Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 8J12Y

Calculation Name: 3H25-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H25

Chain ID: A

ChEMBL ID:

UniProt ID: Q52349

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2043592.814936
FMO2-HF: Nuclear repulsion 1969243.003614
FMO2-HF: Total energy -74349.811322
FMO2-MP2: Total energy -74565.992591


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:ACE )


Summations of interaction energy for fragment #1(A:3: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.
3.1174.1630.018-0.417-0.6470.001
Interaction energy analysis for fragmet #1(A:3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.023
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].
3A5ARG 10.9580.9543.8752.2902.907-0.005-0.296-0.3160.001
4A6THR 0-0.022-0.0207.1290.2500.2500.0000.0000.0000.000
5A7LEU 00.0120.0033.411-0.0700.1440.018-0.062-0.1700.000
6A8GLN 00.0430.0103.5490.3710.5860.005-0.059-0.1610.000
7A9ALA 0-0.033-0.0017.3590.0360.0360.0000.0000.0000.000
8A10ILE 00.0620.0329.3920.0420.0420.0000.0000.0000.000
9A11GLY 00.0300.0199.7410.0170.0170.0000.0000.0000.000
10A12ARG 10.8620.93311.039-0.034-0.0340.0000.0000.0000.000
11A13GLN 00.0650.03913.041-0.026-0.0260.0000.0000.0000.000
12A14LEU 0-0.015-0.01113.484-0.007-0.0070.0000.0000.0000.000
13A15LYS 10.9420.97815.009-0.210-0.2100.0000.0000.0000.000
14A16ALA 0-0.054-0.02416.851-0.013-0.0130.0000.0000.0000.000
15A17MET 0-0.054-0.03318.968-0.011-0.0110.0000.0000.0000.000
16A18GLY 0-0.010-0.00119.746-0.007-0.0070.0000.0000.0000.000
17A19CYS 0-0.059-0.00521.325-0.002-0.0020.0000.0000.0000.000
18A20GLU -1-0.922-0.95620.4990.1300.1300.0000.0000.0000.000
19A21ARG 10.8260.90020.978-0.075-0.0750.0000.0000.0000.000
20A22PHE 0-0.017-0.02618.168-0.007-0.0070.0000.0000.0000.000
21A23ASP -1-0.845-0.91721.6600.0390.0390.0000.0000.0000.000
22A24ILE 0-0.053-0.04917.577-0.004-0.0040.0000.0000.0000.000
23A25GLY 00.0310.01620.788-0.001-0.0010.0000.0000.0000.000
24A26VAL 0-0.046-0.03819.735-0.011-0.0110.0000.0000.0000.000
25A27ARG 10.9770.97622.2060.0430.0430.0000.0000.0000.000
26A28ASP -1-0.780-0.87024.210-0.066-0.0660.0000.0000.0000.000
27A29ALA 0-0.050-0.03625.2220.0040.0040.0000.0000.0000.000
28A30THR 0-0.005-0.00327.0570.0000.0000.0000.0000.0000.000
29A31THR 0-0.028-0.04630.1220.0040.0040.0000.0000.0000.000
30A32GLY 0-0.051-0.00929.7040.0040.0040.0000.0000.0000.000
31A33GLN 0-0.016-0.01229.6680.0050.0050.0000.0000.0000.000
32A34MET 0-0.0300.01325.546-0.006-0.0060.0000.0000.0000.000
33A35MET 00.0040.01723.7670.0060.0060.0000.0000.0000.000
34A36ASN 00.0700.03024.191-0.004-0.0040.0000.0000.0000.000
35A37ARG 10.9250.96721.029-0.035-0.0350.0000.0000.0000.000
36A38GLU -1-0.815-0.88822.2260.0610.0610.0000.0000.0000.000
37A39TRP 0-0.060-0.03817.5000.0000.0000.0000.0000.0000.000
38A40SER 00.0450.02819.4090.0060.0060.0000.0000.0000.000
39A41ALA 00.0530.01316.3380.0080.0080.0000.0000.0000.000
40A42ALA 00.002-0.00814.3290.0270.0270.0000.0000.0000.000
41A43GLU -1-0.829-0.91814.1650.1510.1510.0000.0000.0000.000
42A44VAL 0-0.024-0.00313.782-0.011-0.0110.0000.0000.0000.000
43A45LEU 0-0.018-0.0129.027-0.008-0.0080.0000.0000.0000.000
44A46GLN 0-0.0010.03210.2650.0230.0230.0000.0000.0000.000
45A47ASN 0-0.054-0.03012.361-0.036-0.0360.0000.0000.0000.000
46A48THR 00.025-0.0108.170-0.077-0.0770.0000.0000.0000.000
47A49PRO 0-0.004-0.0129.473-0.094-0.0940.0000.0000.0000.000
48A50TRP 00.0240.01211.347-0.044-0.0440.0000.0000.0000.000
49A51LEU 00.0320.01613.194-0.025-0.0250.0000.0000.0000.000
50A52LYS 10.9340.9656.3470.4970.4970.0000.0000.0000.000
51A53ARG 10.9540.99012.9900.0750.0750.0000.0000.0000.000
52A54MET 0-0.001-0.00315.9390.0000.0000.0000.0000.0000.000
53A55ASN 00.0370.03915.463-0.043-0.0430.0000.0000.0000.000
54A56ALA 0-0.023-0.02215.860-0.002-0.0020.0000.0000.0000.000
55A57GLN 0-0.076-0.04417.7690.0040.0040.0000.0000.0000.000
56A58GLY 0-0.0020.01820.5480.0130.0130.0000.0000.0000.000
57A59ASN 0-0.004-0.00720.4120.0210.0210.0000.0000.0000.000
58A60ASP -1-0.798-0.88519.807-0.114-0.1140.0000.0000.0000.000
59A61VAL 00.000-0.00216.0520.0130.0130.0000.0000.0000.000
60A62TYR 0-0.019-0.02419.119-0.009-0.0090.0000.0000.0000.000
61A63ILE 0-0.039-0.02817.2170.0100.0100.0000.0000.0000.000
62A64ARG 10.9040.94820.809-0.020-0.0200.0000.0000.0000.000
63A65PRO 00.0190.00823.0710.0070.0070.0000.0000.0000.000
64A66ALA 00.0450.03424.569-0.007-0.0070.0000.0000.0000.000
65A67GLU -1-0.791-0.89426.0560.0250.0250.0000.0000.0000.000
66A68GLN 0-0.036-0.02329.547-0.005-0.0050.0000.0000.0000.000
67A69GLU -1-0.815-0.89325.2160.0920.0920.0000.0000.0000.000
68A70ARG 10.8720.93228.413-0.052-0.0520.0000.0000.0000.000
69A71HIS 00.0630.02327.1330.0040.0040.0000.0000.0000.000
70A72GLY 00.0330.01128.723-0.005-0.0050.0000.0000.0000.000
71A73LEU 0-0.057-0.02023.168-0.003-0.0030.0000.0000.0000.000
72A74VAL 00.0140.00627.860-0.001-0.0010.0000.0000.0000.000
73A75LEU 0-0.041-0.00425.0790.0000.0000.0000.0000.0000.000
74A76VAL 00.0300.02128.0200.0000.0000.0000.0000.0000.000
75A77ASP -1-0.841-0.93827.552-0.040-0.0400.0000.0000.0000.000
76A78ASP -1-0.941-0.95328.508-0.039-0.0390.0000.0000.0000.000
77A79LEU 00.0530.03028.0590.0030.0030.0000.0000.0000.000
78A80SER 00.005-0.00428.829-0.008-0.0080.0000.0000.0000.000
79A81GLU -1-0.930-1.01627.265-0.063-0.0630.0000.0000.0000.000
80A82PHE 0-0.028-0.00429.0160.0020.0020.0000.0000.0000.000
81A83ASP -1-0.723-0.85431.542-0.024-0.0240.0000.0000.0000.000
82A84LEU 0-0.112-0.06225.5990.0050.0050.0000.0000.0000.000
83A85ASP -1-0.970-0.98729.705-0.020-0.0200.0000.0000.0000.000
84A86ASP -1-0.836-0.91031.703-0.013-0.0130.0000.0000.0000.000
85A87MET 0-0.062-0.02829.3870.0030.0030.0000.0000.0000.000
86A88LYS 10.7480.84925.1330.0200.0200.0000.0000.0000.000
87A89ALA 0-0.0120.01131.5640.0040.0040.0000.0000.0000.000
88A90GLU -1-0.845-0.89335.091-0.003-0.0030.0000.0000.0000.000
89A91GLY 0-0.067-0.01634.2690.0020.0020.0000.0000.0000.000
90A92ARG 10.8020.87432.5650.0010.0010.0000.0000.0000.000
91A93GLU -1-0.770-0.89028.1160.0160.0160.0000.0000.0000.000
92A94PRO 00.0230.01024.8290.0050.0050.0000.0000.0000.000
93A95ALA 0-0.066-0.03123.2910.0040.0040.0000.0000.0000.000
94A96LEU 0-0.050-0.05618.7940.0110.0110.0000.0000.0000.000
95A97VAL 00.0040.02320.586-0.004-0.0040.0000.0000.0000.000
96A98VAL 0-0.026-0.02918.412-0.007-0.0070.0000.0000.0000.000
97A99GLU -1-0.826-0.91919.599-0.123-0.1230.0000.0000.0000.000
98A100THR 00.0140.00120.074-0.021-0.0210.0000.0000.0000.000
99A101SER 00.0360.02421.726-0.014-0.0140.0000.0000.0000.000
100A102PRO 0-0.019-0.01022.2460.0050.0050.0000.0000.0000.000
101A103LYS 10.9150.96024.0640.1010.1010.0000.0000.0000.000
102A104ASN 00.0050.02225.1960.0150.0150.0000.0000.0000.000
103A105TYR 0-0.013-0.02022.595-0.012-0.0120.0000.0000.0000.000
104A106GLN 00.0490.04922.9770.0040.0040.0000.0000.0000.000
105A107ALA 00.001-0.01624.006-0.001-0.0010.0000.0000.0000.000
106A108TRP 00.0320.03022.1090.0070.0070.0000.0000.0000.000
107A109VAL 00.0650.02825.4800.0040.0040.0000.0000.0000.000
108A110LYS 10.8970.96625.984-0.065-0.0650.0000.0000.0000.000
109A111VAL 00.0160.01028.486-0.001-0.0010.0000.0000.0000.000
110A112ALA 00.009-0.01131.1660.0000.0000.0000.0000.0000.000
111A113ASP -1-0.877-0.94229.1600.0670.0670.0000.0000.0000.000
112A114ALA 0-0.031-0.02129.7610.0030.0030.0000.0000.0000.000
113A115ALA 00.0220.01332.298-0.003-0.0030.0000.0000.0000.000
114A116GLY 0-0.0080.00533.6720.0010.0010.0000.0000.0000.000
115A117GLY 00.0530.01334.712-0.001-0.0010.0000.0000.0000.000
116A118GLU -1-0.894-0.94635.6880.0130.0130.0000.0000.0000.000
117A119LEU 0-0.0120.00037.391-0.001-0.0010.0000.0000.0000.000
118A120ARG 10.8870.93631.117-0.032-0.0320.0000.0000.0000.000
119A121GLY 00.0120.01034.732-0.002-0.0020.0000.0000.0000.000
120A122GLN 00.0010.00636.665-0.003-0.0030.0000.0000.0000.000
121A123ILE 00.010-0.01034.537-0.002-0.0020.0000.0000.0000.000
122A124ALA 00.0180.01233.624-0.002-0.0020.0000.0000.0000.000
123A125ARG 10.9500.98034.895-0.007-0.0070.0000.0000.0000.000
124A126THR 0-0.062-0.02238.173-0.002-0.0020.0000.0000.0000.000
125A127LEU 0-0.016-0.02232.251-0.001-0.0010.0000.0000.0000.000
126A128ALA 00.0110.00635.096-0.002-0.0020.0000.0000.0000.000
127A129SER 0-0.043-0.00935.971-0.003-0.0030.0000.0000.0000.000
128A130GLU -1-0.838-0.92437.3970.0010.0010.0000.0000.0000.000
129A131TYR 0-0.039-0.04334.3630.0010.0010.0000.0000.0000.000
130A132ASP -1-0.943-0.95235.318-0.020-0.0200.0000.0000.0000.000
131A133ALA 00.0090.00932.586-0.002-0.0020.0000.0000.0000.000
132A134ASP -1-0.873-0.95032.624-0.025-0.0250.0000.0000.0000.000
133A135PRO 0-0.029-0.02734.2840.0030.0030.0000.0000.0000.000
134A136ALA 0-0.056-0.02534.8090.0030.0030.0000.0000.0000.000
135A137SER 0-0.012-0.00630.4440.0010.0010.0000.0000.0000.000
136A138ALA 0-0.0290.00131.8220.0030.0030.0000.0000.0000.000
137A139ASP -1-0.875-0.95433.0350.0020.0020.0000.0000.0000.000
138A140SER 0-0.079-0.04632.1080.0010.0010.0000.0000.0000.000
139A141ARG 10.7550.87628.671-0.025-0.0250.0000.0000.0000.000
140A142HIS 00.0620.07328.447-0.001-0.0010.0000.0000.0000.000
141A143TYR 0-0.103-0.07323.1940.0050.0050.0000.0000.0000.000
142A144GLY 00.0370.03123.313-0.005-0.0050.0000.0000.0000.000
143A145ARG 10.8320.88919.9140.0870.0870.0000.0000.0000.000
144A146LEU 0-0.036-0.00314.5340.0120.0120.0000.0000.0000.000
145A147ALA 00.010-0.00214.576-0.028-0.0280.0000.0000.0000.000
146A148GLY 0-0.042-0.02311.3430.0130.0130.0000.0000.0000.000
147A149PHE 0-0.0050.00211.722-0.079-0.0790.0000.0000.0000.000
148A150THR 0-0.022-0.01314.4860.0030.0030.0000.0000.0000.000
149A151ASN 0-0.028-0.04517.2510.0300.0300.0000.0000.0000.000
150A152ARG 10.8500.89718.6760.1630.1630.0000.0000.0000.000
151A153LYS 10.8650.97022.9450.0710.0710.0000.0000.0000.000
152A154ASP -1-0.806-0.90624.592-0.088-0.0880.0000.0000.0000.000
153A155LYS 10.9020.95824.9080.0580.0580.0000.0000.0000.000
154A156NME 0-0.010-0.01127.040-0.005-0.0050.0000.0000.0000.000
155A162ACE 00.007-0.00721.855-0.002-0.0020.0000.0000.0000.000
156A163GLN 0-0.039-0.01420.0410.0190.0190.0000.0000.0000.000
157A164PRO 00.0310.05019.095-0.032-0.0320.0000.0000.0000.000
158A165TRP 0-0.007-0.01112.284-0.009-0.0090.0000.0000.0000.000
159A166VAL 00.0180.02716.4470.0190.0190.0000.0000.0000.000
160A167LEU 0-0.053-0.01914.656-0.038-0.0380.0000.0000.0000.000
161A168LEU 0-0.018-0.00114.0360.0310.0310.0000.0000.0000.000
162A169ARG 10.9140.97715.7830.0560.0560.0000.0000.0000.000
163A170GLU -1-0.841-0.92218.142-0.004-0.0040.0000.0000.0000.000
164A171SER 00.018-0.00416.286-0.005-0.0050.0000.0000.0000.000
165A172LYS 10.8880.94218.4180.0080.0080.0000.0000.0000.000
166A173GLY 00.0330.01521.0020.0110.0110.0000.0000.0000.000
167A174LYS 10.7650.93522.288-0.024-0.0240.0000.0000.0000.000
168A175THR 0-0.006-0.02225.713-0.003-0.0030.0000.0000.0000.000
169A176ALA 0-0.0100.00428.984-0.001-0.0010.0000.0000.0000.000
170A177THR 0-0.027-0.04030.9120.0040.0040.0000.0000.0000.000
171A178ALA 00.0000.00433.9840.0010.0010.0000.0000.0000.000
172A179GLY 0-0.018-0.00233.656-0.001-0.0010.0000.0000.0000.000
173A180PRO 00.041-0.00234.480-0.001-0.0010.0000.0000.0000.000
174A181ALA 00.0120.01037.337-0.001-0.0010.0000.0000.0000.000
175A182LEU 00.0330.00734.915-0.001-0.0010.0000.0000.0000.000
176A183VAL 0-0.036-0.01436.256-0.001-0.0010.0000.0000.0000.000
177A184GLN 0-0.031-0.02138.9290.0010.0010.0000.0000.0000.000
178A185GLN 0-0.0080.00441.974-0.001-0.0010.0000.0000.0000.000
179A186ALA 00.0330.01640.119-0.001-0.0010.0000.0000.0000.000
180A187GLY 00.0160.00342.1270.0000.0000.0000.0000.0000.000
181A188GLN 00.0200.01343.945-0.001-0.0010.0000.0000.0000.000
182A189GLN 0-0.022-0.02643.6380.0000.0000.0000.0000.0000.000
183A190ILE 00.0020.01041.485-0.001-0.0010.0000.0000.0000.000
184A191GLU -1-0.832-0.90946.0920.0130.0130.0000.0000.0000.000
185A192GLN 0-0.030-0.01149.1010.0000.0000.0000.0000.0000.000
186A193ALA 0-0.007-0.01148.392-0.001-0.0010.0000.0000.0000.000
187A194GLN 0-0.032-0.00849.1970.0000.0000.0000.0000.0000.000
188A195ARG 10.8280.90151.075-0.011-0.0110.0000.0000.0000.000
189A196GLN 0-0.100-0.03553.683-0.001-0.0010.0000.0000.0000.000
190A197GLN 0-0.0030.00454.5370.0000.0000.0000.0000.0000.000
191A198GLU -1-0.951-0.97255.9360.0060.0060.0000.0000.0000.000
192A199NME 0-0.046-0.01859.117-0.001-0.0010.0000.0000.0000.000