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: MNQJZ

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 OptHSide
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 -2639459.070584
FMO2-HF: Nuclear repulsion 2547850.23735
FMO2-HF: Total energy -91608.833234
FMO2-MP2: Total energy -91876.357443


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.
0.7533.5360.522-1.314-1.9910
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 : 0.051 / q_NPA : 0.016
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].
3A56MET0-0.016-0.0263.152-0.0191.4230.029-0.695-0.7760.002
4A57GLU-1-0.763-0.8422.647-2.078-0.8890.493-0.593-1.089-0.002
5A58LYS10.9890.9964.5601.7691.9210.000-0.026-0.1260.000
6A59PHE0-0.048-0.0257.1030.3330.3330.0000.0000.0000.000
7A60LYS10.8050.9025.9131.5261.5260.0000.0000.0000.000
8A61THR0-0.050-0.0416.7880.1090.1090.0000.0000.0000.000
9A62LEU00.0030.0168.713-0.131-0.1310.0000.0000.0000.000
10A63LEU0-0.056-0.0364.909-0.176-0.1760.0000.0000.0000.000
11A64TYR0-0.065-0.0658.1480.1670.1670.0000.0000.0000.000
12A65ASP-1-0.915-0.94510.797-0.184-0.1840.0000.0000.0000.000
13A66ILE0-0.029-0.01812.6030.0270.0270.0000.0000.0000.000
14A67PRO00.0330.01715.3540.0200.0200.0000.0000.0000.000
15A68ILE00.0470.01219.048-0.013-0.0130.0000.0000.0000.000
16A69GLU-1-0.872-0.94120.909-0.093-0.0930.0000.0000.0000.000
17A70CYS0-0.055-0.01819.6470.0070.0070.0000.0000.0000.000
18A71MET0-0.010-0.00416.050-0.003-0.0030.0000.0000.0000.000
19A72GLU-1-0.865-0.91621.117-0.096-0.0960.0000.0000.0000.000
20A73VAL00.0290.00624.7580.0050.0050.0000.0000.0000.000
21A74SER0-0.053-0.01421.3150.0070.0070.0000.0000.0000.000
22A75GLU-1-0.951-0.98624.151-0.139-0.1390.0000.0000.0000.000
23A76GLU-1-0.928-0.96625.580-0.087-0.0870.0000.0000.0000.000
24A77ILE00.021-0.00526.4650.0060.0060.0000.0000.0000.000
25A78ILE0-0.041-0.01023.5680.0050.0050.0000.0000.0000.000
26A79SER0-0.051-0.01428.0190.0060.0060.0000.0000.0000.000
27A80TYR00.0310.01330.5140.0060.0060.0000.0000.0000.000
28A81ALA00.018-0.00330.1100.0050.0050.0000.0000.0000.000
29A82LYS10.8880.94026.4120.1490.1490.0000.0000.0000.000
30A83LEU0-0.0420.00032.5960.0050.0050.0000.0000.0000.000
31A84GLN0-0.048-0.03035.5870.0050.0050.0000.0000.0000.000
32A85LEU0-0.019-0.01132.2790.0030.0030.0000.0000.0000.000
33A86GLY0-0.0030.01335.7390.0030.0030.0000.0000.0000.000
34A87LYS10.8360.91933.3390.1060.1060.0000.0000.0000.000
35A88LYS10.8660.93024.7220.1580.1580.0000.0000.0000.000
36A89LEU0-0.002-0.00426.917-0.002-0.0020.0000.0000.0000.000
37A90ASN0-0.015-0.01421.425-0.010-0.0100.0000.0000.0000.000
38A91ASP-1-0.775-0.89320.960-0.192-0.1920.0000.0000.0000.000
39A92SER0-0.005-0.00118.549-0.007-0.0070.0000.0000.0000.000
40A93ILE0-0.025-0.00919.493-0.018-0.0180.0000.0000.0000.000
41A94TYR00.1000.04020.0690.0060.0060.0000.0000.0000.000
42A95VAL0-0.0070.01214.3560.0020.0020.0000.0000.0000.000
43A96SER0-0.026-0.01117.3830.0060.0060.0000.0000.0000.000
44A97LEU00.0390.01019.2330.0100.0100.0000.0000.0000.000
45A98THR0-0.013-0.01517.5130.0220.0220.0000.0000.0000.000
46A99ASP-1-0.830-0.90415.192-0.355-0.3550.0000.0000.0000.000
47A100HIS0-0.028-0.02017.7320.0090.0090.0000.0000.0000.000
48A101ILE00.011-0.00521.0850.0200.0200.0000.0000.0000.000
49A102ASN00.0310.02417.5170.0320.0320.0000.0000.0000.000
50A103PHE0-0.018-0.02515.0570.0320.0320.0000.0000.0000.000
51A104ALA0-0.025-0.00620.9180.0170.0170.0000.0000.0000.000
52A105ILE00.0170.01023.8290.0160.0160.0000.0000.0000.000
53A106GLN0-0.020-0.01418.662-0.004-0.0040.0000.0000.0000.000
54A107ARG10.7900.88822.1710.1600.1600.0000.0000.0000.000
55A108ASN00.0310.01625.6190.0110.0110.0000.0000.0000.000
56A109GLN00.0300.01526.1570.0100.0100.0000.0000.0000.000
57A110LYS10.8620.94823.1810.0920.0920.0000.0000.0000.000
58A111GLY00.0060.00728.0040.0050.0050.0000.0000.0000.000
59A112LEU0-0.097-0.04025.9540.0010.0010.0000.0000.0000.000
60A113ASP-1-0.867-0.93329.372-0.070-0.0700.0000.0000.0000.000
61A114ILE0-0.077-0.03627.1150.0020.0020.0000.0000.0000.000
62A115LYS10.8430.90130.5180.0760.0760.0000.0000.0000.000
63A116ASN0-0.035-0.01531.163-0.004-0.0040.0000.0000.0000.000
64A117ALA00.004-0.00832.5840.0050.0050.0000.0000.0000.000
65A118LEU00.0530.04031.8030.0040.0040.0000.0000.0000.000
66A119LEU0-0.0100.02134.529-0.001-0.0010.0000.0000.0000.000
67A120TRP00.054-0.00535.8670.0000.0000.0000.0000.0000.000
68A121GLU-1-0.868-0.93637.188-0.071-0.0710.0000.0000.0000.000
69A122THR0-0.023-0.02133.044-0.003-0.0030.0000.0000.0000.000
70A123LYS10.7850.89736.0790.0670.0670.0000.0000.0000.000
71A124ARG10.9120.95838.5850.0590.0590.0000.0000.0000.000
72A125LEU0-0.029-0.02237.7720.0030.0030.0000.0000.0000.000
73A126TYR00.0160.02034.077-0.001-0.0010.0000.0000.0000.000
74A127LYS10.9080.95336.5020.0670.0670.0000.0000.0000.000
75A128ASP-1-0.839-0.92237.549-0.073-0.0730.0000.0000.0000.000
76A129GLU-1-0.774-0.85932.304-0.100-0.1000.0000.0000.0000.000
77A130PHE0-0.014-0.02133.400-0.002-0.0020.0000.0000.0000.000
78A131ALA0-0.049-0.01835.2790.0010.0010.0000.0000.0000.000
79A132ILE00.0320.02131.5240.0010.0010.0000.0000.0000.000
80A133GLY00.0210.01531.362-0.003-0.0030.0000.0000.0000.000
81A134LYS10.8200.87432.3630.0690.0690.0000.0000.0000.000
82A135GLU-1-0.899-0.94634.803-0.069-0.0690.0000.0000.0000.000
83A136ALA00.0330.00929.4970.0000.0000.0000.0000.0000.000
84A137LEU0-0.063-0.03430.496-0.001-0.0010.0000.0000.0000.000
85A138VAL0-0.034-0.00232.3480.0040.0040.0000.0000.0000.000
86A139MET00.0060.01330.892-0.001-0.0010.0000.0000.0000.000
87A140VAL00.0190.00927.4060.0000.0000.0000.0000.0000.000
88A141LYS10.8480.95529.9400.0600.0600.0000.0000.0000.000
89A142ASN0-0.039-0.02932.9420.0070.0070.0000.0000.0000.000
90A143LYS10.8380.92427.1870.0990.0990.0000.0000.0000.000
91A144THR00.019-0.00226.6120.0020.0020.0000.0000.0000.000
92A145GLY0-0.0160.00029.7340.0050.0050.0000.0000.0000.000
93A146VAL0-0.041-0.02428.8870.0050.0050.0000.0000.0000.000
94A147SER0-0.014-0.01531.782-0.002-0.0020.0000.0000.0000.000
95A148LEU00.0330.02627.5500.0020.0020.0000.0000.0000.000
96A149PRO00.0290.02131.0000.0030.0030.0000.0000.0000.000
97A150GLU-1-0.755-0.86832.837-0.072-0.0720.0000.0000.0000.000
98A151ASP-1-0.772-0.89232.291-0.080-0.0800.0000.0000.0000.000
99A152GLU-1-0.730-0.86626.982-0.136-0.1360.0000.0000.0000.000
100A153ALA0-0.0150.01429.400-0.008-0.0080.0000.0000.0000.000
101A154GLY00.006-0.00531.577-0.003-0.0030.0000.0000.0000.000
102A155PHE00.000-0.01126.389-0.003-0.0030.0000.0000.0000.000
103A156ILE00.0050.01326.558-0.011-0.0110.0000.0000.0000.000
104A157ALA00.0260.01427.825-0.006-0.0060.0000.0000.0000.000
105A158LEU00.013-0.00427.681-0.002-0.0020.0000.0000.0000.000
106A159HIS0-0.033-0.01422.118-0.012-0.0120.0000.0000.0000.000
107A160ILE0-0.003-0.00725.622-0.008-0.0080.0000.0000.0000.000
108A161VAL00.0330.01628.088-0.001-0.0010.0000.0000.0000.000
109A162ASN00.001-0.01024.6160.0050.0050.0000.0000.0000.000
110A163ALA0-0.078-0.02525.067-0.005-0.0050.0000.0000.0000.000
111A164GLH0-0.038-0.07926.2450.0060.0060.0000.0000.0000.000
112A165LEU0-0.017-0.00626.7550.0080.0080.0000.0000.0000.000
113A166ASN0-0.099-0.03325.1690.0010.0010.0000.0000.0000.000
114A167GLU-1-0.852-0.90929.326-0.103-0.1030.0000.0000.0000.000
115A168GLU-1-0.920-0.95833.002-0.081-0.0810.0000.0000.0000.000
116A169MET0-0.018-0.00531.6960.0020.0020.0000.0000.0000.000
117A170PRO00.0420.00337.2220.0020.0020.0000.0000.0000.000
118A171ASN00.0170.01140.7730.0050.0050.0000.0000.0000.000
119A172ILE00.0300.01536.5510.0020.0020.0000.0000.0000.000
120A173ILE00.0350.03638.2980.0020.0020.0000.0000.0000.000
121A174ASN0-0.015-0.00541.1830.0030.0030.0000.0000.0000.000
122A175ILE0-0.013-0.00741.9980.0030.0030.0000.0000.0000.000
123A176THR0-0.012-0.04039.4990.0020.0020.0000.0000.0000.000
124A177LYS10.8980.95242.9360.0540.0540.0000.0000.0000.000
125A178VAL00.0200.01645.5580.0020.0020.0000.0000.0000.000
126A179MET0-0.052-0.01542.3950.0010.0010.0000.0000.0000.000
127A180GLU-1-0.899-0.94742.326-0.063-0.0630.0000.0000.0000.000
128A181GLU-1-0.746-0.79946.819-0.046-0.0460.0000.0000.0000.000
129A182ILE0-0.003-0.01250.2760.0030.0030.0000.0000.0000.000
130A183LEU00.0040.00445.7280.0020.0020.0000.0000.0000.000
131A184SER0-0.023-0.02549.4270.0020.0020.0000.0000.0000.000
132A185ILE0-0.050-0.01851.4990.0020.0020.0000.0000.0000.000
133A186VAL00.003-0.01053.0380.0020.0020.0000.0000.0000.000
134A187LYS10.8390.91748.3910.0480.0480.0000.0000.0000.000
135A188TYR00.015-0.00453.5860.0020.0020.0000.0000.0000.000
136A189HIS00.0050.00156.2820.0010.0010.0000.0000.0000.000
137A190PHE00.003-0.01356.9970.0020.0020.0000.0000.0000.000
138A191LYS10.7870.92656.6210.0330.0330.0000.0000.0000.000
139A192ILE00.0040.00853.3650.0010.0010.0000.0000.0000.000
140A193GLU-1-0.806-0.89348.675-0.047-0.0470.0000.0000.0000.000
141A194PHE00.006-0.00447.3650.0020.0020.0000.0000.0000.000
142A195ASN0-0.0010.00246.378-0.003-0.0030.0000.0000.0000.000
143A196GLU-1-0.856-0.94042.598-0.060-0.0600.0000.0000.0000.000
144A197GLU-1-0.860-0.92039.887-0.065-0.0650.0000.0000.0000.000
145A198SER0-0.094-0.03042.9430.0010.0010.0000.0000.0000.000
146A199LEU00.0440.00143.421-0.002-0.0020.0000.0000.0000.000
147A200HIS0-0.006-0.01045.971-0.001-0.0010.0000.0000.0000.000
148A201TYR0-0.007-0.02243.3820.0020.0020.0000.0000.0000.000
149A202TYR00.0220.02140.1760.0000.0000.0000.0000.0000.000
150A203ARG10.8600.92244.3350.0430.0430.0000.0000.0000.000
151A204PHE00.0140.00547.0400.0000.0000.0000.0000.0000.000
152A205VAL00.0530.02642.7140.0000.0000.0000.0000.0000.000
153A206THR0-0.038-0.02843.350-0.003-0.0030.0000.0000.0000.000
154A207ASP-1-0.788-0.85244.737-0.046-0.0460.0000.0000.0000.000
155A208LEU0-0.027-0.00447.0950.0000.0000.0000.0000.0000.000
156A209LYS10.9880.98840.2600.0680.0680.0000.0000.0000.000
157A210PHE0-0.084-0.03945.000-0.001-0.0010.0000.0000.0000.000
158A211PHE00.010-0.00547.1770.0010.0010.0000.0000.0000.000
159A212ALA00.0300.02046.4340.0010.0010.0000.0000.0000.000
160A213GLN00.0050.00242.5680.0000.0000.0000.0000.0000.000
161A214ARG10.7620.85346.5170.0410.0410.0000.0000.0000.000
162A215LEU0-0.041-0.01349.9450.0010.0010.0000.0000.0000.000
163A216PHE00.0280.00746.8760.0010.0010.0000.0000.0000.000
164A217ASN0-0.110-0.05345.340-0.001-0.0010.0000.0000.0000.000
165A218GLY00.0500.03548.9820.0010.0010.0000.0000.0000.000
166A219THR0-0.069-0.02351.0400.0010.0010.0000.0000.0000.000
167A220HIS0-0.038-0.03353.2340.0010.0010.0000.0000.0000.000
168A221MET0-0.003-0.00454.775-0.001-0.0010.0000.0000.0000.000
169A222GLU-1-0.914-0.95658.243-0.031-0.0310.0000.0000.0000.000
170A223SER0-0.0120.01660.7890.0010.0010.0000.0000.0000.000
171A224GLU-1-0.993-1.01759.604-0.033-0.0330.0000.0000.0000.000
172A225ASP-1-0.837-0.93263.517-0.024-0.0240.0000.0000.0000.000
173A226ASP-1-0.773-0.86564.444-0.029-0.0290.0000.0000.0000.000
174A227PHE00.0020.01364.1900.0000.0000.0000.0000.0000.000
175A228LEU0-0.043-0.01660.5500.0000.0000.0000.0000.0000.000
176A229LEU0-0.059-0.02261.531-0.001-0.0010.0000.0000.0000.000
177A230ASP-1-0.836-0.92764.374-0.024-0.0240.0000.0000.0000.000
178A231THR0-0.029-0.00365.8920.0010.0010.0000.0000.0000.000
179A232VAL0-0.063-0.03761.0580.0000.0000.0000.0000.0000.000
180A233LYS10.7950.88264.5050.0260.0260.0000.0000.0000.000
181A234GLU-1-0.907-0.93966.603-0.022-0.0220.0000.0000.0000.000
182A235LYS10.8910.93765.5810.0230.0230.0000.0000.0000.000
183A236TYR00.0020.00559.9930.0000.0000.0000.0000.0000.000
184A237HIS00.0710.03863.730-0.001-0.0010.0000.0000.0000.000
185A238ARG10.8770.92763.6050.0240.0240.0000.0000.0000.000
186A239ALA00.0300.01959.454-0.001-0.0010.0000.0000.0000.000
187A240TYR00.0760.02560.7270.0000.0000.0000.0000.0000.000
188A241GLU-1-0.911-0.95462.879-0.026-0.0260.0000.0000.0000.000
189A242CYS0-0.035-0.00357.9160.0000.0000.0000.0000.0000.000
190A243THR00.020-0.00758.801-0.001-0.0010.0000.0000.0000.000
191A244LYS10.9591.00259.8700.0260.0260.0000.0000.0000.000
192A245LYS10.8380.93259.6920.0330.0330.0000.0000.0000.000
193A246ILE00.0040.00555.0910.0000.0000.0000.0000.0000.000
194A247GLN00.0300.01657.9000.0000.0000.0000.0000.0000.000
195A248THR0-0.046-0.03459.7860.0000.0000.0000.0000.0000.000
196A249TYR0-0.084-0.06352.8080.0010.0010.0000.0000.0000.000
197A250ILE00.0280.01353.312-0.001-0.0010.0000.0000.0000.000
198A251GLU-1-0.863-0.93156.935-0.031-0.0310.0000.0000.0000.000
199A252ARG10.8500.90659.9740.0310.0310.0000.0000.0000.000
200A253GLU-1-0.971-0.97154.832-0.039-0.0390.0000.0000.0000.000
201A254TYR0-0.065-0.07250.939-0.002-0.0020.0000.0000.0000.000
202A255GLU-1-0.965-0.96055.961-0.036-0.0360.0000.0000.0000.000
203A256HIS0-0.0040.00454.0880.0000.0000.0000.0000.0000.000
204A257LYS10.8850.95157.5350.0310.0310.0000.0000.0000.000
205A258LEU0-0.011-0.01054.612-0.001-0.0010.0000.0000.0000.000
206A259THR00.0390.00856.9880.0010.0010.0000.0000.0000.000
207A260SER00.034-0.02359.0930.0000.0000.0000.0000.0000.000
208A261ASP-1-0.823-0.89556.279-0.034-0.0340.0000.0000.0000.000
209A262GLU-1-0.798-0.86453.622-0.042-0.0420.0000.0000.0000.000
210A263LEU00.0020.00155.8870.0000.0000.0000.0000.0000.000
211A264LEU00.0130.02158.3600.0000.0000.0000.0000.0000.000
212A265TYR0-0.071-0.06853.2600.0000.0000.0000.0000.0000.000
213A266LEU00.0050.02153.568-0.001-0.0010.0000.0000.0000.000
214A267THR00.013-0.00855.3280.0000.0000.0000.0000.0000.000
215A268ILE0-0.042-0.01755.2080.0010.0010.0000.0000.0000.000
216A269ASH0-0.062-0.08451.1990.0000.0000.0000.0000.0000.000
217A270ILE00.0170.01553.6230.0000.0000.0000.0000.0000.000
218A271GLU-1-0.852-0.92255.521-0.029-0.0290.0000.0000.0000.000
219A272ARG10.7730.88253.2430.0330.0330.0000.0000.0000.000
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