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: G6GZ1

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 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 199
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1446671.318873
FMO2-HF: Nuclear repulsion 1363478.035158
FMO2-HF: Total energy -83193.283714
FMO2-MP2: Total energy -83431.320528


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.
-1.836-0.160.002-0.787-0.8920.003
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 : 0.014 / q_NPA : 0.000
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-1-0.697-0.8363.932-3.401-1.7250.002-0.787-0.8920.003
4A5PRO0-0.011-0.0055.5960.8660.8660.0000.0000.0000.000
5A6MET0-0.056-0.0248.1580.3790.3790.0000.0000.0000.000
6A7THR0-0.006-0.01710.8860.1690.1690.0000.0000.0000.000
7A8TYR0-0.020-0.00113.5680.0670.0670.0000.0000.0000.000
8A9GLU-1-0.746-0.84212.695-0.587-0.5870.0000.0000.0000.000
9A10ALA0-0.043-0.02615.1460.0810.0810.0000.0000.0000.000
10A11GLN0-0.038-0.03117.053-0.034-0.0340.0000.0000.0000.000
11A12PHE0-0.015-0.00119.5300.0350.0350.0000.0000.0000.000
12A13PHE00.002-0.00617.6320.0330.0330.0000.0000.0000.000
13A14GLY0-0.0190.00220.5600.0230.0230.0000.0000.0000.000
14A15PHE0-0.042-0.04318.7390.0090.0090.0000.0000.0000.000
15A16THR0-0.005-0.00813.3810.0010.0010.0000.0000.0000.000
16A17PRO00.0280.02312.6730.0640.0640.0000.0000.0000.000
17A18GLN00.0880.0319.2580.1860.1860.0000.0000.0000.000
18A19THR00.0210.00512.5870.0820.0820.0000.0000.0000.000
19A20CYS0-0.0430.00015.5620.0280.0280.0000.0000.0000.000
20A21MET00.0340.03114.1650.0300.0300.0000.0000.0000.000
21A22LEU00.0120.01914.5890.0260.0260.0000.0000.0000.000
22A23ARG10.8810.92016.6360.0460.0460.0000.0000.0000.000
23A24ILE00.0040.00319.2950.0030.0030.0000.0000.0000.000
24A25TYR0-0.072-0.05317.4210.0110.0110.0000.0000.0000.000
25A26ILE00.012-0.00319.5520.0030.0030.0000.0000.0000.000
26A27ALA00.0310.02821.910-0.003-0.0030.0000.0000.0000.000
27A28PHE0-0.018-0.02422.494-0.003-0.0030.0000.0000.0000.000
28A29GLN0-0.0010.01222.2780.0190.0190.0000.0000.0000.000
29A30ASP-1-0.865-0.94024.3110.1030.1030.0000.0000.0000.000
30A31TYR0-0.004-0.00127.201-0.006-0.0060.0000.0000.0000.000
31A32LEU0-0.019-0.00225.708-0.003-0.0030.0000.0000.0000.000
32A33PHE0-0.002-0.02425.8690.0000.0000.0000.0000.0000.000
33A34GLU-1-0.924-0.95130.1910.0490.0490.0000.0000.0000.000
34A35VAL0-0.021-0.01631.718-0.004-0.0040.0000.0000.0000.000
35A36MET0-0.020-0.00631.037-0.001-0.0010.0000.0000.0000.000
36A37GLN00.0060.00834.0440.0020.0020.0000.0000.0000.000
37A38ALA0-0.0110.00036.157-0.004-0.0040.0000.0000.0000.000
38A39VAL0-0.001-0.00736.552-0.003-0.0030.0000.0000.0000.000
39A40GLU-1-0.759-0.84337.8240.0710.0710.0000.0000.0000.000
40A41GLN00.0450.00639.758-0.005-0.0050.0000.0000.0000.000
41A42VAL0-0.0060.00142.065-0.003-0.0030.0000.0000.0000.000
42A43ILE0-0.019-0.01640.814-0.002-0.0020.0000.0000.0000.000
43A44LEU0-0.011-0.00142.452-0.001-0.0010.0000.0000.0000.000
44A45LYS10.8890.96145.328-0.046-0.0460.0000.0000.0000.000
45A46LYS10.8620.92347.734-0.039-0.0390.0000.0000.0000.000
46A47LEU0-0.0430.00146.359-0.001-0.0010.0000.0000.0000.000
47A48ASP-1-0.853-0.94149.4000.0400.0400.0000.0000.0000.000
48A49GLY0-0.086-0.02751.868-0.002-0.0020.0000.0000.0000.000
49A50ILE0-0.055-0.02852.6880.0000.0000.0000.0000.0000.000
50A51PRO0-0.018-0.00555.438-0.001-0.0010.0000.0000.0000.000
51A52ASP-1-0.915-0.95457.8090.0340.0340.0000.0000.0000.000
52A53CYS0-0.065-0.04555.4300.0000.0000.0000.0000.0000.000
53A54ASP-1-0.878-0.93451.7520.0440.0440.0000.0000.0000.000
54A55ILE0-0.052-0.03347.0350.0010.0010.0000.0000.0000.000
55A56SER00.0250.01646.4790.0020.0020.0000.0000.0000.000
56A57PRO00.0910.01744.9520.0030.0030.0000.0000.0000.000
57A58VAL0-0.014-0.00941.9370.0030.0030.0000.0000.0000.000
58A59GLN0-0.0070.00641.1460.0020.0020.0000.0000.0000.000
59A60ILE00.0260.01240.7210.0040.0040.0000.0000.0000.000
60A61ARG10.8360.91734.736-0.079-0.0790.0000.0000.0000.000
61A62LYS10.8550.90135.344-0.091-0.0910.0000.0000.0000.000
62A63CYM-1-0.855-0.88935.9040.0850.0850.0000.0000.0000.000
63A64THR00.032-0.01034.3880.0040.0040.0000.0000.0000.000
64A65GLU-1-0.835-0.90032.3910.1050.1050.0000.0000.0000.000
65A66LYS10.8130.88631.148-0.080-0.0800.0000.0000.0000.000
66A67PHE00.002-0.00531.1040.0070.0070.0000.0000.0000.000
67A68LEU00.0460.01128.5910.0040.0040.0000.0000.0000.000
68A69CYS0-0.069-0.02726.8290.0110.0110.0000.0000.0000.000
69A70PHE0-0.013-0.00525.9520.0140.0140.0000.0000.0000.000
70A71MET0-0.023-0.01126.2840.0050.0050.0000.0000.0000.000
71A72LYS10.8700.92320.329-0.207-0.2070.0000.0000.0000.000
72A73GLY00.0090.01921.9040.0150.0150.0000.0000.0000.000
73A74HIS0-0.036-0.01821.2730.0190.0190.0000.0000.0000.000
74A75PHE0-0.0040.00421.0760.0030.0030.0000.0000.0000.000
75A76ASP-1-0.743-0.85317.6950.2260.2260.0000.0000.0000.000
76A77ASN00.0120.02216.990-0.004-0.0040.0000.0000.0000.000
77A78LEU0-0.019-0.02617.3770.0010.0010.0000.0000.0000.000
78A79PHE00.0300.02516.101-0.014-0.0140.0000.0000.0000.000
79A80SER0-0.014-0.02113.1590.0040.0040.0000.0000.0000.000
80A81LYS10.8590.93113.736-0.201-0.2010.0000.0000.0000.000
81A82MET0-0.040-0.00515.924-0.034-0.0340.0000.0000.0000.000
82A83GLU-1-0.888-0.96011.3220.1320.1320.0000.0000.0000.000
83A84GLN00.0350.01010.707-0.047-0.0470.0000.0000.0000.000
84A85LEU0-0.032-0.01412.579-0.053-0.0530.0000.0000.0000.000
85A86PHE00.008-0.01915.691-0.036-0.0360.0000.0000.0000.000
86A87LEU0-0.039-0.00510.462-0.039-0.0390.0000.0000.0000.000
87A88GLN0-0.070-0.03411.861-0.072-0.0720.0000.0000.0000.000
88A89LEU0-0.015-0.01713.918-0.020-0.0200.0000.0000.0000.000
89A90ILE0-0.043-0.01416.9430.0080.0080.0000.0000.0000.000
90A91LEU0-0.046-0.02916.015-0.020-0.0200.0000.0000.0000.000
91A92ARG10.8300.9048.4120.7560.7560.0000.0000.0000.000
92A93ILE00.0040.00514.6980.0550.0550.0000.0000.0000.000
93A94PRO00.007-0.00614.845-0.054-0.0540.0000.0000.0000.000
94A95SER0-0.064-0.02113.9700.0050.0050.0000.0000.0000.000
95A96ASN0-0.030-0.02416.0850.0070.0070.0000.0000.0000.000
96A97ILE0-0.047-0.01819.1350.0290.0290.0000.0000.0000.000
97A98LEU00.0490.04119.731-0.034-0.0340.0000.0000.0000.000
98A99LEU0-0.013-0.00319.6960.0270.0270.0000.0000.0000.000
99A100PRO00.012-0.00523.4390.0070.0070.0000.0000.0000.000
100A101GLU-1-0.819-0.90823.398-0.207-0.2070.0000.0000.0000.000
101A102ASP-1-0.791-0.87722.203-0.274-0.2740.0000.0000.0000.000
102A103LYS10.9330.95925.4040.1470.1470.0000.0000.0000.000
103A104CYS0-0.071-0.02827.310-0.001-0.0010.0000.0000.0000.000
104A105LYS10.8440.89321.4500.2970.2970.0000.0000.0000.000
105A106GLU-1-0.936-0.96124.145-0.181-0.1810.0000.0000.0000.000
106A107THR0-0.038-0.02225.8820.0020.0020.0000.0000.0000.000
107A108PRO0-0.046-0.02124.0470.0090.0090.0000.0000.0000.000
108A109TYR0-0.0130.00527.1070.0100.0100.0000.0000.0000.000
109A110SER0-0.005-0.02227.954-0.014-0.0140.0000.0000.0000.000
110A111GLU-1-0.952-0.96826.855-0.192-0.1920.0000.0000.0000.000
111A112GLU-1-0.883-0.95628.928-0.164-0.1640.0000.0000.0000.000
112A113ASP-1-0.833-0.89732.121-0.127-0.1270.0000.0000.0000.000
113A114PHE0-0.035-0.01631.7810.0090.0090.0000.0000.0000.000
114A115GLN00.0280.01833.4220.0160.0160.0000.0000.0000.000
115A116HIS0-0.047-0.01935.2220.0100.0100.0000.0000.0000.000
116A117LEU00.0280.01336.7540.0060.0060.0000.0000.0000.000
117A118GLN0-0.028-0.02735.3600.0030.0030.0000.0000.0000.000
118A119LYS10.8730.94338.9830.1010.1010.0000.0000.0000.000
119A120GLU-1-0.907-0.94541.206-0.082-0.0820.0000.0000.0000.000
120A121ILE00.001-0.00940.3660.0050.0050.0000.0000.0000.000
121A122GLU-1-0.925-0.96343.020-0.079-0.0790.0000.0000.0000.000
122A123GLN0-0.029-0.02044.9270.0070.0070.0000.0000.0000.000
123A124LEU00.0110.00245.6450.0050.0050.0000.0000.0000.000
124A125GLN0-0.031-0.01145.8720.0030.0030.0000.0000.0000.000
125A126GLU-1-0.804-0.86949.351-0.052-0.0520.0000.0000.0000.000
126A127LYS10.8840.93950.9530.0550.0550.0000.0000.0000.000
127A128TYR00.0290.01852.2560.0030.0030.0000.0000.0000.000
128A129LYS10.8240.89053.1200.0570.0570.0000.0000.0000.000
129A130THR0-0.030-0.03655.3090.0020.0020.0000.0000.0000.000
130A131GLU-1-0.839-0.90056.454-0.045-0.0450.0000.0000.0000.000
131A132LEU0-0.031-0.00158.0640.0020.0020.0000.0000.0000.000
132A133CYS0-0.062-0.03659.4180.0020.0020.0000.0000.0000.000
133A134THR00.018-0.01360.8280.0020.0020.0000.0000.0000.000
134A135LYS10.9570.99162.6370.0390.0390.0000.0000.0000.000
135A136GLN0-0.017-0.02364.4250.0010.0010.0000.0000.0000.000
136A137ALA0-0.0050.00365.9940.0010.0010.0000.0000.0000.000
137A138LEU00.0440.01965.6440.0010.0010.0000.0000.0000.000
138A139LEU0-0.057-0.01768.6880.0010.0010.0000.0000.0000.000
139A140ALA00.001-0.01270.4120.0010.0010.0000.0000.0000.000
140A141GLU-1-0.910-0.94871.613-0.030-0.0300.0000.0000.0000.000
141A142LEU0-0.0050.00073.2130.0010.0010.0000.0000.0000.000
142A143GLU-1-0.850-0.92674.591-0.026-0.0260.0000.0000.0000.000
143A144GLU-1-0.952-0.97076.391-0.026-0.0260.0000.0000.0000.000
144A145GLN0-0.025-0.02076.1640.0010.0010.0000.0000.0000.000
145A146LYS10.8240.89477.4010.0270.0270.0000.0000.0000.000
146A147ILE0-0.0090.00981.2610.0010.0010.0000.0000.0000.000
147A148VAL00.0200.00881.6650.0010.0010.0000.0000.0000.000
148A149GLN0-0.0060.00681.8190.0010.0010.0000.0000.0000.000
149A150ALA0-0.008-0.00884.9940.0010.0010.0000.0000.0000.000
150A151LYS10.9280.97087.2740.0200.0200.0000.0000.0000.000
151A152LEU00.0310.01285.8390.0010.0010.0000.0000.0000.000
152A153LYS11.0041.00087.8430.0210.0210.0000.0000.0000.000
153A154GLN00.0010.02191.1820.0000.0000.0000.0000.0000.000
154A155THR0-0.048-0.03692.5940.0000.0000.0000.0000.0000.000
155A156LEU0-0.016-0.00491.3000.0000.0000.0000.0000.0000.000
156A157THR00.0270.00094.7900.0000.0000.0000.0000.0000.000
157A158PHE00.0110.01097.1750.0000.0000.0000.0000.0000.000
158A159PHE0-0.032-0.01897.6640.0000.0000.0000.0000.0000.000
159A160ASP-1-0.889-0.93797.919-0.016-0.0160.0000.0000.0000.000
160A161GLU-1-0.986-1.001100.825-0.015-0.0150.0000.0000.0000.000
161A162LEU0-0.031-0.006102.9830.0000.0000.0000.0000.0000.000
162A163HIS0-0.004-0.001103.8600.0000.0000.0000.0000.0000.000
163A164ASN00.0090.002103.2290.0000.0000.0000.0000.0000.000
164A165VAL00.005-0.003106.9660.0000.0000.0000.0000.0000.000
165A166GLY00.0050.018108.6540.0000.0000.0000.0000.0000.000
166A167ARG10.8460.898105.5200.0140.0140.0000.0000.0000.000
167A168ASP-1-0.928-0.956110.881-0.013-0.0130.0000.0000.0000.000
168A169HIS0-0.050-0.036113.1960.0000.0000.0000.0000.0000.000
169A170GLY0-0.0220.001115.0100.0000.0000.0000.0000.0000.000
170A171THR0-0.077-0.029113.2010.0000.0000.0000.0000.0000.000
171A172SER00.0480.016109.8620.0000.0000.0000.0000.0000.000
172A173ASP-1-0.789-0.894108.742-0.014-0.0140.0000.0000.0000.000
173A174PHE00.0220.026109.4340.0000.0000.0000.0000.0000.000
174A175ARG10.8280.896108.7930.0130.0130.0000.0000.0000.000
175A176GLU-1-0.818-0.910110.905-0.012-0.0120.0000.0000.0000.000
176A177SER0-0.011-0.017113.5780.0000.0000.0000.0000.0000.000
177A178LEU00.000-0.008113.5720.0000.0000.0000.0000.0000.000
178A179VAL0-0.027-0.001114.1820.0000.0000.0000.0000.0000.000
179A180SER00.0110.009116.1820.0000.0000.0000.0000.0000.000
180A181LEU00.0220.027118.7600.0000.0000.0000.0000.0000.000
181A182VAL00.019-0.002117.6180.0000.0000.0000.0000.0000.000
182A183GLN00.0230.030119.9560.0000.0000.0000.0000.0000.000
183A184ASN0-0.029-0.041121.9360.0000.0000.0000.0000.0000.000
184A185SER00.0420.022123.4950.0000.0000.0000.0000.0000.000
185A186ARG10.8910.945119.4990.0110.0110.0000.0000.0000.000
186A187LYS10.8980.948125.5690.0100.0100.0000.0000.0000.000
187A188LEU00.0100.016128.1720.0000.0000.0000.0000.0000.000
188A189GLN00.0280.010127.8370.0000.0000.0000.0000.0000.000
189A190ASN0-0.043-0.020129.8700.0000.0000.0000.0000.0000.000
190A191ILE00.0270.009131.5980.0000.0000.0000.0000.0000.000
191A192ARG10.7970.870132.3790.0090.0090.0000.0000.0000.000
192A193ASP-1-0.813-0.890133.441-0.009-0.0090.0000.0000.0000.000
193A194ASN0-0.023-0.014135.3990.0000.0000.0000.0000.0000.000
194A195VAL00.0080.004137.7700.0000.0000.0000.0000.0000.000
195A196GLU-1-0.814-0.890136.102-0.008-0.0080.0000.0000.0000.000
196A197LYS10.7760.879136.3010.0090.0090.0000.0000.0000.000
197A198GLU-1-0.923-0.962141.414-0.008-0.0080.0000.0000.0000.000
198A199SER0-0.089-0.031142.8440.0000.0000.0000.0000.0000.000
199A200LYS10.9140.972144.7210.0070.0070.0000.0000.0000.000