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: 947Y2

Calculation Name: 1VAV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I4H0

Base Structure: X-ray

Registration Date: 2023-06-22

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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2812779.07111
FMO2-HF: Nuclear repulsion 2726294.907514
FMO2-HF: Total energy -86484.163596
FMO2-MP2: Total energy -86741.868297


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-18.888-9.2065.267-4.845-10.104-0.02
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.003
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].
3A4LEU0-0.024-0.0233.100-2.1260.1010.065-0.827-1.4650.003
4A5SER0-0.004-0.0205.6080.0680.0680.0000.0000.0000.000
5A6THR0-0.034-0.0188.0410.0000.0000.0000.0000.0000.000
6A7TRP00.0320.0285.3210.0320.0320.0000.0000.0000.000
7A8ASN0-0.0450.0139.4560.0890.0890.0000.0000.0000.000
8A9LEU00.0440.0129.891-0.048-0.0480.0000.0000.0000.000
9A10THR0-0.036-0.00112.1380.0110.0110.0000.0000.0000.000
10A11ILE00.0020.00314.269-0.008-0.0080.0000.0000.0000.000
11A12PRO0-0.0200.00716.297-0.013-0.0130.0000.0000.0000.000
12A13GLN00.0960.06419.3440.0030.0030.0000.0000.0000.000
13A14GLY00.0090.01221.2580.0030.0030.0000.0000.0000.000
14A15ARG10.9541.00023.957-0.046-0.0460.0000.0000.0000.000
15A16PRO00.030-0.01724.940-0.001-0.0010.0000.0000.0000.000
16A17ALA0-0.018-0.00620.2100.0070.0070.0000.0000.0000.000
17A18ILE00.0060.01218.595-0.004-0.0040.0000.0000.0000.000
18A19THR00.002-0.00815.833-0.003-0.0030.0000.0000.0000.000
19A20ILE0-0.049-0.00813.5930.0010.0010.0000.0000.0000.000
20A21SER00.026-0.02014.052-0.003-0.0030.0000.0000.0000.000
21A22THR00.0830.01411.0320.0310.0310.0000.0000.0000.000
22A23SER00.0120.00712.1330.0620.0620.0000.0000.0000.000
23A24GLN00.0030.01514.1160.0370.0370.0000.0000.0000.000
24A25LEU0-0.0090.0057.7490.0440.0440.0000.0000.0000.000
25A26GLN0-0.027-0.0378.8830.2790.2790.0000.0000.0000.000
26A27ARG10.8690.96711.036-0.187-0.1870.0000.0000.0000.000
27A28ASP-1-0.892-0.9669.6621.2831.2830.0000.0000.0000.000
28A29TYR0-0.0310.01211.461-0.112-0.1120.0000.0000.0000.000
29A30ARG10.8820.9249.333-0.707-0.7070.0000.0000.0000.000
30A31SER0-0.026-0.02212.510-0.071-0.0710.0000.0000.0000.000
31A32ASP-1-0.858-0.93713.5000.2160.2160.0000.0000.0000.000
32A33TYR0-0.046-0.04914.277-0.022-0.0220.0000.0000.0000.000
33A34PHE00.0240.0175.900-0.041-0.0410.0000.0000.0000.000
34A35GLN0-0.0040.0079.0180.0940.0940.0000.0000.0000.000
35A36ARG10.9571.0083.100-8.646-7.3090.104-0.561-0.8790.005
36A37THR0-0.062-0.0525.696-0.416-0.4160.0000.0000.0000.000
37A38ALA00.0440.0176.3070.2980.2980.0000.0000.0000.000
38A39ASP-1-0.801-0.8736.983-0.116-0.1160.0000.0000.0000.000
39A40GLY00.0320.0113.002-0.983-0.6030.128-0.178-0.3300.000
40A41ILE0-0.047-0.0022.113-0.1170.4742.333-0.643-2.2820.000
41A42ARG10.8990.9514.719-0.605-0.538-0.001-0.008-0.0590.000
42A43PHE00.0210.0025.9600.1370.1370.0000.0000.0000.000
43A44TRP0-0.013-0.02410.703-0.042-0.0420.0000.0000.0000.000
44A45VAL0-0.047-0.01514.4980.0190.0190.0000.0000.0000.000
45A46PRO00.0610.04317.297-0.015-0.0150.0000.0000.0000.000
46A47VAL00.053-0.00720.913-0.003-0.0030.0000.0000.0000.000
47A48ASN0-0.0150.00123.122-0.002-0.0020.0000.0000.0000.000
48A49GLY0-0.0110.00222.0350.0070.0070.0000.0000.0000.000
49A50SER0-0.112-0.07522.669-0.008-0.0080.0000.0000.0000.000
50A51HIS00.0570.02122.019-0.003-0.0030.0000.0000.0000.000
51A52THR0-0.019-0.01220.0360.0030.0030.0000.0000.0000.000
52A53ARG10.9860.96523.012-0.017-0.0170.0000.0000.0000.000
53A54ASN00.0130.01725.1900.0040.0040.0000.0000.0000.000
54A55SER0-0.040-0.02123.249-0.006-0.0060.0000.0000.0000.000
55A56GLU-1-0.843-0.91525.192-0.008-0.0080.0000.0000.0000.000
56A57PHE0-0.025-0.01222.4380.0010.0010.0000.0000.0000.000
57A58PRO0-0.0540.01120.4010.0000.0000.0000.0000.0000.000
58A59ARG10.8250.89016.0910.0330.0330.0000.0000.0000.000
59A60SER00.0250.00312.6370.0270.0270.0000.0000.0000.000
60A61GLU-1-0.845-0.89511.466-0.162-0.1620.0000.0000.0000.000
61A62LEU00.0240.0235.6150.0620.0620.0000.0000.0000.000
62A63ARG10.8120.88410.1270.0390.0390.0000.0000.0000.000
63A64GLU-1-0.714-0.82411.285-0.231-0.2310.0000.0000.0000.000
64A65THR0-0.051-0.04011.9910.0280.0280.0000.0000.0000.000
65A66LEU00.0290.01812.901-0.024-0.0240.0000.0000.0000.000
66A67SER00.0700.03913.0990.0140.0140.0000.0000.0000.000
67A68SER0-0.045-0.02914.1210.0350.0350.0000.0000.0000.000
68A69GLY0-0.008-0.01614.9080.0170.0170.0000.0000.0000.000
69A70ARG10.9200.96815.924-0.001-0.0010.0000.0000.0000.000
70A71PRO00.0130.00516.662-0.013-0.0130.0000.0000.0000.000
71A72TYR0-0.031-0.01214.2240.0210.0210.0000.0000.0000.000
72A73ASN0-0.012-0.00416.647-0.024-0.0240.0000.0000.0000.000
73A74TRP0-0.025-0.02714.7650.0180.0180.0000.0000.0000.000
74A75ARG10.9190.98419.8750.0680.0680.0000.0000.0000.000
75A76TYR00.0920.03820.6630.0000.0000.0000.0000.0000.000
76A77ALA0-0.0010.02221.713-0.004-0.0040.0000.0000.0000.000
77A78ARG10.8520.91821.4100.0850.0850.0000.0000.0000.000
78A79ALA0-0.039-0.01218.6750.0040.0040.0000.0000.0000.000
79A80ASP-1-0.806-0.89418.561-0.166-0.1660.0000.0000.0000.000
80A81ASN0-0.019-0.02815.335-0.007-0.0070.0000.0000.0000.000
81A82TRP00.0340.00512.6020.0020.0020.0000.0000.0000.000
82A83LEU0-0.0090.0107.799-0.046-0.0460.0000.0000.0000.000
83A84GLU-1-0.823-0.8948.117-0.464-0.4640.0000.0000.0000.000
84A85ALA00.0230.0036.571-0.276-0.2760.0000.0000.0000.000
85A86THR00.0200.0016.3200.2610.2610.0000.0000.0000.000
86A87LEU0-0.041-0.0126.386-0.204-0.2040.0000.0000.0000.000
87A88ARG10.8010.9078.6690.2070.2070.0000.0000.0000.000
88A89ILE00.000-0.00211.4390.0100.0100.0000.0000.0000.000
89A90GLU-1-0.765-0.87111.994-0.027-0.0270.0000.0000.0000.000
90A91ALA0-0.014-0.00715.5650.0200.0200.0000.0000.0000.000
91A92VAL00.0010.00517.298-0.015-0.0150.0000.0000.0000.000
92A93PRO00.0210.00919.7520.0090.0090.0000.0000.0000.000
93A94SER00.0530.00422.785-0.007-0.0070.0000.0000.0000.000
94A95THR0-0.119-0.09625.049-0.003-0.0030.0000.0000.0000.000
95A96ARG10.8620.94422.7310.0530.0530.0000.0000.0000.000
96A97ARG10.9110.95120.8730.0790.0790.0000.0000.0000.000
97A98MET0-0.068-0.00714.7070.0210.0210.0000.0000.0000.000
98A99ILE0-0.028-0.00715.918-0.017-0.0170.0000.0000.0000.000
99A100ILE00.0450.01711.9650.0100.0100.0000.0000.0000.000
100A101GLY00.0620.03611.320-0.078-0.0780.0000.0000.0000.000
101A102GLN0-0.080-0.05813.1360.0590.0590.0000.0000.0000.000
102A103ILE00.0460.05814.245-0.030-0.0300.0000.0000.0000.000
103A104HIS0-0.086-0.07116.7060.0220.0220.0000.0000.0000.000
104A105SER00.0730.04318.974-0.005-0.0050.0000.0000.0000.000
105A106ASP-1-0.796-0.89621.651-0.065-0.0650.0000.0000.0000.000
106A107GLY0-0.008-0.00222.9750.0080.0080.0000.0000.0000.000
107A108SER0-0.086-0.05525.6540.0060.0060.0000.0000.0000.000
108A109ASN0-0.076-0.04327.8810.0070.0070.0000.0000.0000.000
109A110SER00.0060.01228.590-0.004-0.0040.0000.0000.0000.000
110A111GLY0-0.0060.01030.9500.0030.0030.0000.0000.0000.000
111A112GLN0-0.084-0.05028.2390.0060.0060.0000.0000.0000.000
112A113ALA00.0180.01924.118-0.004-0.0040.0000.0000.0000.000
113A114ALA00.002-0.01024.1930.0020.0020.0000.0000.0000.000
114A115PRO0-0.041-0.02020.053-0.006-0.0060.0000.0000.0000.000
115A116LEU00.0370.02720.6310.0070.0070.0000.0000.0000.000
116A117VAL00.034-0.00218.4570.0040.0040.0000.0000.0000.000
117A118LYS10.8730.95518.0370.0970.0970.0000.0000.0000.000
118A119LEU00.0200.01813.8370.0150.0150.0000.0000.0000.000
119A120LEU0-0.051-0.03716.6920.0020.0020.0000.0000.0000.000
120A121TYR00.0370.02716.1830.0040.0040.0000.0000.0000.000
121A122GLN00.0350.00018.2600.0130.0130.0000.0000.0000.000
122A123LEU00.0190.01720.960-0.004-0.0040.0000.0000.0000.000
123A124ARG10.8230.89722.6250.1020.1020.0000.0000.0000.000
124A125LEU00.006-0.00526.267-0.001-0.0010.0000.0000.0000.000
125A126ASP-1-0.834-0.91824.996-0.059-0.0590.0000.0000.0000.000
126A127GLN0-0.009-0.01123.244-0.016-0.0160.0000.0000.0000.000
127A128GLY00.0150.00520.2380.0070.0070.0000.0000.0000.000
128A129ARG10.8500.95021.0800.0970.0970.0000.0000.0000.000
129A130VAL00.001-0.01416.2040.0000.0000.0000.0000.0000.000
130A131GLN0-0.068-0.05119.3250.0100.0100.0000.0000.0000.000
131A132ALA00.0500.03820.025-0.012-0.0120.0000.0000.0000.000
132A133LEU0-0.062-0.03521.1510.0160.0160.0000.0000.0000.000
133A134VAL00.0620.02122.192-0.007-0.0070.0000.0000.0000.000
134A135ARG10.8380.92024.2960.0950.0950.0000.0000.0000.000
135A136GLU-1-0.800-0.87626.456-0.096-0.0960.0000.0000.0000.000
136A137ARG10.9110.95829.0170.0600.0600.0000.0000.0000.000
137A138PRO00.0140.00827.3120.0000.0000.0000.0000.0000.000
138A139ASP-1-0.812-0.90428.419-0.054-0.0540.0000.0000.0000.000
139A140ASP-1-0.821-0.87930.090-0.065-0.0650.0000.0000.0000.000
140A141GLY00.0440.02230.321-0.002-0.0020.0000.0000.0000.000
141A142GLY0-0.029-0.01729.9490.0010.0010.0000.0000.0000.000
142A143THR0-0.046-0.02425.033-0.003-0.0030.0000.0000.0000.000
143A144ARG10.8440.90527.4030.0880.0880.0000.0000.0000.000
144A145ALA0-0.019-0.01225.509-0.009-0.0090.0000.0000.0000.000
145A146TYR00.0440.03124.3560.0070.0070.0000.0000.0000.000
146A147THR0-0.022-0.02123.424-0.010-0.0100.0000.0000.0000.000
147A148LEU00.0170.02919.1920.0040.0040.0000.0000.0000.000
148A149MET00.0120.01819.1360.0020.0020.0000.0000.0000.000
149A150ASP-1-0.798-0.90321.434-0.110-0.1100.0000.0000.0000.000
150A151GLY00.0090.00422.217-0.007-0.0070.0000.0000.0000.000
151A152ILE0-0.027-0.00216.344-0.006-0.0060.0000.0000.0000.000
152A153PRO00.0370.03419.6280.0020.0020.0000.0000.0000.000
153A154LEU00.002-0.01017.660-0.018-0.0180.0000.0000.0000.000
154A155GLY0-0.039-0.01715.3550.0110.0110.0000.0000.0000.000
155A156GLN0-0.037-0.02015.0210.0020.0020.0000.0000.0000.000
156A157PRO0-0.014-0.01711.564-0.017-0.0170.0000.0000.0000.000
157A158PHE0-0.035-0.01611.9020.0340.0340.0000.0000.0000.000
158A159SER00.0540.02110.915-0.055-0.0550.0000.0000.0000.000
159A160TYR0-0.025-0.04210.1650.0500.0500.0000.0000.0000.000
160A161ARG10.8660.93011.3390.2830.2830.0000.0000.0000.000
161A162ILE0-0.033-0.01812.8700.0560.0560.0000.0000.0000.000
162A163GLY00.0330.00713.837-0.041-0.0410.0000.0000.0000.000
163A164VAL0-0.044-0.01016.2920.0220.0220.0000.0000.0000.000
164A165SER00.0490.04719.262-0.004-0.0040.0000.0000.0000.000
165A166ARG10.9630.97821.2960.1240.1240.0000.0000.0000.000
166A167SER0-0.019-0.02723.1760.0090.0090.0000.0000.0000.000
167A168GLY0-0.004-0.02024.2270.0090.0090.0000.0000.0000.000
168A169LEU0-0.0270.00522.9760.0050.0050.0000.0000.0000.000
169A170LEU0-0.010-0.00719.868-0.016-0.0160.0000.0000.0000.000
170A171SER00.020-0.01418.7940.0110.0110.0000.0000.0000.000
171A172VAL0-0.039-0.02717.351-0.026-0.0260.0000.0000.0000.000
172A173SER0-0.036-0.01716.5460.0150.0150.0000.0000.0000.000
173A174VAL00.042-0.00315.540-0.039-0.0390.0000.0000.0000.000
174A175ASN00.002-0.00315.233-0.002-0.0020.0000.0000.0000.000
175A176GLY00.0160.01516.6490.0180.0180.0000.0000.0000.000
176A177SER0-0.061-0.02118.3380.0210.0210.0000.0000.0000.000
177A178ALA00.015-0.02020.190-0.016-0.0160.0000.0000.0000.000
178A179LEU0-0.0190.00621.7530.0160.0160.0000.0000.0000.000
179A180GLU-1-0.878-0.92922.331-0.187-0.1870.0000.0000.0000.000
180A181GLN0-0.020-0.02324.3990.0100.0100.0000.0000.0000.000
181A182GLN0-0.039-0.00125.355-0.011-0.0110.0000.0000.0000.000
182A183LEU0-0.046-0.02322.7550.0040.0040.0000.0000.0000.000
183A184ASP-1-0.810-0.90827.231-0.067-0.0670.0000.0000.0000.000
184A185PRO00.047-0.00229.200-0.004-0.0040.0000.0000.0000.000
185A186GLN0-0.027-0.02030.6650.0000.0000.0000.0000.0000.000
186A187TRP0-0.012-0.03824.116-0.001-0.0010.0000.0000.0000.000
187A188ALA0-0.029-0.00125.760-0.005-0.0050.0000.0000.0000.000
188A189TYR0-0.063-0.03927.026-0.001-0.0010.0000.0000.0000.000
189A190GLN0-0.028-0.01224.9240.0080.0080.0000.0000.0000.000
190A191GLY0-0.023-0.00322.737-0.007-0.0070.0000.0000.0000.000
191A192LEU0-0.024-0.02218.9920.0020.0020.0000.0000.0000.000
192A193TYR0-0.028-0.00515.1820.0060.0060.0000.0000.0000.000
193A194PHE00.0300.01911.1900.0000.0000.0000.0000.0000.000
194A195LYS10.8190.89311.8250.1430.1430.0000.0000.0000.000
195A196ALA00.0410.0208.115-0.037-0.0370.0000.0000.0000.000
196A197GLY00.0310.0289.2960.0500.0500.0000.0000.0000.000
197A198LEU0-0.013-0.01210.187-0.023-0.0230.0000.0000.0000.000
198A199TYR00.0350.01513.4890.0410.0410.0000.0000.0000.000
199A200LEU00.0170.01516.862-0.015-0.0150.0000.0000.0000.000
200A201GLN0-0.045-0.03719.739-0.008-0.0080.0000.0000.0000.000
201A202ASP-1-0.789-0.88623.043-0.031-0.0310.0000.0000.0000.000
202A203ASN0-0.039-0.03023.9020.0000.0000.0000.0000.0000.000
203A204ARG10.9270.98526.3040.0330.0330.0000.0000.0000.000
204A205GLY00.0740.03827.760-0.004-0.0040.0000.0000.0000.000
205A206PRO0-0.026-0.00727.7620.0050.0050.0000.0000.0000.000
206A207SER00.0390.01124.3010.0000.0000.0000.0000.0000.000
207A208SER0-0.007-0.00523.7980.0060.0060.0000.0000.0000.000
208A209GLU-1-0.834-0.88923.436-0.019-0.0190.0000.0000.0000.000
209A210GLY00.0490.00820.2920.0080.0080.0000.0000.0000.000
210A211GLY0-0.048-0.00917.083-0.010-0.0100.0000.0000.0000.000
211A212ARG10.9030.93613.8520.0160.0160.0000.0000.0000.000
212A213ALA00.0060.00910.696-0.023-0.0230.0000.0000.0000.000
213A214THR0-0.001-0.0106.9630.1010.1010.0000.0000.0000.000
214A215PHE0-0.027-0.0133.979-0.1090.0380.000-0.020-0.1260.000
215A216SER00.0360.0093.573-0.952-0.3320.015-0.252-0.383-0.002
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