FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QY5MY

Calculation Name: 2C7Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C7Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q56WD9

Base Structure: X-ray

Registration Date: 2023-06-26

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 390
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6301298.135887
FMO2-HF: Nuclear repulsion 6155934.2699
FMO2-HF: Total energy -145363.865987
FMO2-MP2: Total energy -145781.715899


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:38:ASP)


Summations of interaction energy for fragment #1(A:38:ASP)
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.
-51.327-90.2492.96238.859-2.897-0.014
Interaction energy analysis for fragmet #1(A:38:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.966 / q_NPA : -0.906
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].
3A40ALA0-0.048-0.0502.30128.155-11.800-0.41841.050-0.677-0.020
4A41ALA0-0.013-0.0034.511-0.254-0.154-0.001-0.012-0.0870.000
5A42TYR0-0.006-0.0128.056-1.857-1.8570.0000.0000.0000.000
6A43GLN00.044-0.0036.172-0.751-0.7510.0000.0000.0000.000
7A44ARG10.7770.9019.184-18.848-18.8480.0000.0000.0000.000
8A45THR00.0460.01010.3000.7900.7900.0000.0000.0000.000
9A46SER0-0.048-0.00712.918-1.292-1.2920.0000.0000.0000.000
10A47LEU00.0450.01713.9120.4240.4240.0000.0000.0000.000
11A48TYR0-0.002-0.02717.405-0.423-0.4230.0000.0000.0000.000
12A49GLY0-0.034-0.01220.124-0.735-0.7350.0000.0000.0000.000
13A50ASP-1-0.844-0.93121.99713.51113.5110.0000.0000.0000.000
14A51ASP-1-0.933-0.96924.70810.65710.6570.0000.0000.0000.000
15A52VAL0-0.0130.01123.859-0.458-0.4580.0000.0000.0000.000
16A53VAL0-0.0020.00225.0230.4330.4330.0000.0000.0000.000
17A54ILE0-0.031-0.01823.585-0.099-0.0990.0000.0000.0000.000
18A55VAL00.0280.00727.866-0.066-0.0660.0000.0000.0000.000
19A56ALA00.0290.01330.513-0.294-0.2940.0000.0000.0000.000
20A57ALA0-0.0060.00127.4070.2840.2840.0000.0000.0000.000
21A58HIS0-0.034-0.00929.435-0.219-0.2190.0000.0000.0000.000
22A59ARG10.7780.85428.242-9.744-9.7440.0000.0000.0000.000
23A60THR00.0320.04231.043-0.195-0.1950.0000.0000.0000.000
24A61PRO0-0.033-0.01032.1890.2830.2830.0000.0000.0000.000
25A62LEU0-0.045-0.01527.4270.0470.0470.0000.0000.0000.000
26A63CYS0-0.0100.00732.013-0.215-0.2150.0000.0000.0000.000
27A64LYS10.9010.95331.501-9.080-9.0800.0000.0000.0000.000
28A65SER00.031-0.00432.830-0.119-0.1190.0000.0000.0000.000
29A66LYS10.8340.91534.703-8.780-8.7800.0000.0000.0000.000
30A67ARG10.9260.95136.777-7.457-7.4570.0000.0000.0000.000
31A68GLY00.0830.06737.432-0.111-0.1110.0000.0000.0000.000
32A69ASN00.004-0.02738.470-0.241-0.2410.0000.0000.0000.000
33A70PHE00.0180.00435.055-0.136-0.1360.0000.0000.0000.000
34A71LYS10.7670.88039.093-6.876-6.8760.0000.0000.0000.000
35A72ASP-1-0.775-0.87140.5316.7896.7890.0000.0000.0000.000
36A73THR00.0000.02439.338-0.165-0.1650.0000.0000.0000.000
37A74TYR00.0440.04739.3000.1580.1580.0000.0000.0000.000
38A75PRO00.0200.00234.7880.0710.0710.0000.0000.0000.000
39A76ASP-1-0.819-0.92836.0757.7437.7430.0000.0000.0000.000
40A77ASP-1-0.868-0.93737.9007.2507.2500.0000.0000.0000.000
41A78LEU0-0.102-0.04534.2480.0140.0140.0000.0000.0000.000
42A79LEU0-0.006-0.01731.3810.1340.1340.0000.0000.0000.000
43A80ALA00.0340.03134.5980.0740.0740.0000.0000.0000.000
44A81PRO0-0.018-0.01737.366-0.056-0.0560.0000.0000.0000.000
45A82VAL0-0.016-0.00431.7270.0110.0110.0000.0000.0000.000
46A83LEU0-0.024-0.01932.3690.1200.1200.0000.0000.0000.000
47A84ARG10.9900.99535.196-7.395-7.3950.0000.0000.0000.000
48A85ALA00.0220.02436.011-0.094-0.0940.0000.0000.0000.000
49A86LEU0-0.060-0.03331.2960.0320.0320.0000.0000.0000.000
50A87ILE00.0090.03635.3380.0000.0000.0000.0000.0000.000
51A88GLU-1-0.911-0.97538.4607.3067.3060.0000.0000.0000.000
52A89LYS10.8420.93436.532-8.406-8.4060.0000.0000.0000.000
53A90THR0-0.042-0.04535.4440.0420.0420.0000.0000.0000.000
54A91ASN0-0.055-0.02138.819-0.156-0.1560.0000.0000.0000.000
55A92LEU00.0030.02136.127-0.095-0.0950.0000.0000.0000.000
56A93ASN00.0480.01740.379-0.044-0.0440.0000.0000.0000.000
57A94PRO00.0500.01839.3350.1890.1890.0000.0000.0000.000
58A95SER0-0.053-0.03838.6840.1980.1980.0000.0000.0000.000
59A96GLU-1-0.806-0.90538.5207.7437.7430.0000.0000.0000.000
60A97VAL0-0.092-0.03033.1660.2550.2550.0000.0000.0000.000
61A98GLY00.0290.00733.526-0.138-0.1380.0000.0000.0000.000
62A99ASP-1-0.780-0.85028.51710.53610.5360.0000.0000.0000.000
63A100ILE00.0130.02630.3180.1230.1230.0000.0000.0000.000
64A101VAL0-0.0140.00824.613-0.063-0.0630.0000.0000.0000.000
65A102VAL00.014-0.00226.8220.2250.2250.0000.0000.0000.000
66A103GLY00.002-0.02724.1250.1440.1440.0000.0000.0000.000
67A104THR0-0.055-0.02124.954-0.283-0.2830.0000.0000.0000.000
68A105VAL0-0.030-0.03123.5610.0960.0960.0000.0000.0000.000
69A106LEU0-0.011-0.01826.669-0.166-0.1660.0000.0000.0000.000
70A107ALA00.0300.02429.758-0.221-0.2210.0000.0000.0000.000
71A108PRO00.0080.00630.9240.3310.3310.0000.0000.0000.000
72A109GLY00.0360.00131.706-0.210-0.2100.0000.0000.0000.000
73A110SER00.005-0.00132.4820.1950.1950.0000.0000.0000.000
74A111GLN0-0.020-0.01735.065-0.104-0.1040.0000.0000.0000.000
75A112ARG10.8080.88725.571-10.767-10.7670.0000.0000.0000.000
76A113ALA00.0500.02232.3220.0290.0290.0000.0000.0000.000
77A114SER00.011-0.00233.758-0.042-0.0420.0000.0000.0000.000
78A115GLU-1-0.786-0.87934.2798.4568.4560.0000.0000.0000.000
79A116CYS0-0.028-0.01631.7800.0450.0450.0000.0000.0000.000
80A117ARG10.9600.97134.369-8.525-8.5250.0000.0000.0000.000
81A118MET00.0150.03237.201-0.131-0.1310.0000.0000.0000.000
82A119ALA00.0390.00535.779-0.129-0.1290.0000.0000.0000.000
83A120ALA0-0.021-0.01235.953-0.050-0.0500.0000.0000.0000.000
84A121PHE00.0090.01137.763-0.104-0.1040.0000.0000.0000.000
85A122TYR00.006-0.00541.019-0.148-0.1480.0000.0000.0000.000
86A123ALA0-0.109-0.04238.447-0.091-0.0910.0000.0000.0000.000
87A124GLY00.0000.01140.4370.0040.0040.0000.0000.0000.000
88A125PHE0-0.033-0.02236.225-0.004-0.0040.0000.0000.0000.000
89A126PRO00.0190.01140.519-0.104-0.1040.0000.0000.0000.000
90A127GLU-1-0.930-0.97940.6527.0117.0110.0000.0000.0000.000
91A128THR0-0.062-0.03640.0950.1320.1320.0000.0000.0000.000
92A129VAL0-0.0030.02235.5100.1540.1540.0000.0000.0000.000
93A130ALA00.0050.01233.966-0.006-0.0060.0000.0000.0000.000
94A131VAL0-0.001-0.00532.3300.2140.2140.0000.0000.0000.000
95A132ARG10.7810.85326.094-10.962-10.9620.0000.0000.0000.000
96A133THR00.0130.00827.6770.0850.0850.0000.0000.0000.000
97A134VAL00.0010.00020.9370.2230.2230.0000.0000.0000.000
98A135ASN0-0.0140.00923.144-0.259-0.2590.0000.0000.0000.000
99A136ARG10.9300.96016.069-15.245-15.2450.0000.0000.0000.000
100A137GLN00.0560.05322.107-0.068-0.0680.0000.0000.0000.000
101A138CYS0-0.0030.00920.486-0.066-0.0660.0000.0000.0000.000
102A139SER0-0.042-0.02418.6460.7380.7380.0000.0000.0000.000
103A140SER00.0330.01218.026-0.685-0.6850.0000.0000.0000.000
104A141GLY00.0410.01320.004-0.200-0.2000.0000.0000.0000.000
105A142LEU00.0510.01815.006-0.355-0.3550.0000.0000.0000.000
106A143GLN0-0.101-0.05816.4590.8020.8020.0000.0000.0000.000
107A144ALA00.0240.02418.569-0.160-0.1600.0000.0000.0000.000
108A145VAL00.0130.00520.818-0.337-0.3370.0000.0000.0000.000
109A146ALA00.0120.01517.618-0.193-0.1930.0000.0000.0000.000
110A147ASP-1-0.775-0.88919.56314.68114.6810.0000.0000.0000.000
111A148VAL00.0100.02721.658-0.273-0.2730.0000.0000.0000.000
112A149ALA00.0200.01121.360-0.294-0.2940.0000.0000.0000.000
113A150ALA0-0.058-0.02820.379-0.060-0.0600.0000.0000.0000.000
114A151ALA0-0.003-0.00422.278-0.177-0.1770.0000.0000.0000.000
115A152ILE0-0.0060.01125.823-0.297-0.2970.0000.0000.0000.000
116A153LYS10.8990.96522.211-13.103-13.1030.0000.0000.0000.000
117A154ALA0-0.070-0.02825.027-0.066-0.0660.0000.0000.0000.000
118A155GLY0-0.011-0.00526.485-0.307-0.3070.0000.0000.0000.000
119A156PHE0-0.062-0.03326.428-0.244-0.2440.0000.0000.0000.000
120A157TYR0-0.008-0.03727.988-0.206-0.2060.0000.0000.0000.000
121A158ASP-1-0.827-0.91530.8559.4709.4700.0000.0000.0000.000
122A159ILE0-0.006-0.01331.6960.2100.2100.0000.0000.0000.000
123A160GLY00.0350.02929.525-0.141-0.1410.0000.0000.0000.000
124A161ILE0-0.012-0.00329.2300.0850.0850.0000.0000.0000.000
125A162GLY00.0130.02025.2410.1220.1220.0000.0000.0000.000
126A163ALA0-0.016-0.02426.193-0.111-0.1110.0000.0000.0000.000
127A164GLY00.0090.00025.9240.4240.4240.0000.0000.0000.000
128A165LEU00.005-0.00127.074-0.280-0.2800.0000.0000.0000.000
129A166GLU-1-0.726-0.84926.66110.93310.9330.0000.0000.0000.000
130A167SER00.0770.03430.316-0.212-0.2120.0000.0000.0000.000
131A168MET0-0.064-0.04831.3590.0290.0290.0000.0000.0000.000
132A169THR0-0.040-0.00535.097-0.139-0.1390.0000.0000.0000.000
133A170THR0-0.004-0.03537.3510.2840.2840.0000.0000.0000.000
134A171ASN0-0.020-0.00639.690-0.276-0.2760.0000.0000.0000.000
135A172PRO00.0080.02542.2210.0470.0470.0000.0000.0000.000
136A185LYS10.9040.95732.914-8.719-8.7190.0000.0000.0000.000
137A186PHE00.026-0.00431.5950.3290.3290.0000.0000.0000.000
138A187ALA00.0110.00431.4030.2280.2280.0000.0000.0000.000
139A188GLN0-0.036-0.00827.7980.4330.4330.0000.0000.0000.000
140A189ALA00.0360.00027.2890.4000.4000.0000.0000.0000.000
141A190GLN0-0.0050.00126.5370.5800.5800.0000.0000.0000.000
142A191ASN0-0.009-0.00825.1970.3680.3680.0000.0000.0000.000
143A193LEU00.007-0.00921.8230.6170.6170.0000.0000.0000.000
144A194LEU0-0.0050.00422.9610.2720.2720.0000.0000.0000.000
145A195PRO00.0350.02221.1740.2310.2310.0000.0000.0000.000
146A196MET0-0.0160.00816.1080.8900.8900.0000.0000.0000.000
147A197GLY00.0060.01718.8690.7200.7200.0000.0000.0000.000
148A198VAL00.009-0.00421.0900.1650.1650.0000.0000.0000.000
149A199THR0-0.006-0.01016.3060.3610.3610.0000.0000.0000.000
150A200SER00.006-0.02316.0870.9040.9040.0000.0000.0000.000
151A201GLU-1-0.862-0.93417.14412.30012.3000.0000.0000.0000.000
152A202ASN0-0.010-0.00418.621-0.382-0.3820.0000.0000.0000.000
153A203VAL0-0.016-0.00212.5000.1870.1870.0000.0000.0000.000
154A204ALA0-0.011-0.00415.4850.5220.5220.0000.0000.0000.000
155A205GLN00.003-0.00817.331-0.047-0.0470.0000.0000.0000.000
156A206ARG10.9030.96414.650-19.778-19.7780.0000.0000.0000.000
157A207PHE0-0.049-0.04111.8140.5020.5020.0000.0000.0000.000
158A208GLY00.0120.02615.2480.3220.3220.0000.0000.0000.000
159A209VAL0-0.0320.00615.186-0.207-0.2070.0000.0000.0000.000
160A210SER00.0380.01618.123-0.631-0.6310.0000.0000.0000.000
161A211ARG10.8710.90921.923-10.086-10.0860.0000.0000.0000.000
162A212GLN00.0280.00324.6960.2400.2400.0000.0000.0000.000
163A213GLU-1-0.823-0.89918.51214.97114.9710.0000.0000.0000.000
164A214GLN0-0.003-0.00720.2040.5800.5800.0000.0000.0000.000
165A215ASP-1-0.819-0.90522.21510.56910.5690.0000.0000.0000.000
166A216GLN0-0.014-0.02023.880-0.495-0.4950.0000.0000.0000.000
167A217ALA00.0270.01720.874-0.107-0.1070.0000.0000.0000.000
168A218ALA00.0500.02022.801-0.017-0.0170.0000.0000.0000.000
169A219VAL0-0.060-0.03025.507-0.340-0.3400.0000.0000.0000.000
170A220ASP-1-0.855-0.93223.83411.49911.4990.0000.0000.0000.000
171A221SER0-0.048-0.04723.801-0.252-0.2520.0000.0000.0000.000
172A222HIS00.0620.02025.542-0.376-0.3760.0000.0000.0000.000
173A223ARG10.8990.96926.261-10.971-10.9710.0000.0000.0000.000
174A224LYS10.8690.93922.025-13.106-13.1060.0000.0000.0000.000
175A225ALA00.0910.05228.107-0.143-0.1430.0000.0000.0000.000
176A226ALA0-0.050-0.01429.534-0.296-0.2960.0000.0000.0000.000
177A227ALA0-0.012-0.00531.212-0.238-0.2380.0000.0000.0000.000
178A228ALA00.0060.00529.594-0.192-0.1920.0000.0000.0000.000
179A229THR0-0.021-0.03031.749-0.209-0.2090.0000.0000.0000.000
180A230ALA0-0.055-0.02834.399-0.237-0.2370.0000.0000.0000.000
181A231ALA0-0.021-0.00334.233-0.218-0.2180.0000.0000.0000.000
182A232GLY0-0.045-0.01936.332-0.062-0.0620.0000.0000.0000.000
183A233LYS10.9580.97430.190-9.817-9.8170.0000.0000.0000.000
184A234PHE00.0220.01327.9490.1710.1710.0000.0000.0000.000
185A235LYS10.9170.95332.653-7.763-7.7630.0000.0000.0000.000
186A236ASP-1-0.905-0.93233.0618.7538.7530.0000.0000.0000.000
187A237GLU-1-0.815-0.90328.49610.62410.6240.0000.0000.0000.000
188A238ILE0-0.046-0.01832.0370.0000.0000.0000.0000.0000.000
189A239ILE0-0.026-0.00834.111-0.232-0.2320.0000.0000.0000.000
190A240PRO0-0.003-0.02336.7580.0580.0580.0000.0000.0000.000
191A241VAL00.0020.01237.378-0.058-0.0580.0000.0000.0000.000
192A242LYS10.9540.98540.359-6.680-6.6800.0000.0000.0000.000
193A243THR0-0.031-0.06341.661-0.043-0.0430.0000.0000.0000.000
194A244LYS10.9030.97144.532-6.832-6.8320.0000.0000.0000.000
195A245LEU0-0.042-0.01643.7260.1530.1530.0000.0000.0000.000
196A246VAL00.0230.03646.697-0.135-0.1350.0000.0000.0000.000
197A247ASP-1-0.853-0.93747.5296.2586.2580.0000.0000.0000.000
198A248PRO0-0.049-0.03946.195-0.077-0.0770.0000.0000.0000.000
199A249LYS10.8890.94649.144-6.053-6.0530.0000.0000.0000.000
200A250THR0-0.015-0.01152.287-0.076-0.0760.0000.0000.0000.000
201A251GLY00.0170.01852.183-0.081-0.0810.0000.0000.0000.000
202A252ASP-1-0.890-0.93253.2035.5395.5390.0000.0000.0000.000
203A253GLU-1-0.926-0.98250.1536.3296.3290.0000.0000.0000.000
204A254LYS10.9420.97350.353-6.061-6.0610.0000.0000.0000.000
205A255PRO0-0.016-0.02148.9410.1540.1540.0000.0000.0000.000
206A256ILE0-0.020-0.01443.731-0.040-0.0400.0000.0000.0000.000
207A257THR00.0100.00442.5650.0480.0480.0000.0000.0000.000
208A258VAL0-0.0210.00238.130-0.012-0.0120.0000.0000.0000.000
209A259SER00.024-0.01038.5960.0690.0690.0000.0000.0000.000
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211A261ASP-1-0.722-0.83231.7269.5219.5210.0000.0000.0000.000
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