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: 7615K

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2644945.275272
FMO2-HF: Nuclear repulsion 2553336.067324
FMO2-HF: Total energy -91609.207949
FMO2-MP2: Total energy -91876.679237


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.
-0.0791.9531.293-1.585-1.74-0.002
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 : 0.072 / q_NPA : 0.024
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].
3A56MET00.004-0.0123.528-0.9700.4050.001-0.675-0.7010.001
4A57GLU-1-0.747-0.8312.471-0.3870.1691.292-0.884-0.964-0.003
5A58LYS10.9620.9824.3491.4591.5600.000-0.026-0.0750.000
6A59PHE0-0.035-0.0196.9860.2370.2370.0000.0000.0000.000
7A60LYS10.7770.8806.5380.5810.5810.0000.0000.0000.000
8A61THR0-0.044-0.0416.7720.0670.0670.0000.0000.0000.000
9A62LEU00.0060.0168.763-0.136-0.1360.0000.0000.0000.000
10A63LEU0-0.068-0.0345.049-0.095-0.0950.0000.0000.0000.000
11A64TYR0-0.049-0.0608.3410.0140.0140.0000.0000.0000.000
12A65ASP-1-0.903-0.94711.419-0.406-0.4060.0000.0000.0000.000
13A66ILE0-0.046-0.02212.9580.0430.0430.0000.0000.0000.000
14A67PRO00.0360.01715.8360.0240.0240.0000.0000.0000.000
15A68ILE00.0350.00819.599-0.002-0.0020.0000.0000.0000.000
16A69GLU-1-0.869-0.93821.362-0.132-0.1320.0000.0000.0000.000
17A70CYS0-0.059-0.01420.0160.0110.0110.0000.0000.0000.000
18A71MET0-0.015-0.00316.2210.0070.0070.0000.0000.0000.000
19A72GLU-1-0.869-0.92321.130-0.105-0.1050.0000.0000.0000.000
20A73VAL00.0170.00124.8700.0080.0080.0000.0000.0000.000
21A74SER0-0.038-0.00521.1510.0110.0110.0000.0000.0000.000
22A75GLU-1-0.869-0.93724.011-0.104-0.1040.0000.0000.0000.000
23A76GLU-1-0.905-0.95325.624-0.088-0.0880.0000.0000.0000.000
24A77ILE00.027-0.00326.3600.0080.0080.0000.0000.0000.000
25A78ILE0-0.046-0.01123.4490.0070.0070.0000.0000.0000.000
26A79SER0-0.042-0.00827.7590.0080.0080.0000.0000.0000.000
27A80TYR0-0.019-0.03130.3640.0060.0060.0000.0000.0000.000
28A81ALA00.005-0.01029.6260.0040.0040.0000.0000.0000.000
29A82LYS10.8630.92625.6100.1060.1060.0000.0000.0000.000
30A83LEU0-0.043-0.00831.9820.0050.0050.0000.0000.0000.000
31A84GLN0-0.044-0.02835.2160.0050.0050.0000.0000.0000.000
32A85LEU0-0.022-0.00931.9290.0020.0020.0000.0000.0000.000
33A86GLY0-0.0120.00835.6840.0030.0030.0000.0000.0000.000
34A87LYS10.8280.91933.3140.0690.0690.0000.0000.0000.000
35A88LYS10.8400.92625.0200.0840.0840.0000.0000.0000.000
36A89LEU00.0090.00826.637-0.002-0.0020.0000.0000.0000.000
37A90ASN0-0.018-0.02721.7630.0010.0010.0000.0000.0000.000
38A91ASP-1-0.766-0.88821.683-0.114-0.1140.0000.0000.0000.000
39A92SER00.0110.00118.468-0.007-0.0070.0000.0000.0000.000
40A93ILE0-0.026-0.01019.218-0.022-0.0220.0000.0000.0000.000
41A94TYR00.028-0.00219.835-0.007-0.0070.0000.0000.0000.000
42A95VAL0-0.0010.01814.158-0.008-0.0080.0000.0000.0000.000
43A96SER0-0.026-0.01317.227-0.008-0.0080.0000.0000.0000.000
44A97LEU00.0270.00519.118-0.002-0.0020.0000.0000.0000.000
45A98THR00.000-0.01317.5020.0110.0110.0000.0000.0000.000
46A99ASP-1-0.829-0.90315.510-0.382-0.3820.0000.0000.0000.000
47A100HIS0-0.029-0.01417.930-0.002-0.0020.0000.0000.0000.000
48A101ILE00.002-0.00821.2800.0120.0120.0000.0000.0000.000
49A102ASN00.0440.01718.0380.0240.0240.0000.0000.0000.000
50A103PHE0-0.042-0.03815.3400.0170.0170.0000.0000.0000.000
51A104ALA0-0.001-0.00221.2280.0130.0130.0000.0000.0000.000
52A105ILE00.0020.00823.9920.0130.0130.0000.0000.0000.000
53A106GLN0-0.030-0.01919.152-0.007-0.0070.0000.0000.0000.000
54A107ARG10.8030.90622.3370.1830.1830.0000.0000.0000.000
55A108ASN00.004-0.01326.1000.0090.0090.0000.0000.0000.000
56A109GLN00.0220.00926.7830.0130.0130.0000.0000.0000.000
57A110LYS10.8580.94223.5900.1720.1720.0000.0000.0000.000
58A111GLY00.0180.01628.9440.0030.0030.0000.0000.0000.000
59A112LEU0-0.083-0.03726.0540.0020.0020.0000.0000.0000.000
60A113ASP-1-0.843-0.92329.341-0.107-0.1070.0000.0000.0000.000
61A114ILE0-0.046-0.01527.4390.0060.0060.0000.0000.0000.000
62A115LYS10.8260.89830.8290.0950.0950.0000.0000.0000.000
63A116ASN0-0.029-0.01331.294-0.001-0.0010.0000.0000.0000.000
64A117ALA0-0.010-0.01532.8690.0050.0050.0000.0000.0000.000
65A118LEU00.0620.04332.0550.0040.0040.0000.0000.0000.000
66A119LEU0-0.0080.01834.4780.0010.0010.0000.0000.0000.000
67A120TRP00.0420.00136.0250.0020.0020.0000.0000.0000.000
68A121GLU-1-0.867-0.93936.968-0.063-0.0630.0000.0000.0000.000
69A122THR0-0.027-0.02933.1630.0000.0000.0000.0000.0000.000
70A123LYS10.7880.89636.0280.0710.0710.0000.0000.0000.000
71A124ARG10.9100.97238.8740.0520.0520.0000.0000.0000.000
72A125LEU0-0.032-0.00937.6830.0040.0040.0000.0000.0000.000
73A126TYR00.0290.01434.0580.0000.0000.0000.0000.0000.000
74A127LYS10.8600.92136.1110.0540.0540.0000.0000.0000.000
75A128ASP-1-0.836-0.90637.455-0.058-0.0580.0000.0000.0000.000
76A129GLU-1-0.759-0.86031.942-0.078-0.0780.0000.0000.0000.000
77A130PHE0-0.012-0.02133.018-0.005-0.0050.0000.0000.0000.000
78A131ALA0-0.033-0.00535.085-0.001-0.0010.0000.0000.0000.000
79A132ILE00.0360.02231.138-0.001-0.0010.0000.0000.0000.000
80A133GLY00.0100.00431.226-0.004-0.0040.0000.0000.0000.000
81A134LYS10.8240.88132.2550.0710.0710.0000.0000.0000.000
82A135GLU-1-0.830-0.89534.289-0.071-0.0710.0000.0000.0000.000
83A136ALA00.0290.01129.305-0.002-0.0020.0000.0000.0000.000
84A137LEU0-0.066-0.03130.719-0.005-0.0050.0000.0000.0000.000
85A138VAL0-0.0240.00132.4970.0000.0000.0000.0000.0000.000
86A139MET0-0.0040.00930.542-0.002-0.0020.0000.0000.0000.000
87A140VAL00.0150.00627.578-0.003-0.0030.0000.0000.0000.000
88A141LYS10.8350.94730.0750.0780.0780.0000.0000.0000.000
89A142ASN0-0.032-0.03233.3920.0040.0040.0000.0000.0000.000
90A143LYS10.7930.90727.4610.1080.1080.0000.0000.0000.000
91A144THR00.012-0.00627.047-0.002-0.0020.0000.0000.0000.000
92A145GLY0-0.025-0.00130.3040.0010.0010.0000.0000.0000.000
93A146VAL0-0.015-0.02228.9990.0050.0050.0000.0000.0000.000
94A147SER0-0.022-0.01432.0250.0040.0040.0000.0000.0000.000
95A148LEU00.0400.02927.8080.0020.0020.0000.0000.0000.000
96A149PRO00.0240.02331.1870.0060.0060.0000.0000.0000.000
97A150GLU-1-0.779-0.88232.896-0.075-0.0750.0000.0000.0000.000
98A151ASP-1-0.772-0.89632.326-0.090-0.0900.0000.0000.0000.000
99A152GLU-1-0.739-0.85927.084-0.155-0.1550.0000.0000.0000.000
100A153ALA00.0030.02029.337-0.005-0.0050.0000.0000.0000.000
101A154GLY00.0130.00031.5090.0010.0010.0000.0000.0000.000
102A155PHE0-0.002-0.01026.3750.0000.0000.0000.0000.0000.000
103A156ILE0-0.0050.00526.596-0.006-0.0060.0000.0000.0000.000
104A157ALA00.0280.01827.758-0.001-0.0010.0000.0000.0000.000
105A158LEU00.007-0.00627.6620.0010.0010.0000.0000.0000.000
106A159HIS0-0.029-0.01522.062-0.001-0.0010.0000.0000.0000.000
107A160ILE00.0060.00025.470-0.001-0.0010.0000.0000.0000.000
108A161VAL00.0170.00827.8800.0040.0040.0000.0000.0000.000
109A162ASN00.001-0.01124.4190.0100.0100.0000.0000.0000.000
110A163ALA0-0.058-0.01824.6930.0010.0010.0000.0000.0000.000
111A164GLH0-0.020-0.05425.8400.0070.0070.0000.0000.0000.000
112A165LEU0-0.018-0.00126.5110.0070.0070.0000.0000.0000.000
113A166ASN0-0.089-0.03224.8740.0040.0040.0000.0000.0000.000
114A167GLU-1-0.834-0.90829.101-0.059-0.0590.0000.0000.0000.000
115A168GLU-1-0.919-0.95432.808-0.046-0.0460.0000.0000.0000.000
116A169MET0-0.020-0.01631.470-0.001-0.0010.0000.0000.0000.000
117A170PRO00.0460.01337.1260.0010.0010.0000.0000.0000.000
118A171ASN00.0030.00040.7920.0040.0040.0000.0000.0000.000
119A172ILE00.0330.01736.4490.0010.0010.0000.0000.0000.000
120A173ILE00.0260.03138.1750.0010.0010.0000.0000.0000.000
121A174ASN0-0.018-0.00541.0400.0030.0030.0000.0000.0000.000
122A175ILE0-0.021-0.01341.6550.0020.0020.0000.0000.0000.000
123A176THR0-0.013-0.02839.2660.0020.0020.0000.0000.0000.000
124A177LYS10.8960.94242.6990.0330.0330.0000.0000.0000.000
125A178VAL00.0170.01545.4800.0020.0020.0000.0000.0000.000
126A179MET0-0.051-0.01942.1810.0000.0000.0000.0000.0000.000
127A180GLU-1-0.890-0.95042.134-0.038-0.0380.0000.0000.0000.000
128A181GLU-1-0.745-0.79846.661-0.028-0.0280.0000.0000.0000.000
129A182ILE0-0.003-0.00950.1440.0020.0020.0000.0000.0000.000
130A183LEU00.0070.00545.5080.0020.0020.0000.0000.0000.000
131A184SER0-0.013-0.01949.3900.0020.0020.0000.0000.0000.000
132A185ILE0-0.044-0.01951.5300.0020.0020.0000.0000.0000.000
133A186VAL00.031-0.00152.8980.0020.0020.0000.0000.0000.000
134A187LYS10.8240.90848.3800.0280.0280.0000.0000.0000.000
135A188TYR00.024-0.00353.6710.0020.0020.0000.0000.0000.000
136A189HIS0-0.011-0.00156.4710.0010.0010.0000.0000.0000.000
137A190PHE0-0.001-0.01456.7380.0010.0010.0000.0000.0000.000
138A191LYS10.7840.91156.7560.0180.0180.0000.0000.0000.000
139A192ILE00.0010.01453.1270.0010.0010.0000.0000.0000.000
140A193GLU-1-0.784-0.88348.430-0.026-0.0260.0000.0000.0000.000
141A194PHE00.002-0.00646.9980.0010.0010.0000.0000.0000.000
142A195ASN0-0.011-0.00846.342-0.002-0.0020.0000.0000.0000.000
143A196GLU-1-0.830-0.90942.461-0.040-0.0400.0000.0000.0000.000
144A197GLU-1-0.885-0.94239.964-0.044-0.0440.0000.0000.0000.000
145A198SER0-0.070-0.01642.595-0.001-0.0010.0000.0000.0000.000
146A199LEU00.037-0.00143.099-0.001-0.0010.0000.0000.0000.000
147A200HIS0-0.009-0.00345.772-0.002-0.0020.0000.0000.0000.000
148A201TYR0-0.020-0.03043.4650.0010.0010.0000.0000.0000.000
149A202TYR00.0390.02540.1190.0000.0000.0000.0000.0000.000
150A203ARG10.8310.89943.9570.0360.0360.0000.0000.0000.000
151A204PHE00.0100.00346.7260.0000.0000.0000.0000.0000.000
152A205VAL00.0620.02842.1670.0000.0000.0000.0000.0000.000
153A206THR0-0.046-0.03843.119-0.002-0.0020.0000.0000.0000.000
154A207ASP-1-0.793-0.83444.551-0.038-0.0380.0000.0000.0000.000
155A208LEU0-0.026-0.00746.9150.0000.0000.0000.0000.0000.000
156A209LYS10.9780.98540.3170.0550.0550.0000.0000.0000.000
157A210PHE0-0.074-0.03344.940-0.001-0.0010.0000.0000.0000.000
158A211PHE00.0260.00447.0420.0000.0000.0000.0000.0000.000
159A212ALA00.0290.02546.1600.0010.0010.0000.0000.0000.000
160A213GLN00.0250.00142.4390.0020.0020.0000.0000.0000.000
161A214ARG10.7010.80546.2750.0320.0320.0000.0000.0000.000
162A215LEU0-0.025-0.00149.8220.0010.0010.0000.0000.0000.000
163A216PHE00.0410.00646.4610.0010.0010.0000.0000.0000.000
164A217ASN0-0.099-0.04744.958-0.002-0.0020.0000.0000.0000.000
165A218GLY00.0480.02948.6660.0000.0000.0000.0000.0000.000
166A219THR0-0.070-0.02050.9520.0010.0010.0000.0000.0000.000
167A220HIS0-0.032-0.02253.1400.0010.0010.0000.0000.0000.000
168A221MET0-0.003-0.01055.165-0.002-0.0020.0000.0000.0000.000
169A222GLU-1-0.904-0.95658.231-0.027-0.0270.0000.0000.0000.000
170A223SER0-0.058-0.00560.9950.0010.0010.0000.0000.0000.000
171A224GLU-1-0.983-0.99659.216-0.030-0.0300.0000.0000.0000.000
172A225ASP-1-0.840-0.94863.148-0.021-0.0210.0000.0000.0000.000
173A226ASP-1-0.781-0.85764.132-0.023-0.0230.0000.0000.0000.000
174A227PHE00.0290.02464.7850.0000.0000.0000.0000.0000.000
175A228LEU0-0.0050.00660.7290.0000.0000.0000.0000.0000.000
176A229LEU0-0.0250.00461.3560.0000.0000.0000.0000.0000.000
177A230ASP-1-0.835-0.92264.069-0.019-0.0190.0000.0000.0000.000
178A231THR0-0.072-0.03865.6680.0010.0010.0000.0000.0000.000
179A232VAL0-0.069-0.04061.1830.0000.0000.0000.0000.0000.000
180A233LYS10.7600.86764.6120.0210.0210.0000.0000.0000.000
181A234GLU-1-0.878-0.93566.549-0.017-0.0170.0000.0000.0000.000
182A235LYS10.8950.94065.5540.0200.0200.0000.0000.0000.000
183A236TYR00.0380.02160.1250.0000.0000.0000.0000.0000.000
184A237HIS00.0290.02463.3110.0000.0000.0000.0000.0000.000
185A238ARG10.8590.91263.3360.0170.0170.0000.0000.0000.000
186A239ALA00.0340.02359.1240.0000.0000.0000.0000.0000.000
187A240TYR00.0760.02560.4120.0000.0000.0000.0000.0000.000
188A241GLU-1-0.910-0.96262.605-0.018-0.0180.0000.0000.0000.000
189A242CYS0-0.0350.01357.5590.0000.0000.0000.0000.0000.000
190A243THR00.013-0.01458.5910.0000.0000.0000.0000.0000.000
191A244LYS10.9480.99759.6450.0190.0190.0000.0000.0000.000
192A245LYS10.8120.92458.5660.0210.0210.0000.0000.0000.000
193A246ILE00.0120.01154.8980.0000.0000.0000.0000.0000.000
194A247GLN00.0430.01957.6220.0000.0000.0000.0000.0000.000
195A248THR0-0.053-0.03859.6740.0000.0000.0000.0000.0000.000
196A249TYR0-0.084-0.06952.6270.0010.0010.0000.0000.0000.000
197A250ILE00.0170.00652.9800.0000.0000.0000.0000.0000.000
198A251GLU-1-0.799-0.87256.600-0.022-0.0220.0000.0000.0000.000
199A252ARG10.8570.91059.7020.0190.0190.0000.0000.0000.000
200A253GLU-1-0.960-0.96354.739-0.023-0.0230.0000.0000.0000.000
201A254TYR0-0.069-0.06850.661-0.001-0.0010.0000.0000.0000.000
202A255GLU-1-0.951-0.96055.621-0.024-0.0240.0000.0000.0000.000
203A256HIS0-0.0170.00553.5670.0000.0000.0000.0000.0000.000
204A257LYS10.8150.88357.1810.0230.0230.0000.0000.0000.000
205A258LEU0-0.005-0.00554.607-0.001-0.0010.0000.0000.0000.000
206A259THR00.0450.01956.9790.0010.0010.0000.0000.0000.000
207A260SER00.018-0.03158.9400.0000.0000.0000.0000.0000.000
208A261ASP-1-0.826-0.89956.157-0.030-0.0300.0000.0000.0000.000
209A262GLU-1-0.779-0.84753.378-0.033-0.0330.0000.0000.0000.000
210A263LEU00.0060.00455.6330.0000.0000.0000.0000.0000.000
211A264LEU00.0060.02058.4430.0010.0010.0000.0000.0000.000
212A265TYR0-0.054-0.05853.1300.0000.0000.0000.0000.0000.000
213A266LEU00.0150.02953.2510.0000.0000.0000.0000.0000.000
214A267THR0-0.001-0.01754.9330.0010.0010.0000.0000.0000.000
215A268ILE0-0.047-0.02454.8850.0010.0010.0000.0000.0000.000
216A269ASH0-0.046-0.08051.0070.0000.0000.0000.0000.0000.000
217A270ILE00.0140.01553.3750.0000.0000.0000.0000.0000.000
218A271GLU-1-0.853-0.92255.305-0.022-0.0220.0000.0000.0000.000
219A272ARG10.7730.88953.0790.0280.0280.0000.0000.0000.000
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