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: 85JMY

Calculation Name: 1SE8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SE8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RY51

Base Structure: X-ray

Registration Date: 2023-06-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2587778.370682
FMO2-HF: Nuclear repulsion 2499373.32232
FMO2-HF: Total energy -88405.048362
FMO2-MP2: Total energy -88661.416426


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:ARG)


Summations of interaction energy for fragment #1(A:3:ARG)
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.
-86.342-78.62410.709-7.575-10.849-0.065
Interaction energy analysis for fragmet #1(A:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.916 / q_NPA : 0.958
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].
3A5MET0-0.044-0.0233.6621.8884.552-0.018-1.363-1.2830.008
4A6ASN00.002-0.0156.5550.1880.1880.0000.0000.0000.000
5A7HIS00.0360.0318.6820.7120.7120.0000.0000.0000.000
6A8VAL00.006-0.00312.778-0.172-0.1720.0000.0000.0000.000
7A9TYR00.0040.00714.4600.0990.0990.0000.0000.0000.000
8A10LEU0-0.051-0.02119.2470.1380.1380.0000.0000.0000.000
9A11ILE00.0160.00622.8490.2060.2060.0000.0000.0000.000
10A12GLY00.0400.00526.181-0.007-0.0070.0000.0000.0000.000
11A13ALA00.0150.00928.9250.1170.1170.0000.0000.0000.000
12A14LEU0-0.0090.00028.988-0.370-0.3700.0000.0000.0000.000
13A15ALA0-0.014-0.01031.8360.3180.3180.0000.0000.0000.000
14A16ARG10.9340.95333.0539.6299.6290.0000.0000.0000.000
15A17ASP-1-0.817-0.90634.003-8.400-8.4000.0000.0000.0000.000
16A18PRO0-0.059-0.02430.462-0.125-0.1250.0000.0000.0000.000
17A19GLU-1-0.929-0.96131.448-8.568-8.5680.0000.0000.0000.000
18A20LEU0-0.0040.00329.782-0.382-0.3820.0000.0000.0000.000
19A21ARG10.8940.94930.8339.1119.1110.0000.0000.0000.000
20A22TYR00.0110.00630.341-0.179-0.1790.0000.0000.0000.000
21A23THR0-0.0110.00126.3890.1530.1530.0000.0000.0000.000
22A24GLY00.0390.01329.8430.2470.2470.0000.0000.0000.000
23A25ASN0-0.042-0.03128.1920.2010.2010.0000.0000.0000.000
24A26GLY00.0270.02430.2520.0470.0470.0000.0000.0000.000
25A27MET0-0.079-0.02622.918-0.071-0.0710.0000.0000.0000.000
26A28ALA00.0390.02427.6290.0380.0380.0000.0000.0000.000
27A29VAL0-0.004-0.02125.381-0.570-0.5700.0000.0000.0000.000
28A30PHE00.0490.02826.1330.3750.3750.0000.0000.0000.000
29A31GLU-1-0.959-0.98525.971-11.535-11.5350.0000.0000.0000.000
30A32ALA00.0570.03227.0600.4870.4870.0000.0000.0000.000
31A33THR0-0.072-0.03927.296-0.413-0.4130.0000.0000.0000.000
32A34VAL00.0280.03725.6270.3800.3800.0000.0000.0000.000
33A35ALA00.001-0.01127.914-0.336-0.3360.0000.0000.0000.000
34A36GLY00.0490.01929.1940.2670.2670.0000.0000.0000.000
35A37GLU-1-0.852-0.92529.276-9.395-9.3950.0000.0000.0000.000
36A38ASP-1-0.803-0.88525.680-12.166-12.1660.0000.0000.0000.000
37A39ARG10.9210.95928.7279.5999.5990.0000.0000.0000.000
38A40VAL00.0190.01124.054-0.090-0.0900.0000.0000.0000.000
39A48ARG10.9730.97230.6719.6919.6910.0000.0000.0000.000
40A49ASN00.0010.00630.647-0.477-0.4770.0000.0000.0000.000
41A50LEU0-0.0170.00026.5300.2210.2210.0000.0000.0000.000
42A51PRO00.008-0.00428.653-0.253-0.2530.0000.0000.0000.000
43A52TRP0-0.093-0.05525.473-0.375-0.3750.0000.0000.0000.000
44A53TYR00.0120.00227.1210.2750.2750.0000.0000.0000.000
45A54HIS0-0.028-0.02622.515-0.176-0.1760.0000.0000.0000.000
46A55ARG10.9360.97125.48011.10011.1000.0000.0000.0000.000
47A56VAL00.0160.00921.649-0.648-0.6480.0000.0000.0000.000
48A57SER0-0.008-0.00722.0610.4730.4730.0000.0000.0000.000
49A58ILE0-0.0190.00621.277-0.659-0.6590.0000.0000.0000.000
50A59LEU0-0.008-0.01219.6820.3890.3890.0000.0000.0000.000
51A60GLY00.0060.00122.554-0.170-0.1700.0000.0000.0000.000
52A61LYS10.9370.95824.5919.6949.6940.0000.0000.0000.000
53A62PRO00.0260.01221.2490.2920.2920.0000.0000.0000.000
54A63ALA00.0030.00624.3040.1150.1150.0000.0000.0000.000
55A64GLU-1-0.847-0.94326.248-9.062-9.0620.0000.0000.0000.000
56A65TRP00.0100.00123.206-0.081-0.0810.0000.0000.0000.000
57A66GLN00.0260.02626.145-0.072-0.0720.0000.0000.0000.000
58A67ALA0-0.008-0.01328.2090.2000.2000.0000.0000.0000.000
59A68GLU-1-0.937-0.96131.330-8.533-8.5330.0000.0000.0000.000
60A69ARG10.8420.91325.84310.51310.5130.0000.0000.0000.000
61A70ASN0-0.061-0.01932.6470.0490.0490.0000.0000.0000.000
62A71LEU0-0.032-0.00729.6630.1120.1120.0000.0000.0000.000
63A72LYS10.9460.96833.7137.9107.9100.0000.0000.0000.000
64A73GLY0-0.010-0.01734.943-0.219-0.2190.0000.0000.0000.000
65A74GLY0-0.049-0.03235.3250.2570.2570.0000.0000.0000.000
66A75ASP-1-0.842-0.90033.345-8.571-8.5710.0000.0000.0000.000
67A76ALA00.009-0.00131.529-0.274-0.2740.0000.0000.0000.000
68A77VAL0-0.028-0.02326.7790.0950.0950.0000.0000.0000.000
69A78VAL00.0170.00622.691-0.181-0.1810.0000.0000.0000.000
70A79VAL0-0.034-0.02920.4010.1470.1470.0000.0000.0000.000
71A80GLU-1-0.904-0.94815.859-16.434-16.4340.0000.0000.0000.000
72A81GLY0-0.024-0.02916.5250.5080.5080.0000.0000.0000.000
73A82THR0-0.057-0.01411.754-1.068-1.0680.0000.0000.0000.000
74A83LEU0-0.003-0.01513.2731.4991.4990.0000.0000.0000.000
75A84GLU-1-0.824-0.92914.018-20.270-20.2700.0000.0000.0000.000
76A85TYR0-0.019-0.02814.2631.1261.1260.0000.0000.0000.000
77A86ARG10.9210.95816.08113.50613.5060.0000.0000.0000.000
78A87GLN00.0350.02017.782-0.647-0.6470.0000.0000.0000.000
79A88TRP0-0.0150.00020.500-0.001-0.0010.0000.0000.0000.000
80A89GLU-1-0.890-0.94924.148-12.451-12.4510.0000.0000.0000.000
81A90ALA0-0.022-0.00326.9340.2830.2830.0000.0000.0000.000
82A91PRO00.0440.00229.825-0.046-0.0460.0000.0000.0000.000
83A92GLU-1-0.825-0.90130.896-9.807-9.8070.0000.0000.0000.000
84A93GLY00.0090.02628.895-0.086-0.0860.0000.0000.0000.000
85A94GLY0-0.018-0.01226.710-0.523-0.5230.0000.0000.0000.000
86A95LYS10.8950.94721.46313.77913.7790.0000.0000.0000.000
87A96ARG10.9260.96223.66811.21211.2120.0000.0000.0000.000
88A97SER0-0.005-0.00118.584-0.031-0.0310.0000.0000.0000.000
89A98ALA0-0.018-0.00919.9840.5820.5820.0000.0000.0000.000
90A99VAL00.0400.02815.716-0.568-0.5680.0000.0000.0000.000
91A100ASN0-0.027-0.01118.4820.5350.5350.0000.0000.0000.000
92A101VAL00.0660.03918.516-0.933-0.9330.0000.0000.0000.000
93A102LYS10.9000.98115.60117.78517.7850.0000.0000.0000.000
94A103ALA00.0600.02117.252-0.699-0.6990.0000.0000.0000.000
95A104LEU0-0.027-0.02815.8760.2760.2760.0000.0000.0000.000
96A105ARG10.9200.95318.69613.63913.6390.0000.0000.0000.000
97A106MET0-0.0270.00321.958-0.405-0.4050.0000.0000.0000.000
98A107GLU-1-0.897-0.93424.043-10.843-10.8430.0000.0000.0000.000
99A108GLN0-0.013-0.01026.7950.0090.0090.0000.0000.0000.000
100A109LEU0-0.040-0.02028.378-0.011-0.0110.0000.0000.0000.000
101A110GLY00.0240.00931.4480.1940.1940.0000.0000.0000.000
102A111THR0-0.044-0.01533.7160.3160.3160.0000.0000.0000.000
103A112GLN00.0200.00435.507-0.238-0.2380.0000.0000.0000.000
104A113PRO0-0.017-0.00434.4320.0220.0220.0000.0000.0000.000
105A114GLU-1-0.879-0.93636.470-7.583-7.5830.0000.0000.0000.000
106A115LEU0-0.045-0.03236.063-0.296-0.2960.0000.0000.0000.000
107A116ILE0-0.026-0.00735.8360.2390.2390.0000.0000.0000.000
108A117GLN0-0.002-0.00637.780-0.204-0.2040.0000.0000.0000.000
109A118ASP-1-0.871-0.93836.592-8.630-8.6300.0000.0000.0000.000
110A119ALA00.015-0.02439.4760.1300.1300.0000.0000.0000.000
111A120GLY0-0.063-0.01839.6390.1620.1620.0000.0000.0000.000
112A121GLY0-0.043-0.01840.6470.0320.0320.0000.0000.0000.000
113A122GLY0-0.0430.00137.000-0.053-0.0530.0000.0000.0000.000
114A123VAL00.0120.00635.7660.1410.1410.0000.0000.0000.000
115A124ARG10.8340.91832.4088.9358.9350.0000.0000.0000.000
116A125MET00.0030.00931.0610.2520.2520.0000.0000.0000.000
117A126SER0-0.013-0.00432.373-0.273-0.2730.0000.0000.0000.000
118A127GLY0-0.022-0.02131.9290.0340.0340.0000.0000.0000.000
119A128ALA0-0.0440.00628.307-0.059-0.0590.0000.0000.0000.000
120A129MET00.006-0.00720.9160.1430.1430.0000.0000.0000.000
121A130ASN0-0.003-0.00920.963-0.799-0.7990.0000.0000.0000.000
122A131GLU-1-0.900-0.94617.192-17.210-17.2100.0000.0000.0000.000
123A132VAL0-0.028-0.01313.238-0.261-0.2610.0000.0000.0000.000
124A133LEU00.0000.00211.630-0.282-0.2820.0000.0000.0000.000
125A134VAL0-0.0100.0038.745-0.615-0.6150.0000.0000.0000.000
126A135LEU0-0.008-0.0042.517-2.556-2.1281.961-0.449-1.940-0.001
127A136GLY00.0330.0133.129-1.922-1.4020.076-0.219-0.3760.000
128A137ASN0-0.044-0.0271.940-42.367-39.4306.621-4.749-4.809-0.067
129A138VAL00.0570.0484.2735.4035.504-0.001-0.033-0.0670.000
130A139THR00.010-0.0057.8780.1170.1170.0000.0000.0000.000
131A140ARG10.8530.91610.29121.12021.1200.0000.0000.0000.000
132A141ASP-1-0.822-0.91512.981-20.500-20.5000.0000.0000.0000.000
133A142PRO0-0.024-0.00213.1650.6990.6990.0000.0000.0000.000
134A143GLU-1-0.896-0.93415.550-13.236-13.2360.0000.0000.0000.000
135A144ILE0-0.0020.00319.129-0.221-0.2210.0000.0000.0000.000
136A145ARG10.8230.90621.02113.61713.6170.0000.0000.0000.000
137A146TYR0-0.012-0.02524.099-0.318-0.3180.0000.0000.0000.000
138A147THR0-0.020-0.00726.8690.3380.3380.0000.0000.0000.000
139A148PRO00.024-0.00329.2280.0530.0530.0000.0000.0000.000
140A149ALA0-0.028-0.01632.3200.1650.1650.0000.0000.0000.000
141A150GLY00.0180.02329.9600.0800.0800.0000.0000.0000.000
142A151ASP-1-0.944-0.95926.561-11.020-11.0200.0000.0000.0000.000
143A152ALA00.0120.00822.469-0.054-0.0540.0000.0000.0000.000
144A153VAL0-0.019-0.01221.192-0.185-0.1850.0000.0000.0000.000
145A154LEU00.0000.00414.9370.1210.1210.0000.0000.0000.000
146A155SER0-0.025-0.00316.994-0.409-0.4090.0000.0000.0000.000
147A156LEU00.0140.00510.143-0.202-0.2020.0000.0000.0000.000
148A157SER0-0.013-0.02911.9490.6230.6230.0000.0000.0000.000
149A158ILE0-0.010-0.0086.536-1.529-1.5290.0000.0000.0000.000
150A159ALA0-0.014-0.0106.4483.2733.2730.0000.0000.0000.000
151A160VAL00.005-0.0035.009-9.074-9.003-0.001-0.005-0.0640.000
152A161ASN0-0.084-0.0555.0946.4406.4400.0000.0000.0000.000
153A162GLU-1-0.834-0.9025.351-25.780-25.7800.0000.0000.0000.000
154A163ASN00.0290.0054.8002.0852.0850.0000.0000.0000.000
155A164TYR0-0.026-0.0167.7171.4321.4320.0000.0000.0000.000
156A165GLN00.0120.00611.2980.6270.6270.0000.0000.0000.000
157A166ASP-1-0.766-0.88114.449-14.047-14.0470.0000.0000.0000.000
158A167ARG10.9320.93817.51811.52911.5290.0000.0000.0000.000
159A168GLN0-0.058-0.03120.1110.3380.3380.0000.0000.0000.000
160A169GLY0-0.0040.02117.8410.3050.3050.0000.0000.0000.000
161A170GLN0-0.043-0.01016.437-0.366-0.3660.0000.0000.0000.000
162A171ARG10.8660.9287.38124.97324.9730.0000.0000.0000.000
163A172GLN0-0.016-0.00112.065-0.396-0.3960.0000.0000.0000.000
164A173GLU-1-0.849-0.9187.735-31.765-31.7650.0000.0000.0000.000
165A174LYS10.8830.9509.62321.58921.5890.0000.0000.0000.000
166A175VAL0-0.023-0.0058.461-2.748-2.7480.0000.0000.0000.000
167A176HIS0-0.027-0.0319.6243.7363.7360.0000.0000.0000.000
168A177TYR0-0.025-0.0209.736-3.141-3.1410.0000.0000.0000.000
169A178ILE00.0110.00810.6092.1472.1470.0000.0000.0000.000
170A179ASP-1-0.873-0.90811.712-20.693-20.6930.0000.0000.0000.000
171A180ALA0-0.015-0.01312.6540.3960.3960.0000.0000.0000.000
172A181THR0-0.026-0.02214.5290.1300.1300.0000.0000.0000.000
173A182LEU0-0.004-0.00213.263-0.165-0.1650.0000.0000.0000.000
174A183TRP00.0500.01417.5310.8340.8340.0000.0000.0000.000
175A184ARG10.9440.95720.77311.83711.8370.0000.0000.0000.000
176A185ASP-1-0.830-0.91321.344-13.121-13.1210.0000.0000.0000.000
177A186LEU0-0.034-0.01116.191-0.615-0.6150.0000.0000.0000.000
178A187ALA0-0.026-0.01416.669-1.039-1.0390.0000.0000.0000.000
179A188GLU-1-0.787-0.90418.083-13.556-13.5560.0000.0000.0000.000
180A189ASN0-0.059-0.03816.4190.2290.2290.0000.0000.0000.000
181A190MET0-0.034-0.01110.583-0.751-0.7510.0000.0000.0000.000
182A191LYS10.9050.96714.11213.60013.6000.0000.0000.0000.000
183A192GLU-1-0.927-0.97115.943-15.578-15.5780.0000.0000.0000.000
184A193LEU0-0.070-0.0149.053-1.061-1.0610.0000.0000.0000.000
185A194ARG10.8790.93711.12820.15520.1550.0000.0000.0000.000
186A195LYS10.9290.9709.95419.88519.8850.0000.0000.0000.000
187A196GLY0-0.030-0.0227.5311.1321.1320.0000.0000.0000.000
188A197ASP-1-0.787-0.8886.211-34.289-34.2890.0000.0000.0000.000
189A198PRO0-0.073-0.0252.390-4.805-4.7321.974-0.560-1.486-0.002
190A199VAL00.0180.0073.5008.7038.8800.0040.049-0.2300.000
191A200MET0-0.011-0.0134.812-6.314-6.254-0.001-0.003-0.0560.000
192A201ILE0-0.005-0.0117.0783.2413.2410.0000.0000.0000.000
193A202MET00.0290.01410.378-0.636-0.6360.0000.0000.0000.000
194A203GLY00.0240.00713.6090.5760.5760.0000.0000.0000.000
195A204ARG10.9120.98616.69913.22713.2270.0000.0000.0000.000
196A205LEU00.0080.00417.139-0.432-0.4320.0000.0000.0000.000
197A206VAL00.0050.01819.5661.0491.0490.0000.0000.0000.000
198A207ASN0-0.010-0.01021.442-0.806-0.8060.0000.0000.0000.000
199A208GLU-1-0.824-0.92021.348-13.967-13.9670.0000.0000.0000.000
200A209GLY0-0.051-0.03024.620-0.049-0.0490.0000.0000.0000.000
201A210TRP00.007-0.02524.0260.2310.2310.0000.0000.0000.000
202A211THR00.0050.00028.2050.1340.1340.0000.0000.0000.000
203A212ASP-1-0.813-0.86928.548-10.974-10.9740.0000.0000.0000.000
204A213LYS10.8200.87730.3769.8509.8500.0000.0000.0000.000
205A214ASP-1-0.913-0.94732.924-9.049-9.0490.0000.0000.0000.000
206A215GLY00.0240.02235.0720.2380.2380.0000.0000.0000.000
207A216ASN0-0.055-0.02730.666-0.290-0.2900.0000.0000.0000.000
208A217LYS10.8800.93729.96510.03310.0330.0000.0000.0000.000
209A218ARG10.8490.90724.66811.75611.7560.0000.0000.0000.000
210A219ASN0-0.014-0.03325.600-0.139-0.1390.0000.0000.0000.000
211A220SER00.0410.03420.903-0.044-0.0440.0000.0000.0000.000
212A221THR00.0050.02219.0400.3300.3300.0000.0000.0000.000
213A222ARG10.8710.95316.36915.94415.9440.0000.0000.0000.000
214A223VAL00.0140.00413.4240.5760.5760.0000.0000.0000.000
215A224GLU-1-0.898-0.94116.233-13.952-13.9520.0000.0000.0000.000
216A225ALA0-0.010-0.00814.6140.0130.0130.0000.0000.0000.000
217A226THR0-0.025-0.02716.2830.6470.6470.0000.0000.0000.000
218A227ARG10.8390.90313.72819.97619.9760.0000.0000.0000.000
219A228VAL0-0.008-0.00710.366-1.168-1.1680.0000.0000.0000.000
220A229GLU-1-0.802-0.8788.867-20.845-20.8450.0000.0000.0000.000
221A230ALA00.0210.0137.685-4.214-4.2140.0000.0000.0000.000
222A231LEU0-0.031-0.0182.684-1.685-0.9980.094-0.243-0.538-0.003
223A232ALA00.001-0.0036.1371.5551.5550.0000.0000.0000.000
224A233ARG10.9170.9666.31221.42821.4280.0000.0000.0000.000