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: V5VZ1

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 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 1033
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -29025455.999471
FMO2-HF: Nuclear repulsion 28630693.274313
FMO2-HF: Total energy -394762.725159
FMO2-MP2: Total energy -395920.40145


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.
-4.612-4.0066.13-1.897-4.840.008
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 : 0.051 / q_NPA : 0.013
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].
3A3SER00.0430.0033.411-2.028-0.4750.015-0.565-1.0030.002
4A4LYS10.9100.9512.922-3.745-4.9326.116-1.292-3.6370.006
5A5PHE0-0.025-0.0084.3870.0510.291-0.001-0.040-0.2000.000
6A6PHE00.0860.0235.7190.1000.1000.0000.0000.0000.000
7A7ILE0-0.0110.0196.6170.0190.0190.0000.0000.0000.000
8A8GLU-1-0.839-0.9007.4441.3511.3510.0000.0000.0000.000
9A9ARG10.8360.9387.174-0.413-0.4130.0000.0000.0000.000
10A10PRO00.1060.04511.915-0.047-0.0470.0000.0000.0000.000
11A11VAL0-0.0050.00014.728-0.025-0.0250.0000.0000.0000.000
12A12PHE0-0.010-0.00312.138-0.022-0.0220.0000.0000.0000.000
13A13ALA00.0490.01812.912-0.012-0.0120.0000.0000.0000.000
14A14SER0-0.015-0.01914.662-0.008-0.0080.0000.0000.0000.000
15A15VAL00.0180.02118.213-0.011-0.0110.0000.0000.0000.000
16A16VAL00.0240.03215.398-0.009-0.0090.0000.0000.0000.000
17A17ALA00.0530.03617.873-0.006-0.0060.0000.0000.0000.000
18A18ILE00.0040.00819.428-0.010-0.0100.0000.0000.0000.000
19A19ILE0-0.022-0.01321.097-0.009-0.0090.0000.0000.0000.000
20A20ILE0-0.004-0.00317.936-0.006-0.0060.0000.0000.0000.000
21A21SER0-0.008-0.02322.331-0.005-0.0050.0000.0000.0000.000
22A22LEU0-0.045-0.03224.783-0.006-0.0060.0000.0000.0000.000
23A23ALA0-0.003-0.00225.391-0.007-0.0070.0000.0000.0000.000
24A24GLY00.025-0.00126.319-0.005-0.0050.0000.0000.0000.000
25A25ALA0-0.033-0.01427.807-0.005-0.0050.0000.0000.0000.000
26A26ILE00.002-0.00830.538-0.005-0.0050.0000.0000.0000.000
27A27GLY00.0030.00030.832-0.004-0.0040.0000.0000.0000.000
28A28LEU0-0.039-0.02831.732-0.003-0.0030.0000.0000.0000.000
29A29THR0-0.066-0.02233.336-0.003-0.0030.0000.0000.0000.000
30A30ASN0-0.034-0.01435.648-0.003-0.0030.0000.0000.0000.000
31A31LEU0-0.0100.01032.250-0.001-0.0010.0000.0000.0000.000
32A32PRO0-0.0200.00436.724-0.001-0.0010.0000.0000.0000.000
33A33ILE00.0170.00239.2470.0020.0020.0000.0000.0000.000
34A34GLU-1-0.881-0.92040.6380.0440.0440.0000.0000.0000.000
35A35GLN0-0.012-0.01141.9780.0010.0010.0000.0000.0000.000
36A36TYR00.011-0.01141.4100.0020.0020.0000.0000.0000.000
37A37PRO00.0670.04238.619-0.001-0.0010.0000.0000.0000.000
38A38SER00.0170.00341.047-0.003-0.0030.0000.0000.0000.000
39A39LEU0-0.029-0.01440.9320.0000.0000.0000.0000.0000.000
40A40THR0-0.031-0.00744.693-0.001-0.0010.0000.0000.0000.000
41A41PRO00.0030.00148.2960.0000.0000.0000.0000.0000.000
42A42PRO0-0.0150.01448.829-0.001-0.0010.0000.0000.0000.000
43A43THR00.000-0.01751.688-0.001-0.0010.0000.0000.0000.000
44A44VAL0-0.021-0.01355.4640.0000.0000.0000.0000.0000.000
45A45LYS10.8470.92558.255-0.020-0.0200.0000.0000.0000.000
46A46VAL00.0120.00461.8040.0000.0000.0000.0000.0000.000
47A47SER0-0.050-0.02364.7520.0000.0000.0000.0000.0000.000
48A48ALA00.0430.00768.0840.0000.0000.0000.0000.0000.000
49A49THR00.0290.01271.6720.0000.0000.0000.0000.0000.000
50A50TYR0-0.023-0.01175.1950.0000.0000.0000.0000.0000.000
51A51THR00.009-0.01278.4580.0000.0000.0000.0000.0000.000
52A52GLY00.0060.00680.6670.0000.0000.0000.0000.0000.000
53A53ALA0-0.058-0.01079.9940.0000.0000.0000.0000.0000.000
54A54ASP-1-0.776-0.88780.1520.0120.0120.0000.0000.0000.000
55A55ALA00.0440.02675.7300.0000.0000.0000.0000.0000.000
56A56GLN00.0240.00176.1960.0000.0000.0000.0000.0000.000
57A57THR0-0.023-0.02577.3830.0000.0000.0000.0000.0000.000
58A58ILE0-0.0230.00273.9450.0000.0000.0000.0000.0000.000
59A59ALA00.0280.01272.8360.0000.0000.0000.0000.0000.000
60A60SER0-0.034-0.02272.8040.0000.0000.0000.0000.0000.000
61A61THR0-0.076-0.04475.0090.0000.0000.0000.0000.0000.000
62A62VAL0-0.047-0.02972.3120.0000.0000.0000.0000.0000.000
63A63ALA00.011-0.00469.5440.0000.0000.0000.0000.0000.000
64A64SER00.0130.00868.8590.0000.0000.0000.0000.0000.000
65A65PRO0-0.025-0.00769.0150.0000.0000.0000.0000.0000.000
66A66ILE00.0150.00265.7430.0000.0000.0000.0000.0000.000
67A67GLU-1-0.788-0.87964.7240.0160.0160.0000.0000.0000.000
68A68ASP-1-0.862-0.94364.2090.0140.0140.0000.0000.0000.000
69A69ALA0-0.075-0.02264.9720.0000.0000.0000.0000.0000.000
70A70ILE0-0.024-0.02360.1050.0000.0000.0000.0000.0000.000
71A71ASN0-0.061-0.03960.0740.0010.0010.0000.0000.0000.000
72A72GLY00.0450.02458.019-0.001-0.0010.0000.0000.0000.000
73A73ALA0-0.034-0.02056.3210.0000.0000.0000.0000.0000.000
74A74ASP-1-0.878-0.93551.4650.0210.0210.0000.0000.0000.000
75A75ASN0-0.014-0.01548.4330.0010.0010.0000.0000.0000.000
76A76MET0-0.0230.00750.8660.0010.0010.0000.0000.0000.000
77A77ILE0-0.025-0.00950.4290.0000.0000.0000.0000.0000.000
78A78TYR0-0.023-0.02453.6140.0000.0000.0000.0000.0000.000
79A79MET0-0.0210.00157.2220.0000.0000.0000.0000.0000.000
80A80ASP-1-0.818-0.89460.1470.0190.0190.0000.0000.0000.000
81A81SER0-0.019-0.00762.8230.0000.0000.0000.0000.0000.000
82A82THR00.003-0.00866.3090.0000.0000.0000.0000.0000.000
83A83SER00.002-0.00369.0060.0000.0000.0000.0000.0000.000
84A84SER00.0210.00072.4820.0000.0000.0000.0000.0000.000
85A85SER00.009-0.01474.9360.0000.0000.0000.0000.0000.000
86A86SER0-0.067-0.02075.7140.0000.0000.0000.0000.0000.000
87A87GLY00.0120.00277.8360.0000.0000.0000.0000.0000.000
88A88THR0-0.021-0.01472.4470.0000.0000.0000.0000.0000.000
89A89MET0-0.0170.00767.8850.0000.0000.0000.0000.0000.000
90A90SER0-0.004-0.00466.0860.0000.0000.0000.0000.0000.000
91A91LEU00.0410.01463.3950.0000.0000.0000.0000.0000.000
92A92THR0-0.048-0.03659.0440.0000.0000.0000.0000.0000.000
93A93VAL00.0220.01257.0230.0000.0000.0000.0000.0000.000
94A94TYR0-0.021-0.01154.2190.0010.0010.0000.0000.0000.000
95A95PHE0-0.005-0.00351.119-0.001-0.0010.0000.0000.0000.000
96A96ASP-1-0.860-0.93247.1930.0320.0320.0000.0000.0000.000
97A97ILE0-0.079-0.04443.8420.0000.0000.0000.0000.0000.000
98A98GLY0-0.0260.00243.3420.0010.0010.0000.0000.0000.000
99A99THR00.000-0.01744.3630.0000.0000.0000.0000.0000.000
100A100ASP-1-0.882-0.93246.8380.0280.0280.0000.0000.0000.000
101A101PRO00.0450.00547.894-0.001-0.0010.0000.0000.0000.000
102A102ASP-1-0.838-0.93450.9920.0240.0240.0000.0000.0000.000
103A103GLN00.0120.01150.150-0.002-0.0020.0000.0000.0000.000
104A104ALA00.0540.02652.342-0.001-0.0010.0000.0000.0000.000
105A105THR0-0.037-0.03154.140-0.001-0.0010.0000.0000.0000.000
106A106ILE0-0.040-0.02054.678-0.001-0.0010.0000.0000.0000.000
107A107ASP-1-0.840-0.88655.0460.0180.0180.0000.0000.0000.000
108A108VAL00.005-0.01357.120-0.001-0.0010.0000.0000.0000.000
109A109ASN0-0.035-0.03859.770-0.001-0.0010.0000.0000.0000.000
110A110ASN00.0070.01059.070-0.001-0.0010.0000.0000.0000.000
111A111ARG10.8010.89556.496-0.019-0.0190.0000.0000.0000.000
112A112ILE00.0310.02263.516-0.001-0.0010.0000.0000.0000.000
113A113SER00.0080.00965.904-0.001-0.0010.0000.0000.0000.000
114A114ALA0-0.0100.00866.695-0.001-0.0010.0000.0000.0000.000
115A115ALA00.0290.00968.050-0.001-0.0010.0000.0000.0000.000
116A116THR00.010-0.01669.6840.0000.0000.0000.0000.0000.000
117A117ALA0-0.033-0.02071.9080.0000.0000.0000.0000.0000.000
118A118LYS10.8360.91071.117-0.012-0.0120.0000.0000.0000.000
119A119MET0-0.0200.03372.2530.0000.0000.0000.0000.0000.000
120A120PRO00.0560.01275.6520.0000.0000.0000.0000.0000.000
121A121ASP-1-0.818-0.90278.6170.0100.0100.0000.0000.0000.000
122A122ALA0-0.091-0.04780.5870.0000.0000.0000.0000.0000.000
123A123VAL00.0190.00474.3310.0000.0000.0000.0000.0000.000
124A124LYS10.8720.93175.523-0.010-0.0100.0000.0000.0000.000
125A125LYS10.8900.96176.605-0.010-0.0100.0000.0000.0000.000
126A126LEU0-0.035-0.01275.9770.0000.0000.0000.0000.0000.000
127A127GLY0-0.0100.01373.4290.0000.0000.0000.0000.0000.000
128A128VAL0-0.020-0.01368.6300.0000.0000.0000.0000.0000.000
129A129THR0-0.033-0.00767.1950.0000.0000.0000.0000.0000.000
130A130VAL00.0360.01761.3550.0000.0000.0000.0000.0000.000
131A131ARG10.8750.94560.711-0.021-0.0210.0000.0000.0000.000
132A132LYS10.9380.99853.273-0.026-0.0260.0000.0000.0000.000
133A133THR0-0.043-0.03657.2420.0000.0000.0000.0000.0000.000
134A134SER00.0720.05853.7190.0000.0000.0000.0000.0000.000
135A135SER00.0080.00856.109-0.001-0.0010.0000.0000.0000.000
136A136THR00.0110.00152.4430.0010.0010.0000.0000.0000.000
137A137THR0-0.027-0.02155.7950.0000.0000.0000.0000.0000.000
138A138LEU00.0220.03254.8380.0010.0010.0000.0000.0000.000
139A139ALA00.0340.01656.5950.0010.0010.0000.0000.0000.000
140A140ALA00.0080.00259.536-0.001-0.0010.0000.0000.0000.000
141A141ILE0-0.0070.00163.2760.0000.0000.0000.0000.0000.000
142A142SER00.0230.00065.529-0.001-0.0010.0000.0000.0000.000
143A143MET0-0.0330.00068.8590.0000.0000.0000.0000.0000.000
144A144TYR00.0460.01070.3750.0000.0000.0000.0000.0000.000
145A145SER00.0240.02774.9330.0000.0000.0000.0000.0000.000
146A146SER0-0.065-0.05775.7710.0000.0000.0000.0000.0000.000
147A147ASP-1-0.791-0.87577.7070.0150.0150.0000.0000.0000.000
148A148GLY00.0060.00680.9610.0000.0000.0000.0000.0000.000
149A149SER0-0.043-0.03082.4710.0000.0000.0000.0000.0000.000
150A150MET0-0.043-0.03378.9780.0000.0000.0000.0000.0000.000
151A151SER00.030-0.03381.3240.0000.0000.0000.0000.0000.000
152A152ALA00.0220.00379.5150.0000.0000.0000.0000.0000.000
153A153VAL0-0.042-0.01979.2930.0000.0000.0000.0000.0000.000
154A154ASP-1-0.824-0.87181.1070.0130.0130.0000.0000.0000.000
155A155VAL0-0.007-0.00275.5200.0000.0000.0000.0000.0000.000
156A156TYR00.0090.01674.9580.0000.0000.0000.0000.0000.000
157A157ASN00.040-0.00276.5730.0000.0000.0000.0000.0000.000
158A158TYR00.0070.00373.5810.0000.0000.0000.0000.0000.000
159A159ILE00.023-0.01071.0130.0000.0000.0000.0000.0000.000
160A160THR0-0.042-0.00572.6230.0000.0000.0000.0000.0000.000
161A161LEU0-0.050-0.00573.8470.0000.0000.0000.0000.0000.000
162A162ASN0-0.003-0.01073.3150.0000.0000.0000.0000.0000.000
163A163VAL00.0100.01668.6380.0000.0000.0000.0000.0000.000
164A164LEU0-0.008-0.01968.3700.0010.0010.0000.0000.0000.000
165A165ASP-1-0.800-0.89067.6630.0170.0170.0000.0000.0000.000
166A166GLU-1-0.823-0.89965.9450.0190.0190.0000.0000.0000.000
167A167LEU0-0.037-0.02663.5400.0010.0010.0000.0000.0000.000
168A168LYS10.8550.92062.670-0.020-0.0200.0000.0000.0000.000
169A169ARG10.8050.89862.775-0.018-0.0180.0000.0000.0000.000
170A170VAL00.0120.01658.0970.0000.0000.0000.0000.0000.000
171A171PRO00.0500.01654.9150.0000.0000.0000.0000.0000.000
172A172GLY00.0250.00954.4150.0010.0010.0000.0000.0000.000
173A173VAL0-0.0010.00455.1240.0000.0000.0000.0000.0000.000
174A174GLY00.0080.02158.321-0.001-0.0010.0000.0000.0000.000
175A175ASP-1-0.940-0.97759.6640.0190.0190.0000.0000.0000.000
176A176ALA00.013-0.01362.1430.0010.0010.0000.0000.0000.000
177A177ASN0-0.030-0.00564.758-0.001-0.0010.0000.0000.0000.000
178A178ALA00.0480.02967.9640.0000.0000.0000.0000.0000.000
179A179ILE0-0.002-0.00168.1410.0000.0000.0000.0000.0000.000
180A180GLY00.0590.02771.7800.0000.0000.0000.0000.0000.000
181A181ASN0-0.077-0.03274.4860.0000.0000.0000.0000.0000.000
182A182ARG11.0011.00272.003-0.014-0.0140.0000.0000.0000.000
183A183ASN0-0.025-0.02174.050-0.001-0.0010.0000.0000.0000.000
184A184TYR00.0480.02475.6930.0000.0000.0000.0000.0000.000
185A185SER0-0.029-0.00779.3610.0000.0000.0000.0000.0000.000
186A186LEU00.0300.02382.5280.0000.0000.0000.0000.0000.000
187A187ARG10.8590.95283.890-0.012-0.0120.0000.0000.0000.000
188A188ILE00.0180.01187.8930.0000.0000.0000.0000.0000.000
189A189TRP0-0.003-0.03787.6490.0000.0000.0000.0000.0000.000
190A190LEU00.008-0.00892.9610.0000.0000.0000.0000.0000.000
191A191LYS10.8960.97895.998-0.009-0.0090.0000.0000.0000.000
192A192PRO00.018-0.00697.9540.0000.0000.0000.0000.0000.000
193A193ASP-1-0.861-0.922100.7510.0080.0080.0000.0000.0000.000
194A194LEU0-0.006-0.022102.2510.0000.0000.0000.0000.0000.000
195A195LEU00.0100.01798.7410.0000.0000.0000.0000.0000.000
196A196ASN0-0.010-0.022103.3100.0000.0000.0000.0000.0000.000
197A197LYS10.8610.962106.171-0.007-0.0070.0000.0000.0000.000
198A198PHE0-0.025-0.018105.7710.0000.0000.0000.0000.0000.000
199A199GLY00.0370.030107.4240.0000.0000.0000.0000.0000.000
200A200ILE0-0.054-0.021101.4850.0000.0000.0000.0000.0000.000
201A201THR00.004-0.007100.7300.0000.0000.0000.0000.0000.000
202A202ALA00.0780.02495.9850.0000.0000.0000.0000.0000.000
203A203THR0-0.011-0.00896.4210.0000.0000.0000.0000.0000.000
204A204ASP-1-0.741-0.84797.7000.0080.0080.0000.0000.0000.000
205A205VAL0-0.0050.00395.0960.0000.0000.0000.0000.0000.000
206A206ILE0-0.046-0.03092.3770.0000.0000.0000.0000.0000.000
207A207SER0-0.023-0.02294.1180.0000.0000.0000.0000.0000.000
208A208ALA0-0.0090.01396.3450.0000.0000.0000.0000.0000.000
209A209VAL0-0.004-0.02691.0670.0000.0000.0000.0000.0000.000
210A210ASN0-0.075-0.04190.7040.0000.0000.0000.0000.0000.000
211A211ASP-1-0.931-0.96291.9320.0080.0080.0000.0000.0000.000
212A212GLN0-0.006-0.00794.5350.0000.0000.0000.0000.0000.000
213A213ASN0-0.066-0.03087.5100.0000.0000.0000.0000.0000.000
214A214ALA00.0400.03090.0420.0000.0000.0000.0000.0000.000
215A215GLN0-0.013-0.02184.7650.0000.0000.0000.0000.0000.000
216A216TYR00.014-0.00184.5520.0000.0000.0000.0000.0000.000
217A217ALA00.0080.01888.8560.0000.0000.0000.0000.0000.000
218A218THR0-0.030-0.03186.9050.0000.0000.0000.0000.0000.000
219A219GLY00.0400.02789.8430.0000.0000.0000.0000.0000.000
220A220LYS10.8090.88486.984-0.008-0.0080.0000.0000.0000.000
221A221ILE0-0.0270.00992.2600.0000.0000.0000.0000.0000.000
222A222GLY00.018-0.00194.4840.0000.0000.0000.0000.0000.000
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