FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 37NVL

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 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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280914.817537
FMO2-HF: Nuclear repulsion 2204057.178798
FMO2-HF: Total energy -76857.638739
FMO2-MP2: Total energy -77085.258253


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.
-24.282-22.616-0.023-0.656-0.9880.002
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 : -1.005 / q_NPA : -1.007
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-1-0.922-0.9623.81730.41031.988-0.022-0.654-0.9030.002
4A8TYR0-0.032-0.0195.334-2.715-2.627-0.001-0.002-0.0850.000
5A9LEU0-0.057-0.0249.498-0.862-0.8620.0000.0000.0000.000
6A10VAL00.000-0.00212.692-1.272-1.2720.0000.0000.0000.000
7A11PRO00.0310.02111.1341.7531.7530.0000.0000.0000.000
8A12PRO00.037-0.0018.060-1.377-1.3770.0000.0000.0000.000
9A13ASP-1-0.822-0.91611.23317.31717.3170.0000.0000.0000.000
10A14ASP-1-0.897-0.93714.33214.97614.9760.0000.0000.0000.000
11A15TYR0-0.065-0.09512.155-1.435-1.4350.0000.0000.0000.000
12A16LEU0-0.045-0.03112.844-0.973-0.9730.0000.0000.0000.000
13A17ALA0-0.031-0.01416.537-0.830-0.8300.0000.0000.0000.000
14A18ALA0-0.031-0.02918.957-0.783-0.7830.0000.0000.0000.000
15A19GLY0-0.034-0.01319.576-0.571-0.5710.0000.0000.0000.000
16A20VAL0-0.030-0.01916.413-0.340-0.3400.0000.0000.0000.000
17A21HIS00.0580.02915.857-0.078-0.0780.0000.0000.0000.000
18A22ILE0-0.055-0.01417.812-0.117-0.1170.0000.0000.0000.000
19A23GLY00.0810.05921.231-0.262-0.2620.0000.0000.0000.000
20A24THR0-0.015-0.03323.129-0.526-0.5260.0000.0000.0000.000
21A25GLN00.019-0.00525.9230.2130.2130.0000.0000.0000.000
22A26ILE00.0080.01128.315-0.010-0.0100.0000.0000.0000.000
23A27LYS10.9260.96722.498-12.183-12.1830.0000.0000.0000.000
24A28THR0-0.029-0.00426.008-0.151-0.1510.0000.0000.0000.000
25A29GLY00.012-0.00525.3420.4050.4050.0000.0000.0000.000
26A30ASP-1-0.801-0.90124.68011.76011.7600.0000.0000.0000.000
27A31MET00.0060.01620.9430.8110.8110.0000.0000.0000.000
28A32LYS10.9130.96620.574-13.205-13.2050.0000.0000.0000.000
29A33LYS10.8850.93917.749-15.175-15.1750.0000.0000.0000.000
30A34PHE0-0.002-0.00816.1901.1581.1580.0000.0000.0000.000
31A35ILE0-0.046-0.01216.5690.1090.1090.0000.0000.0000.000
32A36PHE0-0.0100.01511.180-0.053-0.0530.0000.0000.0000.000
33A37LYS10.9400.97515.365-13.524-13.5240.0000.0000.0000.000
34A38VAL0-0.013-0.00418.176-0.149-0.1490.0000.0000.0000.000
35A39ARG10.8980.94320.218-11.888-11.8880.0000.0000.0000.000
36A40GLN00.0330.00522.444-0.624-0.6240.0000.0000.0000.000
37A41ASP-1-0.832-0.91025.49710.99310.9930.0000.0000.0000.000
38A42GLY00.0350.01026.125-0.276-0.2760.0000.0000.0000.000
39A43LEU0-0.077-0.01524.111-0.007-0.0070.0000.0000.0000.000
40A44TYR0-0.021-0.02521.5460.6030.6030.0000.0000.0000.000
41A45VAL0-0.0030.00115.822-0.105-0.1050.0000.0000.0000.000
42A46LEU0-0.020-0.00517.0870.5430.5430.0000.0000.0000.000
43A47ASP-1-0.868-0.96010.73324.93024.9300.0000.0000.0000.000
44A48ILE00.0700.02810.344-0.065-0.0650.0000.0000.0000.000
45A49ARG10.9020.9884.929-42.362-42.3620.0000.0000.0000.000
46A50LYS10.9000.9479.514-24.607-24.6070.0000.0000.0000.000
47A51LEU0-0.0040.00912.685-0.453-0.4530.0000.0000.0000.000
48A52ASP-1-0.714-0.80710.93624.15324.1530.0000.0000.0000.000
49A53GLU-1-0.913-0.96510.00028.02328.0230.0000.0000.0000.000
50A54ARG10.8710.92313.285-18.207-18.2070.0000.0000.0000.000
51A55ILE00.0220.02816.275-1.019-1.0190.0000.0000.0000.000
52A56ARG10.9250.96810.427-26.325-26.3250.0000.0000.0000.000
53A57VAL0-0.032-0.01515.621-0.702-0.7020.0000.0000.0000.000
54A58ALA00.013-0.00217.996-0.833-0.8330.0000.0000.0000.000
55A59ALA00.0330.03019.722-0.740-0.7400.0000.0000.0000.000
56A60LYS10.9660.98119.274-15.286-15.2860.0000.0000.0000.000
57A61PHE0-0.050-0.01521.295-0.604-0.6040.0000.0000.0000.000
58A62LEU00.0450.00223.578-0.521-0.5210.0000.0000.0000.000
59A63SER0-0.081-0.04424.167-0.394-0.3940.0000.0000.0000.000
60A64ARG10.8880.93624.305-12.435-12.4350.0000.0000.0000.000
61A65TYR00.0110.02927.788-0.313-0.3130.0000.0000.0000.000
62A66GLU-1-0.910-0.94930.8698.6008.6000.0000.0000.0000.000
63A67PRO00.005-0.01432.855-0.062-0.0620.0000.0000.0000.000
64A68SER00.0450.02334.0680.1550.1550.0000.0000.0000.000
65A69LYS10.9160.97934.794-8.534-8.5340.0000.0000.0000.000
66A70ILE0-0.0120.00629.3700.1780.1780.0000.0000.0000.000
67A71LEU00.0060.00833.296-0.200-0.2000.0000.0000.0000.000
68A72LEU0-0.035-0.01429.3200.2200.2200.0000.0000.0000.000
69A73VAL0-0.020-0.01332.407-0.359-0.3590.0000.0000.0000.000
70A74ALA0-0.006-0.01632.2090.3250.3250.0000.0000.0000.000
71A75ALA00.0170.03234.012-0.217-0.2170.0000.0000.0000.000
72A76ARG10.8210.91630.048-10.023-10.0230.0000.0000.0000.000
73A77GLN00.1210.05633.9580.0770.0770.0000.0000.0000.000
74A78TYR0-0.064-0.04330.6050.0350.0350.0000.0000.0000.000
75A79ALA00.0290.00530.4170.2690.2690.0000.0000.0000.000
76A80HIS0-0.0170.00131.4120.0580.0580.0000.0000.0000.000
77A81LYS10.9100.97932.138-9.148-9.1480.0000.0000.0000.000
78A82PRO00.000-0.00127.8560.0400.0400.0000.0000.0000.000
79A83VAL00.0260.01329.8460.1770.1770.0000.0000.0000.000
80A84GLN0-0.015-0.00131.4100.1580.1580.0000.0000.0000.000
81A85MET0-0.021-0.01430.399-0.108-0.1080.0000.0000.0000.000
82A86PHE00.014-0.00125.4560.2120.2120.0000.0000.0000.000
83A87SER00.0290.00829.5420.1560.1560.0000.0000.0000.000
84A88LYS10.9010.98932.898-8.919-8.9190.0000.0000.0000.000
85A89VAL0-0.036-0.01227.763-0.088-0.0880.0000.0000.0000.000
86A90VAL0-0.011-0.00727.9000.0550.0550.0000.0000.0000.000
87A91GLY00.0300.00130.664-0.043-0.0430.0000.0000.0000.000
88A92SER0-0.059-0.01932.064-0.065-0.0650.0000.0000.0000.000
89A93ASP-1-0.765-0.86034.1547.9627.9620.0000.0000.0000.000
90A94TYR0-0.069-0.06134.9350.3200.3200.0000.0000.0000.000
91A95ILE00.0110.01536.517-0.265-0.2650.0000.0000.0000.000
92A96VAL0-0.017-0.00235.2290.1980.1980.0000.0000.0000.000
93A97GLY00.0000.00237.758-0.238-0.2380.0000.0000.0000.000
94A98ARG10.9250.94539.422-6.772-6.7720.0000.0000.0000.000
95A99PHE00.0540.03138.830-0.066-0.0660.0000.0000.0000.000
96A100ILE0-0.0040.00541.451-0.078-0.0780.0000.0000.0000.000
97A101PRO0-0.062-0.01644.3530.0590.0590.0000.0000.0000.000
98A102GLY00.0280.00144.612-0.183-0.1830.0000.0000.0000.000
99A103THR0-0.056-0.06741.898-0.046-0.0460.0000.0000.0000.000
100A104LEU0-0.007-0.01338.1300.0580.0580.0000.0000.0000.000
101A105THR0-0.028-0.00342.753-0.035-0.0350.0000.0000.0000.000
102A106ASN0-0.020-0.00345.340-0.191-0.1910.0000.0000.0000.000
103A107PRO00.0530.01448.362-0.012-0.0120.0000.0000.0000.000
104A108MET0-0.056-0.02549.672-0.114-0.1140.0000.0000.0000.000
105A109LEU0-0.050-0.00146.949-0.114-0.1140.0000.0000.0000.000
106A110SER0-0.041-0.03650.0990.0210.0210.0000.0000.0000.000
107A111GLU-1-0.870-0.94345.1576.7076.7070.0000.0000.0000.000
108A112TYR0-0.092-0.06444.8370.2090.2090.0000.0000.0000.000
109A113ARG10.8130.88840.257-7.683-7.6830.0000.0000.0000.000
110A114GLU-1-0.872-0.90641.1497.3327.3320.0000.0000.0000.000
111A115PRO0-0.059-0.01135.8470.0750.0750.0000.0000.0000.000
112A116GLU-1-0.868-0.96334.1329.0589.0580.0000.0000.0000.000
113A117VAL0-0.033-0.01729.0330.2800.2800.0000.0000.0000.000
114A118VAL00.0340.02932.275-0.136-0.1360.0000.0000.0000.000
115A119PHE0-0.054-0.03125.1130.4550.4550.0000.0000.0000.000
116A120VAL00.0200.01729.848-0.220-0.2200.0000.0000.0000.000
117A121ASN0-0.002-0.01328.2060.2130.2130.0000.0000.0000.000
118A122ASP-1-0.761-0.89428.13510.43510.4350.0000.0000.0000.000
119A123PRO00.0370.02628.370-0.359-0.3590.0000.0000.0000.000
120A124ALA0-0.053-0.02031.270-0.287-0.2870.0000.0000.0000.000
121A125ILE0-0.065-0.04733.181-0.309-0.3090.0000.0000.0000.000
122A126ASP-1-0.758-0.89332.7808.9888.9880.0000.0000.0000.000
123A127LYS11.0010.99435.203-7.910-7.9100.0000.0000.0000.000
124A128GLN0-0.077-0.04736.392-0.061-0.0610.0000.0000.0000.000
125A129ALA00.0370.02235.845-0.083-0.0830.0000.0000.0000.000
126A130VAL00.0170.01032.7110.0350.0350.0000.0000.0000.000
127A131SER0-0.023-0.00335.297-0.010-0.0100.0000.0000.0000.000
128A132GLU-1-0.735-0.84938.4717.4017.4010.0000.0000.0000.000
129A133ALA00.0070.01135.192-0.072-0.0720.0000.0000.0000.000
130A134THR00.007-0.00735.8790.0970.0970.0000.0000.0000.000
131A135ALA0-0.082-0.03737.141-0.066-0.0660.0000.0000.0000.000
132A136VAL0-0.012-0.00739.196-0.138-0.1380.0000.0000.0000.000
133A137GLY0-0.0240.00436.746-0.028-0.0280.0000.0000.0000.000
134A138ILE0-0.085-0.02533.9220.2210.2210.0000.0000.0000.000
135A139PRO0-0.0070.00129.4670.1240.1240.0000.0000.0000.000
136A140VAL00.021-0.00129.519-0.084-0.0840.0000.0000.0000.000
137A141VAL0-0.040-0.02824.7520.5020.5020.0000.0000.0000.000
138A142ALA00.0370.00325.749-0.418-0.4180.0000.0000.0000.000
139A143LEU0-0.0370.00822.6550.6060.6060.0000.0000.0000.000
140A144CYS0-0.075-0.03923.110-0.612-0.6120.0000.0000.0000.000
141A145ASP-1-0.678-0.85122.51212.74212.7420.0000.0000.0000.000
142A146SER0-0.043-0.02822.822-0.101-0.1010.0000.0000.0000.000
143A147ASN00.005-0.01124.0540.1080.1080.0000.0000.0000.000
144A148ASN0-0.017-0.00826.498-0.169-0.1690.0000.0000.0000.000
145A149SER00.0030.00826.7850.3560.3560.0000.0000.0000.000
146A150SER0-0.054-0.05825.4920.1640.1640.0000.0000.0000.000
147A151ALA0-0.009-0.02327.6260.0570.0570.0000.0000.0000.000
148A152ASP-1-0.866-0.91630.9399.3729.3720.0000.0000.0000.000
149A153VAL0-0.077-0.03026.1930.0400.0400.0000.0000.0000.000
150A154ASP-1-0.794-0.88527.28010.94610.9460.0000.0000.0000.000
151A155LEU0-0.075-0.03520.6820.7270.7270.0000.0000.0000.000
152A156VAL0-0.006-0.01121.246-0.149-0.1490.0000.0000.0000.000
153A157ILE00.0080.00519.3501.0091.0090.0000.0000.0000.000
154A158PRO0-0.056-0.02116.876-0.616-0.6160.0000.0000.0000.000
155A159THR00.064-0.00918.0691.0551.0550.0000.0000.0000.000
156A160ASN00.0580.07920.180-0.986-0.9860.0000.0000.0000.000
157A161ASN0-0.027-0.03122.800-0.013-0.0130.0000.0000.0000.000
158A162LYS10.8400.89125.736-11.105-11.1050.0000.0000.0000.000
159A163GLY0-0.013-0.01025.961-0.356-0.3560.0000.0000.0000.000
160A164ARG10.9160.95726.641-9.541-9.5410.0000.0000.0000.000
161A165ARG10.9090.94821.923-12.042-12.0420.0000.0000.0000.000
162A166ALA0-0.0120.01222.0510.3720.3720.0000.0000.0000.000
163A167LEU00.0130.00322.6230.3610.3610.0000.0000.0000.000
164A168ALA00.0040.01524.7080.2010.2010.0000.0000.0000.000
165A169ILE00.0320.01118.1070.0750.0750.0000.0000.0000.000
166A170VAL00.0210.01419.4700.5460.5460.0000.0000.0000.000
167A171TYR00.002-0.01921.3580.1840.1840.0000.0000.0000.000
168A172TRP0-0.031-0.02019.1010.3250.3250.0000.0000.0000.000
169A173LEU0-0.002-0.00516.7270.0740.0740.0000.0000.0000.000
170A174LEU0-0.035-0.00220.4650.2730.2730.0000.0000.0000.000
171A175ALA00.0170.00322.178-0.030-0.0300.0000.0000.0000.000
172A176ARG10.8430.94016.032-16.557-16.5570.0000.0000.0000.000
173A177GLU-1-0.875-0.96917.83817.49117.4910.0000.0000.0000.000
174A178ILE0-0.0180.00320.9860.0360.0360.0000.0000.0000.000
175A179ALA0-0.0080.00224.173-0.273-0.2730.0000.0000.0000.000
176A180LYS10.9850.99116.662-17.754-17.7540.0000.0000.0000.000
177A181ILE0-0.099-0.04120.6230.0890.0890.0000.0000.0000.000
178A182ARG10.8220.90323.242-10.969-10.9690.0000.0000.0000.000
179A183GLY0-0.0040.02225.634-0.342-0.3420.0000.0000.0000.000
180A184GLN0-0.086-0.04426.814-0.452-0.4520.0000.0000.0000.000
181A185ASP-1-0.929-0.96527.25410.59410.5940.0000.0000.0000.000
182A186PHE0-0.018-0.02424.010-0.149-0.1490.0000.0000.0000.000
183A187THR0-0.001-0.00426.2140.3150.3150.0000.0000.0000.000
184A188TYR00.0050.01627.381-0.338-0.3380.0000.0000.0000.000
185A189SER00.0230.01525.0940.4970.4970.0000.0000.0000.000
186A190ILE00.021-0.00420.240-0.115-0.1150.0000.0000.0000.000
187A191GLU-1-0.811-0.89624.81711.22211.2220.0000.0000.0000.000
188A192ASP-1-0.849-0.89728.0499.6749.6740.0000.0000.0000.000
189A193PHE0-0.047-0.04926.764-0.249-0.2490.0000.0000.0000.000
190A194GLU-1-0.871-0.94827.09310.66110.6610.0000.0000.0000.000
191A195ALA0-0.034-0.00929.519-0.306-0.3060.0000.0000.0000.000
192A196GLU-1-0.859-0.91532.7098.3028.3020.0000.0000.0000.000
193A197LEU0-0.037-0.02633.184-0.047-0.0470.0000.0000.0000.000
194A198GLU-1-0.926-0.95536.9086.8856.8850.0000.0000.0000.000
195A199GLY00.0190.00740.1830.0120.0120.0000.0000.0000.000
196A200GLY0-0.053-0.02236.9480.0500.0500.0000.0000.0000.000
197A201SER0-0.019-0.00734.395-0.174-0.1740.0000.0000.0000.000
198A202HIS10.8880.92636.468-7.779-7.7790.0000.0000.0000.000