FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 537GZ

Calculation Name: 1ES6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ES6

Chain ID: A

ChEMBL ID:

UniProt ID: Q77DJ6

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3475039.667627
FMO2-HF: Nuclear repulsion 3373410.412228
FMO2-HF: Total energy -101629.255399
FMO2-MP2: Total energy -101927.403266


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:44:GLY)


Summations of interaction energy for fragment #1(A:44: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.
-3.738-7.99315.409-4.356-6.796-0.001
Interaction energy analysis for fragmet #1(A:44:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.044
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].
3A46THR0-0.026-0.0043.798-0.1881.546-0.023-0.954-0.757-0.003
4A47PRO0-0.074-0.0297.2640.3000.3000.0000.0000.0000.000
5A48SER00.0270.0249.349-0.035-0.0350.0000.0000.0000.000
6A49ASN00.003-0.00812.378-0.023-0.0230.0000.0000.0000.000
7A50PRO00.005-0.01215.7370.0400.0400.0000.0000.0000.000
8A51LEU0-0.013-0.00217.394-0.008-0.0080.0000.0000.0000.000
9A52ARG10.9300.95519.9810.0090.0090.0000.0000.0000.000
10A53PRO0-0.037-0.01122.035-0.003-0.0030.0000.0000.0000.000
11A54ILE00.0180.01923.927-0.011-0.0110.0000.0000.0000.000
12A55ALA00.011-0.00826.7860.0130.0130.0000.0000.0000.000
13A56ASP-1-0.802-0.88428.3520.0970.0970.0000.0000.0000.000
14A57ASP-1-0.887-0.94729.9180.0590.0590.0000.0000.0000.000
15A58THR0-0.131-0.08532.179-0.002-0.0020.0000.0000.0000.000
16A59ILE0-0.064-0.02029.3000.0020.0020.0000.0000.0000.000
17A60ASP-1-0.801-0.87533.9160.0570.0570.0000.0000.0000.000
18A61HIS0-0.077-0.05835.9170.0000.0000.0000.0000.0000.000
19A62ALA00.0160.00537.0440.0020.0020.0000.0000.0000.000
20A63SER0-0.027-0.03937.8370.0000.0000.0000.0000.0000.000
21A64HIS0-0.073-0.06632.5030.0030.0030.0000.0000.0000.000
22A65THR0-0.017-0.00436.3890.0020.0020.0000.0000.0000.000
23A66PRO0-0.0010.01538.363-0.001-0.0010.0000.0000.0000.000
24A67GLY00.0360.00839.1500.0040.0040.0000.0000.0000.000
25A68SER0-0.030-0.01338.8430.0030.0030.0000.0000.0000.000
26A69VAL0-0.0230.00535.8350.0050.0050.0000.0000.0000.000
27A70SER00.0280.02232.7690.0010.0010.0000.0000.0000.000
28A71SER0-0.006-0.00730.850-0.004-0.0040.0000.0000.0000.000
29A72ALA00.0000.01127.3220.0080.0080.0000.0000.0000.000
30A73PHE00.026-0.00724.583-0.012-0.0120.0000.0000.0000.000
31A74ILE00.001-0.01321.6260.0250.0250.0000.0000.0000.000
32A75LEU00.0060.01819.086-0.024-0.0240.0000.0000.0000.000
33A76GLU-1-0.890-0.96119.5980.1990.1990.0000.0000.0000.000
34A77ALA00.0060.00016.386-0.032-0.0320.0000.0000.0000.000
35A78MET00.0020.02217.9820.0310.0310.0000.0000.0000.000
36A79VAL0-0.011-0.01614.265-0.029-0.0290.0000.0000.0000.000
37A80ASN0-0.0200.01216.7230.0320.0320.0000.0000.0000.000
38A81VAL00.009-0.00212.411-0.021-0.0210.0000.0000.0000.000
39A82ILE00.0230.00713.3040.0020.0020.0000.0000.0000.000
40A83SER00.017-0.00211.275-0.063-0.0630.0000.0000.0000.000
41A84GLY00.0340.02313.0240.0200.0200.0000.0000.0000.000
42A85PRO00.003-0.00314.7220.0350.0350.0000.0000.0000.000
43A86LYS10.9570.99016.7860.0690.0690.0000.0000.0000.000
44A87VAL00.0210.00416.653-0.012-0.0120.0000.0000.0000.000
45A88LEU0-0.085-0.04513.0510.0120.0120.0000.0000.0000.000
46A89MET00.0010.00416.7980.0460.0460.0000.0000.0000.000
47A90LYS10.8850.93118.442-0.028-0.0280.0000.0000.0000.000
48A91GLN0-0.011-0.00820.622-0.004-0.0040.0000.0000.0000.000
49A92ILE00.0280.01017.5640.0110.0110.0000.0000.0000.000
50A93PRO00.0350.01718.4560.0050.0050.0000.0000.0000.000
51A94ILE0-0.041-0.02513.1430.0410.0410.0000.0000.0000.000
52A95TRP0-0.0070.00217.196-0.019-0.0190.0000.0000.0000.000
53A96LEU0-0.023-0.01714.0890.0620.0620.0000.0000.0000.000
54A97PRO00.0240.02317.754-0.039-0.0390.0000.0000.0000.000
55A98LEU00.0230.01618.8380.0270.0270.0000.0000.0000.000
56A99GLY00.0110.00220.7090.0130.0130.0000.0000.0000.000
57A100VAL0-0.005-0.01023.559-0.013-0.0130.0000.0000.0000.000
58A101ALA0-0.020-0.01027.1750.0030.0030.0000.0000.0000.000
59A102ASP-1-0.751-0.83729.1620.1040.1040.0000.0000.0000.000
60A103GLN0-0.010-0.02032.202-0.003-0.0030.0000.0000.0000.000
61A104LYS10.7690.87934.422-0.106-0.1060.0000.0000.0000.000
62A105THR0-0.0200.00431.168-0.004-0.0040.0000.0000.0000.000
63A106TYR0-0.040-0.04829.009-0.009-0.0090.0000.0000.0000.000
64A107SER00.0630.04732.5380.0040.0040.0000.0000.0000.000
65A108PHE00.0610.01030.9190.0040.0040.0000.0000.0000.000
66A109ASP-1-0.810-0.89831.7890.0630.0630.0000.0000.0000.000
67A110SER0-0.033-0.02531.660-0.004-0.0040.0000.0000.0000.000
68A111THR0-0.0190.00026.7010.0030.0030.0000.0000.0000.000
69A112THR00.014-0.00127.2730.0070.0070.0000.0000.0000.000
70A113ALA0-0.0080.00028.084-0.001-0.0010.0000.0000.0000.000
71A114ALA0-0.010-0.00125.677-0.005-0.0050.0000.0000.0000.000
72A115ILE0-0.0040.00122.6940.0010.0010.0000.0000.0000.000
73A116MET00.0380.02123.5950.0010.0010.0000.0000.0000.000
74A117LEU0-0.052-0.00626.000-0.011-0.0110.0000.0000.0000.000
75A118ALA0-0.006-0.00721.474-0.010-0.0100.0000.0000.0000.000
76A119SER0-0.034-0.01319.5560.0050.0050.0000.0000.0000.000
77A120TYR0-0.004-0.01616.2330.0150.0150.0000.0000.0000.000
78A121THR0-0.0140.00612.101-0.006-0.0060.0000.0000.0000.000
79A122ILE00.0270.01110.6660.0850.0850.0000.0000.0000.000
80A123THR00.014-0.0034.677-0.231-0.218-0.001-0.002-0.0090.000
81A124HIS10.8510.9475.673-1.365-1.3650.0000.0000.0000.000
82A125PHE0-0.022-0.0171.948-1.572-3.75012.462-6.869-3.4150.000
83A126GLY00.0390.0182.7083.386-1.2552.0093.956-1.3240.001
84A127LYS10.9300.9723.959-4.843-4.4650.027-0.017-0.3880.001
85A128ALA00.0260.0124.766-0.520-0.520-0.001-0.0060.0080.000
86A129THR0-0.007-0.0087.983-0.209-0.2090.0000.0000.0000.000
87A130ASN0-0.017-0.0068.4470.1980.1980.0000.0000.0000.000
88A131PRO00.0130.0266.5590.3520.3520.0000.0000.0000.000
89A132LEU0-0.016-0.0085.770-0.859-0.8590.0000.0000.0000.000
90A133VAL0-0.001-0.0026.3640.5700.5700.0000.0000.0000.000
91A134ARG10.8810.9327.495-0.677-0.6770.0000.0000.0000.000
92A135VAL00.0430.0329.021-0.132-0.1320.0000.0000.0000.000
93A136ASN00.003-0.00510.0620.0830.0830.0000.0000.0000.000
94A137ARG10.9000.95413.117-0.127-0.1270.0000.0000.0000.000
95A138LEU0-0.051-0.02914.789-0.011-0.0110.0000.0000.0000.000
96A139GLY00.0070.00517.9750.0050.0050.0000.0000.0000.000
97A140PRO0-0.009-0.01720.0580.0120.0120.0000.0000.0000.000
98A141GLY00.0390.03921.4650.0080.0080.0000.0000.0000.000
99A142ILE0-0.056-0.04321.977-0.014-0.0140.0000.0000.0000.000
100A143PRO00.0330.01024.8700.0150.0150.0000.0000.0000.000
101A144ASP-1-0.850-0.92126.0410.1020.1020.0000.0000.0000.000
102A145HIS0-0.0040.00624.3360.0120.0120.0000.0000.0000.000
103A146PRO00.0510.02324.6440.0160.0160.0000.0000.0000.000
104A147LEU0-0.0120.01222.1850.0210.0210.0000.0000.0000.000
105A148ARG10.8830.85916.967-0.358-0.3580.0000.0000.0000.000
106A149LEU0-0.0220.01215.505-0.002-0.0020.0000.0000.0000.000
107A150LEU0-0.001-0.00818.179-0.017-0.0170.0000.0000.0000.000
108A151ARG10.7780.91621.163-0.211-0.2110.0000.0000.0000.000
109A152ILE0-0.034-0.02915.859-0.011-0.0110.0000.0000.0000.000
110A153GLY00.0480.03516.763-0.013-0.0130.0000.0000.0000.000
111A154ASN0-0.113-0.07311.6840.0870.0870.0000.0000.0000.000
112A155GLN00.0360.02012.782-0.035-0.0350.0000.0000.0000.000
113A156ALA0-0.006-0.0039.4510.0580.0580.0000.0000.0000.000
114A157PHE00.0510.03010.843-0.099-0.0990.0000.0000.0000.000
115A158LEU00.0460.02610.5350.2860.2860.0000.0000.0000.000
116A159GLN00.0540.0089.3680.1770.1770.0000.0000.0000.000
117A160GLU-1-0.849-0.91511.4390.4900.4900.0000.0000.0000.000
118A161PHE00.0270.00814.476-0.090-0.0900.0000.0000.0000.000
119A162VAL0-0.036-0.01912.895-0.077-0.0770.0000.0000.0000.000
120A163LEU0-0.024-0.00811.612-0.048-0.0480.0000.0000.0000.000
121A164PRO00.0050.00715.5530.0100.0100.0000.0000.0000.000
122A165PRO00.0090.01817.0490.0440.0440.0000.0000.0000.000
123A166VAL0-0.018-0.01417.310-0.054-0.0540.0000.0000.0000.000
124A167GLN0-0.023-0.02016.1960.0760.0760.0000.0000.0000.000
125A168LEU00.0190.01112.489-0.041-0.0410.0000.0000.0000.000
126A169PRO0-0.0040.00710.7240.0400.0400.0000.0000.0000.000
127A170GLN00.0330.0146.0970.0660.0660.0000.0000.0000.000
128A171TYR0-0.023-0.0112.1120.8421.2810.936-0.464-0.9110.000
129A172PHE0-0.035-0.0216.6970.0460.0460.0000.0000.0000.000
130A173THR00.0370.0207.6070.0420.0420.0000.0000.0000.000
131A174PHE0-0.014-0.0178.8770.1680.1680.0000.0000.0000.000
132A175ASP-1-0.824-0.88812.194-0.143-0.1430.0000.0000.0000.000
133A176LEU0-0.037-0.01715.2880.0520.0520.0000.0000.0000.000
134A177THR00.0180.00616.910-0.017-0.0170.0000.0000.0000.000
135A178ALA00.005-0.00220.191-0.008-0.0080.0000.0000.0000.000
136A179LEU0-0.002-0.00218.2480.0210.0210.0000.0000.0000.000
137A180LYS10.8640.95321.430-0.136-0.1360.0000.0000.0000.000
138A181LEU00.0020.00923.1460.0220.0220.0000.0000.0000.000
139A182ILE0-0.009-0.00624.680-0.011-0.0110.0000.0000.0000.000
140A183THR00.015-0.00426.3080.0150.0150.0000.0000.0000.000
141A184GLN00.0070.01629.000-0.006-0.0060.0000.0000.0000.000
142A185PRO00.0520.03831.5030.0060.0060.0000.0000.0000.000
143A186LEU0-0.026-0.01030.2660.0050.0050.0000.0000.0000.000
144A187PRO00.0200.00534.596-0.007-0.0070.0000.0000.0000.000
145A188ALA00.0450.03237.5940.0020.0020.0000.0000.0000.000
146A189ALA0-0.0310.00040.050-0.002-0.0020.0000.0000.0000.000
147A190THR0-0.018-0.02633.5840.0070.0070.0000.0000.0000.000
148A191TRP00.000-0.00635.438-0.004-0.0040.0000.0000.0000.000
149A192THR0-0.018-0.05431.8260.0070.0070.0000.0000.0000.000
150A193ASP-1-0.733-0.84432.2160.1200.1200.0000.0000.0000.000
151A194ASP-1-0.825-0.88034.7550.0850.0850.0000.0000.0000.000
152A195THR0-0.044-0.03635.6590.0000.0000.0000.0000.0000.000
153A196PRO00.0020.02234.6780.0010.0010.0000.0000.0000.000
154A197THR00.030-0.00329.6220.0040.0040.0000.0000.0000.000
155A198GLY0-0.015-0.01131.286-0.010-0.0100.0000.0000.0000.000
156A199SER0-0.056-0.05027.4570.0080.0080.0000.0000.0000.000
157A200ASN0-0.105-0.05628.801-0.015-0.0150.0000.0000.0000.000
158A201GLY00.0570.01030.180-0.001-0.0010.0000.0000.0000.000
159A202ALA0-0.049-0.01230.0560.0070.0070.0000.0000.0000.000
160A203LEU00.0040.00630.7110.0080.0080.0000.0000.0000.000
161A204ARG10.8030.86230.066-0.145-0.1450.0000.0000.0000.000
162A205PRO00.0200.02630.7220.0110.0110.0000.0000.0000.000
163A206GLY00.0110.00229.3630.0010.0010.0000.0000.0000.000
164A207ILE0-0.008-0.00129.736-0.005-0.0050.0000.0000.0000.000
165A208SER0-0.017-0.00126.2880.0210.0210.0000.0000.0000.000
166A209PHE00.0390.01325.144-0.012-0.0120.0000.0000.0000.000
167A210HIS00.1010.03722.4590.0160.0160.0000.0000.0000.000
168A211PRO00.0060.01022.9240.0160.0160.0000.0000.0000.000
169A212LYS10.7790.87317.826-0.503-0.5030.0000.0000.0000.000
170A213LEU0-0.053-0.01219.0040.0610.0610.0000.0000.0000.000
171A214ARG10.8320.91416.557-0.537-0.5370.0000.0000.0000.000
172A215PRO00.0120.00221.807-0.009-0.0090.0000.0000.0000.000
173A216ILE00.0080.00625.0200.0080.0080.0000.0000.0000.000
174A217LEU0-0.018-0.01526.657-0.013-0.0130.0000.0000.0000.000
175A218LEU00.0140.01229.404-0.003-0.0030.0000.0000.0000.000
176A219PRO00.0000.01033.075-0.003-0.0030.0000.0000.0000.000
177A220ASN0-0.042-0.04234.617-0.011-0.0110.0000.0000.0000.000
178A221LYS10.8690.94636.361-0.081-0.0810.0000.0000.0000.000
179A222SER0-0.024-0.04639.090-0.002-0.0020.0000.0000.0000.000
180A223GLY00.0710.03441.7490.0010.0010.0000.0000.0000.000
181A224LYS10.8450.90845.260-0.058-0.0580.0000.0000.0000.000
182A225LYS10.8660.94044.178-0.064-0.0640.0000.0000.0000.000
183A226GLY00.1050.04440.2210.0020.0020.0000.0000.0000.000
184A227ASN0-0.035-0.00438.0510.0000.0000.0000.0000.0000.000
185A228SER00.0910.03835.2250.0020.0020.0000.0000.0000.000
186A229ALA0-0.0150.01337.0310.0030.0030.0000.0000.0000.000
187A230ASP-1-0.781-0.87840.5020.0690.0690.0000.0000.0000.000
188A231LEU00.0070.01834.5880.0000.0000.0000.0000.0000.000
189A232THR0-0.010-0.01735.7930.0040.0040.0000.0000.0000.000
190A233SER0-0.0130.00238.701-0.003-0.0030.0000.0000.0000.000
191A234PRO00.0560.01641.9990.0030.0030.0000.0000.0000.000
192A235GLU-1-0.869-0.93444.0060.0730.0730.0000.0000.0000.000
193A236LYS10.7910.90840.174-0.085-0.0850.0000.0000.0000.000
194A237ILE0-0.004-0.00338.2770.0040.0040.0000.0000.0000.000
195A238GLN00.0000.00240.4250.0040.0040.0000.0000.0000.000
196A239ALA0-0.0020.00042.7610.0010.0010.0000.0000.0000.000
197A240ILE00.0040.00636.4160.0010.0010.0000.0000.0000.000
198A241MET00.007-0.00637.8810.0060.0060.0000.0000.0000.000
199A242THR0-0.044-0.01040.3540.0010.0010.0000.0000.0000.000
200A243SER00.003-0.02041.2540.0010.0010.0000.0000.0000.000
201A244LEU0-0.0280.00435.0160.0020.0020.0000.0000.0000.000
202A245GLN0-0.051-0.02738.6770.0040.0040.0000.0000.0000.000
203A246ASP-1-0.920-0.97041.0130.0910.0910.0000.0000.0000.000
204A247PHE0-0.070-0.03734.9470.0010.0010.0000.0000.0000.000
205A248LYS10.8360.91637.532-0.105-0.1050.0000.0000.0000.000
206A249ILE0-0.0240.00030.6870.0010.0010.0000.0000.0000.000
207A250VAL0-0.020-0.01034.265-0.004-0.0040.0000.0000.0000.000
208A251PRO00.003-0.02532.8500.0090.0090.0000.0000.0000.000
209A252ILE0-0.0260.00331.968-0.008-0.0080.0000.0000.0000.000
210A253ASP-1-0.761-0.87931.1480.1270.1270.0000.0000.0000.000
211A254PRO00.010-0.00830.3000.0120.0120.0000.0000.0000.000
212A255THR0-0.079-0.03529.4790.0090.0090.0000.0000.0000.000
213A256LYS10.8380.90827.057-0.123-0.1230.0000.0000.0000.000
214A257ASN0-0.068-0.03623.637-0.001-0.0010.0000.0000.0000.000
215A258ILE0-0.0080.00326.0130.0170.0170.0000.0000.0000.000
216A259MET00.0380.02228.337-0.017-0.0170.0000.0000.0000.000
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