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: 7647K

Calculation Name: 5I61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I61

Chain ID: A

ChEMBL ID:

UniProt ID: Q50LE4

Base Structure: X-ray

Registration Date: 2023-09-23

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 534
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11821299.574089
FMO2-HF: Nuclear repulsion 11604741.685547
FMO2-HF: Total energy -216557.888543
FMO2-MP2: Total energy -217180.765647


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.7853.8061.053-2.736-2.906-0.01
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.015
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].
3A3VAL0-0.041-0.0153.8081.4742.476-0.011-0.563-0.4280.003
4A4ALA00.0510.0366.6030.0810.0810.0000.0000.0000.000
5A5PRO00.0660.01210.201-0.133-0.1330.0000.0000.0000.000
6A6ASN00.0200.00512.875-0.052-0.0520.0000.0000.0000.000
7A7VAL00.0270.0168.1660.0140.0140.0000.0000.0000.000
8A8TRP00.0610.0328.320-0.038-0.0380.0000.0000.0000.000
9A9SER0-0.019-0.02711.2980.0230.0230.0000.0000.0000.000
10A10LYS10.9410.97513.1330.2720.2720.0000.0000.0000.000
11A11TYR00.0080.0378.501-0.004-0.0040.0000.0000.0000.000
12A12PHE00.003-0.01510.7320.0670.0670.0000.0000.0000.000
13A13ASN0-0.030-0.01415.3890.0400.0400.0000.0000.0000.000
14A14ILE0-0.040-0.00714.951-0.004-0.0040.0000.0000.0000.000
15A15PRO00.0330.00518.8080.0210.0210.0000.0000.0000.000
16A16ASN00.008-0.00317.4850.0190.0190.0000.0000.0000.000
17A17PRO00.0500.01918.618-0.027-0.0270.0000.0000.0000.000
18A18GLY00.0470.02420.155-0.005-0.0050.0000.0000.0000.000
19A19LEU0-0.0050.00713.7580.0020.0020.0000.0000.0000.000
20A20ARG10.9400.97315.0740.2490.2490.0000.0000.0000.000
21A21ALA00.0140.00416.535-0.007-0.0070.0000.0000.0000.000
22A22TYR0-0.048-0.03714.4340.0380.0380.0000.0000.0000.000
23A23PHE00.0470.00610.946-0.008-0.0080.0000.0000.0000.000
24A24SER00.0000.01014.1580.0040.0040.0000.0000.0000.000
25A25ASN0-0.032-0.02316.3560.0370.0370.0000.0000.0000.000
26A26VAL0-0.0270.00012.5450.0140.0140.0000.0000.0000.000
27A27VAL0-0.027-0.02111.9590.0160.0160.0000.0000.0000.000
28A28SER0-0.030-0.01714.4860.0270.0270.0000.0000.0000.000
29A29GLY00.0050.01318.0390.0220.0220.0000.0000.0000.000
30A30GLN0-0.037-0.04119.3380.0100.0100.0000.0000.0000.000
31A31PRO00.0320.01322.9080.0020.0020.0000.0000.0000.000
32A32GLU-1-0.925-0.95025.337-0.076-0.0760.0000.0000.0000.000
33A33VAL00.0050.00228.317-0.007-0.0070.0000.0000.0000.000
34A34TYR0-0.012-0.00627.5040.0010.0010.0000.0000.0000.000
35A35ARG10.8310.90832.3990.0540.0540.0000.0000.0000.000
36A36THR0-0.072-0.05836.0280.0000.0000.0000.0000.0000.000
37A37PRO0-0.021-0.03238.2740.0030.0030.0000.0000.0000.000
38A38PHE00.0190.03141.3060.0030.0030.0000.0000.0000.000
39A39TYR00.017-0.02142.7540.0000.0000.0000.0000.0000.000
40A40LYS10.9270.97543.6560.0450.0450.0000.0000.0000.000
41A41GLY0-0.033-0.01844.2310.0020.0020.0000.0000.0000.000
42A42MET00.0090.02545.4510.0020.0020.0000.0000.0000.000
43A43SER0-0.022-0.03241.688-0.002-0.0020.0000.0000.0000.000
44A44LEU00.0490.01436.7930.0000.0000.0000.0000.0000.000
45A45GLU-1-0.816-0.89339.327-0.043-0.0430.0000.0000.0000.000
46A46SER00.0140.01142.6300.0010.0010.0000.0000.0000.000
47A47ILE0-0.028-0.01142.3900.0010.0010.0000.0000.0000.000
48A48CYS0-0.045-0.02841.6190.0000.0000.0000.0000.0000.000
49A49ASP-1-0.825-0.90544.391-0.031-0.0310.0000.0000.0000.000
50A50GLU-1-0.851-0.90847.223-0.028-0.0280.0000.0000.0000.000
51A51TRP0-0.004-0.01245.9030.0010.0010.0000.0000.0000.000
52A52TYR00.002-0.01246.6050.0010.0010.0000.0000.0000.000
53A53LYS10.8410.90448.7610.0290.0290.0000.0000.0000.000
54A54LYS10.8120.90751.7950.0320.0320.0000.0000.0000.000
55A55LEU00.0060.01346.2620.0010.0010.0000.0000.0000.000
56A56VAL00.037-0.00250.7050.0000.0000.0000.0000.0000.000
57A57SER0-0.029-0.00952.2750.0010.0010.0000.0000.0000.000
58A58ILE0-0.013-0.01848.8050.0000.0000.0000.0000.0000.000
59A59ASP-1-0.924-0.96551.536-0.026-0.0260.0000.0000.0000.000
60A60THR0-0.013-0.00753.0560.0000.0000.0000.0000.0000.000
61A61GLN0-0.011-0.00555.9360.0000.0000.0000.0000.0000.000
62A62TRP0-0.021-0.02251.1360.0000.0000.0000.0000.0000.000
63A63PRO00.0880.05550.601-0.002-0.0020.0000.0000.0000.000
64A64THR00.035-0.01146.939-0.001-0.0010.0000.0000.0000.000
65A65LEU0-0.069-0.02245.614-0.002-0.0020.0000.0000.0000.000
66A66MET0-0.0100.01245.873-0.003-0.0030.0000.0000.0000.000
67A67GLU-1-0.865-0.93544.638-0.031-0.0310.0000.0000.0000.000
68A68PHE0-0.033-0.01939.474-0.003-0.0030.0000.0000.0000.000
69A69GLU-1-0.742-0.80841.197-0.049-0.0490.0000.0000.0000.000
70A70ASP-1-0.798-0.91641.707-0.036-0.0360.0000.0000.0000.000
71A71ASP-1-0.824-0.88437.029-0.048-0.0480.0000.0000.0000.000
72A72LEU0-0.032-0.02735.831-0.004-0.0040.0000.0000.0000.000
73A73ARG10.9060.94237.1430.0330.0330.0000.0000.0000.000
74A74LYS10.8380.91936.6800.0380.0380.0000.0000.0000.000
75A75LYS10.7650.86632.4160.0520.0520.0000.0000.0000.000
76A76VAL0-0.0320.00233.182-0.006-0.0060.0000.0000.0000.000
77A77GLY00.0390.00433.3980.0040.0040.0000.0000.0000.000
78A78PRO0-0.041-0.00629.585-0.004-0.0040.0000.0000.0000.000
79A79MET0-0.008-0.01328.0410.0000.0000.0000.0000.0000.000
80A80SER0-0.003-0.00926.724-0.007-0.0070.0000.0000.0000.000
81A81VAL0-0.0290.01524.163-0.007-0.0070.0000.0000.0000.000
82A82MET0-0.046-0.00618.241-0.013-0.0130.0000.0000.0000.000
83A83LEU00.0180.00318.7720.0040.0040.0000.0000.0000.000
84A84PRO00.0210.00716.656-0.030-0.0300.0000.0000.0000.000
85A85LEU00.0250.0308.9770.0050.0050.0000.0000.0000.000
86A86LYS10.8800.91611.9980.0770.0770.0000.0000.0000.000
87A87GLU-1-0.861-0.92813.021-0.055-0.0550.0000.0000.0000.000
88A88ARG10.8950.94613.7540.2940.2940.0000.0000.0000.000
89A89MET0-0.022-0.0067.000-0.056-0.0560.0000.0000.0000.000
90A90SER00.0470.03511.406-0.024-0.0240.0000.0000.0000.000
91A91ASP-1-0.862-0.93913.951-0.169-0.1690.0000.0000.0000.000
92A92ILE0-0.047-0.0318.540-0.032-0.0320.0000.0000.0000.000
93A93ASP-1-0.767-0.8639.941-0.206-0.2060.0000.0000.0000.000
94A94SER0-0.0020.02312.0220.0140.0140.0000.0000.0000.000
95A95TYR0-0.025-0.02612.9910.0140.0140.0000.0000.0000.000
96A96TYR0-0.021-0.0309.016-0.074-0.0740.0000.0000.0000.000
97A97ASP-1-0.866-0.92812.682-0.063-0.0630.0000.0000.0000.000
98A98SER0-0.084-0.07115.0460.0310.0310.0000.0000.0000.000
99A99ILE0-0.064-0.01615.2720.0140.0140.0000.0000.0000.000
100A100SER0-0.056-0.02417.3460.0140.0140.0000.0000.0000.000
101A101LYS10.8930.96819.5000.0710.0710.0000.0000.0000.000
102A102ASP-1-0.877-0.93022.514-0.009-0.0090.0000.0000.0000.000
103A103GLN0-0.062-0.03321.855-0.014-0.0140.0000.0000.0000.000
104A104VAL00.0030.00627.1680.0040.0040.0000.0000.0000.000
105A105PRO00.004-0.00330.238-0.006-0.0060.0000.0000.0000.000
106A106PHE00.015-0.01028.7670.0020.0020.0000.0000.0000.000
107A107ASP-1-0.790-0.89733.536-0.030-0.0300.0000.0000.0000.000
108A108THR00.005-0.00537.252-0.002-0.0020.0000.0000.0000.000
109A109LYS10.9390.96038.7220.0220.0220.0000.0000.0000.000
110A110ALA00.0350.03537.489-0.001-0.0010.0000.0000.0000.000
111A111ILE0-0.0110.00034.030-0.003-0.0030.0000.0000.0000.000
112A112SER0-0.019-0.01237.569-0.002-0.0020.0000.0000.0000.000
113A113ALA00.0040.01041.0610.0000.0000.0000.0000.0000.000
114A114ALA00.0240.01137.646-0.001-0.0010.0000.0000.0000.000
115A115LYS10.8670.91736.7660.0510.0510.0000.0000.0000.000
116A116SER0-0.109-0.07440.3710.0010.0010.0000.0000.0000.000
117A117GLU-1-0.790-0.84140.788-0.051-0.0510.0000.0000.0000.000
118A118TRP0-0.040-0.03336.087-0.002-0.0020.0000.0000.0000.000
119A119LYS10.9510.97642.7420.0430.0430.0000.0000.0000.000
120A120GLY0-0.015-0.00645.7020.0000.0000.0000.0000.0000.000
121A121VAL0-0.0390.00441.7330.0000.0000.0000.0000.0000.000
122A122SER00.008-0.00643.9510.0010.0010.0000.0000.0000.000
123A123ARG10.7960.89540.1590.0510.0510.0000.0000.0000.000
124A124LEU0-0.028-0.01435.269-0.001-0.0010.0000.0000.0000.000
125A125ARG10.8510.91135.6480.0740.0740.0000.0000.0000.000
126A126LEU0-0.0080.00430.775-0.003-0.0030.0000.0000.0000.000
127A127ARG10.8860.95134.2100.0970.0970.0000.0000.0000.000
128A128SER00.0760.03233.663-0.007-0.0070.0000.0000.0000.000
129A129GLU-1-0.704-0.84728.946-0.132-0.1320.0000.0000.0000.000
130A130VAL00.0320.01632.252-0.005-0.0050.0000.0000.0000.000
131A131ASN00.0190.00134.744-0.002-0.0020.0000.0000.0000.000
132A132THR0-0.023-0.02230.0360.0010.0010.0000.0000.0000.000
133A133VAL00.0210.00929.398-0.005-0.0050.0000.0000.0000.000
134A134ALA00.0020.01331.708-0.002-0.0020.0000.0000.0000.000
135A135VAL0-0.0090.00033.8750.0010.0010.0000.0000.0000.000
136A136MET0-0.0280.02327.301-0.006-0.0060.0000.0000.0000.000
137A137LYS10.9140.95828.9110.1290.1290.0000.0000.0000.000
138A138LYS10.8320.87428.5770.1070.1070.0000.0000.0000.000
139A139SER0-0.060-0.04329.283-0.006-0.0060.0000.0000.0000.000
140A140THR00.0460.01524.6630.0000.0000.0000.0000.0000.000
141A141ASN00.0250.00420.055-0.010-0.0100.0000.0000.0000.000
142A142SER0-0.020-0.01220.7960.0040.0040.0000.0000.0000.000
143A143GLY00.0490.03517.505-0.005-0.0050.0000.0000.0000.000
144A144SER00.0300.04414.2790.0110.0110.0000.0000.0000.000
145A145PRO00.0670.01916.4010.0260.0260.0000.0000.0000.000
146A146TYR0-0.002-0.03817.594-0.007-0.0070.0000.0000.0000.000
147A147PHE0-0.0220.00817.0780.0090.0090.0000.0000.0000.000
148A148SER00.0110.00519.5800.0260.0260.0000.0000.0000.000
149A149LYS10.9510.97023.3960.1480.1480.0000.0000.0000.000
150A150ARG10.9210.97722.7460.2090.2090.0000.0000.0000.000
151A151LYS10.9740.98326.7220.1220.1220.0000.0000.0000.000
152A152ALA0-0.054-0.01927.9020.0070.0070.0000.0000.0000.000
153A153VAL00.0160.00624.1210.0020.0020.0000.0000.0000.000
154A154VAL00.0280.03327.102-0.006-0.0060.0000.0000.0000.000
155A155SER00.0430.02729.120-0.005-0.0050.0000.0000.0000.000
156A156LYS10.9290.98825.0130.1830.1830.0000.0000.0000.000
157A157THR0-0.030-0.03523.825-0.020-0.0200.0000.0000.0000.000
158A158ILE0-0.0050.01026.019-0.002-0.0020.0000.0000.0000.000
159A159PRO00.0290.01228.8900.0030.0030.0000.0000.0000.000
160A160CYS0-0.139-0.08724.520-0.007-0.0070.0000.0000.0000.000
161A161ASP-1-0.810-0.90924.412-0.124-0.1240.0000.0000.0000.000
162A162VAL0-0.051-0.01320.022-0.016-0.0160.0000.0000.0000.000
163A163TYR00.0500.02619.5430.0180.0180.0000.0000.0000.000
164A164MET0-0.020-0.00113.047-0.037-0.0370.0000.0000.0000.000
165A165ASP-1-0.912-0.94615.795-0.088-0.0880.0000.0000.0000.000
166A166GLY00.0370.01514.516-0.014-0.0140.0000.0000.0000.000
167A167ARG10.9120.9525.0620.1250.1250.0000.0000.0000.000
168A168TYR00.0070.0028.771-0.141-0.1410.0000.0000.0000.000
169A169CYS00.0370.02512.1570.0690.0690.0000.0000.0000.000
170A170VAL00.0300.03714.715-0.038-0.0380.0000.0000.0000.000
171A171MET0-0.022-0.01116.8350.0080.0080.0000.0000.0000.000
172A172ARG10.9310.98419.5880.1300.1300.0000.0000.0000.000
173A173GLN0-0.037-0.04121.081-0.017-0.0170.0000.0000.0000.000
174A174ASN0-0.068-0.03424.7230.0080.0080.0000.0000.0000.000
175A175GLY00.0450.02227.3260.0050.0050.0000.0000.0000.000
176A176ARG10.9190.97520.0130.2070.2070.0000.0000.0000.000
177A177GLU-1-0.938-0.96018.214-0.188-0.1880.0000.0000.0000.000
178A178TRP0-0.090-0.05117.188-0.002-0.0020.0000.0000.0000.000
179A179SER00.014-0.00211.6310.0390.0390.0000.0000.0000.000
180A180GLY0-0.017-0.03114.030-0.037-0.0370.0000.0000.0000.000
181A181ALA00.010-0.0229.934-0.075-0.0750.0000.0000.0000.000
182A182ALA0-0.0260.00111.9130.0800.0800.0000.0000.0000.000
183A183VAL0-0.033-0.00611.100-0.135-0.1350.0000.0000.0000.000
184A184LEU00.0200.02210.5250.0770.0770.0000.0000.0000.000
185A185GLY00.0280.01612.6360.0280.0280.0000.0000.0000.000
186A186TRP0-0.046-0.02616.099-0.014-0.0140.0000.0000.0000.000
187A187ARG10.7460.85418.6310.1740.1740.0000.0000.0000.000
188A188GLY00.0560.04921.928-0.003-0.0030.0000.0000.0000.000
189A189GLN0-0.052-0.03524.4140.0040.0040.0000.0000.0000.000
190A190GLU-1-0.746-0.81726.951-0.089-0.0890.0000.0000.0000.000
191A191GLY00.008-0.03128.9850.0000.0000.0000.0000.0000.000
192A192GLY00.0330.02729.9680.0040.0040.0000.0000.0000.000
193A193PRO00.0670.03032.213-0.005-0.0050.0000.0000.0000.000
194A194LYS10.8380.91131.0920.0460.0460.0000.0000.0000.000
195A195PRO00.0430.00828.310-0.005-0.0050.0000.0000.0000.000
196A196THR00.0200.00126.008-0.007-0.0070.0000.0000.0000.000
197A197ASP-1-0.829-0.88826.271-0.054-0.0540.0000.0000.0000.000
198A198VAL0-0.0560.00224.577-0.003-0.0030.0000.0000.0000.000
199A199LYS10.8550.92523.7770.0750.0750.0000.0000.0000.000
200A200GLN00.0370.01418.831-0.023-0.0230.0000.0000.0000.000
201A201ARG10.8450.91119.1420.1520.1520.0000.0000.0000.000
202A202VAL00.009-0.00313.930-0.018-0.0180.0000.0000.0000.000
203A203VAL0-0.017-0.00416.6840.0150.0150.0000.0000.0000.000
204A204TRP0-0.0140.00211.281-0.070-0.0700.0000.0000.0000.000
205A205MET0-0.044-0.03215.4840.0470.0470.0000.0000.0000.000
206A206PHE00.0170.01215.931-0.057-0.0570.0000.0000.0000.000
207A207PRO0-0.0140.00815.8170.0240.0240.0000.0000.0000.000
208A208PHE00.006-0.01718.4100.0330.0330.0000.0000.0000.000
209A209ALA00.0370.01421.3080.0190.0190.0000.0000.0000.000
210A210VAL00.0670.03118.0100.0160.0160.0000.0000.0000.000
211A211ASN0-0.016-0.01221.3210.0180.0180.0000.0000.0000.000
212A212ILE0-0.045-0.03123.4270.0200.0200.0000.0000.0000.000
213A213ARG10.9050.94624.4060.1480.1480.0000.0000.0000.000
214A214GLU-1-0.729-0.82321.902-0.213-0.2130.0000.0000.0000.000
215A215LEU0-0.033-0.03225.8240.0160.0160.0000.0000.0000.000
216A216GLN0-0.023-0.00328.6070.0050.0050.0000.0000.0000.000
217A217VAL00.0310.03129.6970.0110.0110.0000.0000.0000.000
218A218TYR0-0.009-0.04125.5560.0030.0030.0000.0000.0000.000
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