Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YZQV2

Calculation Name: 5L7Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5L7Z

Chain ID: A

ChEMBL ID:

UniProt ID: P28750

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 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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3098876.958824
FMO2-HF: Nuclear repulsion 3004530.980548
FMO2-HF: Total energy -94345.978276
FMO2-MP2: Total energy -94622.929308


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:26:VAL)


Summations of interaction energy for fragment #1(A:26: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.
-4.4442.4353.346-3.582-6.646-0.013
Interaction energy analysis for fragmet #1(A:26:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.010
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].
3A28LEU00.0220.0293.454-1.7581.2410.004-1.528-1.4750.003
4A29PRO00.0370.0243.045-1.192-0.1950.156-0.493-0.661-0.005
5A30ALA00.012-0.0055.4350.2310.2310.0000.0000.0000.000
6A31GLY00.0500.0217.292-0.054-0.0540.0000.0000.0000.000
7A32ASN0-0.038-0.02010.6830.0730.0730.0000.0000.0000.000
8A33TYR0-0.040-0.0327.5610.0020.0020.0000.0000.0000.000
9A34ILE00.0070.01213.2300.0410.0410.0000.0000.0000.000
10A35LEU00.0060.00211.254-0.015-0.0150.0000.0000.0000.000
11A36VAL00.011-0.00714.7690.0050.0050.0000.0000.0000.000
12A37GLY0-0.0090.02916.1660.0090.0090.0000.0000.0000.000
13A38VAL0-0.029-0.03217.172-0.021-0.0210.0000.0000.0000.000
14A39ASP-1-0.787-0.87919.4820.1060.1060.0000.0000.0000.000
15A40ILE0-0.002-0.01322.071-0.016-0.0160.0000.0000.0000.000
16A41ASP-1-0.791-0.86325.0280.0570.0570.0000.0000.0000.000
17A42THR00.029-0.01726.162-0.007-0.0070.0000.0000.0000.000
18A43THR0-0.018-0.01729.3660.0060.0060.0000.0000.0000.000
19A44GLY00.011-0.01730.1900.0010.0010.0000.0000.0000.000
20A45ARG10.8150.94121.900-0.085-0.0850.0000.0000.0000.000
21A46ARG10.8970.92325.479-0.012-0.0120.0000.0000.0000.000
22A47LEU00.0990.03621.5760.0030.0030.0000.0000.0000.000
23A48MET00.0410.03725.658-0.003-0.0030.0000.0000.0000.000
24A49ASP-1-0.856-0.89028.4790.0280.0280.0000.0000.0000.000
25A50GLU-1-0.721-0.87429.166-0.013-0.0130.0000.0000.0000.000
26A51ILE00.0170.00825.0610.0090.0090.0000.0000.0000.000
27A52VAL0-0.053-0.03028.961-0.003-0.0030.0000.0000.0000.000
28A53GLN0-0.059-0.06028.776-0.005-0.0050.0000.0000.0000.000
29A54LEU00.0210.03122.8950.0050.0050.0000.0000.0000.000
30A55ALA0-0.022-0.01724.752-0.004-0.0040.0000.0000.0000.000
31A56ALA00.0210.00321.2180.0040.0040.0000.0000.0000.000
32A57TYR0-0.076-0.05621.094-0.008-0.0080.0000.0000.0000.000
33A58THR00.0510.02819.6120.0010.0010.0000.0000.0000.000
34A59PRO00.0220.00420.835-0.003-0.0030.0000.0000.0000.000
35A60THR0-0.032-0.00423.9460.0000.0000.0000.0000.0000.000
36A61ASP-1-0.789-0.85924.286-0.036-0.0360.0000.0000.0000.000
37A62HIS10.8130.88924.300-0.002-0.0020.0000.0000.0000.000
38A63PHE00.0200.02625.182-0.006-0.0060.0000.0000.0000.000
39A64GLU-1-0.795-0.88826.4870.0160.0160.0000.0000.0000.000
40A65GLN0-0.025-0.00828.955-0.005-0.0050.0000.0000.0000.000
41A66TYR00.0290.00830.4030.0010.0010.0000.0000.0000.000
42A67ILE0-0.019-0.01629.132-0.005-0.0050.0000.0000.0000.000
43A68MET0-0.052-0.02033.4010.0060.0060.0000.0000.0000.000
44A69PRO0-0.0170.02033.981-0.003-0.0030.0000.0000.0000.000
45A70TYR00.0250.00134.7500.0020.0020.0000.0000.0000.000
46A71MET00.0000.01235.8510.0030.0030.0000.0000.0000.000
47A72ASN0-0.001-0.01937.740-0.001-0.0010.0000.0000.0000.000
48A73LEU00.0030.01034.4140.0010.0010.0000.0000.0000.000
49A74ASN00.0570.04432.7000.0030.0030.0000.0000.0000.000
50A75PRO00.010-0.01436.5760.0010.0010.0000.0000.0000.000
51A76ALA00.0620.03333.5790.0010.0010.0000.0000.0000.000
52A77ALA0-0.031-0.01032.5440.0040.0040.0000.0000.0000.000
53A78ARG10.9040.94033.494-0.027-0.0270.0000.0000.0000.000
54A79GLN00.0240.01536.455-0.003-0.0030.0000.0000.0000.000
55A80ARG10.8820.94728.444-0.061-0.0610.0000.0000.0000.000
56A81HIS00.0470.02628.3350.0030.0030.0000.0000.0000.000
57A82GLN0-0.072-0.03033.393-0.006-0.0060.0000.0000.0000.000
58A83VAL00.0060.01735.580-0.004-0.0040.0000.0000.0000.000
59A84ARG10.9080.91737.557-0.022-0.0220.0000.0000.0000.000
60A85VAL00.0210.01838.619-0.001-0.0010.0000.0000.0000.000
61A86ILE0-0.069-0.03241.0680.0030.0030.0000.0000.0000.000
62A87SER00.0440.00344.782-0.002-0.0020.0000.0000.0000.000
63A88ILE0-0.009-0.00147.4500.0010.0010.0000.0000.0000.000
64A89GLY00.0360.02350.549-0.002-0.0020.0000.0000.0000.000
65A90PHE00.0300.01249.9710.0010.0010.0000.0000.0000.000
66A91TYR0-0.0070.01447.419-0.002-0.0020.0000.0000.0000.000
67A92ARG10.8470.90439.0390.0040.0040.0000.0000.0000.000
68A93MET00.000-0.00442.023-0.002-0.0020.0000.0000.0000.000
69A94LEU00.0280.01835.9050.0020.0020.0000.0000.0000.000
70A95LYS10.8930.94040.346-0.016-0.0160.0000.0000.0000.000
71A96SER00.0320.03039.1840.0030.0030.0000.0000.0000.000
72A97MET0-0.0260.00240.023-0.003-0.0030.0000.0000.0000.000
73A98GLN00.0130.01535.940-0.001-0.0010.0000.0000.0000.000
74A99THR00.0310.00040.735-0.001-0.0010.0000.0000.0000.000
75A100TYR0-0.0040.00043.329-0.003-0.0030.0000.0000.0000.000
76A101LYS10.9741.00043.201-0.018-0.0180.0000.0000.0000.000
77A102ILE00.0160.00042.8780.0020.0020.0000.0000.0000.000
78A103ILE0-0.020-0.00736.6110.0000.0000.0000.0000.0000.000
79A104LYS10.9070.95139.0180.0110.0110.0000.0000.0000.000
80A105SER00.0310.02436.1570.0000.0000.0000.0000.0000.000
81A106LYS10.8190.90533.7670.0250.0250.0000.0000.0000.000
82A107SER00.0790.02935.3790.0020.0020.0000.0000.0000.000
83A108GLU-1-0.713-0.80928.786-0.036-0.0360.0000.0000.0000.000
84A109ILE00.0380.02330.343-0.003-0.0030.0000.0000.0000.000
85A110ALA0-0.044-0.01631.542-0.005-0.0050.0000.0000.0000.000
86A111ALA00.0520.02130.001-0.002-0.0020.0000.0000.0000.000
87A112LEU00.0330.01324.8770.0000.0000.0000.0000.0000.000
88A113LYS10.9450.98326.9300.0570.0570.0000.0000.0000.000
89A114ASP-1-0.857-0.91728.899-0.039-0.0390.0000.0000.0000.000
90A115PHE00.0160.00320.499-0.002-0.0020.0000.0000.0000.000
91A116LEU00.0160.00922.764-0.004-0.0040.0000.0000.0000.000
92A117ASN00.0370.02025.045-0.012-0.0120.0000.0000.0000.000
93A118TRP0-0.050-0.03221.380-0.004-0.0040.0000.0000.0000.000
94A119LEU00.0380.01019.2870.0000.0000.0000.0000.0000.000
95A120GLU-1-0.775-0.85022.080-0.126-0.1260.0000.0000.0000.000
96A121GLN0-0.0440.00324.0050.0000.0000.0000.0000.0000.000
97A122LEU0-0.011-0.00120.5020.0020.0020.0000.0000.0000.000
98A123LYS10.8800.93917.0520.2350.2350.0000.0000.0000.000
99A124THR0-0.049-0.03721.306-0.004-0.0040.0000.0000.0000.000
100A125LYS10.7660.85324.6120.0440.0440.0000.0000.0000.000
101A126ALA0-0.0130.01119.9890.0090.0090.0000.0000.0000.000
102A127GLY00.0110.02121.752-0.003-0.0030.0000.0000.0000.000
103A128PRO0-0.035-0.03721.469-0.012-0.0120.0000.0000.0000.000
104A129SER00.0090.01319.430-0.015-0.0150.0000.0000.0000.000
105A130SER0-0.0070.01316.334-0.009-0.0090.0000.0000.0000.000
106A131ASP-1-0.802-0.90112.625-0.351-0.3510.0000.0000.0000.000
107A132GLY0-0.062-0.05614.567-0.021-0.0210.0000.0000.0000.000
108A133ILE0-0.0220.00714.8160.0260.0260.0000.0000.0000.000
109A134VAL00.0170.0059.365-0.048-0.0480.0000.0000.0000.000
110A135LEU0-0.009-0.00312.3400.0500.0500.0000.0000.0000.000
111A136ILE00.0330.01412.1940.0210.0210.0000.0000.0000.000
112A137TYR00.0350.00812.1610.0030.0030.0000.0000.0000.000
113A138HIS00.000-0.01015.2050.0430.0430.0000.0000.0000.000
114A139GLU-1-0.724-0.85416.9340.0900.0900.0000.0000.0000.000
115A140GLU-1-0.804-0.86916.9860.3060.3060.0000.0000.0000.000
116A141ARG10.8440.92718.038-0.079-0.0790.0000.0000.0000.000
117A142LYS10.7430.85711.143-0.072-0.0720.0000.0000.0000.000
118A143PHE0-0.030-0.02716.976-0.020-0.0200.0000.0000.0000.000
119A144ILE0-0.001-0.00718.318-0.025-0.0250.0000.0000.0000.000
120A145PRO00.0120.01614.544-0.017-0.0170.0000.0000.0000.000
121A146TYR0-0.035-0.03714.885-0.014-0.0140.0000.0000.0000.000
122A147MET00.0320.02918.971-0.016-0.0160.0000.0000.0000.000
123A148ILE0-0.030-0.00819.628-0.010-0.0100.0000.0000.0000.000
124A149LEU0-0.004-0.00315.413-0.015-0.0150.0000.0000.0000.000
125A150GLU-1-0.866-0.93420.108-0.055-0.0550.0000.0000.0000.000
126A151SER0-0.062-0.07423.094-0.003-0.0030.0000.0000.0000.000
127A152LEU0-0.034-0.01420.8780.0000.0000.0000.0000.0000.000
128A153LYS10.8010.88320.8520.1570.1570.0000.0000.0000.000
129A154LYS10.8600.92324.5390.0400.0400.0000.0000.0000.000
130A155TYR0-0.079-0.07227.6190.0070.0070.0000.0000.0000.000
131A156GLY00.0290.01926.8720.0000.0000.0000.0000.0000.000
132A157LEU0-0.046-0.02425.616-0.008-0.0080.0000.0000.0000.000
133A158LEU0-0.003-0.00118.534-0.004-0.0040.0000.0000.0000.000
134A159GLU-1-0.879-0.93020.706-0.205-0.2050.0000.0000.0000.000
135A160ARG10.8120.86221.2470.0900.0900.0000.0000.0000.000
136A161PHE00.000-0.01216.807-0.002-0.0020.0000.0000.0000.000
137A162THR0-0.035-0.01916.464-0.013-0.0130.0000.0000.0000.000
138A163ALA00.0300.04016.940-0.038-0.0380.0000.0000.0000.000
139A164SER0-0.005-0.01318.152-0.015-0.0150.0000.0000.0000.000
140A165VAL0-0.014-0.00714.723-0.012-0.0120.0000.0000.0000.000
141A166LYS10.8330.91710.9320.3300.3300.0000.0000.0000.000
142A167SER0-0.034-0.0418.686-0.072-0.0720.0000.0000.0000.000
143A168PHE00.0300.02110.8050.0720.0720.0000.0000.0000.000
144A169ALA00.0420.0168.987-0.003-0.0030.0000.0000.0000.000
145A170ASN0-0.012-0.01210.215-0.047-0.0470.0000.0000.0000.000
146A171SER00.0570.00811.5380.1080.1080.0000.0000.0000.000
147A172ILE0-0.057-0.02413.2810.0250.0250.0000.0000.0000.000
148A173ASN0-0.016-0.0079.283-0.161-0.1610.0000.0000.0000.000
149A174LEU00.0150.01810.3960.0350.0350.0000.0000.0000.000
150A175ALA00.0000.00013.068-0.032-0.0320.0000.0000.0000.000
151A176LYS10.8590.89814.556-0.412-0.4120.0000.0000.0000.000
152A177ALA00.0070.02212.523-0.004-0.0040.0000.0000.0000.000
153A178SER0-0.075-0.03914.668-0.045-0.0450.0000.0000.0000.000
154A179ILE0-0.020-0.00617.811-0.044-0.0440.0000.0000.0000.000
155A180GLY00.0190.01119.222-0.020-0.0200.0000.0000.0000.000
156A181ASP-1-0.873-0.93620.2060.2510.2510.0000.0000.0000.000
157A182ALA0-0.016-0.00623.188-0.020-0.0200.0000.0000.0000.000
158A183ASN0-0.010-0.00123.644-0.026-0.0260.0000.0000.0000.000
159A184ILE0-0.0010.01422.698-0.018-0.0180.0000.0000.0000.000
160A185LYS10.8640.92821.294-0.208-0.2080.0000.0000.0000.000
161A186ASN0-0.031-0.04420.8220.0180.0180.0000.0000.0000.000
162A187TYR00.019-0.00222.182-0.028-0.0280.0000.0000.0000.000
163A188SER0-0.0030.00222.2630.0110.0110.0000.0000.0000.000
164A189LEU00.0870.04220.222-0.001-0.0010.0000.0000.0000.000
165A190ARG10.8350.91023.717-0.085-0.0850.0000.0000.0000.000
166A191LYS10.8770.95625.988-0.142-0.1420.0000.0000.0000.000
167A192LEU00.0740.03919.795-0.005-0.0050.0000.0000.0000.000
168A193SER00.0560.03423.741-0.005-0.0050.0000.0000.0000.000
169A194LYS10.9270.97025.117-0.104-0.1040.0000.0000.0000.000
170A195ILE00.0080.02124.896-0.008-0.0080.0000.0000.0000.000
171A196LEU0-0.0060.01420.771-0.002-0.0020.0000.0000.0000.000
172A197SER0-0.065-0.05025.127-0.018-0.0180.0000.0000.0000.000
173A256LEU00.0490.02528.685-0.002-0.0020.0000.0000.0000.000
174A257PHE00.009-0.00532.0880.0070.0070.0000.0000.0000.000
175A258ASP-1-0.784-0.89527.1600.0960.0960.0000.0000.0000.000
176A259GLY00.0720.03428.1190.0030.0030.0000.0000.0000.000
177A260ASN0-0.0460.00730.048-0.006-0.0060.0000.0000.0000.000
178A261ALA00.0530.00525.6070.0070.0070.0000.0000.0000.000
179A262SER00.0310.00025.1940.0050.0050.0000.0000.0000.000
180A263VAL0-0.051-0.01625.9680.0040.0040.0000.0000.0000.000
181A264ARG10.7040.82423.153-0.067-0.0670.0000.0000.0000.000
182A265ALA00.0250.02021.1050.0140.0140.0000.0000.0000.000
183A266LYS10.8330.91320.896-0.065-0.0650.0000.0000.0000.000
184A267LEU0-0.009-0.01621.8370.0090.0090.0000.0000.0000.000
185A268ALA0-0.002-0.00617.7850.0180.0180.0000.0000.0000.000
186A269PHE00.0000.00617.1850.0250.0250.0000.0000.0000.000
187A270ASP-1-0.760-0.86717.9590.1020.1020.0000.0000.0000.000
188A271VAL00.0050.00018.4970.0080.0080.0000.0000.0000.000
189A272ALA00.0040.00714.0910.0280.0280.0000.0000.0000.000
190A273LEU00.0240.03015.4050.0270.0270.0000.0000.0000.000
191A274GLN0-0.043-0.03317.3900.0110.0110.0000.0000.0000.000
192A275LEU0-0.016-0.01315.8950.0070.0070.0000.0000.0000.000
193A276SER0-0.069-0.05413.2630.0100.0100.0000.0000.0000.000
194A277ASN0-0.020-0.01614.754-0.008-0.0080.0000.0000.0000.000
195A278SER0-0.045-0.00917.553-0.007-0.0070.0000.0000.0000.000
196A279ASP-1-0.798-0.89519.6660.1130.1130.0000.0000.0000.000
197A280GLY00.0180.01722.3750.0060.0060.0000.0000.0000.000
198A281LYS10.7350.83925.103-0.120-0.1200.0000.0000.0000.000
199A282PRO00.0720.06820.715-0.010-0.0100.0000.0000.0000.000
200A283GLU-1-0.841-0.93223.3350.0430.0430.0000.0000.0000.000
201A284PRO0-0.017-0.01621.5290.0000.0000.0000.0000.0000.000
202A285LYS10.8560.90621.488-0.015-0.0150.0000.0000.0000.000
203A286SER00.0320.02621.424-0.013-0.0130.0000.0000.0000.000
204A287SER00.0380.00517.9000.0020.0020.0000.0000.0000.000
205A288GLU-1-0.913-0.94317.0150.0890.0890.0000.0000.0000.000
206A289ALA00.0160.01616.2120.0190.0190.0000.0000.0000.000
207A290LEU0-0.013-0.01715.8710.0280.0280.0000.0000.0000.000
208A291GLU-1-0.910-0.94912.2680.0010.0010.0000.0000.0000.000
209A292ASN00.0080.00111.3910.0300.0300.0000.0000.0000.000
210A293MET0-0.062-0.01511.5270.0620.0620.0000.0000.0000.000
211A294PHE0-0.019-0.0166.7900.0590.0590.0000.0000.0000.000
212A295ASN0-0.033-0.0386.9340.0230.0230.0000.0000.0000.000
213A296ALA00.0040.0136.9200.2070.2070.0000.0000.0000.000
214A297ILE0-0.026-0.0267.8600.2010.2010.0000.0000.0000.000
215A298ARG10.8790.9462.479-0.3740.8511.304-0.518-2.012-0.001
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217A300PHE0-0.022-0.0213.1971.3351.033-0.0090.681-0.370-0.001
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