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: LJLV9

Calculation Name: 4RFA-A-Xray322

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2619530.172097
FMO2-HF: Nuclear repulsion 2532143.765507
FMO2-HF: Total energy -87386.40659
FMO2-MP2: Total energy -87643.196695


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:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
2.4472.1995.806-3.087-2.474-0.014
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.015
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].
3A4LYS 10.9730.9893.7480.8821.636-0.002-0.330-0.4240.000
4A5LEU 00.0410.0174.441-0.0160.0770.000-0.009-0.0840.000
5A6ASP -1-0.891-0.9414.424-2.129-2.1170.000-0.0320.0190.000
6A7THR 0-0.007-0.0126.6840.2650.2650.0000.0000.0000.000
7A8VAL 0-0.0240.0038.7070.1280.1280.0000.0000.0000.000
8A9LEU 0-0.032-0.0177.9440.0630.0630.0000.0000.0000.000
9A10GLY 0-0.025-0.01910.7410.0470.0470.0000.0000.0000.000
10A11TYR 00.0520.00512.6220.0480.0480.0000.0000.0000.000
11A12LEU 0-0.076-0.03013.3010.0380.0380.0000.0000.0000.000
12A13LYS 10.9090.94513.5060.2890.2890.0000.0000.0000.000
13A14GLU -1-0.928-0.94217.347-0.168-0.1680.0000.0000.0000.000
14A15PHE 0-0.030-0.01318.5710.0170.0170.0000.0000.0000.000
15A16PRO 00.016-0.00521.7010.0010.0010.0000.0000.0000.000
16A17ASP -1-0.933-0.95924.052-0.033-0.0330.0000.0000.0000.000
17A18TYR 00.0120.00914.5170.0060.0060.0000.0000.0000.000
18A19TYR 00.001-0.02819.5310.0060.0060.0000.0000.0000.000
19A20LYS 10.8900.97021.7400.0250.0250.0000.0000.0000.000
20A21TYR 00.0230.00720.8360.0120.0120.0000.0000.0000.000
21A22VAL 0-0.0040.02215.2800.0160.0160.0000.0000.0000.000
22A23THR 0-0.018-0.00217.677-0.013-0.0130.0000.0000.0000.000
23A24LYS 10.9210.97814.3250.0300.0300.0000.0000.0000.000
24A25LYS 10.9470.96716.103-0.077-0.0770.0000.0000.0000.000
25A26THR 0-0.023-0.01615.6880.0150.0150.0000.0000.0000.000
26A27TYR 0-0.042-0.01417.175-0.013-0.0130.0000.0000.0000.000
27A28THR 0-0.019-0.04518.3070.0040.0040.0000.0000.0000.000
28A29LEU 00.0630.02620.5890.0050.0050.0000.0000.0000.000
29A30ASN 0-0.055-0.04721.640-0.005-0.0050.0000.0000.0000.000
30A31GLU -1-0.872-0.88521.8900.0830.0830.0000.0000.0000.000
31A32LYS 10.8880.93822.383-0.093-0.0930.0000.0000.0000.000
32A33ILE 00.0080.01017.083-0.007-0.0070.0000.0000.0000.000
33A34ILE 0-0.032-0.02621.3260.0020.0020.0000.0000.0000.000
34A35PHE 0-0.036-0.02919.0630.0000.0000.0000.0000.0000.000
35A36GLU -1-0.888-0.93723.6770.0580.0580.0000.0000.0000.000
36A37ASP -1-0.998-0.97626.1580.0600.0600.0000.0000.0000.000
37A38GLU -1-0.907-0.96726.1800.0380.0380.0000.0000.0000.000
38A39LYS 10.8970.93228.850-0.024-0.0240.0000.0000.0000.000
39A40ALA 00.0210.01926.6350.0030.0030.0000.0000.0000.000
40A41LYS 10.9710.99624.423-0.061-0.0610.0000.0000.0000.000
41A42SER 00.018-0.01719.621-0.006-0.0060.0000.0000.0000.000
42A43ILE 0-0.0220.01215.0130.0120.0120.0000.0000.0000.000
43A44PHE 0-0.030-0.02115.221-0.019-0.0190.0000.0000.0000.000
44A45PHE 00.0660.0279.2600.0090.0090.0000.0000.0000.000
45A46ILE 0-0.0170.0009.827-0.080-0.0800.0000.0000.0000.000
46A47VAL 0-0.002-0.0036.8160.1840.1840.0000.0000.0000.000
47A48GLU -1-0.911-0.9546.7670.3020.3020.0000.0000.0000.000
48A49GLY 00.0450.0179.093-0.098-0.0980.0000.0000.0000.000
49A50TYR 00.0300.00410.0460.1070.1070.0000.0000.0000.000
50A51ALA 00.000-0.00514.084-0.063-0.0630.0000.0000.0000.000
51A52ALA 0-0.017-0.00617.0360.0270.0270.0000.0000.0000.000
52A53VAL 00.0030.01219.169-0.022-0.0220.0000.0000.0000.000
53A54GLU -1-0.855-0.95121.7280.1250.1250.0000.0000.0000.000
54A55LEU 0-0.006-0.00625.434-0.004-0.0040.0000.0000.0000.000
55A56GLU -1-0.924-0.96028.4330.0950.0950.0000.0000.0000.000
56A57ASP -1-0.856-0.93630.9980.0710.0710.0000.0000.0000.000
57A58ASN 00.009-0.00634.3310.0020.0020.0000.0000.0000.000
58A59LEU 0-0.0270.00336.758-0.004-0.0040.0000.0000.0000.000
59A60ARG 10.8190.91832.297-0.089-0.0890.0000.0000.0000.000
60A61LYS 10.9550.99134.703-0.068-0.0680.0000.0000.0000.000
61A62THR 0-0.013-0.02530.5740.0010.0010.0000.0000.0000.000
62A63ASN 00.0510.04828.851-0.006-0.0060.0000.0000.0000.000
63A64TYR 0-0.0160.00128.3620.0040.0040.0000.0000.0000.000
64A65ILE 00.0040.00721.746-0.002-0.0020.0000.0000.0000.000
65A66SER 0-0.059-0.05223.489-0.003-0.0030.0000.0000.0000.000
66A67ILE 00.0320.00917.807-0.001-0.0010.0000.0000.0000.000
67A68PHE 00.0420.02216.006-0.022-0.0220.0000.0000.0000.000
68A69VAL 0-0.0300.01513.2030.0130.0130.0000.0000.0000.000
69A70LEU 00.047-0.00210.168-0.037-0.0370.0000.0000.0000.000
70A71PRO 00.007-0.0016.383-0.075-0.0750.0000.0000.0000.000
71A72TYR 00.027-0.0052.5701.9200.8135.808-2.716-1.985-0.014
72A73ASN 0-0.0150.0236.832-0.264-0.2640.0000.0000.0000.000
73A74VAL 00.0370.02110.551-0.044-0.0440.0000.0000.0000.000
74A75LEU 00.002-0.01313.036-0.012-0.0120.0000.0000.0000.000
75A76GLY 00.0250.01216.206-0.023-0.0230.0000.0000.0000.000
76A77ILE 00.0610.02317.081-0.019-0.0190.0000.0000.0000.000
77A78ASP -1-0.819-0.90320.4150.1450.1450.0000.0000.0000.000
78A79ALA 0-0.060-0.02223.011-0.012-0.0120.0000.0000.0000.000
79A80PHE 0-0.022-0.01721.705-0.011-0.0110.0000.0000.0000.000
80A81SER 0-0.057-0.01825.796-0.005-0.0050.0000.0000.0000.000
81A82SER 00.0090.00427.645-0.001-0.0010.0000.0000.0000.000
82A83TYR 00.0070.02130.144-0.005-0.0050.0000.0000.0000.000
83A84PRO 00.0210.01331.270-0.001-0.0010.0000.0000.0000.000
84A85LYS 10.9050.90923.681-0.132-0.1320.0000.0000.0000.000
85A86LYS 10.8890.94229.127-0.066-0.0660.0000.0000.0000.000
86A87LYS 10.9940.98929.581-0.071-0.0710.0000.0000.0000.000
87A88HIS 0-0.0130.01824.8990.0060.0060.0000.0000.0000.000
88A89SER 0-0.040-0.01225.159-0.002-0.0020.0000.0000.0000.000
89A90ILE 00.0300.01318.9280.0100.0100.0000.0000.0000.000
90A91THR 00.0080.01121.554-0.013-0.0130.0000.0000.0000.000
91A92VAL 00.0120.02117.3860.0280.0280.0000.0000.0000.000
92A93MET 0-0.044-0.02417.808-0.027-0.0270.0000.0000.0000.000
93A94SER 0-0.0150.00115.0470.0030.0030.0000.0000.0000.000
94A95GLU -1-0.915-0.96117.2070.0810.0810.0000.0000.0000.000
95A96SER 0-0.005-0.01815.008-0.013-0.0130.0000.0000.0000.000
96A97LEU 00.0160.02813.1150.0350.0350.0000.0000.0000.000
97A98MET 0-0.0040.01211.453-0.075-0.0750.0000.0000.0000.000
98A99LEU 0-0.0090.00411.5260.0750.0750.0000.0000.0000.000
99A100TYR 00.008-0.01010.536-0.070-0.0700.0000.0000.0000.000
100A101LYS 10.8900.94913.854-0.028-0.0280.0000.0000.0000.000
101A102ILE 00.019-0.00913.062-0.025-0.0250.0000.0000.0000.000
102A103ASP -1-0.883-0.93617.5580.0400.0400.0000.0000.0000.000
103A104ALA 00.0490.00520.103-0.002-0.0020.0000.0000.0000.000
104A105ASP -1-0.895-0.93321.1570.0270.0270.0000.0000.0000.000
105A106PHE 0-0.037-0.02718.062-0.007-0.0070.0000.0000.0000.000
106A107LEU 00.003-0.00615.076-0.006-0.0060.0000.0000.0000.000
107A108LEU 0-0.039-0.04618.781-0.002-0.0020.0000.0000.0000.000
108A109ASN 0-0.0200.00221.236-0.002-0.0020.0000.0000.0000.000
109A110ILE 0-0.087-0.02917.135-0.009-0.0090.0000.0000.0000.000
110A111LEU 0-0.047-0.01516.852-0.011-0.0110.0000.0000.0000.000
111A112SER 00.007-0.01319.045-0.007-0.0070.0000.0000.0000.000
112A113ILE 0-0.029-0.00920.893-0.007-0.0070.0000.0000.0000.000
113A114LYS 10.8510.96712.5160.0550.0550.0000.0000.0000.000
114A115PRO 00.008-0.00917.3870.0170.0170.0000.0000.0000.000
115A116ASP -1-0.861-0.93810.948-0.091-0.0910.0000.0000.0000.000
116A117VAL 00.0710.04114.2230.0330.0330.0000.0000.0000.000
117A118ASN 00.0140.01415.7570.0320.0320.0000.0000.0000.000
118A119ASP -1-0.860-0.94214.1200.0730.0730.0000.0000.0000.000
119A120PHE 0-0.0060.0056.7300.0350.0350.0000.0000.0000.000
120A121LEU 00.0050.03011.4720.0850.0850.0000.0000.0000.000
121A122LEU 0-0.006-0.01513.7790.0360.0360.0000.0000.0000.000
122A123THR 0-0.001-0.00610.7400.0030.0030.0000.0000.0000.000
123A124SER 0-0.004-0.03510.6660.0740.0740.0000.0000.0000.000
124A125ILE 0-0.088-0.03911.7950.0140.0140.0000.0000.0000.000
125A126ALA 0-0.0080.00215.167-0.002-0.0020.0000.0000.0000.000
126A127ASP -1-0.833-0.92410.9870.5390.5390.0000.0000.0000.000
127A128VAL 0-0.089-0.04513.881-0.002-0.0020.0000.0000.0000.000
128A129PHE 0-0.014-0.01815.823-0.031-0.0310.0000.0000.0000.000
129A130ALA 00.0200.02416.613-0.023-0.0230.0000.0000.0000.000
130A131ARG 10.8580.89813.667-0.465-0.4650.0000.0000.0000.000
131A132HIS 0-0.046-0.02718.138-0.034-0.0340.0000.0000.0000.000
132A133TYR 0-0.026-0.02421.157-0.022-0.0220.0000.0000.0000.000
133A134ALA 00.0510.03820.510-0.015-0.0150.0000.0000.0000.000
134A135LEU 0-0.025-0.01720.601-0.018-0.0180.0000.0000.0000.000
135A136LEU 0-0.046-0.02223.832-0.017-0.0170.0000.0000.0000.000
136A137GLY 00.0260.02725.986-0.013-0.0130.0000.0000.0000.000
137A138MET 0-0.072-0.03724.221-0.009-0.0090.0000.0000.0000.000
138A139ILE 0-0.066-0.03628.740-0.009-0.0090.0000.0000.0000.000
139A140ALA 0-0.048-0.02431.674-0.003-0.0030.0000.0000.0000.000
140A141LYS 10.9771.02330.622-0.102-0.1020.0000.0000.0000.000
141A142THR 0-0.032-0.03933.7940.0000.0000.0000.0000.0000.000
142A143PRO 0-0.036-0.03632.7630.0050.0050.0000.0000.0000.000
143A144LYS 10.8570.93231.657-0.070-0.0700.0000.0000.0000.000
144A145GLU -1-0.799-0.90031.1740.0910.0910.0000.0000.0000.000
145A146ARG 10.8130.89028.638-0.096-0.0960.0000.0000.0000.000
146A147ILE 00.002-0.00527.0190.0120.0120.0000.0000.0000.000
147A148TYR 0-0.034-0.07726.0750.0110.0110.0000.0000.0000.000
148A149MET 00.0270.02524.7150.0060.0060.0000.0000.0000.000
149A150ALA 0-0.037-0.03222.8850.0180.0180.0000.0000.0000.000
150A151LEU 0-0.026-0.01921.3270.0240.0240.0000.0000.0000.000
151A152GLU -1-0.853-0.92620.4890.1940.1940.0000.0000.0000.000
152A153ASN 0-0.023-0.00718.8050.0220.0220.0000.0000.0000.000
153A154LEU 0-0.064-0.05016.8600.0410.0410.0000.0000.0000.000
154A155ALA 00.0130.01315.7030.0490.0490.0000.0000.0000.000
155A156VAL 00.0080.01214.1880.0390.0390.0000.0000.0000.000
156A157GLU -1-0.925-0.96512.6200.4710.4710.0000.0000.0000.000
157A158MET 0-0.079-0.04211.2710.1020.1020.0000.0000.0000.000
158A159GLY 0-0.0280.00112.942-0.027-0.0270.0000.0000.0000.000
159A160THR 0-0.068-0.05011.1410.0400.0400.0000.0000.0000.000
160A161GLU -1-0.912-0.96613.6900.1190.1190.0000.0000.0000.000
161A162ASP -1-0.943-0.96715.8710.0660.0660.0000.0000.0000.000
162A163GLU -1-0.904-0.94817.9470.0480.0480.0000.0000.0000.000
163A164GLU -1-0.937-0.96720.2460.0120.0120.0000.0000.0000.000
164A165ARG 10.7690.88222.413-0.056-0.0560.0000.0000.0000.000
165A166ASN 00.0070.00322.2540.0080.0080.0000.0000.0000.000
166A167GLU -1-0.809-0.88221.2690.0980.0980.0000.0000.0000.000
167A168ILE 00.0110.01016.3720.0130.0130.0000.0000.0000.000
168A169VAL 0-0.0030.00317.320-0.012-0.0120.0000.0000.0000.000
169A170LEU 0-0.0090.00816.2720.0420.0420.0000.0000.0000.000
170A171PRO 00.0210.00314.013-0.034-0.0340.0000.0000.0000.000
171A172ASN 00.014-0.00716.586-0.023-0.0230.0000.0000.0000.000
172A173PHE 0-0.048-0.02614.799-0.024-0.0240.0000.0000.0000.000
173A174ILE 00.0100.02118.405-0.013-0.0130.0000.0000.0000.000
174A175ASN 00.0630.03021.158-0.010-0.0100.0000.0000.0000.000
175A176GLN 00.0650.01724.7860.0050.0050.0000.0000.0000.000
176A177SER 0-0.056-0.03327.9350.0000.0000.0000.0000.0000.000
177A178VAL 00.0370.01621.797-0.002-0.0020.0000.0000.0000.000
178A179LEU 00.0550.03923.7620.0050.0050.0000.0000.0000.000
179A180ALA 00.009-0.00725.514-0.001-0.0010.0000.0000.0000.000
180A181ARG 10.8340.90125.775-0.133-0.1330.0000.0000.0000.000
181A182TYR 00.0330.02720.132-0.008-0.0080.0000.0000.0000.000
182A183CYS 00.0130.02325.1890.0010.0010.0000.0000.0000.000
183A184ARG 10.8580.95424.563-0.163-0.1630.0000.0000.0000.000
184A185THR 00.0220.02130.297-0.010-0.0100.0000.0000.0000.000
185A186THR 0-0.0010.00832.4480.0020.0020.0000.0000.0000.000
186A187GLN 00.0770.01331.5760.0020.0020.0000.0000.0000.000
187A188PRO 0-0.021-0.01633.7080.0010.0010.0000.0000.0000.000
188A189ASN 00.003-0.00135.211-0.004-0.0040.0000.0000.0000.000
189A190ILE 00.0560.03729.1780.0000.0000.0000.0000.0000.000
190A191SER 0-0.019-0.00532.3060.0010.0010.0000.0000.0000.000
191A192ASN 0-0.018-0.02533.904-0.002-0.0020.0000.0000.0000.000
192A193LEU 00.0300.02132.4920.0000.0000.0000.0000.0000.000
193A194LEU 0-0.015-0.00627.8390.0020.0020.0000.0000.0000.000
194A195THR 0-0.036-0.01631.5510.0010.0010.0000.0000.0000.000
195A196GLU -1-0.840-0.91734.6620.0690.0690.0000.0000.0000.000
196A197LEU 00.0080.00527.9290.0000.0000.0000.0000.0000.000
197A198VAL 0-0.058-0.00431.0360.0010.0010.0000.0000.0000.000
198A199GLU -1-0.966-0.99032.1740.0550.0550.0000.0000.0000.000
199A200GLU -1-0.819-0.85132.7710.0760.0760.0000.0000.0000.000
200A201GLU -1-0.949-0.96431.2930.0610.0610.0000.0000.0000.000
201A202PHE 00.0310.02724.1690.0060.0060.0000.0000.0000.000
202A203LEU 0-0.062-0.04425.1540.0110.0110.0000.0000.0000.000
203A204ILE 00.0670.04625.722-0.008-0.0080.0000.0000.0000.000
204A205ASN 0-0.028-0.03427.529-0.011-0.0110.0000.0000.0000.000
205A206LYS 10.8830.94528.087-0.064-0.0640.0000.0000.0000.000
206A207LYS 10.8830.93928.072-0.071-0.0710.0000.0000.0000.000
207A208SER 00.0260.03423.5030.0020.0020.0000.0000.0000.000
208A209PRO 0-0.029-0.03820.317-0.013-0.0130.0000.0000.0000.000
209A210TYR 0-0.006-0.00821.982-0.009-0.0090.0000.0000.0000.000
210A211ARG 10.8560.91921.011-0.082-0.0820.0000.0000.0000.000
211A212ILE 0-0.017-0.01020.161-0.010-0.0100.0000.0000.0000.000
212A213ASP -1-0.861-0.93222.3770.0940.0940.0000.0000.0000.000
213A214LYS 10.9220.96117.545-0.160-0.1600.0000.0000.0000.000
214A215ASP -1-0.852-0.91722.4950.0820.0820.0000.0000.0000.000
215A216SER 0-0.071-0.04425.3410.0010.0010.0000.0000.0000.000
216A217LEU 0-0.081-0.04019.4590.0080.0080.0000.0000.0000.000
217A218ASP -1-0.946-0.96920.7890.1460.1460.0000.0000.0000.000
218A219NME 0-0.054-0.01220.9710.0070.0070.0000.0000.0000.000