FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 6N1JZ

Calculation Name: 3SIR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SIR

Chain ID: A

ChEMBL ID:

UniProt ID: O01382

Base Structure: X-ray

Registration Date: 2023-09-20

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 214
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2656356.393763
FMO2-HF: Nuclear repulsion 2568471.540478
FMO2-HF: Total energy -87884.853285
FMO2-MP2: Total energy -88136.05174


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-4.1170.6150.086-2.329-2.4870.005
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / 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].
3A3GLY00.0330.0123.572-2.2270.710-0.023-1.533-1.3800.000
4A4SER0-0.029-0.0233.256-0.5280.1110.020-0.202-0.4570.000
5A5VAL0-0.0480.0093.433-0.2480.9350.090-0.593-0.6800.005
6A6THR0-0.029-0.0135.760-0.918-0.945-0.001-0.0010.0300.000
7A7ASP-1-0.874-0.9899.4240.9140.9140.0000.0000.0000.000
8A8ARG11.0441.03812.372-0.627-0.6270.0000.0000.0000.000
9A9HIS0-0.151-0.03114.930-0.067-0.0670.0000.0000.0000.000
10A10ALA00.046-0.01212.891-0.040-0.0400.0000.0000.0000.000
11A11ALA00.0650.0478.9190.0160.0160.0000.0000.0000.000
12A12GLU-1-0.820-0.8889.948-0.301-0.3010.0000.0000.0000.000
13A13TYR0-0.053-0.04912.6940.0100.0100.0000.0000.0000.000
14A14ASN00.010-0.00616.347-0.046-0.0460.0000.0000.0000.000
15A15MET0-0.091-0.03017.8220.0120.0120.0000.0000.0000.000
16A16ARG10.9710.96718.5390.0510.0510.0000.0000.0000.000
17A17HIS0-0.070-0.02022.0000.0090.0090.0000.0000.0000.000
18A18LYS10.8500.92825.112-0.017-0.0170.0000.0000.0000.000
19A19ASN00.013-0.00528.599-0.010-0.0100.0000.0000.0000.000
20A20ARG10.8290.91121.8990.0470.0470.0000.0000.0000.000
21A21GLY00.0790.02326.0350.0100.0100.0000.0000.0000.000
22A22MET0-0.0210.00628.629-0.005-0.0050.0000.0000.0000.000
23A23ALA0-0.0040.00529.7300.0030.0030.0000.0000.0000.000
24A24LEU0-0.032-0.01231.273-0.002-0.0020.0000.0000.0000.000
25A25ILE00.0280.01432.6540.0030.0030.0000.0000.0000.000
26A26PHE00.009-0.00434.957-0.001-0.0010.0000.0000.0000.000
27A27ASN0-0.043-0.08837.3980.0000.0000.0000.0000.0000.000
28A28HIS10.8640.94539.397-0.014-0.0140.0000.0000.0000.000
29A29GLU-1-0.772-0.87541.2590.0020.0020.0000.0000.0000.000
30A30HIS0-0.042-0.03744.4300.0010.0010.0000.0000.0000.000
31A31PHE00.0110.02047.522-0.001-0.0010.0000.0000.0000.000
32A43ASN00.012-0.00638.8480.0010.0010.0000.0000.0000.000
33A44VAL00.0320.01037.687-0.001-0.0010.0000.0000.0000.000
34A45ASP-1-0.822-0.92634.628-0.015-0.0150.0000.0000.0000.000
35A46CYM-1-0.798-0.83934.425-0.005-0.0050.0000.0000.0000.000
36A47GLU-1-0.829-0.87836.131-0.020-0.0200.0000.0000.0000.000
37A48ASN0-0.012-0.01532.426-0.004-0.0040.0000.0000.0000.000
38A49LEU00.0520.02728.776-0.003-0.0030.0000.0000.0000.000
39A50THR00.029-0.01130.841-0.002-0.0020.0000.0000.0000.000
40A51ARG10.8280.90532.2950.0260.0260.0000.0000.0000.000
41A52VAL0-0.0110.00726.213-0.003-0.0030.0000.0000.0000.000
42A53LEU0-0.009-0.01326.737-0.004-0.0040.0000.0000.0000.000
43A54LYS10.9350.97328.7090.0180.0180.0000.0000.0000.000
44A55GLN0-0.035-0.01427.2280.0020.0020.0000.0000.0000.000
45A56LEU0-0.030-0.01122.427-0.009-0.0090.0000.0000.0000.000
46A57ASP-1-0.823-0.86725.124-0.057-0.0570.0000.0000.0000.000
47A58PHE0-0.043-0.03224.1940.0060.0060.0000.0000.0000.000
48A59GLU-1-0.888-0.95629.340-0.012-0.0120.0000.0000.0000.000
49A60VAL0-0.081-0.03431.6350.0040.0040.0000.0000.0000.000
50A61THR0-0.0270.00034.141-0.002-0.0020.0000.0000.0000.000
51A62VAL00.0330.00436.5610.0020.0020.0000.0000.0000.000
52A63TYR0-0.0030.00337.3500.0000.0000.0000.0000.0000.000
53A64LYS10.8700.90640.5490.0000.0000.0000.0000.0000.000
54A65ASP-1-0.770-0.87442.7760.0120.0120.0000.0000.0000.000
55A66CYS0-0.073-0.03743.5010.0000.0000.0000.0000.0000.000
56A67ARG10.8830.94645.947-0.012-0.0120.0000.0000.0000.000
57A68TYR00.1170.05237.3540.0020.0020.0000.0000.0000.000
58A69LYS10.8320.88842.018-0.022-0.0220.0000.0000.0000.000
59A70ASP-1-0.767-0.87143.3580.0190.0190.0000.0000.0000.000
60A71ILE0-0.0020.02637.8600.0010.0010.0000.0000.0000.000
61A72LEU0-0.087-0.03837.9590.0020.0020.0000.0000.0000.000
62A73ARG10.9080.94938.963-0.021-0.0210.0000.0000.0000.000
63A74THR00.001-0.00538.9350.0010.0010.0000.0000.0000.000
64A75ILE0-0.022-0.00634.1450.0010.0010.0000.0000.0000.000
65A76GLU-1-0.959-0.97036.3400.0370.0370.0000.0000.0000.000
66A77TYR0-0.001-0.02237.9310.0010.0010.0000.0000.0000.000
67A78SER00.0200.00234.9150.0000.0000.0000.0000.0000.000
68A79ALA0-0.026-0.00733.6070.0010.0010.0000.0000.0000.000
69A80SER0-0.054-0.01834.6670.0030.0030.0000.0000.0000.000
70A81GLN0-0.033-0.00335.401-0.001-0.0010.0000.0000.0000.000
71A82ASN00.0380.03833.7550.0080.0080.0000.0000.0000.000
72A83HIS00.010-0.02529.593-0.006-0.0060.0000.0000.0000.000
73A84SER00.000-0.03729.2400.0040.0040.0000.0000.0000.000
74A85ASP-1-0.867-0.90828.8420.0200.0200.0000.0000.0000.000
75A86SER0-0.044-0.03127.760-0.009-0.0090.0000.0000.0000.000
76A87ASP-1-0.734-0.84422.3560.0070.0070.0000.0000.0000.000
77A88CYS0-0.119-0.06222.6890.0110.0110.0000.0000.0000.000
78A89ILE00.0160.00824.761-0.004-0.0040.0000.0000.0000.000
79A90LEU0-0.0170.00525.3180.0050.0050.0000.0000.0000.000
80A91VAL00.0140.01427.915-0.004-0.0040.0000.0000.0000.000
81A92ALA00.012-0.00729.6390.0020.0020.0000.0000.0000.000
82A93ILE0-0.039-0.00831.713-0.002-0.0020.0000.0000.0000.000
83A94LEU00.0480.01832.5480.0000.0000.0000.0000.0000.000
84A95SER0-0.009-0.01435.9060.0000.0000.0000.0000.0000.000
85A96HIS0-0.050-0.04638.133-0.003-0.0030.0000.0000.0000.000
86A97GLY00.0540.00740.6080.0010.0010.0000.0000.0000.000
87A98GLU-1-0.873-0.89541.3890.0000.0000.0000.0000.0000.000
88A99MET0-0.055-0.04244.4590.0000.0000.0000.0000.0000.000
89A100GLY00.0230.02644.6040.0010.0010.0000.0000.0000.000
90A101TYR0-0.003-0.00941.9260.0000.0000.0000.0000.0000.000
91A102ILE00.0060.00346.3430.0010.0010.0000.0000.0000.000
92A103TYR00.0140.00941.3880.0000.0000.0000.0000.0000.000
93A104ALA00.0030.00147.0060.0000.0000.0000.0000.0000.000
94A105LYS11.0140.99747.346-0.020-0.0200.0000.0000.0000.000
95A106ASP-1-0.748-0.85546.7090.0270.0270.0000.0000.0000.000
96A107THR0-0.011-0.02443.2830.0010.0010.0000.0000.0000.000
97A108GLN00.0390.05639.8070.0050.0050.0000.0000.0000.000
98A109TYR00.1390.05640.5650.0020.0020.0000.0000.0000.000
99A110LYS10.9040.95140.452-0.028-0.0280.0000.0000.0000.000
100A111LEU00.0430.01137.2660.0020.0020.0000.0000.0000.000
101A112ASH0-0.137-0.09336.5340.0030.0030.0000.0000.0000.000
102A113ASN00.0120.00236.0250.0060.0060.0000.0000.0000.000
103A114ILE0-0.0250.00733.7500.0040.0040.0000.0000.0000.000
104A115TRP00.0800.03729.4960.0030.0030.0000.0000.0000.000
105A116SER0-0.094-0.05431.9020.0040.0040.0000.0000.0000.000
106A117PHE00.020-0.00133.6520.0040.0040.0000.0000.0000.000
107A118PHE00.0910.02829.2940.0000.0000.0000.0000.0000.000
108A119THR0-0.105-0.04128.8440.0070.0070.0000.0000.0000.000
109A120ALA00.0980.04126.651-0.004-0.0040.0000.0000.0000.000
110A121ASN0-0.029-0.02228.7160.0010.0010.0000.0000.0000.000
111A122HIS10.8550.92132.163-0.075-0.0750.0000.0000.0000.000
112A123CYS00.0030.01930.865-0.007-0.0070.0000.0000.0000.000
113A124PRO00.0480.03130.0360.0040.0040.0000.0000.0000.000
114A125SER00.0060.01229.6410.0020.0020.0000.0000.0000.000
115A126LEU0-0.006-0.00826.532-0.001-0.0010.0000.0000.0000.000
116A127ALA00.0220.01526.1020.0050.0050.0000.0000.0000.000
117A128GLY00.0090.01421.7270.0020.0020.0000.0000.0000.000
118A129LYS10.8050.91220.912-0.054-0.0540.0000.0000.0000.000
119A130PRO00.0260.01819.0850.0040.0040.0000.0000.0000.000
120A131LYS10.8140.92421.745-0.121-0.1210.0000.0000.0000.000
121A132LEU0-0.005-0.00620.9030.0070.0070.0000.0000.0000.000
122A133PHE0-0.024-0.02224.766-0.004-0.0040.0000.0000.0000.000
123A134PHE00.0170.00923.3580.0020.0020.0000.0000.0000.000
124A135ILE0-0.012-0.00728.449-0.001-0.0010.0000.0000.0000.000
125A136GLN00.0080.02231.018-0.003-0.0030.0000.0000.0000.000
126A137ALA0-0.021-0.01433.4770.0010.0010.0000.0000.0000.000
127A138CYS00.0430.02835.872-0.004-0.0040.0000.0000.0000.000
128A139GLN0-0.025-0.01536.0480.0020.0020.0000.0000.0000.000
129A140GLY0-0.039-0.01938.6210.0000.0000.0000.0000.0000.000
130A141ASP-1-0.926-0.95337.2080.0260.0260.0000.0000.0000.000
131A142ARG10.8800.91336.229-0.043-0.0430.0000.0000.0000.000
132A143LEU00.0190.02028.2660.0000.0000.0000.0000.0000.000
133A144ASP-1-0.791-0.89431.7540.0520.0520.0000.0000.0000.000
134A145GLY00.0270.05129.1020.0040.0040.0000.0000.0000.000
135A163SER00.0080.00937.1700.0010.0010.0000.0000.0000.000
136A164TYR0-0.049-0.04932.4920.0010.0010.0000.0000.0000.000
137A165LYS10.8910.94232.488-0.047-0.0470.0000.0000.0000.000
138A166ILE0-0.001-0.02226.1380.0000.0000.0000.0000.0000.000
139A167PRO0-0.051-0.00527.3890.0050.0050.0000.0000.0000.000
140A168VAL00.0550.03425.5280.0040.0040.0000.0000.0000.000
141A169HIS10.8330.90025.513-0.110-0.1100.0000.0000.0000.000
142A170ALA00.0910.04221.6510.0030.0030.0000.0000.0000.000
143A171ASP-1-0.807-0.89620.1760.1590.1590.0000.0000.0000.000
144A172PHE0-0.046-0.02521.248-0.018-0.0180.0000.0000.0000.000
145A173LEU00.0170.01518.8870.0140.0140.0000.0000.0000.000
146A174ILE0-0.015-0.00722.582-0.012-0.0120.0000.0000.0000.000
147A175ALA00.0220.02423.7410.0030.0030.0000.0000.0000.000
148A176TYR00.0250.01025.271-0.004-0.0040.0000.0000.0000.000
149A177SER00.0360.01428.330-0.002-0.0020.0000.0000.0000.000
150A178THR0-0.001-0.00330.7170.0000.0000.0000.0000.0000.000
151A179VAL0-0.0110.01234.380-0.003-0.0030.0000.0000.0000.000
152A180PRO00.0300.01737.1110.0030.0030.0000.0000.0000.000
153A181GLY00.0420.01940.127-0.001-0.0010.0000.0000.0000.000
154A182PHE0-0.055-0.03742.4710.0010.0010.0000.0000.0000.000
155A183TYR00.0450.01245.169-0.001-0.0010.0000.0000.0000.000
156A184SER0-0.0040.01146.1980.0000.0000.0000.0000.0000.000
157A185TRP00.0330.02142.0020.0000.0000.0000.0000.0000.000
158A186ARG10.9780.98546.7440.0130.0130.0000.0000.0000.000
159A187ASN0-0.021-0.02444.0720.0010.0010.0000.0000.0000.000
160A188THR00.0140.01043.609-0.001-0.0010.0000.0000.0000.000
161A189THR0-0.057-0.03241.058-0.002-0.0020.0000.0000.0000.000
162A190ARG10.9230.96837.7450.0190.0190.0000.0000.0000.000
163A191GLY00.0640.03836.9960.0020.0020.0000.0000.0000.000
164A192SER00.005-0.00533.121-0.002-0.0020.0000.0000.0000.000
165A193TRP00.0800.03031.206-0.001-0.0010.0000.0000.0000.000
166A194PHE00.0100.01025.772-0.004-0.0040.0000.0000.0000.000
167A195MET00.0150.01228.298-0.002-0.0020.0000.0000.0000.000
168A196GLN0-0.017-0.01730.012-0.007-0.0070.0000.0000.0000.000
169A197SER00.013-0.00326.159-0.007-0.0070.0000.0000.0000.000
170A198LEU0-0.0260.00223.983-0.008-0.0080.0000.0000.0000.000
171A199CYS0-0.043-0.03625.205-0.004-0.0040.0000.0000.0000.000
172A200ALA00.0180.02026.662-0.007-0.0070.0000.0000.0000.000
173A201GLU-1-0.782-0.88920.628-0.112-0.1120.0000.0000.0000.000
174A202LEU00.0670.02021.919-0.012-0.0120.0000.0000.0000.000
175A203ALA0-0.034-0.00322.958-0.009-0.0090.0000.0000.0000.000
176A204ALA0-0.070-0.02022.760-0.003-0.0030.0000.0000.0000.000
177A205ASN0-0.046-0.06117.483-0.034-0.0340.0000.0000.0000.000
178A206GLY00.0250.02318.062-0.012-0.0120.0000.0000.0000.000
179A207LYS10.7820.86318.6340.0820.0820.0000.0000.0000.000
180A208ARG10.8490.93915.5810.1620.1620.0000.0000.0000.000
181A209LEU00.0180.00812.642-0.061-0.0610.0000.0000.0000.000
182A210ASP-1-0.866-0.90811.295-0.074-0.0740.0000.0000.0000.000
183A211ILE00.0300.00413.5470.0120.0120.0000.0000.0000.000
184A212LEU00.0110.00713.0380.0010.0010.0000.0000.0000.000
185A213THR00.006-0.00211.3200.0020.0020.0000.0000.0000.000
186A214LEU00.0210.02614.567-0.007-0.0070.0000.0000.0000.000
187A215LEU0-0.041-0.04117.7440.0040.0040.0000.0000.0000.000
188A216THR00.0320.01716.0940.0170.0170.0000.0000.0000.000
189A217PHE0-0.013-0.01815.1030.0010.0010.0000.0000.0000.000
190A218VAL0-0.061-0.02920.0180.0030.0030.0000.0000.0000.000
191A219CYS0-0.044-0.01321.5300.0080.0080.0000.0000.0000.000
192A220GLN00.0390.00820.177-0.002-0.0020.0000.0000.0000.000
193A221ARG10.8430.92722.9640.0810.0810.0000.0000.0000.000
194A222VAL00.0130.00725.7940.0030.0030.0000.0000.0000.000
195A223ALA00.0030.01325.9850.0040.0040.0000.0000.0000.000
196A224VAL0-0.124-0.07625.6060.0000.0000.0000.0000.0000.000
197A225ASP-1-0.903-0.95728.222-0.043-0.0430.0000.0000.0000.000
198A226PHE0-0.081-0.02231.1970.0030.0030.0000.0000.0000.000
199A241GLN0-0.063-0.04132.1090.0050.0050.0000.0000.0000.000
200A242ILE00.0550.03025.223-0.005-0.0050.0000.0000.0000.000
201A243PRO0-0.079-0.03124.7330.0060.0060.0000.0000.0000.000
202A244CYS00.0330.01524.9760.0050.0050.0000.0000.0000.000
203A245ILE0-0.022-0.01219.9530.0020.0020.0000.0000.0000.000
204A246THR00.0020.00421.9190.0140.0140.0000.0000.0000.000
205A247THR0-0.006-0.01016.717-0.009-0.0090.0000.0000.0000.000
206A248MET0-0.012-0.00619.4060.0080.0080.0000.0000.0000.000
207A249LEU0-0.045-0.01216.2070.0100.0100.0000.0000.0000.000
208A250THR0-0.021-0.01315.9910.0280.0280.0000.0000.0000.000
209A251ARG10.9030.96812.703-0.198-0.1980.0000.0000.0000.000
210A252ILE00.0300.0167.524-0.056-0.0560.0000.0000.0000.000
211A253LEU0-0.0010.00512.031-0.032-0.0320.0000.0000.0000.000
212A254ARG10.8820.8929.8990.2800.2800.0000.0000.0000.000
213A255PHE0-0.0020.00715.7580.0100.0100.0000.0000.0000.000
214A256SER00.0430.03116.475-0.004-0.0040.0000.0000.0000.000