FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: R88Y8

Calculation Name: 4HA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HA7

Chain ID: A

ChEMBL ID:

UniProt ID: P33312

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2765638.718076
FMO2-HF: Nuclear repulsion 2677494.691078
FMO2-HF: Total energy -88144.026998
FMO2-MP2: Total energy -88402.069473


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:8:GLU)


Summations of interaction energy for fragment #1(A:8: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.
-82.509-75.1354.471-5.435-6.410.022
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.946 / q_NPA : -0.973
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].
3A10LEU00.0360.0081.797-16.387-10.7144.436-4.948-5.1620.020
4A11PRO00.019-0.0103.409-9.215-8.0460.036-0.437-0.7680.002
5A12GLN0-0.040-0.0296.438-3.680-3.6800.0000.0000.0000.000
6A13PHE00.0080.0076.469-2.466-2.4660.0000.0000.0000.000
7A14LEU00.019-0.0086.914-3.232-3.2320.0000.0000.0000.000
8A15GLN00.0220.0329.970-2.196-2.1960.0000.0000.0000.000
9A16ASN0-0.014-0.02611.906-1.918-1.9180.0000.0000.0000.000
10A17TYR0-0.062-0.03512.912-1.384-1.3840.0000.0000.0000.000
11A18LEU00.0130.03411.113-0.469-0.4690.0000.0000.0000.000
12A19PRO00.0380.00215.294-0.837-0.8370.0000.0000.0000.000
13A20ASN0-0.063-0.02817.576-1.382-1.3820.0000.0000.0000.000
14A21ALA00.0410.04316.3930.0620.0620.0000.0000.0000.000
15A22GLY0-0.049-0.02718.507-0.501-0.5010.0000.0000.0000.000
16A23GLN0-0.108-0.07220.610-1.012-1.0120.0000.0000.0000.000
17A24THR00.0180.00023.6530.1830.1830.0000.0000.0000.000
18A25GLU-1-0.918-0.92727.1259.7889.7880.0000.0000.0000.000
19A26ASN00.0070.00528.2690.5450.5450.0000.0000.0000.000
20A27THR0-0.026-0.01427.999-0.249-0.2490.0000.0000.0000.000
21A28ILE00.0720.03130.7020.0390.0390.0000.0000.0000.000
22A29VAL0-0.015-0.00327.968-0.056-0.0560.0000.0000.0000.000
23A30PRO0-0.0470.00325.0550.1750.1750.0000.0000.0000.000
24A31PHE00.0420.02118.395-0.077-0.0770.0000.0000.0000.000
25A32VAL00.001-0.00721.9950.2980.2980.0000.0000.0000.000
26A33THR0-0.021-0.02616.4720.2480.2480.0000.0000.0000.000
27A34LEU0-0.012-0.00219.003-0.260-0.2600.0000.0000.0000.000
28A35THR0-0.072-0.04814.3651.1271.1270.0000.0000.0000.000
29A36TYR00.0580.01516.243-0.690-0.6900.0000.0000.0000.000
30A37ALA00.0070.00814.4020.9990.9990.0000.0000.0000.000
31A38GLN0-0.032-0.01416.055-1.440-1.4400.0000.0000.0000.000
32A39SER0-0.014-0.03117.5421.0701.0700.0000.0000.0000.000
33A40LEU00.0460.01518.796-0.076-0.0760.0000.0000.0000.000
34A41ASP-1-0.802-0.86221.17112.91112.9110.0000.0000.0000.000
35A42ALA00.0210.01822.289-0.553-0.5530.0000.0000.0000.000
36A43ARG10.7670.88922.850-12.241-12.2410.0000.0000.0000.000
37A44VAL00.0090.00320.0360.7320.7320.0000.0000.0000.000
38A45SER0-0.055-0.03421.7650.5230.5230.0000.0000.0000.000
39A46ARG10.9510.96721.974-14.420-14.4200.0000.0000.0000.000
40A47GLY00.0330.03425.678-0.450-0.4500.0000.0000.0000.000
41A57PRO0-0.017-0.0288.757-1.199-1.1990.0000.0000.0000.000
42A58GLU-1-0.828-0.9164.83140.67840.847-0.001-0.007-0.1610.000
43A59THR00.0540.0256.0903.5633.5630.0000.0000.0000.000
44A60LYS10.9350.9798.531-24.303-24.3030.0000.0000.0000.000
45A61THR00.008-0.0055.362-6.204-6.2040.0000.0000.0000.000
46A62MET00.0550.0506.033-0.925-0.9250.0000.0000.0000.000
47A63THR0-0.003-0.0076.926-3.965-3.9650.0000.0000.0000.000
48A64HIS0-0.006-0.01110.016-2.376-2.3760.0000.0000.0000.000
49A65TYR00.0870.0535.586-3.028-3.0280.0000.0000.0000.000
50A66LEU0-0.0070.0019.233-2.418-2.4180.0000.0000.0000.000
51A67ARG10.7830.86411.603-21.794-21.7940.0000.0000.0000.000
52A68HIS0-0.036-0.00612.461-2.926-2.9260.0000.0000.0000.000
53A69HIS0-0.051-0.03010.752-1.401-1.4010.0000.0000.0000.000
54A70HIS0-0.024-0.01714.920-1.488-1.4880.0000.0000.0000.000
55A71ASP-1-0.753-0.81418.19813.74413.7440.0000.0000.0000.000
56A72GLY00.0050.00921.301-0.405-0.4050.0000.0000.0000.000
57A73ILE0-0.046-0.01817.3520.6680.6680.0000.0000.0000.000
58A74LEU00.0000.00420.846-0.629-0.6290.0000.0000.0000.000
59A75VAL00.0130.00021.9560.5540.5540.0000.0000.0000.000
60A76GLY00.0470.02424.465-0.571-0.5710.0000.0000.0000.000
61A77SER0-0.004-0.01727.3970.2240.2240.0000.0000.0000.000
62A78GLY0-0.029-0.02630.001-0.128-0.1280.0000.0000.0000.000
63A79THR0-0.037-0.03324.2880.2200.2200.0000.0000.0000.000
64A80VAL00.0110.00625.6440.2800.2800.0000.0000.0000.000
65A81LEU0-0.056-0.02827.056-0.174-0.1740.0000.0000.0000.000
66A82ALA0-0.0300.00127.227-0.177-0.1770.0000.0000.0000.000
67A83ASP-1-0.947-0.96722.67214.51914.5190.0000.0000.0000.000
68A84ASN00.0540.02425.440-0.157-0.1570.0000.0000.0000.000
69A85PRO00.0030.00921.3750.2790.2790.0000.0000.0000.000
70A86GLY0-0.022-0.03321.040-0.375-0.3750.0000.0000.0000.000
71A87LEU0-0.002-0.01919.163-0.308-0.3080.0000.0000.0000.000
72A88ASN00.0160.02318.9660.3580.3580.0000.0000.0000.000
73A89CYS0-0.063-0.02113.3690.8000.8000.0000.0000.0000.000
74A90LYS10.8840.9469.214-32.681-32.6810.0000.0000.0000.000
75A91TRP00.0560.01310.9451.5331.5330.0000.0000.0000.000
76A92GLY00.0190.0167.5031.0101.0100.0000.0000.0000.000
77A93PRO0-0.0110.0085.0852.3332.3330.0000.0000.0000.000
78A94ASP-1-0.859-0.9476.08529.36729.3670.0000.0000.0000.000
79A95PRO0-0.066-0.0239.195-2.504-2.5040.0000.0000.0000.000
80A96ALA0-0.018-0.02912.6380.5590.5590.0000.0000.0000.000
81A97ALA00.0560.01615.885-0.752-0.7520.0000.0000.0000.000
82A98ASN0-0.078-0.01619.085-0.855-0.8550.0000.0000.0000.000
83A99SER00.0160.00518.1600.5830.5830.0000.0000.0000.000
84A100PRO00.0480.04617.444-0.820-0.8200.0000.0000.0000.000
85A101ARG10.7700.83620.340-10.946-10.9460.0000.0000.0000.000
86A102PRO00.000-0.00423.0510.2000.2000.0000.0000.0000.000
87A103ILE00.0130.02324.252-0.585-0.5850.0000.0000.0000.000
88A104ILE00.0060.00225.9000.3550.3550.0000.0000.0000.000
89A105ILE0-0.008-0.00228.162-0.436-0.4360.0000.0000.0000.000
90A106ASP-1-0.750-0.87930.5459.3609.3600.0000.0000.0000.000
91A107THR00.0480.03233.656-0.221-0.2210.0000.0000.0000.000
92A108LYS10.8890.94036.512-8.463-8.4630.0000.0000.0000.000
93A109GLN00.0100.02437.104-0.207-0.2070.0000.0000.0000.000
94A110LYS10.9040.95335.508-9.089-9.0890.0000.0000.0000.000
95A111TRP0-0.036-0.02728.959-0.003-0.0030.0000.0000.0000.000
96A112ARG10.8340.91133.801-8.851-8.8510.0000.0000.0000.000
97A113PHE00.0170.01129.0360.3550.3550.0000.0000.0000.000
98A114ASP-1-0.873-0.92132.4869.0409.0400.0000.0000.0000.000
99A115GLY00.0220.01133.977-0.077-0.0770.0000.0000.0000.000
100A116SER0-0.088-0.04929.1470.4010.4010.0000.0000.0000.000
101A117LYS10.9670.97321.887-14.453-14.4530.0000.0000.0000.000
102A118MET00.0130.01224.2460.0690.0690.0000.0000.0000.000
103A119GLN0-0.012-0.00226.4720.1420.1420.0000.0000.0000.000
104A120GLU-1-0.806-0.89226.98511.91511.9150.0000.0000.0000.000
105A121LEU0-0.040-0.02621.9840.1280.1280.0000.0000.0000.000
106A122PHE0-0.0180.00925.7130.0490.0490.0000.0000.0000.000
107A123ILE00.0190.01627.913-0.151-0.1510.0000.0000.0000.000
108A124LYS10.7290.85825.735-12.552-12.5520.0000.0000.0000.000
109A125ARG10.9130.95526.556-10.009-10.0090.0000.0000.0000.000
110A126GLN00.0190.00522.2040.5510.5510.0000.0000.0000.000
111A127GLY0-0.019-0.01121.6640.9260.9260.0000.0000.0000.000
112A128LYS10.8570.92922.388-14.240-14.2400.0000.0000.0000.000
113A129PRO00.0330.03325.6780.1940.1940.0000.0000.0000.000
114A130PRO00.0340.01427.5450.2520.2520.0000.0000.0000.000
115A131ILE00.0020.00728.052-0.361-0.3610.0000.0000.0000.000
116A132VAL0-0.027-0.01929.4780.3330.3330.0000.0000.0000.000
117A133VAL00.0290.01530.411-0.284-0.2840.0000.0000.0000.000
118A134VAL0-0.031-0.01533.1050.0180.0180.0000.0000.0000.000
119A135THR00.021-0.00536.6370.1080.1080.0000.0000.0000.000
120A136SER0-0.039-0.01739.168-0.146-0.1460.0000.0000.0000.000
121A137GLU-1-0.788-0.89941.0617.5557.5550.0000.0000.0000.000
122A138PRO0-0.0210.00239.1090.0000.0000.0000.0000.0000.000
123A139ILE0-0.010-0.00541.265-0.169-0.1690.0000.0000.0000.000
124A140ILE0-0.027-0.01340.652-0.163-0.1630.0000.0000.0000.000
125A141LYS10.8290.91839.421-7.284-7.2840.0000.0000.0000.000
126A142GLU-1-0.752-0.88836.0728.9538.9530.0000.0000.0000.000
127A143GLN00.016-0.01237.4350.1290.1290.0000.0000.0000.000
128A144HIS0-0.008-0.01533.5820.3050.3050.0000.0000.0000.000
129A145VAL0-0.0370.00232.7200.3870.3870.0000.0000.0000.000
130A146ASP-1-0.810-0.86132.3939.2759.2750.0000.0000.0000.000
131A147TYR0-0.007-0.01733.4550.1730.1730.0000.0000.0000.000
132A148ALA00.0450.02933.267-0.130-0.1300.0000.0000.0000.000
133A149ILE0-0.015-0.00935.2120.0780.0780.0000.0000.0000.000
134A150CYS0-0.0160.01035.058-0.006-0.0060.0000.0000.0000.000
135A151PRO00.0140.00237.198-0.083-0.0830.0000.0000.0000.000
136A152ILE00.002-0.00638.2310.2610.2610.0000.0000.0000.000
137A153ASN00.005-0.00937.944-0.271-0.2710.0000.0000.0000.000
138A154ASP-1-0.882-0.94939.9777.1927.1920.0000.0000.0000.000
139A155THR0-0.064-0.01541.037-0.147-0.1470.0000.0000.0000.000
140A156THR00.004-0.00236.723-0.070-0.0700.0000.0000.0000.000
141A157LYS10.8960.95338.590-8.139-8.1390.0000.0000.0000.000
142A158LEU0-0.055-0.03134.6330.0130.0130.0000.0000.0000.000
143A159VAL00.0420.01332.611-0.154-0.1540.0000.0000.0000.000
144A160ASP-1-0.839-0.90434.7798.9558.9550.0000.0000.0000.000
145A161TRP0-0.006-0.02628.5740.2150.2150.0000.0000.0000.000
146A162LYS10.8730.93531.284-9.632-9.6320.0000.0000.0000.000
147A163LYS10.9350.94632.768-8.386-8.3860.0000.0000.0000.000
148A164LEU00.0280.01130.0930.0080.0080.0000.0000.0000.000
149A165PHE0-0.027-0.03025.5930.1920.1920.0000.0000.0000.000
150A166GLU-1-0.812-0.89729.8089.2349.2340.0000.0000.0000.000
151A167ILE00.0250.02732.458-0.008-0.0080.0000.0000.0000.000
152A168LEU0-0.024-0.01727.2480.0480.0480.0000.0000.0000.000
153A169LYS10.8300.90928.063-10.785-10.7850.0000.0000.0000.000
154A170GLU-1-0.999-1.00530.1128.7458.7450.0000.0000.0000.000
155A171GLU-1-0.952-0.97633.7078.4838.4830.0000.0000.0000.000
156A172PHE0-0.044-0.03330.4280.0600.0600.0000.0000.0000.000
157A173ASN0-0.053-0.01428.8090.2940.2940.0000.0000.0000.000
158A174ILE0-0.036-0.01124.3570.5090.5090.0000.0000.0000.000
159A175ARG10.8680.87122.108-13.505-13.5050.0000.0000.0000.000
160A176SER00.001-0.00119.9890.0090.0090.0000.0000.0000.000
161A177VAL0-0.043-0.02521.2970.0040.0040.0000.0000.0000.000
162A178MET00.0050.03513.8100.2070.2070.0000.0000.0000.000
163A179VAL0-0.016-0.02118.983-0.411-0.4110.0000.0000.0000.000
164A180GLU-1-0.716-0.84615.98219.80219.8020.0000.0000.0000.000
165A181GLY0-0.003-0.00519.3870.1400.1400.0000.0000.0000.000
166A182GLY00.0130.00322.418-0.597-0.5970.0000.0000.0000.000
167A183ALA00.0630.03524.9590.1840.1840.0000.0000.0000.000
168A184ASN00.0070.00025.884-0.219-0.2190.0000.0000.0000.000
169A185VAL00.0010.01025.599-0.278-0.2780.0000.0000.0000.000
170A186ILE00.0280.00921.447-0.173-0.1730.0000.0000.0000.000
171A187ASN00.015-0.01124.8410.2100.2100.0000.0000.0000.000
172A188GLN0-0.0220.00727.851-0.468-0.4680.0000.0000.0000.000
173A189LEU00.0230.00324.795-0.165-0.1650.0000.0000.0000.000
174A190LEU00.0280.02022.6140.0740.0740.0000.0000.0000.000
175A191LEU0-0.018-0.01526.186-0.052-0.0520.0000.0000.0000.000
176A192ARG10.8030.87728.165-10.186-10.1860.0000.0000.0000.000
177A193SER00.0670.02727.3040.2470.2470.0000.0000.0000.000
178A194ASP-1-0.833-0.86828.24010.06510.0650.0000.0000.0000.000
179A195ILE0-0.080-0.04626.435-0.123-0.1230.0000.0000.0000.000
180A196VAL00.0000.00821.9490.3260.3260.0000.0000.0000.000
181A197ASN0-0.0110.01621.416-0.276-0.2760.0000.0000.0000.000
182A198SER0-0.049-0.05116.988-0.135-0.1350.0000.0000.0000.000
183A199LEU0-0.0240.00718.370-0.277-0.2770.0000.0000.0000.000
184A200ILE00.0190.00111.7570.5810.5810.0000.0000.0000.000
185A201ILE00.0020.01814.671-0.122-0.1220.0000.0000.0000.000
186A202THR00.0160.01311.5682.1732.1730.0000.0000.0000.000
187A203ILE0-0.047-0.02913.414-1.757-1.7570.0000.0000.0000.000
188A204GLY00.0530.03414.2521.3351.3350.0000.0000.0000.000
189A205SER0-0.027-0.05314.836-1.573-1.5730.0000.0000.0000.000
190A206THR0-0.043-0.02717.177-0.776-0.7760.0000.0000.0000.000
191A207PHE00.0100.00620.0460.1050.1050.0000.0000.0000.000
192A208LEU0-0.040-0.03121.323-0.102-0.1020.0000.0000.0000.000
193A209GLY00.0060.01224.521-0.446-0.4460.0000.0000.0000.000
194A210SER00.010-0.01828.0750.1720.1720.0000.0000.0000.000
195A211SER0-0.013-0.00530.503-0.114-0.1140.0000.0000.0000.000
196A212GLY00.0060.01327.247-0.075-0.0750.0000.0000.0000.000
197A213THR0-0.032-0.02526.001-0.174-0.1740.0000.0000.0000.000
198A214GLU-1-0.822-0.90225.76311.55211.5520.0000.0000.0000.000
199A215VAL0-0.059-0.02921.865-0.234-0.2340.0000.0000.0000.000
200A216SER00.0310.00925.2840.3060.3060.0000.0000.0000.000
201A217PRO0-0.0450.00526.643-0.280-0.2800.0000.0000.0000.000
202A218PRO0-0.012-0.01629.431-0.140-0.1400.0000.0000.0000.000
203A219GLN0-0.009-0.00232.122-0.335-0.3350.0000.0000.0000.000
204A220THR00.0170.00530.8460.2470.2470.0000.0000.0000.000
205A221VAL00.0130.00526.227-0.161-0.1610.0000.0000.0000.000
206A222ASN0-0.0160.00727.0370.3720.3720.0000.0000.0000.000
207A223LEU00.0310.00620.5300.1060.1060.0000.0000.0000.000
208A224LYS10.9060.95622.742-12.611-12.6110.0000.0000.0000.000
209A225ASP-1-0.810-0.90919.76314.14114.1410.0000.0000.0000.000
210A226MET0-0.0180.01617.6990.7130.7130.0000.0000.0000.000
211A227SER00.007-0.00713.1390.3070.3070.0000.0000.0000.000
212A228TRP0-0.017-0.01612.8770.6530.6530.0000.0000.0000.000
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