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: JQ1V9

Calculation Name: 2O6S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O6S

Chain ID: A

ChEMBL ID:

UniProt ID: Q4G1L3

Base Structure: X-ray

Registration Date: 2023-09-24

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2343514.192268
FMO2-HF: Nuclear repulsion 2262882.308819
FMO2-HF: Total energy -80631.883449
FMO2-MP2: Total energy -80865.245344


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:24:CYS)


Summations of interaction energy for fragment #1(A:24: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.
-27.032-18.16121.297-12.766-17.4060.028
Interaction energy analysis for fragmet #1(A:24:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.004
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].
3A26SER00.0400.0173.640-1.6880.109-0.001-0.946-0.8500.004
4A27ARG10.8850.9276.0982.4132.4130.0000.0000.0000.000
5A28CYS0-0.083-0.0273.397-6.039-2.7320.240-0.994-2.553-0.001
8A32GLY00.0240.0163.8411.2783.257-0.023-0.978-0.9780.002
9A33THR0-0.034-0.0165.1660.5120.628-0.002-0.008-0.1060.000
10A34THR00.0110.0093.6960.4490.8640.002-0.102-0.3150.000
11A35VAL0-0.015-0.0292.391-5.453-2.5637.771-4.323-6.337-0.018
12A36GLU-1-0.808-0.8581.787-13.714-18.56912.145-3.926-3.3650.049
13A38TYR0-0.001-0.0116.063-1.785-1.7850.0000.0000.0000.000
14A39SER0-0.012-0.0108.837-0.758-0.7580.0000.0000.0000.000
15A40GLN0-0.007-0.0045.8660.2530.2530.0000.0000.0000.000
16A41GLY00.0020.00511.453-0.115-0.1150.0000.0000.0000.000
17A42ARG10.8210.9097.827-1.128-1.1280.0000.0000.0000.000
18A43THR00.0600.01314.1400.0810.0810.0000.0000.0000.000
19A44SER0-0.067-0.03814.647-0.056-0.0560.0000.0000.0000.000
20A45VAL00.0470.02310.5120.0830.0830.0000.0000.0000.000
21A46PRO0-0.029-0.0087.083-0.515-0.5150.0000.0000.0000.000
22A47THR00.0370.0098.0420.5730.5730.0000.0000.0000.000
23A48GLY00.0310.0024.503-0.430-0.404-0.002-0.017-0.0080.000
24A49ILE0-0.0010.0032.845-0.6251.3000.360-0.969-1.317-0.008
25A50PRO00.0150.0172.804-3.277-2.1400.809-0.496-1.4510.000
26A51ALA00.0930.0625.7080.0150.0150.0000.0000.0000.000
27A52GLN00.0010.0078.4330.2940.2940.0000.0000.0000.000
28A53THR0-0.043-0.0406.2140.3700.504-0.002-0.007-0.1260.000
29A54THR00.0110.0148.019-0.446-0.4460.0000.0000.0000.000
30A55TYR0-0.045-0.0176.604-0.869-0.8690.0000.0000.0000.000
31A56LEU00.0210.0076.7481.9271.9270.0000.0000.0000.000
32A57ASP-1-0.825-0.9066.6752.0012.0010.0000.0000.0000.000
33A58LEU00.003-0.0117.1561.0271.0270.0000.0000.0000.000
34A59GLU-1-0.729-0.8379.9050.9880.9880.0000.0000.0000.000
35A60THR0-0.043-0.01311.776-0.154-0.1540.0000.0000.0000.000
36A61ASN0-0.055-0.02810.209-0.561-0.5610.0000.0000.0000.000
37A62SER0-0.065-0.04114.607-0.266-0.2660.0000.0000.0000.000
38A63LEU00.0310.03213.572-0.131-0.1310.0000.0000.0000.000
39A64LYS10.9680.97817.665-0.671-0.6710.0000.0000.0000.000
40A65SER0-0.010-0.00120.628-0.039-0.0390.0000.0000.0000.000
41A66LEU00.0290.01016.5880.1010.1010.0000.0000.0000.000
42A67PRO00.0300.01217.133-0.098-0.0980.0000.0000.0000.000
43A68ASN00.004-0.01519.1960.1090.1090.0000.0000.0000.000
44A69GLY00.0650.04218.727-0.032-0.0320.0000.0000.0000.000
45A70VAL0-0.069-0.02613.7680.0860.0860.0000.0000.0000.000
46A71PHE00.0430.00612.3980.2550.2550.0000.0000.0000.000
47A72ASP-1-0.875-0.95714.1401.5221.5220.0000.0000.0000.000
48A73GLU-1-0.929-0.96911.9341.5391.5390.0000.0000.0000.000
49A74LEU0-0.051-0.0228.8100.2540.2540.0000.0000.0000.000
50A75THR00.0450.01212.3510.0500.0500.0000.0000.0000.000
51A76SER0-0.054-0.02811.605-0.403-0.4030.0000.0000.0000.000
52A77LEU0-0.033-0.00910.0990.0120.0120.0000.0000.0000.000
53A78THR0-0.004-0.01112.533-0.429-0.4290.0000.0000.0000.000
54A79GLN0-0.0170.00211.728-0.281-0.2810.0000.0000.0000.000
55A80LEU0-0.0020.00611.6740.6320.6320.0000.0000.0000.000
56A81TYR0-0.025-0.02010.656-0.643-0.6430.0000.0000.0000.000
57A82LEU00.014-0.00611.7530.4120.4120.0000.0000.0000.000
58A83GLY00.0500.02914.462-0.253-0.2530.0000.0000.0000.000
59A84GLY00.0250.00815.3910.1080.1080.0000.0000.0000.000
60A85ASN0-0.081-0.04513.862-0.085-0.0850.0000.0000.0000.000
61A86LYS10.8790.92018.075-0.598-0.5980.0000.0000.0000.000
62A87LEU00.0100.01717.770-0.065-0.0650.0000.0000.0000.000
63A88GLN00.018-0.00321.763-0.037-0.0370.0000.0000.0000.000
64A89SER0-0.035-0.01424.657-0.025-0.0250.0000.0000.0000.000
65A90LEU00.0260.00820.9470.0860.0860.0000.0000.0000.000
66A91PRO00.0000.01821.627-0.080-0.0800.0000.0000.0000.000
67A92ASN00.025-0.02024.3570.0620.0620.0000.0000.0000.000
68A93GLY0-0.008-0.01124.5440.0020.0020.0000.0000.0000.000
69A94VAL0-0.007-0.00818.9650.0520.0520.0000.0000.0000.000
70A95PHE00.1010.04217.8810.1540.1540.0000.0000.0000.000
71A96ASN0-0.0040.01020.059-0.035-0.0350.0000.0000.0000.000
72A97LYS10.9250.99417.892-1.274-1.2740.0000.0000.0000.000
73A98LEU0-0.0030.01015.0880.0300.0300.0000.0000.0000.000
74A99THR00.0370.00918.242-0.001-0.0010.0000.0000.0000.000
75A100SER0-0.051-0.02516.720-0.210-0.2100.0000.0000.0000.000
76A101LEU0-0.047-0.00415.3100.0130.0130.0000.0000.0000.000
77A102THR0-0.085-0.05316.682-0.213-0.2130.0000.0000.0000.000
78A103TYR00.0180.00515.668-0.200-0.2000.0000.0000.0000.000
79A104LEU0-0.001-0.00516.3310.2570.2570.0000.0000.0000.000
80A105ASN00.0120.03815.616-0.356-0.3560.0000.0000.0000.000
81A106LEU00.017-0.00916.6890.1640.1640.0000.0000.0000.000
82A107SER0-0.050-0.03519.409-0.131-0.1310.0000.0000.0000.000
83A108THR0-0.044-0.02719.6320.0540.0540.0000.0000.0000.000
84A109ASN0-0.052-0.02318.1300.0430.0430.0000.0000.0000.000
85A110GLN0-0.007-0.00822.113-0.097-0.0970.0000.0000.0000.000
86A111LEU00.0170.02622.303-0.038-0.0380.0000.0000.0000.000
87A112GLN00.0260.00426.120-0.033-0.0330.0000.0000.0000.000
88A113SER0-0.044-0.01729.050-0.022-0.0220.0000.0000.0000.000
89A114LEU00.0280.00625.4390.0570.0570.0000.0000.0000.000
90A115PRO00.0080.00726.588-0.047-0.0470.0000.0000.0000.000
91A116ASN00.0410.00729.4940.0340.0340.0000.0000.0000.000
92A117GLY00.0310.02629.9050.0120.0120.0000.0000.0000.000
93A118VAL0-0.043-0.02024.0860.0470.0470.0000.0000.0000.000
94A119PHE00.0620.01722.5550.0920.0920.0000.0000.0000.000
95A120ASP-1-0.851-0.91025.6380.6520.6520.0000.0000.0000.000
96A121LYS10.9070.94524.544-0.894-0.8940.0000.0000.0000.000
97A122LEU00.0030.01520.8350.0350.0350.0000.0000.0000.000
98A123THR00.008-0.00123.7580.0060.0060.0000.0000.0000.000
99A124GLN0-0.054-0.02621.272-0.138-0.1380.0000.0000.0000.000
100A125LEU0-0.0110.01220.0320.0130.0130.0000.0000.0000.000
101A126LYS10.8280.89721.299-0.996-0.9960.0000.0000.0000.000
102A127GLU-1-0.847-0.93018.7251.1541.1540.0000.0000.0000.000
103A128LEU00.0250.01621.0690.0930.0930.0000.0000.0000.000
104A129ALA00.0070.01220.070-0.124-0.1240.0000.0000.0000.000
105A130LEU00.0360.00221.2600.0860.0860.0000.0000.0000.000
106A131ASN0-0.021-0.01022.936-0.001-0.0010.0000.0000.0000.000
107A132THR0-0.031-0.02623.7220.0670.0670.0000.0000.0000.000
108A133ASN0-0.041-0.01522.8000.0430.0430.0000.0000.0000.000
109A134GLN00.0190.00426.424-0.058-0.0580.0000.0000.0000.000
110A135LEU0-0.0060.01126.795-0.027-0.0270.0000.0000.0000.000
111A136GLN00.0310.00330.539-0.021-0.0210.0000.0000.0000.000
112A137SER0-0.068-0.03033.342-0.021-0.0210.0000.0000.0000.000
113A138LEU00.005-0.00730.1040.0370.0370.0000.0000.0000.000
114A139PRO00.0050.00331.389-0.030-0.0300.0000.0000.0000.000
115A140ASP-1-0.861-0.94134.2640.4060.4060.0000.0000.0000.000
116A141GLY00.0170.01135.2490.0170.0170.0000.0000.0000.000
117A142VAL0-0.067-0.02429.0000.0300.0300.0000.0000.0000.000
118A143PHE00.0510.00627.4110.0550.0550.0000.0000.0000.000
119A144ASP-1-0.846-0.91830.5150.4760.4760.0000.0000.0000.000
120A145LYS10.8040.88529.239-0.614-0.6140.0000.0000.0000.000
121A146LEU0-0.0030.00925.4710.0300.0300.0000.0000.0000.000
122A147THR00.0310.02028.4660.0030.0030.0000.0000.0000.000
123A148GLN00.0130.02325.729-0.026-0.0260.0000.0000.0000.000
124A149LEU0-0.0270.00224.6150.0170.0170.0000.0000.0000.000
125A150LYS10.8910.93525.281-0.596-0.5960.0000.0000.0000.000
126A151ASP-1-0.828-0.88223.7050.6040.6040.0000.0000.0000.000
127A152LEU00.0510.03624.8950.0620.0620.0000.0000.0000.000
128A153ARG10.8080.86823.035-0.718-0.7180.0000.0000.0000.000
129A154LEU00.0710.02325.9340.0400.0400.0000.0000.0000.000
130A155TYR0-0.0010.01225.111-0.008-0.0080.0000.0000.0000.000
131A156GLN00.0420.03127.2970.0630.0630.0000.0000.0000.000
132A157ASN0-0.0180.00327.2340.0410.0410.0000.0000.0000.000
133A158GLN0-0.045-0.03830.840-0.054-0.0540.0000.0000.0000.000
134A159LEU00.0160.02731.473-0.015-0.0150.0000.0000.0000.000
135A160LYS10.8480.91235.274-0.268-0.2680.0000.0000.0000.000
136A161SER0-0.034-0.01738.080-0.013-0.0130.0000.0000.0000.000
137A162VAL0-0.009-0.00734.9110.0220.0220.0000.0000.0000.000
138A163PRO00.0360.02736.094-0.022-0.0220.0000.0000.0000.000
139A164ASP-1-0.823-0.91138.8510.2910.2910.0000.0000.0000.000
140A165GLY00.0260.01040.0100.0040.0040.0000.0000.0000.000
141A166VAL0-0.067-0.01933.6980.0160.0160.0000.0000.0000.000
142A167PHE00.035-0.00731.9250.0350.0350.0000.0000.0000.000
143A168ASP-1-0.851-0.91235.1860.3460.3460.0000.0000.0000.000
144A169ARG10.8540.92634.536-0.448-0.4480.0000.0000.0000.000
145A170LEU0-0.0120.00830.1110.0190.0190.0000.0000.0000.000
146A171THR0-0.010-0.02332.721-0.012-0.0120.0000.0000.0000.000
147A172SER0-0.044-0.02729.230-0.029-0.0290.0000.0000.0000.000
148A173LEU0-0.049-0.01029.1300.0090.0090.0000.0000.0000.000
149A174GLN0-0.012-0.00529.184-0.013-0.0130.0000.0000.0000.000
150A175TYR0-0.060-0.03226.345-0.058-0.0580.0000.0000.0000.000
151A176ILE00.0270.01828.8470.0390.0390.0000.0000.0000.000
152A177TRP0-0.028-0.00926.532-0.025-0.0250.0000.0000.0000.000
153A178LEU00.0400.00430.2130.0220.0220.0000.0000.0000.000
154A179HIS0-0.027-0.02229.974-0.001-0.0010.0000.0000.0000.000
155A180ASP-1-0.860-0.92531.9410.3210.3210.0000.0000.0000.000
156A181ASN00.0230.00731.4850.0300.0300.0000.0000.0000.000
157A182PRO00.0140.03435.212-0.021-0.0210.0000.0000.0000.000
158A183TRP0-0.009-0.01934.415-0.007-0.0070.0000.0000.0000.000
159A184ASP-1-0.805-0.89140.0800.2050.2050.0000.0000.0000.000
160A185CYS0-0.070-0.03340.4660.0150.0150.0000.0000.0000.000
161A186THR00.0410.01945.946-0.014-0.0140.0000.0000.0000.000
162A187CYS0-0.065-0.01348.0350.0050.0050.0000.0000.0000.000
163A188PRO00.0320.00150.115-0.006-0.0060.0000.0000.0000.000
164A189GLY00.0340.01446.4360.0070.0070.0000.0000.0000.000
165A190ILE0-0.0060.00342.0840.0130.0130.0000.0000.0000.000
166A191ARG10.8300.88544.144-0.246-0.2460.0000.0000.0000.000
167A192TYR0-0.033-0.01738.1920.0020.0020.0000.0000.0000.000
168A193LEU00.0430.02337.1720.0030.0030.0000.0000.0000.000
169A194SER0-0.015-0.02441.0090.0000.0000.0000.0000.0000.000
170A195GLU-1-0.802-0.89643.8810.2300.2300.0000.0000.0000.000
171A196TRP0-0.045-0.00934.584-0.008-0.0080.0000.0000.0000.000
172A197ILE00.015-0.00538.0370.0020.0020.0000.0000.0000.000
173A198ASN0-0.068-0.05440.259-0.010-0.0100.0000.0000.0000.000
174A199LYS10.8500.93142.483-0.253-0.2530.0000.0000.0000.000
175A200HIS10.8870.95137.334-0.319-0.3190.0000.0000.0000.000
176A201SER00.0540.03637.7720.0160.0160.0000.0000.0000.000
177A202GLY00.014-0.00237.590-0.001-0.0010.0000.0000.0000.000
178A203VAL0-0.0010.00332.8000.0040.0040.0000.0000.0000.000
179A204VAL00.0030.00532.7760.0240.0240.0000.0000.0000.000
180A205ARG10.8650.94530.124-0.354-0.3540.0000.0000.0000.000
181A206ASN00.0520.00932.2950.0180.0180.0000.0000.0000.000
182A207SER00.0470.01528.9850.0140.0140.0000.0000.0000.000
183A208ALA0-0.0020.01328.6710.0050.0050.0000.0000.0000.000
184A209GLY00.0170.01729.173-0.008-0.0080.0000.0000.0000.000
185A210SER0-0.016-0.00329.8300.0040.0040.0000.0000.0000.000
186A211VAL00.007-0.00233.5180.0190.0190.0000.0000.0000.000
187A212ALA0-0.012-0.01135.255-0.021-0.0210.0000.0000.0000.000
188A213PRO00.0530.03937.0170.0120.0120.0000.0000.0000.000
189A214ASP-1-0.813-0.88338.9690.2020.2020.0000.0000.0000.000
190A215SER0-0.050-0.03435.624-0.004-0.0040.0000.0000.0000.000
191A216ALA00.0410.03636.9150.0040.0040.0000.0000.0000.000
192A217LYS10.8750.93337.938-0.215-0.2150.0000.0000.0000.000
193A219SER00.014-0.01941.467-0.007-0.0070.0000.0000.0000.000
194A220GLY00.0170.01942.497-0.001-0.0010.0000.0000.0000.000
195A221SER0-0.023-0.00845.393-0.007-0.0070.0000.0000.0000.000
196A222GLY00.0300.03143.283-0.007-0.0070.0000.0000.0000.000
197A223LYS10.9170.95343.828-0.160-0.1600.0000.0000.0000.000
198A224PRO00.0050.01342.5330.0110.0110.0000.0000.0000.000
199A225VAL00.0570.03340.255-0.010-0.0100.0000.0000.0000.000
200A226ARG10.8040.87842.117-0.206-0.2060.0000.0000.0000.000
201A227SER0-0.058-0.04044.191-0.011-0.0110.0000.0000.0000.000
202A228ILE0-0.015-0.02046.717-0.013-0.0130.0000.0000.0000.000
203A229ILE00.0250.02548.4100.0100.0100.0000.0000.0000.000
204A231PRO00.0270.02752.0680.0010.0010.0000.0000.0000.000