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: 4J3JN

Calculation Name: 5N1I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N1I

Chain ID: A

ChEMBL ID:

UniProt ID: O53623

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1869017.345192
FMO2-HF: Nuclear repulsion 1797274.957075
FMO2-HF: Total energy -71742.388117
FMO2-MP2: Total energy -71951.720253


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:12:SER)


Summations of interaction energy for fragment #1(A:12: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.
-6.506-1.2821.688-2.903-4.007-0.014
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.013
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].
3A14ALA00.0590.0233.397-1.746-0.0800.014-0.726-0.9530.001
4A15THR0-0.010-0.0052.642-3.200-1.0531.640-1.641-2.145-0.014
5A16ARG10.8270.9064.2782.4422.6840.000-0.070-0.1710.000
6A17GLU-1-0.857-0.9306.248-0.392-0.3920.0000.0000.0000.000
7A18ALA0-0.0120.0137.4690.3320.3320.0000.0000.0000.000
8A19LEU0-0.023-0.0166.7350.3070.3070.0000.0000.0000.000
9A20ILE00.0150.0079.9620.1950.1950.0000.0000.0000.000
10A21THR0-0.019-0.01811.9770.1650.1650.0000.0000.0000.000
11A22GLY00.005-0.00412.9640.0850.0850.0000.0000.0000.000
12A23ALA0-0.012-0.02213.9070.0740.0740.0000.0000.0000.000
13A24ARG10.7640.86015.7040.3350.3350.0000.0000.0000.000
14A25LYS10.8530.92516.6940.3650.3650.0000.0000.0000.000
15A26LEU0-0.022-0.02017.1740.0350.0350.0000.0000.0000.000
16A27TRP00.003-0.01016.2260.0160.0160.0000.0000.0000.000
17A28GLY00.0370.01721.3980.0220.0220.0000.0000.0000.000
18A29LEU0-0.068-0.02623.2160.0180.0180.0000.0000.0000.000
19A30ARG10.7380.83222.6090.1650.1650.0000.0000.0000.000
20A31GLY00.0530.04425.0300.0120.0120.0000.0000.0000.000
21A32TYR0-0.010-0.02319.294-0.009-0.0090.0000.0000.0000.000
22A33ALA0-0.019-0.00222.393-0.004-0.0040.0000.0000.0000.000
23A34GLU-1-0.891-0.93824.175-0.093-0.0930.0000.0000.0000.000
24A35VAL00.0190.02219.304-0.004-0.0040.0000.0000.0000.000
25A36GLY00.0020.01319.7110.0030.0030.0000.0000.0000.000
26A37THR00.011-0.01714.598-0.017-0.0170.0000.0000.0000.000
27A38PRO0-0.013-0.02314.626-0.031-0.0310.0000.0000.0000.000
28A39GLU-1-0.791-0.85015.774-0.179-0.1790.0000.0000.0000.000
29A40ILE00.0420.02012.763-0.020-0.0200.0000.0000.0000.000
30A41ALA0-0.032-0.02011.318-0.066-0.0660.0000.0000.0000.000
31A42THR0-0.040-0.03311.964-0.044-0.0440.0000.0000.0000.000
32A43GLU-1-0.876-0.92514.548-0.343-0.3430.0000.0000.0000.000
33A44ALA00.0190.01910.065-0.011-0.0110.0000.0000.0000.000
34A45GLY0-0.0110.01110.013-0.127-0.1270.0000.0000.0000.000
35A46VAL0-0.055-0.0326.701-0.059-0.0590.0000.0000.0000.000
36A47THR00.0260.0058.8530.1330.1330.0000.0000.0000.000
37A48ARG11.0200.9889.203-0.002-0.0020.0000.0000.0000.000
38A49GLY0-0.0060.00710.055-0.011-0.0110.0000.0000.0000.000
39A50ALA00.010-0.0014.9260.2540.2540.0000.0000.0000.000
40A51MET00.0220.0285.636-0.181-0.1810.0000.0000.0000.000
41A52TYR0-0.002-0.0078.173-0.086-0.0860.0000.0000.0000.000
42A53HIS0-0.034-0.0023.506-2.122-1.5190.011-0.212-0.4020.001
43A54GLN0-0.045-0.0103.691-1.546-0.9800.023-0.254-0.336-0.002
44A55PHE00.0020.0046.813-0.075-0.0750.0000.0000.0000.000
45A56ALA00.0330.01710.6200.0600.0600.0000.0000.0000.000
46A57ASP-1-0.801-0.90613.184-0.104-0.1040.0000.0000.0000.000
47A58LYS10.8060.88815.1120.1050.1050.0000.0000.0000.000
48A59ALA00.0580.02816.858-0.033-0.0330.0000.0000.0000.000
49A60ALA0-0.067-0.03313.313-0.015-0.0150.0000.0000.0000.000
50A61LEU0-0.014-0.00210.987-0.030-0.0300.0000.0000.0000.000
51A62PHE00.013-0.00613.723-0.027-0.0270.0000.0000.0000.000
52A63ARG10.8650.94215.9460.1790.1790.0000.0000.0000.000
53A64ASP-1-0.753-0.87511.084-0.664-0.6640.0000.0000.0000.000
54A65VAL0-0.036-0.01414.6210.0060.0060.0000.0000.0000.000
55A66VAL00.0070.00916.5270.0240.0240.0000.0000.0000.000
56A67GLU-1-0.841-0.90417.105-0.220-0.2200.0000.0000.0000.000
57A68VAL0-0.049-0.02314.6110.0150.0150.0000.0000.0000.000
58A69VAL00.0070.00217.9680.0260.0260.0000.0000.0000.000
59A70GLU-1-0.860-0.95121.143-0.124-0.1240.0000.0000.0000.000
60A71GLN0-0.0210.00517.7020.0330.0330.0000.0000.0000.000
61A72ASP-1-0.800-0.88220.905-0.228-0.2280.0000.0000.0000.000
62A73VAL0-0.040-0.02023.4670.0190.0190.0000.0000.0000.000
63A74MET00.0170.00626.1450.0170.0170.0000.0000.0000.000
64A75ALA00.0040.01424.9430.0120.0120.0000.0000.0000.000
65A76ARG10.8320.90626.9520.1230.1230.0000.0000.0000.000
66A77MET00.0020.00028.9850.0080.0080.0000.0000.0000.000
67A78ALA00.0020.00529.9270.0080.0080.0000.0000.0000.000
68A79THR0-0.054-0.03629.3770.0070.0070.0000.0000.0000.000
69A80LEU0-0.020-0.01232.0420.0060.0060.0000.0000.0000.000
70A81VAL0-0.012-0.00534.8290.0060.0060.0000.0000.0000.000
71A82ALA0-0.0180.01034.6630.0050.0050.0000.0000.0000.000
72A83ALA0-0.026-0.02035.7520.0040.0040.0000.0000.0000.000
73A84SER0-0.071-0.05037.6010.0040.0040.0000.0000.0000.000
74A85GLY0-0.0080.00240.5990.0030.0030.0000.0000.0000.000
75A86ALA0-0.047-0.02641.5460.0030.0030.0000.0000.0000.000
76A87ALA00.0180.01843.4570.0000.0000.0000.0000.0000.000
77A88THR0-0.055-0.04246.0360.0020.0020.0000.0000.0000.000
78A89PRO00.0600.01443.246-0.002-0.0020.0000.0000.0000.000
79A90ALA00.0140.01043.623-0.002-0.0020.0000.0000.0000.000
80A91ASP-1-0.837-0.88544.965-0.043-0.0430.0000.0000.0000.000
81A92ALA00.0340.02039.889-0.003-0.0030.0000.0000.0000.000
82A93ILE0-0.018-0.00640.030-0.004-0.0040.0000.0000.0000.000
83A94ARG10.7270.82641.2130.0390.0390.0000.0000.0000.000
84A95ALA00.0260.01739.441-0.002-0.0020.0000.0000.0000.000
85A96ALA00.0300.01236.790-0.004-0.0040.0000.0000.0000.000
86A97VAL00.0000.00336.806-0.004-0.0040.0000.0000.0000.000
87A98ASP-1-0.839-0.90938.658-0.059-0.0590.0000.0000.0000.000
88A99ALA00.0280.01334.715-0.002-0.0020.0000.0000.0000.000
89A100TRP00.015-0.00330.336-0.007-0.0070.0000.0000.0000.000
90A101LEU00.0130.02434.483-0.004-0.0040.0000.0000.0000.000
91A102GLU-1-0.877-0.90434.364-0.089-0.0890.0000.0000.0000.000
92A103VAL00.0150.00129.219-0.004-0.0040.0000.0000.0000.000
93A104SER0-0.002-0.01930.656-0.006-0.0060.0000.0000.0000.000
94A105GLY0-0.068-0.06032.4320.0030.0030.0000.0000.0000.000
95A106ASP-1-0.888-0.93427.568-0.144-0.1440.0000.0000.0000.000
96A107PRO0-0.031-0.02228.5680.0000.0000.0000.0000.0000.000
97A108GLU-1-0.791-0.87121.587-0.239-0.2390.0000.0000.0000.000
98A109VAL00.0100.00525.597-0.004-0.0040.0000.0000.0000.000
99A110ARG10.8850.93926.8910.0990.0990.0000.0000.0000.000
100A111GLN0-0.079-0.03425.7700.0130.0130.0000.0000.0000.000
101A112LEU00.029-0.00320.7360.0010.0010.0000.0000.0000.000
102A113ILE00.006-0.00823.3510.0000.0000.0000.0000.0000.000
103A114LEU0-0.020-0.01226.5830.0090.0090.0000.0000.0000.000
104A115LEU0-0.045-0.01628.5780.0100.0100.0000.0000.0000.000
105A116ASP-1-0.789-0.88724.259-0.139-0.1390.0000.0000.0000.000
106A117ALA00.0080.00524.3050.0050.0050.0000.0000.0000.000
107A118PRO0-0.025-0.01025.4600.0050.0050.0000.0000.0000.000
108A119VAL0-0.037-0.00927.8010.0090.0090.0000.0000.0000.000
109A120VAL0-0.060-0.03421.4870.0070.0070.0000.0000.0000.000
110A121LEU0-0.028-0.01120.870-0.002-0.0020.0000.0000.0000.000
111A122GLY00.0230.02024.3490.0100.0100.0000.0000.0000.000
112A123TRP00.0320.00327.969-0.005-0.0050.0000.0000.0000.000
113A124ALA0-0.005-0.01328.885-0.002-0.0020.0000.0000.0000.000
114A125GLY00.0340.02625.078-0.001-0.0010.0000.0000.0000.000
115A126PHE00.0110.00325.241-0.008-0.0080.0000.0000.0000.000
116A127ARG10.8930.94226.9130.0570.0570.0000.0000.0000.000
117A128ASP-1-0.917-0.95424.119-0.107-0.1070.0000.0000.0000.000
118A129VAL00.0300.01922.3670.0000.0000.0000.0000.0000.000
119A130ALA00.0870.04925.097-0.001-0.0010.0000.0000.0000.000
120A131GLN0-0.0170.00828.3480.0100.0100.0000.0000.0000.000
121A132ARG10.7500.86120.3420.1630.1630.0000.0000.0000.000
122A133TYR0-0.031-0.02120.1620.0000.0000.0000.0000.0000.000
123A134SER00.024-0.00226.9920.0060.0060.0000.0000.0000.000
124A135LEU0-0.046-0.01230.7810.0070.0070.0000.0000.0000.000
125A136GLY00.0220.00731.3600.0050.0050.0000.0000.0000.000
126A137MET00.0620.02731.5320.0050.0050.0000.0000.0000.000
127A138THR0-0.009-0.00433.9230.0050.0050.0000.0000.0000.000
128A139GLU-1-0.856-0.97035.736-0.049-0.0490.0000.0000.0000.000
129A140GLN0-0.062-0.01734.9260.0010.0010.0000.0000.0000.000
130A141LEU00.0440.01937.2890.0040.0040.0000.0000.0000.000
131A142ILE00.0040.01139.9420.0040.0040.0000.0000.0000.000
132A143THR0-0.045-0.04140.5390.0040.0040.0000.0000.0000.000
133A144GLU-1-0.919-0.95939.278-0.048-0.0480.0000.0000.0000.000
134A145ALA00.0440.01643.4030.0020.0020.0000.0000.0000.000
135A146ILE0-0.073-0.03245.3200.0020.0020.0000.0000.0000.000
136A147ARG10.8910.94044.1180.0370.0370.0000.0000.0000.000
137A148ALA0-0.0060.01247.4800.0010.0010.0000.0000.0000.000
138A149GLY0-0.0120.00049.1910.0010.0010.0000.0000.0000.000
139A150GLN00.0330.01247.986-0.001-0.0010.0000.0000.0000.000
140A151LEU00.0050.00945.633-0.001-0.0010.0000.0000.0000.000
141A152ALA00.0280.02049.6330.0010.0010.0000.0000.0000.000
142A153ARG10.9680.97249.2990.0240.0240.0000.0000.0000.000
143A154GLN0-0.017-0.00146.8360.0020.0020.0000.0000.0000.000
144A155PRO0-0.019-0.01645.075-0.001-0.0010.0000.0000.0000.000
145A156VAL00.0640.02640.042-0.001-0.0010.0000.0000.0000.000
146A157ARG10.9931.01534.0910.0490.0490.0000.0000.0000.000
147A158PRO0-0.030-0.02639.821-0.002-0.0020.0000.0000.0000.000
148A159LEU00.0370.03542.055-0.001-0.0010.0000.0000.0000.000
149A160ALA00.0370.01137.578-0.002-0.0020.0000.0000.0000.000
150A161GLN0-0.030-0.02335.650-0.005-0.0050.0000.0000.0000.000
151A162VAL0-0.032-0.00638.635-0.001-0.0010.0000.0000.0000.000
152A163LEU0-0.004-0.00940.220-0.001-0.0010.0000.0000.0000.000
153A164ILE00.0230.01634.000-0.001-0.0010.0000.0000.0000.000
154A165GLY00.0350.02336.880-0.002-0.0020.0000.0000.0000.000
155A166ALA0-0.019-0.01538.3510.0000.0000.0000.0000.0000.000
156A167LEU0-0.026-0.01936.9260.0000.0000.0000.0000.0000.000
157A168ASP-1-0.877-0.92933.451-0.085-0.0850.0000.0000.0000.000
158A169GLU-1-0.927-0.96335.738-0.060-0.0600.0000.0000.0000.000
159A170ALA0-0.039-0.01838.6590.0000.0000.0000.0000.0000.000
160A171ALA0-0.010-0.00234.1650.0000.0000.0000.0000.0000.000
161A172MET00.0110.00933.623-0.004-0.0040.0000.0000.0000.000
162A173PHE00.0220.02236.2820.0010.0010.0000.0000.0000.000
163A174ILE0-0.044-0.03437.3760.0010.0010.0000.0000.0000.000
164A175ALA0-0.039-0.01533.839-0.001-0.0010.0000.0000.0000.000
165A176THR0-0.053-0.05035.721-0.001-0.0010.0000.0000.0000.000
166A177ALA0-0.0040.01638.1120.0030.0030.0000.0000.0000.000
167A178ASP-1-0.895-0.95040.953-0.051-0.0510.0000.0000.0000.000
168A179ASP-1-0.860-0.93243.152-0.054-0.0540.0000.0000.0000.000
169A180PRO00.0470.02138.3830.0010.0010.0000.0000.0000.000
170A181LYS10.9040.95037.9440.0720.0720.0000.0000.0000.000
171A182ARG10.8060.85742.3940.0440.0440.0000.0000.0000.000
172A183ALA00.0450.03741.8550.0010.0010.0000.0000.0000.000
173A184ARG10.8720.96235.8120.0800.0800.0000.0000.0000.000
174A185ARG10.9050.96241.9710.0490.0490.0000.0000.0000.000
175A186GLU-1-0.823-0.88845.439-0.042-0.0420.0000.0000.0000.000
176A187THR00.032-0.00542.1440.0020.0020.0000.0000.0000.000
177A188ARG10.8820.94539.7990.0640.0640.0000.0000.0000.000
178A189GLN00.0110.02044.4090.0030.0030.0000.0000.0000.000
179A190VAL0-0.018-0.01147.0340.0020.0020.0000.0000.0000.000
180A191LEU00.0430.01841.3920.0010.0010.0000.0000.0000.000
181A192ARG10.8480.92444.8640.0490.0490.0000.0000.0000.000
182A193ARG10.8740.92047.2790.0370.0370.0000.0000.0000.000
183A194LEU0-0.0050.00945.6790.0020.0020.0000.0000.0000.000
184A195ILE00.007-0.00343.3860.0010.0010.0000.0000.0000.000
185A196ASP-1-0.785-0.90147.510-0.040-0.0400.0000.0000.0000.000
186A197GLY0-0.041-0.00150.6200.0020.0020.0000.0000.0000.000
187A198MET0-0.074-0.04047.8180.0010.0010.0000.0000.0000.000
188A199LEU0-0.0190.00646.0770.0000.0000.0000.0000.0000.000
189A200ASN0-0.054-0.01250.5790.0010.0010.0000.0000.0000.000
190A201GLY0-0.005-0.00251.174-0.002-0.0020.0000.0000.0000.000