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

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FMODB ID: G58L1

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2284472.838499
FMO2-HF: Nuclear repulsion 2203006.906245
FMO2-HF: Total energy -81465.932254
FMO2-MP2: Total energy -81703.660977


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.
-20.884-2.9618.84-8.727-18.034-0.08
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 : 0.006 / q_NPA : 0.025
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].
3A3ALA00.0110.0003.201-3.221-0.133-0.022-1.539-1.5270.001
4A4VAL0-0.0030.0093.205-1.321-0.2330.094-0.341-0.841-0.002
5A5ILE0-0.042-0.0205.1810.1850.215-0.001-0.001-0.0280.000
6A6PHE00.0190.0078.363-0.090-0.0900.0000.0000.0000.000
7A7ASP-1-0.698-0.81711.000-0.106-0.1060.0000.0000.0000.000
8A8LEU0-0.067-0.07214.330-0.019-0.0190.0000.0000.0000.000
9A9ASP-1-0.817-0.88217.393-0.175-0.1750.0000.0000.0000.000
10A10GLY00.0050.03917.939-0.018-0.0180.0000.0000.0000.000
11A11VAL0-0.044-0.01912.659-0.037-0.0370.0000.0000.0000.000
12A12ILE0-0.043-0.04313.710-0.019-0.0190.0000.0000.0000.000
13A13THR00.021-0.00416.8370.0210.0210.0000.0000.0000.000
14A14ASP-1-0.821-0.91520.543-0.209-0.2090.0000.0000.0000.000
15A15THR0-0.062-0.07622.5030.0120.0120.0000.0000.0000.000
16A16ALA00.0310.02124.0610.0160.0160.0000.0000.0000.000
17A17GLU-1-0.707-0.80825.790-0.124-0.1240.0000.0000.0000.000
18A18TYR0-0.061-0.05124.8020.0130.0130.0000.0000.0000.000
19A19HIS0-0.016-0.01726.4260.0200.0200.0000.0000.0000.000
20A20PHE0-0.031-0.00730.0730.0110.0110.0000.0000.0000.000
21A21LEU0-0.013-0.01731.1200.0110.0110.0000.0000.0000.000
22A22ALA0-0.017-0.00233.0890.0070.0070.0000.0000.0000.000
23A23TRP0-0.011-0.01533.4500.0090.0090.0000.0000.0000.000
24A24LYS10.8870.94736.1390.0920.0920.0000.0000.0000.000
25A25HIS10.8440.91436.0160.0870.0870.0000.0000.0000.000
26A26ILE0-0.048-0.01638.5520.0050.0050.0000.0000.0000.000
27A27ALA00.0610.03240.7940.0040.0040.0000.0000.0000.000
28A28GLU-1-0.776-0.85740.572-0.075-0.0750.0000.0000.0000.000
29A29GLN0-0.044-0.01641.6640.0060.0060.0000.0000.0000.000
30A30ILE0-0.051-0.01544.6650.0030.0030.0000.0000.0000.000
31A31ASP-1-0.955-0.96946.881-0.051-0.0510.0000.0000.0000.000
32A32ILE0-0.087-0.04644.1580.0010.0010.0000.0000.0000.000
33A33PRO0-0.044-0.02143.594-0.003-0.0030.0000.0000.0000.000
34A34PHE00.012-0.01135.145-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.841-0.93337.474-0.099-0.0990.0000.0000.0000.000
36A36ARG10.8700.87230.1390.1370.1370.0000.0000.0000.000
37A37ASP-1-0.794-0.84333.799-0.113-0.1130.0000.0000.0000.000
38A38MET0-0.004-0.01235.4810.0000.0000.0000.0000.0000.000
39A39ASN00.000-0.01030.6960.0050.0050.0000.0000.0000.000
40A40GLU-1-0.927-0.97630.894-0.150-0.1500.0000.0000.0000.000
41A41ARG10.8050.87732.0310.0970.0970.0000.0000.0000.000
42A42LEU0-0.044-0.01734.3170.0030.0030.0000.0000.0000.000
43A43LYS10.8760.96227.7890.1580.1580.0000.0000.0000.000
44A44GLY0-0.005-0.00329.1680.0000.0000.0000.0000.0000.000
45A45ILE0-0.0270.01129.8950.0070.0070.0000.0000.0000.000
46A46SER00.0370.02033.0960.0000.0000.0000.0000.0000.000
47A47ARG10.8360.89134.1320.0550.0550.0000.0000.0000.000
48A48GLU-1-0.724-0.88135.500-0.053-0.0530.0000.0000.0000.000
49A49GLU-1-0.922-0.95836.821-0.072-0.0720.0000.0000.0000.000
50A50SER0-0.001-0.01135.296-0.002-0.0020.0000.0000.0000.000
51A51LEU0-0.014-0.00937.7860.0010.0010.0000.0000.0000.000
52A52GLU-1-0.780-0.87540.571-0.048-0.0480.0000.0000.0000.000
53A53SER0-0.014-0.00640.1050.0010.0010.0000.0000.0000.000
54A54ILE0-0.043-0.02138.3170.0000.0000.0000.0000.0000.000
55A55LEU0-0.009-0.00942.5160.0020.0020.0000.0000.0000.000
56A56ILE00.0160.01745.0620.0020.0020.0000.0000.0000.000
57A57PHE0-0.065-0.01444.1880.0010.0010.0000.0000.0000.000
58A58GLY00.0060.00946.3840.0010.0010.0000.0000.0000.000
59A59GLY0-0.0130.00448.5230.0030.0030.0000.0000.0000.000
60A60ALA0-0.058-0.04948.7960.0030.0030.0000.0000.0000.000
61A61GLU-1-0.803-0.87547.963-0.046-0.0460.0000.0000.0000.000
62A62THR0-0.031-0.04849.1380.0020.0020.0000.0000.0000.000
63A63LYS10.7900.89451.6270.0480.0480.0000.0000.0000.000
64A64TYR00.0120.02348.6340.0010.0010.0000.0000.0000.000
65A65THR0-0.001-0.03850.4320.0000.0000.0000.0000.0000.000
66A66ASN00.0490.00545.833-0.004-0.0040.0000.0000.0000.000
67A67ALA00.0040.00146.535-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.778-0.86346.822-0.037-0.0370.0000.0000.0000.000
69A69LYS10.8270.89544.1500.0440.0440.0000.0000.0000.000
70A70GLN0-0.063-0.03841.689-0.003-0.0030.0000.0000.0000.000
71A71GLU-1-0.853-0.93641.957-0.044-0.0440.0000.0000.0000.000
72A72LEU0-0.0140.00042.404-0.002-0.0020.0000.0000.0000.000
73A73MET0-0.058-0.00938.258-0.005-0.0050.0000.0000.0000.000
74A74HIS0-0.085-0.03037.723-0.002-0.0020.0000.0000.0000.000
75A75ARG10.9050.92938.2630.0490.0490.0000.0000.0000.000
76A76LYS10.8640.96632.5320.0900.0900.0000.0000.0000.000
77A77ASN00.0250.00032.624-0.007-0.0070.0000.0000.0000.000
78A78ARG10.9690.98833.8900.0430.0430.0000.0000.0000.000
79A79ASP-1-0.889-0.95235.532-0.077-0.0770.0000.0000.0000.000
80A80TYR00.0260.00825.894-0.003-0.0030.0000.0000.0000.000
81A81GLN0-0.019-0.00129.101-0.005-0.0050.0000.0000.0000.000
82A82MET0-0.029-0.02131.4720.0010.0010.0000.0000.0000.000
83A83LEU0-0.031-0.01930.8620.0000.0000.0000.0000.0000.000
84A84ILE00.0310.02625.628-0.003-0.0030.0000.0000.0000.000
85A85SER0-0.145-0.09028.0880.0010.0010.0000.0000.0000.000
86A86LYS10.8560.92030.6050.0830.0830.0000.0000.0000.000
87A87LEU0-0.0120.02224.213-0.001-0.0010.0000.0000.0000.000
88A88THR0-0.031-0.04726.8600.0080.0080.0000.0000.0000.000
89A89PRO00.0440.00423.271-0.009-0.0090.0000.0000.0000.000
90A90GLU-1-0.944-0.93623.030-0.147-0.1470.0000.0000.0000.000
91A91ASP-1-0.856-0.90924.270-0.148-0.1480.0000.0000.0000.000
92A92LEU0-0.065-0.01516.939-0.009-0.0090.0000.0000.0000.000
93A93LEU00.0070.01617.134-0.001-0.0010.0000.0000.0000.000
94A94PRO00.0380.00617.617-0.020-0.0200.0000.0000.0000.000
95A95GLY00.0040.00614.776-0.024-0.0240.0000.0000.0000.000
96A96ILE00.0230.01912.743-0.053-0.0530.0000.0000.0000.000
97A97GLY00.0590.03112.870-0.030-0.0300.0000.0000.0000.000
98A98ARG10.8030.87911.2620.6410.6410.0000.0000.0000.000
99A99LEU00.0260.0216.930-0.021-0.0210.0000.0000.0000.000
100A100LEU00.0240.0129.364-0.091-0.0910.0000.0000.0000.000
101A101CYS0-0.037-0.01310.9870.0030.0030.0000.0000.0000.000
102A102GLN00.000-0.0108.6430.0260.0260.0000.0000.0000.000
103A103LEU00.0730.0334.611-0.116-0.033-0.001-0.006-0.0760.000
104A104LYS10.8050.9267.8640.2100.2100.0000.0000.0000.000
105A105ASN0-0.095-0.03510.7390.1390.1390.0000.0000.0000.000
106A106GLU-1-0.856-0.9346.250-1.403-1.4030.0000.0000.0000.000
107A107ASN0-0.177-0.0868.0930.1350.1350.0000.0000.0000.000
108A108ILE0-0.0190.0013.174-0.5620.2400.078-0.161-0.7180.000
109A109LYS10.8450.9225.987-0.897-0.8970.0000.0000.0000.000
110A110ILE00.0420.0326.816-0.158-0.1580.0000.0000.0000.000
111A111GLY00.0180.0039.2410.1160.1160.0000.0000.0000.000
112A112LEU0-0.060-0.03111.057-0.076-0.0760.0000.0000.0000.000
113A113ALA0-0.002-0.01413.0150.0540.0540.0000.0000.0000.000
114A114SER00.0420.02514.571-0.007-0.0070.0000.0000.0000.000
115A115SER00.0210.00717.8000.0260.0260.0000.0000.0000.000
116A116SER0-0.034-0.01321.1120.0210.0210.0000.0000.0000.000
117A117ARG11.0150.99122.3650.0400.0400.0000.0000.0000.000
118A118ASN0-0.033-0.02824.8380.0150.0150.0000.0000.0000.000
119A119ALA00.0930.06819.532-0.004-0.0040.0000.0000.0000.000
120A120PRO00.0730.04121.197-0.010-0.0100.0000.0000.0000.000
121A121LYS10.8640.92122.1500.0340.0340.0000.0000.0000.000
122A122ILE00.004-0.00321.5640.0010.0010.0000.0000.0000.000
123A123LEU00.0900.04216.633-0.004-0.0040.0000.0000.0000.000
124A124ARG10.8680.93920.6400.0350.0350.0000.0000.0000.000
125A125ARG10.8340.93023.5710.0790.0790.0000.0000.0000.000
126A126LEU00.0170.01720.0260.0000.0000.0000.0000.0000.000
127A127ALA0-0.066-0.02621.541-0.013-0.0130.0000.0000.0000.000
128A128ILE00.0880.03416.147-0.006-0.0060.0000.0000.0000.000
129A129ILE0-0.079-0.03417.090-0.005-0.0050.0000.0000.0000.000
130A130ASP-1-0.886-0.94318.151-0.040-0.0400.0000.0000.0000.000
131A131ASP-1-0.849-0.94613.527-0.199-0.1990.0000.0000.0000.000
132A132PHE0-0.021-0.01112.483-0.007-0.0070.0000.0000.0000.000
133A133HIS0-0.015-0.00912.5210.0090.0090.0000.0000.0000.000
134A134ALA00.0120.00512.9590.0510.0510.0000.0000.0000.000
135A135ILE0-0.049-0.02814.259-0.051-0.0510.0000.0000.0000.000
136A136VAL0-0.0060.00714.9710.0270.0270.0000.0000.0000.000
137A137ASP-1-0.967-0.96917.7530.0280.0280.0000.0000.0000.000
138A138PRO0-0.054-0.02521.4310.0120.0120.0000.0000.0000.000
139A148PRO0-0.025-0.03717.863-0.003-0.0030.0000.0000.0000.000
140A149ASP-1-0.882-0.94215.8910.0640.0640.0000.0000.0000.000
141A150ILE00.0050.00615.7260.0300.0300.0000.0000.0000.000
142A151PHE00.0650.01710.9420.0180.0180.0000.0000.0000.000
143A152LEU00.0190.01712.1550.0430.0430.0000.0000.0000.000
144A153THR00.0100.00413.7330.0540.0540.0000.0000.0000.000
145A154ALA00.0180.00711.6360.0390.0390.0000.0000.0000.000
146A155ALA00.0070.0059.6430.0150.0150.0000.0000.0000.000
147A156ALA00.0010.00910.7300.1200.1200.0000.0000.0000.000
148A157MET0-0.075-0.03814.0440.0330.0330.0000.0000.0000.000
149A158LEU0-0.0100.0029.048-0.033-0.0330.0000.0000.0000.000
150A159ASP-1-0.989-0.98111.1930.8830.8830.0000.0000.0000.000
151A160VAL0-0.030-0.0277.0190.2810.2810.0000.0000.0000.000
152A161SER0-0.013-0.0127.198-0.474-0.4740.0000.0000.0000.000
153A162PRO00.0930.0287.0120.1320.1320.0000.0000.0000.000
154A163ALA00.0220.0196.879-0.189-0.1890.0000.0000.0000.000
155A164ASP-1-0.873-0.9223.6978.3619.1150.020-0.239-0.535-0.001
156A165CYS0-0.045-0.0212.508-3.284-0.9971.478-1.684-2.082-0.021
157A166ALA00.0200.0212.878-1.007-0.2230.249-0.218-0.815-0.001
158A167ALA0-0.006-0.0074.1750.1550.1730.000-0.003-0.0150.000
159A168ILE0-0.029-0.0117.169-0.058-0.0580.0000.0000.0000.000
160A169GLU-1-0.836-0.9319.797-0.181-0.1810.0000.0000.0000.000
161A170ASP-1-0.875-0.95413.404-0.289-0.2890.0000.0000.0000.000
162A171ALA0-0.025-0.00116.8370.0250.0250.0000.0000.0000.000
163A172GLU-1-0.949-0.98217.799-0.206-0.2060.0000.0000.0000.000
164A173ALA0-0.041-0.02818.729-0.002-0.0020.0000.0000.0000.000
165A174GLY00.0730.03816.3550.0110.0110.0000.0000.0000.000
166A175ILE00.0370.01913.982-0.011-0.0110.0000.0000.0000.000
167A176SER0-0.0070.00414.6720.0010.0010.0000.0000.0000.000
168A177ALA0-0.032-0.01115.9020.0220.0220.0000.0000.0000.000
169A178ILE00.0170.0179.7160.0320.0320.0000.0000.0000.000
170A179LYS10.8460.91110.8460.4220.4220.0000.0000.0000.000
171A180SER0-0.043-0.02713.4600.0490.0490.0000.0000.0000.000
172A181ALA0-0.086-0.04812.7420.0490.0490.0000.0000.0000.000
173A182GLY0-0.047-0.03111.8290.0680.0680.0000.0000.0000.000
174A183MET0-0.096-0.0257.5220.0600.0600.0000.0000.0000.000
175A184PHE0-0.002-0.0024.575-0.260-0.121-0.001-0.005-0.1330.000
176A185ALA00.004-0.0206.955-0.045-0.0450.0000.0000.0000.000
177A186VAL0-0.017-0.0177.066-0.045-0.0450.0000.0000.0000.000
178A187GLY00.0260.0169.9150.0840.0840.0000.0000.0000.000
179A188VAL0-0.025-0.02213.546-0.026-0.0260.0000.0000.0000.000
180A196GLY0-0.014-0.01718.139-0.005-0.0050.0000.0000.0000.000
181A197ALA00.0020.00113.0420.0160.0160.0000.0000.0000.000
182A198ASP-1-0.832-0.8839.746-0.541-0.5410.0000.0000.0000.000
183A199LEU00.0100.0069.073-0.048-0.0480.0000.0000.0000.000
184A200VAL0-0.022-0.00811.6200.0300.0300.0000.0000.0000.000
185A201VAL0-0.028-0.00711.7580.0020.0020.0000.0000.0000.000
186A202ARG10.9180.97014.6330.3690.3690.0000.0000.0000.000
187A203GLN0-0.044-0.04117.1890.0560.0560.0000.0000.0000.000
188A204THR00.0880.02414.281-0.032-0.0320.0000.0000.0000.000
189A205SER0-0.069-0.03213.696-0.037-0.0370.0000.0000.0000.000
190A206ASP-1-0.854-0.92614.173-0.461-0.4610.0000.0000.0000.000
191A207LEU0-0.0160.0018.973-0.081-0.0810.0000.0000.0000.000
192A208THR0-0.022-0.0039.5800.0140.0140.0000.0000.0000.000
193A209LEU00.0310.0113.492-0.335-0.0680.013-0.048-0.2310.000
194A210GLU-1-0.770-0.8725.295-1.315-1.3150.0000.0000.0000.000
195A211LEU00.0010.0077.561-0.129-0.1290.0000.0000.0000.000
196A212LEU00.008-0.0063.394-0.485-0.0680.022-0.083-0.3560.000
197A213HIS0-0.048-0.0272.728-4.109-2.1071.277-0.943-2.336-0.011
198A214GLU-1-0.918-0.9564.049-1.286-1.1930.0000.010-0.1020.000
199A215GLU-1-0.921-0.9787.183-0.869-0.8690.0000.0000.0000.000
200A216TRP0-0.019-0.0032.520-9.469-3.5285.635-3.463-8.113-0.045
201A217GLU-1-0.937-0.9825.037-1.960-1.830-0.001-0.003-0.1260.000
202A218GLN0-0.055-0.0356.6700.6450.6450.0000.0000.0000.000
203A219TYR0-0.104-0.0906.3240.2510.2510.0000.0000.0000.000
204A220ARG10.9250.9605.8750.2500.2500.0000.0000.0000.000
205A221ILE00.0260.0398.9630.3280.3280.0000.0000.0000.000
206A222ARG10.8020.94611.4040.8190.8190.0000.0000.0000.000
207A223GLU-1-0.920-0.94710.377-0.134-0.1340.0000.0000.0000.000