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: YY242

Calculation Name: 2H8R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8R

Chain ID: A

ChEMBL ID:

UniProt ID: P35680

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1842920.52899
FMO2-HF: Nuclear repulsion 1769848.985138
FMO2-HF: Total energy -73071.543852
FMO2-MP2: Total energy -73283.412268


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:90:SER)


Summations of interaction energy for fragment #1(A:90:SER)
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.
-11.505-7.1260.659-1.89-3.1490.008
Interaction energy analysis for fragmet #1(A:90:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.006
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].
3A92LEU00.0330.0272.904-2.3280.4120.364-1.378-1.7270.007
4A93LYS10.9510.9622.849-6.874-5.5520.296-0.395-1.2230.001
5A94GLU-1-0.932-0.9564.315-0.858-0.541-0.001-0.117-0.1990.000
6A95LEU00.0420.0096.376-0.174-0.1740.0000.0000.0000.000
7A96GLN0-0.002-0.0017.2180.0440.0440.0000.0000.0000.000
8A97ALA0-0.039-0.0118.458-0.210-0.2100.0000.0000.0000.000
9A98LEU0-0.023-0.01410.188-0.191-0.1910.0000.0000.0000.000
10A99ASN0-0.022-0.00212.028-0.178-0.1780.0000.0000.0000.000
11A100THR00.0170.02012.9820.0020.0020.0000.0000.0000.000
12A101GLU-1-0.884-0.94615.3360.3640.3640.0000.0000.0000.000
13A102GLU-1-0.768-0.88618.2780.3840.3840.0000.0000.0000.000
14A103ALA0-0.044-0.01715.096-0.030-0.0300.0000.0000.0000.000
15A104ALA0-0.0040.00317.065-0.032-0.0320.0000.0000.0000.000
16A105GLU-1-0.810-0.89519.1840.2470.2470.0000.0000.0000.000
17A106GLN0-0.044-0.04418.356-0.045-0.0450.0000.0000.0000.000
18A107ARG10.8160.89915.680-0.416-0.4160.0000.0000.0000.000
19A108ALA00.0460.03321.141-0.025-0.0250.0000.0000.0000.000
20A109GLU-1-0.795-0.86224.5750.1360.1360.0000.0000.0000.000
21A110VAL0-0.062-0.04322.164-0.017-0.0170.0000.0000.0000.000
22A111ASP-1-0.911-0.96224.7770.1020.1020.0000.0000.0000.000
23A112ARG10.8570.89426.356-0.142-0.1420.0000.0000.0000.000
24A113MET0-0.055-0.03427.744-0.008-0.0080.0000.0000.0000.000
25A114LEU0-0.144-0.06725.434-0.012-0.0120.0000.0000.0000.000
26A115SER0-0.022-0.01329.406-0.013-0.0130.0000.0000.0000.000
27A116GLU-1-0.870-0.90832.4310.0870.0870.0000.0000.0000.000
28A117ASP-1-0.798-0.90334.1840.0550.0550.0000.0000.0000.000
29A118PRO0-0.002-0.01333.1430.0050.0050.0000.0000.0000.000
30A119TRP00.0130.00734.1050.0040.0040.0000.0000.0000.000
31A120ARG10.9340.94436.595-0.076-0.0760.0000.0000.0000.000
32A121ALA00.0300.02731.1650.0050.0050.0000.0000.0000.000
33A122ALA0-0.025-0.01032.3330.0060.0060.0000.0000.0000.000
34A123LYS10.8030.89133.348-0.057-0.0570.0000.0000.0000.000
35A124MET00.0330.04532.373-0.003-0.0030.0000.0000.0000.000
36A125ILE00.0130.01728.2470.0040.0040.0000.0000.0000.000
37A126LYS10.8780.93431.198-0.063-0.0630.0000.0000.0000.000
38A127GLY00.0290.01733.928-0.001-0.0010.0000.0000.0000.000
39A128TYR00.0600.02627.414-0.002-0.0020.0000.0000.0000.000
40A129MET0-0.022-0.01628.8630.0020.0020.0000.0000.0000.000
41A130GLN0-0.053-0.03031.687-0.006-0.0060.0000.0000.0000.000
42A131GLN00.0030.01733.9570.0040.0040.0000.0000.0000.000
43A132HIS00.0880.03530.527-0.001-0.0010.0000.0000.0000.000
44A133ASN0-0.0310.00032.271-0.002-0.0020.0000.0000.0000.000
45A134ILE00.0170.01326.878-0.001-0.0010.0000.0000.0000.000
46A135PRO0-0.019-0.01728.016-0.009-0.0090.0000.0000.0000.000
47A136GLN00.0350.00227.7250.0030.0030.0000.0000.0000.000
48A137ARG10.8610.90923.744-0.095-0.0950.0000.0000.0000.000
49A138GLU-1-0.797-0.88222.4740.1860.1860.0000.0000.0000.000
50A139VAL00.0570.03222.3320.0110.0110.0000.0000.0000.000
51A140VAL0-0.0360.00922.5550.0030.0030.0000.0000.0000.000
52A141ASP-1-0.832-0.91320.3110.0700.0700.0000.0000.0000.000
53A142VAL0-0.038-0.01217.2190.0010.0010.0000.0000.0000.000
54A143THR0-0.057-0.05417.7860.0090.0090.0000.0000.0000.000
55A144GLY00.0420.03919.894-0.014-0.0140.0000.0000.0000.000
56A145LEU0-0.070-0.04220.670-0.022-0.0220.0000.0000.0000.000
57A146ASN00.0660.03624.3710.0020.0020.0000.0000.0000.000
58A147GLN00.0590.01827.326-0.001-0.0010.0000.0000.0000.000
59A148SER00.0470.02629.1910.0040.0040.0000.0000.0000.000
60A149HIS0-0.027-0.02629.3530.0010.0010.0000.0000.0000.000
61A150LEU00.0400.02126.8060.0030.0030.0000.0000.0000.000
62A151SER0-0.008-0.00730.2460.0050.0050.0000.0000.0000.000
63A152GLN00.0280.01833.4710.0030.0030.0000.0000.0000.000
64A153HIS0-0.024-0.02030.3770.0070.0070.0000.0000.0000.000
65A154LEU00.0220.01230.7710.0020.0020.0000.0000.0000.000
66A155ASN0-0.078-0.03633.7430.0040.0040.0000.0000.0000.000
67A156LYS10.9290.94137.352-0.028-0.0280.0000.0000.0000.000
68A157GLY00.0700.04636.958-0.001-0.0010.0000.0000.0000.000
69A158THR0-0.048-0.01135.712-0.001-0.0010.0000.0000.0000.000
70A159PRO00.0590.03834.7260.0050.0050.0000.0000.0000.000
71A160MET0-0.0040.00428.286-0.002-0.0020.0000.0000.0000.000
72A161LYS10.9930.98828.4530.0050.0050.0000.0000.0000.000
73A162THR00.0920.03226.7280.0020.0020.0000.0000.0000.000
74A163GLN00.0870.05920.0430.0200.0200.0000.0000.0000.000
75A164LYS10.8830.94722.064-0.004-0.0040.0000.0000.0000.000
76A165ARG10.9190.96024.724-0.055-0.0550.0000.0000.0000.000
77A166ALA00.0740.04722.5410.0120.0120.0000.0000.0000.000
78A167ALA0-0.0120.00920.4660.0250.0250.0000.0000.0000.000
79A168LEU0-0.014-0.00721.4510.0180.0180.0000.0000.0000.000
80A169TYR00.0460.00724.2740.0080.0080.0000.0000.0000.000
81A170THR00.019-0.00418.9480.0200.0200.0000.0000.0000.000
82A171TRP0-0.036-0.01020.4290.0210.0210.0000.0000.0000.000
83A172TYR0-0.017-0.03221.3530.0130.0130.0000.0000.0000.000
84A173VAL00.0080.00422.1810.0070.0070.0000.0000.0000.000
85A174ARG10.9660.98815.257-0.374-0.3740.0000.0000.0000.000
86A175LYS10.7630.86920.587-0.212-0.2120.0000.0000.0000.000
87A176GLN00.0290.02422.918-0.017-0.0170.0000.0000.0000.000
88A177ARG10.8600.92920.818-0.296-0.2960.0000.0000.0000.000
89A178GLU-1-0.857-0.92120.0020.2670.2670.0000.0000.0000.000
90A179ILE00.000-0.00521.818-0.008-0.0080.0000.0000.0000.000
91A180LEU00.0080.00425.227-0.008-0.0080.0000.0000.0000.000
92A181ARG10.8640.92618.317-0.408-0.4080.0000.0000.0000.000
93A182GLN0-0.055-0.01723.9380.0090.0090.0000.0000.0000.000
94A183PHE0-0.016-0.00925.252-0.016-0.0160.0000.0000.0000.000
95A184ASN0-0.055-0.02928.392-0.005-0.0050.0000.0000.0000.000
96A185GLN00.0090.00925.940-0.012-0.0120.0000.0000.0000.000
97A186THR0-0.027-0.01124.791-0.001-0.0010.0000.0000.0000.000
98A187VAL0-0.018-0.04427.768-0.014-0.0140.0000.0000.0000.000
99A231MET00.0860.05117.654-0.003-0.0030.0000.0000.0000.000
100A232ARG10.8860.92719.191-0.056-0.0560.0000.0000.0000.000
101A233ARG10.9881.00422.638-0.083-0.0830.0000.0000.0000.000
102A234ASN0-0.024-0.01924.815-0.021-0.0210.0000.0000.0000.000
103A235ARG10.9080.94727.029-0.061-0.0610.0000.0000.0000.000
104A236PHE00.0080.01530.7480.0000.0000.0000.0000.0000.000
105A237LYS10.8440.91833.731-0.081-0.0810.0000.0000.0000.000
106A238TRP00.0910.05035.7000.0060.0060.0000.0000.0000.000
107A239GLY00.0540.02838.6410.0000.0000.0000.0000.0000.000
108A240PRO0-0.037-0.02039.452-0.004-0.0040.0000.0000.0000.000
109A241ALA00.0490.02642.089-0.004-0.0040.0000.0000.0000.000
110A242SER00.000-0.04640.533-0.002-0.0020.0000.0000.0000.000
111A243GLN00.006-0.00143.329-0.004-0.0040.0000.0000.0000.000
112A244GLN0-0.032-0.00445.120-0.004-0.0040.0000.0000.0000.000
113A245ILE00.0570.02445.384-0.002-0.0020.0000.0000.0000.000
114A246LEU0-0.023-0.00744.347-0.002-0.0020.0000.0000.0000.000
115A247TYR00.004-0.01447.640-0.003-0.0030.0000.0000.0000.000
116A248GLN00.0200.01451.116-0.001-0.0010.0000.0000.0000.000
117A249ALA0-0.023-0.00251.229-0.001-0.0010.0000.0000.0000.000
118A250TYR0-0.109-0.06251.759-0.001-0.0010.0000.0000.0000.000
119A251ASP-1-0.901-0.95253.8460.0330.0330.0000.0000.0000.000
120A252ARG10.8310.90453.428-0.042-0.0420.0000.0000.0000.000
121A253GLN0-0.063-0.05255.839-0.001-0.0010.0000.0000.0000.000
122A254LYS11.0831.04455.065-0.025-0.0250.0000.0000.0000.000
123A255ASN0-0.031-0.02154.1640.0010.0010.0000.0000.0000.000
124A256PRO00.0700.06051.283-0.001-0.0010.0000.0000.0000.000
125A257SER00.0630.04052.5230.0000.0000.0000.0000.0000.000
126A258LYS10.7740.86545.447-0.051-0.0510.0000.0000.0000.000
127A259GLU-1-0.830-0.90549.5330.0430.0430.0000.0000.0000.000
128A260GLU-1-0.795-0.86250.8670.0430.0430.0000.0000.0000.000
129A261ARG10.8180.89047.171-0.038-0.0380.0000.0000.0000.000
130A262GLU-1-0.828-0.93145.9950.0550.0550.0000.0000.0000.000
131A263ALA00.0320.02946.4830.0030.0030.0000.0000.0000.000
132A264LEU00.0270.00247.4340.0030.0030.0000.0000.0000.000
133A265VAL0-0.091-0.03841.5070.0020.0020.0000.0000.0000.000
134A266GLU-1-0.799-0.90141.8310.0850.0850.0000.0000.0000.000
135A267GLU-1-0.898-0.92744.1150.0610.0610.0000.0000.0000.000
136A268CYS0-0.050-0.02341.9230.0010.0010.0000.0000.0000.000
137A269ASN0-0.009-0.01338.6590.0070.0070.0000.0000.0000.000
138A270ARG10.8800.93639.448-0.062-0.0620.0000.0000.0000.000
139A271ALA00.0200.01741.2920.0030.0030.0000.0000.0000.000
140A272GLU-1-0.797-0.88836.9840.0900.0900.0000.0000.0000.000
141A273CYS0-0.046-0.00136.7830.0080.0080.0000.0000.0000.000
142A274LEU00.0340.01937.8160.0040.0040.0000.0000.0000.000
143A275GLN0-0.098-0.05136.937-0.004-0.0040.0000.0000.0000.000
144A276ARG10.7380.85832.229-0.118-0.1180.0000.0000.0000.000
145A277GLY00.0020.02234.7010.0080.0080.0000.0000.0000.000
146A278VAL0-0.029-0.00832.7990.0060.0060.0000.0000.0000.000
147A279SER00.0400.01736.206-0.010-0.0100.0000.0000.0000.000
148A280PRO00.0380.00137.2820.0030.0030.0000.0000.0000.000
149A281SER0-0.043-0.01337.715-0.001-0.0010.0000.0000.0000.000
150A282LYN00.0220.04828.2850.0050.0050.0000.0000.0000.000
151A283ALA00.1180.04633.8340.0070.0070.0000.0000.0000.000
152A284HIS0-0.020-0.01029.796-0.007-0.0070.0000.0000.0000.000
153A285GLY00.0350.02029.7520.0060.0060.0000.0000.0000.000
154A286LEU0-0.025-0.00829.7570.0080.0080.0000.0000.0000.000
155A287GLY00.0210.01229.0300.0000.0000.0000.0000.0000.000
156A288SER0-0.074-0.04928.198-0.011-0.0110.0000.0000.0000.000
157A289ASN0-0.045-0.04430.210-0.016-0.0160.0000.0000.0000.000
158A290LEU00.0340.05133.239-0.005-0.0050.0000.0000.0000.000
159A291VAL0-0.0010.00035.162-0.006-0.0060.0000.0000.0000.000
160A292THR00.0590.02037.4160.0010.0010.0000.0000.0000.000
161A293GLU-1-0.735-0.87140.3060.0590.0590.0000.0000.0000.000
162A294VAL0-0.020-0.00439.697-0.003-0.0030.0000.0000.0000.000
163A295ARG10.8340.92433.723-0.086-0.0860.0000.0000.0000.000
164A296VAL00.0710.03341.159-0.003-0.0030.0000.0000.0000.000
165A297TYR0-0.024-0.01344.473-0.003-0.0030.0000.0000.0000.000
166A298ASN0-0.044-0.03842.540-0.005-0.0050.0000.0000.0000.000
167A299TRP0-0.058-0.02343.711-0.002-0.0020.0000.0000.0000.000
168A300PHE00.0800.02445.256-0.002-0.0020.0000.0000.0000.000
169A301ALA0-0.014-0.00347.194-0.003-0.0030.0000.0000.0000.000
170A302ASN0-0.085-0.04443.485-0.005-0.0050.0000.0000.0000.000
171A303ARG10.8180.89347.384-0.034-0.0340.0000.0000.0000.000
172A304ARG10.9070.94950.270-0.033-0.0330.0000.0000.0000.000
173A305LYS10.8460.92246.056-0.027-0.0270.0000.0000.0000.000
174A306GLU-1-0.881-0.92047.5210.0300.0300.0000.0000.0000.000
175A307GLU-1-0.843-0.89951.5480.0240.0240.0000.0000.0000.000
176A308ALA0-0.075-0.02954.851-0.002-0.0020.0000.0000.0000.000