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: 981K2

Calculation Name: 1H99-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H99

Chain ID: A

ChEMBL ID:

UniProt ID: P39805

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2639156.249454
FMO2-HF: Nuclear repulsion 2547548.788285
FMO2-HF: Total energy -91607.461168
FMO2-MP2: Total energy -91875.019289


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:54:GLY)


Summations of interaction energy for fragment #1(A:54: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.
-0.2172.6670.388-1.283-1.9880.001
Interaction energy analysis for fragmet #1(A:54:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.021
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].
3A56MET0-0.026-0.0353.151-0.0151.4430.031-0.697-0.7920.002
4A57GLU-1-0.853-0.9182.691-3.104-1.8090.358-0.568-1.084-0.001
5A58LYS10.9720.9824.5602.1582.289-0.001-0.018-0.1120.000
6A59PHE0-0.062-0.0237.1010.4130.4130.0000.0000.0000.000
7A60LYS10.9050.9576.4911.2601.2600.0000.0000.0000.000
8A61THR0-0.036-0.0066.8330.1570.1570.0000.0000.0000.000
9A62LEU00.0130.0188.781-0.155-0.1550.0000.0000.0000.000
10A63LEU0-0.045-0.0305.006-0.159-0.1590.0000.0000.0000.000
11A64TYR0-0.063-0.0638.1800.1760.1760.0000.0000.0000.000
12A65ASP-1-0.906-0.94010.837-0.233-0.2330.0000.0000.0000.000
13A66ILE0-0.030-0.02112.6970.0320.0320.0000.0000.0000.000
14A67PRO00.0160.00715.4450.0280.0280.0000.0000.0000.000
15A68ILE00.0640.02419.136-0.016-0.0160.0000.0000.0000.000
16A69GLU-1-0.878-0.94621.024-0.117-0.1170.0000.0000.0000.000
17A70CYS0-0.051-0.01419.7130.0010.0010.0000.0000.0000.000
18A71MET0-0.017-0.01115.8890.0000.0000.0000.0000.0000.000
19A72GLU-1-0.858-0.92821.236-0.116-0.1160.0000.0000.0000.000
20A73VAL00.0300.00524.8810.0060.0060.0000.0000.0000.000
21A74SER0-0.052-0.00921.5070.0090.0090.0000.0000.0000.000
22A75GLU-1-0.938-0.98424.258-0.156-0.1560.0000.0000.0000.000
23A76GLU-1-0.928-0.96825.709-0.104-0.1040.0000.0000.0000.000
24A77ILE00.012-0.00826.5730.0080.0080.0000.0000.0000.000
25A78ILE0-0.045-0.01523.7450.0070.0070.0000.0000.0000.000
26A79SER0-0.049-0.01128.1350.0070.0070.0000.0000.0000.000
27A80TYR00.0430.01830.6440.0070.0070.0000.0000.0000.000
28A81ALA00.021-0.00630.2310.0060.0060.0000.0000.0000.000
29A82LYS10.8940.94326.6060.1730.1730.0000.0000.0000.000
30A83LEU0-0.046-0.00132.7190.0060.0060.0000.0000.0000.000
31A84GLN0-0.047-0.02935.7100.0070.0070.0000.0000.0000.000
32A85LEU0-0.026-0.01632.3770.0030.0030.0000.0000.0000.000
33A86GLY0-0.0030.01435.8790.0030.0030.0000.0000.0000.000
34A87LYS10.9120.96633.4800.1210.1210.0000.0000.0000.000
35A88LYS10.9730.98626.3770.1590.1590.0000.0000.0000.000
36A89LEU0-0.004-0.00526.962-0.002-0.0020.0000.0000.0000.000
37A90ASN0-0.017-0.01021.590-0.014-0.0140.0000.0000.0000.000
38A91ASP-1-0.815-0.91520.728-0.231-0.2310.0000.0000.0000.000
39A92SER0-0.089-0.04418.696-0.013-0.0130.0000.0000.0000.000
40A93ILE0-0.0050.00119.590-0.022-0.0220.0000.0000.0000.000
41A94TYR00.0830.03620.1430.0080.0080.0000.0000.0000.000
42A95VAL0-0.0100.00614.537-0.001-0.0010.0000.0000.0000.000
43A96SER00.0160.00017.487-0.005-0.0050.0000.0000.0000.000
44A97LEU00.0410.01319.3050.0100.0100.0000.0000.0000.000
45A98THR0-0.010-0.00617.3280.0270.0270.0000.0000.0000.000
46A99ASP-1-0.843-0.91415.456-0.440-0.4400.0000.0000.0000.000
47A100HIS0-0.029-0.02817.7880.0080.0080.0000.0000.0000.000
48A101ILE00.007-0.00821.1260.0230.0230.0000.0000.0000.000
49A102ASN00.0340.02616.9430.0480.0480.0000.0000.0000.000
50A103PHE0-0.014-0.02315.2390.0370.0370.0000.0000.0000.000
51A104ALA0-0.022-0.00820.9290.0210.0210.0000.0000.0000.000
52A105ILE00.0220.01123.9060.0190.0190.0000.0000.0000.000
53A106GLN0-0.028-0.01618.582-0.005-0.0050.0000.0000.0000.000
54A107ARG10.7880.89322.1240.2060.2060.0000.0000.0000.000
55A108ASN00.0360.02125.6010.0140.0140.0000.0000.0000.000
56A109GLN00.0370.01726.1130.0110.0110.0000.0000.0000.000
57A110LYS10.8510.94222.8650.1420.1420.0000.0000.0000.000
58A111GLY00.0050.00627.9710.0060.0060.0000.0000.0000.000
59A112LEU0-0.091-0.03625.9520.0010.0010.0000.0000.0000.000
60A113ASP-1-0.893-0.94629.349-0.092-0.0920.0000.0000.0000.000
61A114ILE0-0.081-0.04227.1400.0020.0020.0000.0000.0000.000
62A115LYS10.9420.96630.4940.0910.0910.0000.0000.0000.000
63A116ASN0-0.027-0.00931.272-0.005-0.0050.0000.0000.0000.000
64A117ALA0-0.002-0.01532.5720.0060.0060.0000.0000.0000.000
65A118LEU00.0510.03831.5790.0050.0050.0000.0000.0000.000
66A119LEU0-0.0040.02734.5740.0000.0000.0000.0000.0000.000
67A120TRP00.047-0.00535.8750.0010.0010.0000.0000.0000.000
68A121GLU-1-0.870-0.94237.253-0.091-0.0910.0000.0000.0000.000
69A122THR0-0.025-0.02033.099-0.003-0.0030.0000.0000.0000.000
70A123LYS10.7720.89236.1050.0870.0870.0000.0000.0000.000
71A124ARG10.9020.95538.6210.0740.0740.0000.0000.0000.000
72A125LEU00.005-0.01737.8840.0040.0040.0000.0000.0000.000
73A126TYR00.0110.02233.537-0.002-0.0020.0000.0000.0000.000
74A127LYS10.9810.99436.5570.0770.0770.0000.0000.0000.000
75A128ASP-1-0.879-0.94237.372-0.091-0.0910.0000.0000.0000.000
76A129GLU-1-0.780-0.86132.387-0.122-0.1220.0000.0000.0000.000
77A130PHE0-0.016-0.02133.468-0.003-0.0030.0000.0000.0000.000
78A131ALA0-0.049-0.02035.3360.0010.0010.0000.0000.0000.000
79A132ILE00.0240.02331.5690.0010.0010.0000.0000.0000.000
80A133GLY00.0200.01531.429-0.003-0.0030.0000.0000.0000.000
81A134LYS10.8110.87632.4280.0880.0880.0000.0000.0000.000
82A135GLU-1-0.884-0.93534.936-0.087-0.0870.0000.0000.0000.000
83A136ALA00.0310.00929.5880.0000.0000.0000.0000.0000.000
84A137LEU0-0.071-0.03830.551-0.002-0.0020.0000.0000.0000.000
85A138VAL0-0.0260.00232.4090.0040.0040.0000.0000.0000.000
86A139MET0-0.0080.01030.999-0.001-0.0010.0000.0000.0000.000
87A140VAL00.0250.01327.5340.0000.0000.0000.0000.0000.000
88A141LYS10.8720.97130.0130.0770.0770.0000.0000.0000.000
89A142ASN0-0.035-0.02633.0070.0080.0080.0000.0000.0000.000
90A143LYS10.8320.93327.1520.1210.1210.0000.0000.0000.000
91A144THR00.0240.00526.6890.0020.0020.0000.0000.0000.000
92A145GLY0-0.018-0.00229.8000.0060.0060.0000.0000.0000.000
93A146VAL0-0.041-0.02228.8860.0060.0060.0000.0000.0000.000
94A147SER0-0.028-0.02731.823-0.002-0.0020.0000.0000.0000.000
95A148LEU00.0180.01527.6720.0020.0020.0000.0000.0000.000
96A149PRO00.0180.01930.9910.0050.0050.0000.0000.0000.000
97A150GLU-1-0.737-0.87632.860-0.091-0.0910.0000.0000.0000.000
98A151ASP-1-0.816-0.92232.246-0.106-0.1060.0000.0000.0000.000
99A152GLU-1-0.737-0.87727.075-0.175-0.1750.0000.0000.0000.000
100A153ALA0-0.0200.01129.436-0.009-0.0090.0000.0000.0000.000
101A154GLY00.001-0.00831.622-0.003-0.0030.0000.0000.0000.000
102A155PHE00.002-0.00926.403-0.004-0.0040.0000.0000.0000.000
103A156ILE00.0080.01526.633-0.013-0.0130.0000.0000.0000.000
104A157ALA00.0270.01327.877-0.006-0.0060.0000.0000.0000.000
105A158LEU00.015-0.00627.705-0.001-0.0010.0000.0000.0000.000
106A159HIS0-0.033-0.00821.735-0.014-0.0140.0000.0000.0000.000
107A160ILE0-0.009-0.00825.679-0.009-0.0090.0000.0000.0000.000
108A161VAL00.0310.01128.1630.0000.0000.0000.0000.0000.000
109A162ASN0-0.004-0.00924.3830.0090.0090.0000.0000.0000.000
110A163ALA0-0.084-0.02925.242-0.005-0.0050.0000.0000.0000.000
111A164GLH0-0.040-0.08226.2940.0080.0080.0000.0000.0000.000
112A165LEU0-0.008-0.01126.8830.0100.0100.0000.0000.0000.000
113A166ASN0-0.109-0.03825.0660.0030.0030.0000.0000.0000.000
114A167GLU-1-0.937-0.95929.326-0.119-0.1190.0000.0000.0000.000
115A168GLU-1-0.932-0.96233.003-0.095-0.0950.0000.0000.0000.000
116A169MET0-0.019-0.00331.6390.0020.0020.0000.0000.0000.000
117A170PRO00.0370.00237.2220.0020.0020.0000.0000.0000.000
118A171ASN00.0190.01040.7610.0060.0060.0000.0000.0000.000
119A172ILE00.0250.01536.6540.0020.0020.0000.0000.0000.000
120A173ILE00.0440.03238.5550.0020.0020.0000.0000.0000.000
121A174ASN0-0.036-0.01541.1840.0040.0040.0000.0000.0000.000
122A175ILE0-0.004-0.00342.0000.0030.0030.0000.0000.0000.000
123A176THR0-0.022-0.03739.4800.0030.0030.0000.0000.0000.000
124A177LYS10.9951.02342.9360.0660.0660.0000.0000.0000.000
125A178VAL00.0200.01445.5590.0030.0030.0000.0000.0000.000
126A179MET0-0.062-0.02242.5070.0010.0010.0000.0000.0000.000
127A180GLU-1-0.915-0.95442.465-0.076-0.0760.0000.0000.0000.000
128A181GLU-1-0.788-0.83946.820-0.055-0.0550.0000.0000.0000.000
129A182ILE00.002-0.00650.2810.0030.0030.0000.0000.0000.000
130A183LEU00.0050.00045.6820.0030.0030.0000.0000.0000.000
131A184SER0-0.034-0.03649.4800.0020.0020.0000.0000.0000.000
132A185ILE0-0.046-0.01451.5000.0030.0030.0000.0000.0000.000
133A186VAL0-0.004-0.00952.9840.0020.0020.0000.0000.0000.000
134A187LYS10.9490.98447.9490.0600.0600.0000.0000.0000.000
135A188TYR0-0.001-0.01053.5870.0020.0020.0000.0000.0000.000
136A189HIS0-0.030-0.03156.2830.0020.0020.0000.0000.0000.000
137A190PHE0-0.002-0.01757.0170.0020.0020.0000.0000.0000.000
138A191LYS10.8180.94956.6360.0410.0410.0000.0000.0000.000
139A192ILE0-0.0070.00153.4680.0010.0010.0000.0000.0000.000
140A193GLU-1-0.907-0.95348.609-0.056-0.0560.0000.0000.0000.000
141A194PHE00.003-0.01447.3670.0020.0020.0000.0000.0000.000
142A195ASN00.0090.00946.065-0.004-0.0040.0000.0000.0000.000
143A196GLU-1-0.938-1.00142.222-0.076-0.0760.0000.0000.0000.000
144A197GLU-1-0.855-0.91839.713-0.083-0.0830.0000.0000.0000.000
145A198SER0-0.097-0.03042.8860.0010.0010.0000.0000.0000.000
146A199LEU00.0440.00143.407-0.002-0.0020.0000.0000.0000.000
147A200HIS0-0.006-0.01445.918-0.001-0.0010.0000.0000.0000.000
148A201TYR00.0650.04043.2420.0020.0020.0000.0000.0000.000
149A202TYR00.0210.01939.6960.0000.0000.0000.0000.0000.000
150A203ARG10.9330.97144.3020.0550.0550.0000.0000.0000.000
151A204PHE00.0290.01247.0120.0000.0000.0000.0000.0000.000
152A205VAL00.0530.02542.6910.0000.0000.0000.0000.0000.000
153A206THR0-0.038-0.02643.329-0.004-0.0040.0000.0000.0000.000
154A207ASP-1-0.808-0.86344.728-0.058-0.0580.0000.0000.0000.000
155A208LEU0-0.049-0.01847.0240.0010.0010.0000.0000.0000.000
156A209LYS10.9450.97540.1630.0870.0870.0000.0000.0000.000
157A210PHE0-0.084-0.03744.928-0.001-0.0010.0000.0000.0000.000
158A211PHE00.006-0.00647.1920.0010.0010.0000.0000.0000.000
159A212ALA00.0230.01746.4700.0010.0010.0000.0000.0000.000
160A213GLN0-0.006-0.00342.3330.0000.0000.0000.0000.0000.000
161A214ARG10.7940.86546.5530.0520.0520.0000.0000.0000.000
162A215LEU0-0.053-0.01149.9820.0010.0010.0000.0000.0000.000
163A216PHE00.0210.00246.9950.0010.0010.0000.0000.0000.000
164A217ASN0-0.095-0.04345.363-0.001-0.0010.0000.0000.0000.000
165A218GLY00.0520.03649.0380.0010.0010.0000.0000.0000.000
166A219THR0-0.029-0.00850.4400.0020.0020.0000.0000.0000.000
167A220HIS0-0.053-0.03053.2840.0010.0010.0000.0000.0000.000
168A221MET00.0080.00154.488-0.001-0.0010.0000.0000.0000.000
169A222GLU-1-0.918-0.96058.279-0.039-0.0390.0000.0000.0000.000
170A223SER0-0.0160.01760.8010.0010.0010.0000.0000.0000.000
171A224GLU-1-0.989-1.01760.036-0.041-0.0410.0000.0000.0000.000
172A225ASP-1-0.834-0.92663.535-0.031-0.0310.0000.0000.0000.000
173A226ASP-1-0.868-0.93364.447-0.036-0.0360.0000.0000.0000.000
174A227PHE0-0.0310.00264.2410.0000.0000.0000.0000.0000.000
175A228LEU0-0.039-0.01360.7520.0000.0000.0000.0000.0000.000
176A229LEU0-0.057-0.03061.824-0.001-0.0010.0000.0000.0000.000
177A230ASP-1-0.821-0.94764.366-0.031-0.0310.0000.0000.0000.000
178A231THR0-0.0060.01065.8960.0010.0010.0000.0000.0000.000
179A232VAL0-0.061-0.03361.0790.0000.0000.0000.0000.0000.000
180A233LYS10.8500.93064.4820.0320.0320.0000.0000.0000.000
181A234GLU-1-0.908-0.94066.585-0.028-0.0280.0000.0000.0000.000
182A235LYS10.8900.93965.5950.0290.0290.0000.0000.0000.000
183A236TYR0-0.011-0.00259.836-0.001-0.0010.0000.0000.0000.000
184A237HIS00.0880.04463.706-0.001-0.0010.0000.0000.0000.000
185A238ARG10.9290.96663.5150.0300.0300.0000.0000.0000.000
186A239ALA00.0370.02359.429-0.001-0.0010.0000.0000.0000.000
187A240TYR00.0670.02260.7120.0000.0000.0000.0000.0000.000
188A241GLU-1-0.967-0.98862.865-0.032-0.0320.0000.0000.0000.000
189A242CYS0-0.038-0.00357.7990.0000.0000.0000.0000.0000.000
190A243THR00.015-0.00858.796-0.001-0.0010.0000.0000.0000.000
191A244LYS10.9640.99559.8670.0320.0320.0000.0000.0000.000
192A245LYS10.8690.95060.2520.0390.0390.0000.0000.0000.000
193A246ILE00.0140.01355.1170.0000.0000.0000.0000.0000.000
194A247GLN00.0230.01157.9180.0000.0000.0000.0000.0000.000
195A248THR0-0.030-0.01959.8030.0000.0000.0000.0000.0000.000
196A249TYR0-0.089-0.06552.8670.0010.0010.0000.0000.0000.000
197A250ILE00.0250.01253.413-0.001-0.0010.0000.0000.0000.000
198A251GLU-1-0.914-0.95056.953-0.038-0.0380.0000.0000.0000.000
199A252ARG10.8430.90060.0100.0380.0380.0000.0000.0000.000
200A253GLU-1-0.955-0.96354.713-0.047-0.0470.0000.0000.0000.000
201A254TYR0-0.083-0.07851.117-0.002-0.0020.0000.0000.0000.000
202A255GLU-1-0.964-0.96155.961-0.043-0.0430.0000.0000.0000.000
203A256HIS0-0.0120.00154.0450.0000.0000.0000.0000.0000.000
204A257LYS10.9330.96457.5770.0380.0380.0000.0000.0000.000
205A258LEU0-0.013-0.01254.621-0.001-0.0010.0000.0000.0000.000
206A259THR00.0190.00256.6650.0020.0020.0000.0000.0000.000
207A260SER00.0520.00859.105-0.001-0.0010.0000.0000.0000.000
208A261ASP-1-0.851-0.92756.388-0.043-0.0430.0000.0000.0000.000
209A262GLU-1-0.817-0.89253.368-0.052-0.0520.0000.0000.0000.000
210A263LEU00.0020.00055.893-0.001-0.0010.0000.0000.0000.000
211A264LEU00.0030.02058.2620.0000.0000.0000.0000.0000.000
212A265TYR0-0.010-0.01653.2220.0000.0000.0000.0000.0000.000
213A266LEU00.0130.02453.576-0.001-0.0010.0000.0000.0000.000
214A267THR00.016-0.00755.3190.0000.0000.0000.0000.0000.000
215A268ILE0-0.054-0.02355.2050.0010.0010.0000.0000.0000.000
216A269ASH0-0.077-0.10251.2880.0000.0000.0000.0000.0000.000
217A270ILE0-0.0040.00453.5930.0000.0000.0000.0000.0000.000
218A271GLU-1-0.859-0.94455.496-0.037-0.0370.0000.0000.0000.000
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