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: R5L98

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2516575.711761
FMO2-HF: Nuclear repulsion 2432090.57844
FMO2-HF: Total energy -84485.133322
FMO2-MP2: Total energy -84735.473951


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.
-21.611-15.0678.958-6.864-8.638-0.013
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 : 0.030 / q_NPA : -0.001
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].
3A54VAL00.0420.0073.800-2.2610.030-0.007-1.027-1.2570.006
4A55GLN00.0160.0121.977-17.927-14.7088.905-5.451-6.672-0.020
5A56THR00.0370.0272.975-1.333-0.2990.060-0.386-0.7090.001
6A57SER00.0120.0035.5150.6380.6380.0000.0000.0000.000
7A58SER00.011-0.0047.0550.0650.0650.0000.0000.0000.000
8A59LEU0-0.036-0.0047.7050.0420.0420.0000.0000.0000.000
9A60ILE00.0210.0069.0310.1640.1640.0000.0000.0000.000
10A61GLN00.0100.00811.3490.0890.0890.0000.0000.0000.000
11A62SER0-0.035-0.01712.1960.0280.0280.0000.0000.0000.000
12A63LEU0-0.022-0.00912.1260.0520.0520.0000.0000.0000.000
13A64PHE0-0.005-0.00915.2180.0520.0520.0000.0000.0000.000
14A65ASP-1-0.851-0.93316.884-0.130-0.1300.0000.0000.0000.000
15A66PHE0-0.071-0.03117.8560.0280.0280.0000.0000.0000.000
16A67ARG10.9530.98519.6000.1830.1830.0000.0000.0000.000
17A68LEU00.0280.01121.4940.0220.0220.0000.0000.0000.000
18A69ALA0-0.043-0.02322.5630.0200.0200.0000.0000.0000.000
19A70ALA00.0140.01323.9420.0150.0150.0000.0000.0000.000
20A71LEU00.0140.01025.8960.0130.0130.0000.0000.0000.000
21A72ARG10.9430.98224.2350.1140.1140.0000.0000.0000.000
22A73ILE0-0.054-0.02626.3830.0110.0110.0000.0000.0000.000
23A74HIS00.0190.00029.9820.0140.0140.0000.0000.0000.000
24A75GLN0-0.0110.00831.7010.0050.0050.0000.0000.0000.000
25A76ASP-1-0.780-0.86832.028-0.061-0.0610.0000.0000.0000.000
26A77SER0-0.074-0.02334.2630.0070.0070.0000.0000.0000.000
27A78THR0-0.004-0.02335.8090.0040.0040.0000.0000.0000.000
28A79ALA0-0.037-0.01337.4260.0040.0040.0000.0000.0000.000
29A80LYS10.9160.95536.5160.0590.0590.0000.0000.0000.000
30A81ASN00.0400.04041.0230.0040.0040.0000.0000.0000.000
31A82ALA00.0730.02842.7610.0010.0010.0000.0000.0000.000
32A83SER0-0.023-0.01545.2400.0020.0020.0000.0000.0000.000
33A84LEU00.0010.02741.0490.0020.0020.0000.0000.0000.000
34A85ILE00.0200.00043.7630.0020.0020.0000.0000.0000.000
35A86ASN0-0.022-0.02346.8890.0030.0030.0000.0000.0000.000
36A87ALA00.0280.01047.5430.0020.0020.0000.0000.0000.000
37A88LEU00.0050.01645.4090.0010.0010.0000.0000.0000.000
38A89VAL00.0300.01848.8110.0020.0020.0000.0000.0000.000
39A90SER0-0.080-0.03951.7160.0020.0020.0000.0000.0000.000
40A91ARG10.8220.89649.8010.0290.0290.0000.0000.0000.000
41A92ASP-1-0.807-0.86152.454-0.032-0.0320.0000.0000.0000.000
42A93SER0-0.004-0.01249.470-0.002-0.0020.0000.0000.0000.000
43A94SER00.0540.01348.642-0.001-0.0010.0000.0000.0000.000
44A95ARG10.8040.89849.8210.0330.0330.0000.0000.0000.000
45A96LEU0-0.077-0.04345.259-0.002-0.0020.0000.0000.0000.000
46A97ASP-1-0.825-0.89944.757-0.047-0.0470.0000.0000.0000.000
47A98GLU-1-0.937-0.96744.326-0.049-0.0490.0000.0000.0000.000
48A99PHE00.004-0.00341.040-0.003-0.0030.0000.0000.0000.000
49A100PHE00.023-0.01438.715-0.003-0.0030.0000.0000.0000.000
50A101SER00.0310.02939.523-0.004-0.0040.0000.0000.0000.000
51A102SER0-0.013-0.01640.592-0.002-0.0020.0000.0000.0000.000
52A103VAL0-0.103-0.04436.204-0.003-0.0030.0000.0000.0000.000
53A104ASP-1-0.737-0.83035.418-0.087-0.0870.0000.0000.0000.000
54A105GLU-1-0.949-0.94636.173-0.070-0.0700.0000.0000.0000.000
55A106LEU0-0.055-0.03535.710-0.002-0.0020.0000.0000.0000.000
56A107GLU-1-0.817-0.90130.116-0.136-0.1360.0000.0000.0000.000
57A108LEU0-0.0110.00532.066-0.006-0.0060.0000.0000.0000.000
58A109SER0-0.054-0.02228.243-0.001-0.0010.0000.0000.0000.000
59A110ASN0-0.146-0.09026.285-0.019-0.0190.0000.0000.0000.000
60A111ALA00.0370.02928.8630.0040.0040.0000.0000.0000.000
61A112PRO0-0.071-0.04830.033-0.007-0.0070.0000.0000.0000.000
62A113ASP-1-0.787-0.87028.955-0.106-0.1060.0000.0000.0000.000
63A114LEU0-0.028-0.02032.0950.0060.0060.0000.0000.0000.000
64A115ARG10.7900.85034.6380.0750.0750.0000.0000.0000.000
65A116PHE00.0630.03237.0230.0030.0030.0000.0000.0000.000
66A117ILE0-0.024-0.01439.839-0.001-0.0010.0000.0000.0000.000
67A118SER00.0020.00542.1450.0020.0020.0000.0000.0000.000
68A119SER00.012-0.00943.8220.0000.0000.0000.0000.0000.000
69A120HIS00.0270.01145.6350.0010.0010.0000.0000.0000.000
70A121ASP-1-0.843-0.88445.549-0.020-0.0200.0000.0000.0000.000
71A122ASN0-0.020-0.00146.6200.0000.0000.0000.0000.0000.000
72A123ILE00.023-0.00142.985-0.001-0.0010.0000.0000.0000.000
73A124LEU0-0.099-0.03846.3600.0010.0010.0000.0000.0000.000
74A125TRP0-0.012-0.04140.4050.0000.0000.0000.0000.0000.000
75A126ASP-1-0.798-0.91541.240-0.046-0.0460.0000.0000.0000.000
76A127ASP-1-0.825-0.89537.717-0.062-0.0620.0000.0000.0000.000
77A128GLY00.0180.02341.447-0.001-0.0010.0000.0000.0000.000
78A129ASN0-0.023-0.02436.4880.0000.0000.0000.0000.0000.000
79A130ALA0-0.004-0.00837.231-0.001-0.0010.0000.0000.0000.000
80A131SER00.0260.00638.2980.0010.0010.0000.0000.0000.000
81A132PHE0-0.0370.00633.6780.0020.0020.0000.0000.0000.000
82A133TYR0-0.043-0.04331.307-0.001-0.0010.0000.0000.0000.000
83A134GLY00.0680.03936.0060.0010.0010.0000.0000.0000.000
84A135ILE0-0.099-0.04634.4380.0030.0030.0000.0000.0000.000
85A136ALA00.0050.00638.8240.0010.0010.0000.0000.0000.000
86A137GLN00.027-0.00742.0220.0000.0000.0000.0000.0000.000
87A138GLN00.0330.00843.794-0.001-0.0010.0000.0000.0000.000
88A139GLU-1-0.835-0.91039.335-0.023-0.0230.0000.0000.0000.000
89A140LEU00.0480.03038.1120.0000.0000.0000.0000.0000.000
90A141ASN0-0.021-0.03040.3840.0010.0010.0000.0000.0000.000
91A142LYS10.8120.88740.3660.0230.0230.0000.0000.0000.000
92A143LEU0-0.015-0.01234.9820.0020.0020.0000.0000.0000.000
93A144ILE0-0.0150.01737.5090.0000.0000.0000.0000.0000.000
94A145ARG10.7910.85439.2420.0170.0170.0000.0000.0000.000
95A146ARG10.8590.92134.9300.0280.0280.0000.0000.0000.000
96A147VAL0-0.0100.01932.9920.0010.0010.0000.0000.0000.000
97A148ALA00.0000.00835.054-0.001-0.0010.0000.0000.0000.000
98A149ILE0-0.017-0.01731.3570.0000.0000.0000.0000.0000.000
99A150SER00.013-0.00834.347-0.002-0.0020.0000.0000.0000.000
100A151GLY0-0.019-0.00631.7290.0020.0020.0000.0000.0000.000
101A152ASN0-0.050-0.01627.2870.0000.0000.0000.0000.0000.000
102A153TRP0-0.017-0.02725.5710.0030.0030.0000.0000.0000.000
103A154HIS0-0.022-0.01027.5270.0090.0090.0000.0000.0000.000
104A155LEU0-0.0030.01523.897-0.007-0.0070.0000.0000.0000.000
105A156VAL0-0.025-0.01727.5450.0100.0100.0000.0000.0000.000
106A157GLN00.0320.00228.620-0.004-0.0040.0000.0000.0000.000
107A158THR0-0.0150.00031.8780.0070.0070.0000.0000.0000.000
108A159PRO0-0.028-0.00734.710-0.003-0.0030.0000.0000.0000.000
109A160SER00.0090.00635.643-0.001-0.0010.0000.0000.0000.000
110A161GLU-1-0.971-0.97437.531-0.040-0.0400.0000.0000.0000.000
111A162GLY00.021-0.01636.7710.0010.0010.0000.0000.0000.000
112A163LYS10.8000.90328.5950.0760.0760.0000.0000.0000.000
113A164SER0-0.010-0.00531.0800.0000.0000.0000.0000.0000.000
114A165VAL00.0100.00030.795-0.005-0.0050.0000.0000.0000.000
115A166HIS00.0530.03726.7290.0050.0050.0000.0000.0000.000
116A167ILE0-0.012-0.01828.219-0.009-0.0090.0000.0000.0000.000
117A168LEU00.0180.03723.1560.0070.0070.0000.0000.0000.000
118A169MET0-0.029-0.02227.779-0.001-0.0010.0000.0000.0000.000
119A170ARG10.8510.89928.7980.0730.0730.0000.0000.0000.000
120A171ARG10.9030.98631.8700.0310.0310.0000.0000.0000.000
121A172SER0-0.025-0.04534.7660.0020.0020.0000.0000.0000.000
122A173SER0-0.028-0.03436.7330.0010.0010.0000.0000.0000.000
123A174LEU00.0330.04440.158-0.002-0.0020.0000.0000.0000.000
124A175ILE0-0.033-0.01142.2550.0030.0030.0000.0000.0000.000
125A176GLU-1-0.897-0.95445.105-0.031-0.0310.0000.0000.0000.000
126A177ALA0-0.014-0.01548.1840.0010.0010.0000.0000.0000.000
127A178GLY00.0810.06348.5680.0010.0010.0000.0000.0000.000
128A179THR0-0.096-0.10949.7210.0020.0020.0000.0000.0000.000
129A180GLY00.0500.04951.3580.0020.0020.0000.0000.0000.000
130A181GLN0-0.058-0.02646.522-0.002-0.0020.0000.0000.0000.000
131A182VAL0-0.056-0.03144.095-0.001-0.0010.0000.0000.0000.000
132A183VAL00.0260.02746.5380.0020.0020.0000.0000.0000.000
133A184GLY0-0.013-0.01745.1920.0010.0010.0000.0000.0000.000
134A185TYR0-0.049-0.01539.6350.0000.0000.0000.0000.0000.000
135A186LEU00.0490.03737.0390.0000.0000.0000.0000.0000.000
136A187TYR0-0.046-0.03335.9700.0000.0000.0000.0000.0000.000
137A188VAL00.0160.00431.159-0.001-0.0010.0000.0000.0000.000
138A189GLY0-0.003-0.01330.9030.0020.0020.0000.0000.0000.000
139A190ILE00.0030.01425.201-0.004-0.0040.0000.0000.0000.000
140A191VAL0-0.037-0.01228.0200.0050.0050.0000.0000.0000.000
141A192LEU00.0310.00022.713-0.010-0.0100.0000.0000.0000.000
142A193ASN0-0.042-0.02024.988-0.011-0.0110.0000.0000.0000.000
143A194ASP-1-0.781-0.89526.200-0.088-0.0880.0000.0000.0000.000
144A195ASN00.0130.02224.299-0.015-0.0150.0000.0000.0000.000
145A196PHE0-0.004-0.02322.184-0.020-0.0200.0000.0000.0000.000
146A197ALA00.0180.00922.018-0.021-0.0210.0000.0000.0000.000
147A198LEU00.0110.01220.432-0.021-0.0210.0000.0000.0000.000
148A199LEU00.016-0.00116.570-0.031-0.0310.0000.0000.0000.000
149A200GLU-1-0.770-0.84517.115-0.348-0.3480.0000.0000.0000.000
150A201ASN0-0.049-0.00917.615-0.036-0.0360.0000.0000.0000.000
151A202ILE00.0360.01913.445-0.039-0.0390.0000.0000.0000.000
152A203ARG10.7780.86113.2470.2630.2630.0000.0000.0000.000
153A204SER0-0.020-0.02113.001-0.077-0.0770.0000.0000.0000.000
154A205GLY00.0040.01913.937-0.041-0.0410.0000.0000.0000.000
155A206SER0-0.063-0.0549.093-0.088-0.0880.0000.0000.0000.000
156A207ASN0-0.123-0.0689.088-0.111-0.1110.0000.0000.0000.000
157A208SER00.0170.0189.626-0.083-0.0830.0000.0000.0000.000
158A209GLU-1-0.811-0.87410.566-0.142-0.1420.0000.0000.0000.000
159A210ASN0-0.042-0.05412.5930.0740.0740.0000.0000.0000.000
160A211LEU0-0.0060.01011.296-0.076-0.0760.0000.0000.0000.000
161A212VAL0-0.005-0.00214.8000.0500.0500.0000.0000.0000.000
162A213LEU0-0.0080.02316.777-0.010-0.0100.0000.0000.0000.000
163A214ALA00.0240.00618.8880.0170.0170.0000.0000.0000.000
164A215VAL0-0.013-0.00520.6940.0010.0010.0000.0000.0000.000
165A216ASP-1-0.893-0.94222.1040.0020.0020.0000.0000.0000.000
166A217THR00.0060.00621.659-0.004-0.0040.0000.0000.0000.000
167A218THR0-0.055-0.02423.755-0.005-0.0050.0000.0000.0000.000
168A219PRO0-0.005-0.01022.170-0.006-0.0060.0000.0000.0000.000
169A220LEU0-0.088-0.04222.6130.0090.0090.0000.0000.0000.000
170A221VAL00.0350.01621.1300.0040.0040.0000.0000.0000.000
171A222SER00.0230.00719.734-0.021-0.0210.0000.0000.0000.000
172A223THR00.0660.03017.293-0.003-0.0030.0000.0000.0000.000
173A224LEU0-0.088-0.02217.5100.0000.0000.0000.0000.0000.000
174A225LYS10.8180.89318.3480.2270.2270.0000.0000.0000.000
175A226GLY0-0.013-0.00722.7210.0130.0130.0000.0000.0000.000
176A227ASN0-0.077-0.03822.8250.0060.0060.0000.0000.0000.000
177A228GLU-1-0.732-0.83418.456-0.165-0.1650.0000.0000.0000.000
178A229PRO0-0.026-0.01518.9540.0110.0110.0000.0000.0000.000
179A230TYR0-0.037-0.02015.1070.0120.0120.0000.0000.0000.000
180A231SER00.0410.01220.243-0.012-0.0120.0000.0000.0000.000
181A232LEU00.0430.00720.563-0.006-0.0060.0000.0000.0000.000
182A233ASP-1-0.873-0.94420.989-0.040-0.0400.0000.0000.0000.000
183A234TYR00.0010.00015.3640.0170.0170.0000.0000.0000.000
184A235VAL00.013-0.00315.5250.0040.0040.0000.0000.0000.000
185A236VAL0-0.0070.00817.293-0.005-0.0050.0000.0000.0000.000
186A237HIS0-0.089-0.02719.4690.0140.0140.0000.0000.0000.000
187A238SER0-0.064-0.03015.6800.0150.0150.0000.0000.0000.000
188A239ALA0-0.021-0.01615.6650.0080.0080.0000.0000.0000.000
189A240LYS10.8670.9178.638-0.321-0.3210.0000.0000.0000.000
190A241ASP-1-0.870-0.9186.247-0.129-0.1290.0000.0000.0000.000
191A242ALA00.0260.0248.9540.1290.1290.0000.0000.0000.000
192A243MET00.005-0.0166.2110.0460.0460.0000.0000.0000.000
193A244ARG10.7760.8659.761-0.091-0.0910.0000.0000.0000.000
194A245ASP-1-0.814-0.86613.1990.0750.0750.0000.0000.0000.000
195A246SER0-0.024-0.01113.2810.0100.0100.0000.0000.0000.000
196A247PHE00.017-0.01013.051-0.007-0.0070.0000.0000.0000.000
197A248ILE00.0060.0237.1890.0340.0340.0000.0000.0000.000
198A249VAL00.0440.01810.236-0.132-0.1320.0000.0000.0000.000
199A250GLY0-0.0090.0118.4420.0910.0910.0000.0000.0000.000
200A251GLN0-0.001-0.0369.2330.0620.0620.0000.0000.0000.000
201A252THR00.0260.02310.1790.0660.0660.0000.0000.0000.000
202A253PHE0-0.0250.00112.346-0.031-0.0310.0000.0000.0000.000
203A254LEU00.0110.01115.0360.0170.0170.0000.0000.0000.000
204A255GLU-1-0.929-0.95016.0890.0900.0900.0000.0000.0000.000
205A256VAL0-0.001-0.01918.386-0.032-0.0320.0000.0000.0000.000
206A257GLU-1-0.860-0.92521.701-0.053-0.0530.0000.0000.0000.000
207A258SER0-0.034-0.02118.8320.0060.0060.0000.0000.0000.000
208A259VAL00.0020.01620.1780.0240.0240.0000.0000.0000.000
209A260PRO00.0010.00218.851-0.017-0.0170.0000.0000.0000.000
210A261THR0-0.031-0.02419.610-0.011-0.0110.0000.0000.0000.000
211A262TYR0-0.015-0.02420.1440.0130.0130.0000.0000.0000.000
212A263LEU0-0.027-0.00619.989-0.005-0.0050.0000.0000.0000.000
213A264CYS0-0.0040.02516.1240.0040.0040.0000.0000.0000.000
214A265VAL00.020-0.00312.787-0.008-0.0080.0000.0000.0000.000
215A266TYR00.002-0.00512.877-0.035-0.0350.0000.0000.0000.000
216A267SER00.004-0.0098.728-0.064-0.0640.0000.0000.0000.000
217A268ILE0-0.018-0.00810.2700.0060.0060.0000.0000.0000.000
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