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: M9VRZ

Calculation Name: 4TRT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TRT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RYE8

Base Structure: X-ray

Registration Date: 2023-09-26

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 361
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5063663.694748
FMO2-HF: Nuclear repulsion 4929082.222417
FMO2-HF: Total energy -134581.472331
FMO2-MP2: Total energy -134977.524714


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:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-14.644-8.93911.923-7.422-10.205-0.047
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.000
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].
3A3LYS10.7930.8532.390-1.4251.5630.862-1.388-2.4620.004
4A4ALA00.0200.0065.0460.1960.230-0.001-0.005-0.0270.000
5A5ASN0-0.053-0.0148.8050.0760.0760.0000.0000.0000.000
6A6VAL00.003-0.00811.6770.0430.0430.0000.0000.0000.000
7A7THR00.008-0.00414.8840.0220.0220.0000.0000.0000.000
8A8LYS10.8210.92118.3700.2070.2070.0000.0000.0000.000
9A9LYS10.8950.93519.3480.2100.2100.0000.0000.0000.000
10A10THR00.0290.00320.1700.0170.0170.0000.0000.0000.000
11A11LEU00.0390.03015.190-0.001-0.0010.0000.0000.0000.000
12A12ASN00.017-0.00419.2700.0060.0060.0000.0000.0000.000
13A13GLU-1-0.905-0.92922.114-0.214-0.2140.0000.0000.0000.000
14A14GLY00.0460.01121.4110.0150.0150.0000.0000.0000.000
15A15LEU0-0.009-0.01317.2790.0120.0120.0000.0000.0000.000
16A16GLY00.0330.02721.4880.0200.0200.0000.0000.0000.000
17A17LEU0-0.088-0.05425.0850.0230.0230.0000.0000.0000.000
18A18LEU00.0260.01421.2370.0150.0150.0000.0000.0000.000
19A19GLU-1-0.802-0.90423.438-0.170-0.1700.0000.0000.0000.000
20A20ARG10.7640.87525.0010.1730.1730.0000.0000.0000.000
21A21VAL0-0.0130.02027.3010.0100.0100.0000.0000.0000.000
22A22ILE00.0070.01222.1340.0100.0100.0000.0000.0000.000
23A23PRO00.0190.00426.3830.0050.0050.0000.0000.0000.000
24A24SER00.0110.00426.467-0.002-0.0020.0000.0000.0000.000
25A25ARG10.9120.93927.3450.0680.0680.0000.0000.0000.000
26A26SER00.0390.01828.0270.0010.0010.0000.0000.0000.000
27A27SER0-0.0020.00829.1880.0010.0010.0000.0000.0000.000
28A28ASN00.0240.01426.1040.0020.0020.0000.0000.0000.000
29A29PRO00.012-0.01023.341-0.009-0.0090.0000.0000.0000.000
30A30LEU00.0500.02919.737-0.008-0.0080.0000.0000.0000.000
31A31LEU0-0.037-0.00922.687-0.016-0.0160.0000.0000.0000.000
32A32THR0-0.007-0.00223.722-0.006-0.0060.0000.0000.0000.000
33A33ALA0-0.041-0.01618.767-0.009-0.0090.0000.0000.0000.000
34A34LEU0-0.022-0.00316.6400.0060.0060.0000.0000.0000.000
35A35LYS10.8840.95016.6360.3100.3100.0000.0000.0000.000
36A36VAL0-0.055-0.03012.6530.0170.0170.0000.0000.0000.000
37A37GLU-1-0.808-0.89613.209-0.433-0.4330.0000.0000.0000.000
38A38THR0-0.032-0.03510.146-0.069-0.0690.0000.0000.0000.000
39A39SER0-0.018-0.01312.5850.0620.0620.0000.0000.0000.000
40A40GLU-1-0.911-0.96913.225-0.598-0.5980.0000.0000.0000.000
41A41GLY00.0260.02314.2140.0070.0070.0000.0000.0000.000
42A42GLY0-0.019-0.01515.1920.0690.0690.0000.0000.0000.000
43A43LEU00.0070.00712.021-0.064-0.0640.0000.0000.0000.000
44A44THR0-0.022-0.01815.1620.1010.1010.0000.0000.0000.000
45A45LEU00.0090.02016.181-0.018-0.0180.0000.0000.0000.000
46A46SER0-0.013-0.02518.5050.0370.0370.0000.0000.0000.000
47A47GLY00.0560.02720.488-0.009-0.0090.0000.0000.0000.000
48A48THR0-0.002-0.02423.1860.0100.0100.0000.0000.0000.000
49A49ASN0-0.024-0.02326.7720.0050.0050.0000.0000.0000.000
50A50LEU0-0.028-0.00829.6260.0110.0110.0000.0000.0000.000
51A51GLU-1-0.942-0.95431.750-0.078-0.0780.0000.0000.0000.000
52A52ILE0-0.009-0.00430.3180.0030.0030.0000.0000.0000.000
53A53ASP-1-0.810-0.86626.903-0.154-0.1540.0000.0000.0000.000
54A54LEU0-0.018-0.01825.5730.0040.0040.0000.0000.0000.000
55A55SER0-0.016-0.01521.648-0.017-0.0170.0000.0000.0000.000
56A56CYS0-0.017-0.00621.9040.0290.0290.0000.0000.0000.000
57A57PHE0-0.0270.00418.125-0.017-0.0170.0000.0000.0000.000
58A58VAL0-0.016-0.02517.6060.0410.0410.0000.0000.0000.000
59A59PRO0-0.025-0.00917.293-0.059-0.0590.0000.0000.0000.000
60A60ALA0-0.013-0.01013.4080.0250.0250.0000.0000.0000.000
61A61GLU-1-0.870-0.90912.162-0.639-0.6390.0000.0000.0000.000
62A62VAL00.001-0.0139.027-0.103-0.1030.0000.0000.0000.000
63A63GLN0-0.076-0.0273.4891.0131.6300.009-0.218-0.4080.000
64A64GLN0-0.010-0.0241.930-5.030-7.6638.717-3.235-2.849-0.026
65A65PRO00.0070.0135.754-0.388-0.3880.0000.0000.0000.000
66A66GLU-1-0.881-0.9394.963-1.393-1.264-0.001-0.002-0.1250.000
67A67ASN00.0070.0058.352-0.080-0.0800.0000.0000.0000.000
68A68PHE00.0390.0169.7490.0680.0680.0000.0000.0000.000
69A69VAL00.0320.01912.2020.0210.0210.0000.0000.0000.000
70A70VAL00.0350.01713.0990.0120.0120.0000.0000.0000.000
71A71PRO00.0260.00515.8770.0070.0070.0000.0000.0000.000
72A72ALA00.0150.02018.996-0.015-0.0150.0000.0000.0000.000
73A73HIS00.017-0.00320.353-0.016-0.0160.0000.0000.0000.000
74A74LEU0-0.0260.00418.2610.0050.0050.0000.0000.0000.000
75A75PHE00.0680.02313.379-0.003-0.0030.0000.0000.0000.000
76A76ALA00.0190.01717.555-0.014-0.0140.0000.0000.0000.000
77A77GLN0-0.056-0.03620.4550.0060.0060.0000.0000.0000.000
78A78ILE0-0.019-0.01215.8080.0100.0100.0000.0000.0000.000
79A79VAL00.0150.00015.9650.0010.0010.0000.0000.0000.000
80A80ARG10.8170.90318.5250.1790.1790.0000.0000.0000.000
81A81ASN0-0.051-0.02521.5300.0140.0140.0000.0000.0000.000
82A82LEU0-0.0140.01715.8200.0140.0140.0000.0000.0000.000
83A83GLY00.0130.00419.8800.0050.0050.0000.0000.0000.000
84A84GLY00.0030.00319.7470.0080.0080.0000.0000.0000.000
85A85GLU-1-0.828-0.93520.197-0.234-0.2340.0000.0000.0000.000
86A86LEU0-0.038-0.00315.897-0.016-0.0160.0000.0000.0000.000
87A87VAL0-0.0160.00112.8780.0490.0490.0000.0000.0000.000
88A88GLU-1-0.776-0.8466.547-0.842-0.8420.0000.0000.0000.000
89A89LEU0-0.043-0.0248.9610.1520.1520.0000.0000.0000.000
90A90GLU-1-0.756-0.8692.970-2.592-1.0940.270-0.694-1.074-0.006
91A91LEU0-0.0050.0103.3960.4240.8010.003-0.079-0.3010.000
92A92SER0-0.005-0.0052.481-3.792-1.1102.053-1.871-2.865-0.019
93A93GLY00.002-0.0023.686-0.014-0.0010.0110.070-0.0940.000
94A94GLN00.0150.0246.371-0.227-0.2270.0000.0000.0000.000
95A95GLU-1-0.885-0.9407.6160.0270.0270.0000.0000.0000.000
96A96LEU00.0210.0176.876-0.163-0.1630.0000.0000.0000.000
97A97SER0-0.006-0.0016.7800.3020.3020.0000.0000.0000.000
98A98VAL00.005-0.0028.667-0.188-0.1880.0000.0000.0000.000
99A99ARG10.7510.8525.8530.5570.5570.0000.0000.0000.000
100A100SER00.014-0.02012.272-0.029-0.0290.0000.0000.0000.000
101A101GLY0-0.0120.00315.4710.0370.0370.0000.0000.0000.000
102A102GLY0-0.027-0.01315.808-0.001-0.0010.0000.0000.0000.000
103A103SER0-0.039-0.01816.1450.0300.0300.0000.0000.0000.000
104A104ASP-1-0.775-0.88510.287-0.222-0.2220.0000.0000.0000.000
105A105PHE0-0.017-0.00213.1230.0560.0560.0000.0000.0000.000
106A106LYS10.8320.9068.5810.0550.0550.0000.0000.0000.000
107A107LEU0-0.042-0.02411.6870.0330.0330.0000.0000.0000.000
108A108GLN0-0.039-0.02011.604-0.035-0.0350.0000.0000.0000.000
109A109THR0-0.036-0.03510.090-0.037-0.0370.0000.0000.0000.000
110A110GLY0-0.033-0.02212.8560.0640.0640.0000.0000.0000.000
111A111ASP-1-0.891-0.96014.374-0.078-0.0780.0000.0000.0000.000
112A112ILE0-0.018-0.01912.581-0.016-0.0160.0000.0000.0000.000
113A113GLU-1-0.907-0.94415.382-0.150-0.1500.0000.0000.0000.000
114A114ALA0-0.055-0.02117.7820.0060.0060.0000.0000.0000.000
115A115TYR0-0.054-0.03318.9600.0010.0010.0000.0000.0000.000
116A116PRO0-0.0080.00220.744-0.003-0.0030.0000.0000.0000.000
117A117PRO00.0320.01421.872-0.024-0.0240.0000.0000.0000.000
118A118LEU0-0.051-0.02222.9080.0100.0100.0000.0000.0000.000
119A119SER0-0.015-0.00723.425-0.023-0.0230.0000.0000.0000.000
120A120PHE0-0.034-0.01123.8570.0100.0100.0000.0000.0000.000
121A121PRO0-0.0170.00427.650-0.011-0.0110.0000.0000.0000.000
122A122ALA00.036-0.00329.132-0.003-0.0030.0000.0000.0000.000
123A123GLN0-0.074-0.03631.265-0.001-0.0010.0000.0000.0000.000
124A124ALA00.0080.01834.8310.0020.0020.0000.0000.0000.000
125A125ASP-1-0.799-0.87836.774-0.102-0.1020.0000.0000.0000.000
126A126VAL0-0.026-0.01039.3430.0060.0060.0000.0000.0000.000
127A127SER0-0.070-0.05339.131-0.006-0.0060.0000.0000.0000.000
128A128LEU00.0420.00939.5080.0070.0070.0000.0000.0000.000
129A129ASP-1-0.737-0.86139.469-0.121-0.1210.0000.0000.0000.000
130A130GLY00.0440.00037.0130.0040.0040.0000.0000.0000.000
131A131GLY00.0020.00938.0940.0010.0010.0000.0000.0000.000
132A132GLU-1-0.848-0.92239.652-0.083-0.0830.0000.0000.0000.000
133A133LEU00.0060.01838.9400.0040.0040.0000.0000.0000.000
134A134SER0-0.0010.00538.0350.0050.0050.0000.0000.0000.000
135A135ARG10.8030.88040.3530.1000.1000.0000.0000.0000.000
136A136ALA00.0060.02543.4190.0050.0050.0000.0000.0000.000
137A137PHE00.037-0.00739.5080.0040.0040.0000.0000.0000.000
138A138SER0-0.032-0.03741.8030.0030.0030.0000.0000.0000.000
139A139SER0-0.076-0.03044.0490.0040.0040.0000.0000.0000.000
140A140VAL0-0.011-0.01046.8700.0040.0040.0000.0000.0000.000
141A141ARG10.8270.88842.1550.0780.0780.0000.0000.0000.000
142A142TYR0-0.009-0.02145.9990.0020.0020.0000.0000.0000.000
143A143ALA0-0.005-0.00248.4660.0030.0030.0000.0000.0000.000
144A144ALA0-0.0100.02246.7390.0020.0020.0000.0000.0000.000
145A145SER0-0.030-0.02348.086-0.001-0.0010.0000.0000.0000.000
146A146ASN0-0.045-0.05144.887-0.002-0.0020.0000.0000.0000.000
147A147GLU-1-0.845-0.92047.421-0.049-0.0490.0000.0000.0000.000
148A148ALA0-0.0210.01150.6340.0030.0030.0000.0000.0000.000
149A149PHE00.010-0.00751.904-0.001-0.0010.0000.0000.0000.000
150A150GLN00.0000.00453.553-0.001-0.0010.0000.0000.0000.000
151A151ALA00.0530.01448.400-0.001-0.0010.0000.0000.0000.000
152A152VAL00.0480.03048.425-0.002-0.0020.0000.0000.0000.000
153A153PHE00.0030.00049.083-0.002-0.0020.0000.0000.0000.000
154A154ARG10.8250.93346.1270.0510.0510.0000.0000.0000.000
155A155GLY00.0380.00444.920-0.004-0.0040.0000.0000.0000.000
156A156ILE0-0.056-0.01743.8100.0030.0030.0000.0000.0000.000
157A157LYS10.8520.94445.5500.0550.0550.0000.0000.0000.000
158A158LEU00.015-0.00543.200-0.001-0.0010.0000.0000.0000.000
159A159GLU-1-0.779-0.88347.031-0.057-0.0570.0000.0000.0000.000
160A160HIS00.0440.03044.408-0.001-0.0010.0000.0000.0000.000
161A161HIS10.7850.87949.6600.0650.0650.0000.0000.0000.000
162A162GLY00.0720.04851.2370.0020.0020.0000.0000.0000.000
163A163GLU-1-0.948-0.96950.267-0.065-0.0650.0000.0000.0000.000
164A164SER0-0.036-0.01749.823-0.002-0.0020.0000.0000.0000.000
165A165ALA00.0160.00847.2010.0000.0000.0000.0000.0000.000
166A166ARG10.7640.85849.2460.0580.0580.0000.0000.0000.000
167A167VAL0-0.0130.00445.044-0.001-0.0010.0000.0000.0000.000
168A168VAL00.008-0.00848.4020.0030.0030.0000.0000.0000.000
169A169ALA0-0.0200.00148.503-0.002-0.0020.0000.0000.0000.000
170A170SER0-0.017-0.04050.4580.0030.0030.0000.0000.0000.000
171A171ASP-1-0.768-0.88352.096-0.048-0.0480.0000.0000.0000.000
172A172GLY0-0.046-0.01954.2120.0020.0020.0000.0000.0000.000
173A173TYR0-0.082-0.03757.5380.0020.0020.0000.0000.0000.000
174A174ARG10.8110.90651.6050.0520.0520.0000.0000.0000.000
175A175VAL0-0.030-0.00954.968-0.001-0.0010.0000.0000.0000.000
176A176ALA00.0010.02151.3360.0010.0010.0000.0000.0000.000
177A177ILE00.020-0.00552.113-0.001-0.0010.0000.0000.0000.000
178A178ARG10.8460.90048.4060.0690.0690.0000.0000.0000.000
179A179ASP-1-0.791-0.85649.958-0.062-0.0620.0000.0000.0000.000
180A180PHE0-0.049-0.03544.0560.0000.0000.0000.0000.0000.000
181A181PRO00.0570.01946.7750.0010.0010.0000.0000.0000.000
182A182ALA0-0.042-0.01845.323-0.004-0.0040.0000.0000.0000.000
183A183SER0-0.0150.00043.9410.0050.0050.0000.0000.0000.000
184A184GLY00.0190.01445.423-0.002-0.0020.0000.0000.0000.000
185A185ASP-1-0.932-0.96746.855-0.066-0.0660.0000.0000.0000.000
186A186GLY00.0210.00945.704-0.005-0.0050.0000.0000.0000.000
187A187LYS10.8830.95942.0800.0870.0870.0000.0000.0000.000
188A188ASN00.018-0.00646.010-0.004-0.0040.0000.0000.0000.000
189A189LEU0-0.030-0.00941.671-0.001-0.0010.0000.0000.0000.000
190A190ILE00.0070.00544.8840.0020.0020.0000.0000.0000.000
191A191ILE00.0160.01939.727-0.002-0.0020.0000.0000.0000.000
192A192PRO00.0510.02539.6990.0040.0040.0000.0000.0000.000
193A193ALA00.026-0.00240.788-0.004-0.0040.0000.0000.0000.000
194A194ARG10.9570.96935.4150.0850.0850.0000.0000.0000.000
195A195SER00.0520.02536.409-0.003-0.0030.0000.0000.0000.000
196A196VAL00.0070.01336.957-0.006-0.0060.0000.0000.0000.000
197A197ASP-1-0.837-0.89638.132-0.088-0.0880.0000.0000.0000.000
198A198GLU-1-0.876-0.95232.491-0.131-0.1310.0000.0000.0000.000
199A199LEU00.023-0.00133.620-0.008-0.0080.0000.0000.0000.000
200A200ILE0-0.0240.00235.059-0.006-0.0060.0000.0000.0000.000
201A201ARG10.8840.95632.3650.1080.1080.0000.0000.0000.000
202A202VAL0-0.0010.00429.580-0.009-0.0090.0000.0000.0000.000
203A203LEU00.0040.01631.782-0.008-0.0080.0000.0000.0000.000
204A204LYS10.7920.88631.9200.1520.1520.0000.0000.0000.000
205A205ASP-1-0.813-0.90535.222-0.114-0.1140.0000.0000.0000.000
206A206GLY0-0.0050.01135.915-0.008-0.0080.0000.0000.0000.000
207A207GLU-1-0.840-0.87435.898-0.134-0.1340.0000.0000.0000.000
208A208ALA0-0.019-0.01934.763-0.011-0.0110.0000.0000.0000.000
209A209ARG10.8120.90631.0240.1760.1760.0000.0000.0000.000
210A210PHE0-0.008-0.02135.079-0.005-0.0050.0000.0000.0000.000
211A211THR00.004-0.02033.639-0.003-0.0030.0000.0000.0000.000
212A212TYR0-0.012-0.02436.2160.0020.0020.0000.0000.0000.000
213A213GLY00.0280.01336.878-0.005-0.0050.0000.0000.0000.000
214A214ASP-1-0.943-0.97237.750-0.069-0.0690.0000.0000.0000.000
215A215GLY00.0400.01838.513-0.003-0.0030.0000.0000.0000.000
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