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: JL179

Calculation Name: 5DDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DDT

Chain ID: A

ChEMBL ID:

UniProt ID: Q06755

Base Structure: X-ray

Registration Date: 2023-09-20

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2832022.683751
FMO2-HF: Nuclear repulsion 2741657.325185
FMO2-HF: Total energy -90365.358566
FMO2-MP2: Total energy -90630.362287


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.
-22.25-21.73515.74-8.468-7.791-0.062
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 : -0.056 / q_NPA : -0.033
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].
3A3TYR0-0.002-0.0413.8691.9273.692-0.011-0.908-0.8470.003
4A4ASP-1-0.791-0.8876.839-0.462-0.4620.0000.0000.0000.000
5A5VAL0-0.005-0.01210.2570.0560.0560.0000.0000.0000.000
6A6VAL0-0.029-0.00312.4490.0160.0160.0000.0000.0000.000
7A7ILE00.0120.01015.785-0.023-0.0230.0000.0000.0000.000
8A8PRO0-0.046-0.00518.5020.0200.0200.0000.0000.0000.000
9A9ALA00.0590.00621.817-0.009-0.0090.0000.0000.0000.000
10A10ALA0-0.047-0.00825.0040.0040.0040.0000.0000.0000.000
11A11GLY00.0360.00724.966-0.010-0.0100.0000.0000.0000.000
12A12GLN0-0.030-0.01522.670-0.019-0.0190.0000.0000.0000.000
13A13GLY00.0830.03626.689-0.001-0.0010.0000.0000.0000.000
14A14LYS10.8980.96030.2760.0800.0800.0000.0000.0000.000
15A15ARG10.8510.90531.2830.0740.0740.0000.0000.0000.000
16A16MET00.0000.01034.5000.0030.0030.0000.0000.0000.000
17A17LYS10.9420.96036.2270.0550.0550.0000.0000.0000.000
18A18ALA00.0590.02335.568-0.003-0.0030.0000.0000.0000.000
19A19GLY00.0300.01234.7460.0040.0040.0000.0000.0000.000
20A20ARG10.8230.90135.2880.0600.0600.0000.0000.0000.000
21A21ASN00.000-0.00528.980-0.008-0.0080.0000.0000.0000.000
22A22LYS10.8700.91830.3720.1020.1020.0000.0000.0000.000
23A23LEU00.0200.02124.761-0.004-0.0040.0000.0000.0000.000
24A24PHE0-0.029-0.02228.065-0.004-0.0040.0000.0000.0000.000
25A25ILE0-0.043-0.00930.7050.0060.0060.0000.0000.0000.000
26A26GLU-1-0.926-0.95830.699-0.102-0.1020.0000.0000.0000.000
27A27LEU0-0.011-0.01227.0570.0020.0020.0000.0000.0000.000
28A28LYS10.8120.87530.1700.1100.1100.0000.0000.0000.000
29A29GLY00.0240.03532.3170.0020.0020.0000.0000.0000.000
30A30ASP-1-0.727-0.81728.013-0.135-0.1350.0000.0000.0000.000
31A31PRO0-0.018-0.00328.238-0.005-0.0050.0000.0000.0000.000
32A32VAL00.0070.00825.259-0.012-0.0120.0000.0000.0000.000
33A33ILE0-0.017-0.01421.689-0.015-0.0150.0000.0000.0000.000
34A34ILE00.0170.01822.458-0.020-0.0200.0000.0000.0000.000
35A35HIS00.000-0.00622.433-0.031-0.0310.0000.0000.0000.000
36A36THR0-0.034-0.03818.689-0.028-0.0280.0000.0000.0000.000
37A37LEU0-0.044-0.01118.107-0.038-0.0380.0000.0000.0000.000
38A38ARG10.8300.89517.5460.1420.1420.0000.0000.0000.000
39A39VAL0-0.0250.03014.704-0.028-0.0280.0000.0000.0000.000
40A40PHE00.024-0.00911.979-0.046-0.0460.0000.0000.0000.000
41A41ASP-1-0.771-0.86312.772-0.354-0.3540.0000.0000.0000.000
42A42SER0-0.032-0.02614.185-0.007-0.0070.0000.0000.0000.000
43A43HIS0-0.0360.0017.6620.0590.0590.0000.0000.0000.000
44A44ARG10.9590.9696.402-0.270-0.2700.0000.0000.0000.000
45A45GLN0-0.056-0.0334.1350.2250.556-0.001-0.054-0.2760.000
46A46CYS0-0.0120.0086.049-0.090-0.0900.0000.0000.0000.000
47A47ASP-1-0.806-0.8615.241-1.586-1.5860.0000.0000.0000.000
48A48LYS10.7690.8738.0740.3000.3000.0000.0000.0000.000
49A49ILE00.0270.02111.699-0.008-0.0080.0000.0000.0000.000
50A50ILE0-0.054-0.03014.2800.0400.0400.0000.0000.0000.000
51A51LEU00.0310.02217.308-0.001-0.0010.0000.0000.0000.000
52A52VAL0-0.0340.00520.0760.0190.0190.0000.0000.0000.000
53A53ILE00.0160.00622.654-0.006-0.0060.0000.0000.0000.000
54A54ASN0-0.018-0.01526.3080.0110.0110.0000.0000.0000.000
55A55GLU-1-0.731-0.85729.708-0.052-0.0520.0000.0000.0000.000
56A56GLN0-0.062-0.03431.3830.0010.0010.0000.0000.0000.000
57A57GLU-1-0.810-0.90631.009-0.084-0.0840.0000.0000.0000.000
58A58ARG10.7710.87725.8800.0520.0520.0000.0000.0000.000
59A59GLU-1-0.850-0.92729.512-0.053-0.0530.0000.0000.0000.000
60A60HIS0-0.0070.00431.491-0.003-0.0030.0000.0000.0000.000
61A61PHE00.030-0.00325.795-0.005-0.0050.0000.0000.0000.000
62A62GLN0-0.015-0.01826.684-0.006-0.0060.0000.0000.0000.000
63A63GLN0-0.049-0.01927.7930.0030.0030.0000.0000.0000.000
64A64LEU00.0200.02626.810-0.002-0.0020.0000.0000.0000.000
65A65LEU0-0.027-0.02821.720-0.009-0.0090.0000.0000.0000.000
66A66SER0-0.100-0.05024.6550.0030.0030.0000.0000.0000.000
67A67ASP-1-0.882-0.93627.390-0.072-0.0720.0000.0000.0000.000
68A68TYR0-0.069-0.05824.471-0.001-0.0010.0000.0000.0000.000
69A69PRO0-0.034-0.00422.653-0.003-0.0030.0000.0000.0000.000
70A70PHE0-0.017-0.02517.901-0.013-0.0130.0000.0000.0000.000
71A71GLN0-0.089-0.05214.0690.0780.0780.0000.0000.0000.000
72A72THR0-0.023-0.02111.470-0.018-0.0180.0000.0000.0000.000
73A73SER0-0.041-0.01412.9580.0490.0490.0000.0000.0000.000
74A74ILE00.0480.01114.614-0.036-0.0360.0000.0000.0000.000
75A75GLU-1-0.813-0.88016.788-0.042-0.0420.0000.0000.0000.000
76A76LEU00.0220.01318.949-0.003-0.0030.0000.0000.0000.000
77A77VAL0-0.017-0.01220.2990.0160.0160.0000.0000.0000.000
78A78ALA00.0370.02723.233-0.007-0.0070.0000.0000.0000.000
79A79GLY00.010-0.01125.9520.0060.0060.0000.0000.0000.000
80A80GLY0-0.012-0.00426.5350.0080.0080.0000.0000.0000.000
81A81ASP-1-0.812-0.88928.405-0.073-0.0730.0000.0000.0000.000
82A82GLU-1-0.874-0.93427.984-0.095-0.0950.0000.0000.0000.000
83A83ARG10.8310.90918.8300.1740.1740.0000.0000.0000.000
84A84GLN00.0720.03722.866-0.007-0.0070.0000.0000.0000.000
85A85HIS0-0.009-0.00922.8520.0000.0000.0000.0000.0000.000
86A86SER00.012-0.00523.7950.0080.0080.0000.0000.0000.000
87A87VAL00.0160.00817.6690.0010.0010.0000.0000.0000.000
88A88TYR00.0450.02119.2550.0110.0110.0000.0000.0000.000
89A89LYS10.8400.91020.6830.0560.0560.0000.0000.0000.000
90A90GLY00.0380.01319.0210.0060.0060.0000.0000.0000.000
91A91LEU00.0210.00314.5740.0080.0080.0000.0000.0000.000
92A92LYS10.7700.88216.8190.0460.0460.0000.0000.0000.000
93A93ALA0-0.0330.00517.8140.0090.0090.0000.0000.0000.000
94A94VAL0-0.027-0.00411.476-0.016-0.0160.0000.0000.0000.000
95A95LYS10.7810.86512.2410.0430.0430.0000.0000.0000.000
96A96GLN0-0.047-0.0217.051-0.081-0.0810.0000.0000.0000.000
97A97GLU-1-0.777-0.8719.9200.3020.3020.0000.0000.0000.000
98A98LYS10.7530.8705.7090.3220.3220.0000.0000.0000.000
99A99ILE00.0350.0303.317-0.948-0.3720.041-0.186-0.4320.001
100A100VAL0-0.025-0.0146.198-0.258-0.2580.0000.0000.0000.000
101A101LEU00.0120.0007.247-0.078-0.0780.0000.0000.0000.000
102A102VAL0-0.029-0.00610.6860.0430.0430.0000.0000.0000.000
103A103HIS00.0720.02214.460-0.054-0.0540.0000.0000.0000.000
104A104ASP-1-0.757-0.86816.467-0.172-0.1720.0000.0000.0000.000
105A105GLY00.0700.02120.223-0.014-0.0140.0000.0000.0000.000
106A106ALA0-0.0010.00321.436-0.001-0.0010.0000.0000.0000.000
107A107ARG10.8350.92619.4820.2580.2580.0000.0000.0000.000
108A108PRO00.0360.02219.781-0.031-0.0310.0000.0000.0000.000
109A109PHE0-0.0030.00020.829-0.008-0.0080.0000.0000.0000.000
110A110ILE0-0.0190.01113.707-0.004-0.0040.0000.0000.0000.000
111A111LYS10.8390.90215.9920.3490.3490.0000.0000.0000.000
112A112HIS00.015-0.00711.669-0.074-0.0740.0000.0000.0000.000
113A113GLU-1-0.874-0.93810.847-0.734-0.7340.0000.0000.0000.000
114A114GLN00.0240.00911.023-0.116-0.1160.0000.0000.0000.000
115A115ILE0-0.052-0.0188.0360.0070.0070.0000.0000.0000.000
116A116ASP-1-0.775-0.8766.414-2.418-2.4180.0000.0000.0000.000
117A117GLU-1-0.944-0.9746.671-1.106-1.1060.0000.0000.0000.000
118A118LEU0-0.043-0.0228.618-0.040-0.0400.0000.0000.0000.000
119A119ILE0-0.045-0.0122.333-0.186-0.1611.786-0.655-1.1570.003
120A120ALA00.0540.0334.778-0.212-0.117-0.001-0.006-0.0880.000
121A121GLU-1-0.773-0.8435.844-0.319-0.3190.0000.0000.0000.000
122A122ALA0-0.018-0.0056.3250.2110.2110.0000.0000.0000.000
123A123GLU-1-0.873-0.9481.847-17.498-19.77513.926-6.659-4.991-0.069
124A124GLN0-0.046-0.0025.9620.4900.4900.0000.0000.0000.000
125A125THR0-0.070-0.0649.2160.2230.2230.0000.0000.0000.000
126A126GLY00.000-0.00510.3040.1130.1130.0000.0000.0000.000
127A127ALA0-0.016-0.01611.0750.0840.0840.0000.0000.0000.000
128A128ALA0-0.0020.02110.257-0.014-0.0140.0000.0000.0000.000
129A129ILE00.0210.00112.2350.0260.0260.0000.0000.0000.000
130A130LEU00.0500.04213.993-0.018-0.0180.0000.0000.0000.000
131A131ALA0-0.008-0.00916.1720.0460.0460.0000.0000.0000.000
132A132VAL0-0.0030.02419.855-0.019-0.0190.0000.0000.0000.000
133A133PRO00.0590.04522.8000.0190.0190.0000.0000.0000.000
134A134VAL0-0.0010.01025.9840.0060.0060.0000.0000.0000.000
135A135LYS10.9240.96328.9120.1650.1650.0000.0000.0000.000
136A136ASP-1-0.862-0.92331.990-0.121-0.1210.0000.0000.0000.000
137A137THR0-0.057-0.04334.220-0.004-0.0040.0000.0000.0000.000
138A138ILE00.0530.03931.8610.0060.0060.0000.0000.0000.000
139A139LYS10.9140.94235.3580.0860.0860.0000.0000.0000.000
140A140ARG10.8660.91834.3770.0840.0840.0000.0000.0000.000
141A141VAL0-0.016-0.01138.9190.0030.0030.0000.0000.0000.000
142A142GLN00.0280.01840.650-0.001-0.0010.0000.0000.0000.000
143A143ASP-1-0.885-0.93844.098-0.052-0.0520.0000.0000.0000.000
144A144LEU0-0.057-0.04344.2790.0010.0010.0000.0000.0000.000
145A145GLN00.0140.02946.0050.0000.0000.0000.0000.0000.000
146A146VAL0-0.039-0.03342.709-0.002-0.0020.0000.0000.0000.000
147A147SER0-0.034-0.02242.2120.0030.0030.0000.0000.0000.000
148A148GLU-1-0.805-0.87037.783-0.081-0.0810.0000.0000.0000.000
149A149THR0-0.061-0.04138.575-0.001-0.0010.0000.0000.0000.000
150A150ILE0-0.0200.00532.7410.0020.0020.0000.0000.0000.000
151A151GLU-1-0.779-0.86233.084-0.122-0.1220.0000.0000.0000.000
152A152ARG10.9090.93631.9380.1170.1170.0000.0000.0000.000
153A153SER0-0.119-0.08630.815-0.011-0.0110.0000.0000.0000.000
154A154SER00.0220.01127.809-0.008-0.0080.0000.0000.0000.000
155A155LEU0-0.039-0.00626.802-0.008-0.0080.0000.0000.0000.000
156A156TRP00.006-0.00921.079-0.007-0.0070.0000.0000.0000.000
157A157ALA0-0.035-0.01624.5390.0070.0070.0000.0000.0000.000
158A158VAL00.0330.01119.509-0.021-0.0210.0000.0000.0000.000
159A159GLN0-0.064-0.04118.612-0.011-0.0110.0000.0000.0000.000
160A160THR0-0.046-0.01716.2470.0170.0170.0000.0000.0000.000
161A161PRO00.0400.00611.9260.0130.0130.0000.0000.0000.000
162A162GLN0-0.052-0.03313.2230.0040.0040.0000.0000.0000.000
163A163ALA00.0190.0127.8400.0340.0340.0000.0000.0000.000
164A164PHE00.0220.0009.262-0.057-0.0570.0000.0000.0000.000
165A165ARG10.8990.9588.0880.4970.4970.0000.0000.0000.000
166A166LEU00.0210.0119.725-0.104-0.1040.0000.0000.0000.000
167A167SER0-0.052-0.05512.132-0.086-0.0860.0000.0000.0000.000
168A168LEU0-0.0120.00013.449-0.023-0.0230.0000.0000.0000.000
169A169LEU00.0460.02813.468-0.018-0.0180.0000.0000.0000.000
170A170MET0-0.005-0.00415.576-0.022-0.0220.0000.0000.0000.000
171A171LYS10.8300.90917.8240.0270.0270.0000.0000.0000.000
172A172ALA00.0470.01818.532-0.003-0.0030.0000.0000.0000.000
173A173HIS00.028-0.01718.2060.0080.0080.0000.0000.0000.000
174A174ALA0-0.054-0.01521.4360.0010.0010.0000.0000.0000.000
175A175GLU-1-0.827-0.91623.264-0.042-0.0420.0000.0000.0000.000
176A176ALA0-0.026-0.00424.1950.0000.0000.0000.0000.0000.000
177A177GLU-1-0.838-0.92825.480-0.029-0.0290.0000.0000.0000.000
178A178ARG10.8920.94827.3100.0130.0130.0000.0000.0000.000
179A179LYS10.7910.88326.5500.0580.0580.0000.0000.0000.000
180A180GLY0-0.0020.01230.397-0.002-0.0020.0000.0000.0000.000
181A181PHE0-0.027-0.00125.170-0.001-0.0010.0000.0000.0000.000
182A182LEU0-0.006-0.01227.5990.0000.0000.0000.0000.0000.000
183A183GLY00.0420.02624.770-0.001-0.0010.0000.0000.0000.000
184A184THR0-0.036-0.02624.4800.0030.0030.0000.0000.0000.000
185A185ASP-1-0.841-0.89620.148-0.201-0.2010.0000.0000.0000.000
186A186ASP-1-0.745-0.86216.862-0.143-0.1430.0000.0000.0000.000
187A187ALA00.0180.01817.4040.0110.0110.0000.0000.0000.000
188A188SER00.009-0.02118.4540.0180.0180.0000.0000.0000.000
189A189LEU0-0.043-0.01820.1580.0160.0160.0000.0000.0000.000
190A190VAL0-0.025-0.02315.9510.0160.0160.0000.0000.0000.000
191A191GLU-1-0.917-0.97219.357-0.177-0.1770.0000.0000.0000.000
192A192GLN0-0.0420.00221.9290.0080.0080.0000.0000.0000.000
193A193MET0-0.0480.00518.1570.0220.0220.0000.0000.0000.000
194A194GLU-1-0.915-0.96323.628-0.068-0.0680.0000.0000.0000.000
195A195GLY0-0.055-0.02823.0640.0050.0050.0000.0000.0000.000
196A196GLY0-0.0260.00719.743-0.008-0.0080.0000.0000.0000.000
197A197SER0-0.049-0.03316.934-0.002-0.0020.0000.0000.0000.000
198A198VAL0-0.0060.00015.307-0.009-0.0090.0000.0000.0000.000
199A199ARG10.7960.87313.9300.4980.4980.0000.0000.0000.000
200A200VAL00.001-0.00815.079-0.014-0.0140.0000.0000.0000.000
201A201VAL00.0110.01911.742-0.010-0.0100.0000.0000.0000.000
202A202GLU-1-0.918-0.97115.189-0.246-0.2460.0000.0000.0000.000
203A203GLY00.0350.00517.492-0.036-0.0360.0000.0000.0000.000
204A204SER00.008-0.01418.7140.0220.0220.0000.0000.0000.000
205A205TYR0-0.031-0.04621.4260.0050.0050.0000.0000.0000.000
206A206THR00.0240.02822.8410.0080.0080.0000.0000.0000.000
207A207ASN0-0.038-0.01817.8820.0150.0150.0000.0000.0000.000
208A208ILE0-0.001-0.00921.8520.0030.0030.0000.0000.0000.000
209A209LYS10.7870.88723.5070.1610.1610.0000.0000.0000.000
210A210LEU0-0.040-0.01625.2320.0130.0130.0000.0000.0000.000
211A211THR0-0.049-0.03228.0050.0090.0090.0000.0000.0000.000
212A212THR0-0.050-0.04030.7160.0120.0120.0000.0000.0000.000
213A213PRO00.038-0.00333.452-0.005-0.0050.0000.0000.0000.000
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