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: 432GN

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 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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3475148.705716
FMO2-HF: Nuclear repulsion 3373520.428821
FMO2-HF: Total energy -101628.276896
FMO2-MP2: Total energy -101926.547408


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.
0.05-7.93323.364-7.808-7.571-0.008
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 : -0.016 / q_NPA : -0.054
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].
3A46THR0-0.011-0.0013.7980.0012.034-0.024-1.155-0.853-0.002
4A47PRO0-0.098-0.0327.2390.2550.2550.0000.0000.0000.000
5A48SER00.0360.0239.337-0.055-0.0550.0000.0000.0000.000
6A49ASN00.011-0.00112.340-0.026-0.0260.0000.0000.0000.000
7A50PRO0-0.012-0.01715.7130.0440.0440.0000.0000.0000.000
8A51LEU00.002-0.00217.387-0.012-0.0120.0000.0000.0000.000
9A52ARG10.9370.95019.9780.0130.0130.0000.0000.0000.000
10A53PRO0-0.034-0.00822.027-0.008-0.0080.0000.0000.0000.000
11A54ILE00.0230.02723.915-0.009-0.0090.0000.0000.0000.000
12A55ALA00.020-0.00726.7640.0130.0130.0000.0000.0000.000
13A56ASP-1-0.828-0.89528.4120.0870.0870.0000.0000.0000.000
14A57ASP-1-0.878-0.94329.8890.0470.0470.0000.0000.0000.000
15A58THR0-0.153-0.09432.0880.0000.0000.0000.0000.0000.000
16A59ILE0-0.058-0.02129.3560.0040.0040.0000.0000.0000.000
17A60ASP-1-0.796-0.84933.9000.0620.0620.0000.0000.0000.000
18A61HIS0-0.057-0.04836.0430.0010.0010.0000.0000.0000.000
19A62ALA00.0140.00137.0460.0040.0040.0000.0000.0000.000
20A63SER0-0.050-0.06637.6500.0010.0010.0000.0000.0000.000
21A64HIS0-0.065-0.06932.3320.0030.0030.0000.0000.0000.000
22A65THR0-0.019-0.00336.4070.0040.0040.0000.0000.0000.000
23A66PRO00.0030.01838.3860.0000.0000.0000.0000.0000.000
24A67GLY00.0400.00839.1780.0050.0050.0000.0000.0000.000
25A68SER0-0.044-0.01938.8820.0040.0040.0000.0000.0000.000
26A69VAL0-0.0100.01235.8250.0060.0060.0000.0000.0000.000
27A70SER00.0380.02232.7240.0040.0040.0000.0000.0000.000
28A71SER0-0.016-0.00330.905-0.007-0.0070.0000.0000.0000.000
29A72ALA00.0080.01627.2960.0120.0120.0000.0000.0000.000
30A73PHE00.030-0.00324.589-0.015-0.0150.0000.0000.0000.000
31A74ILE00.009-0.01021.4800.0300.0300.0000.0000.0000.000
32A75LEU00.0010.01518.633-0.028-0.0280.0000.0000.0000.000
33A76GLU-1-0.924-0.97419.5720.1790.1790.0000.0000.0000.000
34A77ALA00.002-0.00116.351-0.033-0.0330.0000.0000.0000.000
35A78MET0-0.0150.01317.9190.0200.0200.0000.0000.0000.000
36A79VAL00.003-0.00314.382-0.031-0.0310.0000.0000.0000.000
37A80ASN0-0.0100.01816.6410.0470.0470.0000.0000.0000.000
38A81VAL00.003-0.00312.360-0.039-0.0390.0000.0000.0000.000
39A82ILE00.0150.00313.1970.0230.0230.0000.0000.0000.000
40A83SER00.018-0.00211.158-0.124-0.1240.0000.0000.0000.000
41A84GLY00.0320.02112.7740.0560.0560.0000.0000.0000.000
42A85PRO00.004-0.00314.4990.0490.0490.0000.0000.0000.000
43A86LYS10.9600.99016.5330.2820.2820.0000.0000.0000.000
44A87VAL00.0240.00816.322-0.039-0.0390.0000.0000.0000.000
45A88LEU0-0.083-0.04612.7470.0240.0240.0000.0000.0000.000
46A89MET00.0040.00916.6980.0560.0560.0000.0000.0000.000
47A90LYS10.9480.97018.3300.0550.0550.0000.0000.0000.000
48A91GLN0-0.016-0.00920.4900.0010.0010.0000.0000.0000.000
49A92ILE00.0210.00917.4830.0160.0160.0000.0000.0000.000
50A93PRO00.0270.01218.3720.0010.0010.0000.0000.0000.000
51A94ILE0-0.030-0.01913.0680.0390.0390.0000.0000.0000.000
52A95TRP00.0040.00017.133-0.014-0.0140.0000.0000.0000.000
53A96LEU0-0.030-0.01714.1510.0700.0700.0000.0000.0000.000
54A97PRO00.0210.02417.732-0.041-0.0410.0000.0000.0000.000
55A98LEU00.0320.02118.8840.0400.0400.0000.0000.0000.000
56A99GLY00.008-0.00120.7250.0230.0230.0000.0000.0000.000
57A100VAL0-0.002-0.00723.581-0.019-0.0190.0000.0000.0000.000
58A101ALA0-0.023-0.01027.2130.0080.0080.0000.0000.0000.000
59A102ASP-1-0.772-0.85329.2000.1380.1380.0000.0000.0000.000
60A103GLN0-0.019-0.02932.246-0.002-0.0020.0000.0000.0000.000
61A104LYS10.8180.91534.456-0.138-0.1380.0000.0000.0000.000
62A105THR0-0.0140.01231.078-0.003-0.0030.0000.0000.0000.000
63A106TYR0-0.041-0.05328.968-0.011-0.0110.0000.0000.0000.000
64A107SER00.0510.03532.5950.0050.0050.0000.0000.0000.000
65A108PHE00.0740.01431.0240.0050.0050.0000.0000.0000.000
66A109ASP-1-0.821-0.90531.8190.0770.0770.0000.0000.0000.000
67A110SER0-0.035-0.02131.672-0.005-0.0050.0000.0000.0000.000
68A111THR0-0.0130.00826.7040.0070.0070.0000.0000.0000.000
69A112THR00.0220.00727.3070.0080.0080.0000.0000.0000.000
70A113ALA0-0.008-0.00328.108-0.002-0.0020.0000.0000.0000.000
71A114ALA0-0.0100.00125.688-0.006-0.0060.0000.0000.0000.000
72A115ILE00.0040.01222.6890.0030.0030.0000.0000.0000.000
73A116MET00.0330.02523.615-0.003-0.0030.0000.0000.0000.000
74A117LEU0-0.0450.00026.014-0.014-0.0140.0000.0000.0000.000
75A118ALA0-0.007-0.00121.469-0.008-0.0080.0000.0000.0000.000
76A119SER0-0.041-0.01319.4600.0010.0010.0000.0000.0000.000
77A120TYR0-0.028-0.04516.2850.0300.0300.0000.0000.0000.000
78A121THR0-0.0060.01111.870-0.010-0.0100.0000.0000.0000.000
79A122ILE00.0400.01810.5510.1170.1170.0000.0000.0000.000
80A123THR00.016-0.0024.627-0.285-0.269-0.001-0.003-0.0110.000
81A124HIS10.8590.9615.592-0.495-0.4950.0000.0000.0000.000
82A125PHE0-0.021-0.0041.8670.031-6.15221.169-10.846-4.140-0.001
83A126GLY00.0320.0142.4525.6850.5281.7474.754-1.344-0.003
84A127LYS10.9240.9733.701-5.494-5.1140.029-0.004-0.4040.001
85A128ALA00.0560.0265.038-0.781-0.789-0.001-0.0070.0160.000
86A129THR0-0.038-0.0248.053-0.289-0.2890.0000.0000.0000.000
87A130ASN0-0.015-0.0058.8140.2820.2820.0000.0000.0000.000
88A131PRO00.0070.0296.5310.5680.5680.0000.0000.0000.000
89A132LEU00.008-0.0055.784-0.843-0.8430.0000.0000.0000.000
90A133VAL0-0.010-0.0066.3100.4460.4460.0000.0000.0000.000
91A134ARG10.8820.9317.380-1.031-1.0310.0000.0000.0000.000
92A135VAL00.0520.0409.031-0.185-0.1850.0000.0000.0000.000
93A136ASN00.014-0.00510.0780.1370.1370.0000.0000.0000.000
94A137ARG10.8960.94913.159-0.198-0.1980.0000.0000.0000.000
95A138LEU0-0.052-0.03314.856-0.002-0.0020.0000.0000.0000.000
96A139GLY0-0.0010.00218.0290.0000.0000.0000.0000.0000.000
97A140PRO0-0.009-0.01520.1340.0200.0200.0000.0000.0000.000
98A141GLY00.0410.03621.5430.0060.0060.0000.0000.0000.000
99A142ILE0-0.067-0.04422.058-0.020-0.0200.0000.0000.0000.000
100A143PRO00.0240.00824.9490.0200.0200.0000.0000.0000.000
101A144ASP-1-0.840-0.92326.1350.1590.1590.0000.0000.0000.000
102A145HIS0-0.0130.00224.3930.0120.0120.0000.0000.0000.000
103A146PRO00.0330.00824.7120.0240.0240.0000.0000.0000.000
104A147LEU0-0.0010.01422.2170.0270.0270.0000.0000.0000.000
105A148ARG10.9470.93516.758-0.496-0.4960.0000.0000.0000.000
106A149LEU0-0.0230.01415.7120.0070.0070.0000.0000.0000.000
107A150LEU0-0.003-0.00918.230-0.015-0.0150.0000.0000.0000.000
108A151ARG10.8940.98521.221-0.305-0.3050.0000.0000.0000.000
109A152ILE0-0.044-0.03415.694-0.010-0.0100.0000.0000.0000.000
110A153GLY00.0440.03416.840-0.005-0.0050.0000.0000.0000.000
111A154ASN0-0.117-0.07311.7400.0850.0850.0000.0000.0000.000
112A155GLN00.0320.01412.841-0.037-0.0370.0000.0000.0000.000
113A156ALA0-0.011-0.0079.5210.0610.0610.0000.0000.0000.000
114A157PHE00.0530.03110.837-0.109-0.1090.0000.0000.0000.000
115A158LEU00.0440.02310.5130.3100.3100.0000.0000.0000.000
116A159GLN00.0450.0029.3310.0670.0670.0000.0000.0000.000
117A160GLU-1-0.956-0.98311.3710.5450.5450.0000.0000.0000.000
118A161PHE00.0240.00814.424-0.092-0.0920.0000.0000.0000.000
119A162VAL0-0.042-0.02312.723-0.080-0.0800.0000.0000.0000.000
120A163LEU0-0.036-0.01511.284-0.064-0.0640.0000.0000.0000.000
121A164PRO0-0.0030.00615.4650.0210.0210.0000.0000.0000.000
122A165PRO00.0050.01616.8550.0230.0230.0000.0000.0000.000
123A166VAL0-0.009-0.00916.856-0.047-0.0470.0000.0000.0000.000
124A167GLN0-0.015-0.02315.6770.0500.0500.0000.0000.0000.000
125A168LEU00.0040.00412.073-0.047-0.0470.0000.0000.0000.000
126A169PRO0-0.0150.00810.4630.0500.0500.0000.0000.0000.000
127A170GLN00.0390.0115.6890.2890.2890.0000.0000.0000.000
128A171TYR0-0.015-0.0152.3650.2151.1510.445-0.547-0.835-0.003
129A172PHE0-0.046-0.0266.3580.3660.3660.0000.0000.0000.000
130A173THR00.0260.0207.489-0.116-0.1160.0000.0000.0000.000
131A174PHE00.010-0.0158.9290.1950.1950.0000.0000.0000.000
132A175ASP-1-0.843-0.90712.108-0.271-0.2710.0000.0000.0000.000
133A176LEU0-0.046-0.02315.3110.0600.0600.0000.0000.0000.000
134A177THR00.005-0.00516.852-0.006-0.0060.0000.0000.0000.000
135A178ALA00.0060.00020.147-0.001-0.0010.0000.0000.0000.000
136A179LEU00.0030.00318.4040.0180.0180.0000.0000.0000.000
137A180LYS10.9060.97021.396-0.111-0.1110.0000.0000.0000.000
138A181LEU00.0020.00623.1210.0250.0250.0000.0000.0000.000
139A182ILE00.000-0.00324.703-0.014-0.0140.0000.0000.0000.000
140A183THR0-0.011-0.01326.3000.0180.0180.0000.0000.0000.000
141A184GLN0-0.015-0.00628.995-0.009-0.0090.0000.0000.0000.000
142A185PRO00.0390.03231.4970.0090.0090.0000.0000.0000.000
143A186LEU0-0.016-0.01430.3460.0040.0040.0000.0000.0000.000
144A187PRO00.0150.00534.602-0.009-0.0090.0000.0000.0000.000
145A188ALA00.0490.02737.6090.0030.0030.0000.0000.0000.000
146A189ALA0-0.0300.00140.067-0.001-0.0010.0000.0000.0000.000
147A190THR0-0.014-0.02033.5610.0090.0090.0000.0000.0000.000
148A191TRP0-0.007-0.01135.473-0.004-0.0040.0000.0000.0000.000
149A192THR0-0.017-0.03432.0530.0080.0080.0000.0000.0000.000
150A193ASP-1-0.775-0.87332.8600.1590.1590.0000.0000.0000.000
151A194ASP-1-0.835-0.89534.8130.1120.1120.0000.0000.0000.000
152A195THR0-0.070-0.05335.7280.0000.0000.0000.0000.0000.000
153A196PRO00.0050.02434.6410.0010.0010.0000.0000.0000.000
154A197THR00.0370.00229.3690.0040.0040.0000.0000.0000.000
155A198GLY0-0.018-0.01431.181-0.013-0.0130.0000.0000.0000.000
156A199SER0-0.075-0.05427.3990.0140.0140.0000.0000.0000.000
157A200ASN0-0.132-0.07028.742-0.020-0.0200.0000.0000.0000.000
158A201GLY00.0790.03330.115-0.001-0.0010.0000.0000.0000.000
159A202ALA0-0.036-0.01030.1510.0080.0080.0000.0000.0000.000
160A203LEU0-0.0020.00330.7980.0120.0120.0000.0000.0000.000
161A204ARG10.8580.89730.296-0.205-0.2050.0000.0000.0000.000
162A205PRO00.0170.02930.7870.0160.0160.0000.0000.0000.000
163A206GLY00.0270.00629.4130.0010.0010.0000.0000.0000.000
164A207ILE0-0.0050.00229.783-0.007-0.0070.0000.0000.0000.000
165A208SER0-0.020-0.00126.4800.0240.0240.0000.0000.0000.000
166A209PHE00.0520.01925.560-0.015-0.0150.0000.0000.0000.000
167A210HIS00.1130.04422.3040.0230.0230.0000.0000.0000.000
168A211PRO00.0100.00723.2350.0220.0220.0000.0000.0000.000
169A212LYS10.8790.93918.548-0.460-0.4600.0000.0000.0000.000
170A213LEU0-0.054-0.00919.0050.0660.0660.0000.0000.0000.000
171A214ARG10.8810.93916.571-0.677-0.6770.0000.0000.0000.000
172A215PRO00.001-0.00121.840-0.016-0.0160.0000.0000.0000.000
173A216ILE00.0240.01225.0610.0120.0120.0000.0000.0000.000
174A217LEU0-0.023-0.02026.808-0.016-0.0160.0000.0000.0000.000
175A218LEU00.0050.00629.455-0.006-0.0060.0000.0000.0000.000
176A219PRO0-0.0110.00433.124-0.001-0.0010.0000.0000.0000.000
177A220ASN0-0.035-0.03634.671-0.016-0.0160.0000.0000.0000.000
178A221LYS10.8650.95636.431-0.109-0.1090.0000.0000.0000.000
179A222SER0-0.027-0.07139.161-0.002-0.0020.0000.0000.0000.000
180A223GLY00.0600.03241.8430.0000.0000.0000.0000.0000.000
181A224LYS10.8490.91045.425-0.083-0.0830.0000.0000.0000.000
182A225LYS10.8760.94444.304-0.095-0.0950.0000.0000.0000.000
183A226GLY00.1150.04640.4320.0020.0020.0000.0000.0000.000
184A227ASN0-0.0290.00138.1520.0030.0030.0000.0000.0000.000
185A228SER00.0510.01835.3480.0020.0020.0000.0000.0000.000
186A229ALA00.0200.03237.1190.0030.0030.0000.0000.0000.000
187A230ASP-1-0.789-0.87540.5870.1020.1020.0000.0000.0000.000
188A231LEU00.0070.01434.654-0.001-0.0010.0000.0000.0000.000
189A232THR0-0.026-0.02635.9540.0040.0040.0000.0000.0000.000
190A233SER0-0.0170.00338.773-0.005-0.0050.0000.0000.0000.000
191A234PRO00.0550.01642.0640.0040.0040.0000.0000.0000.000
192A235GLU-1-0.925-0.95044.0710.0950.0950.0000.0000.0000.000
193A236LYS10.7900.90640.141-0.119-0.1190.0000.0000.0000.000
194A237ILE00.0060.00638.4120.0050.0050.0000.0000.0000.000
195A238GLN00.0090.00240.4810.0040.0040.0000.0000.0000.000
196A239ALA00.0030.00242.7280.0000.0000.0000.0000.0000.000
197A240ILE00.000-0.00936.4670.0010.0010.0000.0000.0000.000
198A241MET0-0.008-0.00937.5510.0060.0060.0000.0000.0000.000
199A242THR0-0.033-0.00740.3910.0000.0000.0000.0000.0000.000
200A243SER0-0.008-0.01740.9880.0000.0000.0000.0000.0000.000
201A244LEU0-0.0040.00835.0720.0010.0010.0000.0000.0000.000
202A245GLN0-0.049-0.02238.6920.0040.0040.0000.0000.0000.000
203A246ASP-1-0.929-0.96641.0250.1090.1090.0000.0000.0000.000
204A247PHE0-0.076-0.04034.9630.0010.0010.0000.0000.0000.000
205A248LYS10.9060.96637.510-0.121-0.1210.0000.0000.0000.000
206A249ILE0-0.0150.00630.8340.0020.0020.0000.0000.0000.000
207A250VAL0-0.026-0.01434.256-0.007-0.0070.0000.0000.0000.000
208A251PRO0-0.001-0.02532.8260.0110.0110.0000.0000.0000.000
209A252ILE0-0.0220.00731.916-0.008-0.0080.0000.0000.0000.000
210A253ASP-1-0.808-0.92830.9510.1300.1300.0000.0000.0000.000
211A254PRO00.013-0.00630.2700.0130.0130.0000.0000.0000.000
212A255THR0-0.065-0.02129.4360.0080.0080.0000.0000.0000.000
213A256LYS10.8910.96327.022-0.132-0.1320.0000.0000.0000.000
214A257ASN0-0.055-0.02624.0700.0000.0000.0000.0000.0000.000
215A258ILE0-0.0030.00725.9920.0230.0230.0000.0000.0000.000
216A259MET00.0360.01728.331-0.022-0.0220.0000.0000.0000.000
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