FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: L7L39

Calculation Name: 1VI5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VI5

Chain ID: A

ChEMBL ID:

UniProt ID: O29132

Base Structure: X-ray

Registration Date: 2023-09-26

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280394.636563
FMO2-HF: Nuclear repulsion 2203536.132383
FMO2-HF: Total energy -76858.504181
FMO2-MP2: Total energy -77086.048549


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:5:GLU)


Summations of interaction energy for fragment #1(A:5: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.
-30.606-28.749-0.022-0.735-1.10.003
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.997 / q_NPA : -1.008
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].
3A7GLU-1-0.911-0.9493.81727.60629.290-0.020-0.723-0.9410.003
4A8TYR0-0.026-0.0055.257-2.713-2.619-0.001-0.004-0.0890.000
5A9LEU0-0.051-0.0279.498-1.029-1.0290.0000.0000.0000.000
6A10VAL00.0020.00012.707-1.366-1.3660.0000.0000.0000.000
7A11PRO00.0460.02411.1041.8691.8690.0000.0000.0000.000
8A12PRO00.023-0.0018.066-1.404-1.4040.0000.0000.0000.000
9A13ASP-1-0.858-0.93111.23318.33318.3330.0000.0000.0000.000
10A14ASP-1-0.863-0.92214.33215.31415.3140.0000.0000.0000.000
11A15TYR0-0.064-0.07512.205-1.552-1.5520.0000.0000.0000.000
12A16LEU0-0.033-0.02512.867-0.988-0.9880.0000.0000.0000.000
13A17ALA0-0.032-0.01816.537-0.874-0.8740.0000.0000.0000.000
14A18ALA0-0.029-0.01418.956-0.811-0.8110.0000.0000.0000.000
15A19GLY0-0.030-0.01219.566-0.593-0.5930.0000.0000.0000.000
16A20VAL0-0.032-0.01716.354-0.349-0.3490.0000.0000.0000.000
17A21HIS00.0490.02315.8330.0550.0550.0000.0000.0000.000
18A22ILE0-0.070-0.02117.756-0.125-0.1250.0000.0000.0000.000
19A23GLY00.0810.05821.183-0.273-0.2730.0000.0000.0000.000
20A24THR0-0.008-0.02923.077-0.571-0.5710.0000.0000.0000.000
21A25GLN00.015-0.01625.8840.1830.1830.0000.0000.0000.000
22A26ILE00.0060.01428.292-0.012-0.0120.0000.0000.0000.000
23A27LYS10.9260.98921.709-13.004-13.0040.0000.0000.0000.000
24A28THR0-0.0110.00025.952-0.158-0.1580.0000.0000.0000.000
25A29GLY00.011-0.00825.2940.4340.4340.0000.0000.0000.000
26A30ASP-1-0.818-0.89824.63212.03312.0330.0000.0000.0000.000
27A31MET00.0020.01320.8790.8460.8460.0000.0000.0000.000
28A32LYS10.9320.97320.560-13.419-13.4190.0000.0000.0000.000
29A33LYS10.8870.94217.779-15.212-15.2120.0000.0000.0000.000
30A34PHE00.015-0.00316.1311.2301.2300.0000.0000.0000.000
31A35ILE0-0.052-0.01516.5150.1170.1170.0000.0000.0000.000
32A36PHE0-0.0010.01711.159-0.101-0.1010.0000.0000.0000.000
33A37LYS10.9330.97215.339-14.252-14.2520.0000.0000.0000.000
34A38VAL00.0120.00218.165-0.141-0.1410.0000.0000.0000.000
35A39ARG10.8730.92120.340-12.193-12.1930.0000.0000.0000.000
36A40GLN00.0280.00822.436-0.635-0.6350.0000.0000.0000.000
37A41ASP-1-0.820-0.89225.04811.42611.4260.0000.0000.0000.000
38A42GLY00.0410.01526.114-0.298-0.2980.0000.0000.0000.000
39A43LEU0-0.066-0.00724.165-0.034-0.0340.0000.0000.0000.000
40A44TYR0-0.007-0.02021.5380.7150.7150.0000.0000.0000.000
41A45VAL0-0.013-0.00215.963-0.103-0.1030.0000.0000.0000.000
42A46LEU0-0.014-0.00917.0340.5890.5890.0000.0000.0000.000
43A47ASP-1-0.825-0.92310.65126.68926.6890.0000.0000.0000.000
44A48ILE00.0630.02510.757-0.109-0.1090.0000.0000.0000.000
45A49ARG10.8500.9414.668-45.975-45.896-0.001-0.008-0.0700.000
46A50LYS10.8490.9149.431-26.675-26.6750.0000.0000.0000.000
47A51LEU0-0.0140.00412.602-0.552-0.5520.0000.0000.0000.000
48A52ASP-1-0.688-0.79310.84224.92924.9290.0000.0000.0000.000
49A53GLU-1-0.827-0.9069.24231.10131.1010.0000.0000.0000.000
50A54ARG10.8770.92213.031-18.531-18.5310.0000.0000.0000.000
51A55ILE00.0190.02316.170-1.102-1.1020.0000.0000.0000.000
52A56ARG10.8630.90810.193-28.197-28.1970.0000.0000.0000.000
53A57VAL0-0.045-0.02415.479-0.778-0.7780.0000.0000.0000.000
54A58ALA00.0160.00217.968-0.879-0.8790.0000.0000.0000.000
55A59ALA00.0230.02519.781-0.770-0.7700.0000.0000.0000.000
56A60LYS10.9720.98119.628-15.570-15.5700.0000.0000.0000.000
57A61PHE0-0.041-0.01521.501-0.544-0.5440.0000.0000.0000.000
58A62LEU00.041-0.00123.671-0.549-0.5490.0000.0000.0000.000
59A63SER0-0.075-0.03624.398-0.411-0.4110.0000.0000.0000.000
60A64ARG10.8930.94224.835-12.430-12.4300.0000.0000.0000.000
61A65TYR00.0070.02527.982-0.130-0.1300.0000.0000.0000.000
62A66GLU-1-0.831-0.89831.0488.6568.6560.0000.0000.0000.000
63A67PRO00.002-0.01933.068-0.069-0.0690.0000.0000.0000.000
64A68SER00.0380.02134.1900.1650.1650.0000.0000.0000.000
65A69LYS10.8070.90134.936-8.603-8.6030.0000.0000.0000.000
66A70ILE0-0.026-0.00329.6320.1910.1910.0000.0000.0000.000
67A71LEU00.0090.01333.245-0.201-0.2010.0000.0000.0000.000
68A72LEU0-0.037-0.01229.1400.2300.2300.0000.0000.0000.000
69A73VAL0-0.026-0.01932.307-0.368-0.3680.0000.0000.0000.000
70A74ALA0-0.004-0.01232.0890.3410.3410.0000.0000.0000.000
71A75ALA00.0230.03333.920-0.230-0.2300.0000.0000.0000.000
72A76ARG10.7890.88729.887-10.357-10.3570.0000.0000.0000.000
73A77GLN00.0820.03833.8730.0240.0240.0000.0000.0000.000
74A78TYR0-0.051-0.03830.662-0.026-0.0260.0000.0000.0000.000
75A79ALA00.0160.00430.3680.2760.2760.0000.0000.0000.000
76A80HIS0-0.013-0.00431.3510.0420.0420.0000.0000.0000.000
77A81LYS10.8260.93732.013-9.275-9.2750.0000.0000.0000.000
78A82PRO00.0210.01027.8230.0320.0320.0000.0000.0000.000
79A83VAL00.0300.01929.8460.1750.1750.0000.0000.0000.000
80A84GLN00.0000.01131.3910.1780.1780.0000.0000.0000.000
81A85MET0-0.006-0.00830.330-0.118-0.1180.0000.0000.0000.000
82A86PHE00.011-0.00525.5540.2140.2140.0000.0000.0000.000
83A87SER00.005-0.00829.5420.0740.0740.0000.0000.0000.000
84A88LYS10.8690.96632.898-9.118-9.1180.0000.0000.0000.000
85A89VAL0-0.035-0.01127.655-0.092-0.0920.0000.0000.0000.000
86A90VAL0-0.012-0.00427.7860.0430.0430.0000.0000.0000.000
87A91GLY00.0480.01430.664-0.049-0.0490.0000.0000.0000.000
88A92SER0-0.053-0.01332.089-0.066-0.0660.0000.0000.0000.000
89A93ASP-1-0.764-0.86334.0938.0478.0470.0000.0000.0000.000
90A94TYR0-0.068-0.05834.8090.2840.2840.0000.0000.0000.000
91A95ILE00.0280.01936.413-0.270-0.2700.0000.0000.0000.000
92A96VAL0-0.027-0.00835.0220.2140.2140.0000.0000.0000.000
93A97GLY00.0050.00837.663-0.244-0.2440.0000.0000.0000.000
94A98ARG10.9220.94539.331-6.874-6.8740.0000.0000.0000.000
95A99PHE00.0610.02938.419-0.072-0.0720.0000.0000.0000.000
96A100ILE0-0.024-0.00441.358-0.075-0.0750.0000.0000.0000.000
97A101PRO0-0.045-0.01844.2540.0620.0620.0000.0000.0000.000
98A102GLY00.0330.00944.500-0.192-0.1920.0000.0000.0000.000
99A103THR0-0.051-0.05541.560-0.044-0.0440.0000.0000.0000.000
100A104LEU0-0.016-0.01338.1280.0660.0660.0000.0000.0000.000
101A105THR0-0.032-0.02342.487-0.026-0.0260.0000.0000.0000.000
102A106ASN0-0.022-0.00845.058-0.203-0.2030.0000.0000.0000.000
103A107PRO00.0490.01648.291-0.017-0.0170.0000.0000.0000.000
104A108MET0-0.057-0.02449.487-0.118-0.1180.0000.0000.0000.000
105A109LEU0-0.081-0.01046.811-0.118-0.1180.0000.0000.0000.000
106A110SER0-0.040-0.04949.9920.0220.0220.0000.0000.0000.000
107A111GLU-1-0.850-0.92645.1476.7426.7420.0000.0000.0000.000
108A112TYR0-0.082-0.04644.7360.2160.2160.0000.0000.0000.000
109A113ARG10.7970.87840.317-7.757-7.7570.0000.0000.0000.000
110A114GLU-1-0.866-0.91341.0237.3647.3640.0000.0000.0000.000
111A115PRO0-0.048-0.00335.6780.0720.0720.0000.0000.0000.000
112A116GLU-1-0.832-0.92934.2379.0229.0220.0000.0000.0000.000
113A117VAL0-0.051-0.03028.8810.2970.2970.0000.0000.0000.000
114A118VAL00.0340.03232.062-0.139-0.1390.0000.0000.0000.000
115A119PHE0-0.047-0.02924.9910.4920.4920.0000.0000.0000.000
116A120VAL00.0130.01429.824-0.219-0.2190.0000.0000.0000.000
117A121ASN0-0.011-0.01628.2660.3020.3020.0000.0000.0000.000
118A122ASP-1-0.749-0.87728.04910.65710.6570.0000.0000.0000.000
119A123PRO00.0490.03228.236-0.366-0.3660.0000.0000.0000.000
120A124ALA0-0.058-0.01831.186-0.296-0.2960.0000.0000.0000.000
121A125ILE0-0.049-0.04033.125-0.324-0.3240.0000.0000.0000.000
122A126ASP-1-0.757-0.88532.5129.2299.2290.0000.0000.0000.000
123A127LYS11.0100.99835.116-8.115-8.1150.0000.0000.0000.000
124A128GLN0-0.074-0.03036.307-0.065-0.0650.0000.0000.0000.000
125A129ALA00.0310.01535.787-0.084-0.0840.0000.0000.0000.000
126A130VAL00.000-0.00132.4950.0440.0440.0000.0000.0000.000
127A131SER0-0.015-0.01635.207-0.015-0.0150.0000.0000.0000.000
128A132GLU-1-0.721-0.83938.3837.4857.4850.0000.0000.0000.000
129A133ALA00.0090.01334.909-0.077-0.0770.0000.0000.0000.000
130A134THR00.0160.00635.2210.0600.0600.0000.0000.0000.000
131A135ALA0-0.081-0.03736.776-0.072-0.0720.0000.0000.0000.000
132A136VAL0-0.022-0.01139.235-0.146-0.1460.0000.0000.0000.000
133A137GLY0-0.0190.00636.503-0.032-0.0320.0000.0000.0000.000
134A138ILE0-0.073-0.02433.8960.2270.2270.0000.0000.0000.000
135A139PRO0-0.010-0.00429.1640.1270.1270.0000.0000.0000.000
136A140VAL00.0200.00029.715-0.091-0.0910.0000.0000.0000.000
137A141VAL0-0.035-0.02724.5200.5350.5350.0000.0000.0000.000
138A142ALA00.0370.00525.653-0.433-0.4330.0000.0000.0000.000
139A143LEU0-0.0270.01322.7310.6540.6540.0000.0000.0000.000
140A144CYS0-0.089-0.04723.027-0.652-0.6520.0000.0000.0000.000
141A145ASP-1-0.673-0.82722.43513.01613.0160.0000.0000.0000.000
142A146SER0-0.039-0.05422.787-0.127-0.1270.0000.0000.0000.000
143A147ASN00.0160.00123.9960.0510.0510.0000.0000.0000.000
144A148ASN0-0.021-0.01626.385-0.194-0.1940.0000.0000.0000.000
145A149SER00.0130.01826.7190.3730.3730.0000.0000.0000.000
146A150SER0-0.089-0.07925.4140.1690.1690.0000.0000.0000.000
147A151ALA00.007-0.01727.5500.0580.0580.0000.0000.0000.000
148A152ASP-1-0.876-0.92230.6539.5149.5140.0000.0000.0000.000
149A153VAL0-0.064-0.02725.9870.0260.0260.0000.0000.0000.000
150A154ASP-1-0.800-0.87726.91711.18311.1830.0000.0000.0000.000
151A155LEU0-0.076-0.04020.2740.7640.7640.0000.0000.0000.000
152A156VAL0-0.013-0.01421.086-0.147-0.1470.0000.0000.0000.000
153A157ILE00.0170.01419.2141.0721.0720.0000.0000.0000.000
154A158PRO0-0.045-0.01716.739-0.641-0.6410.0000.0000.0000.000
155A159THR00.053-0.00517.9881.0841.0840.0000.0000.0000.000
156A160ASN00.0290.04720.102-1.075-1.0750.0000.0000.0000.000
157A161ASN0-0.013-0.01522.729-0.005-0.0050.0000.0000.0000.000
158A162LYS10.7870.85425.658-11.582-11.5820.0000.0000.0000.000
159A163GLY0-0.011-0.00525.922-0.374-0.3740.0000.0000.0000.000
160A164ARG10.8600.92126.624-9.726-9.7260.0000.0000.0000.000
161A165ARG10.8480.89722.506-12.042-12.0420.0000.0000.0000.000
162A166ALA0-0.0080.01022.0600.3860.3860.0000.0000.0000.000
163A167LEU00.0230.00622.6230.3640.3640.0000.0000.0000.000
164A168ALA0-0.0010.01224.7080.1990.1990.0000.0000.0000.000
165A169ILE00.0340.01218.1370.0700.0700.0000.0000.0000.000
166A170VAL00.0190.01319.3780.5580.5580.0000.0000.0000.000
167A171TYR00.019-0.00621.3580.1440.1440.0000.0000.0000.000
168A172TRP0-0.024-0.01719.0580.2980.2980.0000.0000.0000.000
169A173LEU00.0000.00116.6900.0610.0610.0000.0000.0000.000
170A174LEU0-0.041-0.01120.4650.2520.2520.0000.0000.0000.000
171A175ALA00.0160.00422.178-0.053-0.0530.0000.0000.0000.000
172A176ARG10.8030.91015.879-16.873-16.8730.0000.0000.0000.000
173A177GLU-1-0.770-0.88817.73917.65217.6520.0000.0000.0000.000
174A178ILE0-0.0080.00820.9860.0380.0380.0000.0000.0000.000
175A179ALA0-0.0080.00324.279-0.284-0.2840.0000.0000.0000.000
176A180LYS10.8890.92516.274-18.122-18.1220.0000.0000.0000.000
177A181ILE0-0.092-0.03820.5030.0630.0630.0000.0000.0000.000
178A182ARG10.8100.89423.689-11.040-11.0400.0000.0000.0000.000
179A183GLY0-0.0050.02125.879-0.356-0.3560.0000.0000.0000.000
180A184GLN0-0.088-0.04627.098-0.370-0.3700.0000.0000.0000.000
181A185ASP-1-0.911-0.95927.21610.69910.6990.0000.0000.0000.000
182A186PHE0-0.031-0.02824.135-0.143-0.1430.0000.0000.0000.000
183A187THR00.0120.00026.1680.2680.2680.0000.0000.0000.000
184A188TYR00.0000.02527.308-0.365-0.3650.0000.0000.0000.000
185A189SER00.003-0.01225.0390.5500.5500.0000.0000.0000.000
186A190ILE00.023-0.00420.264-0.128-0.1280.0000.0000.0000.000
187A191GLU-1-0.773-0.88124.81711.47011.4700.0000.0000.0000.000
188A192ASP-1-0.831-0.87828.0499.7719.7710.0000.0000.0000.000
189A193PHE0-0.007-0.01626.758-0.254-0.2540.0000.0000.0000.000
190A194GLU-1-0.831-0.90927.12810.79210.7920.0000.0000.0000.000
191A195ALA0-0.018-0.00629.519-0.325-0.3250.0000.0000.0000.000
192A196GLU-1-0.821-0.89532.7098.5578.5570.0000.0000.0000.000
193A197LEU0-0.010-0.00933.165-0.054-0.0540.0000.0000.0000.000
194A198GLU-1-0.925-0.95536.9086.9646.9640.0000.0000.0000.000
195A199GLY00.0160.00440.1830.0120.0120.0000.0000.0000.000
196A200GLY0-0.045-0.01736.9470.0500.0500.0000.0000.0000.000
197A201SER0-0.021-0.01034.412-0.180-0.1800.0000.0000.0000.000
198A202HIS10.8920.93036.468-7.884-7.8840.0000.0000.0000.000