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: LZZ59

Calculation Name: 5MJW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJW

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DJT8

Base Structure: X-ray

Registration Date: 2023-06-21

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2117464.139666
FMO2-HF: Nuclear repulsion 2039658.160123
FMO2-HF: Total energy -77805.979543
FMO2-MP2: Total energy -78035.746151


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-0.6161.312-0.016-0.881-1.030.005
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.020
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].
3A6THR00.0440.0293.854-0.7941.134-0.016-0.881-1.0300.005
4A7VAL00.0620.0106.0350.4300.4300.0000.0000.0000.000
5A8SER0-0.003-0.0159.5020.1990.1990.0000.0000.0000.000
6A9ASP-1-0.836-0.9176.204-1.973-1.9730.0000.0000.0000.000
7A10THR0-0.051-0.0219.0680.2790.2790.0000.0000.0000.000
8A11LYS10.9730.98511.2730.5050.5050.0000.0000.0000.000
9A12ARG10.9680.98110.3710.8830.8830.0000.0000.0000.000
10A13ALA0-0.013-0.00212.0890.0540.0540.0000.0000.0000.000
11A14PHE0-0.0090.00514.0670.0530.0530.0000.0000.0000.000
12A15TYR00.012-0.01117.0780.0200.0200.0000.0000.0000.000
13A16ALA0-0.023-0.00116.7700.0170.0170.0000.0000.0000.000
14A17ALA0-0.025-0.00418.2360.0250.0250.0000.0000.0000.000
15A18HIS0-0.038-0.01419.8900.0280.0280.0000.0000.0000.000
16A19THR00.0210.00722.514-0.012-0.0120.0000.0000.0000.000
17A20ARG10.9280.97224.2840.0430.0430.0000.0000.0000.000
18A21PRO00.0430.02626.506-0.009-0.0090.0000.0000.0000.000
19A22ILE0-0.019-0.01224.1760.0080.0080.0000.0000.0000.000
20A23HIS00.0360.00627.952-0.004-0.0040.0000.0000.0000.000
21A24SER00.0290.00830.445-0.004-0.0040.0000.0000.0000.000
22A25ILE00.0300.01532.4670.0040.0040.0000.0000.0000.000
23A26TYR00.0820.03532.7220.0030.0030.0000.0000.0000.000
24A27ARG10.8940.95428.9270.1050.1050.0000.0000.0000.000
25A28ARG10.8870.94234.8480.0540.0540.0000.0000.0000.000
26A29PHE00.0310.01338.0740.0030.0030.0000.0000.0000.000
27A30ILE00.0130.00735.1470.0020.0020.0000.0000.0000.000
28A31GLU-1-0.938-0.97335.595-0.072-0.0720.0000.0000.0000.000
29A32GLU-1-0.890-0.94239.748-0.047-0.0470.0000.0000.0000.000
30A33LEU0-0.0070.00042.4370.0030.0030.0000.0000.0000.000
31A34LEU0-0.022-0.01038.8320.0010.0010.0000.0000.0000.000
32A35VAL00.0000.01342.8290.0030.0030.0000.0000.0000.000
33A36GLU-1-0.822-0.88145.230-0.044-0.0440.0000.0000.0000.000
34A37ILE0-0.040-0.02245.6290.0030.0030.0000.0000.0000.000
35A38HIS00.0640.04346.3130.0010.0010.0000.0000.0000.000
36A39LEU0-0.067-0.04748.3500.0030.0030.0000.0000.0000.000
37A40LEU0-0.087-0.03650.9690.0020.0020.0000.0000.0000.000
38A41ARG10.9200.96649.4450.0520.0520.0000.0000.0000.000
39A42VAL0-0.0090.00951.1250.0010.0010.0000.0000.0000.000
40A43ASN0-0.067-0.02853.8840.0030.0030.0000.0000.0000.000
41A44VAL00.0390.00957.131-0.001-0.0010.0000.0000.0000.000
42A45ASP-1-0.899-0.94260.154-0.028-0.0280.0000.0000.0000.000
43A46PHE0-0.079-0.02853.6650.0000.0000.0000.0000.0000.000
44A47ARG10.9550.97058.3710.0320.0320.0000.0000.0000.000
45A48TYR0-0.054-0.04851.913-0.001-0.0010.0000.0000.0000.000
46A49SER00.016-0.00155.9400.0010.0010.0000.0000.0000.000
47A50PRO00.1010.02655.214-0.001-0.0010.0000.0000.0000.000
48A51LEU00.0100.03654.823-0.001-0.0010.0000.0000.0000.000
49A52PHE00.000-0.01350.240-0.001-0.0010.0000.0000.0000.000
50A53ALA00.0000.00750.805-0.002-0.0020.0000.0000.0000.000
51A54LEU00.0110.01350.008-0.002-0.0020.0000.0000.0000.000
52A55GLY00.0130.02650.339-0.001-0.0010.0000.0000.0000.000
53A56VAL0-0.022-0.01346.043-0.002-0.0020.0000.0000.0000.000
54A57VAL0-0.009-0.00445.646-0.003-0.0030.0000.0000.0000.000
55A58THR00.014-0.00445.436-0.002-0.0020.0000.0000.0000.000
56A59ALA0-0.037-0.02145.915-0.001-0.0010.0000.0000.0000.000
57A60PHE0-0.048-0.02037.980-0.002-0.0020.0000.0000.0000.000
58A61ASP-1-0.876-0.95041.333-0.076-0.0760.0000.0000.0000.000
59A62GLN00.0300.01941.547-0.001-0.0010.0000.0000.0000.000
60A63PHE0-0.057-0.02739.186-0.001-0.0010.0000.0000.0000.000
61A64MET0-0.045-0.02634.963-0.004-0.0040.0000.0000.0000.000
62A65GLU-1-0.922-0.95236.807-0.075-0.0750.0000.0000.0000.000
63A66GLY0-0.040-0.02535.469-0.002-0.0020.0000.0000.0000.000
64A67TYR0-0.084-0.02730.031-0.004-0.0040.0000.0000.0000.000
65A68GLN00.0100.01828.1100.0050.0050.0000.0000.0000.000
66A69PRO0-0.029-0.03026.779-0.004-0.0040.0000.0000.0000.000
67A70GLU-1-0.856-0.95229.041-0.115-0.1150.0000.0000.0000.000
68A71GLY0-0.0080.00031.4100.0050.0050.0000.0000.0000.000
69A72ASP-1-0.901-0.97228.764-0.162-0.1620.0000.0000.0000.000
70A73ARG10.9610.99932.0960.1070.1070.0000.0000.0000.000
71A74ASP-1-0.830-0.91635.570-0.093-0.0930.0000.0000.0000.000
72A75ARG10.8360.92030.2440.1560.1560.0000.0000.0000.000
73A76ILE00.0000.00532.3400.0030.0030.0000.0000.0000.000
74A77PHE00.0140.01535.9230.0050.0050.0000.0000.0000.000
75A78HIS0-0.038-0.02738.0240.0040.0040.0000.0000.0000.000
76A79ALA00.005-0.01536.1330.0040.0040.0000.0000.0000.000
77A80LEU0-0.0090.00038.2630.0030.0030.0000.0000.0000.000
78A81CYS0-0.0170.00240.6950.0050.0050.0000.0000.0000.000
79A82VAL0-0.024-0.01039.2880.0030.0030.0000.0000.0000.000
80A83ALA0-0.036-0.00840.0520.0030.0030.0000.0000.0000.000
81A84GLU-1-0.838-0.93441.969-0.054-0.0540.0000.0000.0000.000
82A85GLU-1-1.026-1.00945.071-0.050-0.0500.0000.0000.0000.000
83A86MET0-0.055-0.02346.2620.0030.0030.0000.0000.0000.000
84A87ASN00.0380.00546.107-0.006-0.0060.0000.0000.0000.000
85A88PRO00.0560.02042.8360.0020.0020.0000.0000.0000.000
86A89GLN0-0.071-0.04845.455-0.002-0.0020.0000.0000.0000.000
87A90GLN00.0190.00847.0400.0000.0000.0000.0000.0000.000
88A91LEU00.0410.02146.9530.0020.0020.0000.0000.0000.000
89A92LYS10.9650.98442.1030.0810.0810.0000.0000.0000.000
90A93GLU-1-0.900-0.94248.148-0.056-0.0560.0000.0000.0000.000
91A94ASP-1-0.830-0.88451.324-0.047-0.0470.0000.0000.0000.000
92A95ALA0-0.031-0.01349.6800.0020.0020.0000.0000.0000.000
93A96ALA00.0490.01650.0970.0010.0010.0000.0000.0000.000
94A97SER0-0.078-0.04651.9900.0020.0020.0000.0000.0000.000
95A98TRP00.000-0.02454.7110.0030.0030.0000.0000.0000.000
96A99GLN00.0100.01051.038-0.001-0.0010.0000.0000.0000.000
97A100GLN0-0.096-0.03955.6640.0020.0020.0000.0000.0000.000
98A101TYR0-0.053-0.04358.9970.0010.0010.0000.0000.0000.000
99A102GLN00.0230.00853.738-0.001-0.0010.0000.0000.0000.000
100A103GLY0-0.036-0.01358.5560.0010.0010.0000.0000.0000.000
101A104ARG10.8980.96560.9230.0350.0350.0000.0000.0000.000
102A105PRO00.0160.01363.5620.0000.0000.0000.0000.0000.000
103A106LEU00.0990.03064.8030.0000.0000.0000.0000.0000.000
104A107SER0-0.004-0.00866.6130.0000.0000.0000.0000.0000.000
105A108GLN00.0420.00068.1150.0000.0000.0000.0000.0000.000
106A109ILE0-0.0110.01963.8940.0000.0000.0000.0000.0000.000
107A110LEU00.003-0.01367.2360.0000.0000.0000.0000.0000.000
108A111ASP-1-0.948-0.96469.807-0.025-0.0250.0000.0000.0000.000
109A112GLU-1-0.791-0.85666.935-0.032-0.0320.0000.0000.0000.000
110A113LEU0-0.044-0.01865.9410.0000.0000.0000.0000.0000.000
111A114ASN00.0070.00869.9930.0000.0000.0000.0000.0000.000
112A115SER0-0.052-0.03272.0870.0010.0010.0000.0000.0000.000
113A116GLY0-0.014-0.00373.5930.0010.0010.0000.0000.0000.000
114A117GLN0-0.108-0.06071.7580.0010.0010.0000.0000.0000.000
115A118PRO0-0.0030.01267.226-0.001-0.0010.0000.0000.0000.000
116A119SER0-0.017-0.02865.186-0.001-0.0010.0000.0000.0000.000
117A120ALA0-0.0080.02061.8170.0000.0000.0000.0000.0000.000
118A121PRO00.0410.01157.8070.0000.0000.0000.0000.0000.000
119A122LEU00.0450.03460.6580.0000.0000.0000.0000.0000.000
120A123ASN00.015-0.01662.8950.0000.0000.0000.0000.0000.000
121A124SER0-0.074-0.05760.2170.0010.0010.0000.0000.0000.000
122A125LEU00.0170.00160.8450.0000.0000.0000.0000.0000.000
123A126ASN00.000-0.00363.3130.0010.0010.0000.0000.0000.000
124A127HIS0-0.077-0.03063.5330.0010.0010.0000.0000.0000.000
125A128THR00.0050.00560.026-0.001-0.0010.0000.0000.0000.000
126A129GLY0-0.0220.01059.996-0.001-0.0010.0000.0000.0000.000
127A130LYS10.9270.95857.5500.0320.0320.0000.0000.0000.000
128A131TYR0-0.046-0.04557.601-0.001-0.0010.0000.0000.0000.000
129A132SER00.002-0.00153.0520.0000.0000.0000.0000.0000.000
130A133ARG10.8620.90146.8000.0480.0480.0000.0000.0000.000
131A134LEU00.013-0.00548.4580.0000.0000.0000.0000.0000.000
132A135HIS00.0460.01552.5260.0000.0000.0000.0000.0000.000
133A136ALA00.0100.01655.4970.0000.0000.0000.0000.0000.000
134A137VAL00.0050.00549.5060.0000.0000.0000.0000.0000.000
135A138GLY00.0380.02752.972-0.001-0.0010.0000.0000.0000.000
136A139LEU0-0.020-0.01554.1390.0000.0000.0000.0000.0000.000
137A140TYR0-0.022-0.02951.4690.0010.0010.0000.0000.0000.000
138A141ALA00.0400.01851.8880.0000.0000.0000.0000.0000.000
139A142PHE00.017-0.00553.6230.0000.0000.0000.0000.0000.000
140A143LEU0-0.023-0.02056.8180.0010.0010.0000.0000.0000.000
141A144GLN0-0.045-0.03251.4240.0000.0000.0000.0000.0000.000
142A145GLU-1-0.906-0.92752.627-0.048-0.0480.0000.0000.0000.000
143A146LEU0-0.062-0.01156.5890.0010.0010.0000.0000.0000.000
144A147ALA0-0.025-0.01559.8180.0000.0000.0000.0000.0000.000
145A148GLY0-0.031-0.03662.1110.0010.0010.0000.0000.0000.000
146A149GLU-1-0.950-0.96558.353-0.034-0.0340.0000.0000.0000.000
147A150VAL00.0390.01960.4200.0010.0010.0000.0000.0000.000
148A151THR00.0010.00156.3590.0010.0010.0000.0000.0000.000
149A152ILE00.0080.01258.8880.0000.0000.0000.0000.0000.000
150A153HIS00.0190.00960.1680.0000.0000.0000.0000.0000.000
151A154LEU0-0.0050.00057.5550.0000.0000.0000.0000.0000.000
152A155ASN0-0.030-0.04361.501-0.001-0.0010.0000.0000.0000.000
153A156GLU-1-0.914-0.94563.853-0.025-0.0250.0000.0000.0000.000
154A157THR00.0290.00162.8190.0010.0010.0000.0000.0000.000
155A158LEU0-0.061-0.03960.5110.0000.0000.0000.0000.0000.000
156A159ASP-1-0.850-0.92464.881-0.024-0.0240.0000.0000.0000.000
157A160GLN0-0.049-0.02668.2800.0010.0010.0000.0000.0000.000
158A161LEU00.001-0.00663.5950.0000.0000.0000.0000.0000.000
159A162ALA0-0.028-0.00467.7540.0000.0000.0000.0000.0000.000
160A163PRO0-0.050-0.01469.1130.0000.0000.0000.0000.0000.000
161A164VAL0-0.0290.00469.3180.0000.0000.0000.0000.0000.000
162A165ILE0-0.016-0.00863.9720.0000.0000.0000.0000.0000.000
163A166PRO00.0090.00766.1930.0010.0010.0000.0000.0000.000
164A167LEU0-0.014-0.00760.4550.0000.0000.0000.0000.0000.000
165A168PRO0-0.026-0.00962.2120.0010.0010.0000.0000.0000.000
166A169ILE00.0890.02763.242-0.001-0.0010.0000.0000.0000.000
167A170GLU-1-0.886-0.94463.570-0.024-0.0240.0000.0000.0000.000
168A171LYS10.8790.94060.0920.0280.0280.0000.0000.0000.000
169A172VAL00.0190.02058.980-0.001-0.0010.0000.0000.0000.000
170A173LYS10.9240.96758.6380.0230.0230.0000.0000.0000.000
171A174ARG10.8640.93857.3800.0290.0290.0000.0000.0000.000
172A175ASP-1-0.815-0.91155.021-0.034-0.0340.0000.0000.0000.000
173A176LEU0-0.021-0.01854.025-0.002-0.0020.0000.0000.0000.000
174A177GLU-1-0.896-0.94154.561-0.029-0.0290.0000.0000.0000.000
175A178LEU0-0.055-0.01850.7250.0000.0000.0000.0000.0000.000
176A179TYR0-0.034-0.04147.509-0.001-0.0010.0000.0000.0000.000
177A180ARG10.9530.98449.1600.0340.0340.0000.0000.0000.000
178A181SER00.0310.03649.715-0.001-0.0010.0000.0000.0000.000
179A182ASN0-0.038-0.04446.2350.0010.0010.0000.0000.0000.000
180A183LEU00.0070.01244.059-0.002-0.0020.0000.0000.0000.000
181A184ASP-1-0.878-0.93044.901-0.044-0.0440.0000.0000.0000.000
182A185LYS10.9150.94944.4220.0360.0360.0000.0000.0000.000
183A186ILE0-0.027-0.01139.711-0.002-0.0020.0000.0000.0000.000
184A187ASN00.0530.02440.200-0.007-0.0070.0000.0000.0000.000
185A188GLN0-0.0050.00540.863-0.001-0.0010.0000.0000.0000.000
186A189ALA0-0.006-0.00138.158-0.002-0.0020.0000.0000.0000.000
187A190ARG10.9230.95335.9730.0690.0690.0000.0000.0000.000
188A191SER0-0.0170.00136.014-0.004-0.0040.0000.0000.0000.000
189A192LEU00.0150.01936.797-0.001-0.0010.0000.0000.0000.000
190A193MET0-0.056-0.03530.9750.0000.0000.0000.0000.0000.000
191A194LYS10.8180.90531.8480.0750.0750.0000.0000.0000.000
192A195GLU-1-0.946-0.99532.872-0.058-0.0580.0000.0000.0000.000
193A196LEU0-0.044-0.01128.727-0.002-0.0020.0000.0000.0000.000
194A197VAL0-0.085-0.03126.556-0.005-0.0050.0000.0000.0000.000
195A198GLU-1-0.885-0.91527.817-0.088-0.0880.0000.0000.0000.000