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: 5JN3Z

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1836241.801831
FMO2-HF: Nuclear repulsion 1767901.545781
FMO2-HF: Total energy -68340.25605
FMO2-MP2: Total energy -68540.550411


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.
-8.811-6.4972.012-1.848-2.479-0.014
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 : -0.039 / q_NPA : -0.032
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].
3D3TYR0-0.026-0.0213.528-3.113-1.5530.009-0.721-0.8490.001
4D4SER00.0360.0135.6311.0241.0240.0000.0000.0000.000
5D5PRO0-0.031-0.0137.198-0.161-0.1610.0000.0000.0000.000
6D6LEU00.0230.0059.1070.1510.1510.0000.0000.0000.000
7D7GLN0-0.069-0.0262.470-4.342-3.5882.003-1.127-1.630-0.015
8D8ASP-1-0.895-0.9536.445-2.361-2.3610.0000.0000.0000.000
9D9LEU0-0.035-0.0059.0500.3000.3000.0000.0000.0000.000
10D10PRO0-0.028-0.00312.068-0.018-0.0180.0000.0000.0000.000
11D11ALA00.0770.01214.627-0.004-0.0040.0000.0000.0000.000
12D12ASP-1-0.832-0.91515.740-0.442-0.4420.0000.0000.0000.000
13D13LEU0-0.060-0.02515.7960.0440.0440.0000.0000.0000.000
14D14ILE00.0400.01911.9260.0300.0300.0000.0000.0000.000
15D15ASP-1-0.885-0.94116.231-0.445-0.4450.0000.0000.0000.000
16D16ARG10.7990.90119.2290.4580.4580.0000.0000.0000.000
17D17ALA00.019-0.00217.6750.0350.0350.0000.0000.0000.000
18D18ALA00.0130.00818.4690.0240.0240.0000.0000.0000.000
19D19ARG10.8540.92120.0760.3520.3520.0000.0000.0000.000
20D20VAL0-0.052-0.00722.5050.0310.0310.0000.0000.0000.000
21D21ARG10.8620.92124.4240.2770.2770.0000.0000.0000.000
22D22LEU0-0.0120.00227.4920.0160.0160.0000.0000.0000.000
23D23ALA00.0140.00524.984-0.017-0.0170.0000.0000.0000.000
24D24CYS0-0.060-0.01826.8210.0240.0240.0000.0000.0000.000
25D25PHE00.030-0.00423.223-0.022-0.0220.0000.0000.0000.000
26D26ASP-1-0.734-0.84928.622-0.183-0.1830.0000.0000.0000.000
27D27VAL0-0.048-0.04329.676-0.009-0.0090.0000.0000.0000.000
28D28ASP-1-0.800-0.89030.431-0.185-0.1850.0000.0000.0000.000
29D29GLY00.1030.06229.6560.0020.0020.0000.0000.0000.000
30D30THR0-0.027-0.01025.680-0.027-0.0270.0000.0000.0000.000
31D31LEU0-0.031-0.02625.531-0.025-0.0250.0000.0000.0000.000
32D32THR0-0.057-0.02727.5150.0130.0130.0000.0000.0000.000
33D33ASP-1-0.766-0.86228.188-0.211-0.2110.0000.0000.0000.000
34D34GLY00.0070.00029.1180.0050.0050.0000.0000.0000.000
35D35ARG10.7730.87730.8230.1930.1930.0000.0000.0000.000
36D36LEU0-0.017-0.00134.649-0.003-0.0030.0000.0000.0000.000
37D37TYR0-0.046-0.02833.3530.0070.0070.0000.0000.0000.000
38D38TYR0-0.032-0.03139.7960.0010.0010.0000.0000.0000.000
39D39ASP-1-0.818-0.91543.524-0.080-0.0800.0000.0000.0000.000
40D40HIS0-0.047-0.02945.9120.0010.0010.0000.0000.0000.000
41D41ALA0-0.020-0.00449.1860.0030.0030.0000.0000.0000.000
42D42GLY0-0.023-0.00847.5970.0000.0000.0000.0000.0000.000
43D43ASN0-0.071-0.03945.857-0.004-0.0040.0000.0000.0000.000
44D44GLU-1-0.836-0.89740.972-0.123-0.1230.0000.0000.0000.000
45D45SER0-0.087-0.04638.2460.0010.0010.0000.0000.0000.000
46D46LYS10.8590.91234.2820.1570.1570.0000.0000.0000.000
47D47ALA00.0160.01431.1710.0060.0060.0000.0000.0000.000
48D48PHE00.0220.00929.282-0.010-0.0100.0000.0000.0000.000
49D49ASN00.0290.00123.3260.0010.0010.0000.0000.0000.000
50D50VAL00.003-0.01423.524-0.008-0.0080.0000.0000.0000.000
51D51LEU00.0290.02418.5520.0010.0010.0000.0000.0000.000
52D52ASP-1-0.778-0.89321.348-0.419-0.4190.0000.0000.0000.000
53D53GLY0-0.022-0.01723.1240.0020.0020.0000.0000.0000.000
54D54GLN0-0.046-0.02720.6490.0040.0040.0000.0000.0000.000
55D55GLY00.034-0.00820.502-0.006-0.0060.0000.0000.0000.000
56D56LEU00.0150.00521.3090.0010.0010.0000.0000.0000.000
57D57LYS10.9210.98724.7070.1860.1860.0000.0000.0000.000
58D58GLN00.0220.02719.5300.0440.0440.0000.0000.0000.000
59D59LEU00.0210.01120.961-0.002-0.0020.0000.0000.0000.000
60D60GLU-1-0.760-0.88123.769-0.199-0.1990.0000.0000.0000.000
61D61HIS0-0.095-0.05824.4410.0210.0210.0000.0000.0000.000
62D62ALA0-0.020-0.00222.4560.0150.0150.0000.0000.0000.000
63D63GLY0-0.008-0.00724.526-0.005-0.0050.0000.0000.0000.000
64D64ILE0-0.084-0.03022.6380.0040.0040.0000.0000.0000.000
65D65HIS0-0.023-0.00127.1100.0120.0120.0000.0000.0000.000
66D66VAL0-0.018-0.01226.665-0.020-0.0200.0000.0000.0000.000
67D67ALA0-0.004-0.00629.3940.0200.0200.0000.0000.0000.000
68D68LEU0-0.036-0.00629.826-0.017-0.0170.0000.0000.0000.000
69D69ILE00.017-0.00632.5180.0150.0150.0000.0000.0000.000
70D70THR00.0350.02534.082-0.008-0.0080.0000.0000.0000.000
71D71ALA00.0250.00936.5730.0070.0070.0000.0000.0000.000
72D72ARG10.7830.87434.1530.1860.1860.0000.0000.0000.000
73D73ALA00.0570.01840.721-0.003-0.0030.0000.0000.0000.000
74D74SER0-0.008-0.00339.1300.0020.0020.0000.0000.0000.000
75D75LEU00.1010.03340.521-0.005-0.0050.0000.0000.0000.000
76D76SER00.007-0.00137.804-0.001-0.0010.0000.0000.0000.000
77D77ALA00.0100.00835.597-0.004-0.0040.0000.0000.0000.000
78D78GLU-1-0.814-0.88835.923-0.135-0.1350.0000.0000.0000.000
79D79LYS10.8500.90637.5090.1130.1130.0000.0000.0000.000
80D80ARG10.9200.96427.6690.2110.2110.0000.0000.0000.000
81D81GLY00.0600.01933.070-0.008-0.0080.0000.0000.0000.000
82D82GLN0-0.068-0.04634.0070.0010.0010.0000.0000.0000.000
83D83ASP-1-0.869-0.90833.236-0.129-0.1290.0000.0000.0000.000
84D84LEU0-0.107-0.08728.078-0.003-0.0030.0000.0000.0000.000
85D85GLY0-0.0040.01830.542-0.008-0.0080.0000.0000.0000.000
86D86LEU0-0.003-0.00528.755-0.008-0.0080.0000.0000.0000.000
87D87HIS0-0.050-0.02532.7670.0080.0080.0000.0000.0000.000
88D88VAL00.0210.00934.063-0.014-0.0140.0000.0000.0000.000
89D89GLN00.0030.00636.5160.0060.0060.0000.0000.0000.000
90D90ILE0-0.030-0.01237.934-0.007-0.0070.0000.0000.0000.000
91D91GLY00.0000.00840.3380.0060.0060.0000.0000.0000.000
92D92VAL0-0.029-0.01338.5230.0050.0050.0000.0000.0000.000
93D93LYS10.9480.96640.7510.1000.1000.0000.0000.0000.000
94D94ASN00.010-0.01339.650-0.007-0.0070.0000.0000.0000.000
95D95LYS10.8660.92333.5390.2020.2020.0000.0000.0000.000
96D96ARG10.9941.01435.8010.1500.1500.0000.0000.0000.000
97D97LEU0-0.035-0.01936.821-0.001-0.0010.0000.0000.0000.000
98D98ALA00.0330.02637.3930.0030.0030.0000.0000.0000.000
99D99VAL00.0600.01932.4890.0010.0010.0000.0000.0000.000
100D100LEU0-0.012-0.01635.4100.0000.0000.0000.0000.0000.000
101D101ALA0-0.034-0.01337.6240.0040.0040.0000.0000.0000.000
102D102LEU00.0410.01533.9820.0040.0040.0000.0000.0000.000
103D103CYS0-0.064-0.01934.426-0.006-0.0060.0000.0000.0000.000
104D104GLN0-0.025-0.00235.9420.0070.0070.0000.0000.0000.000
105D105GLU-1-0.886-0.94037.720-0.144-0.1440.0000.0000.0000.000
106D106HIS10.8320.91634.4970.1700.1700.0000.0000.0000.000
107D107GLY0-0.0080.01435.634-0.003-0.0030.0000.0000.0000.000
108D108LEU0-0.046-0.02131.036-0.005-0.0050.0000.0000.0000.000
109D109SER00.0130.00432.2180.0140.0140.0000.0000.0000.000
110D110LEU00.041-0.00231.962-0.008-0.0080.0000.0000.0000.000
111D111ASP-1-0.897-0.95628.778-0.257-0.2570.0000.0000.0000.000
112D112GLN00.0360.02927.366-0.009-0.0090.0000.0000.0000.000
113D113VAL0-0.009-0.00427.849-0.003-0.0030.0000.0000.0000.000
114D114LEU00.0130.01621.428-0.013-0.0130.0000.0000.0000.000
115D115PHE0-0.033-0.02925.7150.0260.0260.0000.0000.0000.000
116D116MET00.0110.02021.523-0.017-0.0170.0000.0000.0000.000
117D117GLY00.002-0.01225.9620.0240.0240.0000.0000.0000.000
118D118ASP-1-0.900-0.95927.095-0.263-0.2630.0000.0000.0000.000
119D119ASP-1-0.813-0.89628.916-0.180-0.1800.0000.0000.0000.000
120D120LEU0-0.004-0.02732.447-0.001-0.0010.0000.0000.0000.000
121D121PRO0-0.038-0.02135.2570.0020.0020.0000.0000.0000.000
122D122ASP-1-0.741-0.87031.100-0.222-0.2220.0000.0000.0000.000
123D123LEU0-0.0170.00131.704-0.007-0.0070.0000.0000.0000.000
124D124PRO0-0.051-0.03933.372-0.002-0.0020.0000.0000.0000.000
125D125ALA00.0010.00032.2990.0020.0020.0000.0000.0000.000
126D126LEU0-0.0110.00927.066-0.007-0.0070.0000.0000.0000.000
127D127LEU0-0.022-0.02229.310-0.010-0.0100.0000.0000.0000.000
128D128ALA0-0.054-0.02231.7670.0070.0070.0000.0000.0000.000
129D129VAL0-0.065-0.02327.6060.0060.0060.0000.0000.0000.000
130D130GLY00.0400.02627.134-0.005-0.0050.0000.0000.0000.000
131D131LEU0-0.063-0.03219.949-0.020-0.0200.0000.0000.0000.000
132D132PRO0-0.0070.01524.340-0.005-0.0050.0000.0000.0000.000
133D133VAL0-0.011-0.01619.880-0.029-0.0290.0000.0000.0000.000
134D134ALA00.0120.00522.2650.0370.0370.0000.0000.0000.000
135D135PRO00.0150.01521.639-0.045-0.0450.0000.0000.0000.000
136D136ALA00.0280.01520.1200.0250.0250.0000.0000.0000.000
137D137ASN0-0.087-0.04322.058-0.002-0.0020.0000.0000.0000.000
138D138ALA00.0160.02225.1720.0250.0250.0000.0000.0000.000
139D139HIS00.0700.04027.133-0.003-0.0030.0000.0000.0000.000
140D140PRO00.0420.00428.752-0.010-0.0100.0000.0000.0000.000
141D141TRP0-0.038-0.01429.775-0.002-0.0020.0000.0000.0000.000
142D142ILE0-0.0110.01027.5380.0040.0040.0000.0000.0000.000
143D143ALA00.0310.01425.222-0.012-0.0120.0000.0000.0000.000
144D144GLU-1-0.863-0.92825.681-0.220-0.2200.0000.0000.0000.000
145D145ARG10.7510.85828.0260.2060.2060.0000.0000.0000.000
146D146VAL0-0.0300.00023.2780.0030.0030.0000.0000.0000.000
147D147GLN0-0.014-0.00821.227-0.024-0.0240.0000.0000.0000.000
148D148TRP00.0370.01915.990-0.007-0.0070.0000.0000.0000.000
149D149HIS0-0.010-0.01418.6440.0220.0220.0000.0000.0000.000
150D150THR0-0.039-0.01416.791-0.044-0.0440.0000.0000.0000.000
151D151ARG10.8940.93910.7311.2931.2930.0000.0000.0000.000
152D152ALA0-0.0230.00116.3620.0650.0650.0000.0000.0000.000
153D153ARG10.9710.98918.6810.3120.3120.0000.0000.0000.000
154D154GLY00.0460.02022.457-0.015-0.0150.0000.0000.0000.000
155D155GLY0-0.017-0.00924.9500.0180.0180.0000.0000.0000.000
156D156GLU-1-0.985-1.00822.313-0.297-0.2970.0000.0000.0000.000
157D157GLY00.0180.01619.699-0.037-0.0370.0000.0000.0000.000
158D158ALA00.0000.01718.962-0.060-0.0600.0000.0000.0000.000
159D159ALA00.0970.03019.610-0.036-0.0360.0000.0000.0000.000
160D160ARG10.8250.90715.5000.5910.5910.0000.0000.0000.000
161D161GLU-1-0.810-0.90614.209-0.905-0.9050.0000.0000.0000.000
162D162VAL00.0170.01015.678-0.081-0.0810.0000.0000.0000.000
163D163CYS0-0.065-0.04417.789-0.003-0.0030.0000.0000.0000.000
164D164ASP-1-0.788-0.86613.605-0.868-0.8680.0000.0000.0000.000
165D165VAL0-0.0040.00412.929-0.056-0.0560.0000.0000.0000.000
166D166VAL00.0160.01314.7570.0000.0000.0000.0000.0000.000
167D167LEU0-0.003-0.01216.8480.0310.0310.0000.0000.0000.000
168D168ALA0-0.044-0.02312.1380.0310.0310.0000.0000.0000.000
169D169ALA0-0.011-0.00214.2650.0160.0160.0000.0000.0000.000
170D170GLN0-0.074-0.03215.7310.0950.0950.0000.0000.0000.000
171D171GLY00.0000.01115.8470.0620.0620.0000.0000.0000.000
172D172GLN0-0.016-0.01216.9050.0950.0950.0000.0000.0000.000
173D173VAL00.0010.00112.1060.0580.0580.0000.0000.0000.000
174D174ASP-1-0.866-0.93412.988-0.329-0.3290.0000.0000.0000.000
175D175SER0-0.023-0.01514.8790.0880.0880.0000.0000.0000.000
176D176ILE0-0.032-0.01416.9040.0470.0470.0000.0000.0000.000
177D177ILE00.007-0.01312.1130.0340.0340.0000.0000.0000.000
178D178ALA0-0.0010.02216.4080.0580.0580.0000.0000.0000.000
179D179ARG10.8740.95118.4460.2270.2270.0000.0000.0000.000
180D180PHE0-0.071-0.04719.0850.0120.0120.0000.0000.0000.000
181D181SER0-0.030-0.01417.2630.0290.0290.0000.0000.0000.000
182D182ALA0-0.052-0.01019.3960.0310.0310.0000.0000.0000.000