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: KGRL3

Calculation Name: 4ECB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ECB

Chain ID: A

ChEMBL ID:

UniProt ID: P08515

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2472102.061286
FMO2-HF: Nuclear repulsion 2388806.419686
FMO2-HF: Total energy -83295.6416
FMO2-MP2: Total energy -83534.747201


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-24.529-17.3472.996-4.448-5.729-0.026
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.037
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].
3A4ILE0-0.0110.0133.513-2.298-0.8170.017-0.648-0.8500.001
4A5LEU0-0.010-0.0086.0481.1201.1200.0000.0000.0000.000
5A6GLY00.0170.0169.115-0.045-0.0450.0000.0000.0000.000
6A7TYR00.016-0.01312.0270.2290.2290.0000.0000.0000.000
7A8TRP00.0640.03215.330-0.077-0.0770.0000.0000.0000.000
8A9LYS10.8050.91216.7990.5620.5620.0000.0000.0000.000
9A10ILE0-0.018-0.00818.0070.0540.0540.0000.0000.0000.000
10A11LYS10.8510.94018.2660.1220.1220.0000.0000.0000.000
11A12GLY0-0.020-0.01219.007-0.028-0.0280.0000.0000.0000.000
12A13LEU0-0.022-0.04119.6790.0270.0270.0000.0000.0000.000
13A14VAL00.0050.00913.9070.0260.0260.0000.0000.0000.000
14A15GLN00.0720.06615.541-0.053-0.0530.0000.0000.0000.000
15A16PRO00.0200.00216.6950.0290.0290.0000.0000.0000.000
16A17THR00.008-0.00512.2270.0830.0830.0000.0000.0000.000
17A18ARG10.8240.89711.5750.5890.5890.0000.0000.0000.000
18A19LEU0-0.028-0.00412.9370.0890.0890.0000.0000.0000.000
19A20LEU00.0050.00314.2020.0730.0730.0000.0000.0000.000
20A21LEU00.003-0.0088.1070.1050.1050.0000.0000.0000.000
21A22GLU-1-0.764-0.85310.9120.2930.2930.0000.0000.0000.000
22A23TYR0-0.029-0.01812.4790.0930.0930.0000.0000.0000.000
23A24LEU0-0.033-0.02512.2150.0300.0300.0000.0000.0000.000
24A25GLU-1-0.922-0.95411.1970.7630.7630.0000.0000.0000.000
25A26GLU-1-0.850-0.9077.3281.6721.6720.0000.0000.0000.000
26A27LYS10.9160.9562.580-6.905-4.9580.586-0.967-1.5650.008
27A28TYR0-0.081-0.0672.773-0.5850.0770.176-0.286-0.552-0.002
28A29GLU-1-0.942-0.9682.412-17.195-14.1062.218-2.546-2.761-0.033
29A30GLU-1-0.823-0.9184.953-0.757-0.754-0.001-0.001-0.0010.000
30A31HIS0-0.056-0.0227.6850.2970.2970.0000.0000.0000.000
31A32LEU00.0180.00110.8170.1870.1870.0000.0000.0000.000
32A33TYR00.0230.01913.6470.0660.0660.0000.0000.0000.000
33A34GLU-1-0.777-0.90517.240-0.513-0.5130.0000.0000.0000.000
34A35ARG10.8670.92020.2720.2810.2810.0000.0000.0000.000
35A36ASP-1-0.981-0.97922.617-0.362-0.3620.0000.0000.0000.000
36A60LEU0-0.030-0.03115.1040.0180.0180.0000.0000.0000.000
37A61GLU-1-0.922-0.96917.514-0.451-0.4510.0000.0000.0000.000
38A62PHE0-0.056-0.00620.6000.0230.0230.0000.0000.0000.000
39A63PRO0-0.0100.00916.3880.0060.0060.0000.0000.0000.000
40A64ASN0-0.007-0.02718.5750.0370.0370.0000.0000.0000.000
41A65LEU0-0.0020.03315.737-0.063-0.0630.0000.0000.0000.000
42A66PRO0-0.034-0.02214.6950.0780.0780.0000.0000.0000.000
43A67TYR0-0.003-0.03010.5660.0610.0610.0000.0000.0000.000
44A68TYR0-0.042-0.0257.484-0.308-0.3080.0000.0000.0000.000
45A69ILE0-0.0110.0056.8240.4650.4650.0000.0000.0000.000
46A70ASP-1-0.702-0.8265.536-0.684-0.6840.0000.0000.0000.000
47A71GLY0-0.009-0.0026.478-0.049-0.0490.0000.0000.0000.000
48A72ASP-1-0.872-0.9587.6330.5710.5710.0000.0000.0000.000
49A73VAL0-0.0120.01610.585-0.214-0.2140.0000.0000.0000.000
50A74LYS10.8450.9129.1460.1490.1490.0000.0000.0000.000
51A75LEU0-0.049-0.01712.6130.1120.1120.0000.0000.0000.000
52A76THR00.0490.01514.438-0.110-0.1100.0000.0000.0000.000
53A77GLN00.0290.01217.1630.0710.0710.0000.0000.0000.000
54A78SER00.0460.01217.2280.0040.0040.0000.0000.0000.000
55A79MET00.0370.02217.7110.0090.0090.0000.0000.0000.000
56A80ALA00.0110.00518.2920.0420.0420.0000.0000.0000.000
57A81ILE0-0.026-0.00412.5090.0460.0460.0000.0000.0000.000
58A82ILE00.0070.00914.1250.0500.0500.0000.0000.0000.000
59A83ARG10.8930.92815.9590.0370.0370.0000.0000.0000.000
60A84TYR0-0.010-0.0109.5760.0910.0910.0000.0000.0000.000
61A85ILE00.0270.01410.4170.1050.1050.0000.0000.0000.000
62A86ALA00.0250.00812.8570.1260.1260.0000.0000.0000.000
63A87ASP-1-0.931-0.97016.1710.2950.2950.0000.0000.0000.000
64A88LYS10.8760.9509.991-0.833-0.8330.0000.0000.0000.000
65A89HIS10.7520.86710.396-0.724-0.7240.0000.0000.0000.000
66A90ASN0-0.054-0.02115.439-0.047-0.0470.0000.0000.0000.000
67A91MET0-0.0140.00117.451-0.021-0.0210.0000.0000.0000.000
68A92LEU0-0.0210.00019.381-0.039-0.0390.0000.0000.0000.000
69A93GLY00.0470.02021.921-0.029-0.0290.0000.0000.0000.000
70A94GLY00.0120.00624.9950.0090.0090.0000.0000.0000.000
71A95CYS0-0.074-0.02326.805-0.006-0.0060.0000.0000.0000.000
72A96PRO00.0450.00329.072-0.003-0.0030.0000.0000.0000.000
73A97LYS10.9930.99730.709-0.082-0.0820.0000.0000.0000.000
74A98GLU-1-0.830-0.92827.5320.1540.1540.0000.0000.0000.000
75A99ARG10.9110.95724.700-0.160-0.1600.0000.0000.0000.000
76A100ALA0-0.0090.00227.326-0.011-0.0110.0000.0000.0000.000
77A101GLU-1-0.880-0.91630.0880.0510.0510.0000.0000.0000.000
78A102ILE00.0290.01423.753-0.011-0.0110.0000.0000.0000.000
79A103SER0-0.030-0.03725.852-0.007-0.0070.0000.0000.0000.000
80A104MET0-0.043-0.00427.340-0.017-0.0170.0000.0000.0000.000
81A105LEU0-0.010-0.00727.773-0.010-0.0100.0000.0000.0000.000
82A106GLU-1-0.766-0.86023.086-0.008-0.0080.0000.0000.0000.000
83A107GLY0-0.010-0.00326.367-0.017-0.0170.0000.0000.0000.000
84A108ALA00.0450.02029.114-0.009-0.0090.0000.0000.0000.000
85A109VAL0-0.033-0.01825.583-0.006-0.0060.0000.0000.0000.000
86A110LEU0-0.041-0.03123.917-0.015-0.0150.0000.0000.0000.000
87A111ASP-1-0.879-0.92727.826-0.063-0.0630.0000.0000.0000.000
88A112ILE0-0.0010.00230.102-0.006-0.0060.0000.0000.0000.000
89A113ARG10.8290.90723.2970.1640.1640.0000.0000.0000.000
90A114TYR0-0.015-0.03724.238-0.012-0.0120.0000.0000.0000.000
91A115GLY00.0040.01729.213-0.005-0.0050.0000.0000.0000.000
92A116VAL00.0080.00529.578-0.003-0.0030.0000.0000.0000.000
93A117SER0-0.029-0.02627.377-0.013-0.0130.0000.0000.0000.000
94A118ARG10.9000.95929.7200.0880.0880.0000.0000.0000.000
95A119ILE00.0080.00332.7280.0000.0000.0000.0000.0000.000
96A120ALA00.0010.01830.8250.0010.0010.0000.0000.0000.000
97A121TYR00.009-0.00126.651-0.012-0.0120.0000.0000.0000.000
98A122SER00.0060.02533.4510.0010.0010.0000.0000.0000.000
99A123LYS10.9950.98737.2720.1090.1090.0000.0000.0000.000
100A124ASP-1-0.914-0.95739.989-0.092-0.0920.0000.0000.0000.000
101A125PHE00.0230.00935.1660.0050.0050.0000.0000.0000.000
102A126GLU-1-0.805-0.90038.911-0.082-0.0820.0000.0000.0000.000
103A127THR00.0110.00941.4440.0060.0060.0000.0000.0000.000
104A128LEU0-0.017-0.01438.8150.0050.0050.0000.0000.0000.000
105A129LYS10.8560.91237.9640.0840.0840.0000.0000.0000.000
106A130VAL0-0.0140.00739.3780.0050.0050.0000.0000.0000.000
107A131ASP-1-0.858-0.91141.549-0.051-0.0510.0000.0000.0000.000
108A132PHE0-0.011-0.01833.1300.0030.0030.0000.0000.0000.000
109A133LEU00.015-0.01936.9500.0040.0040.0000.0000.0000.000
110A134SER0-0.046-0.01039.6230.0060.0060.0000.0000.0000.000
111A135LYS10.8690.92339.6310.0530.0530.0000.0000.0000.000
112A136LEU0-0.0050.01134.0040.0040.0040.0000.0000.0000.000
113A137PRO00.0280.01337.4420.0050.0050.0000.0000.0000.000
114A138GLU-1-0.880-0.95139.474-0.020-0.0200.0000.0000.0000.000
115A139MET0-0.076-0.02834.0670.0030.0030.0000.0000.0000.000
116A140LEU0-0.003-0.00233.3250.0050.0050.0000.0000.0000.000
117A141LYS10.8910.92435.736-0.004-0.0040.0000.0000.0000.000
118A142MET0-0.0230.00932.4520.0100.0100.0000.0000.0000.000
119A143PHE00.038-0.00729.7790.0090.0090.0000.0000.0000.000
120A144GLU-1-0.739-0.87134.0010.0260.0260.0000.0000.0000.000
121A145ASP-1-0.846-0.90736.4470.0240.0240.0000.0000.0000.000
122A146ARG10.7550.85231.437-0.052-0.0520.0000.0000.0000.000
123A147LEU0-0.001-0.00930.4420.0080.0080.0000.0000.0000.000
124A148CYS0-0.105-0.03134.5630.0030.0030.0000.0000.0000.000
125A149HIS0-0.033-0.01237.0560.0080.0080.0000.0000.0000.000
126A150LYS10.9180.97632.194-0.076-0.0760.0000.0000.0000.000
127A151THR00.0080.02029.343-0.010-0.0100.0000.0000.0000.000
128A152TYR00.0170.00225.673-0.012-0.0120.0000.0000.0000.000
129A153LEU00.014-0.00126.748-0.002-0.0020.0000.0000.0000.000
130A154ASN0-0.005-0.00427.120-0.019-0.0190.0000.0000.0000.000
131A155GLY0-0.044-0.01629.0200.0070.0070.0000.0000.0000.000
132A156ASP-1-0.890-0.95329.3650.1360.1360.0000.0000.0000.000
133A157HIS0-0.027-0.01224.1020.0140.0140.0000.0000.0000.000
134A158VAL0-0.029-0.00621.027-0.017-0.0170.0000.0000.0000.000
135A159THR0-0.033-0.02121.5230.0190.0190.0000.0000.0000.000
136A160HIS00.041-0.01318.7250.0110.0110.0000.0000.0000.000
137A161PRO00.024-0.00320.277-0.028-0.0280.0000.0000.0000.000
138A162ASP-1-0.730-0.85122.8580.0780.0780.0000.0000.0000.000
139A163PHE00.0450.01018.406-0.012-0.0120.0000.0000.0000.000
140A164MET0-0.038-0.00421.141-0.024-0.0240.0000.0000.0000.000
141A165LEU00.0050.00922.622-0.016-0.0160.0000.0000.0000.000
142A166TYR0-0.073-0.06522.074-0.011-0.0110.0000.0000.0000.000
143A167ASP-1-0.828-0.91921.505-0.169-0.1690.0000.0000.0000.000
144A168ALA0-0.011-0.01123.577-0.011-0.0110.0000.0000.0000.000
145A169LEU0-0.011-0.01126.914-0.002-0.0020.0000.0000.0000.000
146A170ASP-1-0.827-0.91625.101-0.095-0.0950.0000.0000.0000.000
147A171VAL0-0.027-0.01325.493-0.008-0.0080.0000.0000.0000.000
148A172VAL00.004-0.01328.164-0.002-0.0020.0000.0000.0000.000
149A173LEU0-0.0040.00330.2490.0030.0030.0000.0000.0000.000
150A174TYR0-0.021-0.01426.899-0.003-0.0030.0000.0000.0000.000
151A175MET0-0.100-0.03632.228-0.001-0.0010.0000.0000.0000.000
152A176ASP-1-0.824-0.92734.652-0.044-0.0440.0000.0000.0000.000
153A177PRO0-0.041-0.00735.3970.0060.0060.0000.0000.0000.000
154A178MET00.0160.01636.4570.0040.0040.0000.0000.0000.000
155A179CYS0-0.077-0.01435.0930.0060.0060.0000.0000.0000.000
156A180LEU0-0.017-0.03332.1720.0050.0050.0000.0000.0000.000
157A181ASP-1-0.892-0.93836.917-0.013-0.0130.0000.0000.0000.000
158A182ALA0-0.080-0.04240.1640.0050.0050.0000.0000.0000.000
159A183PHE0-0.046-0.02036.8150.0040.0040.0000.0000.0000.000
160A184PRO00.0610.02736.6180.0010.0010.0000.0000.0000.000
161A185LYS10.8810.91835.355-0.036-0.0360.0000.0000.0000.000
162A186LEU00.0220.01631.6710.0060.0060.0000.0000.0000.000
163A187VAL0-0.016-0.00331.7580.0010.0010.0000.0000.0000.000
164A188CYS0-0.103-0.06132.1680.0040.0040.0000.0000.0000.000
165A189PHE0-0.037-0.01925.7940.0100.0100.0000.0000.0000.000
166A190LYS10.8510.92626.6480.0440.0440.0000.0000.0000.000
167A191LYS10.9690.98726.955-0.013-0.0130.0000.0000.0000.000
168A192ARG10.8820.94827.197-0.072-0.0720.0000.0000.0000.000
169A193ILE00.0100.00422.0340.0190.0190.0000.0000.0000.000
170A194GLU-1-0.829-0.89322.7920.0110.0110.0000.0000.0000.000
171A195ALA0-0.015-0.00223.7800.0060.0060.0000.0000.0000.000
172A196ILE0-0.0330.00319.8160.0230.0230.0000.0000.0000.000
173A197PRO00.0280.01720.462-0.009-0.0090.0000.0000.0000.000
174A198GLN0-0.022-0.02515.562-0.064-0.0640.0000.0000.0000.000
175A199ILE0-0.0070.00016.810-0.024-0.0240.0000.0000.0000.000
176A200ASP-1-0.784-0.86618.7350.0560.0560.0000.0000.0000.000
177A201LYS10.8730.93414.526-0.484-0.4840.0000.0000.0000.000
178A202TYR00.005-0.00613.457-0.026-0.0260.0000.0000.0000.000
179A203LEU0-0.0010.01016.558-0.059-0.0590.0000.0000.0000.000
180A204LYS10.7910.88919.723-0.092-0.0920.0000.0000.0000.000
181A205SER0-0.088-0.04315.599-0.019-0.0190.0000.0000.0000.000
182A206SER0-0.002-0.01715.801-0.010-0.0100.0000.0000.0000.000
183A207LYS10.8230.88710.313-0.067-0.0670.0000.0000.0000.000
184A208TYR0-0.0050.02514.321-0.063-0.0630.0000.0000.0000.000
185A209ILE00.0100.01415.352-0.013-0.0130.0000.0000.0000.000
186A210ALA00.009-0.00218.7090.0210.0210.0000.0000.0000.000
187A211TRP0-0.034-0.00622.2690.0300.0300.0000.0000.0000.000
188A212PRO0-0.0040.00722.590-0.023-0.0230.0000.0000.0000.000
189A213LEU0-0.003-0.01223.003-0.019-0.0190.0000.0000.0000.000
190A214GLN0-0.020-0.00224.020-0.005-0.0050.0000.0000.0000.000
191A215GLY00.0570.02424.654-0.021-0.0210.0000.0000.0000.000
192A216TRP00.0480.00720.6560.0260.0260.0000.0000.0000.000
193A217GLN00.0100.00627.3530.0080.0080.0000.0000.0000.000
194A218ALA0-0.065-0.01929.3640.0140.0140.0000.0000.0000.000
195A219THR0-0.037-0.02831.191-0.002-0.0020.0000.0000.0000.000
196A220PHE0-0.013-0.00130.4020.0050.0050.0000.0000.0000.000
197A221GLY00.0440.00829.036-0.008-0.0080.0000.0000.0000.000
198A222GLY00.0110.02427.551-0.021-0.0210.0000.0000.0000.000
199A223GLY0-0.001-0.01929.1730.0110.0110.0000.0000.0000.000
200A224ASP-1-0.847-0.92427.242-0.273-0.2730.0000.0000.0000.000
201A225HIS0-0.0250.00227.0580.0030.0030.0000.0000.0000.000