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: 89LQY

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2338189.374648
FMO2-HF: Nuclear repulsion 2257558.264581
FMO2-HF: Total energy -80631.110067
FMO2-MP2: Total energy -80864.494338


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.
-18.485-8.44516.61-10.718-15.9340.025
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 : -0.018 / q_NPA : -0.039
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].
3A26SER00.0540.0293.798-2.138-1.049-0.006-0.485-0.5980.001
4A27ARG10.9050.9356.1442.7362.7360.0000.0000.0000.000
5A28CYS0-0.117-0.0383.704-6.169-2.9810.067-1.164-2.091-0.003
8A32GLY00.0230.0183.7871.4143.409-0.027-0.873-1.0940.005
9A33THR0-0.035-0.0294.754-0.1020.015-0.002-0.012-0.1030.000
10A34THR00.0110.0074.2050.0700.470-0.001-0.093-0.3060.000
11A35VAL0-0.005-0.0182.306-4.747-2.1848.105-4.351-6.318-0.016
12A36GLU-1-0.889-0.9471.898-8.021-9.9287.279-2.644-2.7290.041
13A38TYR00.0270.0306.400-1.416-1.4160.0000.0000.0000.000
14A39SER00.0140.0019.127-0.735-0.7350.0000.0000.0000.000
15A40GLN0-0.048-0.0156.1500.4900.4900.0000.0000.0000.000
16A41GLY00.002-0.01011.580-0.065-0.0650.0000.0000.0000.000
17A42ARG10.8190.9167.609-0.199-0.1990.0000.0000.0000.000
18A43THR00.022-0.00214.3310.0990.0990.0000.0000.0000.000
19A44SER0-0.030-0.01814.3190.0010.0010.0000.0000.0000.000
20A45VAL00.0360.02210.6280.0170.0170.0000.0000.0000.000
21A46PRO0-0.035-0.0127.350-0.334-0.3340.0000.0000.0000.000
22A47THR00.0390.0118.1860.4870.4870.0000.0000.0000.000
23A48GLY00.030-0.0034.671-0.339-0.328-0.002-0.0090.0000.000
24A49ILE00.0000.0073.1530.9802.2970.090-0.513-0.895-0.004
25A50PRO00.0000.0042.962-2.984-1.8591.109-0.567-1.6670.001
26A51ALA00.0900.0485.783-0.156-0.1560.0000.0000.0000.000
27A52GLN00.000-0.0068.7170.3730.3730.0000.0000.0000.000
28A53THR0-0.051-0.0356.1430.2330.375-0.002-0.007-0.1330.000
29A54THR00.0140.0228.186-0.387-0.3870.0000.0000.0000.000
30A55TYR00.0250.0226.813-0.835-0.8350.0000.0000.0000.000
31A56LEU00.0270.0096.8771.8961.8960.0000.0000.0000.000
32A57ASP-1-0.806-0.9056.7211.8621.8620.0000.0000.0000.000
33A58LEU0-0.027-0.0347.5260.4820.4820.0000.0000.0000.000
34A59GLU-1-0.822-0.91510.1860.9450.9450.0000.0000.0000.000
35A60THR0-0.052-0.01911.983-0.177-0.1770.0000.0000.0000.000
36A61ASN0-0.057-0.02110.647-0.657-0.6570.0000.0000.0000.000
37A62SER0-0.061-0.04214.881-0.128-0.1280.0000.0000.0000.000
38A63LEU00.0040.00913.998-0.105-0.1050.0000.0000.0000.000
39A64LYS10.9430.96918.136-0.578-0.5780.0000.0000.0000.000
40A65SER0-0.008-0.00621.047-0.017-0.0170.0000.0000.0000.000
41A66LEU00.0310.00516.9020.0860.0860.0000.0000.0000.000
42A67PRO00.0190.01917.409-0.083-0.0830.0000.0000.0000.000
43A68ASN00.017-0.01419.4480.0820.0820.0000.0000.0000.000
44A69GLY00.0580.02619.130-0.016-0.0160.0000.0000.0000.000
45A70VAL0-0.067-0.01813.9130.0930.0930.0000.0000.0000.000
46A71PHE00.0310.00113.0870.2240.2240.0000.0000.0000.000
47A72ASP-1-0.925-0.96514.7211.4941.4940.0000.0000.0000.000
48A73GLU-1-0.910-0.95612.2081.6871.6870.0000.0000.0000.000
49A74LEU0-0.064-0.0228.9920.1720.1720.0000.0000.0000.000
50A75THR00.004-0.01612.525-0.039-0.0390.0000.0000.0000.000
51A76SER0-0.0120.00512.006-0.305-0.3050.0000.0000.0000.000
52A77LEU0-0.061-0.01610.3520.0360.0360.0000.0000.0000.000
53A78THR0-0.037-0.02212.900-0.382-0.3820.0000.0000.0000.000
54A79GLN00.0030.01711.853-0.259-0.2590.0000.0000.0000.000
55A80LEU00.0230.02211.6840.5920.5920.0000.0000.0000.000
56A81TYR0-0.032-0.02710.470-0.605-0.6050.0000.0000.0000.000
57A82LEU00.000-0.01712.1080.2660.2660.0000.0000.0000.000
58A83GLY00.0500.04614.794-0.225-0.2250.0000.0000.0000.000
59A84GLY00.0150.00315.4570.0710.0710.0000.0000.0000.000
60A85ASN0-0.065-0.03314.252-0.118-0.1180.0000.0000.0000.000
61A86LYS10.9130.94118.269-0.455-0.4550.0000.0000.0000.000
62A87LEU00.0000.00718.391-0.051-0.0510.0000.0000.0000.000
63A88GLN00.0400.02022.206-0.031-0.0310.0000.0000.0000.000
64A89SER0-0.038-0.01825.003-0.026-0.0260.0000.0000.0000.000
65A90LEU00.0210.00321.5310.0690.0690.0000.0000.0000.000
66A91PRO00.0130.03021.664-0.067-0.0670.0000.0000.0000.000
67A92ASN00.054-0.00724.6000.0390.0390.0000.0000.0000.000
68A93GLY0-0.031-0.02724.7610.0170.0170.0000.0000.0000.000
69A94VAL0-0.0050.01019.4590.0610.0610.0000.0000.0000.000
70A95PHE00.0950.03918.3330.1290.1290.0000.0000.0000.000
71A96ASN0-0.057-0.02920.7560.0060.0060.0000.0000.0000.000
72A97LYS10.9810.98918.421-1.158-1.1580.0000.0000.0000.000
73A98LEU00.0090.01615.4410.0370.0370.0000.0000.0000.000
74A99THR00.012-0.01018.467-0.020-0.0200.0000.0000.0000.000
75A100SER00.0010.02017.416-0.158-0.1580.0000.0000.0000.000
76A101LEU0-0.061-0.01515.6100.0280.0280.0000.0000.0000.000
77A102THR0-0.084-0.04317.191-0.174-0.1740.0000.0000.0000.000
78A103TYR00.008-0.00115.839-0.192-0.1920.0000.0000.0000.000
79A104LEU00.0270.02116.3100.2360.2360.0000.0000.0000.000
80A105ASN00.0660.05715.781-0.287-0.2870.0000.0000.0000.000
81A106LEU00.029-0.00316.9530.1300.1300.0000.0000.0000.000
82A107SER0-0.052-0.02419.144-0.132-0.1320.0000.0000.0000.000
83A108THR0-0.010-0.01419.7190.0320.0320.0000.0000.0000.000
84A109ASN0-0.042-0.00918.5220.0240.0240.0000.0000.0000.000
85A110GLN0-0.042-0.03422.336-0.078-0.0780.0000.0000.0000.000
86A111LEU00.0150.01922.822-0.025-0.0250.0000.0000.0000.000
87A112GLN00.0670.02626.602-0.038-0.0380.0000.0000.0000.000
88A113SER0-0.043-0.02029.390-0.022-0.0220.0000.0000.0000.000
89A114LEU00.0150.00225.9610.0480.0480.0000.0000.0000.000
90A115PRO00.0120.01527.009-0.041-0.0410.0000.0000.0000.000
91A116ASN00.0670.00929.8840.0220.0220.0000.0000.0000.000
92A117GLY00.0270.01430.7320.0200.0200.0000.0000.0000.000
93A118VAL0-0.057-0.01524.6030.0420.0420.0000.0000.0000.000
94A119PHE00.0490.01023.0540.0800.0800.0000.0000.0000.000
95A120ASP-1-0.883-0.94926.1200.6390.6390.0000.0000.0000.000
96A121LYS10.9000.94524.606-0.866-0.8660.0000.0000.0000.000
97A122LEU00.0090.01921.1440.0270.0270.0000.0000.0000.000
98A123THR00.022-0.00124.050-0.002-0.0020.0000.0000.0000.000
99A124GLN0-0.0190.00121.485-0.048-0.0480.0000.0000.0000.000
100A125LEU0-0.038-0.00820.2780.0220.0220.0000.0000.0000.000
101A126LYS10.9110.94921.252-0.887-0.8870.0000.0000.0000.000
102A127GLU-1-0.943-0.97319.5560.9690.9690.0000.0000.0000.000
103A128LEU00.0500.03020.7740.1040.1040.0000.0000.0000.000
104A129ALA00.0040.01720.120-0.113-0.1130.0000.0000.0000.000
105A130LEU00.018-0.01321.6070.0650.0650.0000.0000.0000.000
106A131ASN0-0.0120.00322.8130.0070.0070.0000.0000.0000.000
107A132THR0-0.035-0.02523.9570.0600.0600.0000.0000.0000.000
108A133ASN0-0.0210.00223.0930.0390.0390.0000.0000.0000.000
109A134GLN0-0.026-0.02726.623-0.032-0.0320.0000.0000.0000.000
110A135LEU0-0.0030.01027.393-0.019-0.0190.0000.0000.0000.000
111A136GLN00.0220.00330.965-0.019-0.0190.0000.0000.0000.000
112A137SER0-0.079-0.03133.515-0.020-0.0200.0000.0000.0000.000
113A138LEU00.000-0.00630.5540.0320.0320.0000.0000.0000.000
114A139PRO00.0020.00731.349-0.026-0.0260.0000.0000.0000.000
115A140ASP-1-0.830-0.92834.3910.3780.3780.0000.0000.0000.000
116A141GLY00.003-0.00135.5590.0170.0170.0000.0000.0000.000
117A142VAL0-0.058-0.01929.3570.0300.0300.0000.0000.0000.000
118A143PHE00.028-0.00327.8910.0470.0470.0000.0000.0000.000
119A144ASP-1-0.901-0.94630.9610.4560.4560.0000.0000.0000.000
120A145LYS10.8530.92829.707-0.599-0.5990.0000.0000.0000.000
121A146LEU0-0.0030.01125.9680.0200.0200.0000.0000.0000.000
122A147THR00.0140.00328.914-0.002-0.0020.0000.0000.0000.000
123A148GLN0-0.016-0.00426.032-0.014-0.0140.0000.0000.0000.000
124A149LEU0-0.033-0.00824.6410.0140.0140.0000.0000.0000.000
125A150LYS10.9210.96024.954-0.625-0.6250.0000.0000.0000.000
126A151ASP-1-0.848-0.91423.9290.5900.5900.0000.0000.0000.000
127A152LEU00.0600.03824.9100.0580.0580.0000.0000.0000.000
128A153ARG10.8680.91623.009-0.706-0.7060.0000.0000.0000.000
129A154LEU00.0530.01326.0990.0360.0360.0000.0000.0000.000
130A155TYR0-0.0100.00824.684-0.011-0.0110.0000.0000.0000.000
131A156GLN00.0280.01627.8910.0510.0510.0000.0000.0000.000
132A157ASN0-0.031-0.01627.5900.0410.0410.0000.0000.0000.000
133A158GLN0-0.022-0.02331.040-0.048-0.0480.0000.0000.0000.000
134A159LEU00.0060.02332.000-0.011-0.0110.0000.0000.0000.000
135A160LYS10.9770.98935.622-0.253-0.2530.0000.0000.0000.000
136A161SER0-0.017-0.01338.398-0.012-0.0120.0000.0000.0000.000
137A162VAL00.0060.00635.5580.0190.0190.0000.0000.0000.000
138A163PRO00.0230.02036.270-0.019-0.0190.0000.0000.0000.000
139A164ASP-1-0.896-0.95239.1390.2810.2810.0000.0000.0000.000
140A165GLY00.006-0.02740.3670.0080.0080.0000.0000.0000.000
141A166VAL0-0.048-0.00934.0930.0170.0170.0000.0000.0000.000
142A167PHE00.010-0.01732.5180.0290.0290.0000.0000.0000.000
143A168ASP-1-0.862-0.91535.6400.3310.3310.0000.0000.0000.000
144A169ARG10.9330.97334.983-0.431-0.4310.0000.0000.0000.000
145A170LEU0-0.0150.00430.5330.0170.0170.0000.0000.0000.000
146A171THR0-0.016-0.02133.405-0.005-0.0050.0000.0000.0000.000
147A172SER0-0.0150.00329.884-0.026-0.0260.0000.0000.0000.000
148A173LEU0-0.054-0.01629.3160.0110.0110.0000.0000.0000.000
149A174GLN0-0.056-0.03828.984-0.006-0.0060.0000.0000.0000.000
150A175TYR0-0.059-0.03127.365-0.052-0.0520.0000.0000.0000.000
151A176ILE00.0280.03028.9150.0380.0380.0000.0000.0000.000
152A177TRP0-0.0210.00626.280-0.028-0.0280.0000.0000.0000.000
153A178LEU00.0530.00130.4530.0180.0180.0000.0000.0000.000
154A179HIS0-0.077-0.04330.1330.0020.0020.0000.0000.0000.000
155A180ASP-1-0.836-0.91932.2180.2880.2880.0000.0000.0000.000
156A181ASN00.0420.02131.9480.0260.0260.0000.0000.0000.000
157A182PRO0-0.0140.01135.406-0.019-0.0190.0000.0000.0000.000
158A183TRP0-0.010-0.01834.866-0.004-0.0040.0000.0000.0000.000
159A184ASP-1-0.860-0.93040.3500.1950.1950.0000.0000.0000.000
160A185CYS0-0.093-0.05740.3650.0180.0180.0000.0000.0000.000
161A186THR00.0390.02545.986-0.013-0.0130.0000.0000.0000.000
162A187CYS0-0.106-0.02748.0710.0060.0060.0000.0000.0000.000
163A188PRO00.036-0.01250.317-0.005-0.0050.0000.0000.0000.000
164A189GLY00.0400.01546.5940.0060.0060.0000.0000.0000.000
165A190ILE00.0060.01242.4500.0120.0120.0000.0000.0000.000
166A191ARG10.9380.96944.713-0.231-0.2310.0000.0000.0000.000
167A192TYR0-0.034-0.00638.6440.0020.0020.0000.0000.0000.000
168A193LEU00.0510.02737.5650.0030.0030.0000.0000.0000.000
169A194SER00.002-0.01141.3270.0030.0030.0000.0000.0000.000
170A195GLU-1-0.899-0.96243.8630.2130.2130.0000.0000.0000.000
171A196TRP0-0.023-0.00734.888-0.006-0.0060.0000.0000.0000.000
172A197ILE00.012-0.01338.3780.0020.0020.0000.0000.0000.000
173A198ASN0-0.060-0.04540.500-0.009-0.0090.0000.0000.0000.000
174A199LYS10.9070.97442.710-0.240-0.2400.0000.0000.0000.000
175A200HIS10.8720.94437.594-0.303-0.3030.0000.0000.0000.000
176A201SER00.0430.02438.1280.0140.0140.0000.0000.0000.000
177A202GLY00.014-0.00137.794-0.003-0.0030.0000.0000.0000.000
178A203VAL00.0040.00432.8060.0050.0050.0000.0000.0000.000
179A204VAL0-0.0040.00432.9250.0240.0240.0000.0000.0000.000
180A205ARG10.9020.95830.024-0.344-0.3440.0000.0000.0000.000
181A206ASN00.0410.01932.2030.0210.0210.0000.0000.0000.000
182A207SER00.0600.02729.4840.0110.0110.0000.0000.0000.000
183A208ALA0-0.015-0.00428.8920.0110.0110.0000.0000.0000.000
184A209GLY00.0200.02029.043-0.002-0.0020.0000.0000.0000.000
185A210SER0-0.057-0.01929.782-0.003-0.0030.0000.0000.0000.000
186A211VAL00.0150.00333.2830.0150.0150.0000.0000.0000.000
187A212ALA0-0.002-0.01735.516-0.020-0.0200.0000.0000.0000.000
188A213PRO00.0260.02337.1900.0110.0110.0000.0000.0000.000
189A214ASP-1-0.807-0.86739.2010.1880.1880.0000.0000.0000.000
190A215SER0-0.073-0.04935.692-0.002-0.0020.0000.0000.0000.000
191A216ALA00.0290.04037.1230.0040.0040.0000.0000.0000.000
192A217LYS10.8940.93238.017-0.204-0.2040.0000.0000.0000.000
193A219SER0-0.026-0.01541.806-0.010-0.0100.0000.0000.0000.000
194A220GLY00.0260.01942.806-0.004-0.0040.0000.0000.0000.000
195A221SER0-0.010-0.00746.040-0.005-0.0050.0000.0000.0000.000
196A222GLY00.0700.04743.573-0.008-0.0080.0000.0000.0000.000
197A223LYS10.9150.94944.112-0.143-0.1430.0000.0000.0000.000
198A224PRO00.0390.02142.7500.0100.0100.0000.0000.0000.000
199A225VAL00.0940.04640.409-0.008-0.0080.0000.0000.0000.000
200A226ARG10.8200.87442.381-0.199-0.1990.0000.0000.0000.000
201A227SER0-0.078-0.04744.358-0.010-0.0100.0000.0000.0000.000
202A228ILE0-0.031-0.01746.647-0.011-0.0110.0000.0000.0000.000
203A229ILE00.0150.02148.3830.0090.0090.0000.0000.0000.000
204A231PRO00.0370.02952.156-0.001-0.0010.0000.0000.0000.000