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: KGGN3

Calculation Name: 2IN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IN5

Chain ID: A

ChEMBL ID:

UniProt ID: P75884

Base Structure: X-ray

Registration Date: 2023-09-21

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2273145.194262
FMO2-HF: Nuclear repulsion 2194041.210629
FMO2-HF: Total energy -79103.983632
FMO2-MP2: Total energy -79335.131668


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:3:HIS)


Summations of interaction energy for fragment #1(A:3:HIS)
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.
-3.44-0.135-0.025-1.582-1.6980.006
Interaction energy analysis for fragmet #1(A:3:HIS)
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 : 0.006
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].
3A5GLN0-0.004-0.0043.808-3.2670.038-0.025-1.582-1.6980.006
4A6GLN00.0310.0186.207-0.496-0.4960.0000.0000.0000.000
5A7SER0-0.032-0.0179.803-0.072-0.0720.0000.0000.0000.000
6A8MET00.049-0.00312.229-0.030-0.0300.0000.0000.0000.000
7A9VAL00.0350.02015.509-0.010-0.0100.0000.0000.0000.000
8A10ASP-1-0.809-0.89112.6180.1620.1620.0000.0000.0000.000
9A11THR00.0140.01414.1440.0140.0140.0000.0000.0000.000
10A12PHE0-0.040-0.03416.448-0.015-0.0150.0000.0000.0000.000
11A13ARG10.8240.92116.062-0.093-0.0930.0000.0000.0000.000
12A14ALA00.0180.00417.497-0.019-0.0190.0000.0000.0000.000
13A15SER00.0560.02719.590-0.018-0.0180.0000.0000.0000.000
14A16LEU0-0.062-0.02121.829-0.016-0.0160.0000.0000.0000.000
15A17PHE0-0.068-0.05922.130-0.019-0.0190.0000.0000.0000.000
16A18ASP-1-0.925-0.93820.4470.2090.2090.0000.0000.0000.000
17A19ASN0-0.063-0.02123.9770.0050.0050.0000.0000.0000.000
18A20GLN0-0.053-0.01327.072-0.019-0.0190.0000.0000.0000.000
19A21ASP-1-0.823-0.92729.3820.0680.0680.0000.0000.0000.000
20A22ILE0-0.025-0.01427.926-0.006-0.0060.0000.0000.0000.000
21A23THR0-0.113-0.06731.972-0.010-0.0100.0000.0000.0000.000
22A24VAL0-0.072-0.01332.520-0.001-0.0010.0000.0000.0000.000
23A25ALA00.0650.02935.104-0.004-0.0040.0000.0000.0000.000
24A26ASP-1-0.885-0.95836.6950.0250.0250.0000.0000.0000.000
25A27GLN00.0100.00639.096-0.005-0.0050.0000.0000.0000.000
26A28GLN00.018-0.02133.6920.0000.0000.0000.0000.0000.000
27A29ILE00.0090.01833.3850.0010.0010.0000.0000.0000.000
28A30GLN0-0.038-0.02834.188-0.006-0.0060.0000.0000.0000.000
29A31ALA0-0.0290.00034.588-0.001-0.0010.0000.0000.0000.000
30A32LEU0-0.034-0.00328.8930.0070.0070.0000.0000.0000.000
31A33PRO0-0.0080.00128.047-0.009-0.0090.0000.0000.0000.000
32A34TYR00.0190.00125.571-0.007-0.0070.0000.0000.0000.000
33A35SER0-0.008-0.02228.5780.0040.0040.0000.0000.0000.000
34A36THR00.0190.00927.9190.0000.0000.0000.0000.0000.000
35A37MET0-0.032-0.01528.356-0.006-0.0060.0000.0000.0000.000
36A38TYR0-0.0010.00530.6630.0050.0050.0000.0000.0000.000
37A39LEU00.0240.00128.277-0.006-0.0060.0000.0000.0000.000
38A40ARG10.9080.97531.9530.0200.0200.0000.0000.0000.000
39A41LEU00.0230.00629.065-0.007-0.0070.0000.0000.0000.000
40A42ASN00.006-0.00533.3260.0030.0030.0000.0000.0000.000
41A43GLU-1-0.903-0.94936.407-0.027-0.0270.0000.0000.0000.000
42A44GLY0-0.022-0.00434.9740.0050.0050.0000.0000.0000.000
43A45GLN00.009-0.00933.196-0.001-0.0010.0000.0000.0000.000
44A46ARG10.9020.95633.115-0.014-0.0140.0000.0000.0000.000
45A47ILE00.0140.01327.1950.0080.0080.0000.0000.0000.000
46A48PHE00.006-0.00328.107-0.007-0.0070.0000.0000.0000.000
47A49VAL00.0020.00025.0210.0020.0020.0000.0000.0000.000
48A50VAL00.0190.01122.8520.0030.0030.0000.0000.0000.000
49A51LEU0-0.036-0.01324.053-0.014-0.0140.0000.0000.0000.000
50A52GLY0-0.0070.00620.3590.0150.0150.0000.0000.0000.000
51A53TYR00.010-0.01216.6850.0150.0150.0000.0000.0000.000
52A54ILE0-0.002-0.01121.395-0.010-0.0100.0000.0000.0000.000
53A55GLU-1-0.910-0.94317.589-0.281-0.2810.0000.0000.0000.000
54A56GLN00.0290.00621.071-0.002-0.0020.0000.0000.0000.000
55A57GLU-1-0.878-0.92425.438-0.110-0.1100.0000.0000.0000.000
56A58GLN00.0140.01123.965-0.006-0.0060.0000.0000.0000.000
57A59SER0-0.037-0.01624.3580.0020.0020.0000.0000.0000.000
58A60LYS10.8610.93619.5800.2250.2250.0000.0000.0000.000
59A61TRP0-0.008-0.01722.3550.0240.0240.0000.0000.0000.000
60A62LEU00.0080.00218.089-0.016-0.0160.0000.0000.0000.000
61A63SER00.0410.02221.7680.0210.0210.0000.0000.0000.000
62A64GLN00.0730.02721.527-0.001-0.0010.0000.0000.0000.000
63A65ASP-1-0.967-0.98219.806-0.012-0.0120.0000.0000.0000.000
64A66ASN0-0.050-0.02414.653-0.007-0.0070.0000.0000.0000.000
65A67ALA00.0160.03318.380-0.040-0.0400.0000.0000.0000.000
66A68MET0-0.041-0.03518.7440.0090.0090.0000.0000.0000.000
67A69LEU00.008-0.00121.419-0.014-0.0140.0000.0000.0000.000
68A70VAL0-0.024-0.00922.6080.0020.0020.0000.0000.0000.000
69A71THR00.012-0.00325.2890.0020.0020.0000.0000.0000.000
70A72HIS00.011-0.00828.2370.0000.0000.0000.0000.0000.000
71A73ASN00.0070.00430.9280.0060.0060.0000.0000.0000.000
72A74GLY00.0310.01632.8840.0020.0020.0000.0000.0000.000
73A75ARG10.7860.86533.1910.0860.0860.0000.0000.0000.000
74A76LEU0-0.031-0.01728.467-0.006-0.0060.0000.0000.0000.000
75A77LEU0-0.013-0.02127.888-0.003-0.0030.0000.0000.0000.000
76A78LYS10.9700.98219.8910.2890.2890.0000.0000.0000.000
77A79THR00.0160.03524.4060.0140.0140.0000.0000.0000.000
78A80VAL0-0.042-0.03018.395-0.029-0.0290.0000.0000.0000.000
79A81LYS10.9510.96815.0730.3110.3110.0000.0000.0000.000
80A82LEU00.0520.04521.2320.0240.0240.0000.0000.0000.000
81A83ASN0-0.002-0.00424.748-0.012-0.0120.0000.0000.0000.000
82A84ASN00.0480.02526.814-0.015-0.0150.0000.0000.0000.000
83A85ASN0-0.035-0.02524.0450.0100.0100.0000.0000.0000.000
84A86LEU00.0380.03126.979-0.003-0.0030.0000.0000.0000.000
85A87LEU0-0.060-0.07524.244-0.014-0.0140.0000.0000.0000.000
86A88GLU-1-0.955-0.98025.950-0.231-0.2310.0000.0000.0000.000
87A89VAL00.0130.01628.4660.0160.0160.0000.0000.0000.000
88A90THR00.0430.03430.842-0.003-0.0030.0000.0000.0000.000
89A91ASN00.007-0.03633.1030.0070.0070.0000.0000.0000.000
90A92SER00.0450.02730.6180.0100.0100.0000.0000.0000.000
91A93GLY0-0.005-0.00733.8560.0060.0060.0000.0000.0000.000
92A94GLN0-0.025-0.02134.9600.0020.0020.0000.0000.0000.000
93A95ASP-1-0.770-0.88036.173-0.081-0.0810.0000.0000.0000.000
94A96PRO00.0460.02138.1540.0010.0010.0000.0000.0000.000
95A97LEU0-0.025-0.00237.1280.0040.0040.0000.0000.0000.000
96A98ARG10.8150.91732.0090.1120.1120.0000.0000.0000.000
97A99ASN0-0.048-0.02937.1790.0050.0050.0000.0000.0000.000
98A100ALA00.0540.01439.8030.0020.0020.0000.0000.0000.000
99A101LEU0-0.0010.01141.6100.0020.0020.0000.0000.0000.000
100A102ALA0-0.079-0.01743.9690.0020.0020.0000.0000.0000.000
101A103ILE0-0.0410.00741.935-0.002-0.0020.0000.0000.0000.000
102A104LYS10.9430.97345.9780.0530.0530.0000.0000.0000.000
103A105ASP-1-0.820-0.91548.949-0.044-0.0440.0000.0000.0000.000
104A106GLY00.0360.02950.0620.0000.0000.0000.0000.0000.000
105A107SER0-0.095-0.04545.362-0.003-0.0030.0000.0000.0000.000
106A108ARG10.9560.98445.7630.0660.0660.0000.0000.0000.000
107A109TRP0-0.018-0.01335.2410.0000.0000.0000.0000.0000.000
108A110THR0-0.004-0.00741.2500.0030.0030.0000.0000.0000.000
109A111ARG10.8340.95036.0820.0910.0910.0000.0000.0000.000
110A112ASP-1-0.783-0.84635.435-0.121-0.1210.0000.0000.0000.000
111A113ILE0-0.037-0.01532.954-0.006-0.0060.0000.0000.0000.000
112A114LEU00.0170.00628.2680.0030.0030.0000.0000.0000.000
113A115TRP0-0.018-0.01229.464-0.009-0.0090.0000.0000.0000.000
114A116SER0-0.020-0.00727.588-0.004-0.0040.0000.0000.0000.000
115A117GLU-1-0.904-0.96729.651-0.090-0.0900.0000.0000.0000.000
116A118ASP-1-0.865-0.92030.400-0.092-0.0920.0000.0000.0000.000
117A119ASN0-0.101-0.06024.9430.0070.0070.0000.0000.0000.000
118A120HIS0-0.0050.01228.496-0.009-0.0090.0000.0000.0000.000
119A121PHE00.001-0.00325.7830.0040.0040.0000.0000.0000.000
120A122ARG10.9180.96831.4040.1290.1290.0000.0000.0000.000
121A123SER00.0630.01133.124-0.011-0.0110.0000.0000.0000.000
122A124ALA0-0.080-0.02435.3320.0070.0070.0000.0000.0000.000
123A125THR00.025-0.02237.729-0.003-0.0030.0000.0000.0000.000
124A126LEU0-0.070-0.03737.7770.0070.0070.0000.0000.0000.000
125A127SER0-0.0170.00040.971-0.002-0.0020.0000.0000.0000.000
126A128SER0-0.020-0.01642.2360.0020.0020.0000.0000.0000.000
127A129THR0-0.003-0.02944.620-0.001-0.0010.0000.0000.0000.000
128A130PHE0-0.050-0.02840.6800.0010.0010.0000.0000.0000.000
129A131SER00.0250.01446.7780.0010.0010.0000.0000.0000.000
130A132PHE0-0.009-0.00949.0900.0010.0010.0000.0000.0000.000
131A133ALA00.002-0.00949.4870.0010.0010.0000.0000.0000.000
132A134GLY00.0000.00651.1690.0020.0020.0000.0000.0000.000
133A135LEU0-0.031-0.00750.217-0.001-0.0010.0000.0000.0000.000
134A136GLU-1-0.851-0.93348.031-0.018-0.0180.0000.0000.0000.000
135A137THR0-0.040-0.01548.0760.0000.0000.0000.0000.0000.000
136A138LEU00.0010.01542.5320.0010.0010.0000.0000.0000.000
137A139ASN0-0.005-0.01844.9220.0030.0030.0000.0000.0000.000
138A140ILE0-0.017-0.01538.4120.0000.0000.0000.0000.0000.000
139A141ALA0-0.046-0.02838.0560.0010.0010.0000.0000.0000.000
140A142GLY00.1180.07339.9920.0020.0020.0000.0000.0000.000
141A143ARG10.8980.95641.414-0.007-0.0070.0000.0000.0000.000
142A144ASN0-0.0040.00144.320-0.002-0.0020.0000.0000.0000.000
143A145VAL0-0.039-0.01942.3640.0000.0000.0000.0000.0000.000
144A146LEU00.0200.02445.358-0.001-0.0010.0000.0000.0000.000
145A147CYS0-0.029-0.03944.114-0.002-0.0020.0000.0000.0000.000
146A148ASN00.0070.00045.7790.0030.0030.0000.0000.0000.000
147A149VAL00.003-0.00945.555-0.003-0.0030.0000.0000.0000.000
148A150TRP0-0.003-0.00144.147-0.001-0.0010.0000.0000.0000.000
149A151GLN00.0570.03544.745-0.003-0.0030.0000.0000.0000.000
150A152GLU-1-0.742-0.81340.483-0.077-0.0770.0000.0000.0000.000
151A153GLU-1-0.806-0.90144.573-0.048-0.0480.0000.0000.0000.000
152A154VAL0-0.025-0.03141.024-0.004-0.0040.0000.0000.0000.000
153A155THR00.0100.01344.3620.0020.0020.0000.0000.0000.000
154A156SER00.029-0.00441.615-0.004-0.0040.0000.0000.0000.000
155A157THR00.0190.00043.1270.0040.0040.0000.0000.0000.000
156A158ARG10.8770.96943.0320.0870.0870.0000.0000.0000.000
157A159PRO00.0470.00942.527-0.005-0.0050.0000.0000.0000.000
158A160GLU-1-0.923-0.97444.782-0.064-0.0640.0000.0000.0000.000
159A161LYS10.8490.93142.1080.0740.0740.0000.0000.0000.000
160A162GLN00.0480.02245.660-0.003-0.0030.0000.0000.0000.000
161A163TRP0-0.0200.00139.3290.0020.0020.0000.0000.0000.000
162A164GLN0-0.007-0.00845.0290.0000.0000.0000.0000.0000.000
163A165ASN0-0.064-0.02339.7580.0010.0010.0000.0000.0000.000
164A166THR0-0.015-0.02441.5110.0020.0020.0000.0000.0000.000
165A167PHE0-0.035-0.02537.001-0.002-0.0020.0000.0000.0000.000
166A168TRP00.002-0.01241.045-0.001-0.0010.0000.0000.0000.000
167A169VAL0-0.025-0.01941.0230.0000.0000.0000.0000.0000.000
168A170ASP-1-0.804-0.87041.428-0.017-0.0170.0000.0000.0000.000
169A171SER0-0.057-0.03843.122-0.002-0.0020.0000.0000.0000.000
170A172ALA0-0.0030.00144.945-0.001-0.0010.0000.0000.0000.000
171A173THR0-0.026-0.01339.930-0.003-0.0030.0000.0000.0000.000
172A174GLY00.0100.00040.760-0.004-0.0040.0000.0000.0000.000
173A175GLN00.009-0.00734.392-0.001-0.0010.0000.0000.0000.000
174A176VAL0-0.0300.00136.4370.0040.0040.0000.0000.0000.000
175A177ARG10.8660.92436.5770.0130.0130.0000.0000.0000.000
176A178GLN0-0.001-0.00337.7580.0070.0070.0000.0000.0000.000
177A179SER0-0.045-0.01235.260-0.001-0.0010.0000.0000.0000.000
178A180ARG11.0011.00337.6840.0370.0370.0000.0000.0000.000
179A181GLN00.027-0.00834.431-0.007-0.0070.0000.0000.0000.000
180A182MET0-0.0430.01336.9580.0030.0030.0000.0000.0000.000
181A183LEU0-0.0300.00029.481-0.004-0.0040.0000.0000.0000.000
182A184GLY00.0540.01532.886-0.012-0.0120.0000.0000.0000.000
183A185ALA0-0.027-0.02035.0710.0060.0060.0000.0000.0000.000
184A186GLY0-0.034-0.02238.5560.0030.0030.0000.0000.0000.000
185A187VAL0-0.023-0.00736.0320.0060.0060.0000.0000.0000.000
186A188ILE00.0240.00232.626-0.005-0.0050.0000.0000.0000.000
187A189PRO00.0510.03235.300-0.005-0.0050.0000.0000.0000.000
188A190VAL0-0.012-0.01832.1310.0010.0010.0000.0000.0000.000
189A191GLU-1-0.910-0.95535.058-0.027-0.0270.0000.0000.0000.000
190A192MET0-0.022-0.02331.336-0.001-0.0010.0000.0000.0000.000
191A193THR00.0170.01734.4960.0010.0010.0000.0000.0000.000
192A194PHE0-0.011-0.01331.1320.0030.0030.0000.0000.0000.000
193A195LEU00.0350.02332.9990.0010.0010.0000.0000.0000.000
194A196LYS10.9190.97831.576-0.011-0.0110.0000.0000.0000.000
195A197PRO0-0.058-0.02034.731-0.006-0.0060.0000.0000.0000.000
196A198ALA00.0140.00735.6560.0040.0040.0000.0000.0000.000
197A199PRO0-0.014-0.00536.7180.0000.0000.0000.0000.0000.000
198A200LEU00.0300.01739.602-0.005-0.0050.0000.0000.0000.000