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: NN4LQ

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2338249.623529
FMO2-HF: Nuclear repulsion 2257617.890731
FMO2-HF: Total energy -80631.732798
FMO2-MP2: Total energy -80865.06324


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.
-21.288-10.82917.271-11.163-16.5640.031
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 : 0.017 / q_NPA : -0.010
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].
3A26SER00.0530.0293.817-2.363-0.570-0.010-0.915-0.8680.005
4A27ARG10.8960.9376.1513.0633.0630.0000.0000.0000.000
5A28CYS0-0.122-0.0413.704-6.150-3.0200.066-1.125-2.070-0.003
8A32GLY00.0210.0183.7871.3163.305-0.026-0.866-1.0970.005
9A33THR0-0.030-0.0194.7830.1890.301-0.002-0.011-0.0990.000
10A34THR00.0070.0054.0110.1060.476-0.001-0.083-0.2860.000
11A35VAL0-0.004-0.0222.314-4.537-2.4149.029-4.511-6.641-0.016
12A36GLU-1-0.822-0.8921.900-10.207-11.9297.177-2.569-2.8850.043
13A38TYR00.0160.0116.400-1.477-1.4770.0000.0000.0000.000
14A39SER0-0.003-0.0059.127-0.733-0.7330.0000.0000.0000.000
15A40GLN0-0.021-0.0145.9680.3530.3530.0000.0000.0000.000
16A41GLY0-0.013-0.01011.580-0.091-0.0910.0000.0000.0000.000
17A42ARG10.8340.9227.6560.0060.0060.0000.0000.0000.000
18A43THR00.0410.00814.3310.0660.0660.0000.0000.0000.000
19A44SER0-0.055-0.03114.586-0.015-0.0150.0000.0000.0000.000
20A45VAL00.0280.02010.6340.0310.0310.0000.0000.0000.000
21A46PRO0-0.023-0.0087.303-0.394-0.3940.0000.0000.0000.000
22A47THR00.0390.0118.1880.4600.4600.0000.0000.0000.000
23A48GLY00.026-0.0034.659-0.404-0.384-0.002-0.010-0.0080.000
24A49ILE00.0050.0093.1490.2851.6550.095-0.553-0.911-0.004
25A50PRO00.0120.0102.959-3.137-2.0020.947-0.513-1.5700.001
26A51ALA00.0900.0555.782-0.056-0.0560.0000.0000.0000.000
27A52GLN0-0.002-0.0098.6650.3120.3120.0000.0000.0000.000
28A53THR0-0.050-0.0376.1760.3370.476-0.002-0.007-0.1290.000
29A54THR00.0140.0118.095-0.490-0.4900.0000.0000.0000.000
30A55TYR00.0100.0196.818-0.825-0.8250.0000.0000.0000.000
31A56LEU00.0220.0076.8851.9681.9680.0000.0000.0000.000
32A57ASP-1-0.834-0.9206.7241.8511.8510.0000.0000.0000.000
33A58LEU0-0.013-0.0247.5260.4950.4950.0000.0000.0000.000
34A59GLU-1-0.759-0.86210.1860.9040.9040.0000.0000.0000.000
35A60THR0-0.044-0.01811.983-0.177-0.1770.0000.0000.0000.000
36A61ASN0-0.060-0.02110.535-0.603-0.6030.0000.0000.0000.000
37A62SER0-0.043-0.02914.881-0.128-0.1280.0000.0000.0000.000
38A63LEU00.0120.01514.016-0.117-0.1170.0000.0000.0000.000
39A64LYS10.9750.98418.136-0.431-0.4310.0000.0000.0000.000
40A65SER0-0.009-0.00821.086-0.015-0.0150.0000.0000.0000.000
41A66LEU00.0280.00816.8900.0770.0770.0000.0000.0000.000
42A67PRO00.0220.01717.441-0.071-0.0710.0000.0000.0000.000
43A68ASN00.016-0.01519.4610.0910.0910.0000.0000.0000.000
44A69GLY00.0450.02319.138-0.030-0.0300.0000.0000.0000.000
45A70VAL0-0.061-0.01814.0070.0810.0810.0000.0000.0000.000
46A71PHE00.0390.00412.9620.1920.1920.0000.0000.0000.000
47A72ASP-1-0.900-0.96414.7321.3791.3790.0000.0000.0000.000
48A73GLU-1-0.894-0.94612.1811.4931.4930.0000.0000.0000.000
49A74LEU0-0.066-0.0248.9290.2070.2070.0000.0000.0000.000
50A75THR00.0390.00212.4520.0040.0040.0000.0000.0000.000
51A76SER0-0.056-0.02011.935-0.368-0.3680.0000.0000.0000.000
52A77LEU0-0.053-0.01010.1930.0690.0690.0000.0000.0000.000
53A78THR0-0.040-0.02712.909-0.417-0.4170.0000.0000.0000.000
54A79GLN00.0150.01911.855-0.267-0.2670.0000.0000.0000.000
55A80LEU00.0150.01611.6840.6200.6200.0000.0000.0000.000
56A81TYR0-0.018-0.02210.539-0.595-0.5950.0000.0000.0000.000
57A82LEU00.006-0.01312.1080.2680.2680.0000.0000.0000.000
58A83GLY00.0350.02614.794-0.242-0.2420.0000.0000.0000.000
59A84GLY00.0220.00615.4570.0730.0730.0000.0000.0000.000
60A85ASN0-0.074-0.03614.152-0.141-0.1410.0000.0000.0000.000
61A86LYS10.8740.91718.269-0.397-0.3970.0000.0000.0000.000
62A87LEU00.0070.00918.326-0.055-0.0550.0000.0000.0000.000
63A88GLN00.0210.01322.206-0.036-0.0360.0000.0000.0000.000
64A89SER0-0.020-0.01125.061-0.015-0.0150.0000.0000.0000.000
65A90LEU00.0120.00321.4870.0670.0670.0000.0000.0000.000
66A91PRO00.0090.02321.769-0.063-0.0630.0000.0000.0000.000
67A92ASN00.038-0.01224.6130.0490.0490.0000.0000.0000.000
68A93GLY0-0.015-0.02524.7750.0100.0100.0000.0000.0000.000
69A94VAL0-0.0070.00819.3380.0610.0610.0000.0000.0000.000
70A95PHE00.0960.03318.4740.1270.1270.0000.0000.0000.000
71A96ASN0-0.043-0.01620.6040.0070.0070.0000.0000.0000.000
72A97LYS10.9380.98918.356-1.124-1.1240.0000.0000.0000.000
73A98LEU0-0.0080.00715.1930.0490.0490.0000.0000.0000.000
74A99THR00.0340.00318.366-0.015-0.0150.0000.0000.0000.000
75A100SER0-0.040-0.00617.230-0.180-0.1800.0000.0000.0000.000
76A101LEU0-0.051-0.01115.5770.0370.0370.0000.0000.0000.000
77A102THR0-0.082-0.04717.306-0.175-0.1750.0000.0000.0000.000
78A103TYR00.0040.00515.873-0.188-0.1880.0000.0000.0000.000
79A104LEU00.0150.01516.3100.2400.2400.0000.0000.0000.000
80A105ASN00.0460.04315.727-0.350-0.3500.0000.0000.0000.000
81A106LEU00.005-0.01016.9530.1220.1220.0000.0000.0000.000
82A107SER0-0.047-0.03419.353-0.133-0.1330.0000.0000.0000.000
83A108THR0-0.010-0.01219.7190.0360.0360.0000.0000.0000.000
84A109ASN0-0.049-0.01318.3610.0160.0160.0000.0000.0000.000
85A110GLN0-0.027-0.02522.336-0.074-0.0740.0000.0000.0000.000
86A111LEU00.0210.02022.782-0.028-0.0280.0000.0000.0000.000
87A112GLN00.0410.01526.602-0.032-0.0320.0000.0000.0000.000
88A113SER0-0.027-0.01429.434-0.016-0.0160.0000.0000.0000.000
89A114LEU00.0130.00325.9050.0460.0460.0000.0000.0000.000
90A115PRO00.0110.01126.825-0.040-0.0400.0000.0000.0000.000
91A116ASN00.0540.00329.8840.0270.0270.0000.0000.0000.000
92A117GLY00.0310.01730.5970.0160.0160.0000.0000.0000.000
93A118VAL0-0.061-0.01624.5970.0420.0420.0000.0000.0000.000
94A119PHE00.0520.01022.9420.0780.0780.0000.0000.0000.000
95A120ASP-1-0.835-0.90826.1200.6260.6260.0000.0000.0000.000
96A121LYS10.9150.95424.607-0.815-0.8150.0000.0000.0000.000
97A122LEU00.0010.01621.0860.0320.0320.0000.0000.0000.000
98A123THR00.0300.00424.0610.0040.0040.0000.0000.0000.000
99A124GLN0-0.029-0.00221.015-0.121-0.1210.0000.0000.0000.000
100A125LEU0-0.024-0.00620.3340.0260.0260.0000.0000.0000.000
101A126LYS10.8560.92621.724-0.996-0.9960.0000.0000.0000.000
102A127GLU-1-0.920-0.96818.8801.0731.0730.0000.0000.0000.000
103A128LEU00.0340.02520.7740.1030.1030.0000.0000.0000.000
104A129ALA00.0330.02520.102-0.120-0.1200.0000.0000.0000.000
105A130LEU00.012-0.01321.6070.0590.0590.0000.0000.0000.000
106A131ASN0-0.023-0.00522.862-0.006-0.0060.0000.0000.0000.000
107A132THR0-0.018-0.02823.9790.0630.0630.0000.0000.0000.000
108A133ASN0-0.039-0.00422.8950.0320.0320.0000.0000.0000.000
109A134GLN0-0.007-0.01226.623-0.040-0.0400.0000.0000.0000.000
110A135LEU0-0.0030.00827.366-0.021-0.0210.0000.0000.0000.000
111A136GLN00.0260.00430.965-0.020-0.0200.0000.0000.0000.000
112A137SER0-0.065-0.02633.520-0.018-0.0180.0000.0000.0000.000
113A138LEU0-0.015-0.00930.5420.0310.0310.0000.0000.0000.000
114A139PRO00.0040.00631.368-0.026-0.0260.0000.0000.0000.000
115A140ASP-1-0.834-0.93034.3910.3690.3690.0000.0000.0000.000
116A141GLY0-0.011-0.00735.5590.0150.0150.0000.0000.0000.000
117A142VAL0-0.056-0.01929.3570.0300.0300.0000.0000.0000.000
118A143PHE00.0420.00027.8720.0480.0480.0000.0000.0000.000
119A144ASP-1-0.825-0.90130.9610.4520.4520.0000.0000.0000.000
120A145LYS10.8410.90729.707-0.579-0.5790.0000.0000.0000.000
121A146LEU0-0.0120.00925.8070.0240.0240.0000.0000.0000.000
122A147THR00.0330.01528.9180.0010.0010.0000.0000.0000.000
123A148GLN0-0.0060.01225.989-0.008-0.0080.0000.0000.0000.000
124A149LEU0-0.037-0.00924.6110.0180.0180.0000.0000.0000.000
125A150LYS10.9080.95025.428-0.637-0.6370.0000.0000.0000.000
126A151ASP-1-0.830-0.88023.8980.6070.6070.0000.0000.0000.000
127A152LEU00.0480.03424.9100.0580.0580.0000.0000.0000.000
128A153ARG10.8390.87722.736-0.739-0.7390.0000.0000.0000.000
129A154LEU00.0510.01026.0990.0330.0330.0000.0000.0000.000
130A155TYR0-0.0080.00924.868-0.014-0.0140.0000.0000.0000.000
131A156GLN00.0320.02527.6140.0580.0580.0000.0000.0000.000
132A157ASN0-0.019-0.00227.4710.0350.0350.0000.0000.0000.000
133A158GLN0-0.049-0.03731.040-0.050-0.0500.0000.0000.0000.000
134A159LEU00.0120.02531.902-0.012-0.0120.0000.0000.0000.000
135A160LYS10.9030.94935.622-0.240-0.2400.0000.0000.0000.000
136A161SER0-0.016-0.01638.403-0.011-0.0110.0000.0000.0000.000
137A162VAL00.0000.00235.5530.0190.0190.0000.0000.0000.000
138A163PRO00.0250.02436.225-0.019-0.0190.0000.0000.0000.000
139A164ASP-1-0.824-0.92039.1390.2740.2740.0000.0000.0000.000
140A165GLY00.016-0.00940.3670.0070.0070.0000.0000.0000.000
141A166VAL0-0.057-0.01334.0570.0180.0180.0000.0000.0000.000
142A167PHE00.012-0.01932.2370.0300.0300.0000.0000.0000.000
143A168ASP-1-0.844-0.90635.6400.3370.3370.0000.0000.0000.000
144A169ARG10.8480.92534.843-0.433-0.4330.0000.0000.0000.000
145A170LEU0-0.022-0.00230.3840.0200.0200.0000.0000.0000.000
146A171THR00.009-0.00933.405-0.011-0.0110.0000.0000.0000.000
147A172SER0-0.065-0.03629.965-0.027-0.0270.0000.0000.0000.000
148A173LEU0-0.055-0.01329.4490.0140.0140.0000.0000.0000.000
149A174GLN0-0.031-0.02229.183-0.006-0.0060.0000.0000.0000.000
150A175TYR0-0.057-0.03126.733-0.054-0.0540.0000.0000.0000.000
151A176ILE00.0360.03128.9150.0380.0380.0000.0000.0000.000
152A177TRP0-0.013-0.00226.487-0.023-0.0230.0000.0000.0000.000
153A178LEU00.0470.00130.4530.0160.0160.0000.0000.0000.000
154A179HIS0-0.077-0.04729.9880.0020.0020.0000.0000.0000.000
155A180ASP-1-0.829-0.91032.2250.2940.2940.0000.0000.0000.000
156A181ASN00.0280.01631.7980.0220.0220.0000.0000.0000.000
157A182PRO00.0040.02135.406-0.017-0.0170.0000.0000.0000.000
158A183TRP0-0.008-0.01834.731-0.005-0.0050.0000.0000.0000.000
159A184ASP-1-0.826-0.90840.3500.1870.1870.0000.0000.0000.000
160A185CYS0-0.086-0.05240.3650.0180.0180.0000.0000.0000.000
161A186THR00.0420.02745.986-0.012-0.0120.0000.0000.0000.000
162A187CYS0-0.094-0.02148.0710.0060.0060.0000.0000.0000.000
163A188PRO00.047-0.00650.317-0.006-0.0060.0000.0000.0000.000
164A189GLY00.0330.01146.5950.0070.0070.0000.0000.0000.000
165A190ILE0-0.0050.00642.2670.0130.0130.0000.0000.0000.000
166A191ARG10.8450.90244.713-0.234-0.2340.0000.0000.0000.000
167A192TYR0-0.036-0.00738.6450.0030.0030.0000.0000.0000.000
168A193LEU00.0490.02337.5770.0040.0040.0000.0000.0000.000
169A194SER00.001-0.01341.3270.0040.0040.0000.0000.0000.000
170A195GLU-1-0.822-0.90743.8630.2230.2230.0000.0000.0000.000
171A196TRP0-0.042-0.01234.875-0.005-0.0050.0000.0000.0000.000
172A197ILE00.006-0.01438.2620.0030.0030.0000.0000.0000.000
173A198ASN0-0.069-0.05840.500-0.007-0.0070.0000.0000.0000.000
174A199LYS10.8470.93942.760-0.246-0.2460.0000.0000.0000.000
175A200HIS10.8800.94737.597-0.315-0.3150.0000.0000.0000.000
176A201SER00.0510.02838.1280.0160.0160.0000.0000.0000.000
177A202GLY00.008-0.00337.794-0.003-0.0030.0000.0000.0000.000
178A203VAL0-0.0030.00133.0340.0070.0070.0000.0000.0000.000
179A204VAL0-0.0040.00332.9250.0250.0250.0000.0000.0000.000
180A205ARG10.8990.96130.048-0.371-0.3710.0000.0000.0000.000
181A206ASN00.0390.01532.2030.0180.0180.0000.0000.0000.000
182A207SER00.0660.03029.4810.0140.0140.0000.0000.0000.000
183A208ALA0-0.020-0.00428.8920.0120.0120.0000.0000.0000.000
184A209GLY00.0200.01829.0430.0000.0000.0000.0000.0000.000
185A210SER0-0.013-0.00429.7820.0030.0030.0000.0000.0000.000
186A211VAL0-0.005-0.00333.2830.0130.0130.0000.0000.0000.000
187A212ALA0-0.014-0.02435.516-0.022-0.0220.0000.0000.0000.000
188A213PRO00.0460.03037.1900.0100.0100.0000.0000.0000.000
189A214ASP-1-0.818-0.87439.2010.1970.1970.0000.0000.0000.000
190A215SER0-0.064-0.04035.676-0.004-0.0040.0000.0000.0000.000
191A216ALA00.0280.04037.0580.0030.0030.0000.0000.0000.000
192A217LYS10.8950.92938.017-0.208-0.2080.0000.0000.0000.000
193A219SER0-0.015-0.01641.810-0.008-0.0080.0000.0000.0000.000
194A220GLY00.0190.01842.806-0.004-0.0040.0000.0000.0000.000
195A221SER0-0.003-0.00846.040-0.004-0.0040.0000.0000.0000.000
196A222GLY00.0670.04843.573-0.007-0.0070.0000.0000.0000.000
197A223LYS10.9160.95544.112-0.146-0.1460.0000.0000.0000.000
198A224PRO00.0330.01842.7520.0100.0100.0000.0000.0000.000
199A225VAL00.0830.04240.388-0.008-0.0080.0000.0000.0000.000
200A226ARG10.8160.88242.540-0.206-0.2060.0000.0000.0000.000
201A227SER0-0.065-0.03944.358-0.010-0.0100.0000.0000.0000.000
202A228ILE0-0.037-0.02246.578-0.012-0.0120.0000.0000.0000.000
203A229ILE00.0180.02448.3830.0100.0100.0000.0000.0000.000
204A231PRO00.0360.03052.1560.0000.0000.0000.0000.0000.000