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: N1L7Q

Calculation Name: 3HVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HVE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H2C0

Base Structure: X-ray

Registration Date: 2023-03-14

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 OptH
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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446191.578178
FMO2-HF: Nuclear repulsion 2355211.803151
FMO2-HF: Total energy -90979.775027
FMO2-MP2: Total energy -91242.209174


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:SER)


Summations of interaction energy for fragment #1(A:8: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.
3.8636.696-0.032-1.521-1.2810
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.000
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].
3A10PRO00.0540.0353.788-0.0192.814-0.032-1.521-1.2810.000
4A11GLN0-0.041-0.0116.3881.1011.1010.0000.0000.0000.000
5A12HIS00.0400.0136.6000.2420.2420.0000.0000.0000.000
6A13ALA00.0740.0378.4900.2570.2570.0000.0000.0000.000
7A14ALA00.0540.03411.3960.1090.1090.0000.0000.0000.000
8A15ARG10.8180.9097.0412.1562.1560.0000.0000.0000.000
9A16LEU0-0.022-0.02312.6250.1160.1160.0000.0000.0000.000
10A17LEU0-0.0050.00514.3620.0760.0760.0000.0000.0000.000
11A18ARG10.9920.98914.2870.8740.8740.0000.0000.0000.000
12A19ALA0-0.030-0.01217.0440.0430.0430.0000.0000.0000.000
13A20LEU00.004-0.00117.8000.0410.0410.0000.0000.0000.000
14A21SER0-0.0150.00320.6680.0450.0450.0000.0000.0000.000
15A22SER0-0.032-0.01922.6200.0190.0190.0000.0000.0000.000
16A23PHE0-0.065-0.01021.9550.0150.0150.0000.0000.0000.000
17A24ARG10.8240.89025.2000.2430.2430.0000.0000.0000.000
18A25GLU-1-0.860-0.96628.207-0.147-0.1470.0000.0000.0000.000
19A26GLU-1-0.926-0.97131.111-0.105-0.1050.0000.0000.0000.000
20A27SER00.0320.01132.7300.0090.0090.0000.0000.0000.000
21A28ARG10.8450.93729.2440.1090.1090.0000.0000.0000.000
22A29PHE0-0.037-0.02325.5770.0080.0080.0000.0000.0000.000
23A30CYS0-0.0780.00328.389-0.004-0.0040.0000.0000.0000.000
24A31ASP-1-0.813-0.88828.920-0.075-0.0750.0000.0000.0000.000
25A32ALA0-0.051-0.03831.8440.0100.0100.0000.0000.0000.000
26A33HIS00.0640.01633.808-0.008-0.0080.0000.0000.0000.000
27A34LEU0-0.044-0.01732.6510.0060.0060.0000.0000.0000.000
28A35VAL0-0.001-0.01536.069-0.002-0.0020.0000.0000.0000.000
29A36LEU00.0550.02436.1500.0020.0020.0000.0000.0000.000
30A37ASP-1-0.807-0.89540.278-0.083-0.0830.0000.0000.0000.000
31A38GLY0-0.032-0.02143.4730.0050.0050.0000.0000.0000.000
32A39GLU-1-1.001-1.00740.738-0.090-0.0900.0000.0000.0000.000
33A40GLU-1-0.861-0.91539.001-0.063-0.0630.0000.0000.0000.000
34A41ILE0-0.026-0.01633.602-0.006-0.0060.0000.0000.0000.000
35A42PRO00.0140.03233.0980.0030.0030.0000.0000.0000.000
36A43VAL0-0.004-0.01029.566-0.012-0.0120.0000.0000.0000.000
37A44GLN00.0110.00124.0290.0130.0130.0000.0000.0000.000
38A45LYS10.9480.95326.7560.0440.0440.0000.0000.0000.000
39A46ASN0-0.003-0.00422.462-0.005-0.0050.0000.0000.0000.000
40A47ILE00.0170.00621.3510.0030.0030.0000.0000.0000.000
41A48LEU00.0550.02323.330-0.006-0.0060.0000.0000.0000.000
42A49ALA00.0170.01026.0050.0060.0060.0000.0000.0000.000
43A50ALA0-0.124-0.07320.9940.0130.0130.0000.0000.0000.000
44A51ALA00.0220.01122.018-0.008-0.0080.0000.0000.0000.000
45A52SER00.0320.02923.9640.0020.0020.0000.0000.0000.000
46A53PRO0-0.032-0.01926.6950.0110.0110.0000.0000.0000.000
47A54TYR00.0500.03728.7680.0090.0090.0000.0000.0000.000
48A55ILE00.0180.00129.6040.0080.0080.0000.0000.0000.000
49A56ARG10.8850.94224.3670.0550.0550.0000.0000.0000.000
50A57THR0-0.035-0.01529.7490.0080.0080.0000.0000.0000.000
51A58LYS10.8940.97532.6550.0570.0570.0000.0000.0000.000
52A59LEU0-0.056-0.02029.6220.0000.0000.0000.0000.0000.000
53A71TYR00.0290.00335.0740.0040.0040.0000.0000.0000.000
54A72LYS10.8270.89636.9950.0510.0510.0000.0000.0000.000
55A73ILE0-0.050-0.01033.6580.0060.0060.0000.0000.0000.000
56A74GLU-1-0.906-0.96236.933-0.055-0.0550.0000.0000.0000.000
57A75LEU0-0.108-0.04534.3120.0030.0030.0000.0000.0000.000
58A76GLU-1-0.938-0.98138.693-0.046-0.0460.0000.0000.0000.000
59A77GLY0-0.0120.00641.162-0.001-0.0010.0000.0000.0000.000
60A78ILE00.0220.00035.752-0.002-0.0020.0000.0000.0000.000
61A79SER00.0380.02939.554-0.002-0.0020.0000.0000.0000.000
62A80VAL00.0180.00237.950-0.008-0.0080.0000.0000.0000.000
63A81MET0-0.014-0.01536.822-0.009-0.0090.0000.0000.0000.000
64A82VAL00.0600.03034.488-0.011-0.0110.0000.0000.0000.000
65A83MET0-0.0020.01332.729-0.011-0.0110.0000.0000.0000.000
66A84ARG10.9460.97331.8050.1210.1210.0000.0000.0000.000
67A85GLU-1-0.842-0.91930.404-0.192-0.1920.0000.0000.0000.000
68A86ILE0-0.007-0.00328.903-0.017-0.0170.0000.0000.0000.000
69A87LEU0-0.025-0.02327.584-0.012-0.0120.0000.0000.0000.000
70A88ASP-1-0.814-0.90026.243-0.247-0.2470.0000.0000.0000.000
71A89TYR0-0.096-0.04223.478-0.039-0.0390.0000.0000.0000.000
72A90ILE0-0.029-0.01822.920-0.026-0.0260.0000.0000.0000.000
73A91PHE0-0.062-0.04321.233-0.024-0.0240.0000.0000.0000.000
74A92SER0-0.070-0.04520.172-0.050-0.0500.0000.0000.0000.000
75A93GLY0-0.0270.00019.886-0.054-0.0540.0000.0000.0000.000
76A94GLN0-0.070-0.04821.0220.0320.0320.0000.0000.0000.000
77A95ILE00.0200.02824.0050.0060.0060.0000.0000.0000.000
78A96ARG10.9200.95527.5920.1860.1860.0000.0000.0000.000
79A97LEU00.0250.00930.1680.0100.0100.0000.0000.0000.000
80A98ASN0-0.0110.00032.931-0.012-0.0120.0000.0000.0000.000
81A99GLU-1-0.895-0.97636.016-0.093-0.0930.0000.0000.0000.000
82A100ASP-1-0.884-0.93739.194-0.096-0.0960.0000.0000.0000.000
83A101THR0-0.050-0.01936.4280.0000.0000.0000.0000.0000.000
84A102ILE00.0070.01035.0040.0000.0000.0000.0000.0000.000
85A103GLN00.008-0.01236.335-0.001-0.0010.0000.0000.0000.000
86A104ASP-1-0.907-0.93938.184-0.089-0.0890.0000.0000.0000.000
87A105VAL0-0.028-0.03631.9080.0000.0000.0000.0000.0000.000
88A106VAL0-0.0080.00233.557-0.003-0.0030.0000.0000.0000.000
89A107GLN00.0220.02935.1960.0020.0020.0000.0000.0000.000
90A108ALA00.0150.00334.2070.0040.0040.0000.0000.0000.000
91A109ALA0-0.012-0.00430.9990.0010.0010.0000.0000.0000.000
92A110ASP-1-0.969-0.99032.184-0.062-0.0620.0000.0000.0000.000
93A111LEU00.0140.02234.3330.0030.0030.0000.0000.0000.000
94A112LEU0-0.044-0.04030.8350.0050.0050.0000.0000.0000.000
95A113LEU0-0.055-0.03130.3690.0010.0010.0000.0000.0000.000
96A114LEU00.0130.02026.528-0.001-0.0010.0000.0000.0000.000
97A115THR00.019-0.00825.953-0.004-0.0040.0000.0000.0000.000
98A116ASP-1-0.789-0.86322.832-0.163-0.1630.0000.0000.0000.000
99A117LEU00.0530.01124.608-0.005-0.0050.0000.0000.0000.000
100A118LYS10.9340.96226.9260.0840.0840.0000.0000.0000.000
101A119THR0-0.043-0.02525.7760.0120.0120.0000.0000.0000.000
102A120LEU00.0060.01923.6410.0010.0010.0000.0000.0000.000
103A121CYS0-0.044-0.01327.6100.0050.0050.0000.0000.0000.000
104A122CYS0-0.040-0.01830.6270.0110.0110.0000.0000.0000.000
105A123GLU-1-0.928-0.95225.541-0.183-0.1830.0000.0000.0000.000
106A124PHE0-0.030-0.03530.4260.0040.0040.0000.0000.0000.000
107A125LEU00.034-0.00532.3710.0060.0060.0000.0000.0000.000
108A126GLU-1-0.878-0.92132.300-0.094-0.0940.0000.0000.0000.000
109A127GLY0-0.055-0.01834.0740.0050.0050.0000.0000.0000.000
110A128CYS0-0.040-0.01635.283-0.001-0.0010.0000.0000.0000.000
111A129ILE0-0.059-0.02038.3810.0060.0060.0000.0000.0000.000
112A130ALA0-0.0040.01540.510-0.001-0.0010.0000.0000.0000.000
113A131ALA0-0.024-0.01743.7230.0030.0030.0000.0000.0000.000
114A132GLU-1-0.820-0.93046.562-0.065-0.0650.0000.0000.0000.000
115A133ASN0-0.0090.01442.4650.0050.0050.0000.0000.0000.000
116A134CYS0-0.061-0.02743.117-0.001-0.0010.0000.0000.0000.000
117A135ILE00.006-0.00644.7240.0010.0010.0000.0000.0000.000
118A136GLY00.1140.07246.0560.0010.0010.0000.0000.0000.000
119A137ILE0-0.008-0.01739.4420.0010.0010.0000.0000.0000.000
120A138ARG10.8580.93741.5020.0440.0440.0000.0000.0000.000
121A139ASP-1-0.804-0.88543.604-0.044-0.0440.0000.0000.0000.000
122A140PHE00.006-0.00537.7600.0010.0010.0000.0000.0000.000
123A141ALA00.0140.00039.089-0.001-0.0010.0000.0000.0000.000
124A142LEU0-0.0300.00739.9770.0020.0020.0000.0000.0000.000
125A143HIS0-0.032-0.01541.7670.0040.0040.0000.0000.0000.000
126A144TYR0-0.043-0.00737.5190.0010.0010.0000.0000.0000.000
127A145CYS0-0.029-0.02337.5690.0000.0000.0000.0000.0000.000
128A146LEU0-0.023-0.00234.402-0.001-0.0010.0000.0000.0000.000
129A147HIS00.009-0.01535.1930.0010.0010.0000.0000.0000.000
130A148HIS0-0.037-0.03433.0860.0080.0080.0000.0000.0000.000
131A149VAL00.0730.04434.2580.0000.0000.0000.0000.0000.000
132A150HIS0-0.024-0.02136.5770.0040.0040.0000.0000.0000.000
133A151TYR0-0.040-0.01637.5810.0040.0040.0000.0000.0000.000
134A152LEU00.0410.02534.5180.0030.0030.0000.0000.0000.000
135A153ALA00.0290.02038.9520.0010.0010.0000.0000.0000.000
136A154THR0-0.022-0.00541.6830.0030.0030.0000.0000.0000.000
137A155GLU-1-0.900-0.95240.020-0.050-0.0500.0000.0000.0000.000
138A156TYR0-0.031-0.01141.7850.0030.0030.0000.0000.0000.000
139A157LEU00.0460.00043.9250.0020.0020.0000.0000.0000.000
140A158GLU-1-0.905-0.95446.158-0.036-0.0360.0000.0000.0000.000
141A159THR0-0.067-0.03344.8300.0010.0010.0000.0000.0000.000
142A160HIS10.8370.90944.2010.0570.0570.0000.0000.0000.000
143A161PHE00.0360.04148.7760.0000.0000.0000.0000.0000.000
144A162ARG10.8450.91850.5200.0400.0400.0000.0000.0000.000
145A163ASP-1-0.875-0.93750.367-0.050-0.0500.0000.0000.0000.000
146A164VAL00.0330.03848.9470.0000.0000.0000.0000.0000.000
147A165SER0-0.049-0.05051.6700.0010.0010.0000.0000.0000.000
148A166SER0-0.134-0.08354.6450.0020.0020.0000.0000.0000.000
149A167THR00.0040.00750.596-0.001-0.0010.0000.0000.0000.000
150A168GLU-1-0.852-0.93653.665-0.046-0.0460.0000.0000.0000.000
151A169GLU-1-0.850-0.92448.610-0.056-0.0560.0000.0000.0000.000
152A170PHE0-0.059-0.03752.3270.0030.0030.0000.0000.0000.000
153A171LEU0-0.012-0.00654.0900.0030.0030.0000.0000.0000.000
154A172GLU-1-1.067-1.02554.652-0.046-0.0460.0000.0000.0000.000
155A173LEU00.0660.04953.0290.0010.0010.0000.0000.0000.000
156A174SER00.001-0.00755.9140.0010.0010.0000.0000.0000.000
157A175PRO00.0440.01357.5810.0000.0000.0000.0000.0000.000
158A176GLN00.019-0.00657.2700.0000.0000.0000.0000.0000.000
159A177LYS10.8440.90849.9740.0430.0430.0000.0000.0000.000
160A178LEU00.0810.02354.3530.0000.0000.0000.0000.0000.000
161A179LYS10.8760.93855.3400.0280.0280.0000.0000.0000.000
162A180GLU-1-0.962-1.00350.215-0.035-0.0350.0000.0000.0000.000
163A181VAL0-0.022-0.00651.6050.0000.0000.0000.0000.0000.000
164A182ILE0-0.033-0.02152.8910.0000.0000.0000.0000.0000.000
165A183SER0-0.107-0.03053.0500.0010.0010.0000.0000.0000.000
166A184LEU00.0140.01048.6350.0010.0010.0000.0000.0000.000
167A185GLU-1-0.978-0.97451.113-0.025-0.0250.0000.0000.0000.000
168A193ARG10.8420.88461.6650.0290.0290.0000.0000.0000.000
169A194TYR00.0730.01355.155-0.001-0.0010.0000.0000.0000.000
170A195VAL00.0830.05456.765-0.001-0.0010.0000.0000.0000.000
171A196PHE00.049-0.00259.2010.0000.0000.0000.0000.0000.000
172A197GLU-1-0.859-0.89261.753-0.030-0.0300.0000.0000.0000.000
173A198ALA0-0.0060.00058.011-0.001-0.0010.0000.0000.0000.000
174A199VAL00.0110.00060.130-0.001-0.0010.0000.0000.0000.000
175A200ILE0-0.021-0.01761.9870.0000.0000.0000.0000.0000.000
176A201ARG10.9170.96058.0250.0380.0380.0000.0000.0000.000
177A202TRP0-0.0090.01558.7350.0010.0010.0000.0000.0000.000
178A203ILE0-0.060-0.01461.8240.0000.0000.0000.0000.0000.000
179A204ALA00.0510.03762.9570.0000.0000.0000.0000.0000.000
180A205HIS00.0260.00964.1050.0010.0010.0000.0000.0000.000
181A206ASP-1-0.727-0.83867.583-0.029-0.0290.0000.0000.0000.000
182A207THR00.058-0.00669.6770.0010.0010.0000.0000.0000.000
183A208GLU-1-1.028-0.99470.470-0.027-0.0270.0000.0000.0000.000
184A209ILE0-0.072-0.03466.2250.0010.0010.0000.0000.0000.000
185A210ARG10.8250.92860.1740.0370.0370.0000.0000.0000.000
186A211LYS10.8120.93567.0140.0240.0240.0000.0000.0000.000
187A212VAL0-0.015-0.00969.2640.0010.0010.0000.0000.0000.000
188A213HIS00.0890.02965.7330.0010.0010.0000.0000.0000.000
189A214MET0-0.0320.01268.8270.0000.0000.0000.0000.0000.000
190A215LYS10.8530.89870.0570.0200.0200.0000.0000.0000.000
191A216ASP-1-0.852-0.94267.964-0.020-0.0200.0000.0000.0000.000
192A217VAL0-0.019-0.00466.0060.0000.0000.0000.0000.0000.000
193A218MET0-0.029-0.01968.2800.0000.0000.0000.0000.0000.000
194A219SER0-0.046-0.00771.1890.0010.0010.0000.0000.0000.000
195A220ALA00.0510.02066.4400.0010.0010.0000.0000.0000.000
196A221LEU0-0.009-0.01967.9220.0000.0000.0000.0000.0000.000
197A222TRP0-0.068-0.02269.3710.0000.0000.0000.0000.0000.000
198A223VAL00.012-0.00168.8320.0010.0010.0000.0000.0000.000
199A224SER00.0610.03465.8890.0000.0000.0000.0000.0000.000
200A225GLY0-0.104-0.03867.9230.0000.0000.0000.0000.0000.000
201A226LEU0-0.099-0.05070.5440.0010.0010.0000.0000.0000.000
202A227ASP-1-0.917-0.94166.953-0.014-0.0140.0000.0000.0000.000
203A228SER0-0.026-0.01565.7680.0000.0000.0000.0000.0000.000
204A229SER00.0200.00467.916-0.001-0.0010.0000.0000.0000.000
205A230TYR0-0.017-0.01767.6850.0000.0000.0000.0000.0000.000
206A231LEU00.0350.01665.606-0.001-0.0010.0000.0000.0000.000
207A232ARG10.9520.96168.7210.0160.0160.0000.0000.0000.000
208A233GLU-1-0.866-0.94371.370-0.021-0.0210.0000.0000.0000.000
209A234GLN0-0.049-0.01365.173-0.001-0.0010.0000.0000.0000.000
210A235MET0-0.0020.02465.394-0.001-0.0010.0000.0000.0000.000
211A236LEU0-0.069-0.04268.7750.0000.0000.0000.0000.0000.000
212A237ASN0-0.070-0.03970.0310.0000.0000.0000.0000.0000.000
213A238GLU-1-0.817-0.90065.502-0.032-0.0320.0000.0000.0000.000
214A239PRO0-0.0190.00767.4490.0010.0010.0000.0000.0000.000
215A240LEU00.015-0.00965.6960.0000.0000.0000.0000.0000.000
216A241VAL00.003-0.01469.5700.0010.0010.0000.0000.0000.000
217A242ARG10.8170.87870.1830.0300.0300.0000.0000.0000.000
218A243GLH00.015-0.03868.2890.0010.0010.0000.0000.0000.000
219A244ILE0-0.054-0.02970.8790.0010.0010.0000.0000.0000.000
220A245VAL0-0.059-0.02873.7820.0010.0010.0000.0000.0000.000
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