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: LJ8V9

Calculation Name: 3WRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WRV

Chain ID: A

ChEMBL ID:

UniProt ID: A7M6E7

Base Structure: X-ray

Registration Date: 2023-06-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970591.901629
FMO2-HF: Nuclear repulsion 1898425.970707
FMO2-HF: Total energy -72165.930922
FMO2-MP2: Total energy -72374.835355


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:7:ASN)


Summations of interaction energy for fragment #1(A:7:ASN)
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.
-11.557-7.15.565-4.662-5.36-0.004
Interaction energy analysis for fragmet #1(A:7:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.019
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].
3A9PRO0-0.0010.0123.252-4.166-2.1090.053-1.107-1.0030.001
4A10ARG10.9140.9544.3815.7235.908-0.001-0.007-0.1770.000
5A11VAL00.0090.0216.5120.5790.5790.0000.0000.0000.000
6A12PHE00.0240.0107.448-0.059-0.0590.0000.0000.0000.000
7A13CYS0-0.035-0.01712.1110.1940.1940.0000.0000.0000.000
8A14ILE00.0200.01114.4330.0060.0060.0000.0000.0000.000
9A15GLY00.016-0.01417.3690.0900.0900.0000.0000.0000.000
10A16THR0-0.044-0.00220.200-0.026-0.0260.0000.0000.0000.000
11A17ALA00.0670.02020.4070.0400.0400.0000.0000.0000.000
12A18ASP-1-0.818-0.88522.478-0.395-0.3950.0000.0000.0000.000
13A19THR0-0.078-0.05425.5400.0350.0350.0000.0000.0000.000
14A20LYS10.9010.95624.1160.4470.4470.0000.0000.0000.000
15A21PHE0-0.0120.00820.336-0.034-0.0340.0000.0000.0000.000
16A22ASP-1-0.894-0.94422.683-0.464-0.4640.0000.0000.0000.000
17A23GLU-1-0.843-0.94924.619-0.437-0.4370.0000.0000.0000.000
18A24LEU00.0310.01218.260-0.012-0.0120.0000.0000.0000.000
19A25ARG10.9931.04919.5630.4940.4940.0000.0000.0000.000
20A26PHE0-0.0170.00220.452-0.021-0.0210.0000.0000.0000.000
21A27LEU00.0240.00819.4780.0080.0080.0000.0000.0000.000
22A28SER00.000-0.05416.009-0.043-0.0430.0000.0000.0000.000
23A29GLU-1-0.949-0.97917.106-0.712-0.7120.0000.0000.0000.000
24A30HIS0-0.013-0.01819.1990.0250.0250.0000.0000.0000.000
25A31VAL0-0.0160.00414.9570.0190.0190.0000.0000.0000.000
26A32ARG10.8740.96013.8750.9460.9460.0000.0000.0000.000
27A33SER0-0.006-0.01015.6870.0040.0040.0000.0000.0000.000
28A34SER00.0390.02018.6490.0730.0730.0000.0000.0000.000
29A35LEU0-0.001-0.00512.3260.0410.0410.0000.0000.0000.000
30A36ASN0-0.127-0.06314.5880.0860.0860.0000.0000.0000.000
31A37SER0-0.023-0.02516.6210.0640.0640.0000.0000.0000.000
32A38PHE0-0.029-0.01818.9280.0450.0450.0000.0000.0000.000
33A39SER0-0.072-0.00115.4520.0230.0230.0000.0000.0000.000
34A40ASN0-0.0050.01117.4480.0720.0720.0000.0000.0000.000
35A41LYS10.9920.99013.2340.0160.0160.0000.0000.0000.000
36A42SER0-0.066-0.06814.7200.0290.0290.0000.0000.0000.000
37A43SER0-0.0160.00211.8520.0270.0270.0000.0000.0000.000
38A44PHE00.015-0.0096.8260.0060.0060.0000.0000.0000.000
39A45LYS10.9030.9798.0760.3360.3360.0000.0000.0000.000
40A46VAL00.0730.0507.932-0.272-0.2720.0000.0000.0000.000
41A47GLY0-0.0160.0066.9640.3370.3370.0000.0000.0000.000
42A48VAL00.000-0.0158.005-0.037-0.0370.0000.0000.0000.000
43A49THR0-0.058-0.0617.580-0.200-0.2000.0000.0000.0000.000
44A50VAL0-0.033-0.00410.3020.1900.1900.0000.0000.0000.000
45A51VAL00.0230.00012.174-0.115-0.1150.0000.0000.0000.000
46A52ASP-1-0.785-0.87514.350-0.531-0.5310.0000.0000.0000.000
47A53VAL00.024-0.00117.7170.0010.0010.0000.0000.0000.000
48A54SER0-0.099-0.07219.9230.0740.0740.0000.0000.0000.000
49A55THR0-0.007-0.00422.805-0.002-0.0020.0000.0000.0000.000
50A56SER0-0.115-0.10925.4520.0360.0360.0000.0000.0000.000
51A57TRP00.0350.00326.421-0.014-0.0140.0000.0000.0000.000
52A58LYS10.8950.96626.6290.3740.3740.0000.0000.0000.000
53A59GLU-1-0.889-0.93023.357-0.395-0.3950.0000.0000.0000.000
54A60THR0-0.072-0.04920.0280.0120.0120.0000.0000.0000.000
55A61ASN00.0300.00318.616-0.058-0.0580.0000.0000.0000.000
56A62SER0-0.021-0.00516.500-0.074-0.0740.0000.0000.0000.000
57A63CYS00.0240.00816.4110.1070.1070.0000.0000.0000.000
58A64ALA0-0.027-0.01116.757-0.065-0.0650.0000.0000.0000.000
59A65ASP-1-0.866-0.93615.946-0.802-0.8020.0000.0000.0000.000
60A66PHE0-0.058-0.02213.141-0.074-0.0740.0000.0000.0000.000
61A67ASP-1-0.817-0.8836.935-3.780-3.7800.0000.0000.0000.000
62A68PHE0-0.031-0.02310.2440.1820.1820.0000.0000.0000.000
63A69VAL00.0260.0219.788-0.107-0.1070.0000.0000.0000.000
64A70PRO00.0180.01712.2850.1390.1390.0000.0000.0000.000
65A71SER00.0940.03315.587-0.029-0.0290.0000.0000.0000.000
66A72LYS10.9260.95215.7150.6710.6710.0000.0000.0000.000
67A73ASP-1-0.852-0.93611.829-1.095-1.0950.0000.0000.0000.000
68A74VAL0-0.0240.00113.8190.0140.0140.0000.0000.0000.000
69A75LEU00.001-0.01315.0370.0710.0710.0000.0000.0000.000
70A76SER0-0.073-0.03014.6600.0380.0380.0000.0000.0000.000
71A77CYS0-0.087-0.02812.7020.0510.0510.0000.0000.0000.000
72A78HIS00.0380.01714.6770.0340.0340.0000.0000.0000.000
73A79THR0-0.050-0.01718.0220.0260.0260.0000.0000.0000.000
74A80LEU0-0.031-0.02621.147-0.004-0.0040.0000.0000.0000.000
75A81GLY00.0640.03324.3680.0260.0260.0000.0000.0000.000
76A82GLU-1-0.946-0.98726.564-0.109-0.1090.0000.0000.0000.000
77A83GLU-1-0.852-0.93124.450-0.226-0.2260.0000.0000.0000.000
78A84THR0-0.005-0.01327.882-0.004-0.0040.0000.0000.0000.000
79A85MET0-0.079-0.03530.1150.0080.0080.0000.0000.0000.000
80A86GLY0-0.0080.01032.2930.0080.0080.0000.0000.0000.000
81A87THR0-0.020-0.01933.7280.0000.0000.0000.0000.0000.000
82A88PHE0-0.030-0.01130.707-0.003-0.0030.0000.0000.0000.000
83A89ALA00.0140.01135.7520.0080.0080.0000.0000.0000.000
84A90ASP-1-0.871-0.93234.873-0.203-0.2030.0000.0000.0000.000
85A91THR00.025-0.00232.673-0.010-0.0100.0000.0000.0000.000
86A92ARG10.9731.00530.3780.2620.2620.0000.0000.0000.000
87A93GLY00.0280.00329.908-0.021-0.0210.0000.0000.0000.000
88A94LEU00.0240.02529.619-0.007-0.0070.0000.0000.0000.000
89A95ALA00.004-0.00226.856-0.010-0.0100.0000.0000.0000.000
90A96ILE0-0.047-0.02925.437-0.029-0.0290.0000.0000.0000.000
91A97ALA00.0200.01625.358-0.025-0.0250.0000.0000.0000.000
92A98ILE00.0210.00922.970-0.008-0.0080.0000.0000.0000.000
93A99MET0-0.0370.01019.934-0.032-0.0320.0000.0000.0000.000
94A100SER0-0.066-0.03420.443-0.038-0.0380.0000.0000.0000.000
95A101LYS10.9680.97920.9810.2280.2280.0000.0000.0000.000
96A102ALA00.0100.01318.071-0.002-0.0020.0000.0000.0000.000
97A103LEU0-0.034-0.02915.634-0.067-0.0670.0000.0000.0000.000
98A104GLU-1-0.936-0.97415.924-0.382-0.3820.0000.0000.0000.000
99A105THR0-0.0040.00514.8920.0010.0010.0000.0000.0000.000
100A106PHE00.0450.0239.640-0.015-0.0150.0000.0000.0000.000
101A107LEU0-0.037-0.02311.408-0.144-0.1440.0000.0000.0000.000
102A108SER0-0.0150.00611.509-0.044-0.0440.0000.0000.0000.000
103A109ILE00.0340.0138.9540.0760.0760.0000.0000.0000.000
104A110ALA0-0.0060.0017.4880.1350.1350.0000.0000.0000.000
105A111ASN0-0.068-0.0727.521-0.121-0.1210.0000.0000.0000.000
106A112ASP-1-0.916-0.94210.0480.1160.1160.0000.0000.0000.000
107A113GLU-1-1.019-1.0025.1281.9772.099-0.0010.000-0.1210.000
108A114GLN0-0.075-0.0505.524-0.201-0.2010.0000.0000.0000.000
109A115ASN00.0030.0172.039-11.180-9.1295.515-3.538-4.028-0.005
110A116LEU0-0.067-0.0204.624-0.363-0.321-0.001-0.010-0.0310.000
111A117ALA0-0.018-0.0198.0570.3810.3810.0000.0000.0000.000
112A118GLY00.013-0.01010.0320.2690.2690.0000.0000.0000.000
113A119VAL0-0.050-0.00812.008-0.204-0.2040.0000.0000.0000.000
114A120ILE00.0390.02014.6180.1330.1330.0000.0000.0000.000
115A121GLY00.0830.02617.340-0.074-0.0740.0000.0000.0000.000
116A122LEU0-0.0520.00220.0660.0650.0650.0000.0000.0000.000
117A123GLY00.021-0.00423.515-0.012-0.0120.0000.0000.0000.000
118A124GLY00.0260.02826.3430.0180.0180.0000.0000.0000.000
119A125SER00.0350.02729.189-0.013-0.0130.0000.0000.0000.000
120A126GLY00.0230.00929.565-0.001-0.0010.0000.0000.0000.000
121A127GLY00.0570.02125.405-0.009-0.0090.0000.0000.0000.000
122A128THR00.0480.02024.937-0.028-0.0280.0000.0000.0000.000
123A129SER0-0.0020.03925.9230.0030.0030.0000.0000.0000.000
124A130LEU0-0.0040.01521.2480.0050.0050.0000.0000.0000.000
125A131LEU00.012-0.00619.647-0.012-0.0120.0000.0000.0000.000
126A132SER0-0.059-0.06421.190-0.010-0.0100.0000.0000.0000.000
127A133SER0-0.070-0.02622.6640.0010.0010.0000.0000.0000.000
128A134ALA00.0910.05818.5020.0160.0160.0000.0000.0000.000
129A135PHE0-0.023-0.02417.366-0.029-0.0290.0000.0000.0000.000
130A136ARG10.8510.91819.0950.2820.2820.0000.0000.0000.000
131A137SER0-0.0410.00518.5750.0300.0300.0000.0000.0000.000
132A138LEU00.006-0.00213.9610.0040.0040.0000.0000.0000.000
133A139PRO00.0100.00615.7040.0320.0320.0000.0000.0000.000
134A140ILE0-0.010-0.00118.255-0.057-0.0570.0000.0000.0000.000
135A141GLY0-0.034-0.01818.8820.0260.0260.0000.0000.0000.000
136A142ILE0-0.005-0.00213.304-0.041-0.0410.0000.0000.0000.000
137A143PRO0-0.008-0.00914.5190.0510.0510.0000.0000.0000.000
138A144LYS10.8370.92115.9540.3850.3850.0000.0000.0000.000
139A145VAL00.0090.00518.4610.0750.0750.0000.0000.0000.000
140A146ILE00.0360.00520.439-0.045-0.0450.0000.0000.0000.000
141A147ILE0-0.048-0.02022.8320.0500.0500.0000.0000.0000.000
142A148SER00.031-0.01725.3880.0030.0030.0000.0000.0000.000
143A149THR0-0.028-0.02728.2570.0110.0110.0000.0000.0000.000
144A150VAL0-0.017-0.01630.8800.0200.0200.0000.0000.0000.000
145A151ALA0-0.023-0.00229.8440.0120.0120.0000.0000.0000.000
146A152SER0-0.034-0.00231.5410.0130.0130.0000.0000.0000.000
147A153GLY00.034-0.00235.2860.0040.0040.0000.0000.0000.000
148A154GLN0-0.0100.01036.054-0.002-0.0020.0000.0000.0000.000
149A155THR00.0330.00031.051-0.004-0.0040.0000.0000.0000.000
150A156GLU-1-0.909-0.94031.252-0.174-0.1740.0000.0000.0000.000
151A157SER0-0.036-0.02231.644-0.006-0.0060.0000.0000.0000.000
152A158TYR0-0.002-0.01027.490-0.003-0.0030.0000.0000.0000.000
153A159ILE00.0550.02926.613-0.023-0.0230.0000.0000.0000.000
154A160GLY00.0000.01727.266-0.002-0.0020.0000.0000.0000.000
155A161THR0-0.008-0.00927.4150.0140.0140.0000.0000.0000.000
156A162SER0-0.069-0.02723.231-0.008-0.0080.0000.0000.0000.000
157A163ASP-1-0.737-0.86721.031-0.387-0.3870.0000.0000.0000.000
158A164LEU0-0.041-0.01721.630-0.025-0.0250.0000.0000.0000.000
159A165VAL0-0.0100.00622.9670.0370.0370.0000.0000.0000.000
160A166LEU0-0.005-0.00724.215-0.031-0.0310.0000.0000.0000.000
161A167PHE00.010-0.00824.4460.0190.0190.0000.0000.0000.000
162A168PRO00.0370.01527.610-0.006-0.0060.0000.0000.0000.000
163A169SER0-0.019-0.02529.101-0.006-0.0060.0000.0000.0000.000
164A170VAL0-0.016-0.00831.0390.0010.0010.0000.0000.0000.000
165A171VAL0-0.030-0.00133.1340.0100.0100.0000.0000.0000.000
166A172ASP-1-0.863-0.93434.879-0.213-0.2130.0000.0000.0000.000
167A173ILE0-0.055-0.01634.9630.0080.0080.0000.0000.0000.000
168A174CYS00.0230.02731.633-0.024-0.0240.0000.0000.0000.000
169A175GLY00.002-0.00529.5740.0110.0110.0000.0000.0000.000
170A176ILE0-0.012-0.00226.920-0.004-0.0040.0000.0000.0000.000
171A177ASN0-0.027-0.04930.574-0.002-0.0020.0000.0000.0000.000
172A178ASN00.010-0.00833.034-0.010-0.0100.0000.0000.0000.000
173A179VAL00.0930.04333.599-0.011-0.0110.0000.0000.0000.000
174A180SER00.0350.02630.712-0.010-0.0100.0000.0000.0000.000
175A181LYS10.9550.98728.8830.3090.3090.0000.0000.0000.000
176A182VAL00.0240.02728.431-0.024-0.0240.0000.0000.0000.000
177A183VAL0-0.0010.00728.593-0.007-0.0070.0000.0000.0000.000
178A184LEU0-0.0130.00224.410-0.027-0.0270.0000.0000.0000.000
179A185SER0-0.004-0.00924.239-0.037-0.0370.0000.0000.0000.000
180A186ASN0-0.021-0.00324.327-0.029-0.0290.0000.0000.0000.000
181A187ALA0-0.0040.00823.405-0.015-0.0150.0000.0000.0000.000
182A188GLY00.0330.00620.460-0.039-0.0390.0000.0000.0000.000
183A189ALA00.0120.00719.979-0.054-0.0540.0000.0000.0000.000
184A190ALA0-0.017-0.01621.472-0.001-0.0010.0000.0000.0000.000
185A191PHE0-0.030-0.01514.072-0.007-0.0070.0000.0000.0000.000
186A192ALA0-0.002-0.00316.700-0.049-0.0490.0000.0000.0000.000
187A193GLY00.0160.00017.305-0.021-0.0210.0000.0000.0000.000
188A194MET0-0.052-0.01618.4420.0330.0330.0000.0000.0000.000
189A195VAL0-0.0080.00112.1440.0030.0030.0000.0000.0000.000
190A196ILE0-0.021-0.01314.118-0.031-0.0310.0000.0000.0000.000
191A197GLY00.0060.01515.9510.0490.0490.0000.0000.0000.000
192A198ARG10.9730.98111.6980.8210.8210.0000.0000.0000.000
193A199LEU0-0.059-0.02910.571-0.004-0.0040.0000.0000.0000.000
194A200GLU-1-0.914-0.96314.286-0.376-0.3760.0000.0000.0000.000
195A201SER0-0.055-0.01317.2110.0830.0830.0000.0000.0000.000