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: R8428

Calculation Name: 5I45-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I45

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NFJ9

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2267983.664001
FMO2-HF: Nuclear repulsion 2192131.187083
FMO2-HF: Total energy -75852.476918
FMO2-MP2: Total energy -76077.017691


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:141:GLY)


Summations of interaction energy for fragment #1(A:141:GLY)
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.
-2.4121.1214.913-4.11-4.339-0.019
Interaction energy analysis for fragmet #1(A:141:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.017
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].
3A143ASP-1-0.785-0.8763.876-0.9070.618-0.009-0.812-0.7040.003
4A144THR00.0530.0116.9140.3010.3010.0000.0000.0000.000
5A145GLN0-0.075-0.0439.4110.3530.3530.0000.0000.0000.000
6A146VAL0-0.0200.00310.5690.1230.1230.0000.0000.0000.000
7A147PHE0-0.014-0.0108.7490.1280.1280.0000.0000.0000.000
8A148TYR00.0360.01910.553-0.007-0.0070.0000.0000.0000.000
9A149PRO00.0160.00613.2950.0200.0200.0000.0000.0000.000
10A150ALA00.0070.00716.2830.0070.0070.0000.0000.0000.000
11A151GLU-1-0.941-0.96619.754-0.207-0.2070.0000.0000.0000.000
12A152ASN0-0.002-0.01322.8000.0220.0220.0000.0000.0000.000
13A153ARG10.8740.93417.3690.3170.3170.0000.0000.0000.000
14A154GLN00.0460.03322.9250.0030.0030.0000.0000.0000.000
15A155GLN0-0.067-0.03926.5060.0160.0160.0000.0000.0000.000
16A156GLN0-0.005-0.01821.608-0.034-0.0340.0000.0000.0000.000
17A157TRP0-0.031-0.01124.079-0.023-0.0230.0000.0000.0000.000
18A158GLN0-0.018-0.01725.8290.0030.0030.0000.0000.0000.000
19A159ASP-1-0.830-0.90026.076-0.235-0.2350.0000.0000.0000.000
20A160LYS10.8040.91321.6000.3970.3970.0000.0000.0000.000
21A161LYS10.8050.91127.0030.1810.1810.0000.0000.0000.000
22A162ILE00.0110.01526.0700.0170.0170.0000.0000.0000.000
23A163PRO00.0010.00630.5620.0040.0040.0000.0000.0000.000
24A164GLY00.0520.04230.683-0.008-0.0080.0000.0000.0000.000
25A165LYS10.7900.87730.0520.1150.1150.0000.0000.0000.000
26A166TYR0-0.039-0.01726.094-0.006-0.0060.0000.0000.0000.000
27A167GLY00.0740.03523.6900.0080.0080.0000.0000.0000.000
28A168ILE0-0.009-0.01021.554-0.011-0.0110.0000.0000.0000.000
29A169GLY00.0400.00719.8750.0070.0070.0000.0000.0000.000
30A170ILE0-0.036-0.00517.214-0.003-0.0030.0000.0000.0000.000
31A171PHE00.0600.03014.3280.0120.0120.0000.0000.0000.000
32A172GLY0-0.007-0.00115.379-0.027-0.0270.0000.0000.0000.000
33A173ARG10.7930.87716.6680.2790.2790.0000.0000.0000.000
34A174ILE00.0190.01719.5730.0140.0140.0000.0000.0000.000
35A175ARG10.8680.90521.4420.1680.1680.0000.0000.0000.000
36A176LYS10.9080.95922.1610.0920.0920.0000.0000.0000.000
37A177THR0-0.029-0.04520.2750.0060.0060.0000.0000.0000.000
38A178LYS10.8270.91114.6720.3550.3550.0000.0000.0000.000
39A179GLY00.0600.03918.739-0.019-0.0190.0000.0000.0000.000
40A180THR00.017-0.00520.9710.0050.0050.0000.0000.0000.000
41A181GLN0-0.010-0.01722.6620.0010.0010.0000.0000.0000.000
42A182GLU-1-0.764-0.88123.525-0.108-0.1080.0000.0000.0000.000
43A183PHE00.0350.02021.1070.0090.0090.0000.0000.0000.000
44A184ILE00.0110.01023.7510.0040.0040.0000.0000.0000.000
45A185GLU-1-0.813-0.90826.990-0.077-0.0770.0000.0000.0000.000
46A186ALA00.0240.01825.4750.0080.0080.0000.0000.0000.000
47A187ALA00.0070.01826.4650.0060.0060.0000.0000.0000.000
48A188ILE0-0.032-0.02528.1670.0070.0070.0000.0000.0000.000
49A189VAL0-0.028-0.01530.7690.0060.0060.0000.0000.0000.000
50A190THR0-0.012-0.02827.8170.0070.0070.0000.0000.0000.000
51A191LEU0-0.022-0.02228.0660.0030.0030.0000.0000.0000.000
52A192LYS10.8390.92531.6800.0850.0850.0000.0000.0000.000
53A193LYS10.7980.90632.5220.0630.0630.0000.0000.0000.000
54A194TYR0-0.049-0.05230.5130.0030.0030.0000.0000.0000.000
55A195PRO00.0340.00232.469-0.010-0.0100.0000.0000.0000.000
56A196ASP-1-0.807-0.87832.396-0.122-0.1220.0000.0000.0000.000
57A197TRP0-0.014-0.00523.910-0.013-0.0130.0000.0000.0000.000
58A198THR0-0.022-0.02927.5150.0150.0150.0000.0000.0000.000
59A199ALA0-0.0310.00024.967-0.016-0.0160.0000.0000.0000.000
60A200VAL00.0050.00121.6000.0080.0080.0000.0000.0000.000
61A201VAL0-0.039-0.02721.552-0.011-0.0110.0000.0000.0000.000
62A202ILE00.0220.02418.3100.0170.0170.0000.0000.0000.000
63A203GLY00.0460.01518.631-0.062-0.0620.0000.0000.0000.000
64A204GLU-1-0.826-0.91720.778-0.228-0.2280.0000.0000.0000.000
65A205ALA0-0.036-0.00422.523-0.012-0.0120.0000.0000.0000.000
66A206THR0-0.015-0.03823.1440.0060.0060.0000.0000.0000.000
67A207PRO00.068-0.00125.7920.0110.0110.0000.0000.0000.000
68A208ARG10.9010.96426.1200.1340.1340.0000.0000.0000.000
69A209ASP-1-0.706-0.80324.763-0.186-0.1860.0000.0000.0000.000
70A210LEU00.0380.02727.782-0.003-0.0030.0000.0000.0000.000
71A211ASP-1-0.912-0.96030.256-0.112-0.1120.0000.0000.0000.000
72A212PHE00.0020.00224.6160.0060.0060.0000.0000.0000.000
73A213LYS10.8450.89927.3680.1820.1820.0000.0000.0000.000
74A214LYS10.9760.99028.9770.1120.1120.0000.0000.0000.000
75A215GLU-1-0.822-0.87731.889-0.085-0.0850.0000.0000.0000.000
76A216LEU0-0.043-0.01626.1930.0040.0040.0000.0000.0000.000
77A217GLU-1-0.782-0.88230.459-0.161-0.1610.0000.0000.0000.000
78A218GLN0-0.055-0.03432.4380.0070.0070.0000.0000.0000.000
79A219LYS10.8500.92231.1610.0940.0940.0000.0000.0000.000
80A220VAL00.0210.01330.2260.0050.0050.0000.0000.0000.000
81A221LYS10.8820.93433.3630.1080.1080.0000.0000.0000.000
82A222GLN0-0.016-0.00936.7930.0020.0020.0000.0000.0000.000
83A223ALA0-0.0100.01635.1130.0060.0060.0000.0000.0000.000
84A224GLY00.0260.01137.2230.0030.0030.0000.0000.0000.000
85A225LEU0-0.022-0.00833.0350.0000.0000.0000.0000.0000.000
86A226ASP-1-0.795-0.89433.220-0.119-0.1190.0000.0000.0000.000
87A227LYS10.8250.90233.6730.0960.0960.0000.0000.0000.000
88A228GLN0-0.017-0.00831.4720.0040.0040.0000.0000.0000.000
89A229ILE0-0.015-0.00127.563-0.008-0.0080.0000.0000.0000.000
90A230ILE0-0.0110.00127.5320.0070.0070.0000.0000.0000.000
91A231PHE0-0.010-0.02425.547-0.021-0.0210.0000.0000.0000.000
92A232ILE0-0.0120.00123.4070.0160.0160.0000.0000.0000.000
93A233GLY0-0.0050.00524.455-0.011-0.0110.0000.0000.0000.000
94A234PHE0-0.040-0.03520.823-0.024-0.0240.0000.0000.0000.000
95A235ILE0-0.004-0.00122.8300.0250.0250.0000.0000.0000.000
96A236ALA0-0.029-0.01721.689-0.035-0.0350.0000.0000.0000.000
97A237ASP-1-0.815-0.90920.985-0.495-0.4950.0000.0000.0000.000
98A238SER0-0.032-0.01715.999-0.041-0.0410.0000.0000.0000.000
99A239ASN0-0.029-0.02716.261-0.151-0.1510.0000.0000.0000.000
100A240GLU-1-0.782-0.88718.192-0.404-0.4040.0000.0000.0000.000
101A241ILE00.0170.01714.2140.0070.0070.0000.0000.0000.000
102A242PRO00.010-0.00113.3730.0070.0070.0000.0000.0000.000
103A243SER0-0.048-0.02315.1260.0480.0480.0000.0000.0000.000
104A244TRP00.0320.00118.2870.0580.0580.0000.0000.0000.000
105A245TYR0-0.030-0.04211.5530.1160.1160.0000.0000.0000.000
106A246ARG10.8090.90014.3030.7480.7480.0000.0000.0000.000
107A247ALA0-0.0040.00718.0100.0510.0510.0000.0000.0000.000
108A248LEU0-0.054-0.01418.1770.0420.0420.0000.0000.0000.000
109A249ASP-1-0.765-0.85918.709-0.224-0.2240.0000.0000.0000.000
110A250ILE0-0.040-0.01418.7160.0130.0130.0000.0000.0000.000
111A251VAL0-0.007-0.00314.494-0.023-0.0230.0000.0000.0000.000
112A252VAL0-0.007-0.00316.9180.0410.0410.0000.0000.0000.000
113A253CYS0-0.036-0.00311.774-0.056-0.0560.0000.0000.0000.000
114A254ALA00.0490.01615.1140.0540.0540.0000.0000.0000.000
115A255SER0-0.052-0.03214.8960.0460.0460.0000.0000.0000.000
116A256HIS0-0.047-0.04416.9580.0490.0490.0000.0000.0000.000
117A257LYS10.9230.94916.683-0.009-0.0090.0000.0000.0000.000
118A258GLU-1-0.817-0.87014.830-0.212-0.2120.0000.0000.0000.000
119A259GLY00.0280.02111.117-0.081-0.0810.0000.0000.0000.000
120A260PHE00.0010.0026.3650.1510.1510.0000.0000.0000.000
121A261GLY00.0640.0485.557-0.237-0.2370.0000.0000.0000.000
122A262LEU0-0.012-0.0043.772-0.1270.0420.000-0.047-0.1220.000
123A263PRO00.0550.0235.998-0.010-0.0100.0000.0000.0000.000
124A264ALA00.0290.0149.0070.1260.1260.0000.0000.0000.000
125A265LEU00.0210.0092.433-0.282-0.1050.947-0.413-0.712-0.001
126A266GLU-1-0.843-0.9056.529-1.787-1.7870.0000.0000.0000.000
127A267ALA00.0240.0158.8120.2340.2340.0000.0000.0000.000
128A268MET0-0.042-0.0038.7380.0870.0870.0000.0000.0000.000
129A269ALA00.0120.0067.7000.1570.1570.0000.0000.0000.000
130A270SER0-0.035-0.0369.7800.1320.1320.0000.0000.0000.000
131A271LYS10.8310.91912.6850.3220.3220.0000.0000.0000.000
132A272CYS0-0.044-0.00214.1200.0380.0380.0000.0000.0000.000
133A273ALA0-0.0010.00614.8940.0150.0150.0000.0000.0000.000
134A274VAL0-0.010-0.01412.244-0.045-0.0450.0000.0000.0000.000
135A275ILE00.0130.02215.5040.0620.0620.0000.0000.0000.000
136A276ALA0-0.009-0.01013.754-0.060-0.0600.0000.0000.0000.000
137A277THR00.0170.00115.7760.0430.0430.0000.0000.0000.000
138A278LYS10.8760.90414.356-0.298-0.2980.0000.0000.0000.000
139A279ALA0-0.036-0.01612.8700.0630.0630.0000.0000.0000.000
140A280GLY0-0.027-0.02511.360-0.062-0.0620.0000.0000.0000.000
141A281ALA00.0450.0179.881-0.158-0.1580.0000.0000.0000.000
142A282TRP0-0.0260.0206.9560.2240.2240.0000.0000.0000.000
143A283PRO0-0.037-0.0246.732-0.124-0.1240.0000.0000.0000.000
144A284GLU-1-0.793-0.9169.6280.5790.5790.0000.0000.0000.000
145A285ILE0-0.055-0.0106.0590.0070.0070.0000.0000.0000.000
146A286ILE0-0.013-0.0029.654-0.044-0.0440.0000.0000.0000.000
147A287VAL0-0.012-0.00612.7570.0330.0330.0000.0000.0000.000
148A288ASP-1-0.793-0.88616.1110.0000.0000.0000.0000.0000.000
149A289ASP-1-0.825-0.90419.0310.0430.0430.0000.0000.0000.000
150A290GLU-1-0.949-0.94615.7360.2600.2600.0000.0000.0000.000
151A291ASN0-0.029-0.05513.377-0.055-0.0550.0000.0000.0000.000
152A292GLY00.0300.00513.937-0.059-0.0590.0000.0000.0000.000
153A293TYR0-0.044-0.05715.7690.0240.0240.0000.0000.0000.000
154A294LEU0-0.030-0.01114.856-0.028-0.0280.0000.0000.0000.000
155A295VAL0-0.018-0.01018.516-0.005-0.0050.0000.0000.0000.000
156A296GLU-1-0.894-0.94919.7410.0760.0760.0000.0000.0000.000
157A297PRO0-0.059-0.03820.096-0.027-0.0270.0000.0000.0000.000
158A298LYS10.8740.93321.7710.0490.0490.0000.0000.0000.000
159A299SER00.0160.01524.4280.0050.0050.0000.0000.0000.000
160A300SER0-0.004-0.01025.5500.0000.0000.0000.0000.0000.000
161A301GLN0-0.015-0.01726.955-0.011-0.0110.0000.0000.0000.000
162A302GLN00.0950.06024.4560.0000.0000.0000.0000.0000.000
163A303ILE0-0.024-0.01521.739-0.004-0.0040.0000.0000.0000.000
164A304ALA00.0240.00924.073-0.010-0.0100.0000.0000.0000.000
165A305ASP-1-0.848-0.90727.052-0.036-0.0360.0000.0000.0000.000
166A306LYS10.8090.87921.720-0.007-0.0070.0000.0000.0000.000
167A307LEU0-0.016-0.00522.271-0.012-0.0120.0000.0000.0000.000
168A308ASP-1-0.760-0.85824.683-0.067-0.0670.0000.0000.0000.000
169A309MET0-0.0140.00425.4020.0020.0020.0000.0000.0000.000
170A310LEU0-0.0040.00719.946-0.003-0.0030.0000.0000.0000.000
171A311ILE0-0.032-0.00924.372-0.006-0.0060.0000.0000.0000.000
172A312SER0-0.034-0.02027.0350.0020.0020.0000.0000.0000.000
173A313ASP-1-0.801-0.87127.465-0.033-0.0330.0000.0000.0000.000
174A314SER00.0380.01525.7450.0000.0000.0000.0000.0000.000
175A315LYS10.8420.90124.8390.0280.0280.0000.0000.0000.000
176A316LEU00.0010.01523.3160.0010.0010.0000.0000.0000.000
177A317ARG10.8140.89021.1780.1420.1420.0000.0000.0000.000
178A318TYR0-0.042-0.04920.087-0.010-0.0100.0000.0000.0000.000
179A319LYS10.8930.96319.788-0.054-0.0540.0000.0000.0000.000
180A320ILE0-0.039-0.00117.3060.0030.0030.0000.0000.0000.000
181A321ALA00.0180.00615.7620.0020.0020.0000.0000.0000.000
182A322GLN0-0.066-0.02714.858-0.070-0.0700.0000.0000.0000.000
183A323ASN00.0260.00414.9170.0030.0030.0000.0000.0000.000
184A324GLY00.0530.02412.0100.0710.0710.0000.0000.0000.000
185A325TYR00.002-0.01410.423-0.018-0.0180.0000.0000.0000.000
186A326ASP-1-0.797-0.87110.7540.0000.0000.0000.0000.0000.000
187A327LEU0-0.0030.0188.9000.1120.1120.0000.0000.0000.000
188A328VAL0-0.033-0.0245.7370.2900.2900.0000.0000.0000.000
189A329THR0-0.066-0.0556.2990.1120.1120.0000.0000.0000.000
190A330THR0-0.045-0.0238.8560.0370.0370.0000.0000.0000.000
191A331LYS10.8800.9427.487-1.384-1.3840.0000.0000.0000.000
192A332TYR00.0170.0012.453-0.1310.3890.559-0.464-0.616-0.001
193A333LYS10.9420.9972.598-2.322-1.6963.164-2.178-1.612-0.020
194A334ILE0-0.023-0.0132.8110.4670.9140.252-0.184-0.5150.000
195A335GLN0-0.035-0.0124.5330.4760.5450.000-0.012-0.0580.000