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

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FMODB ID: JLMG9

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 OptAll
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 -2591919.136808
FMO2-HF: Nuclear repulsion 2503512.403472
FMO2-HF: Total energy -88406.733336
FMO2-MP2: Total energy -88663.074661


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.
-90.403-87.92416.32-8.037-10.763-0.073
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 : 0.923 / q_NPA : 0.959
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].
3A5MET0-0.057-0.0183.7562.4364.984-0.013-1.362-1.1730.006
4A6ASN00.016-0.0057.038-0.236-0.2360.0000.0000.0000.000
5A7HIS00.0510.0348.3620.2470.2470.0000.0000.0000.000
6A8VAL0-0.008-0.01012.821-0.180-0.1800.0000.0000.0000.000
7A9TYR0-0.021-0.02714.7760.0500.0500.0000.0000.0000.000
8A10LEU0-0.041-0.00219.4020.1770.1770.0000.0000.0000.000
9A11ILE00.011-0.00522.9800.2080.2080.0000.0000.0000.000
10A12GLY00.0280.00626.403-0.021-0.0210.0000.0000.0000.000
11A13ALA00.0140.00629.3830.1500.1500.0000.0000.0000.000
12A14LEU0-0.026-0.00529.419-0.344-0.3440.0000.0000.0000.000
13A15ALA0-0.002-0.00832.2200.3210.3210.0000.0000.0000.000
14A16ARG10.9230.95233.1539.4029.4020.0000.0000.0000.000
15A17ASP-1-0.813-0.90634.244-8.335-8.3350.0000.0000.0000.000
16A18PRO0-0.050-0.02130.570-0.118-0.1180.0000.0000.0000.000
17A19GLU-1-0.836-0.88831.362-8.479-8.4790.0000.0000.0000.000
18A20LEU0-0.0190.00329.902-0.361-0.3610.0000.0000.0000.000
19A21ARG10.7760.85430.6059.0099.0090.0000.0000.0000.000
20A22TYR0-0.001-0.01629.996-0.134-0.1340.0000.0000.0000.000
21A23THR00.0060.00926.2440.1790.1790.0000.0000.0000.000
22A24GLY00.0320.01229.6980.2460.2460.0000.0000.0000.000
23A25ASN0-0.064-0.03528.0970.0260.0260.0000.0000.0000.000
24A26GLY00.0360.02330.0150.0070.0070.0000.0000.0000.000
25A27MET0-0.061-0.01922.893-0.077-0.0770.0000.0000.0000.000
26A28ALA00.0400.02227.3500.0270.0270.0000.0000.0000.000
27A29VAL0-0.016-0.02425.315-0.536-0.5360.0000.0000.0000.000
28A30PHE00.0250.01925.9080.3920.3920.0000.0000.0000.000
29A31GLU-1-0.820-0.87825.809-11.597-11.5970.0000.0000.0000.000
30A32ALA00.0510.03427.0190.4610.4610.0000.0000.0000.000
31A33THR0-0.047-0.03727.638-0.289-0.2890.0000.0000.0000.000
32A34VAL00.0250.03426.0080.3630.3630.0000.0000.0000.000
33A35ALA00.003-0.00528.422-0.299-0.2990.0000.0000.0000.000
34A36GLY00.0480.01830.0980.2410.2410.0000.0000.0000.000
35A37GLU-1-0.790-0.87230.352-9.239-9.2390.0000.0000.0000.000
36A38ASP-1-0.767-0.85626.640-11.991-11.9910.0000.0000.0000.000
37A39ARG10.9570.97429.6729.4919.4910.0000.0000.0000.000
38A40VAL00.0100.01224.7840.0100.0100.0000.0000.0000.000
39A48ARG10.9740.97730.8629.5629.5620.0000.0000.0000.000
40A49ASN0-0.035-0.02431.154-0.356-0.3560.0000.0000.0000.000
41A50LEU0-0.016-0.00526.9500.2540.2540.0000.0000.0000.000
42A51PRO0-0.024-0.02328.974-0.379-0.3790.0000.0000.0000.000
43A52TRP0-0.053-0.01726.415-0.354-0.3540.0000.0000.0000.000
44A53TYR0-0.023-0.04428.1900.2270.2270.0000.0000.0000.000
45A54HIS0-0.036-0.03623.127-0.197-0.1970.0000.0000.0000.000
46A55ARG10.8010.87525.77510.98510.9850.0000.0000.0000.000
47A56VAL00.0090.00221.960-0.686-0.6860.0000.0000.0000.000
48A57SER0-0.012-0.00621.7140.4630.4630.0000.0000.0000.000
49A58ILE0-0.0030.01021.129-0.649-0.6490.0000.0000.0000.000
50A59LEU00.001-0.00319.3500.4060.4060.0000.0000.0000.000
51A60GLY00.0390.01822.402-0.146-0.1460.0000.0000.0000.000
52A61LYS10.8440.90124.2549.4129.4120.0000.0000.0000.000
53A62PRO00.0280.01221.2850.2690.2690.0000.0000.0000.000
54A63ALA0-0.0020.00324.3270.0860.0860.0000.0000.0000.000
55A64GLU-1-0.757-0.87226.333-8.991-8.9910.0000.0000.0000.000
56A65TRP00.003-0.00423.645-0.078-0.0780.0000.0000.0000.000
57A66GLN0-0.0070.01426.308-0.145-0.1450.0000.0000.0000.000
58A67ALA0-0.007-0.01228.3990.1640.1640.0000.0000.0000.000
59A68GLU-1-0.901-0.95531.718-8.519-8.5190.0000.0000.0000.000
60A69ARG10.8560.92625.48610.46110.4610.0000.0000.0000.000
61A70ASN0-0.070-0.03332.6200.1330.1330.0000.0000.0000.000
62A71LEU0-0.0240.00429.8380.1580.1580.0000.0000.0000.000
63A72LYS10.8520.91133.9418.0938.0930.0000.0000.0000.000
64A73GLY0-0.009-0.01535.188-0.233-0.2330.0000.0000.0000.000
65A74GLY0-0.035-0.02136.0770.2120.2120.0000.0000.0000.000
66A75ASP-1-0.797-0.87633.898-8.446-8.4460.0000.0000.0000.000
67A76ALA00.0450.01532.314-0.282-0.2820.0000.0000.0000.000
68A77VAL0-0.023-0.02627.7250.0840.0840.0000.0000.0000.000
69A78VAL00.0090.00523.322-0.177-0.1770.0000.0000.0000.000
70A79VAL0-0.039-0.03120.6600.1480.1480.0000.0000.0000.000
71A80GLU-1-0.801-0.87116.572-16.064-16.0640.0000.0000.0000.000
72A81GLY0-0.031-0.02716.5640.6220.6220.0000.0000.0000.000
73A82THR0-0.036-0.00911.861-0.553-0.5530.0000.0000.0000.000
74A83LEU00.0170.00513.8561.4631.4630.0000.0000.0000.000
75A84GLU-1-0.807-0.89614.020-19.655-19.6550.0000.0000.0000.000
76A85TYR0-0.019-0.01514.8071.0411.0410.0000.0000.0000.000
77A86ARG10.9310.95716.67413.26513.2650.0000.0000.0000.000
78A87GLN00.0450.01818.441-0.531-0.5310.0000.0000.0000.000
79A88TRP0-0.026-0.00321.275-0.003-0.0030.0000.0000.0000.000
80A89GLU-1-0.779-0.87224.827-12.491-12.4910.0000.0000.0000.000
81A90ALA0-0.016-0.01127.5550.2010.2010.0000.0000.0000.000
82A91PRO00.0380.01030.204-0.057-0.0570.0000.0000.0000.000
83A92GLU-1-0.804-0.89531.203-9.726-9.7260.0000.0000.0000.000
84A93GLY00.0240.03529.062-0.075-0.0750.0000.0000.0000.000
85A94GLY0-0.020-0.00326.950-0.537-0.5370.0000.0000.0000.000
86A95LYS10.7830.85922.35112.97012.9700.0000.0000.0000.000
87A96ARG10.8250.92324.50110.87710.8770.0000.0000.0000.000
88A97SER00.004-0.00519.634-0.046-0.0460.0000.0000.0000.000
89A98ALA0-0.028-0.01020.7600.5120.5120.0000.0000.0000.000
90A99VAL00.0340.01816.591-0.724-0.7240.0000.0000.0000.000
91A100ASN0-0.0250.00319.3930.8710.8710.0000.0000.0000.000
92A101VAL00.0750.03218.690-0.906-0.9060.0000.0000.0000.000
93A102LYS10.8170.92213.25619.47519.4750.0000.0000.0000.000
94A103ALA00.0650.02617.177-0.678-0.6780.0000.0000.0000.000
95A104LEU0-0.029-0.02916.2420.2340.2340.0000.0000.0000.000
96A105ARG10.8620.93117.78913.97813.9780.0000.0000.0000.000
97A106MET0-0.035-0.01122.537-0.468-0.4680.0000.0000.0000.000
98A107GLU-1-0.834-0.90724.760-10.532-10.5320.0000.0000.0000.000
99A108GLN0-0.015-0.01627.3740.0040.0040.0000.0000.0000.000
100A109LEU0-0.023-0.01028.518-0.046-0.0460.0000.0000.0000.000
101A110GLY0-0.005-0.00331.8210.2150.2150.0000.0000.0000.000
102A111THR0-0.068-0.03634.2410.2000.2000.0000.0000.0000.000
103A112GLN00.0540.02735.776-0.312-0.3120.0000.0000.0000.000
104A113PRO0-0.013-0.00334.649-0.027-0.0270.0000.0000.0000.000
105A114GLU-1-0.864-0.93336.635-7.524-7.5240.0000.0000.0000.000
106A115LEU0-0.062-0.02036.353-0.270-0.2700.0000.0000.0000.000
107A116ILE0-0.0080.00436.9490.2240.2240.0000.0000.0000.000
108A117GLN0-0.012-0.00638.327-0.143-0.1430.0000.0000.0000.000
109A118ASP-1-0.848-0.90837.350-8.626-8.6260.0000.0000.0000.000
110A119ALA00.011-0.02040.2370.1430.1430.0000.0000.0000.000
111A120GLY0-0.040-0.00640.2890.1550.1550.0000.0000.0000.000
112A121GLY0-0.038-0.01441.0800.0000.0000.0000.0000.0000.000
113A122GLY0-0.0230.00937.696-0.042-0.0420.0000.0000.0000.000
114A123VAL0-0.003-0.01235.9990.1860.1860.0000.0000.0000.000
115A124ARG10.8200.90233.1048.8108.8100.0000.0000.0000.000
116A125MET00.0050.02231.4050.2290.2290.0000.0000.0000.000
117A126SER0-0.041-0.03132.914-0.300-0.3000.0000.0000.0000.000
118A127GLY0-0.014-0.01532.7760.0680.0680.0000.0000.0000.000
119A128ALA0-0.042-0.00728.664-0.061-0.0610.0000.0000.0000.000
120A129MET00.001-0.00621.2360.1790.1790.0000.0000.0000.000
121A130ASN0-0.013-0.02222.024-0.696-0.6960.0000.0000.0000.000
122A131GLU-1-0.893-0.94117.501-17.008-17.0080.0000.0000.0000.000
123A132VAL0-0.022-0.01514.251-0.123-0.1230.0000.0000.0000.000
124A133LEU00.0100.00612.079-0.315-0.3150.0000.0000.0000.000
125A134VAL0-0.022-0.0069.451-0.555-0.5550.0000.0000.0000.000
126A135LEU0-0.008-0.0102.913-2.215-1.1620.333-0.300-1.0860.000
127A136GLY00.0330.0173.692-1.070-0.8320.006-0.078-0.1670.000
128A137ASN0-0.021-0.0201.859-54.699-57.07513.833-5.559-5.898-0.075
129A138VAL00.0140.0304.2665.9426.048-0.001-0.041-0.0640.000
130A139THR0-0.026-0.0367.9651.4591.4590.0000.0000.0000.000
131A140ARG10.7910.87210.62421.29421.2940.0000.0000.0000.000
132A141ASP-1-0.788-0.89312.950-21.054-21.0540.0000.0000.0000.000
133A142PRO0-0.0260.00213.4220.6620.6620.0000.0000.0000.000
134A143GLU-1-0.847-0.91315.601-12.893-12.8930.0000.0000.0000.000
135A144ILE0-0.0060.00719.246-0.047-0.0470.0000.0000.0000.000
136A145ARG10.7710.86521.12113.51013.5100.0000.0000.0000.000
137A146TYR00.001-0.02424.423-0.249-0.2490.0000.0000.0000.000
138A147THR0-0.051-0.03427.1780.2880.2880.0000.0000.0000.000
139A148PRO0-0.007-0.02329.8490.0520.0520.0000.0000.0000.000
140A149ALA0-0.0180.00132.5350.2280.2280.0000.0000.0000.000
141A150GLY00.0320.02630.4720.1150.1150.0000.0000.0000.000
142A151ASP-1-0.857-0.90026.763-11.065-11.0650.0000.0000.0000.000
143A152ALA00.0300.02622.922-0.038-0.0380.0000.0000.0000.000
144A153VAL0-0.036-0.02421.720-0.128-0.1280.0000.0000.0000.000
145A154LEU0-0.0110.00415.3160.1210.1210.0000.0000.0000.000
146A155SER0-0.0060.01217.496-0.474-0.4740.0000.0000.0000.000
147A156LEU00.0290.02210.418-0.279-0.2790.0000.0000.0000.000
148A157SER0-0.004-0.03512.2410.1450.1450.0000.0000.0000.000
149A158ILE0-0.0040.0196.884-0.979-0.9790.0000.0000.0000.000
150A159ALA0-0.004-0.0016.7373.1763.1760.0000.0000.0000.000
151A160VAL00.005-0.0015.558-8.239-8.2390.0000.0000.0000.000
152A161ASN0-0.057-0.0524.5245.7475.979-0.001-0.014-0.2160.000
153A162GLU-1-0.819-0.8965.733-23.109-23.1090.0000.0000.0000.000
154A163ASN0-0.016-0.0245.4043.7533.7530.0000.0000.0000.000
155A164TYR0-0.046-0.0207.6111.3551.3550.0000.0000.0000.000
156A165GLN00.0350.01511.0980.3500.3500.0000.0000.0000.000
157A166ASP-1-0.757-0.86214.285-13.798-13.7980.0000.0000.0000.000
158A167ARG10.9260.94417.61211.61211.6120.0000.0000.0000.000
159A168GLN0-0.059-0.02820.1070.3430.3430.0000.0000.0000.000
160A169GLY0-0.0080.01517.7940.1720.1720.0000.0000.0000.000
161A170GLN0-0.054-0.02916.271-0.470-0.4700.0000.0000.0000.000
162A171ARG10.8790.9126.82925.32325.3230.0000.0000.0000.000
163A172GLN0-0.036-0.01711.993-0.415-0.4150.0000.0000.0000.000
164A173GLU-1-0.812-0.8696.679-33.011-33.0110.0000.0000.0000.000
165A174LYS10.7930.9049.58521.90121.9010.0000.0000.0000.000
166A175VAL0-0.0140.0028.949-2.669-2.6690.0000.0000.0000.000
167A176HIS0-0.020-0.04410.0473.3983.3980.0000.0000.0000.000
168A177TYR0-0.021-0.01010.291-2.995-2.9950.0000.0000.0000.000
169A178ILE00.0150.01011.1692.2002.2000.0000.0000.0000.000
170A179ASP-1-0.771-0.84512.142-20.485-20.4850.0000.0000.0000.000
171A180ALA0-0.023-0.01213.3990.6040.6040.0000.0000.0000.000
172A181THR0-0.013-0.03015.2530.0070.0070.0000.0000.0000.000
173A182LEU00.0040.01113.583-0.078-0.0780.0000.0000.0000.000
174A183TRP00.0380.00518.0760.7550.7550.0000.0000.0000.000
175A184ARG10.9030.92921.30611.64811.6480.0000.0000.0000.000
176A185ASP-1-0.829-0.90921.667-13.214-13.2140.0000.0000.0000.000
177A186LEU0-0.016-0.00516.945-0.655-0.6550.0000.0000.0000.000
178A187ALA0-0.023-0.00616.923-1.053-1.0530.0000.0000.0000.000
179A188GLU-1-0.776-0.88518.391-13.799-13.7990.0000.0000.0000.000
180A189ASN0-0.064-0.03616.7070.0650.0650.0000.0000.0000.000
181A190MET0-0.023-0.00511.031-0.857-0.8570.0000.0000.0000.000
182A191LYS10.8290.90214.21013.33813.3380.0000.0000.0000.000
183A192GLU-1-0.850-0.91715.880-15.617-15.6170.0000.0000.0000.000
184A193LEU0-0.058-0.0149.012-1.029-1.0290.0000.0000.0000.000
185A194ARG10.8000.88011.03920.28020.2800.0000.0000.0000.000
186A195LYS10.8790.9269.97220.02520.0250.0000.0000.0000.000
187A196GLY0-0.0030.0007.6151.1751.1750.0000.0000.0000.000
188A197ASP-1-0.773-0.8535.975-35.469-35.4690.0000.0000.0000.000
189A198PRO0-0.072-0.0242.367-5.087-5.0912.136-0.593-1.539-0.002
190A199VAL00.008-0.0043.5338.8809.0060.0050.081-0.2120.000
191A200MET0-0.007-0.0095.194-5.719-5.673-0.001-0.001-0.0440.000
192A201ILE0-0.011-0.0097.3772.8982.8980.0000.0000.0000.000
193A202MET00.0090.00611.032-0.915-0.9150.0000.0000.0000.000
194A203GLY00.0410.01714.1030.5460.5460.0000.0000.0000.000
195A204ARG10.7880.89417.40412.78112.7810.0000.0000.0000.000
196A205LEU00.0160.00918.075-0.356-0.3560.0000.0000.0000.000
197A206VAL00.0100.02320.4160.9980.9980.0000.0000.0000.000
198A207ASN00.0230.00722.165-0.779-0.7790.0000.0000.0000.000
199A208GLU-1-0.779-0.83521.529-13.967-13.9670.0000.0000.0000.000
200A209GLY0-0.002-0.01425.123-0.070-0.0700.0000.0000.0000.000
201A210TRP0-0.004-0.01723.7240.3630.3630.0000.0000.0000.000
202A211THR0-0.002-0.01328.8320.1890.1890.0000.0000.0000.000
203A212ASP-1-0.783-0.85328.900-11.187-11.1870.0000.0000.0000.000
204A213LYS10.7890.85230.6369.8749.8740.0000.0000.0000.000
205A214ASP-1-0.870-0.92332.938-9.196-9.1960.0000.0000.0000.000
206A215GLY00.0420.03134.9940.2870.2870.0000.0000.0000.000
207A216ASN0-0.028-0.00830.593-0.244-0.2440.0000.0000.0000.000
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209A218ARG10.8380.90524.35811.99411.9940.0000.0000.0000.000
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