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: YZ972

Calculation Name: 5T0O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T0O

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RTE4

Base Structure: X-ray

Registration Date: 2023-06-22

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 1033
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -29024896.68168
FMO2-HF: Nuclear repulsion 28630140.236287
FMO2-HF: Total energy -394756.445393
FMO2-MP2: Total energy -395914.384453


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.878-1.4293.071-1.446-4.0730.006
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.014
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].
3A3SER00.038-0.0123.578-2.607-1.1260.016-0.546-0.9500.002
4A4LYS10.9300.9792.783-3.061-2.3123.056-0.868-2.9380.004
5A5PHE0-0.019-0.0074.356-0.1150.104-0.001-0.032-0.1850.000
6A6PHE00.0690.0305.7090.1760.1760.0000.0000.0000.000
7A7ILE0-0.0200.0017.0480.0380.0380.0000.0000.0000.000
8A8GLU-1-0.918-0.9747.2600.1800.1800.0000.0000.0000.000
9A9ARG10.8310.9307.2290.4310.4310.0000.0000.0000.000
10A10PRO00.0900.03611.8270.0000.0000.0000.0000.0000.000
11A11VAL0-0.001-0.00314.6020.0040.0040.0000.0000.0000.000
12A12PHE0-0.004-0.00312.843-0.008-0.0080.0000.0000.0000.000
13A13ALA00.0490.01412.9200.0110.0110.0000.0000.0000.000
14A14SER0-0.001-0.00614.6680.0210.0210.0000.0000.0000.000
15A15VAL00.0240.02618.2460.0050.0050.0000.0000.0000.000
16A16VAL00.0260.03015.3680.0040.0040.0000.0000.0000.000
17A17ALA00.0550.03618.0710.0070.0070.0000.0000.0000.000
18A18ILE00.0040.00219.5820.0000.0000.0000.0000.0000.000
19A19ILE0-0.031-0.01721.712-0.002-0.0020.0000.0000.0000.000
20A20ILE0-0.010-0.00418.1500.0000.0000.0000.0000.0000.000
21A21SER0-0.004-0.01622.5020.0020.0020.0000.0000.0000.000
22A22LEU0-0.033-0.02824.943-0.003-0.0030.0000.0000.0000.000
23A23ALA0-0.010-0.00325.575-0.004-0.0040.0000.0000.0000.000
24A24GLY00.0290.00026.489-0.003-0.0030.0000.0000.0000.000
25A25ALA0-0.025-0.01527.977-0.002-0.0020.0000.0000.0000.000
26A26ILE0-0.001-0.00930.702-0.003-0.0030.0000.0000.0000.000
27A27GLY00.004-0.00231.006-0.003-0.0030.0000.0000.0000.000
28A28LEU0-0.042-0.02831.905-0.001-0.0010.0000.0000.0000.000
29A29THR0-0.060-0.01933.503-0.003-0.0030.0000.0000.0000.000
30A30ASN0-0.029-0.01435.842-0.002-0.0020.0000.0000.0000.000
31A31LEU0-0.0280.00832.4790.0000.0000.0000.0000.0000.000
32A32PRO00.0060.00636.896-0.002-0.0020.0000.0000.0000.000
33A33ILE00.0070.00239.3560.0030.0030.0000.0000.0000.000
34A34GLU-1-0.920-0.96740.8150.0450.0450.0000.0000.0000.000
35A35GLN0-0.021-0.01642.1320.0010.0010.0000.0000.0000.000
36A36TYR0-0.002-0.02141.5470.0030.0030.0000.0000.0000.000
37A37PRO00.0680.04738.814-0.002-0.0020.0000.0000.0000.000
38A38SER00.0250.00841.202-0.003-0.0030.0000.0000.0000.000
39A39LEU0-0.025-0.01241.2700.0010.0010.0000.0000.0000.000
40A40THR0-0.030-0.01244.8410.0000.0000.0000.0000.0000.000
41A41PRO0-0.013-0.00348.4490.0000.0000.0000.0000.0000.000
42A42PRO0-0.0150.01749.036-0.001-0.0010.0000.0000.0000.000
43A43THR00.0220.00651.8460.0000.0000.0000.0000.0000.000
44A44VAL0-0.026-0.01255.622-0.001-0.0010.0000.0000.0000.000
45A45LYS10.9200.97658.417-0.023-0.0230.0000.0000.0000.000
46A46VAL0-0.002-0.00861.964-0.001-0.0010.0000.0000.0000.000
47A47SER0-0.013-0.01064.9140.0000.0000.0000.0000.0000.000
48A48ALA00.0270.00568.246-0.001-0.0010.0000.0000.0000.000
49A49THR00.0140.00471.8340.0000.0000.0000.0000.0000.000
50A50TYR0-0.008-0.00875.356-0.001-0.0010.0000.0000.0000.000
51A51THR00.006-0.01478.6170.0000.0000.0000.0000.0000.000
52A52GLY00.0060.00580.8270.0000.0000.0000.0000.0000.000
53A53ALA0-0.054-0.00680.0840.0000.0000.0000.0000.0000.000
54A54ASP-1-0.782-0.87480.3040.0140.0140.0000.0000.0000.000
55A55ALA00.0400.01775.7890.0000.0000.0000.0000.0000.000
56A56GLN00.002-0.00776.3430.0000.0000.0000.0000.0000.000
57A57THR0-0.016-0.03077.5280.0000.0000.0000.0000.0000.000
58A58ILE0-0.0180.00674.0650.0000.0000.0000.0000.0000.000
59A59ALA00.0290.00972.9910.0000.0000.0000.0000.0000.000
60A60SER0-0.009-0.01272.9510.0000.0000.0000.0000.0000.000
61A61THR0-0.079-0.04175.1570.0000.0000.0000.0000.0000.000
62A62VAL0-0.034-0.02272.2980.0000.0000.0000.0000.0000.000
63A63ALA0-0.009-0.01069.7160.0000.0000.0000.0000.0000.000
64A64SER00.0170.01169.0110.0000.0000.0000.0000.0000.000
65A65PRO0-0.029-0.00469.1650.0000.0000.0000.0000.0000.000
66A66ILE0-0.001-0.00465.8510.0000.0000.0000.0000.0000.000
67A67GLU-1-0.841-0.94164.8760.0210.0210.0000.0000.0000.000
68A68ASP-1-0.859-0.94264.3590.0190.0190.0000.0000.0000.000
69A69ALA0-0.075-0.02365.1210.0000.0000.0000.0000.0000.000
70A70ILE0-0.033-0.03560.2960.0000.0000.0000.0000.0000.000
71A71ASN0-0.050-0.02960.2270.0010.0010.0000.0000.0000.000
72A72GLY00.0340.01958.165-0.001-0.0010.0000.0000.0000.000
73A73ALA0-0.067-0.03556.4600.0000.0000.0000.0000.0000.000
74A74ASP-1-0.864-0.92451.5450.0270.0270.0000.0000.0000.000
75A75ASN0-0.020-0.01348.5550.0010.0010.0000.0000.0000.000
76A76MET0-0.029-0.00251.0180.0010.0010.0000.0000.0000.000
77A77ILE0-0.031-0.01350.6430.0000.0000.0000.0000.0000.000
78A78TYR0-0.035-0.03253.7560.0000.0000.0000.0000.0000.000
79A79MET0-0.0130.00457.3640.0000.0000.0000.0000.0000.000
80A80ASP-1-0.881-0.92860.2930.0240.0240.0000.0000.0000.000
81A81SER00.0580.02162.968-0.001-0.0010.0000.0000.0000.000
82A82THR0-0.038-0.02666.4560.0000.0000.0000.0000.0000.000
83A83SER0-0.017-0.01669.1530.0000.0000.0000.0000.0000.000
84A84SER00.0310.02972.6300.0000.0000.0000.0000.0000.000
85A85SER00.0310.00075.086-0.001-0.0010.0000.0000.0000.000
86A86SER0-0.074-0.02776.008-0.001-0.0010.0000.0000.0000.000
87A87GLY00.0090.00477.9920.0000.0000.0000.0000.0000.000
88A88THR0-0.004-0.00972.7140.0000.0000.0000.0000.0000.000
89A89MET0-0.024-0.00268.2590.0000.0000.0000.0000.0000.000
90A90SER0-0.002-0.00165.7800.0000.0000.0000.0000.0000.000
91A91LEU00.0150.00763.6090.0000.0000.0000.0000.0000.000
92A92THR0-0.038-0.02459.1070.0000.0000.0000.0000.0000.000
93A93VAL00.0160.00457.0560.0000.0000.0000.0000.0000.000
94A94TYR0-0.017-0.00754.3380.0010.0010.0000.0000.0000.000
95A95PHE0-0.001-0.00551.240-0.001-0.0010.0000.0000.0000.000
96A96ASP-1-0.856-0.94247.4370.0420.0420.0000.0000.0000.000
97A97ILE0-0.084-0.04744.0380.0000.0000.0000.0000.0000.000
98A98GLY0-0.0180.00543.4980.0020.0020.0000.0000.0000.000
99A99THR00.006-0.00544.5210.0000.0000.0000.0000.0000.000
100A100ASP-1-0.893-0.94246.9990.0300.0300.0000.0000.0000.000
101A101PRO00.029-0.00248.019-0.001-0.0010.0000.0000.0000.000
102A102ASP-1-0.854-0.94451.1750.0230.0230.0000.0000.0000.000
103A103GLN00.0170.01550.302-0.002-0.0020.0000.0000.0000.000
104A104ALA00.0750.04252.512-0.001-0.0010.0000.0000.0000.000
105A105THR0-0.043-0.03454.305-0.001-0.0010.0000.0000.0000.000
106A106ILE0-0.051-0.02154.426-0.001-0.0010.0000.0000.0000.000
107A107ASP-1-0.891-0.93854.9410.0220.0220.0000.0000.0000.000
108A108VAL00.000-0.01557.286-0.001-0.0010.0000.0000.0000.000
109A109ASN0-0.050-0.05059.934-0.001-0.0010.0000.0000.0000.000
110A110ASN00.0240.02560.168-0.001-0.0010.0000.0000.0000.000
111A111ARG10.8720.95857.329-0.023-0.0230.0000.0000.0000.000
112A112ILE00.0270.01963.678-0.001-0.0010.0000.0000.0000.000
113A113SER00.0060.00066.068-0.001-0.0010.0000.0000.0000.000
114A114ALA00.0080.01766.869-0.001-0.0010.0000.0000.0000.000
115A115ALA0-0.011-0.02268.217-0.001-0.0010.0000.0000.0000.000
116A116THR00.0170.00569.9450.0000.0000.0000.0000.0000.000
117A117ALA0-0.039-0.02072.0720.0000.0000.0000.0000.0000.000
118A118LYS10.8380.91770.558-0.014-0.0140.0000.0000.0000.000
119A119MET0-0.0070.03072.0490.0000.0000.0000.0000.0000.000
120A120PRO00.0600.01875.811-0.001-0.0010.0000.0000.0000.000
121A121ASP-1-0.815-0.90578.7790.0110.0110.0000.0000.0000.000
122A122ALA0-0.105-0.05680.7520.0000.0000.0000.0000.0000.000
123A123VAL00.0320.01374.5270.0000.0000.0000.0000.0000.000
124A124LYS10.9020.93775.690-0.012-0.0120.0000.0000.0000.000
125A125LYS10.8760.96576.772-0.011-0.0110.0000.0000.0000.000
126A126LEU0-0.035-0.00776.2010.0000.0000.0000.0000.0000.000
127A127GLY0-0.0180.00773.5990.0000.0000.0000.0000.0000.000
128A128VAL0-0.013-0.01168.7650.0000.0000.0000.0000.0000.000
129A129THR0-0.058-0.02667.5370.0000.0000.0000.0000.0000.000
130A130VAL00.0490.03361.5330.0000.0000.0000.0000.0000.000
131A131ARG10.8970.95360.546-0.022-0.0220.0000.0000.0000.000
132A132LYS10.9911.02053.920-0.024-0.0240.0000.0000.0000.000
133A133THR0-0.099-0.07157.377-0.001-0.0010.0000.0000.0000.000
134A134SER00.1140.06453.7230.0010.0010.0000.0000.0000.000
135A135SER00.0110.00556.268-0.001-0.0010.0000.0000.0000.000
136A136THR00.002-0.00352.6340.0010.0010.0000.0000.0000.000
137A137THR0-0.028-0.02555.9480.0000.0000.0000.0000.0000.000
138A138LEU00.0340.04255.0750.0010.0010.0000.0000.0000.000
139A139ALA00.0410.02356.7470.0010.0010.0000.0000.0000.000
140A140ALA00.0070.00559.687-0.001-0.0010.0000.0000.0000.000
141A141ILE0-0.017-0.00763.4250.0000.0000.0000.0000.0000.000
142A142SER00.0160.00065.6800.0000.0000.0000.0000.0000.000
143A143MET0-0.031-0.00469.0060.0000.0000.0000.0000.0000.000
144A144TYR00.0620.02170.7650.0000.0000.0000.0000.0000.000
145A145SER00.0330.02875.0790.0000.0000.0000.0000.0000.000
146A146SER0-0.073-0.04176.0200.0000.0000.0000.0000.0000.000
147A147ASP-1-0.779-0.90377.8480.0140.0140.0000.0000.0000.000
148A148GLY00.0110.00881.1090.0000.0000.0000.0000.0000.000
149A149SER0-0.047-0.01782.5630.0000.0000.0000.0000.0000.000
150A150MET0-0.037-0.02379.5570.0000.0000.0000.0000.0000.000
151A151SER00.0500.01581.4760.0000.0000.0000.0000.0000.000
152A152ALA00.0430.02179.6630.0000.0000.0000.0000.0000.000
153A153VAL0-0.064-0.03279.4450.0000.0000.0000.0000.0000.000
154A154ASP-1-0.828-0.92181.2640.0130.0130.0000.0000.0000.000
155A155VAL0-0.015-0.01175.6910.0000.0000.0000.0000.0000.000
156A156TYR00.0200.02775.5780.0000.0000.0000.0000.0000.000
157A157ASN00.033-0.00776.7340.0000.0000.0000.0000.0000.000
158A158TYR0-0.0050.00073.8110.0000.0000.0000.0000.0000.000
159A159ILE00.016-0.01871.2120.0000.0000.0000.0000.0000.000
160A160THR0-0.047-0.00472.7870.0000.0000.0000.0000.0000.000
161A161LEU0-0.072-0.02174.0140.0000.0000.0000.0000.0000.000
162A162ASN00.0120.00673.4880.0000.0000.0000.0000.0000.000
163A163VAL00.0130.01768.8100.0000.0000.0000.0000.0000.000
164A164LEU0-0.004-0.02068.5350.0010.0010.0000.0000.0000.000
165A165ASP-1-0.875-0.94267.8300.0150.0150.0000.0000.0000.000
166A166GLU-1-0.929-0.97566.4190.0160.0160.0000.0000.0000.000
167A167LEU0-0.058-0.03863.7360.0010.0010.0000.0000.0000.000
168A168LYS10.8090.88162.837-0.019-0.0190.0000.0000.0000.000
169A169ARG10.8580.95162.946-0.015-0.0150.0000.0000.0000.000
170A170VAL00.0030.01158.2200.0000.0000.0000.0000.0000.000
171A171PRO00.0470.01455.0880.0000.0000.0000.0000.0000.000
172A172GLY00.0330.01054.5870.0010.0010.0000.0000.0000.000
173A173VAL0-0.0140.00655.2930.0010.0010.0000.0000.0000.000
174A174GLY00.0220.02258.487-0.001-0.0010.0000.0000.0000.000
175A175ASP-1-0.941-0.96259.8310.0200.0200.0000.0000.0000.000
176A176ALA00.039-0.00662.3070.0010.0010.0000.0000.0000.000
177A177ASN0-0.053-0.00764.921-0.001-0.0010.0000.0000.0000.000
178A178ALA00.0560.02968.1220.0010.0010.0000.0000.0000.000
179A179ILE0-0.010-0.00668.3650.0000.0000.0000.0000.0000.000
180A180GLY00.0700.03571.9340.0000.0000.0000.0000.0000.000
181A181ASN0-0.056-0.01974.6440.0000.0000.0000.0000.0000.000
182A182ARG10.9940.99872.079-0.015-0.0150.0000.0000.0000.000
183A183ASN0-0.046-0.03174.244-0.001-0.0010.0000.0000.0000.000
184A184TYR00.0530.02075.8590.0000.0000.0000.0000.0000.000
185A185SER0-0.016-0.00379.5270.0000.0000.0000.0000.0000.000
186A186LEU00.0220.02182.6950.0000.0000.0000.0000.0000.000
187A187ARG10.8320.92983.470-0.012-0.0120.0000.0000.0000.000
188A188ILE00.0280.02088.0580.0000.0000.0000.0000.0000.000
189A189TRP0-0.023-0.02587.4320.0000.0000.0000.0000.0000.000
190A190LEU00.0240.00093.1230.0000.0000.0000.0000.0000.000
191A191LYS10.9540.99896.160-0.009-0.0090.0000.0000.0000.000
192A192PRO00.022-0.00598.1260.0000.0000.0000.0000.0000.000
193A193ASP-1-0.873-0.927100.9100.0090.0090.0000.0000.0000.000
194A194LEU0-0.010-0.024102.5200.0000.0000.0000.0000.0000.000
195A195LEU00.0100.02498.9300.0000.0000.0000.0000.0000.000
196A196ASN00.009-0.003103.4720.0000.0000.0000.0000.0000.000
197A197LYS10.8690.964106.332-0.007-0.0070.0000.0000.0000.000
198A198PHE0-0.038-0.021106.0060.0000.0000.0000.0000.0000.000
199A199GLY00.0330.023107.5890.0000.0000.0000.0000.0000.000
200A200ILE0-0.054-0.020101.7030.0000.0000.0000.0000.0000.000
201A201THR0-0.032-0.012100.9560.0000.0000.0000.0000.0000.000
202A202ALA00.0720.01896.1250.0000.0000.0000.0000.0000.000
203A203THR0-0.003-0.00696.8090.0000.0000.0000.0000.0000.000
204A204ASP-1-0.742-0.86397.8690.0080.0080.0000.0000.0000.000
205A205VAL0-0.024-0.00995.2880.0000.0000.0000.0000.0000.000
206A206ILE0-0.057-0.03392.6700.0000.0000.0000.0000.0000.000
207A207SER0-0.027-0.02494.2890.0000.0000.0000.0000.0000.000
208A208ALA00.0050.02096.5180.0000.0000.0000.0000.0000.000
209A209VAL0-0.004-0.02791.2680.0000.0000.0000.0000.0000.000
210A210ASN0-0.090-0.04490.5360.0000.0000.0000.0000.0000.000
211A211ASP-1-0.915-0.95592.1070.0080.0080.0000.0000.0000.000
212A212GLN0-0.022-0.01494.7110.0000.0000.0000.0000.0000.000
213A213ASN0-0.051-0.00787.8090.0000.0000.0000.0000.0000.000
214A214ALA00.0460.03290.2190.0000.0000.0000.0000.0000.000
215A215GLN0-0.003-0.01585.0620.0000.0000.0000.0000.0000.000
216A216TYR00.0160.00784.8450.0000.0000.0000.0000.0000.000
217A217ALA0-0.0040.01489.0380.0000.0000.0000.0000.0000.000
218A218THR0-0.015-0.02287.2830.0000.0000.0000.0000.0000.000
219A219GLY00.0240.01990.0270.0000.0000.0000.0000.0000.000
220A220LYS10.8690.93986.483-0.005-0.0050.0000.0000.0000.000
221A221ILE0-0.0310.00692.4420.0000.0000.0000.0000.0000.000
222A222GLY00.0240.00094.6060.0000.0000.0000.0000.0000.000
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