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

tag_button

FMODB ID: MMK8Z

Calculation Name: 4C47-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C47

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZL65

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 193
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1678294.05837
FMO2-HF: Nuclear repulsion 1602181.846887
FMO2-HF: Total energy -76112.211483
FMO2-MP2: Total energy -76336.62413


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:22:ACE )


Summations of interaction energy for fragment #1(A:22:ACE )
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.
2.2082.853-0.007-0.309-0.3290
Interaction energy analysis for fragmet #1(A:22:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.022
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].
3A24TYR 0-0.064-0.0253.8151.3522.035-0.007-0.305-0.3710.000
4A25PHE 0-0.057-0.0255.8950.5640.5640.0000.0000.0000.000
5A26ALA 0-0.016-0.0054.941-0.123-0.1610.000-0.0040.0420.000
6A27ASP -1-0.824-0.9295.0200.2190.2190.0000.0000.0000.000
7A28LYS 10.9500.9706.6330.1220.1220.0000.0000.0000.000
8A29HIS 00.0090.0109.948-0.028-0.0280.0000.0000.0000.000
9A30LEU 00.0340.0278.110-0.008-0.0080.0000.0000.0000.000
10A31VAL 00.004-0.00510.307-0.036-0.0360.0000.0000.0000.000
11A32GLU -1-0.981-0.99312.2310.0350.0350.0000.0000.0000.000
12A33GLU -1-0.888-0.93913.1420.2430.2430.0000.0000.0000.000
13A34MET 0-0.042-0.02312.800-0.005-0.0050.0000.0000.0000.000
14A35LYS 10.9360.97215.629-0.075-0.0750.0000.0000.0000.000
15A36GLU -1-0.879-0.94518.0980.0700.0700.0000.0000.0000.000
16A37GLN 00.0150.00618.2140.0040.0040.0000.0000.0000.000
17A38GLN 0-0.029-0.01219.783-0.020-0.0200.0000.0000.0000.000
18A39LYS 10.9370.96321.467-0.068-0.0680.0000.0000.0000.000
19A40GLU -1-0.941-0.96223.4660.1090.1090.0000.0000.0000.000
20A41GLN 0-0.068-0.05221.878-0.010-0.0100.0000.0000.0000.000
21A42GLU -1-0.876-0.92725.6040.0480.0480.0000.0000.0000.000
22A43THR 0-0.037-0.00827.605-0.008-0.0080.0000.0000.0000.000
23A44LYS 10.9230.94526.244-0.107-0.1070.0000.0000.0000.000
24A45ILE 00.0390.02627.349-0.003-0.0030.0000.0000.0000.000
25A46ASN 00.0090.00431.120-0.008-0.0080.0000.0000.0000.000
26A47LEU 0-0.094-0.03533.451-0.004-0.0040.0000.0000.0000.000
27A48LEU 00.008-0.00731.880-0.003-0.0030.0000.0000.0000.000
28A49GLU -1-0.897-0.93734.3880.0380.0380.0000.0000.0000.000
29A50LYS 10.9120.95437.139-0.040-0.0400.0000.0000.0000.000
30A51GLN 00.001-0.02037.8220.0000.0000.0000.0000.0000.000
31A52GLN 00.0280.02639.091-0.002-0.0020.0000.0000.0000.000
32A53LYS 10.9820.98740.137-0.031-0.0310.0000.0000.0000.000
33A54GLU -1-0.968-0.98143.3870.0330.0330.0000.0000.0000.000
34A55GLN 0-0.046-0.03642.159-0.002-0.0020.0000.0000.0000.000
35A56GLU -1-0.893-0.92845.1160.0280.0280.0000.0000.0000.000
36A57ALA 0-0.017-0.01346.835-0.002-0.0020.0000.0000.0000.000
37A58LYS 10.9120.94147.285-0.033-0.0330.0000.0000.0000.000
38A59ILE 00.0540.03646.915-0.001-0.0010.0000.0000.0000.000
39A60ASN 00.0280.01550.417-0.003-0.0030.0000.0000.0000.000
40A61LEU 0-0.057-0.03153.017-0.001-0.0010.0000.0000.0000.000
41A62LEU 0-0.005-0.00251.943-0.001-0.0010.0000.0000.0000.000
42A63GLU -1-0.889-0.93252.7690.0240.0240.0000.0000.0000.000
43A64LYS 10.9190.95356.206-0.019-0.0190.0000.0000.0000.000
44A65GLN 0-0.008-0.01758.2230.0000.0000.0000.0000.0000.000
45A66GLN 00.0370.02857.545-0.001-0.0010.0000.0000.0000.000
46A67ALA 00.0260.01760.642-0.001-0.0010.0000.0000.0000.000
47A68THR 0-0.027-0.01962.721-0.001-0.0010.0000.0000.0000.000
48A69ILE 00.0330.01961.739-0.001-0.0010.0000.0000.0000.000
49A70ILE 00.0090.04462.083-0.001-0.0010.0000.0000.0000.000
50A71ASN 0-0.012-0.00466.090-0.001-0.0010.0000.0000.0000.000
51A72THR 00.000-0.01268.433-0.001-0.0010.0000.0000.0000.000
52A73THR 00.008-0.02867.5830.0000.0000.0000.0000.0000.000
53A74LYS 10.9660.99769.742-0.015-0.0150.0000.0000.0000.000
54A75LYS 10.9100.95872.085-0.014-0.0140.0000.0000.0000.000
55A76VAL 00.0340.01972.6420.0000.0000.0000.0000.0000.000
56A77THR 0-0.052-0.04072.5780.0000.0000.0000.0000.0000.000
57A78GLU -1-0.916-0.96375.5240.0120.0120.0000.0000.0000.000
58A79VAL 0-0.038-0.02078.1210.0000.0000.0000.0000.0000.000
59A80VAL 00.0150.00376.9630.0000.0000.0000.0000.0000.000
60A81GLY 00.0550.03679.5980.0000.0000.0000.0000.0000.000
61A82ARG 10.8550.93081.182-0.012-0.0120.0000.0000.0000.000
62A83VAL 00.000-0.00583.2230.0000.0000.0000.0000.0000.000
63A84GLU -1-0.781-0.88581.9560.0130.0130.0000.0000.0000.000
64A85ARG 10.9130.94283.946-0.011-0.0110.0000.0000.0000.000
65A86LYS 10.9250.95986.942-0.010-0.0100.0000.0000.0000.000
66A87GLN 00.009-0.00486.8360.0000.0000.0000.0000.0000.000
67A88ARG 10.8240.93083.465-0.012-0.0120.0000.0000.0000.000
68A89LEU 0-0.084-0.03790.3580.0000.0000.0000.0000.0000.000
69A90PHE 0-0.0200.00193.2730.0000.0000.0000.0000.0000.000
70A91ASP -1-0.891-0.92990.0620.0110.0110.0000.0000.0000.000
71A92TYR 0-0.054-0.04589.2420.0000.0000.0000.0000.0000.000
72A93THR 00.012-0.01495.1890.0000.0000.0000.0000.0000.000
73A94GLU -1-0.915-0.91091.5430.0110.0110.0000.0000.0000.000
74A95LEU 0-0.0040.00696.0890.0000.0000.0000.0000.0000.000
75A96ASP -1-0.764-0.85398.1510.0090.0090.0000.0000.0000.000
76A97PRO 00.0080.00299.5950.0000.0000.0000.0000.0000.000
77A98SER 0-0.049-0.050101.4950.0000.0000.0000.0000.0000.000
78A99GLN 0-0.067-0.034101.3010.0000.0000.0000.0000.0000.000
79A100THR 0-0.014-0.005102.3650.0000.0000.0000.0000.0000.000
80A101HIS 0-0.0080.015105.0050.0000.0000.0000.0000.0000.000
81A102TYR 00.019-0.003107.5930.0000.0000.0000.0000.0000.000
82A103PHE 0-0.016-0.006102.5520.0000.0000.0000.0000.0000.000
83A104ILE 00.0170.004102.3010.0000.0000.0000.0000.0000.000
84A105ILE 00.0150.03699.6070.0000.0000.0000.0000.0000.000
85A106ASN 00.007-0.00899.6550.0000.0000.0000.0000.0000.000
86A107ASN 00.1130.04796.7830.0000.0000.0000.0000.0000.000
87A108GLY 0-0.0200.00196.8850.0000.0000.0000.0000.0000.000
88A109ASN 0-0.123-0.06198.4530.0000.0000.0000.0000.0000.000
89A110ILE 00.0730.032101.1890.0000.0000.0000.0000.0000.000
90A111GLY 0-0.019-0.006102.4390.0000.0000.0000.0000.0000.000
91A112LEU 00.0120.007104.4060.0000.0000.0000.0000.0000.000
92A113ALA 00.0020.000105.2760.0000.0000.0000.0000.0000.000
93A114GLY 00.0240.009107.1700.0000.0000.0000.0000.0000.000
94A115ARG 10.8060.898108.024-0.007-0.0070.0000.0000.0000.000
95A116ILE 0-0.012-0.009104.8730.0000.0000.0000.0000.0000.000
96A117LEU 0-0.056-0.017109.4980.0000.0000.0000.0000.0000.000
97A118SER 00.0080.000111.4470.0000.0000.0000.0000.0000.000
98A119ILE 0-0.024-0.012105.6540.0000.0000.0000.0000.0000.000
99A120GLU -1-0.878-0.955108.8660.0070.0070.0000.0000.0000.000
100A121PRO 0-0.040-0.013107.7380.0000.0000.0000.0000.0000.000
101A122ILE 00.0070.002105.8120.0000.0000.0000.0000.0000.000
102A123ASP -1-0.885-0.951106.6900.0090.0090.0000.0000.0000.000
103A124ASN 0-0.016-0.00699.7010.0000.0000.0000.0000.0000.000
104A125GLY 0-0.0010.010102.0260.0000.0000.0000.0000.0000.000
105A126SER 0-0.021-0.035103.2260.0000.0000.0000.0000.0000.000
106A127VAL 0-0.024-0.014105.3180.0000.0000.0000.0000.0000.000
107A128ILE 0-0.0130.008103.3590.0000.0000.0000.0000.0000.000
108A129HIS 00.0440.033107.8170.0000.0000.0000.0000.0000.000
109A130LEU 0-0.026-0.022106.7230.0000.0000.0000.0000.0000.000
110A131ASP -1-0.765-0.865110.7280.0070.0070.0000.0000.0000.000
111A132LEU 0-0.014-0.020106.3770.0000.0000.0000.0000.0000.000
112A133VAL 00.0110.013109.7970.0000.0000.0000.0000.0000.000
113A134ASN 00.0260.011109.3950.0000.0000.0000.0000.0000.000
114A135LEU 0-0.041-0.030106.2230.0000.0000.0000.0000.0000.000
115A136LEU 0-0.031-0.008105.9680.0000.0000.0000.0000.0000.000
116A137SER 0-0.002-0.011110.1230.0000.0000.0000.0000.0000.000
117A138ILE 00.0080.008109.0790.0000.0000.0000.0000.0000.000
118A139PRO 00.0180.001111.6980.0000.0000.0000.0000.0000.000
119A140VAL 0-0.0190.008107.4270.0000.0000.0000.0000.0000.000
120A141SER 00.0460.014109.1310.0000.0000.0000.0000.0000.000
121A142ASN 0-0.024-0.015106.7690.0000.0000.0000.0000.0000.000
122A143LEU 00.0290.031103.6870.0000.0000.0000.0000.0000.000
123A144ALA 00.0610.041100.6310.0000.0000.0000.0000.0000.000
124A145PHE 0-0.018-0.010100.4650.0000.0000.0000.0000.0000.000
125A146ASN 0-0.0040.00594.8090.0000.0000.0000.0000.0000.000
126A147MET 00.0200.00297.2290.0000.0000.0000.0000.0000.000
127A148THR 0-0.036-0.02991.6410.0000.0000.0000.0000.0000.000
128A149TRP 0-0.012-0.00195.0290.0000.0000.0000.0000.0000.000
129A150GLY 00.0280.00694.4490.0000.0000.0000.0000.0000.000
130A151THR 00.0510.02292.3730.0000.0000.0000.0000.0000.000
131A152LYS 10.8650.92493.410-0.009-0.0090.0000.0000.0000.000
132A153LYS 10.9510.98187.004-0.011-0.0110.0000.0000.0000.000
133A154PRO 0-0.0080.01286.2070.0000.0000.0000.0000.0000.000
134A155SER 00.0260.00286.7300.0000.0000.0000.0000.0000.000
135A156GLU -1-0.930-0.95180.6290.0120.0120.0000.0000.0000.000
136A157ALA 00.025-0.00879.2480.0000.0000.0000.0000.0000.000
137A158LYS 10.9380.97078.137-0.013-0.0130.0000.0000.0000.000
138A159ASP -1-0.875-0.94879.4320.0120.0120.0000.0000.0000.000
139A160LEU 0-0.015-0.00981.6110.0000.0000.0000.0000.0000.000
140A161PRO 0-0.030-0.02378.8720.0000.0000.0000.0000.0000.000
141A162ARG 10.9910.98978.595-0.014-0.0140.0000.0000.0000.000
142A163TRP 00.0380.02683.8360.0000.0000.0000.0000.0000.000
143A164LYS 10.9390.96480.875-0.014-0.0140.0000.0000.0000.000
144A165GLN 0-0.038-0.01780.7550.0000.0000.0000.0000.0000.000
145A166LEU 0-0.019-0.00386.1290.0000.0000.0000.0000.0000.000
146A167LEU 0-0.095-0.02089.1280.0000.0000.0000.0000.0000.000
147A168LEU 00.0070.02091.2850.0000.0000.0000.0000.0000.000
148A169ASN 0-0.024-0.03092.4940.0000.0000.0000.0000.0000.000
149A170THR 0-0.021-0.00794.6610.0000.0000.0000.0000.0000.000
150A171LYS 10.9410.97995.277-0.011-0.0110.0000.0000.0000.000
151A172MET 0-0.045-0.01298.7950.0000.0000.0000.0000.0000.000
152A173ASP -1-0.858-0.928102.3350.0100.0100.0000.0000.0000.000
153A174SER 0-0.093-0.046104.2160.0000.0000.0000.0000.0000.000
154A175THR 00.016-0.004107.5400.0000.0000.0000.0000.0000.000
155A176ILE 0-0.027-0.016110.0330.0000.0000.0000.0000.0000.000
156A177GLU -1-0.899-0.940110.7790.0070.0070.0000.0000.0000.000
157A178LEU 0-0.057-0.027108.8070.0000.0000.0000.0000.0000.000
158A179LEU 00.0640.013112.7860.0000.0000.0000.0000.0000.000
159A180PRO 0-0.031-0.017113.7930.0000.0000.0000.0000.0000.000
160A181GLY 0-0.0100.007114.0540.0000.0000.0000.0000.0000.000
161A182ALA 0-0.029-0.012115.7780.0000.0000.0000.0000.0000.000
162A183TRP 0-0.040-0.029110.9110.0000.0000.0000.0000.0000.000
163A184THR 0-0.001-0.008113.2650.0000.0000.0000.0000.0000.000
164A185ASN 00.0120.006113.0210.0000.0000.0000.0000.0000.000
165A186VAL 0-0.0040.006107.9050.0000.0000.0000.0000.0000.000
166A187THR 00.0000.002109.3010.0000.0000.0000.0000.0000.000
167A188LEU 0-0.013-0.007103.2860.0000.0000.0000.0000.0000.000
168A189THR 0-0.004-0.023104.5050.0000.0000.0000.0000.0000.000
169A190LEU 0-0.0080.012100.4840.0000.0000.0000.0000.0000.000
170A191LYS 10.9150.942100.728-0.009-0.0090.0000.0000.0000.000
171A192GLY 00.007-0.01398.1880.0000.0000.0000.0000.0000.000
172A193VAL 00.0090.00597.0970.0000.0000.0000.0000.0000.000
173A194SER 00.0250.06099.8350.0000.0000.0000.0000.0000.000
174A195PRO 00.1440.053101.9770.0000.0000.0000.0000.0000.000
175A196ASN 0-0.028-0.011102.1810.0000.0000.0000.0000.0000.000
176A197ASN 0-0.085-0.05898.0690.0000.0000.0000.0000.0000.000
177A198LEU 0-0.024-0.00698.1680.0000.0000.0000.0000.0000.000
178A199LYS 10.9180.96196.995-0.009-0.0090.0000.0000.0000.000
179A200TYR 0-0.140-0.12391.7920.0000.0000.0000.0000.0000.000
180A201LEU 00.0480.02196.4590.0000.0000.0000.0000.0000.000
181A202LYS 10.9090.97789.475-0.011-0.0110.0000.0000.0000.000
182A203ILE 00.010-0.00395.9870.0000.0000.0000.0000.0000.000
183A204GLY 00.0420.00896.4260.0000.0000.0000.0000.0000.000
184A205ILE 0-0.026-0.00597.4760.0000.0000.0000.0000.0000.000
185A206ASP -1-0.889-0.95396.7060.0110.0110.0000.0000.0000.000
186A207MET 0-0.001-0.01597.9080.0000.0000.0000.0000.0000.000
187A208GLU -1-0.941-0.93796.5810.0110.0110.0000.0000.0000.000
188A209ASN 0-0.035-0.02899.3920.0000.0000.0000.0000.0000.000
189A210VAL 00.0110.013102.7210.0000.0000.0000.0000.0000.000
190A211ILE 0-0.042-0.015104.7010.0000.0000.0000.0000.0000.000
191A212PHE 0-0.035-0.034104.0540.0000.0000.0000.0000.0000.000
192A213ASP -1-0.894-0.947109.3900.0070.0070.0000.0000.0000.000
193A214NME 0-0.0320.000113.0960.0000.0000.0000.0000.0000.000