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: QV1VY

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1856898.8891
FMO2-HF: Nuclear repulsion 1785157.482536
FMO2-HF: Total energy -71741.406564
FMO2-MP2: Total energy -71950.647652


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.
-8.192-1.9631.106-3.005-4.3310.002
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 : 0.026 / q_NPA : -0.011
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].
3A14ALA00.0280.0162.908-3.922-1.3270.190-1.262-1.5230.004
4A15THR0-0.018-0.0172.512-2.209-0.4560.797-0.954-1.596-0.005
5A16ARG10.9370.9884.1471.0341.2810.000-0.067-0.1800.000
6A17GLU-1-0.872-0.9356.1100.2250.2250.0000.0000.0000.000
7A18ALA0-0.0040.0007.4290.1230.1230.0000.0000.0000.000
8A19LEU0-0.028-0.0116.9240.1240.1240.0000.0000.0000.000
9A20ILE00.0190.0129.9540.0570.0570.0000.0000.0000.000
10A21THR0-0.010-0.00911.8830.0430.0430.0000.0000.0000.000
11A22GLY00.0400.02112.7940.0180.0180.0000.0000.0000.000
12A23ALA0-0.032-0.03113.9890.0140.0140.0000.0000.0000.000
13A24ARG10.8150.91215.8000.0070.0070.0000.0000.0000.000
14A25LYS10.9560.99317.525-0.009-0.0090.0000.0000.0000.000
15A26LEU0-0.034-0.02417.1970.0030.0030.0000.0000.0000.000
16A27TRP0-0.032-0.02016.7750.0020.0020.0000.0000.0000.000
17A28GLY00.0490.02921.2330.0000.0000.0000.0000.0000.000
18A29LEU0-0.085-0.03723.1350.0010.0010.0000.0000.0000.000
19A30ARG10.7970.88422.597-0.024-0.0240.0000.0000.0000.000
20A31GLY00.0830.06124.8330.0000.0000.0000.0000.0000.000
21A32TYR0-0.006-0.02819.7710.0040.0040.0000.0000.0000.000
22A33ALA0-0.046-0.03422.8370.0040.0040.0000.0000.0000.000
23A34GLU-1-0.908-0.93825.3240.0210.0210.0000.0000.0000.000
24A35VAL0-0.0170.01219.3520.0020.0020.0000.0000.0000.000
25A36GLY0-0.004-0.00819.9570.0000.0000.0000.0000.0000.000
26A37THR00.029-0.01314.685-0.008-0.0080.0000.0000.0000.000
27A38PRO0-0.035-0.02814.8800.0120.0120.0000.0000.0000.000
28A39GLU-1-0.801-0.88716.0120.0350.0350.0000.0000.0000.000
29A40ILE00.0280.01912.734-0.003-0.0030.0000.0000.0000.000
30A41ALA0-0.025-0.00811.473-0.012-0.0120.0000.0000.0000.000
31A42THR0-0.040-0.02612.068-0.010-0.0100.0000.0000.0000.000
32A43GLU-1-0.960-0.97914.649-0.002-0.0020.0000.0000.0000.000
33A44ALA00.0600.0369.834-0.006-0.0060.0000.0000.0000.000
34A45GLY0-0.0420.00010.065-0.042-0.0420.0000.0000.0000.000
35A46VAL0-0.053-0.0276.3460.0000.0000.0000.0000.0000.000
36A47THR00.0300.0078.7990.0530.0530.0000.0000.0000.000
37A48ARG11.0100.9809.499-0.067-0.0670.0000.0000.0000.000
38A49GLY00.0090.0139.932-0.007-0.0070.0000.0000.0000.000
39A50ALA00.0190.0165.0830.1600.1600.0000.0000.0000.000
40A51MET00.0190.0166.3230.2370.2370.0000.0000.0000.000
41A52TYR0-0.033-0.0318.521-0.058-0.0580.0000.0000.0000.000
42A53HIS0-0.049-0.0093.480-0.870-0.2080.021-0.293-0.3910.002
43A54GLN0-0.036-0.0083.044-2.807-1.8350.098-0.429-0.6410.001
44A55PHE0-0.012-0.0077.507-0.221-0.2210.0000.0000.0000.000
45A56ALA00.0230.01211.2130.0270.0270.0000.0000.0000.000
46A57ASP-1-0.887-0.95813.8410.0460.0460.0000.0000.0000.000
47A58LYS10.8790.93215.364-0.034-0.0340.0000.0000.0000.000
48A59ALA00.0250.01117.179-0.009-0.0090.0000.0000.0000.000
49A60ALA0-0.031-0.00814.519-0.010-0.0100.0000.0000.0000.000
50A61LEU00.0110.01111.463-0.011-0.0110.0000.0000.0000.000
51A62PHE0-0.006-0.00614.232-0.016-0.0160.0000.0000.0000.000
52A63ARG10.9310.96717.0840.0060.0060.0000.0000.0000.000
53A64ASP-1-0.779-0.89912.131-0.113-0.1130.0000.0000.0000.000
54A65VAL0-0.063-0.02715.239-0.001-0.0010.0000.0000.0000.000
55A66VAL0-0.016-0.00816.9380.0040.0040.0000.0000.0000.000
56A67GLU-1-0.942-0.96816.792-0.050-0.0500.0000.0000.0000.000
57A68VAL0-0.017-0.00714.8700.0060.0060.0000.0000.0000.000
58A69VAL0-0.007-0.00418.2650.0080.0080.0000.0000.0000.000
59A70GLU-1-0.888-0.95621.3670.0000.0000.0000.0000.0000.000
60A71GLN0-0.048-0.02117.462-0.003-0.0030.0000.0000.0000.000
61A72ASP-1-0.837-0.92120.8670.0150.0150.0000.0000.0000.000
62A73VAL0-0.025-0.00523.5190.0030.0030.0000.0000.0000.000
63A74MET0-0.006-0.00326.1220.0020.0020.0000.0000.0000.000
64A75ALA0-0.0040.00325.0730.0010.0010.0000.0000.0000.000
65A76ARG10.8990.93727.017-0.011-0.0110.0000.0000.0000.000
66A77MET00.0160.01428.9160.0000.0000.0000.0000.0000.000
67A78ALA0-0.0040.00230.1980.0000.0000.0000.0000.0000.000
68A79THR0-0.052-0.02129.5410.0010.0010.0000.0000.0000.000
69A80LEU0-0.026-0.01832.1700.0000.0000.0000.0000.0000.000
70A81VAL0-0.0060.00634.9620.0000.0000.0000.0000.0000.000
71A82ALA0-0.023-0.00434.8600.0000.0000.0000.0000.0000.000
72A83ALA0-0.019-0.00635.8500.0000.0000.0000.0000.0000.000
73A84SER0-0.070-0.04337.7130.0000.0000.0000.0000.0000.000
74A85GLY0-0.0070.00540.7810.0000.0000.0000.0000.0000.000
75A86ALA0-0.031-0.00941.803-0.001-0.0010.0000.0000.0000.000
76A87ALA00.0200.00943.2750.0000.0000.0000.0000.0000.000
77A88THR0-0.063-0.04046.0810.0000.0000.0000.0000.0000.000
78A89PRO00.0610.01243.7370.0000.0000.0000.0000.0000.000
79A90ALA0-0.0040.00444.1150.0000.0000.0000.0000.0000.000
80A91ASP-1-0.870-0.93045.4380.0060.0060.0000.0000.0000.000
81A92ALA00.0180.01840.3410.0000.0000.0000.0000.0000.000
82A93ILE0-0.010-0.00340.6130.0000.0000.0000.0000.0000.000
83A94ARG10.7950.88941.630-0.005-0.0050.0000.0000.0000.000
84A95ALA00.0240.02339.8500.0000.0000.0000.0000.0000.000
85A96ALA00.0260.00237.2220.0000.0000.0000.0000.0000.000
86A97VAL0-0.029-0.01237.2840.0000.0000.0000.0000.0000.000
87A98ASP-1-0.925-0.97138.8310.0070.0070.0000.0000.0000.000
88A99ALA0-0.011-0.00934.7550.0000.0000.0000.0000.0000.000
89A100TRP00.0410.01030.6490.0010.0010.0000.0000.0000.000
90A101LEU0-0.021-0.01634.4240.0000.0000.0000.0000.0000.000
91A102GLU-1-0.978-0.97934.5050.0120.0120.0000.0000.0000.000
92A103VAL0-0.010-0.01629.2750.0010.0010.0000.0000.0000.000
93A104SER0-0.009-0.00730.5010.0000.0000.0000.0000.0000.000
94A105GLY0-0.081-0.04132.2310.0000.0000.0000.0000.0000.000
95A106ASP-1-0.892-0.94727.9220.0120.0120.0000.0000.0000.000
96A107PRO0-0.030-0.02229.267-0.001-0.0010.0000.0000.0000.000
97A108GLU-1-0.809-0.89022.0720.0060.0060.0000.0000.0000.000
98A109VAL00.0260.01025.563-0.001-0.0010.0000.0000.0000.000
99A110ARG10.8690.93227.053-0.009-0.0090.0000.0000.0000.000
100A111GLN0-0.060-0.03125.8200.0000.0000.0000.0000.0000.000
101A112LEU00.0280.00421.0060.0000.0000.0000.0000.0000.000
102A113ILE00.0190.00923.671-0.001-0.0010.0000.0000.0000.000
103A114LEU0-0.033-0.02026.6670.0000.0000.0000.0000.0000.000
104A115LEU0-0.052-0.02029.1860.0000.0000.0000.0000.0000.000
105A116ASP-1-0.801-0.91124.8130.0100.0100.0000.0000.0000.000
106A117ALA0-0.013-0.00124.7750.0000.0000.0000.0000.0000.000
107A118PRO0-0.020-0.00225.761-0.001-0.0010.0000.0000.0000.000
108A119VAL0-0.039-0.01528.0800.0000.0000.0000.0000.0000.000
109A120VAL0-0.059-0.02521.9600.0010.0010.0000.0000.0000.000
110A121LEU0-0.039-0.02321.8620.0000.0000.0000.0000.0000.000
111A122GLY00.0130.02525.170-0.001-0.0010.0000.0000.0000.000
112A123TRP00.0420.00028.689-0.001-0.0010.0000.0000.0000.000
113A124ALA0-0.020-0.01729.6480.0000.0000.0000.0000.0000.000
114A125GLY00.0530.02526.010-0.001-0.0010.0000.0000.0000.000
115A126PHE00.0160.00726.199-0.002-0.0020.0000.0000.0000.000
116A127ARG10.9500.98327.7210.0050.0050.0000.0000.0000.000
117A128ASP-1-0.950-0.97225.779-0.016-0.0160.0000.0000.0000.000
118A129VAL0-0.0120.00123.035-0.001-0.0010.0000.0000.0000.000
119A130ALA00.0780.03825.6740.0000.0000.0000.0000.0000.000
120A131GLN0-0.041-0.01328.7400.0010.0010.0000.0000.0000.000
121A132ARG10.9090.96920.1210.0260.0260.0000.0000.0000.000
122A133TYR0-0.025-0.00920.493-0.001-0.0010.0000.0000.0000.000
123A134SER00.039-0.00227.3790.0020.0020.0000.0000.0000.000
124A135LEU0-0.036-0.01231.1580.0010.0010.0000.0000.0000.000
125A136GLY00.0310.01431.6370.0010.0010.0000.0000.0000.000
126A137MET00.0750.03832.2640.0010.0010.0000.0000.0000.000
127A138THR0-0.016-0.01633.7890.0010.0010.0000.0000.0000.000
128A139GLU-1-0.919-0.98836.146-0.004-0.0040.0000.0000.0000.000
129A140GLN0-0.042-0.00835.6500.0000.0000.0000.0000.0000.000
130A141LEU00.0310.01437.4480.0000.0000.0000.0000.0000.000
131A142ILE00.0040.01039.9360.0000.0000.0000.0000.0000.000
132A143THR0-0.050-0.03140.6520.0000.0000.0000.0000.0000.000
133A144GLU-1-0.927-0.98439.7060.0040.0040.0000.0000.0000.000
134A145ALA00.0220.01443.5770.0000.0000.0000.0000.0000.000
135A146ILE0-0.050-0.02045.2600.0000.0000.0000.0000.0000.000
136A147ARG10.8820.94844.193-0.002-0.0020.0000.0000.0000.000
137A148ALA0-0.019-0.00947.6730.0000.0000.0000.0000.0000.000
138A149GLY00.0080.01549.4850.0000.0000.0000.0000.0000.000
139A150GLN00.0260.00648.5310.0000.0000.0000.0000.0000.000
140A151LEU00.0220.01345.9950.0000.0000.0000.0000.0000.000
141A152ALA00.0230.01849.9500.0000.0000.0000.0000.0000.000
142A153ARG10.9940.98449.7150.0010.0010.0000.0000.0000.000
143A154GLN0-0.0080.00147.1380.0000.0000.0000.0000.0000.000
144A155PRO0-0.032-0.02445.5730.0000.0000.0000.0000.0000.000
145A156VAL00.0780.03240.3850.0000.0000.0000.0000.0000.000
146A157ARG10.9761.00235.8630.0070.0070.0000.0000.0000.000
147A158PRO0-0.021-0.02540.4560.0000.0000.0000.0000.0000.000
148A159LEU00.0380.03942.8930.0000.0000.0000.0000.0000.000
149A160ALA00.0470.01437.9310.0000.0000.0000.0000.0000.000
150A161GLN0-0.011-0.00935.7730.0000.0000.0000.0000.0000.000
151A162VAL0-0.0080.00339.1070.0000.0000.0000.0000.0000.000
152A163LEU0-0.018-0.01140.3970.0000.0000.0000.0000.0000.000
153A164ILE00.0240.01134.5400.0000.0000.0000.0000.0000.000
154A165GLY00.0230.01437.3870.0000.0000.0000.0000.0000.000
155A166ALA0-0.009-0.00239.0670.0000.0000.0000.0000.0000.000
156A167LEU0-0.016-0.01737.4060.0010.0010.0000.0000.0000.000
157A168ASP-1-0.882-0.93634.0360.0000.0000.0000.0000.0000.000
158A169GLU-1-0.958-0.97336.2870.0030.0030.0000.0000.0000.000
159A170ALA0-0.038-0.02039.0940.0010.0010.0000.0000.0000.000
160A171ALA0-0.009-0.00634.5780.0010.0010.0000.0000.0000.000
161A172MET00.0260.01234.4010.0010.0010.0000.0000.0000.000
162A173PHE00.0120.01836.5560.0010.0010.0000.0000.0000.000
163A174ILE0-0.068-0.03937.6220.0010.0010.0000.0000.0000.000
164A175ALA0-0.040-0.02134.1370.0010.0010.0000.0000.0000.000
165A176THR0-0.033-0.01436.0970.0010.0010.0000.0000.0000.000
166A177ALA00.0110.01938.2400.0000.0000.0000.0000.0000.000
167A178ASP-1-0.888-0.93840.8960.0070.0070.0000.0000.0000.000
168A179ASP-1-0.911-0.97042.9650.0080.0080.0000.0000.0000.000
169A180PRO00.0390.00838.8960.0000.0000.0000.0000.0000.000
170A181LYS10.9070.95237.422-0.009-0.0090.0000.0000.0000.000
171A182ARG10.9050.96742.631-0.006-0.0060.0000.0000.0000.000
172A183ALA00.0720.04942.3690.0000.0000.0000.0000.0000.000
173A184ARG10.9580.98636.505-0.008-0.0080.0000.0000.0000.000
174A185ARG10.9130.94942.080-0.007-0.0070.0000.0000.0000.000
175A186GLU-1-0.899-0.96345.3210.0050.0050.0000.0000.0000.000
176A187THR00.0360.01142.2060.0000.0000.0000.0000.0000.000
177A188ARG10.9690.99039.863-0.008-0.0080.0000.0000.0000.000
178A189GLN00.0000.01744.5540.0000.0000.0000.0000.0000.000
179A190VAL00.0020.00146.9720.0000.0000.0000.0000.0000.000
180A191LEU00.0420.01941.6140.0000.0000.0000.0000.0000.000
181A192ARG10.9140.97444.814-0.006-0.0060.0000.0000.0000.000
182A193ARG10.8930.91647.610-0.004-0.0040.0000.0000.0000.000
183A194LEU00.0050.01646.2890.0000.0000.0000.0000.0000.000
184A195ILE00.0060.00644.2020.0000.0000.0000.0000.0000.000
185A196ASP-1-0.829-0.93747.9130.0040.0040.0000.0000.0000.000
186A197GLY0-0.054-0.00851.0760.0000.0000.0000.0000.0000.000
187A198MET0-0.074-0.03648.7990.0000.0000.0000.0000.0000.000
188A199LEU0-0.043-0.01646.5710.0000.0000.0000.0000.0000.000
189A200ASN0-0.053-0.00750.8300.0000.0000.0000.0000.0000.000
190A201GLY00.0180.00149.9050.0000.0000.0000.0000.0000.000