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: 9M4L2

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 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 361
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5057656.814387
FMO2-HF: Nuclear repulsion 4923075.702078
FMO2-HF: Total energy -134581.112309
FMO2-MP2: Total energy -134977.026636


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.
-14.271-8.39812.452-7.997-10.325-0.055
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 : -0.017 / q_NPA : -0.008
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].
3A3LYS10.8180.8762.452-1.2932.0600.477-1.532-2.2970.004
4A4ALA00.0060.0004.8820.2480.284-0.001-0.007-0.0290.000
5A5ASN0-0.0180.0088.6660.1360.1360.0000.0000.0000.000
6A6VAL00.0260.00811.4860.0400.0400.0000.0000.0000.000
7A7THR00.0010.00114.6350.0230.0230.0000.0000.0000.000
8A8LYS10.8620.93118.1050.2180.2180.0000.0000.0000.000
9A9LYS10.8900.92919.1210.2210.2210.0000.0000.0000.000
10A10THR00.0300.00319.8740.0200.0200.0000.0000.0000.000
11A11LEU00.0390.02615.0910.0080.0080.0000.0000.0000.000
12A12ASN00.022-0.00419.1060.0090.0090.0000.0000.0000.000
13A13GLU-1-0.913-0.92822.017-0.213-0.2130.0000.0000.0000.000
14A14GLY00.0450.01621.7580.0160.0160.0000.0000.0000.000
15A15LEU0-0.006-0.01217.6040.0150.0150.0000.0000.0000.000
16A16GLY00.0470.03421.7880.0190.0190.0000.0000.0000.000
17A17LEU0-0.104-0.05925.3300.0240.0240.0000.0000.0000.000
18A18LEU00.0110.00321.0750.0140.0140.0000.0000.0000.000
19A19GLU-1-0.828-0.90423.787-0.178-0.1780.0000.0000.0000.000
20A20ARG10.8330.92025.2170.1770.1770.0000.0000.0000.000
21A21VAL00.0190.03727.1540.0100.0100.0000.0000.0000.000
22A22ILE0-0.023-0.00421.9730.0110.0110.0000.0000.0000.000
23A23PRO00.0160.00526.2570.0060.0060.0000.0000.0000.000
24A24SER00.0140.00926.243-0.004-0.0040.0000.0000.0000.000
25A25ARG10.9230.94227.1230.0760.0760.0000.0000.0000.000
26A26SER00.0310.01227.8120.0030.0030.0000.0000.0000.000
27A27SER0-0.0130.00528.680-0.001-0.0010.0000.0000.0000.000
28A28ASN00.0070.00526.1310.0030.0030.0000.0000.0000.000
29A29PRO00.0270.00023.381-0.009-0.0090.0000.0000.0000.000
30A30LEU00.0660.03019.574-0.010-0.0100.0000.0000.0000.000
31A31LEU0-0.054-0.01122.471-0.016-0.0160.0000.0000.0000.000
32A32THR0-0.009-0.00623.574-0.009-0.0090.0000.0000.0000.000
33A33ALA0-0.030-0.01018.547-0.011-0.0110.0000.0000.0000.000
34A34LEU0-0.018-0.00816.6780.0100.0100.0000.0000.0000.000
35A35LYS10.8550.92416.3680.2960.2960.0000.0000.0000.000
36A36VAL0-0.036-0.02212.4690.0150.0150.0000.0000.0000.000
37A37GLU-1-0.844-0.91313.087-0.419-0.4190.0000.0000.0000.000
38A38THR0-0.021-0.0179.964-0.060-0.0600.0000.0000.0000.000
39A39SER0-0.002-0.00212.3810.0650.0650.0000.0000.0000.000
40A40GLU-1-0.905-0.96612.989-0.605-0.6050.0000.0000.0000.000
41A41GLY00.0180.01513.965-0.011-0.0110.0000.0000.0000.000
42A42GLY00.016-0.00314.7830.0530.0530.0000.0000.0000.000
43A43LEU0-0.016-0.00911.766-0.068-0.0680.0000.0000.0000.000
44A44THR0-0.030-0.01715.3370.0970.0970.0000.0000.0000.000
45A45LEU0-0.0060.00516.030-0.021-0.0210.0000.0000.0000.000
46A46SER00.005-0.01518.6180.0430.0430.0000.0000.0000.000
47A47GLY00.0450.02520.406-0.012-0.0120.0000.0000.0000.000
48A48THR00.007-0.01023.1360.0110.0110.0000.0000.0000.000
49A49ASN0-0.010-0.00226.6530.0040.0040.0000.0000.0000.000
50A50LEU0-0.038-0.01929.2320.0110.0110.0000.0000.0000.000
51A51GLU-1-0.944-0.95131.307-0.081-0.0810.0000.0000.0000.000
52A52ILE0-0.014-0.01330.3590.0030.0030.0000.0000.0000.000
53A53ASP-1-0.817-0.88026.683-0.156-0.1560.0000.0000.0000.000
54A54LEU0-0.012-0.01325.6260.0050.0050.0000.0000.0000.000
55A55SER0-0.010-0.00821.887-0.017-0.0170.0000.0000.0000.000
56A56CYS00.001-0.00321.9310.0270.0270.0000.0000.0000.000
57A57PHE0-0.048-0.00718.024-0.020-0.0200.0000.0000.0000.000
58A58VAL0-0.017-0.02417.4850.0380.0380.0000.0000.0000.000
59A59PRO0-0.027-0.01117.207-0.055-0.0550.0000.0000.0000.000
60A60ALA0-0.025-0.02113.1460.0110.0110.0000.0000.0000.000
61A61GLU-1-0.921-0.93312.564-0.608-0.6080.0000.0000.0000.000
62A62VAL00.012-0.0058.778-0.127-0.1270.0000.0000.0000.000
63A63GLN0-0.077-0.0293.2191.2381.8770.014-0.217-0.4360.000
64A64GLN0-0.010-0.0241.905-4.939-7.9119.385-3.475-2.937-0.029
65A65PRO00.0090.0095.497-0.379-0.3790.0000.0000.0000.000
66A66GLU-1-0.891-0.9415.004-1.069-0.918-0.001-0.002-0.1470.000
67A67ASN00.0180.0068.178-0.119-0.1190.0000.0000.0000.000
68A68PHE00.0470.0209.3870.0500.0500.0000.0000.0000.000
69A69VAL00.0260.01711.8000.0130.0130.0000.0000.0000.000
70A70VAL00.0440.02612.7260.0060.0060.0000.0000.0000.000
71A71PRO00.0140.00315.5040.0100.0100.0000.0000.0000.000
72A72ALA00.0280.02418.749-0.019-0.0190.0000.0000.0000.000
73A73HIS0-0.008-0.01920.413-0.012-0.0120.0000.0000.0000.000
74A74LEU0-0.017-0.00518.4830.0020.0020.0000.0000.0000.000
75A75PHE00.0570.02013.893-0.005-0.0050.0000.0000.0000.000
76A76ALA00.0310.02217.972-0.016-0.0160.0000.0000.0000.000
77A77GLN0-0.057-0.03020.7970.0060.0060.0000.0000.0000.000
78A78ILE0-0.017-0.01316.2250.0100.0100.0000.0000.0000.000
79A79VAL00.003-0.00216.258-0.001-0.0010.0000.0000.0000.000
80A80ARG10.8230.91118.8320.1920.1920.0000.0000.0000.000
81A81ASN0-0.054-0.03121.8630.0130.0130.0000.0000.0000.000
82A82LEU0-0.0170.02115.9280.0130.0130.0000.0000.0000.000
83A83GLY00.008-0.00120.2710.0070.0070.0000.0000.0000.000
84A84GLY0-0.0100.00119.6080.0070.0070.0000.0000.0000.000
85A85GLU-1-0.828-0.93320.424-0.239-0.2390.0000.0000.0000.000
86A86LEU0-0.040-0.00415.794-0.015-0.0150.0000.0000.0000.000
87A87VAL0-0.019-0.00312.6740.0390.0390.0000.0000.0000.000
88A88GLU-1-0.784-0.8636.752-0.929-0.9290.0000.0000.0000.000
89A89LEU0-0.042-0.0258.5050.1350.1350.0000.0000.0000.000
90A90GLU-1-0.761-0.8692.725-2.385-1.0500.771-0.766-1.339-0.007
91A91LEU00.0000.0203.6700.3630.7120.000-0.068-0.2810.000
92A92SER00.000-0.0052.421-4.341-1.4541.801-1.936-2.752-0.023
93A93GLY00.0120.0073.8480.0290.1240.0060.006-0.1070.000
94A94GLN00.0060.0136.547-0.254-0.2540.0000.0000.0000.000
95A95GLU-1-0.898-0.9557.914-0.056-0.0560.0000.0000.0000.000
96A96LEU00.0240.0167.031-0.198-0.1980.0000.0000.0000.000
97A97SER0-0.014-0.0146.8910.2680.2680.0000.0000.0000.000
98A98VAL0-0.008-0.0128.775-0.156-0.1560.0000.0000.0000.000
99A99ARG10.7800.8666.0170.6370.6370.0000.0000.0000.000
100A100SER0-0.002-0.02712.386-0.029-0.0290.0000.0000.0000.000
101A101GLY0-0.012-0.00215.3780.0380.0380.0000.0000.0000.000
102A102GLY0-0.005-0.00515.9900.0030.0030.0000.0000.0000.000
103A103SER0-0.070-0.02216.8330.0250.0250.0000.0000.0000.000
104A104ASP-1-0.776-0.88910.926-0.285-0.2850.0000.0000.0000.000
105A105PHE0-0.025-0.00313.0360.0550.0550.0000.0000.0000.000
106A106LYS10.8450.9218.3850.1770.1770.0000.0000.0000.000
107A107LEU0-0.045-0.02311.9100.0570.0570.0000.0000.0000.000
108A108GLN0-0.022-0.00711.763-0.025-0.0250.0000.0000.0000.000
109A109THR0-0.013-0.0179.790-0.031-0.0310.0000.0000.0000.000
110A110GLY0-0.050-0.03512.8440.0620.0620.0000.0000.0000.000
111A111ASP-1-0.912-0.97314.412-0.083-0.0830.0000.0000.0000.000
112A112ILE0-0.029-0.02512.632-0.006-0.0060.0000.0000.0000.000
113A113GLU-1-0.900-0.94415.159-0.150-0.1500.0000.0000.0000.000
114A114ALA0-0.035-0.00417.6910.0090.0090.0000.0000.0000.000
115A115TYR0-0.058-0.03019.0200.0020.0020.0000.0000.0000.000
116A116PRO0-0.020-0.00120.798-0.003-0.0030.0000.0000.0000.000
117A117PRO00.0130.00321.695-0.022-0.0220.0000.0000.0000.000
118A118LEU0-0.012-0.00122.4170.0140.0140.0000.0000.0000.000
119A119SER0-0.008-0.00923.539-0.018-0.0180.0000.0000.0000.000
120A120PHE0-0.019-0.01123.9860.0080.0080.0000.0000.0000.000
121A121PRO0-0.0180.00227.697-0.010-0.0100.0000.0000.0000.000
122A122ALA00.035-0.00429.013-0.003-0.0030.0000.0000.0000.000
123A123GLN0-0.081-0.03731.0370.0000.0000.0000.0000.0000.000
124A124ALA00.0080.01434.6250.0010.0010.0000.0000.0000.000
125A125ASP-1-0.795-0.86736.580-0.099-0.0990.0000.0000.0000.000
126A126VAL0-0.019-0.01139.3460.0060.0060.0000.0000.0000.000
127A127SER0-0.081-0.05338.978-0.007-0.0070.0000.0000.0000.000
128A128LEU00.0290.00839.4970.0070.0070.0000.0000.0000.000
129A129ASP-1-0.759-0.88439.448-0.121-0.1210.0000.0000.0000.000
130A130GLY00.016-0.00937.1850.0040.0040.0000.0000.0000.000
131A131GLY00.0230.01538.2640.0010.0010.0000.0000.0000.000
132A132GLU-1-0.887-0.94539.870-0.083-0.0830.0000.0000.0000.000
133A133LEU0-0.0170.00438.9990.0040.0040.0000.0000.0000.000
134A134SER00.0070.00138.1950.0050.0050.0000.0000.0000.000
135A135ARG10.8550.91840.6210.1020.1020.0000.0000.0000.000
136A136ALA00.0020.02443.8060.0050.0050.0000.0000.0000.000
137A137PHE00.043-0.00539.3650.0040.0040.0000.0000.0000.000
138A138SER0-0.042-0.04142.0560.0020.0020.0000.0000.0000.000
139A139SER0-0.071-0.03344.1800.0040.0040.0000.0000.0000.000
140A140VAL0-0.014-0.00946.9640.0040.0040.0000.0000.0000.000
141A141ARG10.8500.91042.0330.0820.0820.0000.0000.0000.000
142A142TYR0-0.017-0.03246.1290.0020.0020.0000.0000.0000.000
143A143ALA0-0.017-0.00648.3760.0020.0020.0000.0000.0000.000
144A144ALA0-0.0050.02146.8020.0020.0020.0000.0000.0000.000
145A145SER0-0.007-0.00848.5190.0000.0000.0000.0000.0000.000
146A146ASN0-0.050-0.04844.423-0.003-0.0030.0000.0000.0000.000
147A147GLU-1-0.864-0.93447.241-0.052-0.0520.0000.0000.0000.000
148A148ALA0-0.0360.00950.5070.0030.0030.0000.0000.0000.000
149A149PHE00.0420.00351.994-0.001-0.0010.0000.0000.0000.000
150A150GLN0-0.0140.00153.613-0.001-0.0010.0000.0000.0000.000
151A151ALA00.0570.01248.278-0.001-0.0010.0000.0000.0000.000
152A152VAL00.0620.03548.539-0.002-0.0020.0000.0000.0000.000
153A153PHE0-0.019-0.01049.153-0.002-0.0020.0000.0000.0000.000
154A154ARG10.8320.93146.2130.0520.0520.0000.0000.0000.000
155A155GLY0-0.007-0.00944.920-0.004-0.0040.0000.0000.0000.000
156A156ILE0-0.037-0.01543.9380.0030.0030.0000.0000.0000.000
157A157LYS10.8350.92745.5060.0550.0550.0000.0000.0000.000
158A158LEU00.0180.00143.140-0.001-0.0010.0000.0000.0000.000
159A159GLU-1-0.782-0.88246.889-0.057-0.0570.0000.0000.0000.000
160A160HIS00.0480.02444.463-0.001-0.0010.0000.0000.0000.000
161A161HIS10.7960.88049.6960.0640.0640.0000.0000.0000.000
162A162GLY00.0760.04051.5440.0010.0010.0000.0000.0000.000
163A163GLU-1-0.924-0.94750.297-0.065-0.0650.0000.0000.0000.000
164A164SER0-0.045-0.01850.040-0.002-0.0020.0000.0000.0000.000
165A165ALA00.0210.00947.2590.0010.0010.0000.0000.0000.000
166A166ARG10.7980.87949.2840.0580.0580.0000.0000.0000.000
167A167VAL0-0.025-0.00445.055-0.001-0.0010.0000.0000.0000.000
168A168VAL00.020-0.00248.4780.0020.0020.0000.0000.0000.000
169A169ALA0-0.024-0.00148.486-0.002-0.0020.0000.0000.0000.000
170A170SER0-0.027-0.04450.5000.0030.0030.0000.0000.0000.000
171A171ASP-1-0.774-0.88452.340-0.050-0.0500.0000.0000.0000.000
172A172GLY0-0.034-0.01754.5230.0020.0020.0000.0000.0000.000
173A173TYR0-0.081-0.03657.6580.0030.0030.0000.0000.0000.000
174A174ARG10.8170.91151.6960.0530.0530.0000.0000.0000.000
175A175VAL0-0.0120.00354.989-0.001-0.0010.0000.0000.0000.000
176A176ALA0-0.0130.02051.4350.0010.0010.0000.0000.0000.000
177A177ILE00.0290.00252.198-0.001-0.0010.0000.0000.0000.000
178A178ARG10.8790.92948.4240.0720.0720.0000.0000.0000.000
179A179ASP-1-0.816-0.86950.047-0.063-0.0630.0000.0000.0000.000
180A180PHE0-0.033-0.02944.213-0.001-0.0010.0000.0000.0000.000
181A181PRO00.0500.02047.0690.0010.0010.0000.0000.0000.000
182A182ALA0-0.032-0.01545.753-0.004-0.0040.0000.0000.0000.000
183A183SER0-0.025-0.00243.8140.0050.0050.0000.0000.0000.000
184A184GLY00.005-0.01045.027-0.003-0.0030.0000.0000.0000.000
185A185ASP-1-0.930-0.95546.511-0.064-0.0640.0000.0000.0000.000
186A186GLY0-0.0050.00145.439-0.003-0.0030.0000.0000.0000.000
187A187LYS10.9120.96142.5810.0840.0840.0000.0000.0000.000
188A188ASN0-0.002-0.01746.006-0.004-0.0040.0000.0000.0000.000
189A189LEU0-0.0260.00141.4530.0000.0000.0000.0000.0000.000
190A190ILE00.0240.01344.9000.0020.0020.0000.0000.0000.000
191A191ILE00.0070.01539.666-0.002-0.0020.0000.0000.0000.000
192A192PRO00.0590.03339.5800.0040.0040.0000.0000.0000.000
193A193ALA00.0530.01340.652-0.005-0.0050.0000.0000.0000.000
194A194ARG10.9610.96735.9560.0860.0860.0000.0000.0000.000
195A195SER00.0450.02336.207-0.003-0.0030.0000.0000.0000.000
196A196VAL00.0010.00636.719-0.006-0.0060.0000.0000.0000.000
197A197ASP-1-0.829-0.89137.941-0.092-0.0920.0000.0000.0000.000
198A198GLU-1-0.888-0.95632.575-0.136-0.1360.0000.0000.0000.000
199A199LEU00.001-0.00833.558-0.008-0.0080.0000.0000.0000.000
200A200ILE0-0.021-0.00335.190-0.006-0.0060.0000.0000.0000.000
201A201ARG10.8760.94932.5700.1140.1140.0000.0000.0000.000
202A202VAL00.004-0.01229.698-0.009-0.0090.0000.0000.0000.000
203A203LEU0-0.0300.01031.958-0.008-0.0080.0000.0000.0000.000
204A204LYS10.8120.90831.7970.1560.1560.0000.0000.0000.000
205A205ASP-1-0.831-0.92234.900-0.115-0.1150.0000.0000.0000.000
206A206GLY00.0040.01635.286-0.009-0.0090.0000.0000.0000.000
207A207GLU-1-0.840-0.87435.598-0.133-0.1330.0000.0000.0000.000
208A208ALA0-0.018-0.01834.729-0.011-0.0110.0000.0000.0000.000
209A209ARG10.8400.90330.8980.1730.1730.0000.0000.0000.000
210A210PHE0-0.014-0.01435.074-0.005-0.0050.0000.0000.0000.000
211A211THR00.015-0.01133.817-0.001-0.0010.0000.0000.0000.000
212A212TYR0-0.008-0.01936.1070.0010.0010.0000.0000.0000.000
213A213GLY00.0370.01636.707-0.003-0.0030.0000.0000.0000.000
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