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: 769ZK

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 OptAll
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 -11507270.829399
FMO2-HF: Nuclear repulsion 11288364.930182
FMO2-HF: Total energy -218905.899218
FMO2-MP2: Total energy -219548.201856


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.
-19.16-8.58.241-7.858-11.042-0.074
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 : -0.033 / q_NPA : -0.008
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].
3A4THR0-0.019-0.0092.813-2.935-0.0420.655-1.678-1.870-0.008
4A5ARG11.0471.0285.1020.5980.757-0.001-0.007-0.1510.000
5A6GLU-1-0.644-0.8076.462-0.407-0.4070.0000.0000.0000.000
6A7GLN0-0.075-0.0729.2250.0820.0820.0000.0000.0000.000
7A8LEU0-0.048-0.0127.8800.0760.0760.0000.0000.0000.000
8A9MET00.0400.0339.8110.0560.0560.0000.0000.0000.000
9A10LYS10.7450.85611.3380.5630.5630.0000.0000.0000.000
10A11ILE00.0260.02613.1220.0750.0750.0000.0000.0000.000
11A12ALA00.0230.01315.4260.0470.0470.0000.0000.0000.000
12A13SER0-0.048-0.03117.2620.0450.0450.0000.0000.0000.000
13A14ILE0-0.0090.00019.7130.0240.0240.0000.0000.0000.000
14A15PRO00.0420.01123.1300.0100.0100.0000.0000.0000.000
15A16LEU0-0.003-0.00125.6360.0060.0060.0000.0000.0000.000
16A17LYS10.8420.94823.9370.2780.2780.0000.0000.0000.000
17A18ARG10.9890.98923.7150.1310.1310.0000.0000.0000.000
18A19LYS10.9661.00417.4550.2670.2670.0000.0000.0000.000
19A20GLU-1-0.725-0.81921.768-0.274-0.2740.0000.0000.0000.000
20A21PRO0-0.012-0.00420.729-0.019-0.0190.0000.0000.0000.000
21A22GLU-1-0.662-0.82619.504-0.241-0.2410.0000.0000.0000.000
22A23TYR00.002-0.00215.292-0.006-0.0060.0000.0000.0000.000
23A24ASN0-0.031-0.03415.910-0.050-0.0500.0000.0000.0000.000
24A25LEU00.0720.04515.316-0.022-0.0220.0000.0000.0000.000
25A26ILE0-0.0080.01311.940-0.021-0.0210.0000.0000.0000.000
26A27LEU0-0.057-0.02711.218-0.086-0.0860.0000.0000.0000.000
27A28ASP-1-0.878-0.93810.896-0.298-0.2980.0000.0000.0000.000
28A29ALA0-0.006-0.00110.9400.0290.0290.0000.0000.0000.000
29A30LEU0-0.016-0.0015.3610.0520.0520.0000.0000.0000.000
30A31GLU-1-0.928-0.9696.249-0.454-0.4540.0000.0000.0000.000
31A32ASN0-0.038-0.0197.4500.1530.1530.0000.0000.0000.000
32A33PHE00.0130.0102.675-0.815-0.0340.360-0.191-0.9500.001
33A34ASN0-0.105-0.0822.576-2.146-0.4850.526-0.816-1.370-0.003
34A35ARG10.7740.8633.649-0.0390.3030.010-0.018-0.334-0.001
35A36ASP-1-0.846-0.8896.1690.2040.2040.0000.0000.0000.000
36A37ILE0-0.007-0.0162.443-0.893-0.3371.247-0.253-1.550-0.001
37A38GLU-1-0.874-0.9226.3670.9140.9140.0000.0000.0000.000
38A39GLY0-0.049-0.0329.204-0.116-0.1160.0000.0000.0000.000
39A40THR0-0.024-0.0059.037-0.102-0.1020.0000.0000.0000.000
40A41SER00.016-0.00112.4400.0160.0160.0000.0000.0000.000
41A42VAL00.0460.01411.692-0.031-0.0310.0000.0000.0000.000
42A43LYS10.8540.91512.063-0.092-0.0920.0000.0000.0000.000
43A44GLU-1-0.830-0.89412.269-0.134-0.1340.0000.0000.0000.000
44A45ILE00.0010.0096.629-0.074-0.0740.0000.0000.0000.000
45A46TYR00.001-0.0258.994-0.149-0.1490.0000.0000.0000.000
46A47SER0-0.056-0.04311.268-0.094-0.0940.0000.0000.0000.000
47A48LYS10.8870.9408.675-0.042-0.0420.0000.0000.0000.000
48A49LEU00.0020.0045.887-0.060-0.0600.0000.0000.0000.000
49A50SER00.0100.0039.281-0.027-0.0270.0000.0000.0000.000
50A51LYS10.8980.95012.5030.2360.2360.0000.0000.0000.000
51A52LEU0-0.0060.0056.9920.0050.0050.0000.0000.0000.000
52A53ASN00.0320.01611.367-0.061-0.0610.0000.0000.0000.000
53A54GLU-1-0.914-0.95413.697-0.246-0.2460.0000.0000.0000.000
54A55LEU0-0.020-0.01013.3870.0370.0370.0000.0000.0000.000
55A56VAL0-0.017-0.00513.5210.0310.0310.0000.0000.0000.000
56A57ASP-1-0.806-0.89116.373-0.387-0.3870.0000.0000.0000.000
57A58ASN0-0.065-0.02519.2750.0600.0600.0000.0000.0000.000
58A59TYR0-0.053-0.03718.7280.0260.0260.0000.0000.0000.000
59A60GLN0-0.050-0.03819.2370.0320.0320.0000.0000.0000.000
60A61THR0-0.038-0.02721.9820.0290.0290.0000.0000.0000.000
61A62LYS10.7800.89524.0940.2300.2300.0000.0000.0000.000
62A63TYR0-0.078-0.06022.7870.0330.0330.0000.0000.0000.000
63A64PRO00.0910.05924.935-0.019-0.0190.0000.0000.0000.000
64A65SER0-0.026-0.01726.414-0.011-0.0110.0000.0000.0000.000
65A66SER0-0.047-0.03422.5770.0100.0100.0000.0000.0000.000
66A67GLY00.0440.01023.474-0.020-0.0200.0000.0000.0000.000
67A68ARG10.7430.83918.7670.3120.3120.0000.0000.0000.000
68A69ASN0-0.002-0.01218.491-0.072-0.0720.0000.0000.0000.000
69A70LEU00.0630.03618.915-0.033-0.0330.0000.0000.0000.000
70A71ALA0-0.023-0.00415.891-0.052-0.0520.0000.0000.0000.000
71A72LEU00.011-0.01314.002-0.117-0.1170.0000.0000.0000.000
72A73GLU-1-0.805-0.86414.581-0.621-0.6210.0000.0000.0000.000
73A74ASN0-0.014-0.02013.865-0.038-0.0380.0000.0000.0000.000
74A75PHE0-0.0060.0027.311-0.152-0.1520.0000.0000.0000.000
75A76ARG10.8300.89710.4160.2870.2870.0000.0000.0000.000
76A77ASP-1-0.848-0.93211.883-0.861-0.8610.0000.0000.0000.000
77A78SER0-0.107-0.0657.174-0.251-0.2510.0000.0000.0000.000
78A79LEU00.0280.0167.125-0.541-0.5410.0000.0000.0000.000
79A80TYR00.0360.0178.8530.0910.0910.0000.0000.0000.000
80A81SER0-0.074-0.0536.9460.2430.2430.0000.0000.0000.000
81A82GLU-1-0.794-0.9082.380-13.158-8.8905.444-4.895-4.817-0.062
82A83LEU0-0.027-0.0015.6550.7630.7630.0000.0000.0000.000
83A84ARG10.8450.9308.6600.8180.8180.0000.0000.0000.000
84A85GLU-1-0.779-0.8755.0190.2640.2640.0000.0000.0000.000
85A86LEU0-0.0030.0197.4030.3660.3660.0000.0000.0000.000
86A87ILE0-0.0090.0198.9290.1140.1140.0000.0000.0000.000
87A88LYS10.7640.8619.4050.0660.0660.0000.0000.0000.000
88A89ASN0-0.019-0.0137.867-0.220-0.2200.0000.0000.0000.000
89A90SER00.0140.00011.457-0.008-0.0080.0000.0000.0000.000
90A91ARG10.7790.89514.021-0.076-0.0760.0000.0000.0000.000
91A92THR00.0360.01514.648-0.027-0.0270.0000.0000.0000.000
92A93SER0-0.075-0.04117.0230.0110.0110.0000.0000.0000.000
93A94THR00.0100.01318.227-0.018-0.0180.0000.0000.0000.000
94A95ILE00.006-0.01721.0030.0000.0000.0000.0000.0000.000
95A96ALA00.0060.02023.700-0.007-0.0070.0000.0000.0000.000
96A97SER0-0.007-0.01225.8390.0070.0070.0000.0000.0000.000
97A98LYS10.8350.92229.103-0.094-0.0940.0000.0000.0000.000
98A99ASN0-0.013-0.00231.989-0.002-0.0020.0000.0000.0000.000
99A100LEU00.0080.01132.6870.0000.0000.0000.0000.0000.000
100A101SER0-0.025-0.00834.9430.0000.0000.0000.0000.0000.000
101A102PHE00.0440.02136.410-0.003-0.0030.0000.0000.0000.000
102A103ILE0-0.007-0.01237.7400.0010.0010.0000.0000.0000.000
103A104TRP0-0.038-0.02141.241-0.001-0.0010.0000.0000.0000.000
104A105ILE00.0130.00243.4810.0020.0020.0000.0000.0000.000
105A106GLY00.0440.01446.840-0.001-0.0010.0000.0000.0000.000
106A107GLY0-0.010-0.00449.895-0.001-0.0010.0000.0000.0000.000
107A108PRO0-0.0050.01250.9310.0010.0010.0000.0000.0000.000
108A109ILE00.0350.02746.323-0.001-0.0010.0000.0000.0000.000
109A110SER00.0360.02548.2300.0010.0010.0000.0000.0000.000
110A111ASP-1-0.805-0.91449.5140.0000.0000.0000.0000.0000.000
111A112GLN0-0.0040.00747.6000.0010.0010.0000.0000.0000.000
112A113SER00.0340.01045.3000.0010.0010.0000.0000.0000.000
113A114LEU0-0.016-0.00145.4550.0020.0020.0000.0000.0000.000
114A115GLU-1-0.754-0.86247.1280.0100.0100.0000.0000.0000.000
115A116TYR0-0.043-0.06441.9060.0020.0020.0000.0000.0000.000
116A117TYR00.005-0.00341.7100.0030.0030.0000.0000.0000.000
117A118ASN00.000-0.00342.9720.0040.0040.0000.0000.0000.000
118A119MET00.0220.02541.0310.0040.0040.0000.0000.0000.000
119A120TRP0-0.020-0.02833.9370.0060.0060.0000.0000.0000.000
120A121LYS10.9430.97139.504-0.013-0.0130.0000.0000.0000.000
121A122MET0-0.063-0.01442.0380.0030.0030.0000.0000.0000.000
122A123PHE00.0130.00437.9830.0030.0030.0000.0000.0000.000
123A124ASN0-0.0110.00034.9640.0070.0070.0000.0000.0000.000
124A125LYS10.9180.94237.382-0.041-0.0410.0000.0000.0000.000
125A126ASP-1-0.828-0.90033.4830.0660.0660.0000.0000.0000.000
126A127TYR0-0.049-0.04229.7440.0010.0010.0000.0000.0000.000
127A128ASN0-0.046-0.02335.837-0.005-0.0050.0000.0000.0000.000
128A129ILE0-0.023-0.01037.387-0.004-0.0040.0000.0000.0000.000
129A130ARG10.8570.92336.529-0.026-0.0260.0000.0000.0000.000
130A131LEU00.0140.00440.253-0.002-0.0020.0000.0000.0000.000
131A132PHE0-0.0020.00538.4980.0000.0000.0000.0000.0000.000
132A133TYR00.0490.00742.928-0.002-0.0020.0000.0000.0000.000
133A134ASP-1-0.710-0.81946.210-0.013-0.0130.0000.0000.0000.000
134A135LYS10.9380.97548.234-0.002-0.0020.0000.0000.0000.000
135A136ASN0-0.048-0.02750.7760.0010.0010.0000.0000.0000.000
136A137SER0-0.074-0.07148.858-0.002-0.0020.0000.0000.0000.000
137A138LEU00.0070.00850.6140.0000.0000.0000.0000.0000.000
138A139LEU0-0.035-0.01253.1350.0000.0000.0000.0000.0000.000
139A140VAL00.0280.01949.658-0.001-0.0010.0000.0000.0000.000
140A141ASN00.0140.00851.343-0.003-0.0030.0000.0000.0000.000
141A142THR0-0.026-0.01552.738-0.001-0.0010.0000.0000.0000.000
142A143LEU00.0100.00953.4830.0000.0000.0000.0000.0000.000
143A144LYS10.8880.94848.5190.0330.0330.0000.0000.0000.000
144A145THR0-0.029-0.02954.133-0.001-0.0010.0000.0000.0000.000
145A146ALA00.0180.01656.5620.0000.0000.0000.0000.0000.000
146A147ILE0-0.010-0.00155.1750.0000.0000.0000.0000.0000.000
147A148ILE0-0.0170.00852.911-0.001-0.0010.0000.0000.0000.000
148A149GLN00.0280.00657.5040.0000.0000.0000.0000.0000.000
149A150GLU-1-0.787-0.86260.786-0.018-0.0180.0000.0000.0000.000
150A151SER0-0.023-0.03959.1560.0000.0000.0000.0000.0000.000
151A152SER0-0.031-0.04359.970-0.001-0.0010.0000.0000.0000.000
152A153LYS10.8830.94662.1080.0180.0180.0000.0000.0000.000
153A154VAL00.0140.01565.1970.0000.0000.0000.0000.0000.000
154A155ILE00.0010.00362.3610.0000.0000.0000.0000.0000.000
155A156ILE00.0030.00363.4570.0000.0000.0000.0000.0000.000
156A157GLU-1-0.798-0.87967.035-0.017-0.0170.0000.0000.0000.000
157A158GLN0-0.025-0.00767.6530.0000.0000.0000.0000.0000.000
158A159ASN0-0.052-0.03567.5100.0000.0000.0000.0000.0000.000
159A160GLN0-0.008-0.00470.4870.0000.0000.0000.0000.0000.000
160A161SER00.0330.00672.4920.0000.0000.0000.0000.0000.000
161A162ASN0-0.021-0.02069.6200.0000.0000.0000.0000.0000.000
162A163ILE0-0.031-0.00468.208-0.001-0.0010.0000.0000.0000.000
163A164LEU0-0.023-0.00168.7900.0000.0000.0000.0000.0000.000
164A165ASP-1-0.874-0.95565.621-0.028-0.0280.0000.0000.0000.000
165A166GLY0-0.030-0.01267.717-0.001-0.0010.0000.0000.0000.000
166A167THR0-0.021-0.00667.383-0.001-0.0010.0000.0000.0000.000
167A168TYR0-0.070-0.06463.647-0.001-0.0010.0000.0000.0000.000
168A169GLY00.0910.06563.5530.0000.0000.0000.0000.0000.000
169A170HIS0-0.053-0.03855.3550.0000.0000.0000.0000.0000.000
170A171ASN00.0010.00856.9330.0000.0000.0000.0000.0000.000
171A172LYS10.8930.95458.6800.0310.0310.0000.0000.0000.000
172A173PHE00.015-0.00459.171-0.001-0.0010.0000.0000.0000.000
173A174TYR00.002-0.01455.2860.0010.0010.0000.0000.0000.000
174A175SER0-0.009-0.00956.538-0.001-0.0010.0000.0000.0000.000
175A176ASP-1-0.771-0.85557.518-0.033-0.0330.0000.0000.0000.000
176A177ARG10.8820.94755.0380.0310.0310.0000.0000.0000.000
177A178MET0-0.0190.00752.3080.0000.0000.0000.0000.0000.000
178A179LYS10.8750.93556.6460.0350.0350.0000.0000.0000.000
179A180LEU0-0.0180.01559.1270.0000.0000.0000.0000.0000.000
180A181ILE00.000-0.00554.4260.0010.0010.0000.0000.0000.000
181A182TYR0-0.041-0.03953.3390.0000.0000.0000.0000.0000.000
182A183ARG10.8800.92656.4450.0300.0300.0000.0000.0000.000
183A184TYR00.0190.00358.3950.0010.0010.0000.0000.0000.000
184A185LYS10.8530.94350.3400.0370.0370.0000.0000.0000.000
185A186ARG10.8520.92855.2850.0330.0330.0000.0000.0000.000
186A187GLU-1-0.843-0.91256.561-0.024-0.0240.0000.0000.0000.000
187A188LEU0-0.0070.01254.5830.0010.0010.0000.0000.0000.000
188A189LYS10.8870.92749.7550.0340.0340.0000.0000.0000.000
189A190MET0-0.026-0.01055.1090.0000.0000.0000.0000.0000.000
190A191LEU0-0.0020.01258.1360.0010.0010.0000.0000.0000.000
191A192TYR00.018-0.00350.2230.0010.0010.0000.0000.0000.000
192A193GLU-1-0.840-0.91351.990-0.027-0.0270.0000.0000.0000.000
193A194ASN0-0.043-0.02755.2960.0010.0010.0000.0000.0000.000
194A195MET0-0.0070.00157.4470.0020.0020.0000.0000.0000.000
195A196LYS10.8360.91851.0640.0260.0260.0000.0000.0000.000
196A197GLN0-0.042-0.01652.841-0.001-0.0010.0000.0000.0000.000
197A198ASN0-0.022-0.01255.5540.0010.0010.0000.0000.0000.000
198A199ASN0-0.052-0.01356.8240.0010.0010.0000.0000.0000.000
199A200SER0-0.013-0.01254.283-0.001-0.0010.0000.0000.0000.000
200A201VAL00.033-0.00750.576-0.001-0.0010.0000.0000.0000.000
201A202ASP-1-0.692-0.85853.984-0.013-0.0130.0000.0000.0000.000
202A203ASP-1-0.843-0.89756.433-0.009-0.0090.0000.0000.0000.000
203A204ILE0-0.0040.01055.3000.0000.0000.0000.0000.0000.000
204A205ILE0-0.0160.00254.011-0.001-0.0010.0000.0000.0000.000
205A206ILE0-0.012-0.00958.4560.0000.0000.0000.0000.0000.000
206A207ASN0-0.0070.02161.621-0.001-0.0010.0000.0000.0000.000
207A208PHE00.0650.02359.4950.0000.0000.0000.0000.0000.000
208A209LEU0-0.014-0.01059.3530.0000.0000.0000.0000.0000.000
209A210SER0-0.051-0.03363.0910.0000.0000.0000.0000.0000.000
210A211ASN0-0.035-0.03865.5230.0010.0010.0000.0000.0000.000
211A212TYR0-0.078-0.05263.9780.0000.0000.0000.0000.0000.000
212A213PHE0-0.046-0.03060.8220.0000.0000.0000.0000.0000.000
213A214LYS10.9200.97366.6240.0150.0150.0000.0000.0000.000
214A215TYR0-0.060-0.05462.1190.0010.0010.0000.0000.0000.000
215A216ASP-1-0.824-0.90366.935-0.008-0.0080.0000.0000.0000.000
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