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: ZYZ6N

Calculation Name: 3C38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KLK7

Base Structure: X-ray

Registration Date: 2023-03-14

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2517082.67505
FMO2-HF: Nuclear repulsion 2432599.044329
FMO2-HF: Total energy -84483.630721
FMO2-MP2: Total energy -84734.177214


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:52:THR)


Summations of interaction energy for fragment #1(A:52:THR)
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.
-6.945-7.46314.732-5.336-8.8770.022
Interaction energy analysis for fragmet #1(A:52:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.005
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].
3A54VAL00.0380.0043.392-2.293-0.1800.138-0.853-1.3970.003
4A55GLN0-0.040-0.0242.066-4.792-8.70614.565-4.074-6.5770.019
5A56THR00.0240.0253.377-1.768-0.6250.030-0.398-0.7750.000
6A57SER00.017-0.0425.159-0.207-0.067-0.001-0.011-0.1280.000
7A58SER0-0.037-0.0156.917-0.225-0.2250.0000.0000.0000.000
8A59LEU00.0130.0207.476-0.078-0.0780.0000.0000.0000.000
9A60ILE00.0120.0059.016-0.007-0.0070.0000.0000.0000.000
10A61GLN00.0040.00811.0150.0110.0110.0000.0000.0000.000
11A62SER0-0.031-0.01312.008-0.055-0.0550.0000.0000.0000.000
12A63LEU0-0.015-0.00811.954-0.013-0.0130.0000.0000.0000.000
13A64PHE0-0.022-0.01314.951-0.005-0.0050.0000.0000.0000.000
14A65ASP-1-0.837-0.92816.6960.0470.0470.0000.0000.0000.000
15A66PHE0-0.072-0.03317.630-0.015-0.0150.0000.0000.0000.000
16A67ARG10.9710.99219.384-0.077-0.0770.0000.0000.0000.000
17A68LEU00.0360.01021.325-0.006-0.0060.0000.0000.0000.000
18A69ALA0-0.045-0.02222.338-0.008-0.0080.0000.0000.0000.000
19A70ALA00.0180.01223.717-0.006-0.0060.0000.0000.0000.000
20A71LEU00.0220.01325.675-0.002-0.0020.0000.0000.0000.000
21A72ARG10.9360.98024.4810.0020.0020.0000.0000.0000.000
22A73ILE0-0.058-0.02826.279-0.004-0.0040.0000.0000.0000.000
23A74HIS00.0370.02429.275-0.004-0.0040.0000.0000.0000.000
24A75GLN0-0.0040.01531.4710.0000.0000.0000.0000.0000.000
25A76ASP-1-0.801-0.91232.1190.0050.0050.0000.0000.0000.000
26A77SER0-0.081-0.02634.067-0.003-0.0030.0000.0000.0000.000
27A78THR00.000-0.00935.747-0.001-0.0010.0000.0000.0000.000
28A79ALA0-0.038-0.00937.2150.0000.0000.0000.0000.0000.000
29A80LYS10.9180.95337.5600.0090.0090.0000.0000.0000.000
30A81ASN00.0460.03740.907-0.002-0.0020.0000.0000.0000.000
31A82ALA00.0630.02142.5650.0020.0020.0000.0000.0000.000
32A83SER0-0.017-0.00244.9220.0010.0010.0000.0000.0000.000
33A84LEU00.0000.02440.7980.0010.0010.0000.0000.0000.000
34A85ILE00.0240.00543.9760.0010.0010.0000.0000.0000.000
35A86ASN00.005-0.02746.6620.0020.0020.0000.0000.0000.000
36A87ALA00.037-0.00647.2690.0010.0010.0000.0000.0000.000
37A88LEU00.0070.00245.3230.0010.0010.0000.0000.0000.000
38A89VAL00.0060.02048.5450.0010.0010.0000.0000.0000.000
39A90SER0-0.075-0.03251.4640.0000.0000.0000.0000.0000.000
40A91ARG10.8500.90950.259-0.015-0.0150.0000.0000.0000.000
41A92ASP-1-0.863-0.90552.1500.0170.0170.0000.0000.0000.000
42A93SER0-0.019-0.02649.1650.0000.0000.0000.0000.0000.000
43A94SER00.0560.01248.3230.0010.0010.0000.0000.0000.000
44A95ARG10.8450.95449.502-0.011-0.0110.0000.0000.0000.000
45A96LEU0-0.079-0.03445.028-0.001-0.0010.0000.0000.0000.000
46A97ASP-1-0.816-0.89944.4570.0280.0280.0000.0000.0000.000
47A98GLU-1-0.923-0.95644.0140.0150.0150.0000.0000.0000.000
48A99PHE0-0.005-0.00940.782-0.001-0.0010.0000.0000.0000.000
49A100PHE00.013-0.01838.508-0.001-0.0010.0000.0000.0000.000
50A101SER00.0380.03339.2270.0020.0020.0000.0000.0000.000
51A102SER0-0.003-0.00540.2970.0000.0000.0000.0000.0000.000
52A103VAL0-0.074-0.03335.945-0.002-0.0020.0000.0000.0000.000
53A104ASP-1-0.752-0.85635.3270.0310.0310.0000.0000.0000.000
54A105GLU-1-1.001-0.98035.8860.0150.0150.0000.0000.0000.000
55A106LEU0-0.035-0.02435.365-0.001-0.0010.0000.0000.0000.000
56A107GLU-1-0.918-0.97830.9960.0050.0050.0000.0000.0000.000
57A108LEU0-0.021-0.00831.7830.0040.0040.0000.0000.0000.000
58A109SER0-0.036-0.00527.8600.0050.0050.0000.0000.0000.000
59A110ASN0-0.115-0.06226.6490.0120.0120.0000.0000.0000.000
60A111ALA00.0330.02528.575-0.003-0.0030.0000.0000.0000.000
61A112PRO0-0.083-0.05029.7470.0060.0060.0000.0000.0000.000
62A113ASP-1-0.787-0.88428.9410.0870.0870.0000.0000.0000.000
63A114LEU0-0.051-0.02931.924-0.001-0.0010.0000.0000.0000.000
64A115ARG10.7950.86734.324-0.033-0.0330.0000.0000.0000.000
65A116PHE00.0470.02836.8920.0000.0000.0000.0000.0000.000
66A117ILE0-0.013-0.01239.533-0.001-0.0010.0000.0000.0000.000
67A118SER0-0.0210.00441.6090.0000.0000.0000.0000.0000.000
68A119SER00.032-0.00443.530-0.003-0.0030.0000.0000.0000.000
69A120HIS0-0.0020.00045.4150.0010.0010.0000.0000.0000.000
70A121ASP-1-0.836-0.88945.2490.0310.0310.0000.0000.0000.000
71A122ASN0-0.022-0.00546.3240.0020.0020.0000.0000.0000.000
72A123ILE00.0280.00342.6430.0000.0000.0000.0000.0000.000
73A124LEU0-0.111-0.05046.037-0.001-0.0010.0000.0000.0000.000
74A125TRP0-0.011-0.02540.144-0.001-0.0010.0000.0000.0000.000
75A126ASP-1-0.800-0.91441.1910.0450.0450.0000.0000.0000.000
76A127ASP-1-0.804-0.89137.5260.0450.0450.0000.0000.0000.000
77A128GLY0-0.0090.00041.2070.0000.0000.0000.0000.0000.000
78A129ASN0-0.006-0.01836.4260.0030.0030.0000.0000.0000.000
79A130ALA0-0.013-0.01337.1640.0050.0050.0000.0000.0000.000
80A131SER0-0.010-0.00738.2320.0040.0040.0000.0000.0000.000
81A132PHE00.0140.02833.7440.0020.0020.0000.0000.0000.000
82A133TYR0-0.006-0.00331.1260.0030.0030.0000.0000.0000.000
83A134GLY00.0550.03036.1110.0040.0040.0000.0000.0000.000
84A135ILE0-0.074-0.03134.5380.0010.0010.0000.0000.0000.000
85A136ALA00.002-0.00238.848-0.004-0.0040.0000.0000.0000.000
86A137GLN00.0500.02141.950-0.001-0.0010.0000.0000.0000.000
87A138GLN00.012-0.01543.632-0.002-0.0020.0000.0000.0000.000
88A139GLU-1-0.879-0.95639.1770.0590.0590.0000.0000.0000.000
89A140LEU00.0480.02837.9030.0020.0020.0000.0000.0000.000
90A141ASN0-0.002-0.01440.170-0.003-0.0030.0000.0000.0000.000
91A142LYS10.8400.92639.964-0.055-0.0550.0000.0000.0000.000
92A143LEU00.013-0.00334.9180.0010.0010.0000.0000.0000.000
93A144ILE0-0.0150.01937.184-0.001-0.0010.0000.0000.0000.000
94A145ARG10.7830.85638.940-0.033-0.0330.0000.0000.0000.000
95A146ARG10.8260.90534.511-0.070-0.0700.0000.0000.0000.000
96A147VAL00.0010.02332.8100.0010.0010.0000.0000.0000.000
97A148ALA0-0.0020.00634.748-0.004-0.0040.0000.0000.0000.000
98A149ILE0-0.017-0.01631.078-0.004-0.0040.0000.0000.0000.000
99A150SER0-0.021-0.02034.1330.0040.0040.0000.0000.0000.000
100A151GLY0-0.028-0.01731.694-0.002-0.0020.0000.0000.0000.000
101A152ASN0-0.0090.00527.853-0.008-0.0080.0000.0000.0000.000
102A153TRP0-0.043-0.04325.4670.0050.0050.0000.0000.0000.000
103A154HIS0-0.024-0.01627.2620.0060.0060.0000.0000.0000.000
104A155LEU0-0.0070.01323.4800.0010.0010.0000.0000.0000.000
105A156VAL0-0.030-0.01127.171-0.003-0.0030.0000.0000.0000.000
106A157GLN00.0760.02729.2860.0040.0040.0000.0000.0000.000
107A158THR0-0.0020.00331.804-0.009-0.0090.0000.0000.0000.000
108A159PRO0-0.052-0.01834.7780.0060.0060.0000.0000.0000.000
109A160SER00.0380.02235.698-0.004-0.0040.0000.0000.0000.000
110A161GLU-1-0.981-0.97737.6890.0720.0720.0000.0000.0000.000
111A162GLY00.023-0.01437.1240.0010.0010.0000.0000.0000.000
112A163LYS10.9060.97428.550-0.146-0.1460.0000.0000.0000.000
113A164SER0-0.020-0.01131.240-0.003-0.0030.0000.0000.0000.000
114A165VAL00.0060.00430.8130.0100.0100.0000.0000.0000.000
115A166HIS00.0410.03026.707-0.006-0.0060.0000.0000.0000.000
116A167ILE00.002-0.01028.1870.0010.0010.0000.0000.0000.000
117A168LEU00.0100.03422.8960.0000.0000.0000.0000.0000.000
118A169MET0-0.010-0.01627.464-0.006-0.0060.0000.0000.0000.000
119A170ARG10.8500.92328.634-0.021-0.0210.0000.0000.0000.000
120A171ARG10.9150.98231.599-0.025-0.0250.0000.0000.0000.000
121A172SER0-0.019-0.02934.660-0.004-0.0040.0000.0000.0000.000
122A173SER0-0.020-0.03936.5350.0020.0020.0000.0000.0000.000
123A174LEU00.0390.04640.075-0.002-0.0020.0000.0000.0000.000
124A175ILE0-0.065-0.01342.3730.0000.0000.0000.0000.0000.000
125A176GLU-1-0.895-0.95045.0390.0030.0030.0000.0000.0000.000
126A177ALA0-0.004-0.01148.071-0.001-0.0010.0000.0000.0000.000
127A178GLY00.0740.05848.6550.0000.0000.0000.0000.0000.000
128A179THR0-0.070-0.09749.7890.0000.0000.0000.0000.0000.000
129A180GLY00.0290.03351.4640.0000.0000.0000.0000.0000.000
130A181GLN0-0.051-0.02645.953-0.002-0.0020.0000.0000.0000.000
131A182VAL0-0.060-0.03543.9620.0000.0000.0000.0000.0000.000
132A183VAL00.0190.02146.3880.0010.0010.0000.0000.0000.000
133A184GLY0-0.003-0.00544.9430.0020.0020.0000.0000.0000.000
134A185TYR0-0.056-0.01839.301-0.002-0.0020.0000.0000.0000.000
135A186LEU00.0530.04036.8420.0020.0020.0000.0000.0000.000
136A187TYR0-0.028-0.03035.684-0.002-0.0020.0000.0000.0000.000
137A188VAL00.0120.00830.851-0.001-0.0010.0000.0000.0000.000
138A189GLY00.000-0.01530.5720.0010.0010.0000.0000.0000.000
139A190ILE0-0.0080.01224.899-0.002-0.0020.0000.0000.0000.000
140A191VAL0-0.040-0.02427.8480.0060.0060.0000.0000.0000.000
141A192LEU00.024-0.00522.7910.0060.0060.0000.0000.0000.000
142A193ASN0-0.035-0.01925.1340.0130.0130.0000.0000.0000.000
143A194ASP-1-0.875-0.94226.5260.1310.1310.0000.0000.0000.000
144A195ASN0-0.0130.01024.314-0.003-0.0030.0000.0000.0000.000
145A196PHE0-0.004-0.02322.5410.0120.0120.0000.0000.0000.000
146A197ALA00.0230.01122.2280.0110.0110.0000.0000.0000.000
147A198LEU00.0090.00720.169-0.002-0.0020.0000.0000.0000.000
148A199LEU00.009-0.00216.7960.0060.0060.0000.0000.0000.000
149A200GLU-1-0.770-0.85817.2840.2350.2350.0000.0000.0000.000
150A201ASN0-0.062-0.02717.7610.0070.0070.0000.0000.0000.000
151A202ILE00.0460.02613.315-0.012-0.0120.0000.0000.0000.000
152A203ARG10.7940.87613.361-0.263-0.2630.0000.0000.0000.000
153A204SER0-0.045-0.02513.2180.0150.0150.0000.0000.0000.000
154A205GLY00.0240.02813.952-0.010-0.0100.0000.0000.0000.000
155A206SER0-0.055-0.0449.075-0.023-0.0230.0000.0000.0000.000
156A207ASN0-0.117-0.0639.2000.0850.0850.0000.0000.0000.000
157A208SER00.0070.0039.9970.1650.1650.0000.0000.0000.000
158A209GLU-1-0.854-0.94011.1160.5630.5630.0000.0000.0000.000
159A210ASN0-0.045-0.04013.403-0.134-0.1340.0000.0000.0000.000
160A211LEU0-0.0040.00911.7150.0970.0970.0000.0000.0000.000
161A212VAL00.0030.00615.366-0.056-0.0560.0000.0000.0000.000
162A213LEU0-0.0040.02217.2120.0320.0320.0000.0000.0000.000
163A214ALA00.018-0.00119.201-0.027-0.0270.0000.0000.0000.000
164A215VAL0-0.0070.00320.8800.0060.0060.0000.0000.0000.000
165A216ASP-1-0.943-0.97422.1120.1940.1940.0000.0000.0000.000
166A217THR00.0660.03721.6930.0280.0280.0000.0000.0000.000
167A218THR0-0.063-0.03023.795-0.006-0.0060.0000.0000.0000.000
168A219PRO0-0.016-0.01122.8890.0050.0050.0000.0000.0000.000
169A220LEU0-0.100-0.05022.997-0.023-0.0230.0000.0000.0000.000
170A221VAL00.0590.02621.199-0.015-0.0150.0000.0000.0000.000
171A222SER00.0160.00420.2720.0370.0370.0000.0000.0000.000
172A223THR00.0430.02217.894-0.011-0.0110.0000.0000.0000.000
173A224LEU0-0.098-0.04218.324-0.005-0.0050.0000.0000.0000.000
174A225LYS10.8610.93119.482-0.290-0.2900.0000.0000.0000.000
175A226GLY0-0.015-0.01323.644-0.020-0.0200.0000.0000.0000.000
176A227ASN0-0.060-0.03024.069-0.002-0.0020.0000.0000.0000.000
177A228GLU-1-0.758-0.86019.5370.2790.2790.0000.0000.0000.000
178A229PRO0-0.037-0.02319.857-0.015-0.0150.0000.0000.0000.000
179A230TYR00.0130.03216.334-0.012-0.0120.0000.0000.0000.000
180A231SER00.0470.01920.755-0.001-0.0010.0000.0000.0000.000
181A232LEU00.0490.00821.0630.0240.0240.0000.0000.0000.000
182A233ASP-1-0.918-0.96021.3760.2470.2470.0000.0000.0000.000
183A234TYR00.0090.00515.464-0.008-0.0080.0000.0000.0000.000
184A235VAL00.0250.00315.9460.0250.0250.0000.0000.0000.000
185A236VAL0-0.0170.02217.3490.0350.0350.0000.0000.0000.000
186A237HIS0-0.078-0.02819.512-0.009-0.0090.0000.0000.0000.000
187A238SER0-0.049-0.04315.8030.0130.0130.0000.0000.0000.000
188A239ALA0-0.041-0.02015.686-0.006-0.0060.0000.0000.0000.000
189A240LYS10.9320.9518.478-1.083-1.0830.0000.0000.0000.000
190A241ASP-1-0.893-0.9416.6411.9911.9910.0000.0000.0000.000
191A242ALA0-0.0160.0118.969-0.053-0.0530.0000.0000.0000.000
192A243MET00.013-0.0176.241-0.119-0.1190.0000.0000.0000.000
193A244ARG10.7610.8509.777-0.486-0.4860.0000.0000.0000.000
194A245ASP-1-0.809-0.86513.2280.4140.4140.0000.0000.0000.000
195A246SER0-0.035-0.01913.3300.0400.0400.0000.0000.0000.000
196A247PHE00.014-0.00813.3040.0310.0310.0000.0000.0000.000
197A248ILE0-0.0040.0247.244-0.048-0.0480.0000.0000.0000.000
198A249VAL00.0540.02610.4970.0720.0720.0000.0000.0000.000
199A250GLY00.0230.0238.5010.0160.0160.0000.0000.0000.000
200A251GLN00.009-0.0159.282-0.156-0.1560.0000.0000.0000.000
201A252THR00.0340.05910.2700.1640.1640.0000.0000.0000.000
202A253PHE0-0.042-0.00412.162-0.058-0.0580.0000.0000.0000.000
203A254LEU00.0170.01614.6590.0010.0010.0000.0000.0000.000
204A255GLU-1-0.938-0.93715.4990.1130.1130.0000.0000.0000.000
205A256VAL00.014-0.00818.035-0.009-0.0090.0000.0000.0000.000
206A257GLU-1-0.853-0.90621.4210.0260.0260.0000.0000.0000.000
207A258SER0-0.047-0.03018.859-0.015-0.0150.0000.0000.0000.000
208A259VAL0-0.0090.01419.929-0.001-0.0010.0000.0000.0000.000
209A260PRO00.0140.00718.6160.0140.0140.0000.0000.0000.000
210A261THR0-0.033-0.04519.101-0.014-0.0140.0000.0000.0000.000
211A262TYR0-0.028-0.05219.5700.0190.0190.0000.0000.0000.000
212A263LEU0-0.028-0.00819.7100.0100.0100.0000.0000.0000.000
213A264CYS0-0.0300.00216.1180.0440.0440.0000.0000.0000.000
214A265VAL00.0360.00113.004-0.023-0.0230.0000.0000.0000.000
215A266TYR00.017-0.00213.1920.0920.0920.0000.0000.0000.000
216A267SER00.004-0.0108.385-0.066-0.0660.0000.0000.0000.000
217A268ILE0-0.014-0.00410.8710.1110.1110.0000.0000.0000.000
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