Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 1N52Z

Calculation Name: 3NAS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NAS

Chain ID: A

ChEMBL ID:

UniProt ID: O06995

Base Structure: X-ray

Registration Date: 2023-09-22

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2284828.720168
FMO2-HF: Nuclear repulsion 2203364.515097
FMO2-HF: Total energy -81464.205071
FMO2-MP2: Total energy -81702.044756


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-24.55-8.76812.69-9.226-19.245-0.067
Interaction energy analysis for fragmet #1(A:1:LEU)
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 : 0.016
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].
3A3ALA00.007-0.0013.635-3.461-0.143-0.032-1.744-1.5420.004
4A4VAL00.0030.0113.418-1.043-0.2610.028-0.209-0.601-0.001
5A5ILE0-0.037-0.0195.6570.1470.1470.0000.0000.0000.000
6A6PHE00.0090.0018.666-0.086-0.0860.0000.0000.0000.000
7A7ASP-1-0.714-0.83711.378-0.093-0.0930.0000.0000.0000.000
8A8LEU0-0.072-0.06914.6290.0000.0000.0000.0000.0000.000
9A9ASP-1-0.840-0.91817.723-0.113-0.1130.0000.0000.0000.000
10A10GLY00.0030.04018.061-0.015-0.0150.0000.0000.0000.000
11A11VAL0-0.027-0.01812.633-0.023-0.0230.0000.0000.0000.000
12A12ILE0-0.031-0.03813.7150.0000.0000.0000.0000.0000.000
13A13THR0-0.016-0.02716.7870.0190.0190.0000.0000.0000.000
14A14ASP-1-0.802-0.90920.485-0.134-0.1340.0000.0000.0000.000
15A15THR0-0.049-0.04022.2000.0080.0080.0000.0000.0000.000
16A16ALA00.0480.02323.9600.0100.0100.0000.0000.0000.000
17A17GLU-1-0.702-0.80825.732-0.082-0.0820.0000.0000.0000.000
18A18TYR0-0.027-0.01824.8100.0080.0080.0000.0000.0000.000
19A19HIS0-0.026-0.02526.5750.0140.0140.0000.0000.0000.000
20A20PHE0-0.027-0.00829.9840.0060.0060.0000.0000.0000.000
21A21LEU0-0.034-0.02930.6960.0070.0070.0000.0000.0000.000
22A22ALA0-0.032-0.00333.0020.0050.0050.0000.0000.0000.000
23A23TRP00.020-0.00633.2740.0060.0060.0000.0000.0000.000
24A24LYS10.9550.99436.0530.0630.0630.0000.0000.0000.000
25A25HIS10.8590.92735.5800.0530.0530.0000.0000.0000.000
26A26ILE0-0.057-0.02038.5490.0040.0040.0000.0000.0000.000
27A27ALA00.0560.02740.7080.0020.0020.0000.0000.0000.000
28A28GLU-1-0.847-0.91340.510-0.044-0.0440.0000.0000.0000.000
29A29GLN0-0.044-0.02542.0510.0050.0050.0000.0000.0000.000
30A30ILE0-0.048-0.00444.5480.0020.0020.0000.0000.0000.000
31A31ASP-1-0.963-0.97946.836-0.034-0.0340.0000.0000.0000.000
32A32ILE0-0.092-0.04544.2410.0000.0000.0000.0000.0000.000
33A33PRO0-0.045-0.01643.549-0.002-0.0020.0000.0000.0000.000
34A34PHE00.027-0.01135.027-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.811-0.90337.485-0.072-0.0720.0000.0000.0000.000
36A36ARG10.8420.85530.2960.0890.0890.0000.0000.0000.000
37A37ASP-1-0.863-0.91033.730-0.088-0.0880.0000.0000.0000.000
38A38MET0-0.100-0.05835.393-0.001-0.0010.0000.0000.0000.000
39A39ASN0-0.010-0.01230.5530.0020.0020.0000.0000.0000.000
40A40GLU-1-0.968-0.99831.125-0.106-0.1060.0000.0000.0000.000
41A41ARG10.9320.96931.9080.0710.0710.0000.0000.0000.000
42A42LEU0-0.048-0.01834.3690.0010.0010.0000.0000.0000.000
43A43LYS10.9420.99427.5570.1260.1260.0000.0000.0000.000
44A44GLY00.0020.00129.258-0.002-0.0020.0000.0000.0000.000
45A45ILE0-0.0030.02629.9840.0030.0030.0000.0000.0000.000
46A46SER00.0290.01433.2210.0010.0010.0000.0000.0000.000
47A47ARG10.8530.89834.2360.0440.0440.0000.0000.0000.000
48A48GLU-1-0.743-0.89735.661-0.042-0.0420.0000.0000.0000.000
49A49GLU-1-0.939-0.96037.342-0.064-0.0640.0000.0000.0000.000
50A50SER00.006-0.01135.465-0.001-0.0010.0000.0000.0000.000
51A51LEU0-0.018-0.01037.9540.0010.0010.0000.0000.0000.000
52A52GLU-1-0.838-0.92840.772-0.040-0.0400.0000.0000.0000.000
53A53SER0-0.006-0.00640.2400.0010.0010.0000.0000.0000.000
54A54ILE0-0.052-0.02738.5450.0000.0000.0000.0000.0000.000
55A55LEU0-0.033-0.01942.5490.0020.0020.0000.0000.0000.000
56A56ILE00.0330.02645.0120.0020.0020.0000.0000.0000.000
57A57PHE0-0.079-0.02044.0580.0010.0010.0000.0000.0000.000
58A58GLY0-0.006-0.00546.3020.0010.0010.0000.0000.0000.000
59A59GLY0-0.037-0.00648.4410.0020.0020.0000.0000.0000.000
60A60ALA0-0.079-0.06948.9420.0020.0020.0000.0000.0000.000
61A61GLU-1-0.840-0.92548.117-0.038-0.0380.0000.0000.0000.000
62A62THR0-0.041-0.03049.3170.0010.0010.0000.0000.0000.000
63A63LYS10.8560.93951.8420.0350.0350.0000.0000.0000.000
64A64TYR00.0280.03448.9900.0020.0020.0000.0000.0000.000
65A65THR00.0120.00750.616-0.001-0.0010.0000.0000.0000.000
66A66ASN00.0610.01246.024-0.003-0.0030.0000.0000.0000.000
67A67ALA00.0030.00246.716-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.824-0.92847.040-0.026-0.0260.0000.0000.0000.000
69A69LYS10.9660.98544.3680.0350.0350.0000.0000.0000.000
70A70GLN0-0.093-0.04542.607-0.002-0.0020.0000.0000.0000.000
71A71GLU-1-0.880-0.94342.191-0.028-0.0280.0000.0000.0000.000
72A72LEU0-0.0030.00642.574-0.001-0.0010.0000.0000.0000.000
73A73MET0-0.061-0.01138.437-0.003-0.0030.0000.0000.0000.000
74A74HIS0-0.061-0.02137.977-0.001-0.0010.0000.0000.0000.000
75A75ARG10.9030.95038.5710.0310.0310.0000.0000.0000.000
76A76LYS10.8780.97232.5900.0640.0640.0000.0000.0000.000
77A77ASN0-0.002-0.00932.624-0.001-0.0010.0000.0000.0000.000
78A78ARG10.9950.99134.2380.0250.0250.0000.0000.0000.000
79A79ASP-1-0.891-0.94835.765-0.043-0.0430.0000.0000.0000.000
80A80TYR00.0240.00426.140-0.001-0.0010.0000.0000.0000.000
81A81GLN00.0090.01029.329-0.001-0.0010.0000.0000.0000.000
82A82MET0-0.040-0.02631.6640.0030.0030.0000.0000.0000.000
83A83LEU0-0.021-0.01830.7770.0020.0020.0000.0000.0000.000
84A84ILE00.0260.02925.9810.0000.0000.0000.0000.0000.000
85A85SER0-0.160-0.10028.1200.0040.0040.0000.0000.0000.000
86A86LYS10.8500.92030.6800.0420.0420.0000.0000.0000.000
87A87LEU0-0.0160.01623.9930.0000.0000.0000.0000.0000.000
88A88THR0-0.036-0.04726.8940.0060.0060.0000.0000.0000.000
89A89PRO00.0400.00023.386-0.006-0.0060.0000.0000.0000.000
90A90GLU-1-0.946-0.93123.127-0.056-0.0560.0000.0000.0000.000
91A91ASP-1-0.879-0.93624.316-0.075-0.0750.0000.0000.0000.000
92A92LEU0-0.082-0.02416.873-0.007-0.0070.0000.0000.0000.000
93A93LEU0-0.0060.00817.037-0.001-0.0010.0000.0000.0000.000
94A94PRO00.0300.00417.710-0.004-0.0040.0000.0000.0000.000
95A95GLY00.0060.01114.932-0.019-0.0190.0000.0000.0000.000
96A96ILE00.0260.02312.933-0.016-0.0160.0000.0000.0000.000
97A97GLY00.0580.02913.0050.0000.0000.0000.0000.0000.000
98A98ARG10.8000.88011.3490.3250.3250.0000.0000.0000.000
99A99LEU00.0380.0317.0510.0050.0050.0000.0000.0000.000
100A100LEU00.0170.0079.446-0.007-0.0070.0000.0000.0000.000
101A101CYS0-0.038-0.01710.8870.0420.0420.0000.0000.0000.000
102A102GLN00.0170.0118.7920.0230.0230.0000.0000.0000.000
103A103LEU00.0830.0354.9060.0270.0270.0000.0000.0000.000
104A104LYS10.8350.9457.6760.0000.0000.0000.0000.0000.000
105A105ASN0-0.085-0.03510.9480.1040.1040.0000.0000.0000.000
106A106GLU-1-0.873-0.9496.535-0.417-0.4170.0000.0000.0000.000
107A107ASN0-0.179-0.0867.9590.1430.1430.0000.0000.0000.000
108A108ILE0-0.0170.0023.532-0.2550.3020.015-0.114-0.4580.000
109A109LYS10.8640.9396.251-1.057-1.0570.0000.0000.0000.000
110A110ILE00.0570.0436.805-0.089-0.0890.0000.0000.0000.000
111A111GLY00.014-0.0029.3360.0500.0500.0000.0000.0000.000
112A112LEU0-0.062-0.03411.446-0.054-0.0540.0000.0000.0000.000
113A113ALA00.008-0.00913.1310.0330.0330.0000.0000.0000.000
114A114SER00.0790.05714.773-0.011-0.0110.0000.0000.0000.000
115A115SER00.0300.00618.0430.0200.0200.0000.0000.0000.000
116A116SER0-0.030-0.01221.2900.0150.0150.0000.0000.0000.000
117A117ARG11.0070.98922.6530.0260.0260.0000.0000.0000.000
118A118ASN0-0.055-0.04425.1670.0140.0140.0000.0000.0000.000
119A119ALA00.0770.06219.9500.0000.0000.0000.0000.0000.000
120A120PRO00.0740.04221.615-0.002-0.0020.0000.0000.0000.000
121A121LYS10.8950.93622.6010.0010.0010.0000.0000.0000.000
122A122ILE00.0150.00321.6350.0020.0020.0000.0000.0000.000
123A123LEU00.0910.04116.932-0.002-0.0020.0000.0000.0000.000
124A124ARG10.9380.97120.747-0.030-0.0300.0000.0000.0000.000
125A125ARG10.8490.93623.6120.0260.0260.0000.0000.0000.000
126A126LEU00.0250.02019.821-0.002-0.0020.0000.0000.0000.000
127A127ALA0-0.058-0.02221.600-0.005-0.0050.0000.0000.0000.000
128A128ILE00.0720.03316.5770.0010.0010.0000.0000.0000.000
129A129ILE0-0.085-0.03717.1790.0060.0060.0000.0000.0000.000
130A130ASP-1-0.919-0.95118.2230.0690.0690.0000.0000.0000.000
131A131ASP-1-0.878-0.96513.8310.0320.0320.0000.0000.0000.000
132A132PHE0-0.025-0.01612.6510.0240.0240.0000.0000.0000.000
133A133HIS0-0.043-0.02612.6230.0100.0100.0000.0000.0000.000
134A134ALA00.0030.00413.0910.0240.0240.0000.0000.0000.000
135A135ILE0-0.047-0.02714.596-0.034-0.0340.0000.0000.0000.000
136A136VAL0-0.0030.01115.1930.0170.0170.0000.0000.0000.000
137A137ASP-1-0.952-0.96817.9470.0350.0350.0000.0000.0000.000
138A138PRO0-0.062-0.02721.5680.0040.0040.0000.0000.0000.000
139A148PRO0-0.037-0.04017.6440.0000.0000.0000.0000.0000.000
140A149ASP-1-0.863-0.95215.692-0.024-0.0240.0000.0000.0000.000
141A150ILE00.0010.01315.4660.0260.0260.0000.0000.0000.000
142A151PHE00.0450.00710.6960.0230.0230.0000.0000.0000.000
143A152LEU00.0060.02912.1980.0300.0300.0000.0000.0000.000
144A153THR00.0090.00513.8890.0450.0450.0000.0000.0000.000
145A154ALA00.0290.00911.7180.0390.0390.0000.0000.0000.000
146A155ALA00.0040.0049.6950.0350.0350.0000.0000.0000.000
147A156ALA0-0.0020.00811.0600.1030.1030.0000.0000.0000.000
148A157MET0-0.076-0.04014.3300.0360.0360.0000.0000.0000.000
149A158LEU0-0.035-0.0098.8880.0050.0050.0000.0000.0000.000
150A159ASP-1-0.980-0.98511.3370.6680.6680.0000.0000.0000.000
151A160VAL0-0.048-0.0317.0340.2530.2530.0000.0000.0000.000
152A161SER00.0180.0047.555-0.204-0.2040.0000.0000.0000.000
153A162PRO00.0730.0186.9680.0230.0230.0000.0000.0000.000
154A163ALA00.0030.0036.671-0.167-0.1670.0000.0000.0000.000
155A164ASP-1-0.924-0.9633.4540.7202.3860.058-0.725-0.999-0.005
156A165CYS0-0.082-0.0382.537-2.730-0.7421.437-1.461-1.964-0.017
157A166ALA00.0280.0272.896-1.226-0.3020.241-0.288-0.877-0.002
158A167ALA0-0.009-0.0064.0960.2460.2680.000-0.006-0.0170.000
159A168ILE0-0.037-0.0176.974-0.057-0.0570.0000.0000.0000.000
160A169GLU-1-0.871-0.96510.031-0.147-0.1470.0000.0000.0000.000
161A170ASP-1-0.849-0.93513.571-0.222-0.2220.0000.0000.0000.000
162A171ALA0-0.0100.01216.9990.0150.0150.0000.0000.0000.000
163A172GLU-1-0.953-0.97417.783-0.213-0.2130.0000.0000.0000.000
164A173ALA0-0.031-0.02918.603-0.009-0.0090.0000.0000.0000.000
165A174GLY00.0790.04316.3550.0000.0000.0000.0000.0000.000
166A175ILE00.0340.01213.534-0.022-0.0220.0000.0000.0000.000
167A176SER00.0040.01114.426-0.020-0.0200.0000.0000.0000.000
168A177ALA0-0.043-0.02015.6150.0040.0040.0000.0000.0000.000
169A178ILE00.0150.0219.4730.0120.0120.0000.0000.0000.000
170A179LYS10.8310.90910.9940.5320.5320.0000.0000.0000.000
171A180SER0-0.041-0.03113.1240.0170.0170.0000.0000.0000.000
172A181ALA0-0.075-0.05312.4440.0330.0330.0000.0000.0000.000
173A182GLY0-0.051-0.03111.6850.0310.0310.0000.0000.0000.000
174A183MET0-0.094-0.0267.2500.0010.0010.0000.0000.0000.000
175A184PHE00.0000.0064.524-0.209-0.057-0.001-0.006-0.1440.000
176A185ALA00.013-0.0056.7000.0190.0190.0000.0000.0000.000
177A186VAL0-0.004-0.0087.020-0.031-0.0310.0000.0000.0000.000
178A187GLY00.0210.0149.9340.0770.0770.0000.0000.0000.000
179A188VAL0-0.031-0.02813.247-0.010-0.0100.0000.0000.0000.000
180A196GLY0-0.016-0.01918.017-0.002-0.0020.0000.0000.0000.000
181A197ALA0-0.002-0.00112.9280.0050.0050.0000.0000.0000.000
182A198ASP-1-0.825-0.8959.720-0.640-0.6400.0000.0000.0000.000
183A199LEU00.0150.0078.952-0.043-0.0430.0000.0000.0000.000
184A200VAL0-0.023-0.00611.6650.0370.0370.0000.0000.0000.000
185A201VAL0-0.0190.00111.8280.0060.0060.0000.0000.0000.000
186A202ARG10.9330.96714.6230.2770.2770.0000.0000.0000.000
187A203GLN00.0170.01317.3090.0180.0180.0000.0000.0000.000
188A204THR00.0840.01814.311-0.023-0.0230.0000.0000.0000.000
189A205SER0-0.065-0.04013.793-0.015-0.0150.0000.0000.0000.000
190A206ASP-1-0.930-0.96914.308-0.312-0.3120.0000.0000.0000.000
191A207LEU0-0.027-0.0028.627-0.060-0.0600.0000.0000.0000.000
192A208THR0-0.034-0.0049.8350.0240.0240.0000.0000.0000.000
193A209LEU00.0260.0133.831-0.249-0.0650.002-0.030-0.1560.000
194A210GLU-1-0.801-0.9065.498-0.705-0.7050.0000.0000.0000.000
195A211LEU00.0080.0087.578-0.138-0.1380.0000.0000.0000.000
196A212LEU00.002-0.0073.666-0.458-0.1220.007-0.055-0.2880.000
197A213HIS0-0.011-0.0032.694-3.303-1.3710.505-0.689-1.749-0.004
198A214GLU-1-0.914-0.9524.073-1.318-1.225-0.0010.006-0.0970.000
199A215GLU-1-0.951-0.9887.244-0.866-0.8660.0000.0000.0000.000
200A216TRP0-0.025-0.0032.323-8.416-4.76510.432-3.902-10.181-0.042
201A217GLU-1-0.929-0.9755.079-2.742-2.565-0.001-0.003-0.1720.000
202A218GLN0-0.042-0.0346.6880.4760.4760.0000.0000.0000.000
203A219TYR0-0.065-0.0406.2990.2230.2230.0000.0000.0000.000
204A220ARG10.9210.9635.6831.1361.1360.0000.0000.0000.000
205A221ILE0-0.0010.0238.5600.2990.2990.0000.0000.0000.000
206A222ARG10.8010.93411.4200.8720.8720.0000.0000.0000.000
207A223GLU-1-0.932-0.97410.628-0.525-0.5250.0000.0000.0000.000