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: YVNQ2

Calculation Name: 4NAV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NAV

Chain ID: D

ChEMBL ID:

UniProt ID: Q8P716

Base Structure: X-ray

Registration Date: 2023-09-21

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1840057.963823
FMO2-HF: Nuclear repulsion 1771717.266457
FMO2-HF: Total energy -68340.697366
FMO2-MP2: Total energy -68541.001176


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(D:1:MET)


Summations of interaction energy for fragment #1(D:1:MET)
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.
-8.63-6.1151.719-1.806-2.428-0.014
Interaction energy analysis for fragmet #1(D:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.027
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].
3D3TYR0-0.034-0.0273.368-3.393-1.6990.038-0.812-0.9200.000
4D4SER00.0360.0115.4971.0431.0430.0000.0000.0000.000
5D5PRO0-0.030-0.0186.875-0.210-0.2100.0000.0000.0000.000
6D6LEU00.0190.0039.1280.1200.1200.0000.0000.0000.000
7D7GLN0-0.066-0.0282.508-4.148-3.3271.681-0.994-1.508-0.014
8D8ASP-1-0.894-0.9466.612-2.152-2.1520.0000.0000.0000.000
9D9LEU0-0.0270.0028.9750.2740.2740.0000.0000.0000.000
10D10PRO0-0.016-0.00112.025-0.025-0.0250.0000.0000.0000.000
11D11ALA00.0680.01714.584-0.010-0.0100.0000.0000.0000.000
12D12ASP-1-0.843-0.92215.698-0.404-0.4040.0000.0000.0000.000
13D13LEU0-0.051-0.00315.5070.0460.0460.0000.0000.0000.000
14D14ILE00.0380.02211.9220.0220.0220.0000.0000.0000.000
15D15ASP-1-0.861-0.93416.316-0.394-0.3940.0000.0000.0000.000
16D16ARG10.7640.87819.5390.4410.4410.0000.0000.0000.000
17D17ALA00.0290.00017.5880.0290.0290.0000.0000.0000.000
18D18ALA00.0070.00118.5890.0250.0250.0000.0000.0000.000
19D19ARG10.7860.88220.1180.3320.3320.0000.0000.0000.000
20D20VAL0-0.053-0.01022.2110.0280.0280.0000.0000.0000.000
21D21ARG10.8500.90824.2620.2700.2700.0000.0000.0000.000
22D22LEU0-0.0160.00327.5200.0150.0150.0000.0000.0000.000
23D23ALA00.0130.00124.752-0.017-0.0170.0000.0000.0000.000
24D24CYS0-0.042-0.00526.5990.0190.0190.0000.0000.0000.000
25D25PHE00.0460.00922.809-0.027-0.0270.0000.0000.0000.000
26D26ASP-1-0.723-0.83528.227-0.178-0.1780.0000.0000.0000.000
27D27VAL0-0.037-0.03829.180-0.013-0.0130.0000.0000.0000.000
28D28ASP-1-0.743-0.86830.237-0.186-0.1860.0000.0000.0000.000
29D29GLY00.0670.04629.629-0.003-0.0030.0000.0000.0000.000
30D30THR0-0.037-0.01725.274-0.026-0.0260.0000.0000.0000.000
31D31LEU0-0.029-0.02125.251-0.027-0.0270.0000.0000.0000.000
32D32THR0-0.031-0.02627.2180.0060.0060.0000.0000.0000.000
33D33ASP-1-0.754-0.85727.912-0.213-0.2130.0000.0000.0000.000
34D34GLY0-0.031-0.02828.8730.0090.0090.0000.0000.0000.000
35D35ARG10.7950.89330.6230.1980.1980.0000.0000.0000.000
36D36LEU0-0.033-0.00534.395-0.004-0.0040.0000.0000.0000.000
37D37TYR0-0.068-0.04432.5300.0090.0090.0000.0000.0000.000
38D38TYR0-0.053-0.04939.0830.0020.0020.0000.0000.0000.000
39D39ASP-1-0.788-0.89142.828-0.086-0.0860.0000.0000.0000.000
40D40HIS0-0.041-0.01945.3400.0020.0020.0000.0000.0000.000
41D41ALA0-0.041-0.01748.8920.0020.0020.0000.0000.0000.000
42D42GLY0-0.0020.00547.2400.0010.0010.0000.0000.0000.000
43D43ASN0-0.098-0.05745.265-0.004-0.0040.0000.0000.0000.000
44D44GLU-1-0.787-0.88440.197-0.134-0.1340.0000.0000.0000.000
45D45SER0-0.045-0.02538.2610.0020.0020.0000.0000.0000.000
46D46LYS10.8020.90034.0650.1540.1540.0000.0000.0000.000
47D47ALA00.0290.03330.4600.0020.0020.0000.0000.0000.000
48D48PHE00.0330.00928.848-0.006-0.0060.0000.0000.0000.000
49D49ASN00.0100.00623.0420.0030.0030.0000.0000.0000.000
50D50VAL00.0280.00423.3050.0010.0010.0000.0000.0000.000
51D51LEU00.0080.00818.427-0.002-0.0020.0000.0000.0000.000
52D52ASP-1-0.791-0.91121.239-0.432-0.4320.0000.0000.0000.000
53D53GLY00.001-0.00422.9210.0030.0030.0000.0000.0000.000
54D54GLN0-0.025-0.01120.3550.0050.0050.0000.0000.0000.000
55D55GLY00.032-0.00420.434-0.004-0.0040.0000.0000.0000.000
56D56LEU00.0210.00421.2260.0070.0070.0000.0000.0000.000
57D57LYS10.8710.95024.6780.2060.2060.0000.0000.0000.000
58D58GLN00.0220.01520.3280.0380.0380.0000.0000.0000.000
59D59LEU00.0010.00820.8630.0000.0000.0000.0000.0000.000
60D60GLU-1-0.745-0.85523.749-0.198-0.1980.0000.0000.0000.000
61D61HIS0-0.081-0.04424.6350.0220.0220.0000.0000.0000.000
62D62ALA00.0000.01122.5610.0130.0130.0000.0000.0000.000
63D63GLY00.0130.01324.6060.0000.0000.0000.0000.0000.000
64D64ILE0-0.086-0.03622.407-0.001-0.0010.0000.0000.0000.000
65D65HIS0-0.054-0.03626.7440.0050.0050.0000.0000.0000.000
66D66VAL0-0.008-0.00926.375-0.015-0.0150.0000.0000.0000.000
67D67ALA0-0.002-0.00628.9490.0190.0190.0000.0000.0000.000
68D68LEU0-0.029-0.00329.691-0.014-0.0140.0000.0000.0000.000
69D69ILE00.0200.00432.2820.0170.0170.0000.0000.0000.000
70D70THR00.0370.02133.918-0.005-0.0050.0000.0000.0000.000
71D71ALA00.0190.00736.1770.0080.0080.0000.0000.0000.000
72D72ARG10.7770.85333.8810.1890.1890.0000.0000.0000.000
73D73ALA00.0240.00039.968-0.003-0.0030.0000.0000.0000.000
74D74SER0-0.0110.00138.5500.0030.0030.0000.0000.0000.000
75D75LEU00.0840.02539.604-0.007-0.0070.0000.0000.0000.000
76D76SER00.0200.00037.402-0.001-0.0010.0000.0000.0000.000
77D77ALA0-0.0090.00335.137-0.007-0.0070.0000.0000.0000.000
78D78GLU-1-0.816-0.89335.484-0.139-0.1390.0000.0000.0000.000
79D79LYS10.8490.91537.2800.1250.1250.0000.0000.0000.000
80D80ARG10.9000.94927.1950.2330.2330.0000.0000.0000.000
81D81GLY00.0670.02232.685-0.011-0.0110.0000.0000.0000.000
82D82GLN0-0.063-0.05033.867-0.001-0.0010.0000.0000.0000.000
83D83ASP-1-0.860-0.90433.204-0.139-0.1390.0000.0000.0000.000
84D84LEU0-0.100-0.07027.984-0.009-0.0090.0000.0000.0000.000
85D85GLY0-0.0060.01330.338-0.007-0.0070.0000.0000.0000.000
86D86LEU0-0.026-0.01728.438-0.006-0.0060.0000.0000.0000.000
87D87HIS0-0.034-0.02532.5040.0090.0090.0000.0000.0000.000
88D88VAL00.0070.00133.645-0.013-0.0130.0000.0000.0000.000
89D89GLN0-0.017-0.00836.1540.0080.0080.0000.0000.0000.000
90D90ILE00.0110.00637.436-0.008-0.0080.0000.0000.0000.000
91D91GLY0-0.0070.00740.0990.0060.0060.0000.0000.0000.000
92D92VAL0-0.027-0.01737.9690.0060.0060.0000.0000.0000.000
93D93LYS10.9540.96840.0530.0970.0970.0000.0000.0000.000
94D94ASN0-0.003-0.01239.420-0.005-0.0050.0000.0000.0000.000
95D95LYS10.8420.91032.9520.2030.2030.0000.0000.0000.000
96D96ARG10.9771.01035.5100.1430.1430.0000.0000.0000.000
97D97LEU0-0.040-0.02136.6420.0000.0000.0000.0000.0000.000
98D98ALA00.0360.03036.9930.0030.0030.0000.0000.0000.000
99D99VAL00.0520.02132.3200.0000.0000.0000.0000.0000.000
100D100LEU00.0130.00735.0110.0000.0000.0000.0000.0000.000
101D101ALA0-0.022-0.00237.4490.0050.0050.0000.0000.0000.000
102D102LEU00.0400.01433.7960.0030.0030.0000.0000.0000.000
103D103CYS0-0.042-0.00534.009-0.007-0.0070.0000.0000.0000.000
104D104GLN0-0.041-0.02335.5920.0090.0090.0000.0000.0000.000
105D105GLU-1-0.882-0.93137.138-0.144-0.1440.0000.0000.0000.000
106D106HIS10.8230.90834.2880.1670.1670.0000.0000.0000.000
107D107GLY0-0.0130.01135.600-0.002-0.0020.0000.0000.0000.000
108D108LEU0-0.037-0.01130.853-0.003-0.0030.0000.0000.0000.000
109D109SER00.010-0.00332.1920.0110.0110.0000.0000.0000.000
110D110LEU00.010-0.01131.586-0.010-0.0100.0000.0000.0000.000
111D111ASP-1-0.839-0.92528.303-0.240-0.2400.0000.0000.0000.000
112D112GLN00.0280.02526.922-0.011-0.0110.0000.0000.0000.000
113D113VAL0-0.013-0.00327.669-0.003-0.0030.0000.0000.0000.000
114D114LEU00.0100.01621.291-0.013-0.0130.0000.0000.0000.000
115D115PHE0-0.035-0.03025.3830.0270.0270.0000.0000.0000.000
116D116MET0-0.0060.01420.859-0.015-0.0150.0000.0000.0000.000
117D117GLY00.012-0.01025.5780.0240.0240.0000.0000.0000.000
118D118ASP-1-0.896-0.96326.683-0.268-0.2680.0000.0000.0000.000
119D119ASP-1-0.803-0.89328.454-0.175-0.1750.0000.0000.0000.000
120D120LEU00.002-0.02032.079-0.001-0.0010.0000.0000.0000.000
121D121PRO0-0.048-0.03234.7390.0030.0030.0000.0000.0000.000
122D122ASP-1-0.736-0.86330.586-0.223-0.2230.0000.0000.0000.000
123D123LEU00.0080.02231.452-0.004-0.0040.0000.0000.0000.000
124D124PRO0-0.047-0.04132.980-0.001-0.0010.0000.0000.0000.000
125D125ALA0-0.019-0.01132.2600.0060.0060.0000.0000.0000.000
126D126LEU00.0070.01126.739-0.006-0.0060.0000.0000.0000.000
127D127LEU0-0.035-0.01929.100-0.008-0.0080.0000.0000.0000.000
128D128ALA0-0.051-0.02831.3340.0120.0120.0000.0000.0000.000
129D129VAL0-0.025-0.00527.3820.0090.0090.0000.0000.0000.000
130D130GLY00.0060.01126.716-0.004-0.0040.0000.0000.0000.000
131D131LEU0-0.042-0.02219.549-0.018-0.0180.0000.0000.0000.000
132D132PRO0-0.0150.01023.934-0.006-0.0060.0000.0000.0000.000
133D133VAL0-0.008-0.01619.668-0.026-0.0260.0000.0000.0000.000
134D134ALA00.0200.01021.9160.0350.0350.0000.0000.0000.000
135D135PRO0-0.0070.00721.352-0.046-0.0460.0000.0000.0000.000
136D136ALA00.0280.00419.7990.0290.0290.0000.0000.0000.000
137D137ASN0-0.071-0.04021.816-0.004-0.0040.0000.0000.0000.000
138D138ALA0-0.0050.01025.0790.0240.0240.0000.0000.0000.000
139D139HIS00.0570.03627.004-0.003-0.0030.0000.0000.0000.000
140D140PRO00.0490.01528.618-0.010-0.0100.0000.0000.0000.000
141D141TRP0-0.060-0.02729.399-0.003-0.0030.0000.0000.0000.000
142D142ILE0-0.048-0.01326.9720.0050.0050.0000.0000.0000.000
143D143ALA00.0320.01424.894-0.011-0.0110.0000.0000.0000.000
144D144GLU-1-0.841-0.92825.358-0.205-0.2050.0000.0000.0000.000
145D145ARG10.7520.86927.7990.1920.1920.0000.0000.0000.000
146D146VAL00.0010.01623.0650.0040.0040.0000.0000.0000.000
147D147GLN00.007-0.00321.157-0.020-0.0200.0000.0000.0000.000
148D148TRP00.0370.02415.802-0.017-0.0170.0000.0000.0000.000
149D149HIS0-0.003-0.00818.7310.0190.0190.0000.0000.0000.000
150D150THR0-0.035-0.02016.550-0.038-0.0380.0000.0000.0000.000
151D151ARG10.8660.9149.5231.4391.4390.0000.0000.0000.000
152D152ALA00.0010.01815.7640.0550.0550.0000.0000.0000.000
153D153ARG10.9060.94618.2400.3190.3190.0000.0000.0000.000
154D154GLY00.0570.02422.083-0.020-0.0200.0000.0000.0000.000
155D155GLY0-0.032-0.01124.6380.0190.0190.0000.0000.0000.000
156D156GLU-1-0.910-0.95321.774-0.320-0.3200.0000.0000.0000.000
157D157GLY0-0.0050.00519.425-0.035-0.0350.0000.0000.0000.000
158D158ALA0-0.0170.00318.748-0.057-0.0570.0000.0000.0000.000
159D159ALA00.0960.03419.206-0.035-0.0350.0000.0000.0000.000
160D160ARG10.8270.89415.0340.6690.6690.0000.0000.0000.000
161D161GLU-1-0.801-0.87613.615-0.969-0.9690.0000.0000.0000.000
162D162VAL00.0230.00615.454-0.069-0.0690.0000.0000.0000.000
163D163CYS0-0.078-0.03617.8230.0090.0090.0000.0000.0000.000
164D164ASP-1-0.762-0.84513.296-0.925-0.9250.0000.0000.0000.000
165D165VAL0-0.014-0.00512.649-0.053-0.0530.0000.0000.0000.000
166D166VAL00.0180.00314.4870.0090.0090.0000.0000.0000.000
167D167LEU0-0.023-0.01316.8600.0370.0370.0000.0000.0000.000
168D168ALA0-0.033-0.01312.0740.0380.0380.0000.0000.0000.000
169D169ALA0-0.015-0.00714.2030.0270.0270.0000.0000.0000.000
170D170GLN0-0.044-0.01115.8210.0970.0970.0000.0000.0000.000
171D171GLY00.0000.00415.7170.0550.0550.0000.0000.0000.000
172D172GLN0-0.006-0.00216.7850.0820.0820.0000.0000.0000.000
173D173VAL00.0060.01012.0710.0540.0540.0000.0000.0000.000
174D174ASP-1-0.848-0.92512.810-0.356-0.3560.0000.0000.0000.000
175D175SER0-0.049-0.03914.9830.0780.0780.0000.0000.0000.000
176D176ILE0-0.027-0.01317.1850.0410.0410.0000.0000.0000.000
177D177ILE00.0140.00111.8810.0280.0280.0000.0000.0000.000
178D178ALA00.0020.01516.2190.0570.0570.0000.0000.0000.000
179D179ARG10.8490.92918.5000.2610.2610.0000.0000.0000.000
180D180PHE0-0.062-0.03819.1710.0070.0070.0000.0000.0000.000
181D181SER0-0.033-0.02117.2860.0230.0230.0000.0000.0000.000
182D182ALA0-0.054-0.00919.3190.0300.0300.0000.0000.0000.000