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: MV8MZ

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 OptAll
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 -2809912.92871
FMO2-HF: Nuclear repulsion 2723428.331498
FMO2-HF: Total energy -86484.597212
FMO2-MP2: Total energy -86742.286774


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.
-15.459-6.1126.372-4.907-10.807-0.022
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 : 0.022 / q_NPA : 0.002
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].
3A4LEU0-0.025-0.0213.500-1.0001.0020.015-0.867-1.1490.001
4A5SER0-0.023-0.0325.7700.1110.1110.0000.0000.0000.000
5A6THR0-0.017-0.0067.910-0.001-0.0010.0000.0000.0000.000
6A7TRP00.0280.0255.4300.0770.0770.0000.0000.0000.000
7A8ASN0-0.0530.0089.7210.0490.0490.0000.0000.0000.000
8A9LEU00.0570.02710.248-0.014-0.0140.0000.0000.0000.000
9A10THR0-0.055-0.02312.465-0.020-0.0200.0000.0000.0000.000
10A11ILE00.0220.01314.6690.0280.0280.0000.0000.0000.000
11A12PRO0-0.0140.01216.654-0.029-0.0290.0000.0000.0000.000
12A13GLN00.0640.03919.728-0.007-0.0070.0000.0000.0000.000
13A14GLY00.0430.03321.8550.0040.0040.0000.0000.0000.000
14A15ARG10.9540.98524.631-0.100-0.1000.0000.0000.0000.000
15A16PRO00.007-0.01224.948-0.007-0.0070.0000.0000.0000.000
16A17ALA0-0.020-0.00720.3980.0040.0040.0000.0000.0000.000
17A18ILE0-0.0020.00418.962-0.009-0.0090.0000.0000.0000.000
18A19THR00.006-0.00315.9510.0210.0210.0000.0000.0000.000
19A20ILE0-0.0240.01114.063-0.026-0.0260.0000.0000.0000.000
20A21SER00.029-0.01414.2710.0120.0120.0000.0000.0000.000
21A22THR00.042-0.00711.0560.0350.0350.0000.0000.0000.000
22A23SER00.0330.01512.6240.0400.0400.0000.0000.0000.000
23A24GLN0-0.0030.02115.283-0.011-0.0110.0000.0000.0000.000
24A25LEU0-0.0190.0018.2510.0240.0240.0000.0000.0000.000
25A26GLN0-0.007-0.0278.8540.2040.2040.0000.0000.0000.000
26A27ARG10.8450.93411.214-0.241-0.2410.0000.0000.0000.000
27A28ASP-1-0.852-0.9288.3380.9850.9850.0000.0000.0000.000
28A29TYR0-0.050-0.01810.698-0.069-0.0690.0000.0000.0000.000
29A30ARG10.8790.9289.699-0.585-0.5850.0000.0000.0000.000
30A31SER0-0.033-0.00413.005-0.121-0.1210.0000.0000.0000.000
31A32ASP-1-0.840-0.92713.7070.3490.3490.0000.0000.0000.000
32A33TYR0-0.015-0.03814.4660.0120.0120.0000.0000.0000.000
33A34PHE0-0.0010.0196.6270.0090.0090.0000.0000.0000.000
34A35GLN00.0090.0099.093-0.015-0.0150.0000.0000.0000.000
35A36ARG10.9200.9682.993-5.581-4.2330.146-0.599-0.8950.004
36A37THR0-0.050-0.0315.637-0.691-0.6910.0000.0000.0000.000
37A38ALA00.0600.0215.8530.1310.1310.0000.0000.0000.000
38A39ASP-1-0.767-0.8327.1490.0310.0310.0000.0000.0000.000
39A40GLY00.0390.0152.694-0.831-0.4630.279-0.255-0.3910.000
40A41ILE0-0.035-0.0052.305-1.1580.3151.902-0.686-2.6890.000
41A42ARG10.8280.9064.543-1.110-1.025-0.001-0.010-0.0730.000
42A43PHE00.0190.0065.7170.1400.1400.0000.0000.0000.000
43A44TRP0-0.021-0.02710.585-0.079-0.0790.0000.0000.0000.000
44A45VAL0-0.013-0.00314.4300.0160.0160.0000.0000.0000.000
45A46PRO00.0400.03717.322-0.021-0.0210.0000.0000.0000.000
46A47VAL00.012-0.01320.8800.0000.0000.0000.0000.0000.000
47A48ASN00.0020.00623.339-0.001-0.0010.0000.0000.0000.000
48A49GLY0-0.0040.00322.0580.0010.0010.0000.0000.0000.000
49A50SER0-0.108-0.06922.991-0.009-0.0090.0000.0000.0000.000
50A51HIS00.0560.01322.2580.0020.0020.0000.0000.0000.000
51A52THR0-0.0150.00120.2010.0010.0010.0000.0000.0000.000
52A53ARG10.9710.95823.129-0.067-0.0670.0000.0000.0000.000
53A54ASN00.0240.03325.416-0.001-0.0010.0000.0000.0000.000
54A55SER0-0.009-0.01023.724-0.003-0.0030.0000.0000.0000.000
55A56GLU-1-0.857-0.91225.7750.0570.0570.0000.0000.0000.000
56A57PHE00.0170.00422.390-0.001-0.0010.0000.0000.0000.000
57A58PRO0-0.0430.01420.0820.0050.0050.0000.0000.0000.000
58A59ARG10.8000.87316.273-0.113-0.1130.0000.0000.0000.000
59A60SER0-0.003-0.02012.6060.0200.0200.0000.0000.0000.000
60A61GLU-1-0.798-0.87111.6950.0960.0960.0000.0000.0000.000
61A62LEU00.0120.0166.0250.0120.0120.0000.0000.0000.000
62A63ARG10.7880.86510.592-0.086-0.0860.0000.0000.0000.000
63A64GLU-1-0.703-0.82211.346-0.090-0.0900.0000.0000.0000.000
64A65THR0-0.068-0.04811.9190.0120.0120.0000.0000.0000.000
65A66LEU00.0400.03012.944-0.034-0.0340.0000.0000.0000.000
66A67SER00.0630.01813.1750.0290.0290.0000.0000.0000.000
67A68SER0-0.068-0.02814.1440.0280.0280.0000.0000.0000.000
68A69GLY00.0130.00415.3850.0110.0110.0000.0000.0000.000
69A70ARG10.9430.96916.3480.0040.0040.0000.0000.0000.000
70A71PRO00.0110.00416.511-0.008-0.0080.0000.0000.0000.000
71A72TYR0-0.026-0.01114.8330.0020.0020.0000.0000.0000.000
72A73ASN0-0.008-0.00816.9410.0040.0040.0000.0000.0000.000
73A74TRP0-0.057-0.03615.573-0.001-0.0010.0000.0000.0000.000
74A75ARG10.8980.97020.7570.0340.0340.0000.0000.0000.000
75A76TYR00.0900.03821.245-0.001-0.0010.0000.0000.0000.000
76A77ALA0-0.0220.00522.276-0.006-0.0060.0000.0000.0000.000
77A78ARG10.8740.94822.0090.0560.0560.0000.0000.0000.000
78A79ALA00.0360.01419.0090.0010.0010.0000.0000.0000.000
79A80ASP-1-0.779-0.85318.552-0.121-0.1210.0000.0000.0000.000
80A81ASN0-0.014-0.00715.729-0.011-0.0110.0000.0000.0000.000
81A82TRP00.0260.00012.7920.0090.0090.0000.0000.0000.000
82A83LEU0-0.014-0.0018.295-0.030-0.0300.0000.0000.0000.000
83A84GLU-1-0.811-0.8838.476-0.326-0.3260.0000.0000.0000.000
84A85ALA00.0100.0026.211-0.158-0.1580.0000.0000.0000.000
85A86THR00.038-0.0046.0090.1580.1580.0000.0000.0000.000
86A87LEU0-0.054-0.0146.336-0.094-0.0940.0000.0000.0000.000
87A88ARG10.7870.8818.757-0.072-0.0720.0000.0000.0000.000
88A89ILE00.0090.00011.4360.0440.0440.0000.0000.0000.000
89A90GLU-1-0.776-0.87511.8280.1890.1890.0000.0000.0000.000
90A91ALA0-0.022-0.00915.9110.0010.0010.0000.0000.0000.000
91A92VAL0-0.004-0.00317.5290.0020.0020.0000.0000.0000.000
92A93PRO00.0090.00419.8870.0000.0000.0000.0000.0000.000
93A94SER00.0470.00323.061-0.010-0.0100.0000.0000.0000.000
94A95THR0-0.104-0.07925.294-0.007-0.0070.0000.0000.0000.000
95A96ARG10.7960.88623.124-0.032-0.0320.0000.0000.0000.000
96A97ARG10.8620.92221.102-0.014-0.0140.0000.0000.0000.000
97A98MET0-0.0580.00215.0180.0150.0150.0000.0000.0000.000
98A99ILE0-0.040-0.01215.638-0.017-0.0170.0000.0000.0000.000
99A100ILE00.0370.01012.1200.0250.0250.0000.0000.0000.000
100A101GLY00.0540.03211.293-0.017-0.0170.0000.0000.0000.000
101A102GLN0-0.087-0.06013.0860.0010.0010.0000.0000.0000.000
102A103ILE00.0380.03414.683-0.014-0.0140.0000.0000.0000.000
103A104HIS0-0.081-0.04717.3490.0140.0140.0000.0000.0000.000
104A105SER00.0630.04119.616-0.005-0.0050.0000.0000.0000.000
105A106ASP-1-0.785-0.87721.826-0.003-0.0030.0000.0000.0000.000
106A107GLY00.0020.00123.1180.0060.0060.0000.0000.0000.000
107A108SER0-0.102-0.06525.786-0.001-0.0010.0000.0000.0000.000
108A109ASN0-0.051-0.03828.042-0.001-0.0010.0000.0000.0000.000
109A110SER00.0000.00728.575-0.004-0.0040.0000.0000.0000.000
110A111GLY00.0040.01230.9910.0020.0020.0000.0000.0000.000
111A112GLN0-0.083-0.05428.4940.0070.0070.0000.0000.0000.000
112A113ALA00.0210.02324.269-0.004-0.0040.0000.0000.0000.000
113A114ALA00.007-0.00724.3980.0050.0050.0000.0000.0000.000
114A115PRO0-0.020-0.00820.572-0.006-0.0060.0000.0000.0000.000
115A116LEU00.0360.02521.2570.0010.0010.0000.0000.0000.000
116A117VAL00.013-0.00718.570-0.002-0.0020.0000.0000.0000.000
117A118LYS10.8620.94118.011-0.006-0.0060.0000.0000.0000.000
118A119LEU00.0360.03013.861-0.003-0.0030.0000.0000.0000.000
119A120LEU0-0.035-0.02016.5450.0150.0150.0000.0000.0000.000
120A121TYR00.0300.01016.255-0.004-0.0040.0000.0000.0000.000
121A122GLN00.0410.01218.3140.0070.0070.0000.0000.0000.000
122A123LEU00.0370.02721.175-0.008-0.0080.0000.0000.0000.000
123A124ARG10.8230.89022.8100.0210.0210.0000.0000.0000.000
124A125LEU00.0410.01626.463-0.003-0.0030.0000.0000.0000.000
125A126ASP-1-0.815-0.89525.2570.0160.0160.0000.0000.0000.000
126A127GLN00.008-0.00623.597-0.007-0.0070.0000.0000.0000.000
127A128GLY00.0200.01220.7670.0040.0040.0000.0000.0000.000
128A129ARG10.8230.94221.0780.0080.0080.0000.0000.0000.000
129A130VAL00.0180.00216.2080.0080.0080.0000.0000.0000.000
130A131GLN0-0.047-0.03719.3520.0010.0010.0000.0000.0000.000
131A132ALA00.0640.04020.3250.0020.0020.0000.0000.0000.000
132A133LEU0-0.066-0.03621.2840.0060.0060.0000.0000.0000.000
133A134VAL00.0560.02022.486-0.001-0.0010.0000.0000.0000.000
134A135ARG10.7960.89324.7170.0150.0150.0000.0000.0000.000
135A136GLU-1-0.751-0.83427.211-0.040-0.0400.0000.0000.0000.000
136A137ARG10.8880.94929.8510.0150.0150.0000.0000.0000.000
137A138PRO00.0050.00327.4410.0020.0020.0000.0000.0000.000
138A139ASP-1-0.789-0.89528.632-0.006-0.0060.0000.0000.0000.000
139A140ASP-1-0.813-0.87430.305-0.016-0.0160.0000.0000.0000.000
140A141GLY00.0490.01730.3670.0010.0010.0000.0000.0000.000
141A142GLY0-0.027-0.01529.9960.0030.0030.0000.0000.0000.000
142A143THR0-0.059-0.02725.152-0.001-0.0010.0000.0000.0000.000
143A144ARG10.8480.91028.2720.0290.0290.0000.0000.0000.000
144A145ALA0-0.006-0.01525.847-0.001-0.0010.0000.0000.0000.000
145A146TYR00.0460.02224.6290.0010.0010.0000.0000.0000.000
146A147THR0-0.036-0.02423.520-0.002-0.0020.0000.0000.0000.000
147A148LEU00.0310.03919.3390.0000.0000.0000.0000.0000.000
148A149MET00.0100.02019.044-0.004-0.0040.0000.0000.0000.000
149A150ASP-1-0.819-0.92621.338-0.019-0.0190.0000.0000.0000.000
150A151GLY00.0330.02922.722-0.006-0.0060.0000.0000.0000.000
151A152ILE0-0.011-0.00116.594-0.006-0.0060.0000.0000.0000.000
152A153PRO00.0140.02119.7600.0090.0090.0000.0000.0000.000
153A154LEU0-0.003-0.00917.871-0.003-0.0030.0000.0000.0000.000
154A155GLY0-0.023-0.00715.676-0.003-0.0030.0000.0000.0000.000
155A156GLN0-0.031-0.02415.0740.0010.0010.0000.0000.0000.000
156A157PRO0-0.015-0.01011.7180.0020.0020.0000.0000.0000.000
157A158PHE0-0.033-0.01511.9960.0100.0100.0000.0000.0000.000
158A159SER00.0540.02410.596-0.020-0.0200.0000.0000.0000.000
159A160TYR0-0.037-0.04610.1440.0350.0350.0000.0000.0000.000
160A161ARG10.8770.93511.0600.1730.1730.0000.0000.0000.000
161A162ILE0-0.022-0.01013.0520.0390.0390.0000.0000.0000.000
162A163GLY00.0320.00314.084-0.027-0.0270.0000.0000.0000.000
163A164VAL0-0.048-0.00816.5550.0190.0190.0000.0000.0000.000
164A165SER00.0660.05619.463-0.008-0.0080.0000.0000.0000.000
165A166ARG10.8730.92521.6960.0990.0990.0000.0000.0000.000
166A167SER0-0.008-0.01923.5510.0050.0050.0000.0000.0000.000
167A168GLY00.001-0.01224.5640.0070.0070.0000.0000.0000.000
168A169LEU0-0.0160.00823.2330.0050.0050.0000.0000.0000.000
169A170LEU0-0.008-0.00520.528-0.010-0.0100.0000.0000.0000.000
170A171SER00.011-0.03218.8180.0050.0050.0000.0000.0000.000
171A172VAL0-0.034-0.02618.019-0.010-0.0100.0000.0000.0000.000
172A173SER0-0.035-0.01616.4540.0030.0030.0000.0000.0000.000
173A174VAL00.023-0.01415.390-0.016-0.0160.0000.0000.0000.000
174A175ASN00.000-0.00814.986-0.003-0.0030.0000.0000.0000.000
175A176GLY00.0170.02116.3340.0030.0030.0000.0000.0000.000
176A177SER0-0.048-0.01218.3570.0090.0090.0000.0000.0000.000
177A178ALA00.011-0.02119.624-0.010-0.0100.0000.0000.0000.000
178A179LEU0-0.023-0.00121.5730.0100.0100.0000.0000.0000.000
179A180GLU-1-0.872-0.91521.951-0.118-0.1180.0000.0000.0000.000
180A181GLN0-0.016-0.01824.5450.0040.0040.0000.0000.0000.000
181A182GLN0-0.058-0.02025.860-0.008-0.0080.0000.0000.0000.000
182A183LEU0-0.051-0.02623.3530.0050.0050.0000.0000.0000.000
183A184ASP-1-0.793-0.90527.844-0.028-0.0280.0000.0000.0000.000
184A185PRO00.0300.00129.846-0.002-0.0020.0000.0000.0000.000
185A186GLN0-0.032-0.02831.3350.0000.0000.0000.0000.0000.000
186A187TRP0-0.007-0.03124.5350.0020.0020.0000.0000.0000.000
187A188ALA0-0.0340.00026.382-0.003-0.0030.0000.0000.0000.000
188A189TYR0-0.051-0.03127.745-0.003-0.0030.0000.0000.0000.000
189A190GLN0-0.035-0.02525.1580.0070.0070.0000.0000.0000.000
190A191GLY00.0160.01123.056-0.006-0.0060.0000.0000.0000.000
191A192LEU0-0.024-0.01319.5840.0080.0080.0000.0000.0000.000
192A193TYR0-0.018-0.00215.3160.0060.0060.0000.0000.0000.000
193A194PHE00.0240.01111.7550.0060.0060.0000.0000.0000.000
194A195LYS10.8140.88811.878-0.054-0.0540.0000.0000.0000.000
195A196ALA00.0470.0288.109-0.043-0.0430.0000.0000.0000.000
196A197GLY00.0320.0218.9860.0860.0860.0000.0000.0000.000
197A198LEU0-0.018-0.0169.840-0.057-0.0570.0000.0000.0000.000
198A199TYR00.003-0.01913.2840.0180.0180.0000.0000.0000.000
199A200LEU00.0120.02016.751-0.020-0.0200.0000.0000.0000.000
200A201GLN0-0.038-0.03019.841-0.016-0.0160.0000.0000.0000.000
201A202ASP-1-0.747-0.86723.0920.0490.0490.0000.0000.0000.000
202A203ASN0-0.032-0.02923.8310.0050.0050.0000.0000.0000.000
203A204ARG10.8620.94526.257-0.047-0.0470.0000.0000.0000.000
204A205GLY00.0980.05027.846-0.005-0.0050.0000.0000.0000.000
205A206PRO0-0.0060.00527.7950.0040.0040.0000.0000.0000.000
206A207SER00.011-0.00924.7640.0040.0040.0000.0000.0000.000
207A208SER00.0160.01124.1020.0110.0110.0000.0000.0000.000
208A209GLU-1-0.823-0.88123.4860.0680.0680.0000.0000.0000.000
209A210GLY00.0380.00020.2690.0080.0080.0000.0000.0000.000
210A211GLY0-0.023-0.00517.207-0.013-0.0130.0000.0000.0000.000
211A212ARG10.8920.93213.899-0.140-0.1400.0000.0000.0000.000
212A213ALA00.0070.01010.728-0.048-0.0480.0000.0000.0000.000
213A214THR0-0.015-0.0246.7130.1450.1450.0000.0000.0000.000
214A215PHE0-0.008-0.0084.010-0.214-0.0720.000-0.019-0.1230.000
215A216SER0-0.0050.0003.518-0.856-0.0740.029-0.296-0.515-0.002
216A217GLU-1-0.861-0.9022.299-2.731-1.6931.228-0.963-1.303-0.006
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