.00221.5950.0190.0190.0000.0000.0000.000
61A62LYS10.8910.95823.7460.1420.1420.0000.0000.0000.000
62A63TYR0-0.131-0.09922.6720.0240.0240.0000.0000.0000.000
63A64PRO00.0850.05124.500-0.011-0.0110.0000.0000.0000.000
64A65SER0-0.044-0.03226.110-0.007-0.0070.0000.0000.0000.000
65A66SER0-0.054-0.04122.2840.0090.0090.0000.0000.0000.000
66A67GLY00.0200.00223.848-0.009-0.0090.0000.0000.0000.000
67A68ARG10.7790.86518.6070.1550.1550.0000.0000.0000.000
68A69ASN00.0470.01818.373-0.039-0.0390.0000.0000.0000.000
69A70LEU00.0470.03118.580-0.027-0.0270.0000.0000.0000.000
70A71ALA0-0.0040.00215.835-0.036-0.0360.0000.0000.0000.000
71A72LEU0-0.001-0.01313.642-0.070-0.0700.0000.0000.0000.000
72A73GLU-1-0.822-0.89114.186-0.451-0.4510.0000.0000.0000.000
73A74ASN00.0140.00113.657-0.047-0.0470.0000.0000.0000.000
74A75PHE0-0.015-0.0077.109-0.120-0.1200.0000.0000.0000.000
75A76ARG10.8650.9539.9010.2260.2260.0000.0000.0000.000
76A77ASP-1-0.873-0.93211.015-0.722-0.7220.0000.0000.0000.000
77A78SER0-0.135-0.1047.079-0.143-0.1430.0000.0000.0000.000
78A79LEU00.0420.0166.907-0.495-0.4950.0000.0000.0000.000
79A80TYR00.0400.0288.018-0.023-0.0230.0000.0000.0000.000
80A81SER0-0.061-0.0367.1930.1860.1860.0000.0000.0000.000
81A82GLU-1-0.826-0.9162.476-11.864-7.5592.646-3.284-3.668-0.042
82A83LEU0-0.053-0.0125.8370.3530.3530.0000.0000.0000.000
83A84ARG10.9010.9359.0840.8560.8560.0000.0000.0000.000
84A85GLU-1-0.938-0.9624.699-0.303-0.236-0.001-0.001-0.0650.000
85A86LEU00.0130.0267.6450.3330.3330.0000.0000.0000.000
86A87ILE0-0.0180.0058.8440.2010.2010.0000.0000.0000.000
87A88LYS10.9390.96110.6450.5220.5220.0000.0000.0000.000
88A89ASN00.0080.0119.145-0.025-0.0250.0000.0000.0000.000
89A90SER0-0.0260.00211.9630.0670.0670.0000.0000.0000.000
90A91ARG10.8810.96113.6420.2420.2420.0000.0000.0000.000
91A92THR0-0.003-0.00714.9440.0200.0200.0000.0000.0000.000
92A93SER0-0.052-0.04316.9470.0040.0040.0000.0000.0000.000
93A94THR00.0150.01818.434-0.001-0.0010.0000.0000.0000.000
94A95ILE00.001-0.00720.978-0.006-0.0060.0000.0000.0000.000
95A96ALA0-0.0010.00924.024-0.005-0.0050.0000.0000.0000.000
96A97SER0-0.007-0.00926.1960.0110.0110.0000.0000.0000.000
97A98LYS10.8490.93329.3360.0140.0140.0000.0000.0000.000
98A99ASN0-0.049-0.02232.2640.0090.0090.0000.0000.0000.000
99A100LEU00.0160.01833.082-0.005-0.0050.0000.0000.0000.000
100A101SER0-0.027-0.01635.2720.0050.0050.0000.0000.0000.000
101A102PHE00.0430.01836.857-0.003-0.0030.0000.0000.0000.000
102A103ILE00.0120.00737.9830.0020.0020.0000.0000.0000.000
103A104TRP0-0.021-0.01041.549-0.001-0.0010.0000.0000.0000.000
104A105ILE00.004-0.00543.5440.0020.0020.0000.0000.0000.000
105A106GLY00.0410.01646.613-0.001-0.0010.0000.0000.0000.000
106A107GLY0-0.025-0.01449.7240.0010.0010.0000.0000.0000.000
107A108PRO0-0.0070.01351.4100.0000.0000.0000.0000.0000.000
108A109ILE00.0510.04046.708-0.001-0.0010.0000.0000.0000.000
109A110SER00.0320.01549.4160.0020.0020.0000.0000.0000.000
110A111ASP-1-0.799-0.91350.604-0.028-0.0280.0000.0000.0000.000
111A112GLN0-0.0020.00648.4670.0010.0010.0000.0000.0000.000
112A113SER00.0470.02646.2020.0000.0000.0000.0000.0000.000
113A114LEU0-0.008-0.00846.2530.0000.0000.0000.0000.0000.000
114A115GLU-1-0.819-0.90148.150-0.024-0.0240.0000.0000.0000.000
115A116TYR00.004-0.02242.4140.0010.0010.0000.0000.0000.000
116A117TYR0-0.008-0.00242.1140.0010.0010.0000.0000.0000.000
117A118ASN00.0130.00043.4290.0010.0010.0000.0000.0000.000
118A119MET00.0050.01841.7220.0020.0020.0000.0000.0000.000
119A120TRP0-0.020-0.02234.5920.0020.0020.0000.0000.0000.000
120A121LYS10.9410.96940.0040.0290.0290.0000.0000.0000.000
121A122MET0-0.076-0.02742.4580.0020.0020.0000.0000.0000.000
122A123PHE0-0.010-0.01038.4100.0030.0030.0000.0000.0000.000
123A124ASN0-0.0120.00635.4040.0000.0000.0000.0000.0000.000
124A125LYS10.9740.97838.0200.0100.0100.0000.0000.0000.000
125A126ASP-1-0.872-0.92834.279-0.018-0.0180.0000.0000.0000.000
126A127TYR0-0.041-0.03930.739-0.005-0.0050.0000.0000.0000.000
127A128ASN0-0.028-0.00136.5110.0040.0040.0000.0000.0000.000
128A129ILE0-0.022-0.01437.488-0.005-0.0050.0000.0000.0000.000
129A130ARG10.9040.95837.1700.0440.0440.0000.0000.0000.000
130A131LEU00.0250.01640.472-0.003-0.0030.0000.0000.0000.000
131A132PHE0-0.015-0.01138.5230.0020.0020.0000.0000.0000.000
132A133TYR00.014-0.03243.136-0.001-0.0010.0000.0000.0000.000
133A134ASP-1-0.715-0.83946.039-0.046-0.0460.0000.0000.0000.000
134A135LYS10.9520.98247.7910.0310.0310.0000.0000.0000.000
135A136ASN0-0.014-0.00550.5000.0030.0030.0000.0000.0000.000
136A137SER0-0.054-0.05349.193-0.001-0.0010.0000.0000.0000.000
137A138LEU0-0.0260.01050.509-0.002-0.0020.0000.0000.0000.000
138A139LEU0-0.024-0.01552.9970.0010.0010.0000.0000.0000.000
139A140VAL00.0370.02449.3860.0000.0000.0000.0000.0000.000
140A141ASN0-0.0020.00051.561-0.002-0.0020.0000.0000.0000.000
141A142THR0-0.032-0.02752.8690.0000.0000.0000.0000.0000.000
142A143LEU00.0120.00953.6340.0010.0010.0000.0000.0000.000
143A144LYS10.9720.99048.8960.0540.0540.0000.0000.0000.000
144A145THR0-0.016-0.01154.1850.0000.0000.0000.0000.0000.000
145A146ALA00.0110.01956.7860.0000.0000.0000.0000.0000.000
146A147ILE00.0110.01555.5410.0010.0010.0000.0000.0000.000
147A148ILE0-0.028-0.00753.3570.0000.0000.0000.0000.0000.000
148A149GLN00.000-0.01757.7790.0010.0010.0000.0000.0000.000
149A150GLU-1-0.875-0.93861.076-0.031-0.0310.0000.0000.0000.000
150A151SER0-0.043-0.04259.3960.0000.0000.0000.0000.0000.000
151A152SER0-0.036-0.03460.4960.0000.0000.0000.0000.0000.000
152A153LYS10.9540.99462.4530.0290.0290.0000.0000.0000.000
153A154VAL00.0260.01765.2130.0010.0010.0000.0000.0000.000
154A155ILE00.0070.00462.7280.0010.0010.0000.0000.0000.000
155A156ILE0-0.035-0.01564.2240.0000.0000.0000.0000.0000.000
156A157GLU-1-0.924-0.97267.233-0.028-0.0280.0000.0000.0000.000
157A158GLN0-0.053-0.01967.8030.0000.0000.0000.0000.0000.000
158A159ASN0-0.088-0.05467.5940.0000.0000.0000.0000.0000.000
159A160GLN00.0110.01570.6490.0000.0000.0000.0000.0000.000
160A161SER00.0580.01972.8850.0000.0000.0000.0000.0000.000
161A162ASN0-0.025-0.01270.5160.0000.0000.0000.0000.0000.000
162A163ILE00.004-0.00168.871-0.001-0.0010.0000.0000.0000.000
163A164LEU0-0.047-0.01569.6510.0000.0000.0000.0000.0000.000
164A165ASP-1-0.934-0.97266.816-0.033-0.0330.0000.0000.0000.000
165A166GLY0-0.0200.01169.1560.0000.0000.0000.0000.0000.000
166A167THR0-0.002-0.00467.754-0.001-0.0010.0000.0000.0000.000
167A168TYR0-0.093-0.07064.003-0.002-0.0020.0000.0000.0000.000
168A169GLY00.0740.04764.1460.0000.0000.0000.0000.0000.000
169A170HIS00.009-0.00255.7130.0000.0000.0000.0000.0000.000
170A171ASN0-0.041-0.02957.5450.0000.0000.0000.0000.0000.000
171A172LYS10.9771.00658.6550.0370.0370.0000.0000.0000.000
172A173PHE00.003-0.01359.1020.0000.0000.0000.0000.0000.000
173A174TYR00.0270.00555.3420.0000.0000.0000.0000.0000.000
174A175SER0-0.013-0.00156.659-0.002-0.0020.0000.0000.0000.000
175A176ASP-1-0.818-0.91257.742-0.039-0.0390.0000.0000.0000.000
176A177ARG10.8880.95055.2010.0440.0440.0000.0000.0000.000
177A178MET0-0.0260.00951.9650.0000.0000.0000.0000.0000.000
178A179LYS10.9180.96956.4920.0410.0410.0000.0000.0000.000
179A180LEU0-0.0210.00658.6050.0000.0000.0000.0000.0000.000
180A181ILE00.008-0.00454.2610.0000.0000.0000.0000.0000.000
181A182TYR0-0.045-0.03052.702-0.001-0.0010.0000.0000.0000.000
182A183ARG11.0040.98655.7970.0380.0380.0000.0000.0000.000
183A184TYR00.0260.02157.8960.0000.0000.0000.0000.0000.000
184A185LYS10.8820.97049.8180.0550.0550.0000.0000.0000.000
185A186ARG10.8600.91754.7170.0440.0440.0000.0000.0000.000
186A187GLU-1-0.900-0.95556.102-0.036-0.0360.0000.0000.0000.000
187A188LEU0-0.0340.00453.8950.0010.0010.0000.0000.0000.000
188A189LYS10.9060.95649.3690.0530.0530.0000.0000.0000.000
189A190MET00.002-0.00754.5440.0000.0000.0000.0000.0000.000
190A191LEU00.0170.01357.5460.0010.0010.0000.0000.0000.000
191A192TYR0-0.004-0.01049.6800.0000.0000.0000.0000.0000.000
192A193GLU-1-0.907-0.96451.251-0.048-0.0480.0000.0000.0000.000
193A194ASN0-0.010-0.00254.883-0.001-0.0010.0000.0000.0000.000
194A195MET0-0.011-0.00157.3520.0020.0020.0000.0000.0000.000
195A196LYS10.8670.94449.8920.0480.0480.0000.0000.0000.000
196A197GLN0-0.062-0.02652.443-0.002-0.0020.0000.0000.0000.000
197A198ASN0-0.006-0.00355.1530.0000.0000.0000.0000.0000.000
198A199ASN0-0.050-0.00956.5370.0010.0010.0000.0000.0000.000
199A200SER00.0050.01353.757-0.002-0.0020.0000.0000.0000.000
200A201VAL00.052-0.00550.0380.0000.0000.0000.0000.0000.000
201A202ASP-1-0.714-0.85953.453-0.037-0.0370.0000.0000.0000.000
202A203ASP-1-0.889-0.93055.983-0.030-0.0300.0000.0000.0000.000
203A204ILE0-0.021-0.01154.4480.0010.0010.0000.0000.0000.000
204A205ILE0-0.019-0.00653.6250.0000.0000.0000.0000.0000.000
205A206ILE0-0.026-0.01857.9860.0010.0010.0000.0000.0000.000
206A207ASN0-0.013-0.01161.0740.0010.0010.0000.0000.0000.000
207A208PHE00.0570.02059.0470.0010.0010.0000.0000.0000.000
208A209LEU0-0.003-0.00759.2780.0000.0000.0000.0000.0000.000
209A210SER0-0.042-0.00362.7500.0010.0010.0000.0000.0000.000
210A211ASN0-0.048-0.03965.0680.0020.0020.0000.0000.0000.000
211A212TYR0-0.055-0.00963.5040.0010.0010.0000.0000.0000.000
212A213PHE0-0.032-0.01460.7260.0000.0000.0000.0000.0000.000
213A214LYS10.9200.97166.3320.0250.0250.0000.0000.0000.000
214A215TYR0-0.053-0.02662.5430.0010.0010.0000.0000.0000.000
215A216ASP-1-0.871-0.95566.892-0.024-0.0240.0000.0000.0000.000
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217A218GLY00.0230.02665.6260.0000.0000.0000.0000.0000.000
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