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: 17K8Z

Calculation Name: 5LSJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q03188

Base Structure: X-ray

Registration Date: 2023-09-19

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 199
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1445609.927509
FMO2-HF: Nuclear repulsion 1362417.382502
FMO2-HF: Total energy -83192.545007
FMO2-MP2: Total energy -83430.799967


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-2.726-0.808-0.003-0.913-1.0030.004
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.003
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].
3A4ASP-1-0.731-0.8593.826-4.180-2.262-0.003-0.913-1.0030.004
4A5PRO0-0.035-0.0285.5410.8690.8690.0000.0000.0000.000
5A6MET0-0.058-0.0257.9170.4130.4130.0000.0000.0000.000
6A7THR00.010-0.00410.7870.1950.1950.0000.0000.0000.000
7A8TYR0-0.033-0.02413.3550.0960.0960.0000.0000.0000.000
8A9GLU-1-0.772-0.85512.453-0.754-0.7540.0000.0000.0000.000
9A10ALA0-0.046-0.02415.1600.0990.0990.0000.0000.0000.000
10A11GLN0-0.042-0.01317.113-0.040-0.0400.0000.0000.0000.000
11A12PHE0-0.022-0.01619.5150.0350.0350.0000.0000.0000.000
12A13PHE0-0.029-0.01217.8340.0370.0370.0000.0000.0000.000
13A14GLY00.0130.01019.8390.0250.0250.0000.0000.0000.000
14A15PHE0-0.055-0.04818.5540.0210.0210.0000.0000.0000.000
15A16THR00.0020.01512.812-0.006-0.0060.0000.0000.0000.000
16A17PRO00.0310.01012.0590.0750.0750.0000.0000.0000.000
17A18GLN00.1080.0498.6350.2270.2270.0000.0000.0000.000
18A19THR00.0400.01412.8010.0800.0800.0000.0000.0000.000
19A20CYS0-0.044-0.00615.7150.0420.0420.0000.0000.0000.000
20A21MET00.0340.02414.3310.0380.0380.0000.0000.0000.000
21A22LEU00.0160.02414.7130.0370.0370.0000.0000.0000.000
22A23ARG10.8980.93816.7540.0890.0890.0000.0000.0000.000
23A24ILE00.006-0.00519.2870.0090.0090.0000.0000.0000.000
24A25TYR0-0.074-0.04817.5430.0130.0130.0000.0000.0000.000
25A26ILE0-0.011-0.01919.6610.0070.0070.0000.0000.0000.000
26A27ALA00.0210.02521.8800.0000.0000.0000.0000.0000.000
27A28PHE0-0.007-0.01822.6080.0000.0000.0000.0000.0000.000
28A29GLN00.0220.01922.1070.0180.0180.0000.0000.0000.000
29A30ASP-1-0.881-0.94524.3910.0820.0820.0000.0000.0000.000
30A31TYR0-0.010-0.00327.275-0.005-0.0050.0000.0000.0000.000
31A32LEU0-0.039-0.00925.961-0.002-0.0020.0000.0000.0000.000
32A33PHE0-0.004-0.03025.7020.0010.0010.0000.0000.0000.000
33A34GLU-1-0.907-0.93930.1560.0400.0400.0000.0000.0000.000
34A35VAL0-0.024-0.01631.850-0.003-0.0030.0000.0000.0000.000
35A36MET0-0.027-0.01431.2580.0000.0000.0000.0000.0000.000
36A37GLN00.0340.01334.0990.0030.0030.0000.0000.0000.000
37A38ALA0-0.027-0.00236.045-0.003-0.0030.0000.0000.0000.000
38A39VAL00.012-0.00336.626-0.003-0.0030.0000.0000.0000.000
39A40GLU-1-0.771-0.85037.8210.0710.0710.0000.0000.0000.000
40A41GLN00.024-0.01039.737-0.004-0.0040.0000.0000.0000.000
41A42VAL0-0.0120.00541.852-0.003-0.0030.0000.0000.0000.000
42A43ILE0-0.026-0.02141.058-0.002-0.0020.0000.0000.0000.000
43A44LEU0-0.003-0.00342.432-0.001-0.0010.0000.0000.0000.000
44A45LYS10.9060.97245.134-0.045-0.0450.0000.0000.0000.000
45A46LYS10.8800.92547.768-0.037-0.0370.0000.0000.0000.000
46A47LEU0-0.0330.00246.477-0.001-0.0010.0000.0000.0000.000
47A48ASP-1-0.842-0.92149.4530.0390.0390.0000.0000.0000.000
48A49GLY0-0.126-0.04652.156-0.002-0.0020.0000.0000.0000.000
49A50ILE0-0.080-0.02152.343-0.001-0.0010.0000.0000.0000.000
50A51PRO0-0.015-0.01655.224-0.001-0.0010.0000.0000.0000.000
51A52ASP-1-0.917-0.94657.7090.0350.0350.0000.0000.0000.000
52A53CYS0-0.090-0.05655.3940.0010.0010.0000.0000.0000.000
53A54ASP-1-0.851-0.93951.9200.0440.0440.0000.0000.0000.000
54A55ILE0-0.051-0.02347.2150.0020.0020.0000.0000.0000.000
55A56SER00.0000.00946.3510.0010.0010.0000.0000.0000.000
56A57PRO00.1170.02644.8140.0020.0020.0000.0000.0000.000
57A58VAL0-0.015-0.01141.3530.0030.0030.0000.0000.0000.000
58A59GLN0-0.0060.00340.8380.0030.0030.0000.0000.0000.000
59A60ILE00.0550.01840.5500.0040.0040.0000.0000.0000.000
60A61ARG10.8080.92035.068-0.078-0.0780.0000.0000.0000.000
61A62LYS10.8510.89534.736-0.097-0.0970.0000.0000.0000.000
62A63CYM-1-0.875-0.91535.7520.0870.0870.0000.0000.0000.000
63A64THR00.017-0.02134.2760.0040.0040.0000.0000.0000.000
64A65GLU-1-0.820-0.89732.3210.1090.1090.0000.0000.0000.000
65A66LYS10.8530.92431.158-0.083-0.0830.0000.0000.0000.000
66A67PHE00.001-0.00931.0870.0080.0080.0000.0000.0000.000
67A68LEU00.0560.01928.5250.0030.0030.0000.0000.0000.000
68A69CYS0-0.059-0.02526.9240.0110.0110.0000.0000.0000.000
69A70PHE0-0.027-0.01426.0620.0140.0140.0000.0000.0000.000
70A71MET0-0.023-0.01826.2320.0060.0060.0000.0000.0000.000
71A72LYS10.8810.92920.406-0.194-0.1940.0000.0000.0000.000
72A73GLY00.0090.02221.9250.0170.0170.0000.0000.0000.000
73A74HIS0-0.037-0.02321.3360.0140.0140.0000.0000.0000.000
74A75PHE0-0.0080.00521.127-0.001-0.0010.0000.0000.0000.000
75A76ASP-1-0.727-0.83517.9070.2150.2150.0000.0000.0000.000
76A77ASN0-0.011-0.00517.249-0.014-0.0140.0000.0000.0000.000
77A78LEU0-0.021-0.03017.5230.0020.0020.0000.0000.0000.000
78A79PHE00.0340.02716.338-0.019-0.0190.0000.0000.0000.000
79A80SER00.0060.00013.3660.0020.0020.0000.0000.0000.000
80A81LYS10.8640.94114.295-0.203-0.2030.0000.0000.0000.000
81A82MET0-0.029-0.00615.869-0.036-0.0360.0000.0000.0000.000
82A83GLU-1-0.885-0.94811.6670.0470.0470.0000.0000.0000.000
83A84GLN00.0280.00410.638-0.046-0.0460.0000.0000.0000.000
84A85LEU0-0.036-0.02412.670-0.055-0.0550.0000.0000.0000.000
85A86PHE0-0.021-0.02515.736-0.035-0.0350.0000.0000.0000.000
86A87LEU0-0.026-0.0079.741-0.050-0.0500.0000.0000.0000.000
87A88GLN0-0.064-0.02311.454-0.067-0.0670.0000.0000.0000.000
88A89LEU0-0.017-0.01613.827-0.029-0.0290.0000.0000.0000.000
89A90ILE0-0.051-0.02016.6910.0100.0100.0000.0000.0000.000
90A91LEU0-0.045-0.02115.565-0.024-0.0240.0000.0000.0000.000
91A92ARG10.8590.9158.5420.8400.8400.0000.0000.0000.000
92A93ILE00.0250.02915.2490.0610.0610.0000.0000.0000.000
93A94PRO0-0.005-0.01215.327-0.062-0.0620.0000.0000.0000.000
94A95SER0-0.060-0.01913.714-0.014-0.0140.0000.0000.0000.000
95A96ASN0-0.009-0.01515.8460.0080.0080.0000.0000.0000.000
96A97ILE0-0.048-0.01819.2320.0260.0260.0000.0000.0000.000
97A98LEU00.0390.02519.722-0.038-0.0380.0000.0000.0000.000
98A99LEU0-0.0140.00519.8480.0320.0320.0000.0000.0000.000
99A100PRO00.026-0.00323.3420.0080.0080.0000.0000.0000.000
100A101GLU-1-0.847-0.92923.173-0.255-0.2550.0000.0000.0000.000
101A102ASP-1-0.814-0.89822.281-0.316-0.3160.0000.0000.0000.000
102A103LYS10.9560.98424.8560.1730.1730.0000.0000.0000.000
103A104CYS0-0.065-0.03227.491-0.003-0.0030.0000.0000.0000.000
104A105LYS10.8600.89622.2140.3210.3210.0000.0000.0000.000
105A106GLU-1-0.933-0.94924.512-0.210-0.2100.0000.0000.0000.000
106A107THR0-0.020-0.00525.9780.0000.0000.0000.0000.0000.000
107A108PRO0-0.055-0.02824.3950.0100.0100.0000.0000.0000.000
108A109TYR0-0.023-0.01027.1730.0100.0100.0000.0000.0000.000
109A110SER0-0.003-0.01627.871-0.015-0.0150.0000.0000.0000.000
110A111GLU-1-0.936-0.96527.243-0.210-0.2100.0000.0000.0000.000
111A112GLU-1-0.897-0.96429.104-0.184-0.1840.0000.0000.0000.000
112A113ASP-1-0.842-0.90632.265-0.147-0.1470.0000.0000.0000.000
113A114PHE0-0.019-0.00531.8720.0110.0110.0000.0000.0000.000
114A115GLN00.0260.00733.5230.0180.0180.0000.0000.0000.000
115A116HIS0-0.044-0.01535.3200.0110.0110.0000.0000.0000.000
116A117LEU00.0160.01236.9950.0080.0080.0000.0000.0000.000
117A118GLN0-0.015-0.01735.5040.0020.0020.0000.0000.0000.000
118A119LYS10.9140.96038.7880.1150.1150.0000.0000.0000.000
119A120GLU-1-0.923-0.96141.390-0.091-0.0910.0000.0000.0000.000
120A121ILE00.003-0.00340.3140.0060.0060.0000.0000.0000.000
121A122GLU-1-0.948-0.96843.412-0.082-0.0820.0000.0000.0000.000
122A123GLN0-0.032-0.02145.2870.0070.0070.0000.0000.0000.000
123A124LEU00.0160.00245.9020.0050.0050.0000.0000.0000.000
124A125GLN0-0.036-0.01146.4030.0030.0030.0000.0000.0000.000
125A126GLU-1-0.810-0.88049.583-0.058-0.0580.0000.0000.0000.000
126A127LYS10.8870.93851.1930.0620.0620.0000.0000.0000.000
127A128TYR00.0160.00552.4700.0040.0040.0000.0000.0000.000
128A129LYS10.8060.88252.8460.0630.0630.0000.0000.0000.000
129A130THR0-0.032-0.02555.7190.0030.0030.0000.0000.0000.000
130A131GLU-1-0.826-0.91156.624-0.051-0.0510.0000.0000.0000.000
131A132LEU0-0.0280.00458.4540.0020.0020.0000.0000.0000.000
132A133CYS0-0.055-0.03259.7640.0020.0020.0000.0000.0000.000
133A134THR00.0260.00361.1670.0020.0020.0000.0000.0000.000
134A135LYS10.9630.99662.9130.0440.0440.0000.0000.0000.000
135A136GLN0-0.035-0.03064.6690.0010.0010.0000.0000.0000.000
136A137ALA00.0090.01066.1710.0010.0010.0000.0000.0000.000
137A138LEU00.0390.02265.9810.0010.0010.0000.0000.0000.000
138A139LEU0-0.033-0.01468.9030.0010.0010.0000.0000.0000.000
139A140ALA0-0.017-0.01670.5050.0010.0010.0000.0000.0000.000
140A141GLU-1-0.896-0.94071.974-0.033-0.0330.0000.0000.0000.000
141A142LEU0-0.002-0.00373.4740.0010.0010.0000.0000.0000.000
142A143GLU-1-0.870-0.94374.724-0.029-0.0290.0000.0000.0000.000
143A144GLU-1-0.966-0.97376.420-0.029-0.0290.0000.0000.0000.000
144A145GLN0-0.031-0.01376.4070.0010.0010.0000.0000.0000.000
145A146LYS10.8360.89877.9480.0300.0300.0000.0000.0000.000
146A147ILE0-0.0180.00481.5360.0010.0010.0000.0000.0000.000
147A148VAL00.0300.00881.9940.0010.0010.0000.0000.0000.000
148A149GLN0-0.0060.00782.4770.0000.0000.0000.0000.0000.000
149A150ALA0-0.002-0.00985.2560.0010.0010.0000.0000.0000.000
150A151LYS10.9380.97787.5200.0220.0220.0000.0000.0000.000
151A152LEU00.0210.00986.4540.0010.0010.0000.0000.0000.000
152A153LYS11.0000.99088.4660.0240.0240.0000.0000.0000.000
153A154GLN00.0070.03091.3640.0000.0000.0000.0000.0000.000
154A155THR0-0.021-0.01693.2150.0000.0000.0000.0000.0000.000
155A156LEU0-0.016-0.01291.8210.0000.0000.0000.0000.0000.000
156A157THR00.010-0.00594.9620.0000.0000.0000.0000.0000.000
157A158PHE00.0060.00697.2900.0000.0000.0000.0000.0000.000
158A159PHE0-0.031-0.02398.5600.0000.0000.0000.0000.0000.000
159A160ASP-1-0.889-0.94098.206-0.018-0.0180.0000.0000.0000.000
160A161GLU-1-0.982-1.001100.978-0.017-0.0170.0000.0000.0000.000
161A162LEU0-0.044-0.010103.1390.0000.0000.0000.0000.0000.000
162A163HIS0-0.016-0.015104.1680.0000.0000.0000.0000.0000.000
163A164ASN00.0130.007103.4110.0000.0000.0000.0000.0000.000
164A165VAL0-0.004-0.003107.0520.0000.0000.0000.0000.0000.000
165A166GLY0-0.0150.006108.8300.0000.0000.0000.0000.0000.000
166A167ARG10.8770.924105.5890.0160.0160.0000.0000.0000.000
167A168ASP-1-0.969-0.974111.168-0.014-0.0140.0000.0000.0000.000
168A169HIS0-0.030-0.026113.3840.0000.0000.0000.0000.0000.000
169A170GLY0-0.0180.003115.5090.0000.0000.0000.0000.0000.000
170A171THR0-0.068-0.028113.8630.0000.0000.0000.0000.0000.000
171A172SER00.0780.039110.0500.0000.0000.0000.0000.0000.000
172A173ASP-1-0.867-0.929108.496-0.016-0.0160.0000.0000.0000.000
173A174PHE00.0330.012110.0270.0000.0000.0000.0000.0000.000
174A175ARG10.8700.926109.0280.0150.0150.0000.0000.0000.000
175A176GLU-1-0.814-0.904111.351-0.014-0.0140.0000.0000.0000.000
176A177SER00.003-0.003113.8550.0000.0000.0000.0000.0000.000
177A178LEU0-0.006-0.012113.6480.0000.0000.0000.0000.0000.000
178A179VAL0-0.0080.004114.6160.0000.0000.0000.0000.0000.000
179A180SER00.006-0.003116.5920.0000.0000.0000.0000.0000.000
180A181LEU00.0080.015119.0820.0000.0000.0000.0000.0000.000
181A182VAL00.0230.000117.9170.0000.0000.0000.0000.0000.000
182A183GLN0-0.0100.014119.9630.0000.0000.0000.0000.0000.000
183A184ASN0-0.024-0.044122.3030.0000.0000.0000.0000.0000.000
184A185SER00.0530.041123.5560.0000.0000.0000.0000.0000.000
185A186ARG10.9020.955120.0650.0120.0120.0000.0000.0000.000
186A187LYS10.9080.951125.9240.0110.0110.0000.0000.0000.000
187A188LEU00.0100.017128.4320.0000.0000.0000.0000.0000.000
188A189GLN00.0270.007128.1450.0000.0000.0000.0000.0000.000
189A190ASN0-0.050-0.022130.1280.0000.0000.0000.0000.0000.000
190A191ILE00.0250.004131.9190.0000.0000.0000.0000.0000.000
191A192ARG10.8260.897132.8410.0100.0100.0000.0000.0000.000
192A193ASP-1-0.842-0.905134.019-0.009-0.0090.0000.0000.0000.000
193A194ASN0-0.019-0.018135.8900.0000.0000.0000.0000.0000.000
194A195VAL0-0.0010.000138.0770.0000.0000.0000.0000.0000.000
195A196GLU-1-0.838-0.905136.342-0.009-0.0090.0000.0000.0000.000
196A197LYS10.8040.877136.8480.0090.0090.0000.0000.0000.000
197A198GLU-1-0.948-0.957141.600-0.008-0.0080.0000.0000.0000.000
198A199SER0-0.059-0.013143.1600.0000.0000.0000.0000.0000.000
199A200LYS10.9080.964145.0490.0080.0080.0000.0000.0000.000