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: 3J46L

Calculation Name: 2F20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F20

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A8E9

Base Structure: X-ray

Registration Date: 2023-09-23

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3183633.587953
FMO2-HF: Nuclear repulsion 3088012.094202
FMO2-HF: Total energy -95621.493751
FMO2-MP2: Total energy -95900.888514


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-37.151-36.73233.036-14.585-18.872-0.124
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.086 / q_NPA : -0.024
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].
3A4HIS00.0000.0093.301-2.2960.8960.002-1.767-1.4280.005
4A5ASN00.0590.0515.0611.3791.625-0.001-0.012-0.2340.000
5A6SER0-0.010-0.0296.315-0.828-0.8280.0000.0000.0000.000
6A7MET00.0130.0029.7530.1450.1450.0000.0000.0000.000
7A8SER00.0190.01712.943-0.102-0.1020.0000.0000.0000.000
8A9ALA0-0.0120.00015.790-0.056-0.0560.0000.0000.0000.000
9A10LYS10.8030.88318.412-0.151-0.1510.0000.0000.0000.000
10A11ALA00.0750.03519.9770.0250.0250.0000.0000.0000.000
11A12ILE00.0210.00321.0160.0200.0200.0000.0000.0000.000
12A13LYS10.8920.95220.925-0.206-0.2060.0000.0000.0000.000
13A14VAL00.0410.01816.3320.0180.0180.0000.0000.0000.000
14A15ALA00.0110.00119.1240.0140.0140.0000.0000.0000.000
15A16ALA0-0.033-0.01721.690-0.001-0.0010.0000.0000.0000.000
16A17ARG10.7070.81116.289-0.488-0.4880.0000.0000.0000.000
17A18TYR0-0.020-0.02414.5310.0220.0220.0000.0000.0000.000
18A19GLY0-0.0160.00420.964-0.015-0.0150.0000.0000.0000.000
19A20ARG10.7450.85121.090-0.285-0.2850.0000.0000.0000.000
20A21GLN0-0.040-0.02424.606-0.002-0.0020.0000.0000.0000.000
21A22SER00.0630.00324.0440.0150.0150.0000.0000.0000.000
22A23ASP-1-0.836-0.87225.1020.1240.1240.0000.0000.0000.000
23A24VAL00.0080.00022.651-0.009-0.0090.0000.0000.0000.000
24A25VAL00.002-0.00519.383-0.004-0.0040.0000.0000.0000.000
25A26GLU-1-0.846-0.92622.2330.1350.1350.0000.0000.0000.000
26A27ILE0-0.049-0.02025.277-0.011-0.0110.0000.0000.0000.000
27A28TYR0-0.025-0.01421.551-0.023-0.0230.0000.0000.0000.000
28A29GLN00.0280.00721.8570.0030.0030.0000.0000.0000.000
29A30SER0-0.023-0.01921.8370.0100.0100.0000.0000.0000.000
30A31ILE0-0.077-0.02919.074-0.017-0.0170.0000.0000.0000.000
31A32LEU0-0.024-0.01516.7240.0140.0140.0000.0000.0000.000
32A33ASP-1-0.796-0.88517.2390.2300.2300.0000.0000.0000.000
33A34GLU-1-0.902-0.92417.3490.1450.1450.0000.0000.0000.000
34A35GLN00.0030.00513.895-0.062-0.0620.0000.0000.0000.000
35A36TYR0-0.023-0.03112.8020.1390.1390.0000.0000.0000.000
36A37HIS0-0.048-0.0128.2610.0640.0640.0000.0000.0000.000
37A38VAL0-0.0050.0109.069-0.112-0.1120.0000.0000.0000.000
38A39ASN00.0420.0178.1910.0110.0110.0000.0000.0000.000
39A40ALA00.0710.0436.3670.0530.0530.0000.0000.0000.000
40A41PHE0-0.017-0.0197.2340.0670.0670.0000.0000.0000.000
41A42THR0-0.082-0.04711.3040.1030.1030.0000.0000.0000.000
42A43PHE00.0170.00912.3740.0640.0640.0000.0000.0000.000
43A44PRO00.0230.03811.4220.0520.0520.0000.0000.0000.000
44A45ARG10.9120.95413.653-0.046-0.0460.0000.0000.0000.000
45A46TYR0-0.048-0.04110.7280.0050.0050.0000.0000.0000.000
46A47PRO00.0360.01113.878-0.041-0.0410.0000.0000.0000.000
47A48ILE0-0.050-0.01511.9270.0880.0880.0000.0000.0000.000
48A49ILE00.0100.02114.999-0.058-0.0580.0000.0000.0000.000
49A50THR00.0470.00416.3580.0330.0330.0000.0000.0000.000
50A51SER00.0190.00219.0340.0010.0010.0000.0000.0000.000
51A52SER0-0.0170.00122.122-0.019-0.0190.0000.0000.0000.000
52A53ASP-1-0.837-0.92123.1320.1750.1750.0000.0000.0000.000
53A54GLH0-0.086-0.07624.2940.0050.0050.0000.0000.0000.000
54A55VAL0-0.0020.01418.3930.0140.0140.0000.0000.0000.000
55A56GLN0-0.065-0.03518.314-0.045-0.0450.0000.0000.0000.000
56A57VAL00.002-0.00617.5860.0310.0310.0000.0000.0000.000
57A58PHE00.0210.02115.181-0.030-0.0300.0000.0000.0000.000
58A59ASN00.007-0.02115.0890.0490.0490.0000.0000.0000.000
59A60TRP0-0.069-0.0374.684-0.0530.105-0.001-0.039-0.1170.000
60A61GLY00.024-0.01311.290-0.102-0.1020.0000.0000.0000.000
61A62LEU0-0.039-0.01111.8480.0470.0470.0000.0000.0000.000
62A63ILE00.0430.03513.873-0.053-0.0530.0000.0000.0000.000
63A64PRO0-0.030-0.00616.3940.0310.0310.0000.0000.0000.000
64A65PHE0-0.046-0.02119.012-0.009-0.0090.0000.0000.0000.000
65A66TRP0-0.055-0.02718.899-0.008-0.0080.0000.0000.0000.000
66A67VAL0-0.021-0.01219.805-0.006-0.0060.0000.0000.0000.000
67A68ARG10.9090.95123.1670.0450.0450.0000.0000.0000.000
68A69SER00.018-0.00524.9460.0040.0040.0000.0000.0000.000
69A70GLU-1-0.818-0.91123.613-0.094-0.0940.0000.0000.0000.000
70A71GLU-1-0.935-0.95222.559-0.144-0.1440.0000.0000.0000.000
71A72ASP-1-0.858-0.91221.802-0.136-0.1360.0000.0000.0000.000
72A73ALA0-0.025-0.01319.493-0.027-0.0270.0000.0000.0000.000
73A74THR0-0.047-0.03317.927-0.032-0.0320.0000.0000.0000.000
74A75GLU-1-0.800-0.88117.160-0.351-0.3510.0000.0000.0000.000
75A76ILE0-0.020-0.02015.583-0.057-0.0570.0000.0000.0000.000
76A77ARG10.8810.96913.7870.1900.1900.0000.0000.0000.000
77A78LYS10.7640.86111.9920.2640.2640.0000.0000.0000.000
78A79MET0-0.086-0.03810.394-0.175-0.1750.0000.0000.0000.000
79A80THR0-0.036-0.03010.2280.0010.0010.0000.0000.0000.000
80A81LEU00.0430.0407.1170.1060.1060.0000.0000.0000.000
81A82ASN0-0.062-0.0342.356-4.215-2.9401.931-1.361-1.845-0.016
82A83ALA00.0480.0276.0370.1170.1170.0000.0000.0000.000
83A84ARG10.8540.9187.744-0.129-0.1290.0000.0000.0000.000
84A85ALA00.0600.0229.013-0.116-0.1160.0000.0000.0000.000
85A86ASP-1-0.828-0.88311.3050.2760.2760.0000.0000.0000.000
86A87THR0-0.026-0.02713.404-0.075-0.0750.0000.0000.0000.000
87A88ILE0-0.0210.00211.106-0.060-0.0600.0000.0000.0000.000
88A89PHE00.030-0.01214.407-0.027-0.0270.0000.0000.0000.000
89A90GLU-1-0.799-0.89117.6860.1380.1380.0000.0000.0000.000
90A91LYS10.9210.95411.739-0.056-0.0560.0000.0000.0000.000
91A92PRO00.020-0.00417.2010.0130.0130.0000.0000.0000.000
92A93SER00.0040.01114.7440.0170.0170.0000.0000.0000.000
93A94PHE00.0310.00110.8860.0140.0140.0000.0000.0000.000
94A95ARG10.8520.92115.7750.0020.0020.0000.0000.0000.000
95A96GLU-1-0.808-0.88318.8830.0500.0500.0000.0000.0000.000
96A97PRO00.005-0.00115.9810.0170.0170.0000.0000.0000.000
97A98ILE00.0360.02614.4800.0250.0250.0000.0000.0000.000
98A99MET0-0.029-0.00516.9940.0220.0220.0000.0000.0000.000
99A100LYS10.9050.93920.471-0.119-0.1190.0000.0000.0000.000
100A101LYS10.8300.92618.166-0.093-0.0930.0000.0000.0000.000
101A102ARG10.8290.91215.478-0.256-0.2560.0000.0000.0000.000
102A103CYS0-0.054-0.01613.529-0.023-0.0230.0000.0000.0000.000
103A104ILE00.0100.01712.3340.0500.0500.0000.0000.0000.000
104A105VAL00.0130.0097.926-0.103-0.1030.0000.0000.0000.000
105A106PRO00.0530.0329.9500.1850.1850.0000.0000.0000.000
106A107SER00.0370.0087.6600.1120.1120.0000.0000.0000.000
107A108THR0-0.013-0.00510.144-0.204-0.2040.0000.0000.0000.000
108A109GLY00.0200.0108.408-0.262-0.2620.0000.0000.0000.000
109A110TYR0-0.032-0.0212.380-0.8820.4133.291-1.659-2.928-0.004
110A111PHE0-0.023-0.0164.639-1.166-1.044-0.001-0.010-0.1100.000
111A112GLU-1-0.793-0.8941.822-28.185-34.31521.493-8.880-6.483-0.109
112A113TRP0-0.067-0.0415.6250.9760.9760.0000.0000.0000.000
113A114ARG10.8830.9528.9020.3030.3030.0000.0000.0000.000
114A115HIS0-0.019-0.0179.5510.2740.2740.0000.0000.0000.000
115A116GLU-1-0.801-0.88013.700-0.282-0.2820.0000.0000.0000.000
116A117GLY00.0200.01017.3850.0300.0300.0000.0000.0000.000
117A118ALA00.000-0.01518.000-0.044-0.0440.0000.0000.0000.000
118A119ASN0-0.052-0.01217.868-0.036-0.0360.0000.0000.0000.000
119A120LYS10.8790.93112.4980.5950.5950.0000.0000.0000.000
120A121ILE00.0020.01513.3980.0620.0620.0000.0000.0000.000
121A122PRO00.0060.01610.206-0.127-0.1270.0000.0000.0000.000
122A123TYR00.031-0.0119.1180.2060.2060.0000.0000.0000.000
123A124TYR0-0.021-0.0178.263-0.187-0.1870.0000.0000.0000.000
124A125ILE0-0.019-0.0185.605-0.100-0.1000.0000.0000.0000.000
125A126TYR0-0.048-0.0577.9470.4150.4150.0000.0000.0000.000
126A127VAL0-0.0150.00710.202-0.071-0.0710.0000.0000.0000.000
127A128LYS10.8340.89312.604-0.239-0.2390.0000.0000.0000.000
128A129ASP-1-0.925-0.96916.2040.2440.2440.0000.0000.0000.000
129A130GLU-1-0.807-0.89114.9640.5470.5470.0000.0000.0000.000
130A131PRO0-0.031-0.02314.7310.0640.0640.0000.0000.0000.000
131A132ILE0-0.030-0.01013.9840.0300.0300.0000.0000.0000.000
132A133PHE00.0300.0467.712-0.048-0.0480.0000.0000.0000.000
133A134SER00.026-0.02211.8820.0850.0850.0000.0000.0000.000
134A135MET0-0.039-0.0045.9870.4870.4870.0000.0000.0000.000
135A136ALA00.0400.0229.125-0.189-0.1890.0000.0000.0000.000
136A137GLY00.0270.0088.7360.1240.1240.0000.0000.0000.000
137A138ILE0-0.054-0.02710.613-0.052-0.0520.0000.0000.0000.000
138A139TYR00.0420.00812.541-0.026-0.0260.0000.0000.0000.000
139A140ASP-1-0.800-0.90915.3000.0420.0420.0000.0000.0000.000
140A141ARG10.8870.96918.195-0.049-0.0490.0000.0000.0000.000
141A142TRP0-0.018-0.01721.118-0.006-0.0060.0000.0000.0000.000
142A143LEU00.0320.02522.807-0.005-0.0050.0000.0000.0000.000
143A144ASP-1-0.788-0.88425.757-0.065-0.0650.0000.0000.0000.000
144A145LYS10.7820.87926.9860.0420.0420.0000.0000.0000.000
145A146ASP-1-0.903-0.95329.542-0.041-0.0410.0000.0000.0000.000
146A147THR0-0.014-0.00827.5210.0040.0040.0000.0000.0000.000
147A148GLY0-0.027-0.00729.9790.0050.0050.0000.0000.0000.000
148A149GLU-1-0.887-0.93723.753-0.022-0.0220.0000.0000.0000.000
149A150GLU-1-0.888-0.96724.4050.0160.0160.0000.0000.0000.000
150A151HIS10.7850.88520.4870.0520.0520.0000.0000.0000.000
151A152GLU-1-0.867-0.94519.2930.0960.0960.0000.0000.0000.000
152A153THR0-0.058-0.01614.959-0.013-0.0130.0000.0000.0000.000
153A154PHE00.015-0.0058.5370.0090.0090.0000.0000.0000.000
154A155SER0-0.025-0.0328.809-0.106-0.1060.0000.0000.0000.000
155A156ILE00.0100.0163.948-0.0140.2140.001-0.038-0.1920.000
156A157ILE0-0.029-0.0125.993-0.369-0.3690.0000.0000.0000.000
157A158THR0-0.027-0.0113.111-0.2900.3620.097-0.147-0.6020.000
158A159THR0-0.010-0.0185.914-0.801-0.8010.0000.0000.0000.000
159A160ASP-1-0.836-0.9056.5271.2071.2070.0000.0000.0000.000
160A161THR0-0.009-0.0306.8400.1990.1990.0000.0000.0000.000
161A162ASN0-0.009-0.0118.847-0.159-0.1590.0000.0000.0000.000
162A163SER00.016-0.01011.088-0.067-0.0670.0000.0000.0000.000
163A164LEU00.0040.02510.679-0.073-0.0730.0000.0000.0000.000
164A165THR00.023-0.0226.416-0.054-0.0540.0000.0000.0000.000
165A166ASP-1-0.824-0.8757.752-0.215-0.2150.0000.0000.0000.000
166A167TYR0-0.026-0.0069.874-0.091-0.0910.0000.0000.0000.000
167A168ILE0-0.017-0.0097.293-0.038-0.0380.0000.0000.0000.000
168A169ASP-1-0.699-0.8614.915-0.680-0.6800.0000.0000.0000.000
169A170ASN00.0140.0027.0620.2240.2240.0000.0000.0000.000
170A171THR0-0.073-0.0388.9000.0250.0250.0000.0000.0000.000
171A172LYS10.7720.8786.3200.8970.8970.0000.0000.0000.000
172A173HIS0-0.039-0.0107.8970.2280.2280.0000.0000.0000.000
173A174ARG10.7130.8283.470-1.595-1.1850.583-0.244-0.7490.001
174A175MET00.0100.0272.972-2.045-1.8191.775-0.766-1.235-0.002
175A176PRO00.0500.0172.1920.855-0.4573.8590.351-2.8980.001
176A177ALA0-0.010-0.0194.544-0.921-0.8640.007-0.013-0.0510.000
177A178ILE0-0.030-0.0127.085-0.184-0.1840.0000.0000.0000.000
178A179LEU0-0.018-0.0059.519-0.155-0.1550.0000.0000.0000.000
179A180THR0-0.039-0.03413.224-0.004-0.0040.0000.0000.0000.000
180A181GLN00.008-0.01116.181-0.040-0.0400.0000.0000.0000.000
181A182GLU-1-0.908-0.97118.6030.3450.3450.0000.0000.0000.000
182A183GLU-1-0.848-0.90717.8180.3880.3880.0000.0000.0000.000
183A184GLU-1-0.744-0.79616.3970.5110.5110.0000.0000.0000.000
184A185GLU-1-0.755-0.86918.2800.2910.2910.0000.0000.0000.000
185A186LYS10.7870.89720.465-0.344-0.3440.0000.0000.0000.000
186A187TRP0-0.014-0.03213.344-0.011-0.0110.0000.0000.0000.000
187A188LEU0-0.0090.00616.703-0.017-0.0170.0000.0000.0000.000
188A189ASN00.0470.05619.630-0.042-0.0420.0000.0000.0000.000
189A190PRO00.013-0.00422.6440.0040.0040.0000.0000.0000.000
190A191SER0-0.077-0.05524.027-0.011-0.0110.0000.0000.0000.000
191A192LEU0-0.069-0.00120.410-0.008-0.0080.0000.0000.0000.000
192A193SER0-0.028-0.04923.430-0.006-0.0060.0000.0000.0000.000
193A194LYS10.8470.89819.896-0.155-0.1550.0000.0000.0000.000
194A195ALA00.0050.00820.6690.0230.0230.0000.0000.0000.000
195A196GLU-1-0.805-0.87121.3360.2210.2210.0000.0000.0000.000
196A197ILE00.0020.00416.6020.0340.0340.0000.0000.0000.000
197A198ALA00.013-0.00116.5960.0510.0510.0000.0000.0000.000
198A199SER0-0.053-0.03616.6520.0500.0500.0000.0000.0000.000
199A200LEU00.0030.01015.8730.0050.0050.0000.0000.0000.000
200A201LEU0-0.044-0.00511.1130.0850.0850.0000.0000.0000.000
201A202LYS10.8410.92212.463-0.486-0.4860.0000.0000.0000.000
202A203PRO00.0270.01810.0830.1420.1420.0000.0000.0000.000
203A204PHE00.0060.00210.302-0.110-0.1100.0000.0000.0000.000
204A205ASP-1-0.826-0.91912.1690.2510.2510.0000.0000.0000.000
205A206THR00.013-0.01513.4040.0190.0190.0000.0000.0000.000
206A207GLU-1-0.911-0.94614.4210.1260.1260.0000.0000.0000.000
207A208LYS10.8820.96715.109-0.394-0.3940.0000.0000.0000.000
208A209MET00.0040.0367.6340.0830.0830.0000.0000.0000.000
209A210ASP-1-0.823-0.88812.2980.0360.0360.0000.0000.0000.000
210A211ALA0-0.005-0.00410.6280.0310.0310.0000.0000.0000.000
211A212TYR0-0.063-0.02212.418-0.021-0.0210.0000.0000.0000.000
212A213VAL0-0.0020.00712.862-0.032-0.0320.0000.0000.0000.000
213A214ILE00.0120.00710.6700.0700.0700.0000.0000.0000.000
214A215ARG10.8350.89614.6350.0430.0430.0000.0000.0000.000
215A216ASN00.042-0.00314.017-0.065-0.0650.0000.0000.0000.000
216A217ASP-1-0.870-0.94915.285-0.159-0.1590.0000.0000.0000.000
217A218PHE00.0510.0159.0530.0170.0170.0000.0000.0000.000
218A219LEU00.0030.01211.0330.0320.0320.0000.0000.0000.000
219A220LYS10.8010.90814.2250.1740.1740.0000.0000.0000.000
220A221LYS10.7940.93016.7780.1020.1020.0000.0000.0000.000
221A222SER00.0320.01317.189-0.016-0.0160.0000.0000.0000.000
222A223PRO00.0440.01815.0120.0100.0100.0000.0000.0000.000
223A224ASN00.0170.01115.5140.0400.0400.0000.0000.0000.000
224A225ASP-1-0.819-0.88117.8350.0000.0000.0000.0000.0000.000
225A226PRO00.0540.01017.3350.0080.0080.0000.0000.0000.000
226A227THR0-0.118-0.08318.028-0.007-0.0070.0000.0000.0000.000
227A228ILE0-0.046-0.02312.734-0.048-0.0480.0000.0000.0000.000
228A229VAL00.0450.02712.377-0.040-0.0400.0000.0000.0000.000
229A230GLN0-0.043-0.00614.620-0.006-0.0060.0000.0000.0000.000
230A231ARG10.9270.94916.552-0.008-0.0080.0000.0000.0000.000
231A232ALA00.0270.02117.609-0.006-0.0060.0000.0000.0000.000
232A233LEU0-0.034-0.01219.1330.0270.0270.0000.0000.0000.000
233A234GLU-1-0.829-0.88522.686-0.072-0.0720.0000.0000.0000.000