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

tag_button

FMODB ID: 7664K

Calculation Name: 5C5S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C5S

Chain ID: A

ChEMBL ID:

UniProt ID: Q13459

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2444639.111946
FMO2-HF: Nuclear repulsion 2360716.198439
FMO2-HF: Total energy -83922.913507
FMO2-MP2: Total energy -84164.399497


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:109:PHE)


Summations of interaction energy for fragment #1(A:109:PHE)
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.
-5.577-2.5751.249-1.358-2.893-0.001
Interaction energy analysis for fragmet #1(A:109:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.014
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].
3A111GLY0-0.0060.0023.848-1.3180.116-0.021-0.605-0.8080.001
4A112VAL0-0.039-0.0062.428-0.1150.5711.260-0.522-1.423-0.002
5A113GLU-1-0.917-0.9583.743-3.190-2.8110.003-0.136-0.247-0.001
6A114PRO0-0.038-0.0183.807-0.1170.3860.007-0.095-0.4150.001
7A115GLY0-0.0110.0165.6180.3150.3150.0000.0000.0000.000
8A116HIS00.016-0.0289.146-0.081-0.0810.0000.0000.0000.000
9A117PHE0-0.064-0.03811.6040.0540.0540.0000.0000.0000.000
10A118GLY00.0140.01110.6110.0120.0120.0000.0000.0000.000
11A119VAL0-0.0150.0046.320-0.013-0.0130.0000.0000.0000.000
12A120CYS0-0.012-0.0207.7950.0860.0860.0000.0000.0000.000
13A121VAL00.0510.0209.704-0.084-0.0840.0000.0000.0000.000
14A122ASP-1-0.862-0.93611.145-0.575-0.5750.0000.0000.0000.000
15A123SER0-0.075-0.0327.316-0.085-0.0850.0000.0000.0000.000
16A124LEU0-0.063-0.0329.315-0.063-0.0630.0000.0000.0000.000
17A125THR0-0.036-0.00911.7970.0950.0950.0000.0000.0000.000
18A126SER0-0.036-0.03313.404-0.048-0.0480.0000.0000.0000.000
19A127ASP-1-0.862-0.93415.756-0.319-0.3190.0000.0000.0000.000
20A128LYS10.8720.93118.1520.3740.3740.0000.0000.0000.000
21A129ALA0-0.032-0.01316.7510.0190.0190.0000.0000.0000.000
22A130SER00.0830.05817.433-0.042-0.0420.0000.0000.0000.000
23A131VAL0-0.0010.00318.972-0.005-0.0050.0000.0000.0000.000
24A132PRO00.0290.01914.968-0.012-0.0120.0000.0000.0000.000
25A133ILE00.0550.01915.9090.0450.0450.0000.0000.0000.000
26A134VAL00.001-0.00715.0930.0420.0420.0000.0000.0000.000
27A135LEU0-0.0190.00218.0020.0370.0370.0000.0000.0000.000
28A136GLU-1-0.769-0.86919.947-0.215-0.2150.0000.0000.0000.000
29A137LYS10.8310.92020.8180.3030.3030.0000.0000.0000.000
30A138LEU0-0.038-0.02320.5790.0260.0260.0000.0000.0000.000
31A139LEU0-0.038-0.02323.7010.0220.0220.0000.0000.0000.000
32A140GLU-1-0.880-0.94025.699-0.175-0.1750.0000.0000.0000.000
33A141HIS00.0890.04026.8030.0110.0110.0000.0000.0000.000
34A142VAL0-0.045-0.03527.9710.0150.0150.0000.0000.0000.000
35A143GLU-1-0.789-0.87529.052-0.166-0.1660.0000.0000.0000.000
36A144MET0-0.0250.01131.3910.0140.0140.0000.0000.0000.000
37A145HIS0-0.059-0.02531.0760.0120.0120.0000.0000.0000.000
38A146GLY0-0.021-0.01533.2960.0060.0060.0000.0000.0000.000
39A147LEU00.0180.02933.0210.0040.0040.0000.0000.0000.000
40A148TYR00.0360.01535.8300.0040.0040.0000.0000.0000.000
41A149THR0-0.081-0.04335.4000.0060.0060.0000.0000.0000.000
42A150GLU-1-0.837-0.91837.206-0.082-0.0820.0000.0000.0000.000
43A151GLY0-0.034-0.03336.950-0.001-0.0010.0000.0000.0000.000
44A152LEU00.0320.03231.780-0.004-0.0040.0000.0000.0000.000
45A153TYR00.011-0.02026.544-0.002-0.0020.0000.0000.0000.000
46A154ARG10.9620.99930.7260.0860.0860.0000.0000.0000.000
47A155LYS10.8170.90832.9830.0920.0920.0000.0000.0000.000
48A156SER00.0080.01230.212-0.006-0.0060.0000.0000.0000.000
49A157GLY00.0180.00729.7550.0060.0060.0000.0000.0000.000
50A158ALA0-0.0010.00230.0100.0020.0020.0000.0000.0000.000
51A159ALA00.0700.03726.604-0.010-0.0100.0000.0000.0000.000
52A160ASN00.0090.00725.149-0.012-0.0120.0000.0000.0000.000
53A161ARG10.9250.95224.6790.1410.1410.0000.0000.0000.000
54A162THR00.007-0.01623.471-0.012-0.0120.0000.0000.0000.000
55A163ARG10.8990.96120.2470.1240.1240.0000.0000.0000.000
56A164GLU-1-0.897-0.95620.186-0.159-0.1590.0000.0000.0000.000
57A165LEU00.0070.01720.941-0.017-0.0170.0000.0000.0000.000
58A166ARG10.8540.90713.6850.2650.2650.0000.0000.0000.000
59A167GLN0-0.043-0.03616.271-0.016-0.0160.0000.0000.0000.000
60A168ALA0-0.0050.00016.234-0.035-0.0350.0000.0000.0000.000
61A169LEU00.000-0.01017.549-0.022-0.0220.0000.0000.0000.000
62A170GLN00.0340.03411.173-0.084-0.0840.0000.0000.0000.000
63A171THR0-0.0150.00312.633-0.066-0.0660.0000.0000.0000.000
64A172ASP-1-0.759-0.90013.278-0.514-0.5140.0000.0000.0000.000
65A173PRO0-0.0320.00214.8440.0680.0680.0000.0000.0000.000
66A174ALA0-0.006-0.00117.8460.0470.0470.0000.0000.0000.000
67A175ALA00.0010.00819.8550.0420.0420.0000.0000.0000.000
68A176VAL0-0.047-0.02219.9920.0340.0340.0000.0000.0000.000
69A177LYS10.9370.98022.7790.2050.2050.0000.0000.0000.000
70A178LEU00.0550.01923.4020.0090.0090.0000.0000.0000.000
71A179GLU-1-0.789-0.90026.989-0.163-0.1630.0000.0000.0000.000
72A180ASN0-0.113-0.04528.5670.0180.0180.0000.0000.0000.000
73A181PHE0-0.051-0.02824.0030.0040.0040.0000.0000.0000.000
74A182PRO00.0250.01529.1660.0030.0030.0000.0000.0000.000
75A183ILE00.1080.04329.833-0.009-0.0090.0000.0000.0000.000
76A184HIS00.019-0.00629.923-0.011-0.0110.0000.0000.0000.000
77A185ALA0-0.020-0.00926.960-0.001-0.0010.0000.0000.0000.000
78A186ILE00.0150.01825.528-0.013-0.0130.0000.0000.0000.000
79A187THR00.0120.00825.030-0.013-0.0130.0000.0000.0000.000
80A188GLY0-0.026-0.01625.710-0.003-0.0030.0000.0000.0000.000
81A189VAL00.0230.00320.165-0.004-0.0040.0000.0000.0000.000
82A190LEU00.0080.02920.598-0.018-0.0180.0000.0000.0000.000
83A191LYS10.8800.91621.1170.1360.1360.0000.0000.0000.000
84A192GLN0-0.117-0.06318.3870.0070.0070.0000.0000.0000.000
85A193TRP00.022-0.00214.0670.0220.0220.0000.0000.0000.000
86A194LEU00.0100.01016.523-0.018-0.0180.0000.0000.0000.000
87A195ARG10.8930.93218.0170.1700.1700.0000.0000.0000.000
88A196GLU-1-0.795-0.87414.143-0.269-0.2690.0000.0000.0000.000
89A197LEU00.0130.03113.059-0.034-0.0340.0000.0000.0000.000
90A198PRO0-0.022-0.0129.2220.0540.0540.0000.0000.0000.000
91A199GLU-1-0.847-0.91212.111-0.245-0.2450.0000.0000.0000.000
92A200PRO0-0.057-0.01315.154-0.017-0.0170.0000.0000.0000.000
93A201LEU00.0670.02517.578-0.005-0.0050.0000.0000.0000.000
94A202MET0-0.050-0.00319.046-0.003-0.0030.0000.0000.0000.000
95A203THR0-0.026-0.01418.2230.0230.0230.0000.0000.0000.000
96A204PHE00.002-0.03316.2450.0180.0180.0000.0000.0000.000
97A205ALA0-0.033-0.01120.2900.0200.0200.0000.0000.0000.000
98A206GLN00.0560.03222.1360.0010.0010.0000.0000.0000.000
99A207TYR0-0.030-0.02323.9370.0080.0080.0000.0000.0000.000
100A208GLY0-0.009-0.02525.5510.0080.0080.0000.0000.0000.000
101A209ASP-1-0.825-0.91927.204-0.105-0.1050.0000.0000.0000.000
102A210PHE00.022-0.00724.7290.0070.0070.0000.0000.0000.000
103A211LEU0-0.086-0.03729.7370.0070.0070.0000.0000.0000.000
104A212ARG10.8530.90231.1200.0810.0810.0000.0000.0000.000
105A213ALA00.0030.01633.0520.0050.0050.0000.0000.0000.000
106A214VAL0-0.029-0.02733.8790.0040.0040.0000.0000.0000.000
107A215GLU-1-0.870-0.91135.735-0.064-0.0640.0000.0000.0000.000
108A216LEU0-0.0380.00238.1450.0050.0050.0000.0000.0000.000
109A217PRO0-0.0020.00140.412-0.001-0.0010.0000.0000.0000.000
110A218GLU-1-0.847-0.91143.774-0.055-0.0550.0000.0000.0000.000
111A219LYS10.9520.98541.5460.0700.0700.0000.0000.0000.000
112A220GLN0-0.066-0.05540.779-0.004-0.0040.0000.0000.0000.000
113A221GLU-1-0.804-0.91240.617-0.062-0.0620.0000.0000.0000.000
114A222GLN0-0.009-0.00638.054-0.006-0.0060.0000.0000.0000.000
115A223LEU0-0.045-0.03536.443-0.005-0.0050.0000.0000.0000.000
116A224ALA0-0.009-0.00435.670-0.006-0.0060.0000.0000.0000.000
117A225ALA00.0230.02135.218-0.004-0.0040.0000.0000.0000.000
118A226ILE00.014-0.00831.078-0.006-0.0060.0000.0000.0000.000
119A227TYR0-0.021-0.03830.840-0.005-0.0050.0000.0000.0000.000
120A228ALA00.0020.01131.128-0.005-0.0050.0000.0000.0000.000
121A229VAL0-0.018-0.00726.953-0.003-0.0030.0000.0000.0000.000
122A230LEU0-0.044-0.03026.658-0.010-0.0100.0000.0000.0000.000
123A231GLU-1-0.927-0.96026.151-0.151-0.1510.0000.0000.0000.000
124A232HIS0-0.075-0.02825.606-0.007-0.0070.0000.0000.0000.000
125A233LEU0-0.071-0.01121.710-0.009-0.0090.0000.0000.0000.000
126A234PRO00.0040.00017.7330.0000.0000.0000.0000.0000.000
127A235GLU-1-0.878-0.93618.665-0.283-0.2830.0000.0000.0000.000
128A236ALA00.0650.03815.4970.0080.0080.0000.0000.0000.000
129A237ASN0-0.045-0.04516.592-0.020-0.0200.0000.0000.0000.000
130A238HIS00.0080.01918.8510.0030.0030.0000.0000.0000.000
131A239ASN00.0630.02420.0330.0000.0000.0000.0000.0000.000
132A240SER0-0.034-0.02718.2220.0000.0000.0000.0000.0000.000
133A241LEU0-0.021-0.01520.7180.0150.0150.0000.0000.0000.000
134A242GLU-1-0.940-0.95823.367-0.171-0.1710.0000.0000.0000.000
135A243ARG10.7740.85423.3500.2310.2310.0000.0000.0000.000
136A244LEU0-0.007-0.01023.0530.0120.0120.0000.0000.0000.000
137A245ILE00.002-0.01025.5590.0150.0150.0000.0000.0000.000
138A246PHE00.0190.01128.6160.0150.0150.0000.0000.0000.000
139A247HIS0-0.004-0.00327.8070.0140.0140.0000.0000.0000.000
140A248LEU00.007-0.01327.9090.0110.0110.0000.0000.0000.000
141A249VAL0-0.036-0.01331.2490.0100.0100.0000.0000.0000.000
142A250LYS10.8800.93231.7560.1610.1610.0000.0000.0000.000
143A251VAL0-0.018-0.00231.8350.0060.0060.0000.0000.0000.000
144A252ALA00.0070.01334.8950.0070.0070.0000.0000.0000.000
145A253LEU0-0.041-0.02637.1230.0080.0080.0000.0000.0000.000
146A254LEU0-0.0080.00838.0570.0050.0050.0000.0000.0000.000
147A255GLU-1-0.807-0.88540.090-0.080-0.0800.0000.0000.0000.000
148A256ASP-1-0.944-0.98940.908-0.072-0.0720.0000.0000.0000.000
149A257VAL0-0.069-0.02941.8580.0030.0030.0000.0000.0000.000
150A258ASN0-0.027-0.03237.4440.0030.0030.0000.0000.0000.000
151A259ARG10.8340.90638.8750.0750.0750.0000.0000.0000.000
152A260MET0-0.091-0.02334.0020.0030.0030.0000.0000.0000.000
153A261SER00.0600.04737.528-0.004-0.0040.0000.0000.0000.000
154A262PRO00.025-0.01435.677-0.004-0.0040.0000.0000.0000.000
155A263GLY00.0610.04535.077-0.004-0.0040.0000.0000.0000.000
156A264ALA0-0.037-0.02135.616-0.002-0.0020.0000.0000.0000.000
157A265LEU00.003-0.00831.712-0.004-0.0040.0000.0000.0000.000
158A266ALA00.0280.02130.933-0.008-0.0080.0000.0000.0000.000
159A267ILE0-0.007-0.00330.909-0.004-0.0040.0000.0000.0000.000
160A268ILE0-0.089-0.03728.576-0.002-0.0020.0000.0000.0000.000
161A269PHE00.033-0.00924.912-0.007-0.0070.0000.0000.0000.000
162A270ALA00.0270.02525.943-0.011-0.0110.0000.0000.0000.000
163A271PRO00.0080.00726.143-0.006-0.0060.0000.0000.0000.000
164A272CYS0-0.125-0.05622.609-0.006-0.0060.0000.0000.0000.000
165A273LEU0-0.0150.00121.392-0.019-0.0190.0000.0000.0000.000
166A274LEU00.0100.00522.298-0.008-0.0080.0000.0000.0000.000
167A275ARG10.8760.93915.9350.2520.2520.0000.0000.0000.000
168A276CYS0-0.007-0.00222.708-0.004-0.0040.0000.0000.0000.000
169A277PRO00.0400.01721.377-0.004-0.0040.0000.0000.0000.000
170A278ASP-1-0.930-0.94719.587-0.090-0.0900.0000.0000.0000.000
171A279ASN0-0.030-0.01422.3790.0040.0040.0000.0000.0000.000
172A280SER0-0.038-0.02424.4790.0040.0040.0000.0000.0000.000
173A281ASP-1-0.805-0.91627.330-0.036-0.0360.0000.0000.0000.000
174A282PRO00.0130.00829.444-0.004-0.0040.0000.0000.0000.000
175A283LEU0-0.019-0.00930.961-0.001-0.0010.0000.0000.0000.000
176A284THR0-0.030-0.02632.2580.0010.0010.0000.0000.0000.000
177A285SER0-0.043-0.02630.199-0.004-0.0040.0000.0000.0000.000
178A286MET0-0.013-0.00731.720-0.003-0.0030.0000.0000.0000.000
179A287LYS10.9710.97235.0230.0500.0500.0000.0000.0000.000
180A288ASP-1-0.749-0.85330.426-0.081-0.0810.0000.0000.0000.000
181A289VAL00.0530.03430.019-0.006-0.0060.0000.0000.0000.000
182A290LEU00.0070.00731.980-0.004-0.0040.0000.0000.0000.000
183A291LYS10.8230.92433.1830.0690.0690.0000.0000.0000.000
184A292ILE00.0370.01427.559-0.002-0.0020.0000.0000.0000.000
185A293THR0-0.039-0.03230.802-0.008-0.0080.0000.0000.0000.000
186A294THR0-0.024-0.02632.7120.0000.0000.0000.0000.0000.000
187A295CYS0-0.0290.00331.008-0.002-0.0020.0000.0000.0000.000
188A296VAL00.0340.01528.341-0.003-0.0030.0000.0000.0000.000
189A297GLU-1-0.835-0.92331.284-0.088-0.0880.0000.0000.0000.000
190A298MET0-0.066-0.03434.7620.0020.0020.0000.0000.0000.000
191A299LEU00.0340.03529.0370.0020.0020.0000.0000.0000.000
192A300ILE00.014-0.00130.9720.0000.0000.0000.0000.0000.000
193A301LYS10.8500.91334.0120.0870.0870.0000.0000.0000.000
194A302GLU-1-0.770-0.83436.446-0.086-0.0860.0000.0000.0000.000
195A303GLN00.0490.03131.8410.0080.0080.0000.0000.0000.000
196A304MET00.0130.00835.7090.0010.0010.0000.0000.0000.000
197A305ARG10.7950.87037.9370.0850.0850.0000.0000.0000.000
198A306LYS10.8240.89036.2020.1070.1070.0000.0000.0000.000
199A307TYR0-0.0010.01036.4670.0000.0000.0000.0000.0000.000
200A308LYS10.9470.95739.3150.0890.0890.0000.0000.0000.000
201A309VAL0-0.025-0.00142.8250.0030.0030.0000.0000.0000.000
202A310LYS10.9970.99838.3300.1010.1010.0000.0000.0000.000
203A311MET0-0.057-0.01640.3660.0000.0000.0000.0000.0000.000
204A312GLU-1-0.901-0.95543.467-0.070-0.0700.0000.0000.0000.000
205A313GLU-1-0.965-0.96744.615-0.077-0.0770.0000.0000.0000.000
206A314ILE0-0.036-0.03140.5480.0000.0000.0000.0000.0000.000
207A315SER0-0.090-0.02045.0960.0010.0010.0000.0000.0000.000
208A316GLN0-0.048-0.03947.8200.0060.0060.0000.0000.0000.000
209A317LEU0-0.030-0.00449.585-0.002-0.0020.0000.0000.0000.000
210A318GLU-1-0.959-0.97551.531-0.059-0.0590.0000.0000.0000.000