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: R8J18

Calculation Name: 5H5W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H5W

Chain ID: A

ChEMBL ID:

UniProt ID: P24216

Base Structure: X-ray

Registration Date: 2023-09-24

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1729303.042803
FMO2-HF: Nuclear repulsion 1657836.84916
FMO2-HF: Total energy -71466.193644
FMO2-MP2: Total energy -71674.557612


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:70:LEU)


Summations of interaction energy for fragment #1(A:70:LEU)
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.
-5.607-7.4729.825-3.588-4.370.014
Interaction energy analysis for fragmet #1(A:70:LEU)
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 : -0.015
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].
3A72ALA00.0320.0213.888-0.0091.215-0.003-0.566-0.6540.001
4A73THR00.019-0.0056.2320.4670.4670.0000.0000.0000.000
5A74SER00.0170.0099.3690.0350.0350.0000.0000.0000.000
6A75THR0-0.049-0.03812.7550.0670.0670.0000.0000.0000.000
7A76THR0-0.027-0.02115.263-0.024-0.0240.0000.0000.0000.000
8A77SER00.006-0.00819.1160.0270.0270.0000.0000.0000.000
9A78SER0-0.009-0.01022.018-0.008-0.0080.0000.0000.0000.000
10A79THR0-0.026-0.03325.312-0.001-0.0010.0000.0000.0000.000
11A80THR00.0120.00125.3680.0010.0010.0000.0000.0000.000
12A81ALA00.0210.02526.379-0.002-0.0020.0000.0000.0000.000
13A82PHE00.0480.02521.5820.0080.0080.0000.0000.0000.000
14A83SER0-0.0140.00019.961-0.006-0.0060.0000.0000.0000.000
15A84ALA00.0270.00615.6340.0220.0220.0000.0000.0000.000
16A85THR0-0.0240.01012.636-0.024-0.0240.0000.0000.0000.000
17A86THR00.007-0.0078.5630.0570.0570.0000.0000.0000.000
18A87ALA0-0.0050.0146.484-0.193-0.1930.0000.0000.0000.000
19A88GLY0-0.022-0.0222.264-1.073-0.8641.073-0.766-0.5160.001
20A89ASN0-0.040-0.0452.104-4.534-7.9288.756-2.251-3.1110.012
21A90ALA00.0570.0515.173-0.507-0.411-0.001-0.005-0.0890.000
22A91ILE00.0080.0098.366-0.072-0.0720.0000.0000.0000.000
23A92ALA00.0170.01611.389-0.123-0.1230.0000.0000.0000.000
24A93GLY0-0.005-0.00713.0250.0270.0270.0000.0000.0000.000
25A94LYS10.8490.92116.826-0.127-0.1270.0000.0000.0000.000
26A95TYR0-0.013-0.02514.0780.0150.0150.0000.0000.0000.000
27A96THR0-0.0030.00020.222-0.017-0.0170.0000.0000.0000.000
28A97ILE0-0.024-0.00219.9980.0170.0170.0000.0000.0000.000
29A98SER0-0.036-0.00724.556-0.014-0.0140.0000.0000.0000.000
30A99VAL00.0510.00425.5610.0110.0110.0000.0000.0000.000
31A100THR0-0.054-0.03328.355-0.007-0.0070.0000.0000.0000.000
32A101HIS0-0.009-0.01330.599-0.009-0.0090.0000.0000.0000.000
33A102LEU00.0390.03127.8230.0060.0060.0000.0000.0000.000
34A103ALA00.0140.01227.7120.0000.0000.0000.0000.0000.000
35A104GLN0-0.072-0.04829.604-0.008-0.0080.0000.0000.0000.000
36A105ALA00.0560.03732.5000.0040.0040.0000.0000.0000.000
37A106GLN00.0250.02233.7620.0000.0000.0000.0000.0000.000
38A107THR0-0.045-0.03437.374-0.002-0.0020.0000.0000.0000.000
39A108LEU0-0.032-0.00739.9850.0010.0010.0000.0000.0000.000
40A109THR00.012-0.01643.451-0.002-0.0020.0000.0000.0000.000
41A110THR00.0340.01346.4050.0010.0010.0000.0000.0000.000
42A111ARG10.8310.90849.998-0.013-0.0130.0000.0000.0000.000
43A112THR0-0.028-0.00652.327-0.001-0.0010.0000.0000.0000.000
44A113THR0-0.042-0.04753.5450.0000.0000.0000.0000.0000.000
45A114ARG10.8020.89555.2220.0000.0000.0000.0000.0000.000
46A115ASP-1-0.753-0.86556.755-0.001-0.0010.0000.0000.0000.000
47A116ASP-1-0.815-0.87357.020-0.004-0.0040.0000.0000.0000.000
48A117THR00.0240.00252.2930.0010.0010.0000.0000.0000.000
49A118LYS10.8570.92953.1920.0070.0070.0000.0000.0000.000
50A119THR0-0.024-0.04356.4580.0000.0000.0000.0000.0000.000
51A120ALA0-0.025-0.00857.4530.0000.0000.0000.0000.0000.000
52A121ILE0-0.025-0.02253.9670.0000.0000.0000.0000.0000.000
53A122ALA0-0.018-0.00156.4060.0010.0010.0000.0000.0000.000
54A123THR0-0.079-0.05658.361-0.001-0.0010.0000.0000.0000.000
55A124SER0-0.040-0.02059.9380.0000.0000.0000.0000.0000.000
56A125ASP-1-0.883-0.94256.6900.0040.0040.0000.0000.0000.000
57A126SER0-0.077-0.03553.7730.0010.0010.0000.0000.0000.000
58A127LYS10.8360.88550.373-0.011-0.0110.0000.0000.0000.000
59A128LEU00.0300.02645.5410.0010.0010.0000.0000.0000.000
60A129THR0-0.018-0.01044.6670.0000.0000.0000.0000.0000.000
61A130ILE0-0.0060.00240.0020.0000.0000.0000.0000.0000.000
62A131GLN0-0.015-0.02238.388-0.001-0.0010.0000.0000.0000.000
63A132GLN0-0.015-0.01034.6410.0000.0000.0000.0000.0000.000
64A133GLY00.0700.05235.7050.0010.0010.0000.0000.0000.000
65A134GLY00.002-0.00732.1770.0000.0000.0000.0000.0000.000
66A135ASP-1-0.972-0.99332.3850.0660.0660.0000.0000.0000.000
67A136LYS10.8030.90930.578-0.051-0.0510.0000.0000.0000.000
68A137ASP-1-0.908-0.94734.6580.0320.0320.0000.0000.0000.000
69A138PRO0-0.037-0.00637.548-0.002-0.0020.0000.0000.0000.000
70A139ILE0-0.001-0.00937.671-0.002-0.0020.0000.0000.0000.000
71A140THR0-0.045-0.03341.5260.0000.0000.0000.0000.0000.000
72A141ILE0-0.041-0.02742.442-0.001-0.0010.0000.0000.0000.000
73A142ASP-1-0.815-0.88846.4220.0090.0090.0000.0000.0000.000
74A143ILE0-0.035-0.01748.086-0.001-0.0010.0000.0000.0000.000
75A144SER00.0320.02451.8020.0010.0010.0000.0000.0000.000
76A145ALA00.0840.02855.3760.0000.0000.0000.0000.0000.000
77A146ALA0-0.0280.00357.2910.0000.0000.0000.0000.0000.000
78A147ASN0-0.033-0.02851.065-0.001-0.0010.0000.0000.0000.000
79A148SER00.0270.01052.4560.0000.0000.0000.0000.0000.000
80A149SER00.0300.03254.3380.0000.0000.0000.0000.0000.000
81A150LEU00.0100.00250.8260.0000.0000.0000.0000.0000.000
82A151SER0-0.068-0.05949.483-0.001-0.0010.0000.0000.0000.000
83A152GLY00.0130.02248.7390.0000.0000.0000.0000.0000.000
84A153ILE00.0420.01847.4010.0000.0000.0000.0000.0000.000
85A154ARG10.8180.88144.5460.0080.0080.0000.0000.0000.000
86A155ASP-1-0.824-0.88544.113-0.007-0.0070.0000.0000.0000.000
87A156ALA00.0130.01644.468-0.001-0.0010.0000.0000.0000.000
88A157ILE00.0120.00440.8560.0010.0010.0000.0000.0000.000
89A158ASN0-0.002-0.01139.8660.0020.0020.0000.0000.0000.000
90A159ASN0-0.101-0.06439.518-0.003-0.0030.0000.0000.0000.000
91A160ALA00.0300.02040.274-0.001-0.0010.0000.0000.0000.000
92A161LYS10.8170.91535.3400.0070.0070.0000.0000.0000.000
93A162ALA00.0590.04535.8050.0020.0020.0000.0000.0000.000
94A163GLY00.0250.00533.6180.0020.0020.0000.0000.0000.000
95A164VAL0-0.017-0.00634.3620.0020.0020.0000.0000.0000.000
96A165SER0-0.0160.00536.379-0.003-0.0030.0000.0000.0000.000
97A166ALA00.0160.00638.2540.0020.0020.0000.0000.0000.000
98A167SER0-0.046-0.01941.764-0.003-0.0030.0000.0000.0000.000
99A168ILE0-0.011-0.01943.6750.0010.0010.0000.0000.0000.000
100A169ILE00.0050.01344.187-0.002-0.0020.0000.0000.0000.000
101A170ASN0-0.016-0.01648.0440.0010.0010.0000.0000.0000.000
102A171VAL0-0.003-0.00950.4550.0000.0000.0000.0000.0000.000
103A172GLY00.0280.02752.4100.0000.0000.0000.0000.0000.000
104A173ASN0-0.087-0.07955.3390.0000.0000.0000.0000.0000.000
105A174GLY0-0.0170.00857.9070.0000.0000.0000.0000.0000.000
106A175GLU-1-0.842-0.88056.1630.0010.0010.0000.0000.0000.000
107A176TYR0-0.057-0.03451.818-0.002-0.0020.0000.0000.0000.000
108A177ARG10.8850.94849.638-0.004-0.0040.0000.0000.0000.000
109A178LEU0-0.0090.00246.536-0.002-0.0020.0000.0000.0000.000
110A179SER00.0260.01042.7560.0020.0020.0000.0000.0000.000
111A180VAL0-0.019-0.01040.578-0.002-0.0020.0000.0000.0000.000
112A181THR00.0180.01235.6000.0020.0020.0000.0000.0000.000
113A182SER00.0240.01833.462-0.002-0.0020.0000.0000.0000.000
114A183ASN0-0.043-0.03931.531-0.003-0.0030.0000.0000.0000.000
115A184ASP-1-0.897-0.92027.5720.0230.0230.0000.0000.0000.000
116A185THR0-0.076-0.06727.793-0.002-0.0020.0000.0000.0000.000
117A186GLY00.1030.04029.3890.0050.0050.0000.0000.0000.000
118A187LEU0-0.065-0.03530.824-0.005-0.0050.0000.0000.0000.000
119A188ASP-1-0.845-0.89830.0460.0590.0590.0000.0000.0000.000
120A189ASN0-0.021-0.01729.519-0.002-0.0020.0000.0000.0000.000
121A190ALA0-0.0070.00433.694-0.005-0.0050.0000.0000.0000.000
122A191MET0-0.033-0.01337.1150.0010.0010.0000.0000.0000.000
123A192THR0-0.063-0.03339.6470.0010.0010.0000.0000.0000.000
124A193LEU0-0.027-0.00642.549-0.001-0.0010.0000.0000.0000.000
125A194SER0-0.0040.00745.6040.0000.0000.0000.0000.0000.000
126A195VAL00.0320.00248.718-0.001-0.0010.0000.0000.0000.000
127A196SER0-0.033-0.00951.4780.0000.0000.0000.0000.0000.000
128A197GLY00.0390.00054.017-0.001-0.0010.0000.0000.0000.000
129A198ASP-1-0.740-0.87056.5790.0060.0060.0000.0000.0000.000
130A199ASP-1-0.865-0.93156.6890.0110.0110.0000.0000.0000.000
131A200ALA0-0.0260.02258.0360.0000.0000.0000.0000.0000.000
132A201LEU00.003-0.01052.0580.0000.0000.0000.0000.0000.000
133A202GLN00.0700.03451.7460.0000.0000.0000.0000.0000.000
134A203SER0-0.075-0.06353.4320.0010.0010.0000.0000.0000.000
135A204PHE0-0.033-0.01251.8110.0000.0000.0000.0000.0000.000
136A205MET0-0.041-0.02546.858-0.001-0.0010.0000.0000.0000.000
137A206GLY00.0030.02148.7720.0010.0010.0000.0000.0000.000
138A207TYR0-0.038-0.04942.9540.0000.0000.0000.0000.0000.000
139A208ASP-1-0.748-0.84946.1580.0280.0280.0000.0000.0000.000
140A209ALA00.0070.00243.911-0.001-0.0010.0000.0000.0000.000
141A210SER0-0.085-0.05646.0310.0010.0010.0000.0000.0000.000
142A211ALA0-0.022-0.00348.843-0.001-0.0010.0000.0000.0000.000
143A212SER0-0.026-0.02351.2530.0000.0000.0000.0000.0000.000
144A213SER0-0.057-0.02853.768-0.001-0.0010.0000.0000.0000.000
145A214ASN0-0.0070.00349.5990.0000.0000.0000.0000.0000.000
146A215GLY00.0880.05951.760-0.001-0.0010.0000.0000.0000.000
147A216MET0-0.049-0.00846.150-0.002-0.0020.0000.0000.0000.000
148A217GLU-1-0.866-0.93947.7920.0110.0110.0000.0000.0000.000
149A218VAL00.000-0.00341.807-0.001-0.0010.0000.0000.0000.000
150A219SER0-0.038-0.02143.4100.0010.0010.0000.0000.0000.000
151A220VAL00.0130.00736.901-0.001-0.0010.0000.0000.0000.000
152A221ALA00.0230.00938.7990.0010.0010.0000.0000.0000.000
153A222ALA00.0310.02435.385-0.001-0.0010.0000.0000.0000.000
154A223GLN0-0.064-0.04033.0340.0000.0000.0000.0000.0000.000
155A224ASN00.0250.00529.313-0.005-0.0050.0000.0000.0000.000
156A225ALA00.0220.02226.039-0.004-0.0040.0000.0000.0000.000
157A226GLN0-0.037-0.02727.7390.0050.0050.0000.0000.0000.000
158A227LEU00.0060.00522.521-0.009-0.0090.0000.0000.0000.000
159A228THR0-0.017-0.00726.0030.0060.0060.0000.0000.0000.000
160A229VAL00.0350.01019.548-0.011-0.0110.0000.0000.0000.000
161A230ASN0-0.023-0.03020.147-0.007-0.0070.0000.0000.0000.000
162A231ASN0-0.036-0.02523.6760.0020.0020.0000.0000.0000.000
163A232VAL00.0010.02222.548-0.007-0.0070.0000.0000.0000.000
164A233ALA00.0010.00024.845-0.003-0.0030.0000.0000.0000.000
165A234ILE0-0.015-0.01020.8340.0120.0120.0000.0000.0000.000
166A235GLU-1-0.829-0.88625.1580.0650.0650.0000.0000.0000.000
167A236ASN0-0.037-0.03921.902-0.002-0.0020.0000.0000.0000.000
168A237SER00.0290.00425.589-0.006-0.0060.0000.0000.0000.000
169A238SER00.0100.01622.275-0.017-0.0170.0000.0000.0000.000
170A239ASN00.0390.00424.5830.0120.0120.0000.0000.0000.000
171A240THR0-0.047-0.02318.746-0.006-0.0060.0000.0000.0000.000
172A241ILE0-0.0090.00718.9090.0060.0060.0000.0000.0000.000
173A242SER0-0.018-0.01514.412-0.008-0.0080.0000.0000.0000.000
174A243ASP-1-0.840-0.90614.8190.1940.1940.0000.0000.0000.000
175A244ALA0-0.013-0.01017.1090.0290.0290.0000.0000.0000.000
176A245LEU0-0.042-0.02615.1460.0040.0040.0000.0000.0000.000
177A246GLU-1-0.897-0.94611.3560.7560.7560.0000.0000.0000.000
178A247ASN0-0.087-0.0457.315-0.117-0.1170.0000.0000.0000.000
179A248ILE00.0200.0099.281-0.115-0.1150.0000.0000.0000.000
180A249THR0-0.022-0.01312.103-0.011-0.0110.0000.0000.0000.000
181A250LEU0-0.0020.00714.671-0.038-0.0380.0000.0000.0000.000
182A251ASN0-0.011-0.00117.6820.0010.0010.0000.0000.0000.000
183A252LEU0-0.007-0.00120.803-0.003-0.0030.0000.0000.0000.000
184A253ASN0-0.061-0.04823.683-0.004-0.0040.0000.0000.0000.000
185A254ASP-1-0.872-0.93427.1890.0030.0030.0000.0000.0000.000
186A255VAL0-0.0170.00028.8840.0060.0060.0000.0000.0000.000
187A256THR0-0.0330.00427.480-0.002-0.0020.0000.0000.0000.000
188A257THR0-0.005-0.01430.6470.0010.0010.0000.0000.0000.000
189A258GLY00.0020.00332.203-0.003-0.0030.0000.0000.0000.000
190A259ASN0-0.019-0.01828.3230.0100.0100.0000.0000.0000.000
191A260GLN00.0420.05826.561-0.011-0.0110.0000.0000.0000.000
192A261THR0-0.037-0.03422.8940.0120.0120.0000.0000.0000.000
193A262LEU00.0270.04716.468-0.018-0.0180.0000.0000.0000.000
194A263THR0-0.067-0.04318.0820.0220.0220.0000.0000.0000.000
195A264ILE00.0320.02311.770-0.032-0.0320.0000.0000.0000.000
196A265THR0-0.015-0.01713.5600.0570.0570.0000.0000.0000.000
197A266GLN00.0370.0227.6090.1110.1110.0000.0000.0000.000
198A267ASP-1-0.881-0.9088.935-0.640-0.6400.0000.0000.0000.000