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: J3VR9

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446781.045718
FMO2-HF: Nuclear repulsion 2355799.592909
FMO2-HF: Total energy -90981.452809
FMO2-MP2: Total energy -91243.765437


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.
3.6556.982-0.031-1.832-1.4630.003
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 : 0.024 / q_NPA : 0.013
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].
3A10PRO00.0520.0303.733-0.9302.397-0.031-1.832-1.4630.003
4A11GLN0-0.034-0.0016.3861.0271.0270.0000.0000.0000.000
5A12HIS00.0520.0136.6250.1510.1510.0000.0000.0000.000
6A13ALA00.0760.0408.5070.2980.2980.0000.0000.0000.000
7A14ALA00.0670.04011.4140.1250.1250.0000.0000.0000.000
8A15ARG10.8080.8927.1702.7752.7750.0000.0000.0000.000
9A16LEU0-0.046-0.03212.6350.1320.1320.0000.0000.0000.000
10A17LEU00.0050.00614.3760.0890.0890.0000.0000.0000.000
11A18ARG10.9220.95014.1191.0201.0200.0000.0000.0000.000
12A19ALA0-0.042-0.01616.9740.0540.0540.0000.0000.0000.000
13A20LEU0-0.0020.00017.7050.0510.0510.0000.0000.0000.000
14A21SER00.0380.01920.6840.0480.0480.0000.0000.0000.000
15A22SER0-0.089-0.03722.5180.0320.0320.0000.0000.0000.000
16A23PHE0-0.053-0.00921.6240.0150.0150.0000.0000.0000.000
17A24ARG10.8010.87224.9560.3030.3030.0000.0000.0000.000
18A25GLU-1-0.840-0.96528.222-0.206-0.2060.0000.0000.0000.000
19A26GLU-1-0.905-0.97331.123-0.156-0.1560.0000.0000.0000.000
20A27SER0-0.0030.01432.9050.0120.0120.0000.0000.0000.000
21A28ARG10.8370.93629.0780.1790.1790.0000.0000.0000.000
22A29PHE0-0.026-0.01925.5260.0030.0030.0000.0000.0000.000
23A30CYS0-0.097-0.00828.400-0.007-0.0070.0000.0000.0000.000
24A31ASP-1-0.783-0.87629.433-0.136-0.1360.0000.0000.0000.000
25A32ALA0-0.055-0.03731.8550.0120.0120.0000.0000.0000.000
26A33HIS00.0610.02033.820-0.009-0.0090.0000.0000.0000.000
27A34LEU0-0.036-0.01332.6440.0060.0060.0000.0000.0000.000
28A35VAL0-0.013-0.02036.085-0.002-0.0020.0000.0000.0000.000
29A36LEU00.0450.03036.2390.0020.0020.0000.0000.0000.000
30A37ASP-1-0.810-0.89740.296-0.102-0.1020.0000.0000.0000.000
31A38GLY0-0.022-0.01043.4910.0050.0050.0000.0000.0000.000
32A39GLU-1-0.964-0.99240.565-0.118-0.1180.0000.0000.0000.000
33A40GLU-1-0.841-0.92239.153-0.093-0.0930.0000.0000.0000.000
34A41ILE0-0.016-0.01133.370-0.006-0.0060.0000.0000.0000.000
35A42PRO00.0410.04133.0800.0020.0020.0000.0000.0000.000
36A43VAL0-0.019-0.01229.623-0.014-0.0140.0000.0000.0000.000
37A44GLN00.007-0.00923.9540.0040.0040.0000.0000.0000.000
38A45LYS10.8800.91826.7700.1090.1090.0000.0000.0000.000
39A46ASN00.0160.00322.4300.0040.0040.0000.0000.0000.000
40A47ILE00.0090.00521.4090.0040.0040.0000.0000.0000.000
41A48LEU00.0590.02623.344-0.002-0.0020.0000.0000.0000.000
42A49ALA00.0330.02226.1710.0110.0110.0000.0000.0000.000
43A50ALA0-0.111-0.06220.9990.0170.0170.0000.0000.0000.000
44A51ALA00.0140.00522.033-0.009-0.0090.0000.0000.0000.000
45A52SER00.0280.01923.9810.0080.0080.0000.0000.0000.000
46A53PRO0-0.027-0.01326.7630.0080.0080.0000.0000.0000.000
47A54TYR00.0620.03828.7830.0090.0090.0000.0000.0000.000
48A55ILE00.0250.00329.6440.0070.0070.0000.0000.0000.000
49A56ARG10.8450.91823.9430.1140.1140.0000.0000.0000.000
50A57THR0-0.015-0.01029.7620.0070.0070.0000.0000.0000.000
51A58LYS10.8610.96732.6670.0870.0870.0000.0000.0000.000
52A59LEU0-0.027-0.00629.465-0.002-0.0020.0000.0000.0000.000
53A71TYR0-0.009-0.01835.1070.0030.0030.0000.0000.0000.000
54A72LYS10.8180.90337.0060.0800.0800.0000.0000.0000.000
55A73ILE0-0.046-0.00833.6050.0070.0070.0000.0000.0000.000
56A74GLU-1-0.895-0.95136.947-0.082-0.0820.0000.0000.0000.000
57A75LEU0-0.085-0.04734.0740.0030.0030.0000.0000.0000.000
58A76GLU-1-0.942-0.97838.710-0.063-0.0630.0000.0000.0000.000
59A77GLY0-0.0090.00641.1800.0000.0000.0000.0000.0000.000
60A78ILE00.017-0.00635.783-0.002-0.0020.0000.0000.0000.000
61A79SER00.0330.02739.573-0.004-0.0040.0000.0000.0000.000
62A80VAL00.017-0.01337.883-0.010-0.0100.0000.0000.0000.000
63A81MET0-0.021-0.01236.841-0.011-0.0110.0000.0000.0000.000
64A82VAL00.0580.02634.683-0.012-0.0120.0000.0000.0000.000
65A83MET00.0010.02132.535-0.013-0.0130.0000.0000.0000.000
66A84ARG10.9080.96031.7640.1390.1390.0000.0000.0000.000
67A85GLU-1-0.789-0.87330.424-0.218-0.2180.0000.0000.0000.000
68A86ILE00.008-0.00129.112-0.017-0.0170.0000.0000.0000.000
69A87LEU0-0.030-0.02227.604-0.015-0.0150.0000.0000.0000.000
70A88ASP-1-0.807-0.88126.263-0.298-0.2980.0000.0000.0000.000
71A89TYR0-0.076-0.03923.567-0.040-0.0400.0000.0000.0000.000
72A90ILE0-0.020-0.01722.885-0.028-0.0280.0000.0000.0000.000
73A91PHE0-0.046-0.03521.186-0.031-0.0310.0000.0000.0000.000
74A92SER0-0.067-0.03920.192-0.055-0.0550.0000.0000.0000.000
75A93GLY0-0.0270.00019.890-0.052-0.0520.0000.0000.0000.000
76A94GLN0-0.068-0.04721.0660.0340.0340.0000.0000.0000.000
77A95ILE00.0360.02224.0100.0020.0020.0000.0000.0000.000
78A96ARG10.8090.89727.5950.2030.2030.0000.0000.0000.000
79A97LEU00.0290.01930.7180.0100.0100.0000.0000.0000.000
80A98ASN0-0.052-0.02332.936-0.012-0.0120.0000.0000.0000.000
81A99GLU-1-0.847-0.93836.024-0.090-0.0900.0000.0000.0000.000
82A100ASP-1-0.874-0.93239.298-0.099-0.0990.0000.0000.0000.000
83A101THR0-0.047-0.02836.991-0.001-0.0010.0000.0000.0000.000
84A102ILE0-0.0060.00834.833-0.001-0.0010.0000.0000.0000.000
85A103GLN0-0.021-0.02736.3290.0010.0010.0000.0000.0000.000
86A104ASP-1-0.882-0.93138.303-0.098-0.0980.0000.0000.0000.000
87A105VAL0-0.023-0.03031.867-0.002-0.0020.0000.0000.0000.000
88A106VAL00.0020.00933.545-0.004-0.0040.0000.0000.0000.000
89A107GLN00.0000.02135.1830.0010.0010.0000.0000.0000.000
90A108ALA00.0140.00234.3210.0030.0030.0000.0000.0000.000
91A109ALA0-0.005-0.00130.942-0.001-0.0010.0000.0000.0000.000
92A110ASP-1-0.900-0.93532.203-0.073-0.0730.0000.0000.0000.000
93A111LEU00.0100.01534.3510.0020.0020.0000.0000.0000.000
94A112LEU0-0.041-0.03630.8480.0030.0030.0000.0000.0000.000
95A113LEU0-0.036-0.01930.508-0.003-0.0030.0000.0000.0000.000
96A114LEU00.0140.02126.755-0.004-0.0040.0000.0000.0000.000
97A115THR00.016-0.00925.990-0.001-0.0010.0000.0000.0000.000
98A116ASP-1-0.811-0.87522.818-0.190-0.1900.0000.0000.0000.000
99A117LEU00.0680.02524.5890.0000.0000.0000.0000.0000.000
100A118LYS10.8750.91826.9130.0910.0910.0000.0000.0000.000
101A119THR0-0.033-0.01525.7430.0150.0150.0000.0000.0000.000
102A120LEU00.0150.02223.5090.0020.0020.0000.0000.0000.000
103A121CYS0-0.056-0.02927.6040.0060.0060.0000.0000.0000.000
104A122CYS0-0.048-0.02330.6240.0110.0110.0000.0000.0000.000
105A123GLU-1-0.918-0.95225.720-0.162-0.1620.0000.0000.0000.000
106A124PHE0-0.026-0.03030.4240.0040.0040.0000.0000.0000.000
107A125LEU00.021-0.00732.3720.0060.0060.0000.0000.0000.000
108A126GLU-1-0.828-0.90532.554-0.076-0.0760.0000.0000.0000.000
109A127GLY0-0.061-0.01834.0790.0050.0050.0000.0000.0000.000
110A128CYS0-0.047-0.02435.288-0.001-0.0010.0000.0000.0000.000
111A129ILE0-0.063-0.02338.0620.0050.0050.0000.0000.0000.000
112A130ALA00.0310.02540.5130.0000.0000.0000.0000.0000.000
113A131ALA0-0.049-0.02543.7280.0030.0030.0000.0000.0000.000
114A132GLU-1-0.820-0.93746.358-0.059-0.0590.0000.0000.0000.000
115A133ASN0-0.0390.00042.0400.0040.0040.0000.0000.0000.000
116A134CYS0-0.070-0.03143.1160.0000.0000.0000.0000.0000.000
117A135ILE00.027-0.00444.7180.0010.0010.0000.0000.0000.000
118A136GLY00.1080.07246.0440.0000.0000.0000.0000.0000.000
119A137ILE0-0.021-0.02539.2660.0000.0000.0000.0000.0000.000
120A138ARG10.8720.93241.4930.0380.0380.0000.0000.0000.000
121A139ASP-1-0.835-0.91443.593-0.042-0.0420.0000.0000.0000.000
122A140PHE00.001-0.00337.8500.0000.0000.0000.0000.0000.000
123A141ALA00.009-0.00139.124-0.001-0.0010.0000.0000.0000.000
124A142LEU0-0.0270.00339.9590.0020.0020.0000.0000.0000.000
125A143HIS0-0.035-0.01241.7550.0040.0040.0000.0000.0000.000
126A144TYR0-0.026-0.00637.5530.0000.0000.0000.0000.0000.000
127A145CYS0-0.044-0.02437.5460.0000.0000.0000.0000.0000.000
128A146LEU0-0.019-0.00634.2890.0000.0000.0000.0000.0000.000
129A147HIS00.008-0.01435.2180.0030.0030.0000.0000.0000.000
130A148HIS0-0.054-0.04532.8760.0090.0090.0000.0000.0000.000
131A149VAL00.0570.03934.3990.0010.0010.0000.0000.0000.000
132A150HIS0-0.024-0.01936.5660.0040.0040.0000.0000.0000.000
133A151TYR0-0.088-0.03837.5680.0040.0040.0000.0000.0000.000
134A152LEU00.0470.02734.6070.0020.0020.0000.0000.0000.000
135A153ALA00.0160.01438.9450.0010.0010.0000.0000.0000.000
136A154THR0-0.036-0.02941.6770.0030.0030.0000.0000.0000.000
137A155GLU-1-0.861-0.92540.205-0.033-0.0330.0000.0000.0000.000
138A156TYR0-0.027-0.00241.7450.0020.0020.0000.0000.0000.000
139A157LEU00.0670.01243.9230.0020.0020.0000.0000.0000.000
140A158GLU-1-0.895-0.95046.463-0.025-0.0250.0000.0000.0000.000
141A159THR0-0.059-0.03544.8200.0010.0010.0000.0000.0000.000
142A160HIS10.8250.90443.9650.0440.0440.0000.0000.0000.000
143A161PHE00.0410.04248.778-0.001-0.0010.0000.0000.0000.000
144A162ARG10.8320.91150.5080.0290.0290.0000.0000.0000.000
145A163ASP-1-0.877-0.93750.372-0.040-0.0400.0000.0000.0000.000
146A164VAL00.0400.03748.9090.0000.0000.0000.0000.0000.000
147A165SER0-0.053-0.04451.6710.0010.0010.0000.0000.0000.000
148A166SER0-0.134-0.08154.6480.0020.0020.0000.0000.0000.000
149A167THR0-0.0140.00950.652-0.001-0.0010.0000.0000.0000.000
150A168GLU-1-0.842-0.93953.667-0.043-0.0430.0000.0000.0000.000
151A169GLU-1-0.856-0.92748.466-0.055-0.0550.0000.0000.0000.000
152A170PHE0-0.035-0.03352.3250.0020.0020.0000.0000.0000.000
153A171LEU0-0.016-0.00454.0870.0030.0030.0000.0000.0000.000
154A172GLU-1-1.001-0.96854.867-0.045-0.0450.0000.0000.0000.000
155A173LEU00.0320.02152.8730.0000.0000.0000.0000.0000.000
156A174SER00.014-0.00655.9070.0010.0010.0000.0000.0000.000
157A175PRO00.0460.01757.5700.0000.0000.0000.0000.0000.000
158A176GLN00.003-0.00557.2400.0010.0010.0000.0000.0000.000
159A177LYS10.8340.89949.7650.0410.0410.0000.0000.0000.000
160A178LEU00.0720.03754.3410.0000.0000.0000.0000.0000.000
161A179LYS10.8830.93555.5550.0260.0260.0000.0000.0000.000
162A180GLU-1-0.890-0.93550.289-0.033-0.0330.0000.0000.0000.000
163A181VAL0-0.011-0.00451.0850.0000.0000.0000.0000.0000.000
164A182ILE0-0.030-0.02052.8810.0000.0000.0000.0000.0000.000
165A183SER0-0.066-0.01653.3310.0010.0010.0000.0000.0000.000
166A184LEU0-0.0020.01448.2510.0020.0020.0000.0000.0000.000
167A185GLU-1-1.018-1.00051.100-0.016-0.0160.0000.0000.0000.000
168A193ARG10.8350.87461.7500.0220.0220.0000.0000.0000.000
169A194TYR00.0640.01954.890-0.001-0.0010.0000.0000.0000.000
170A195VAL00.0770.05156.845-0.001-0.0010.0000.0000.0000.000
171A196PHE00.050-0.00659.197-0.001-0.0010.0000.0000.0000.000
172A197GLU-1-0.853-0.89561.783-0.024-0.0240.0000.0000.0000.000
173A198ALA00.0020.01257.998-0.001-0.0010.0000.0000.0000.000
174A199VAL00.0120.00460.128-0.001-0.0010.0000.0000.0000.000
175A200ILE0-0.026-0.02561.9820.0000.0000.0000.0000.0000.000
176A201ARG10.8940.95157.8970.0320.0320.0000.0000.0000.000
177A202TRP00.0220.01958.5990.0000.0000.0000.0000.0000.000
178A203ILE0-0.070-0.02461.8210.0000.0000.0000.0000.0000.000
179A204ALA00.0580.03862.9430.0000.0000.0000.0000.0000.000
180A205HIS00.0430.01963.9430.0010.0010.0000.0000.0000.000
181A206ASP-1-0.741-0.82767.580-0.027-0.0270.0000.0000.0000.000
182A207THR00.058-0.00969.6150.0010.0010.0000.0000.0000.000
183A208GLU-1-1.028-0.99570.438-0.027-0.0270.0000.0000.0000.000
184A209ILE0-0.068-0.03566.3620.0000.0000.0000.0000.0000.000
185A210ARG10.7720.87959.5140.0350.0350.0000.0000.0000.000
186A211LYS10.8040.93267.0070.0220.0220.0000.0000.0000.000
187A212VAL0-0.020-0.01069.2550.0010.0010.0000.0000.0000.000
188A213HIS00.0770.02765.8390.0000.0000.0000.0000.0000.000
189A214MET0-0.0240.01468.8170.0000.0000.0000.0000.0000.000
190A215LYS10.8460.89670.0490.0180.0180.0000.0000.0000.000
191A216ASP-1-0.847-0.94167.943-0.018-0.0180.0000.0000.0000.000
192A217VAL0-0.018-0.00465.9600.0010.0010.0000.0000.0000.000
193A218MET0-0.020-0.01468.2710.0010.0010.0000.0000.0000.000
194A219SER0-0.040-0.00571.1200.0010.0010.0000.0000.0000.000
195A220ALA00.0400.01666.4250.0010.0010.0000.0000.0000.000
196A221LEU0-0.001-0.00967.3150.0010.0010.0000.0000.0000.000
197A222TRP0-0.066-0.02069.3640.0010.0010.0000.0000.0000.000
198A223VAL00.0430.00968.4980.0010.0010.0000.0000.0000.000
199A224SER00.0610.03466.2160.0010.0010.0000.0000.0000.000
200A225GLY0-0.108-0.04367.9140.0000.0000.0000.0000.0000.000
201A226LEU0-0.113-0.05570.5170.0010.0010.0000.0000.0000.000
202A227ASP-1-0.905-0.93866.966-0.007-0.0070.0000.0000.0000.000
203A228SER0-0.018-0.01065.7390.0000.0000.0000.0000.0000.000
204A229SER00.0140.00067.886-0.001-0.0010.0000.0000.0000.000
205A230TYR0-0.054-0.04368.0140.0000.0000.0000.0000.0000.000
206A231LEU00.0440.02965.422-0.001-0.0010.0000.0000.0000.000
207A232ARG10.9040.94068.7190.0110.0110.0000.0000.0000.000
208A233GLU-1-0.850-0.92671.773-0.015-0.0150.0000.0000.0000.000
209A234GLN0-0.011-0.00465.153-0.002-0.0020.0000.0000.0000.000
210A235MET0-0.0060.02665.448-0.001-0.0010.0000.0000.0000.000
211A236LEU0-0.065-0.04068.772-0.001-0.0010.0000.0000.0000.000
212A237ASN0-0.070-0.03970.2590.0000.0000.0000.0000.0000.000
213A238GLU-1-0.818-0.90165.554-0.026-0.0260.0000.0000.0000.000
214A239PRO0-0.0190.01167.4550.0010.0010.0000.0000.0000.000
215A240LEU00.016-0.00765.6990.0000.0000.0000.0000.0000.000
216A241VAL00.001-0.01869.5720.0000.0000.0000.0000.0000.000
217A242ARG10.8090.88269.8510.0270.0270.0000.0000.0000.000
218A243GLH00.020-0.03868.3130.0000.0000.0000.0000.0000.000
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