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: RY8N8

Calculation Name: 1ET9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ET9

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0I6

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2363344.87099
FMO2-HF: Nuclear repulsion 2283760.412048
FMO2-HF: Total energy -79584.458942
FMO2-MP2: Total energy -79820.134254


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:ASN)


Summations of interaction energy for fragment #1(A:1:ASN)
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.
-14.827-15.19412.798-4.112-8.320.055
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.039
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].
3A3TYR00.0510.0222.038-8.484-8.94212.734-5.345-6.9320.053
4A4ASN0-0.0130.0043.278-2.818-2.9320.0661.259-1.2110.002
5A5THR00.0800.0224.646-1.459-1.360-0.001-0.016-0.0820.000
6A6THR00.0440.0347.919-0.445-0.4450.0000.0000.0000.000
7A7ASN00.0270.0135.4830.0220.0220.0000.0000.0000.000
8A8ARG10.7630.8775.899-2.890-2.8900.0000.0000.0000.000
9A9HIS00.0240.0149.656-0.161-0.1610.0000.0000.0000.000
10A10ASN00.0040.00712.208-0.121-0.1210.0000.0000.0000.000
11A11LEU0-0.009-0.00210.691-0.076-0.0760.0000.0000.0000.000
12A12GLU-1-0.929-0.97313.4800.5720.5720.0000.0000.0000.000
13A13SER0-0.043-0.03015.471-0.092-0.0920.0000.0000.0000.000
14A14LEU0-0.022-0.00516.490-0.045-0.0450.0000.0000.0000.000
15A15TYR0-0.010-0.04516.167-0.033-0.0330.0000.0000.0000.000
16A16LYS10.9120.96919.211-0.424-0.4240.0000.0000.0000.000
17A17HIS0-0.047-0.02220.776-0.041-0.0410.0000.0000.0000.000
18A18ASP-1-0.838-0.92923.6910.1670.1670.0000.0000.0000.000
19A19SER0-0.052-0.01525.741-0.010-0.0100.0000.0000.0000.000
20A20ASN00.006-0.00321.541-0.021-0.0210.0000.0000.0000.000
21A21LEU0-0.042-0.01824.591-0.007-0.0070.0000.0000.0000.000
22A22ILE0-0.053-0.01326.496-0.004-0.0040.0000.0000.0000.000
23A23GLU-1-0.887-0.95829.4910.0930.0930.0000.0000.0000.000
24A24ALA0-0.066-0.02932.0760.0010.0010.0000.0000.0000.000
25A25ASP-1-0.886-0.94035.4600.0630.0630.0000.0000.0000.000
26A26SER0-0.033-0.02138.268-0.001-0.0010.0000.0000.0000.000
27A27ILE0-0.0440.00636.540-0.001-0.0010.0000.0000.0000.000
28A28LYS10.9941.00139.650-0.036-0.0360.0000.0000.0000.000
29A29ASN0-0.022-0.00138.0880.0020.0020.0000.0000.0000.000
30A30SER00.0040.00339.030-0.001-0.0010.0000.0000.0000.000
31A31PRO0-0.0150.00940.694-0.001-0.0010.0000.0000.0000.000
32A32ASP-1-0.888-0.96739.3090.0410.0410.0000.0000.0000.000
33A33ILE0-0.024-0.01040.063-0.002-0.0020.0000.0000.0000.000
34A34VAL0-0.050-0.02535.7280.0030.0030.0000.0000.0000.000
35A35THR00.0260.00032.450-0.003-0.0030.0000.0000.0000.000
36A36SER00.001-0.00634.3180.0010.0010.0000.0000.0000.000
37A37HIS00.0240.01129.0440.0000.0000.0000.0000.0000.000
38A38MET0-0.036-0.01330.5300.0020.0020.0000.0000.0000.000
39A39LEU0-0.017-0.00332.512-0.003-0.0030.0000.0000.0000.000
40A40LYS10.9720.99833.198-0.042-0.0420.0000.0000.0000.000
41A41TYR00.0510.01733.863-0.003-0.0030.0000.0000.0000.000
42A42SER00.0240.01335.4530.0030.0030.0000.0000.0000.000
43A43VAL00.0250.01033.781-0.001-0.0010.0000.0000.0000.000
44A44LYS10.8700.94934.287-0.085-0.0850.0000.0000.0000.000
45A45ASP-1-0.838-0.93433.7490.0970.0970.0000.0000.0000.000
46A46LYS10.8050.91329.430-0.117-0.1170.0000.0000.0000.000
47A47ASN0-0.003-0.01733.589-0.004-0.0040.0000.0000.0000.000
48A48LEU00.0010.00328.5230.0060.0060.0000.0000.0000.000
49A49SER00.0130.00729.064-0.008-0.0080.0000.0000.0000.000
50A50VAL0-0.0070.00128.4480.0040.0040.0000.0000.0000.000
51A51PHE00.0290.00326.184-0.008-0.0080.0000.0000.0000.000
52A52PHE0-0.010-0.02527.3410.0020.0020.0000.0000.0000.000
53A53GLU-1-0.956-0.98424.780-0.019-0.0190.0000.0000.0000.000
54A54LYS10.8900.93827.4190.0130.0130.0000.0000.0000.000
55A55ASP-1-0.877-0.94730.8320.0050.0050.0000.0000.0000.000
56A56TRP00.0150.01032.6390.0030.0030.0000.0000.0000.000
57A57ILE0-0.054-0.01429.9430.0020.0020.0000.0000.0000.000
58A58SER00.0430.01734.0970.0030.0030.0000.0000.0000.000
59A59GLN0-0.022-0.03035.6100.0010.0010.0000.0000.0000.000
60A60GLU-1-0.841-0.88836.5040.0190.0190.0000.0000.0000.000
61A61PHE00.000-0.02333.7720.0010.0010.0000.0000.0000.000
62A62LYS10.9190.97138.617-0.019-0.0190.0000.0000.0000.000
63A63ASP-1-0.923-0.95640.6020.0260.0260.0000.0000.0000.000
64A64LYS10.8670.93841.280-0.022-0.0220.0000.0000.0000.000
65A65GLU-1-0.971-0.97840.9700.0390.0390.0000.0000.0000.000
66A66VAL0-0.026-0.02536.228-0.002-0.0020.0000.0000.0000.000
67A67ASP-1-0.805-0.90935.4630.0520.0520.0000.0000.0000.000
68A68ILE0-0.062-0.04930.734-0.001-0.0010.0000.0000.0000.000
69A69TYR0-0.015-0.01526.4220.0060.0060.0000.0000.0000.000
70A70ALA0-0.026-0.00325.950-0.004-0.0040.0000.0000.0000.000
71A71LEU00.0060.01520.0850.0060.0060.0000.0000.0000.000
72A72SER0-0.076-0.03623.819-0.014-0.0140.0000.0000.0000.000
73A73ALA00.0250.00120.9350.0200.0200.0000.0000.0000.000
74A74GLN0-0.044-0.02422.824-0.005-0.0050.0000.0000.0000.000
75A75GLU-1-0.940-0.97123.8120.0770.0770.0000.0000.0000.000
76A83ARG10.9290.97030.127-0.082-0.0820.0000.0000.0000.000
77A84TYR00.0130.00126.1710.0060.0060.0000.0000.0000.000
78A85GLU-1-0.865-0.91123.3960.0720.0720.0000.0000.0000.000
79A86ALA00.003-0.00924.8220.0100.0100.0000.0000.0000.000
80A87PHE00.0180.00622.188-0.012-0.0120.0000.0000.0000.000
81A88GLY00.0310.02025.1290.0020.0020.0000.0000.0000.000
82A89GLY00.005-0.01327.7240.0060.0060.0000.0000.0000.000
83A90ILE0-0.023-0.00128.5160.0030.0030.0000.0000.0000.000
84A91THR00.006-0.00632.209-0.004-0.0040.0000.0000.0000.000
85A92LEU0-0.040-0.01034.7590.0020.0020.0000.0000.0000.000
86A93THR00.0260.02138.5420.0000.0000.0000.0000.0000.000
87A94ASN0-0.020-0.01940.235-0.003-0.0030.0000.0000.0000.000
88A95SER00.007-0.00141.8090.0030.0030.0000.0000.0000.000
89A96GLU-1-0.940-0.96542.3580.0310.0310.0000.0000.0000.000
90A97LYS10.9670.98940.405-0.050-0.0500.0000.0000.0000.000
91A98LYS10.9270.95640.970-0.029-0.0290.0000.0000.0000.000
92A99GLU-1-0.944-0.97837.5760.0650.0650.0000.0000.0000.000
93A100ILE0-0.0080.01634.576-0.004-0.0040.0000.0000.0000.000
94A101LYS10.9270.95233.383-0.055-0.0550.0000.0000.0000.000
95A102VAL00.0500.03928.796-0.004-0.0040.0000.0000.0000.000
96A103PRO0-0.012-0.02029.7020.0090.0090.0000.0000.0000.000
97A104VAL00.0080.01223.671-0.002-0.0020.0000.0000.0000.000
98A105ASN0-0.051-0.02624.9430.0080.0080.0000.0000.0000.000
99A106VAL0-0.011-0.00119.750-0.001-0.0010.0000.0000.0000.000
100A107TRP00.0140.01119.535-0.007-0.0070.0000.0000.0000.000
101A108ASP-1-0.803-0.86717.6750.2210.2210.0000.0000.0000.000
102A109LYS10.8470.92212.568-0.318-0.3180.0000.0000.0000.000
103A110SER0-0.015-0.00517.257-0.015-0.0150.0000.0000.0000.000
104A111LYS10.8620.92119.839-0.109-0.1090.0000.0000.0000.000
105A112GLN00.0420.03422.0890.0110.0110.0000.0000.0000.000
106A113GLN0-0.026-0.01322.289-0.004-0.0040.0000.0000.0000.000
107A114PRO0-0.024-0.01925.303-0.008-0.0080.0000.0000.0000.000
108A115PRO00.0510.01927.4320.0070.0070.0000.0000.0000.000
109A116MET0-0.058-0.01024.3510.0140.0140.0000.0000.0000.000
110A117PHE00.0120.00128.370-0.007-0.0070.0000.0000.0000.000
111A118ILE0-0.0140.01525.7810.0130.0130.0000.0000.0000.000
112A119THR0-0.018-0.01229.131-0.007-0.0070.0000.0000.0000.000
113A120VAL00.0190.01530.4930.0070.0070.0000.0000.0000.000
114A121ASN0-0.005-0.00833.244-0.004-0.0040.0000.0000.0000.000
115A122LYS10.9871.01732.281-0.065-0.0650.0000.0000.0000.000
116A123PRO00.0330.04835.6370.0000.0000.0000.0000.0000.000
117A124LYS10.9640.97534.528-0.021-0.0210.0000.0000.0000.000
118A125VAL00.0220.03029.2720.0030.0030.0000.0000.0000.000
119A126THR00.022-0.00227.486-0.003-0.0030.0000.0000.0000.000
120A127ALA00.0700.02823.7940.0060.0060.0000.0000.0000.000
121A128GLN00.0420.00922.9070.0190.0190.0000.0000.0000.000
122A129GLU-1-0.803-0.91423.7490.0860.0860.0000.0000.0000.000
123A130VAL00.0090.00824.5740.0110.0110.0000.0000.0000.000
124A131ASP-1-0.720-0.80818.6360.1160.1160.0000.0000.0000.000
125A132ILE0-0.018-0.00821.1670.0250.0250.0000.0000.0000.000
126A133LYS10.8240.90522.392-0.066-0.0660.0000.0000.0000.000
127A134VAL00.0270.02420.1500.0130.0130.0000.0000.0000.000
128A135ARG10.8640.91414.416-0.128-0.1280.0000.0000.0000.000
129A136LYS10.8660.94419.443-0.158-0.1580.0000.0000.0000.000
130A137LEU0-0.042-0.01322.0040.0170.0170.0000.0000.0000.000
131A138LEU00.010-0.01017.0970.0100.0100.0000.0000.0000.000
132A139ILE00.0050.00816.7650.0330.0330.0000.0000.0000.000
133A140LYS10.9110.95618.766-0.177-0.1770.0000.0000.0000.000
134A141LYS10.8830.95021.942-0.164-0.1640.0000.0000.0000.000
135A142TYR00.0260.00017.404-0.023-0.0230.0000.0000.0000.000
136A143ASP-1-0.855-0.90816.4700.6270.6270.0000.0000.0000.000
137A144ILE0-0.028-0.02513.0830.0990.0990.0000.0000.0000.000
138A145TYR0-0.038-0.05110.9240.1330.1330.0000.0000.0000.000
139A146ASN00.0500.04911.6650.2860.2860.0000.0000.0000.000
140A147ASN00.043-0.0279.0100.7610.7610.0000.0000.0000.000
141A148ARG10.8980.96411.043-0.466-0.4660.0000.0000.0000.000
142A149GLU-1-0.888-0.95712.5650.5200.5200.0000.0000.0000.000
143A150GLN0-0.097-0.0276.1070.0810.0810.0000.0000.0000.000
144A151LYS10.9550.9779.660-0.411-0.4110.0000.0000.0000.000
145A152TYR0-0.081-0.06910.613-0.145-0.1450.0000.0000.0000.000
146A153SER0-0.008-0.0095.1990.2100.2100.0000.0000.0000.000
147A154LYS10.9971.0166.4060.3510.3510.0000.0000.0000.000
148A155GLY00.0470.0068.8370.0730.0730.0000.0000.0000.000
149A156THR0-0.0270.00812.194-0.039-0.0390.0000.0000.0000.000
150A157VAL00.0270.00915.0520.0280.0280.0000.0000.0000.000
151A158THR00.0480.01618.481-0.014-0.0140.0000.0000.0000.000
152A159LEU0-0.061-0.02321.0420.0110.0110.0000.0000.0000.000
153A160ASP-1-0.804-0.90024.392-0.020-0.0200.0000.0000.0000.000
154A161LEU0-0.015-0.01626.7660.0070.0070.0000.0000.0000.000
155A162ASN00.021-0.00929.756-0.002-0.0020.0000.0000.0000.000
156A163SER0-0.079-0.03331.705-0.001-0.0010.0000.0000.0000.000
157A164GLY0-0.0070.00430.969-0.003-0.0030.0000.0000.0000.000
158A165LYS10.9040.94826.4690.0150.0150.0000.0000.0000.000
159A166ASP-1-0.818-0.89223.017-0.028-0.0280.0000.0000.0000.000
160A167ILE0-0.066-0.03521.735-0.007-0.0070.0000.0000.0000.000
161A168VAL0-0.012-0.01016.2430.0100.0100.0000.0000.0000.000
162A169PHE0-0.0030.00216.322-0.008-0.0080.0000.0000.0000.000
163A170ASP-1-0.852-0.9309.564-0.204-0.2040.0000.0000.0000.000
164A171LEU0-0.040-0.02012.3150.0200.0200.0000.0000.0000.000
165A172TYR0-0.058-0.0317.1400.1970.1970.0000.0000.0000.000
166A173TYR00.0390.0537.387-0.300-0.3000.0000.0000.0000.000
167A174PHE00.003-0.0345.1760.1080.214-0.001-0.010-0.0950.000
168A175GLY00.0180.0109.3940.0620.0620.0000.0000.0000.000
169A176ASN0-0.028-0.0289.686-0.066-0.0660.0000.0000.0000.000
170A177GLY00.0060.00310.4490.0250.0250.0000.0000.0000.000
171A178ASP-1-0.893-0.93011.1370.2130.2130.0000.0000.0000.000
172A179PHE00.020-0.02214.886-0.021-0.0210.0000.0000.0000.000
173A180ASN00.0340.01517.032-0.021-0.0210.0000.0000.0000.000
174A181SER0-0.0240.01013.909-0.030-0.0300.0000.0000.0000.000
175A182MET0-0.065-0.03111.172-0.012-0.0120.0000.0000.0000.000
176A183LEU00.0310.02115.078-0.004-0.0040.0000.0000.0000.000
177A184LYS10.9700.99818.294-0.003-0.0030.0000.0000.0000.000
178A185ILE0-0.022-0.01115.698-0.014-0.0140.0000.0000.0000.000
179A186TYR0-0.020-0.02319.0230.0010.0010.0000.0000.0000.000
180A187SER0-0.022-0.00422.3250.0000.0000.0000.0000.0000.000
181A188ASN00.0570.03622.9330.0080.0080.0000.0000.0000.000
182A189ASN0-0.026-0.02726.1490.0040.0040.0000.0000.0000.000
183A190GLU-1-0.921-0.95225.123-0.005-0.0050.0000.0000.0000.000
184A191ARG10.7460.85227.934-0.015-0.0150.0000.0000.0000.000
185A192ILE0-0.0120.00327.524-0.006-0.0060.0000.0000.0000.000
186A193ASP-1-0.892-0.95031.4430.0250.0250.0000.0000.0000.000
187A194SER00.004-0.05832.7540.0000.0000.0000.0000.0000.000
188A195THR0-0.058-0.02433.3780.0020.0020.0000.0000.0000.000
189A196GLN0-0.031-0.00634.266-0.001-0.0010.0000.0000.0000.000
190A197PHE0-0.060-0.02127.344-0.002-0.0020.0000.0000.0000.000
191A198HIS0-0.063-0.00127.0600.0090.0090.0000.0000.0000.000
192A199VAL0-0.017-0.02122.682-0.002-0.0020.0000.0000.0000.000
193A200ASP-1-0.800-0.88722.2690.0200.0200.0000.0000.0000.000
194A201VAL0-0.023-0.03117.6380.0020.0020.0000.0000.0000.000
195A202SER0-0.030-0.00416.2210.0040.0040.0000.0000.0000.000
196A203ILE00.0100.01713.6280.0100.0100.0000.0000.0000.000
197A204SER00.0300.0139.726-0.017-0.0170.0000.0000.0000.000