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: 2N6VR

Calculation Name: 4RFA-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4RFA

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8Y902

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 OptHSide
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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2609118.166593
FMO2-HF: Nuclear repulsion 2521901.326474
FMO2-HF: Total energy -87216.840119
FMO2-MP2: Total energy -87473.09564


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:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
131.691131.9310.294-5.275-5.26-0.042
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.918 / q_NPA : -0.968
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].
3A5LEU00.0400.0133.793-8.639-6.412-0.018-1.016-1.1940.004
4A6ASP-1-0.867-0.9271.86026.73623.99610.299-4.084-3.476-0.046
5A7THR00.0010.0034.460-3.292-2.986-0.001-0.083-0.2220.000
6A8VAL0-0.0140.0076.415-3.353-3.3530.0000.0000.0000.000
7A9LEU0-0.035-0.0236.849-2.536-2.5360.0000.0000.0000.000
8A10GLY0-0.028-0.0198.590-1.828-1.8280.0000.0000.0000.000
9A11TYR00.0470.00610.227-0.749-0.7490.0000.0000.0000.000
10A12LEU0-0.070-0.02811.873-1.533-1.5330.0000.0000.0000.000
11A13LYS10.9090.94311.687-19.573-19.5730.0000.0000.0000.000
12A14GLU-1-0.935-0.94414.63616.48516.4850.0000.0000.0000.000
13A15PHE0-0.023-0.00816.292-0.945-0.9450.0000.0000.0000.000
14A16PRO00.012-0.01119.752-0.002-0.0020.0000.0000.0000.000
15A17ASP-1-0.823-0.89622.41410.70910.7090.0000.0000.0000.000
16A18TYR00.0130.01813.5490.0880.0880.0000.0000.0000.000
17A19TYR00.001-0.02818.3860.2740.2740.0000.0000.0000.000
18A20LYS10.7850.89720.557-10.721-10.7210.0000.0000.0000.000
19A21TYR00.0210.01019.851-0.416-0.4160.0000.0000.0000.000
20A22VAL0-0.0110.01914.2720.4840.4840.0000.0000.0000.000
21A23THR0-0.015-0.00217.216-0.476-0.4760.0000.0000.0000.000
22A24LYS10.8810.94613.775-14.672-14.6720.0000.0000.0000.000
23A25LYS10.8740.94716.320-12.666-12.6660.0000.0000.0000.000
24A26THR0-0.005-0.00116.1990.7340.7340.0000.0000.0000.000
25A27TYR0-0.032-0.02018.137-0.605-0.6050.0000.0000.0000.000
26A28THR0-0.007-0.02119.5880.3650.3650.0000.0000.0000.000
27A29LEU00.0480.02622.086-0.212-0.2120.0000.0000.0000.000
28A30ASN0-0.061-0.04923.523-0.282-0.2820.0000.0000.0000.000
29A31GLU-1-0.839-0.89423.30211.14511.1450.0000.0000.0000.000
30A32LYS10.8520.92123.942-9.894-9.8940.0000.0000.0000.000
31A33ILE00.0060.00718.333-0.057-0.0570.0000.0000.0000.000
32A34ILE0-0.055-0.03722.601-0.183-0.1830.0000.0000.0000.000
33A35PHE00.003-0.00319.8640.0990.0990.0000.0000.0000.000
34A36GLU-1-0.864-0.92224.53510.52510.5250.0000.0000.0000.000
35A37ASP-1-0.923-0.93426.6679.3529.3520.0000.0000.0000.000
36A38GLU-1-0.875-0.93625.83810.09310.0930.0000.0000.0000.000
37A39LYS10.9020.93729.137-8.045-8.0450.0000.0000.0000.000
38A40ALA00.0280.02726.3950.0510.0510.0000.0000.0000.000
39A41LYS10.9440.98124.512-10.024-10.0240.0000.0000.0000.000
40A42SER00.023-0.01119.7050.1590.1590.0000.0000.0000.000
41A43ILE0-0.0250.00415.495-0.174-0.1740.0000.0000.0000.000
42A44PHE0-0.020-0.01815.7090.0130.0130.0000.0000.0000.000
43A45PHE00.0760.0309.8720.0820.0820.0000.0000.0000.000
44A46ILE0-0.0180.00311.429-0.515-0.5150.0000.0000.0000.000
45A47VAL00.0060.0037.2331.6471.6470.0000.0000.0000.000
46A48GLU-1-0.888-0.9458.04420.51620.5160.0000.0000.0000.000
47A49GLY00.0370.00910.648-1.387-1.3870.0000.0000.0000.000
48A50TYR00.0330.00212.3360.5340.5340.0000.0000.0000.000
49A51ALA0-0.008-0.00516.152-0.848-0.8480.0000.0000.0000.000
50A52ALA0-0.011-0.00519.0260.3890.3890.0000.0000.0000.000
51A53VAL00.0190.02021.128-0.424-0.4240.0000.0000.0000.000
52A54GLU-1-0.818-0.91123.72310.24310.2430.0000.0000.0000.000
53A55LEU0-0.008-0.00527.476-0.072-0.0720.0000.0000.0000.000
54A56GLU-1-0.877-0.90130.1939.3129.3120.0000.0000.0000.000
55A57ASP-1-0.844-0.93232.9307.8237.8230.0000.0000.0000.000
56A58ASN0-0.011-0.01236.3460.1210.1210.0000.0000.0000.000
57A59LEU0-0.0200.00638.712-0.181-0.1810.0000.0000.0000.000
58A60ARG10.8090.91134.902-8.629-8.6290.0000.0000.0000.000
59A61LYS10.9470.98337.186-7.863-7.8630.0000.0000.0000.000
60A62THR0-0.011-0.01432.7360.0320.0320.0000.0000.0000.000
61A63ASN00.0470.03130.805-0.323-0.3230.0000.0000.0000.000
62A64TYR0-0.0090.00130.7230.1520.1520.0000.0000.0000.000
63A65ILE0-0.010-0.00124.010-0.032-0.0320.0000.0000.0000.000
64A66SER0-0.057-0.05425.855-0.096-0.0960.0000.0000.0000.000
65A67ILE00.0410.01319.9840.0430.0430.0000.0000.0000.000
66A68PHE00.0210.01718.375-0.465-0.4650.0000.0000.0000.000
67A69VAL0-0.0100.00714.9360.2930.2930.0000.0000.0000.000
68A70LEU00.0290.00312.451-0.396-0.3960.0000.0000.0000.000
69A71PRO0-0.002-0.0088.601-0.265-0.2650.0000.0000.0000.000
70A72TYR00.012-0.0113.2742.0752.5210.014-0.092-0.3680.000
71A73ASN0-0.0250.0078.428-1.663-1.6630.0000.0000.0000.000
72A74VAL00.0320.02312.135-0.150-0.1500.0000.0000.0000.000
73A75LEU0-0.005-0.01614.091-0.694-0.6940.0000.0000.0000.000
74A76GLY00.0370.01817.354-0.040-0.0400.0000.0000.0000.000
75A77ILE00.0420.01717.988-0.426-0.4260.0000.0000.0000.000
76A78ASP-1-0.867-0.93921.31812.03912.0390.0000.0000.0000.000
77A79ALA0-0.067-0.01923.965-0.556-0.5560.0000.0000.0000.000
78A80PHE0-0.029-0.02722.199-0.434-0.4340.0000.0000.0000.000
79A81SER0-0.061-0.01726.474-0.344-0.3440.0000.0000.0000.000
80A82SER00.0280.00528.567-0.101-0.1010.0000.0000.0000.000
81A83TYR0-0.037-0.00531.314-0.421-0.4210.0000.0000.0000.000
82A84PRO00.0130.01032.3400.0440.0440.0000.0000.0000.000
83A85LYS10.9150.92228.859-9.374-9.3740.0000.0000.0000.000
84A86LYS10.9150.95231.189-8.445-8.4450.0000.0000.0000.000
85A87LYS10.9730.98131.236-8.169-8.1690.0000.0000.0000.000
86A88HIS00.0570.05126.7360.0180.0180.0000.0000.0000.000
87A89SER0-0.059-0.04426.738-0.011-0.0110.0000.0000.0000.000
88A90ILE00.0380.01620.4600.1480.1480.0000.0000.0000.000
89A91THR0-0.009-0.01223.402-0.217-0.2170.0000.0000.0000.000
90A92VAL00.0170.02318.9950.4930.4930.0000.0000.0000.000
91A93MET0-0.044-0.02620.023-0.700-0.7000.0000.0000.0000.000
92A94SER0-0.0140.00317.087-0.061-0.0610.0000.0000.0000.000
93A95GLU-1-0.904-0.96519.53311.62411.6240.0000.0000.0000.000
94A96SER00.012-0.00916.403-0.586-0.5860.0000.0000.0000.000
95A97LEU0-0.0140.01914.6320.5620.5620.0000.0000.0000.000
96A98MET00.0250.03711.474-1.598-1.5980.0000.0000.0000.000
97A99LEU0-0.0120.00212.4021.0351.0350.0000.0000.0000.000
98A100TYR00.015-0.01010.049-1.092-1.0920.0000.0000.0000.000
99A101LYS10.8060.89713.884-11.367-11.3670.0000.0000.0000.000
100A102ILE00.010-0.01612.536-0.096-0.0960.0000.0000.0000.000
101A103ASP-1-0.856-0.92717.24811.57411.5740.0000.0000.0000.000
102A104ALA00.0430.00319.6490.4830.4830.0000.0000.0000.000
103A105ASP-1-0.899-0.93420.93311.16611.1660.0000.0000.0000.000
104A106PHE0-0.008-0.00316.7210.2330.2330.0000.0000.0000.000
105A107LEU00.005-0.00114.3270.3500.3500.0000.0000.0000.000
106A108LEU0-0.043-0.04818.0930.5000.5000.0000.0000.0000.000
107A109ASN0-0.071-0.04020.684-0.429-0.4290.0000.0000.0000.000
108A110ILE0-0.065-0.01715.7740.0120.0120.0000.0000.0000.000
109A111LEU0-0.052-0.01616.4220.9410.9410.0000.0000.0000.000
110A112SER00.002-0.01517.5700.5940.5940.0000.0000.0000.000
111A113ILE0-0.033-0.01219.0230.1790.1790.0000.0000.0000.000
112A114LYS10.8180.93711.147-22.008-22.0080.0000.0000.0000.000
113A115PRO00.012-0.00913.3940.1140.1140.0000.0000.0000.000
114A116ASP-1-0.818-0.9019.24728.89828.8980.0000.0000.0000.000
115A117VAL00.0650.03711.562-0.059-0.0590.0000.0000.0000.000
116A118ASN00.0160.01614.419-0.170-0.1700.0000.0000.0000.000
117A119ASP-1-0.870-0.95012.24220.65420.6540.0000.0000.0000.000
118A120PHE0-0.0040.0147.0580.0490.0490.0000.0000.0000.000
119A121LEU0-0.0040.01110.9560.2240.2240.0000.0000.0000.000
120A122LEU0-0.019-0.02313.933-0.571-0.5710.0000.0000.0000.000
121A123THR0-0.001-0.01410.258-0.612-0.6120.0000.0000.0000.000
122A124SER00.013-0.00611.0100.4540.4540.0000.0000.0000.000
123A125ILE0-0.073-0.03112.767-0.812-0.8120.0000.0000.0000.000
124A126ALA0-0.0040.00315.322-0.706-0.7060.0000.0000.0000.000
125A127ASP-1-0.842-0.92811.70023.69623.6960.0000.0000.0000.000
126A128VAL0-0.080-0.03915.275-0.745-0.7450.0000.0000.0000.000
127A129PHE0-0.017-0.02317.483-0.907-0.9070.0000.0000.0000.000
128A130ALA00.0270.02717.709-0.817-0.8170.0000.0000.0000.000
129A131ARG10.8200.87515.673-18.074-18.0740.0000.0000.0000.000
130A132HIS0-0.052-0.02919.995-1.008-1.0080.0000.0000.0000.000
131A133TYR0-0.022-0.02122.967-0.680-0.6800.0000.0000.0000.000
132A134ALA00.0500.03822.296-0.518-0.5180.0000.0000.0000.000
133A135LEU0-0.026-0.02522.886-0.629-0.6290.0000.0000.0000.000
134A136LEU0-0.039-0.01825.876-0.600-0.6000.0000.0000.0000.000
135A137GLY00.0260.02727.873-0.482-0.4820.0000.0000.0000.000
136A138MET0-0.066-0.02926.281-0.411-0.4110.0000.0000.0000.000
137A139ILE0-0.066-0.03930.876-0.417-0.4170.0000.0000.0000.000
138A140ALA0-0.046-0.02533.728-0.046-0.0460.0000.0000.0000.000
139A141LYS10.9000.97632.919-9.608-9.6080.0000.0000.0000.000
140A142THR0-0.032-0.05435.980-0.060-0.0600.0000.0000.0000.000
141A143PRO0-0.024-0.03034.9810.2350.2350.0000.0000.0000.000
142A144LYS10.8050.88433.907-8.559-8.5590.0000.0000.0000.000
143A145GLU-1-0.737-0.84633.3989.2249.2240.0000.0000.0000.000
144A146ARG10.8210.90230.863-9.022-9.0220.0000.0000.0000.000
145A147ILE0-0.019-0.00629.2690.4060.4060.0000.0000.0000.000
146A148TYR00.013-0.02228.3510.4470.4470.0000.0000.0000.000
147A149MET00.0400.02926.7650.2200.2200.0000.0000.0000.000
148A150ALA0-0.050-0.03725.1520.5340.5340.0000.0000.0000.000
149A151LEU0-0.022-0.02123.5890.6280.6280.0000.0000.0000.000
150A152GLU-1-0.864-0.92822.45013.79813.7980.0000.0000.0000.000
151A153ASN00.0020.00320.7870.9630.9630.0000.0000.0000.000
152A154LEU0-0.073-0.05319.1210.8500.8500.0000.0000.0000.000
153A155ALA00.0180.01417.9730.9790.9790.0000.0000.0000.000
154A156VAL00.0200.01515.8551.1591.1590.0000.0000.0000.000
155A157GLU-1-0.889-0.92614.75117.92617.9260.0000.0000.0000.000
156A158MET0-0.082-0.05313.5200.9310.9310.0000.0000.0000.000
157A159GLY0-0.0240.00615.166-0.341-0.3410.0000.0000.0000.000
158A160THR0-0.068-0.04512.8961.3141.3140.0000.0000.0000.000
159A161GLU-1-0.824-0.89514.37717.86617.8660.0000.0000.0000.000
160A162ASP-1-0.883-0.93816.05614.97414.9740.0000.0000.0000.000
161A163GLU-1-0.906-0.95716.51718.63718.6370.0000.0000.0000.000
162A164GLU-1-0.975-0.98019.45113.08913.0890.0000.0000.0000.000
163A165ARG10.7950.89321.753-13.786-13.7860.0000.0000.0000.000
164A166ASN0-0.026-0.01921.7830.2070.2070.0000.0000.0000.000
165A167GLU-1-0.805-0.89421.21812.24712.2470.0000.0000.0000.000
166A168ILE00.0260.01717.2830.9830.9830.0000.0000.0000.000
167A169VAL0-0.017-0.00218.611-1.023-1.0230.0000.0000.0000.000
168A170LEU0-0.0040.01018.4180.9860.9860.0000.0000.0000.000
169A171PRO00.0200.00016.439-0.625-0.6250.0000.0000.0000.000
170A172ASN00.007-0.01019.155-0.803-0.8030.0000.0000.0000.000
171A173PHE0-0.028-0.01117.246-0.682-0.6820.0000.0000.0000.000
172A174ILE00.0020.01520.826-0.626-0.6260.0000.0000.0000.000
173A175ASN00.0550.02323.694-0.409-0.4090.0000.0000.0000.000
174A176GLN00.0980.03227.3460.0020.0020.0000.0000.0000.000
175A177SER0-0.042-0.02730.382-0.190-0.1900.0000.0000.0000.000
176A178VAL00.0170.00824.204-0.168-0.1680.0000.0000.0000.000
177A179LEU00.0600.04126.1770.0160.0160.0000.0000.0000.000
178A180ALA00.0200.00027.889-0.057-0.0570.0000.0000.0000.000
179A181ARG10.8000.87927.771-10.564-10.5640.0000.0000.0000.000
180A182TYR00.0300.02622.195-0.305-0.3050.0000.0000.0000.000
181A183CYS00.0100.02227.5200.0800.0800.0000.0000.0000.000
182A184ARG10.8490.93826.627-11.385-11.3850.0000.0000.0000.000
183A185THR00.0070.01432.635-0.381-0.3810.0000.0000.0000.000
184A186THR00.0020.00834.7550.1020.1020.0000.0000.0000.000
185A187GLN00.0770.02933.8610.1680.1680.0000.0000.0000.000
186A188PRO00.001-0.00936.1440.0900.0900.0000.0000.0000.000
187A189ASN0-0.012-0.00937.428-0.126-0.1260.0000.0000.0000.000
188A190ILE00.0610.03931.6700.0220.0220.0000.0000.0000.000
189A191SER0-0.030-0.02034.6610.0630.0630.0000.0000.0000.000
190A192ASN0-0.040-0.03036.3270.0310.0310.0000.0000.0000.000
191A193LEU00.0190.01734.7840.0060.0060.0000.0000.0000.000
192A194LEU00.006-0.00230.0690.1320.1320.0000.0000.0000.000
193A195THR0-0.050-0.02633.8530.1650.1650.0000.0000.0000.000
194A196GLU-1-0.805-0.88336.5828.3878.3870.0000.0000.0000.000
195A197LEU00.0160.00929.9090.0260.0260.0000.0000.0000.000
196A198VAL0-0.058-0.00732.4460.1740.1740.0000.0000.0000.000
197A199GLU-1-0.975-0.98633.6428.0418.0410.0000.0000.0000.000
198A200GLU-1-0.837-0.89534.0489.0689.0680.0000.0000.0000.000
199A201GLU-1-0.952-0.96531.8909.5299.5290.0000.0000.0000.000
200A202PHE00.0280.02325.5670.3810.3810.0000.0000.0000.000
201A203LEU0-0.064-0.04426.7120.5630.5630.0000.0000.0000.000
202A204ILE00.0720.04626.661-0.443-0.4430.0000.0000.0000.000
203A205ASN0-0.039-0.03929.193-0.649-0.6490.0000.0000.0000.000
204A206LYS10.9180.96730.189-8.406-8.4060.0000.0000.0000.000
205A207LYS10.8510.92429.671-10.456-10.4560.0000.0000.0000.000
206A208SER00.0190.03826.1220.1040.1040.0000.0000.0000.000
207A209PRO0-0.027-0.03722.848-0.519-0.5190.0000.0000.0000.000
208A210TYR00.012-0.00724.434-0.242-0.2420.0000.0000.0000.000
209A211ARG10.8160.90522.628-12.794-12.7940.0000.0000.0000.000
210A212ILE0-0.018-0.01122.068-0.630-0.6300.0000.0000.0000.000
211A213ASP-1-0.842-0.92523.18912.51212.5120.0000.0000.0000.000
212A214LYS10.8560.89517.246-17.654-17.6540.0000.0000.0000.000
213A215ASP-1-0.846-0.90122.62512.42012.4200.0000.0000.0000.000
214A216SER0-0.090-0.04525.345-0.056-0.0560.0000.0000.0000.000
215A217LEU0-0.083-0.02520.279-0.100-0.1000.0000.0000.0000.000
216A218ASP-1-1.001-0.99520.77414.63614.6360.0000.0000.0000.000