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

tag_button

FMODB ID: 4JL3N

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1835936.361328
FMO2-HF: Nuclear repulsion 1767596.940435
FMO2-HF: Total energy -68339.420893
FMO2-MP2: Total energy -68539.749923


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.
-5.781-5.4645.612-2.535-3.395-0.008
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 : -0.029 / q_NPA : -0.031
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].
3D3TYR0-0.0030.0033.455-2.988-1.4450.019-0.715-0.8480.000
4D4SER00.0420.0145.5600.9580.9580.0000.0000.0000.000
5D5PRO0-0.039-0.0136.940-0.073-0.0730.0000.0000.0000.000
6D6LEU00.0320.0068.8260.1730.1730.0000.0000.0000.000
7D7GLN0-0.0210.0081.936-2.107-3.3335.593-1.820-2.547-0.008
8D8ASP-1-0.937-0.9796.809-1.560-1.5600.0000.0000.0000.000
9D9LEU0-0.043-0.0169.0500.2540.2540.0000.0000.0000.000
10D10PRO0-0.023-0.00711.950-0.023-0.0230.0000.0000.0000.000
11D11ALA00.0610.01314.486-0.013-0.0130.0000.0000.0000.000
12D12ASP-1-0.863-0.92415.620-0.385-0.3850.0000.0000.0000.000
13D13LEU0-0.061-0.03015.4360.0370.0370.0000.0000.0000.000
14D14ILE00.0300.01511.6450.0180.0180.0000.0000.0000.000
15D15ASP-1-0.890-0.94715.985-0.440-0.4400.0000.0000.0000.000
16D16ARG10.8500.92619.1480.4070.4070.0000.0000.0000.000
17D17ALA00.011-0.00517.3750.0310.0310.0000.0000.0000.000
18D18ALA00.0290.01218.4440.0190.0190.0000.0000.0000.000
19D19ARG10.8720.93919.9140.3240.3240.0000.0000.0000.000
20D20VAL0-0.042-0.00422.1530.0320.0320.0000.0000.0000.000
21D21ARG10.8710.94224.2160.2690.2690.0000.0000.0000.000
22D22LEU0-0.004-0.00127.1550.0140.0140.0000.0000.0000.000
23D23ALA00.0090.00924.788-0.014-0.0140.0000.0000.0000.000
24D24CYS0-0.059-0.02226.6160.0220.0220.0000.0000.0000.000
25D25PHE00.022-0.00623.274-0.019-0.0190.0000.0000.0000.000
26D26ASP-1-0.775-0.89528.555-0.176-0.1760.0000.0000.0000.000
27D27VAL0-0.062-0.04429.680-0.007-0.0070.0000.0000.0000.000
28D28ASP-1-0.860-0.97030.500-0.170-0.1700.0000.0000.0000.000
29D29GLY00.1020.06829.8150.0020.0020.0000.0000.0000.000
30D30THR0-0.024-0.01025.806-0.024-0.0240.0000.0000.0000.000
31D31LEU0-0.046-0.03425.613-0.023-0.0230.0000.0000.0000.000
32D32THR0-0.061-0.01727.5800.0100.0100.0000.0000.0000.000
33D33ASP-1-0.804-0.90528.396-0.195-0.1950.0000.0000.0000.000
34D34GLY0-0.019-0.02029.3240.0060.0060.0000.0000.0000.000
35D35ARG10.8250.92731.1290.1710.1710.0000.0000.0000.000
36D36LEU0-0.0020.00434.860-0.003-0.0030.0000.0000.0000.000
37D37TYR0-0.046-0.02833.4840.0070.0070.0000.0000.0000.000
38D38TYR0-0.0090.00039.8390.0010.0010.0000.0000.0000.000
39D39ASP-1-0.830-0.91543.599-0.077-0.0770.0000.0000.0000.000
40D40HIS0-0.034-0.02745.8580.0010.0010.0000.0000.0000.000
41D41ALA0-0.0080.00349.1590.0030.0030.0000.0000.0000.000
42D42GLY0-0.037-0.01647.7200.0000.0000.0000.0000.0000.000
43D43ASN0-0.071-0.04146.021-0.003-0.0030.0000.0000.0000.000
44D44GLU-1-0.882-0.93841.188-0.110-0.1100.0000.0000.0000.000
45D45SER0-0.075-0.03738.1770.0000.0000.0000.0000.0000.000
46D46LYS10.9140.95734.5080.1470.1470.0000.0000.0000.000
47D47ALA00.0100.01731.0650.0050.0050.0000.0000.0000.000
48D48PHE00.0280.01529.157-0.009-0.0090.0000.0000.0000.000
49D49ASN00.0800.04522.948-0.007-0.0070.0000.0000.0000.000
50D50VAL0-0.006-0.02123.311-0.008-0.0080.0000.0000.0000.000
51D51LEU00.0110.00818.3080.0000.0000.0000.0000.0000.000
52D52ASP-1-0.771-0.89121.280-0.395-0.3950.0000.0000.0000.000
53D53GLY0-0.026-0.02223.0560.0010.0010.0000.0000.0000.000
54D54GLN0-0.064-0.03520.8020.0030.0030.0000.0000.0000.000
55D55GLY00.0390.00220.428-0.007-0.0070.0000.0000.0000.000
56D56LEU00.0290.00621.2350.0000.0000.0000.0000.0000.000
57D57LYS10.9820.99724.6330.1980.1980.0000.0000.0000.000
58D58GLN0-0.034-0.00319.1180.0480.0480.0000.0000.0000.000
59D59LEU00.0220.01020.799-0.003-0.0030.0000.0000.0000.000
60D60GLU-1-0.820-0.91223.649-0.198-0.1980.0000.0000.0000.000
61D61HIS0-0.105-0.06124.0970.0160.0160.0000.0000.0000.000
62D62ALA0-0.0140.00122.3970.0120.0120.0000.0000.0000.000
63D63GLY0-0.021-0.01024.452-0.004-0.0040.0000.0000.0000.000
64D64ILE0-0.087-0.03222.3690.0060.0060.0000.0000.0000.000
65D65HIS00.0120.01326.7890.0080.0080.0000.0000.0000.000
66D66VAL00.0120.01026.535-0.017-0.0170.0000.0000.0000.000
67D67ALA0-0.006-0.00729.1870.0190.0190.0000.0000.0000.000
68D68LEU0-0.030-0.00629.916-0.015-0.0150.0000.0000.0000.000
69D69ILE00.0240.00232.4250.0150.0150.0000.0000.0000.000
70D70THR00.0040.01134.047-0.006-0.0060.0000.0000.0000.000
71D71ALA00.0280.00836.5550.0060.0060.0000.0000.0000.000
72D72ARG10.8570.94334.3100.1670.1670.0000.0000.0000.000
73D73ALA00.0560.01540.720-0.003-0.0030.0000.0000.0000.000
74D74SER0-0.007-0.00939.1250.0020.0020.0000.0000.0000.000
75D75LEU00.1250.04340.513-0.005-0.0050.0000.0000.0000.000
76D76SER0-0.0050.00037.2660.0000.0000.0000.0000.0000.000
77D77ALA0-0.0010.00135.577-0.005-0.0050.0000.0000.0000.000
78D78GLU-1-0.817-0.88935.852-0.133-0.1330.0000.0000.0000.000
79D79LYS10.8680.91337.4630.1120.1120.0000.0000.0000.000
80D80ARG10.9300.96927.7990.2000.2000.0000.0000.0000.000
81D81GLY00.0620.01932.999-0.009-0.0090.0000.0000.0000.000
82D82GLN0-0.070-0.04633.9330.0010.0010.0000.0000.0000.000
83D83ASP-1-0.899-0.93033.243-0.132-0.1320.0000.0000.0000.000
84D84LEU0-0.124-0.07127.978-0.005-0.0050.0000.0000.0000.000
85D85GLY0-0.0170.01430.468-0.008-0.0080.0000.0000.0000.000
86D86LEU0-0.010-0.01228.954-0.008-0.0080.0000.0000.0000.000
87D87HIS00.0120.02032.6920.0080.0080.0000.0000.0000.000
88D88VAL00.0040.00233.917-0.012-0.0120.0000.0000.0000.000
89D89GLN00.0030.00436.3910.0050.0050.0000.0000.0000.000
90D90ILE0-0.025-0.00637.854-0.006-0.0060.0000.0000.0000.000
91D91GLY0-0.0150.00340.2750.0050.0050.0000.0000.0000.000
92D92VAL0-0.019-0.01138.5020.0050.0050.0000.0000.0000.000
93D93LYS10.9480.97040.7180.0920.0920.0000.0000.0000.000
94D94ASN00.0200.00639.494-0.006-0.0060.0000.0000.0000.000
95D95LYS10.9090.96134.0330.1790.1790.0000.0000.0000.000
96D96ARG10.9921.01435.6720.1340.1340.0000.0000.0000.000
97D97LEU0-0.031-0.02636.697-0.001-0.0010.0000.0000.0000.000
98D98ALA00.0180.01837.2510.0020.0020.0000.0000.0000.000
99D99VAL00.0560.02032.4370.0000.0000.0000.0000.0000.000
100D100LEU0-0.009-0.02635.231-0.001-0.0010.0000.0000.0000.000
101D101ALA0-0.040-0.01237.4100.0030.0030.0000.0000.0000.000
102D102LEU00.0380.00733.8900.0030.0030.0000.0000.0000.000
103D103CYS0-0.054-0.00533.921-0.006-0.0060.0000.0000.0000.000
104D104GLN0-0.033-0.00435.6630.0050.0050.0000.0000.0000.000
105D105GLU-1-0.930-0.96337.286-0.139-0.1390.0000.0000.0000.000
106D106HIS10.8440.92534.1720.1640.1640.0000.0000.0000.000
107D107GLY0-0.0100.01235.328-0.003-0.0030.0000.0000.0000.000
108D108LEU0-0.053-0.02730.786-0.006-0.0060.0000.0000.0000.000
109D109SER00.0220.00232.1120.0140.0140.0000.0000.0000.000
110D110LEU00.040-0.00931.663-0.008-0.0080.0000.0000.0000.000
111D111ASP-1-0.933-0.97428.433-0.235-0.2350.0000.0000.0000.000
112D112GLN00.0390.02927.058-0.010-0.0100.0000.0000.0000.000
113D113VAL0-0.0050.00127.548-0.005-0.0050.0000.0000.0000.000
114D114LEU00.0180.02321.394-0.010-0.0100.0000.0000.0000.000
115D115PHE0-0.030-0.03425.5230.0230.0230.0000.0000.0000.000
116D116MET00.0110.01421.761-0.013-0.0130.0000.0000.0000.000
117D117GLY00.001-0.01025.9210.0200.0200.0000.0000.0000.000
118D118ASP-1-0.863-0.93427.152-0.228-0.2280.0000.0000.0000.000
119D119ASP-1-0.819-0.91029.017-0.158-0.1580.0000.0000.0000.000
120D120LEU0-0.017-0.02932.552-0.001-0.0010.0000.0000.0000.000
121D121PRO0-0.041-0.02335.2000.0020.0020.0000.0000.0000.000
122D122ASP-1-0.777-0.90031.163-0.198-0.1980.0000.0000.0000.000
123D123LEU0-0.006-0.00131.575-0.007-0.0070.0000.0000.0000.000
124D124PRO0-0.074-0.04333.333-0.002-0.0020.0000.0000.0000.000
125D125ALA00.0080.00332.1460.0020.0020.0000.0000.0000.000
126D126LEU0-0.0060.01027.090-0.007-0.0070.0000.0000.0000.000
127D127LEU0-0.019-0.02129.220-0.009-0.0090.0000.0000.0000.000
128D128ALA0-0.052-0.02131.6830.0060.0060.0000.0000.0000.000
129D129VAL0-0.065-0.02127.4180.0040.0040.0000.0000.0000.000
130D130GLY00.0270.02026.886-0.003-0.0030.0000.0000.0000.000
131D131LEU0-0.064-0.03119.775-0.017-0.0170.0000.0000.0000.000
132D132PRO00.0010.01824.157-0.006-0.0060.0000.0000.0000.000
133D133VAL0-0.017-0.02119.857-0.025-0.0250.0000.0000.0000.000
134D134ALA00.0250.00822.2990.0310.0310.0000.0000.0000.000
135D135PRO00.0170.01621.781-0.037-0.0370.0000.0000.0000.000
136D136ALA00.0370.01820.3480.0250.0250.0000.0000.0000.000
137D137ASN0-0.103-0.04522.2820.0000.0000.0000.0000.0000.000
138D138ALA00.0220.02525.3680.0210.0210.0000.0000.0000.000
139D139HIS00.0740.04027.3120.0010.0010.0000.0000.0000.000
140D140PRO00.0410.00328.961-0.009-0.0090.0000.0000.0000.000
141D141TRP0-0.023-0.00629.942-0.002-0.0020.0000.0000.0000.000
142D142ILE0-0.0100.01827.5470.0030.0030.0000.0000.0000.000
143D143ALA00.0280.01125.468-0.010-0.0100.0000.0000.0000.000
144D144GLU-1-0.890-0.95625.792-0.183-0.1830.0000.0000.0000.000
145D145ARG10.7620.87328.1510.1760.1760.0000.0000.0000.000
146D146VAL0-0.0290.00323.2310.0000.0000.0000.0000.0000.000
147D147GLN0-0.010-0.01021.497-0.021-0.0210.0000.0000.0000.000
148D148TRP00.0230.01516.014-0.001-0.0010.0000.0000.0000.000
149D149HIS0-0.020-0.01518.7150.0200.0200.0000.0000.0000.000
150D150THR0-0.046-0.01816.896-0.034-0.0340.0000.0000.0000.000
151D151ARG10.9240.94811.3261.0851.0850.0000.0000.0000.000
152D152ALA0-0.029-0.00116.6010.0580.0580.0000.0000.0000.000
153D153ARG10.9830.98918.9120.2730.2730.0000.0000.0000.000
154D154GLY00.0400.01722.684-0.017-0.0170.0000.0000.0000.000
155D155GLY0-0.021-0.01225.1120.0160.0160.0000.0000.0000.000
156D156GLU-1-1.012-1.02022.312-0.257-0.2570.0000.0000.0000.000
157D157GLY00.0070.00819.639-0.033-0.0330.0000.0000.0000.000
158D158ALA00.0080.02019.053-0.056-0.0560.0000.0000.0000.000
159D159ALA00.0810.02619.647-0.032-0.0320.0000.0000.0000.000
160D160ARG10.8340.92016.5270.5320.5320.0000.0000.0000.000
161D161GLU-1-0.803-0.89914.280-0.785-0.7850.0000.0000.0000.000
162D162VAL00.0170.01015.612-0.075-0.0750.0000.0000.0000.000
163D163CYS0-0.070-0.04217.630-0.006-0.0060.0000.0000.0000.000
164D164ASP-1-0.825-0.91513.542-0.790-0.7900.0000.0000.0000.000
165D165VAL0-0.0060.00412.950-0.063-0.0630.0000.0000.0000.000
166D166VAL00.0160.01014.537-0.007-0.0070.0000.0000.0000.000
167D167LEU0-0.003-0.01016.6720.0250.0250.0000.0000.0000.000
168D168ALA0-0.045-0.02711.8510.0210.0210.0000.0000.0000.000
169D169ALA0-0.020-0.00513.9490.0080.0080.0000.0000.0000.000
170D170GLN0-0.079-0.03815.5490.0800.0800.0000.0000.0000.000
171D171GLY0-0.0030.00915.6930.0590.0590.0000.0000.0000.000
172D172GLN0-0.022-0.02116.7570.0960.0960.0000.0000.0000.000
173D173VAL00.0100.00512.0010.0580.0580.0000.0000.0000.000
174D174ASP-1-0.856-0.92612.507-0.381-0.3810.0000.0000.0000.000
175D175SER0-0.040-0.02214.8790.0890.0890.0000.0000.0000.000
176D176ILE0-0.021-0.00817.2690.0480.0480.0000.0000.0000.000
177D177ILE00.025-0.00312.1370.0310.0310.0000.0000.0000.000
178D178ALA0-0.0020.02816.4100.0580.0580.0000.0000.0000.000
179D179ARG10.9180.97018.4490.2400.2400.0000.0000.0000.000
180D180PHE0-0.076-0.04119.0630.0190.0190.0000.0000.0000.000
181D181SER0-0.037-0.02917.3150.0220.0220.0000.0000.0000.000
182D182ALA0-0.052-0.01119.3940.0310.0310.0000.0000.0000.000