Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: XVQL1

Calculation Name: 3KYJ-A-Xray22

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KYJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KLS0

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandCharge NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1262831.807043
FMO2-HF: Nuclear repulsion 1206665.792831
FMO2-HF: Total energy -56166.014212
FMO2-MP2: Total energy -56323.430572


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:7:ACE)


Summations of interaction energy for fragment #1(A:7:ACE)
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.
1.4140.1445.02-1.955-1.793-0.012
Interaction energy analysis for fragmet #1(A:7:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.018
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].
3A9ASP-1-0.826-0.9013.8550.2401.247-0.007-0.399-0.6010.000
4A10GLU-1-0.829-0.8814.2800.3820.532-0.001-0.009-0.1390.000
5A11ILE00.0360.0215.5530.1640.1640.0000.0000.0000.000
6A12TRP00.0540.0327.4630.2990.2990.0000.0000.0000.000
7A13ALA0-0.0160.0048.8490.1470.1470.0000.0000.0000.000
8A14LEU00.0130.0109.9710.0620.0620.0000.0000.0000.000
9A15TYR0-0.034-0.03011.4950.0550.0550.0000.0000.0000.000
10A16ALA00.0330.01213.4300.0500.0500.0000.0000.0000.000
11A17ASP-1-0.880-0.92314.657-0.065-0.0650.0000.0000.0000.000
12A18ASP-1-0.692-0.83515.615-0.119-0.1190.0000.0000.0000.000
13A19GLY00.0270.00917.0900.0170.0170.0000.0000.0000.000
14A20ALA0-0.026-0.01219.0190.0160.0160.0000.0000.0000.000
15A21GLN0-0.0160.01920.3970.0210.0210.0000.0000.0000.000
16A22ALA00.0140.01521.5120.0110.0110.0000.0000.0000.000
17A23LEU0-0.008-0.01123.0340.0100.0100.0000.0000.0000.000
18A24ASP-1-0.768-0.84824.791-0.073-0.0730.0000.0000.0000.000
19A25ALA0-0.035-0.01226.2370.0080.0080.0000.0000.0000.000
20A26MET0-0.054-0.02427.4640.0020.0020.0000.0000.0000.000
21A27GLU-1-0.898-0.95829.100-0.062-0.0620.0000.0000.0000.000
22A28ALA00.0080.00530.6440.0060.0060.0000.0000.0000.000
23A29SER00.0200.00131.9090.0060.0060.0000.0000.0000.000
24A30LEU0-0.055-0.01732.4520.0040.0040.0000.0000.0000.000
25A31LEU00.0190.01434.2640.0040.0040.0000.0000.0000.000
26A32ALA00.0010.01236.6200.0030.0030.0000.0000.0000.000
27A33LEU0-0.058-0.02937.2330.0030.0030.0000.0000.0000.000
28A34GLN0-0.0030.00939.5550.0020.0020.0000.0000.0000.000
29A35ALA0-0.037-0.01141.1400.0020.0020.0000.0000.0000.000
30A36GLY0-0.031-0.00543.0410.0020.0020.0000.0000.0000.000
31A37GLU-1-0.787-0.84140.078-0.029-0.0290.0000.0000.0000.000
32A38ASP-1-0.621-0.89742.880-0.031-0.0310.0000.0000.0000.000
33A39ALA00.0990.02140.255-0.001-0.0010.0000.0000.0000.000
34A40ALA0-0.004-0.01339.516-0.002-0.0020.0000.0000.0000.000
35A41ALA0-0.0040.02938.9330.0000.0000.0000.0000.0000.000
36A42HIS00.0660.02035.738-0.004-0.0040.0000.0000.0000.000
37A43VAL00.0260.01734.727-0.004-0.0040.0000.0000.0000.000
38A44GLY0-0.013-0.00533.750-0.004-0.0040.0000.0000.0000.000
39A45PRO0-0.009-0.01330.767-0.004-0.0040.0000.0000.0000.000
40A46LEU00.0790.06029.732-0.006-0.0060.0000.0000.0000.000
41A47PHE00.0160.00329.324-0.007-0.0070.0000.0000.0000.000
42A48ARG10.8910.93327.1740.0440.0440.0000.0000.0000.000
43A49ALA00.0600.04425.406-0.008-0.0080.0000.0000.0000.000
44A50VAL00.0410.01324.604-0.013-0.0130.0000.0000.0000.000
45A51HIS0-0.110-0.06524.843-0.014-0.0140.0000.0000.0000.000
46A52THR0-0.0040.01520.166-0.007-0.0070.0000.0000.0000.000
47A53PHE00.0470.03320.319-0.023-0.0230.0000.0000.0000.000
48A54LYS10.8770.94520.3840.0960.0960.0000.0000.0000.000
49A55GLY0-0.0090.00420.153-0.019-0.0190.0000.0000.0000.000
50A56ASN00.0380.01616.357-0.020-0.0200.0000.0000.0000.000
51A57SER0-0.010-0.00715.753-0.046-0.0460.0000.0000.0000.000
52A58ARG10.8130.90117.1930.1410.1410.0000.0000.0000.000
53A59VAL0-0.069-0.02212.248-0.014-0.0140.0000.0000.0000.000
54A60LEU0-0.009-0.00510.039-0.070-0.0700.0000.0000.0000.000
55A61GLY0-0.0020.01313.546-0.022-0.0220.0000.0000.0000.000
56A62LEU0-0.0040.01115.1260.0200.0200.0000.0000.0000.000
57A63SER00.0300.00518.3820.0320.0320.0000.0000.0000.000
58A64VAL00.0020.00821.7630.0270.0270.0000.0000.0000.000
59A65VAL00.0410.02420.2370.0200.0200.0000.0000.0000.000
60A66GLU-1-0.761-0.84621.291-0.176-0.1760.0000.0000.0000.000
61A67SER0-0.049-0.03223.0340.0230.0230.0000.0000.0000.000
62A68ARG10.9290.93026.0680.1460.1460.0000.0000.0000.000
63A69ALA00.0350.02724.5920.0110.0110.0000.0000.0000.000
64A70HIS0-0.031-0.02326.5440.0060.0060.0000.0000.0000.000
65A71LEU0-0.009-0.00228.0810.0090.0090.0000.0000.0000.000
66A72CYS0-0.028-0.00929.4180.0090.0090.0000.0000.0000.000
67A73GLU-1-0.758-0.85327.453-0.095-0.0950.0000.0000.0000.000
68A74ASP-1-0.780-0.87030.797-0.077-0.0770.0000.0000.0000.000
69A75LEU0-0.017-0.00733.6980.0060.0060.0000.0000.0000.000
70A76ILE0-0.008-0.01231.4520.0060.0060.0000.0000.0000.000
71A77GLY00.014-0.00234.4490.0040.0040.0000.0000.0000.000
72A78LEU0-0.0030.00835.6590.0040.0040.0000.0000.0000.000
73A79VAL0-0.043-0.01438.3830.0040.0040.0000.0000.0000.000
74A80ARG10.7580.88032.1710.0600.0600.0000.0000.0000.000
75A81ASP-1-0.810-0.87236.639-0.049-0.0490.0000.0000.0000.000
76A82ALA0-0.052-0.02639.9680.0020.0020.0000.0000.0000.000
77A83GLY0-0.028-0.00342.6430.0010.0010.0000.0000.0000.000
78A84VAL00.0130.01342.0500.0020.0020.0000.0000.0000.000
79A85PRO00.0090.00342.895-0.001-0.0010.0000.0000.0000.000
80A86MET00.0440.03237.050-0.002-0.0020.0000.0000.0000.000
81A87ASP-1-0.797-0.86841.957-0.043-0.0430.0000.0000.0000.000
82A88GLY00.0840.01342.222-0.002-0.0020.0000.0000.0000.000
83A89GLU-1-0.715-0.82041.997-0.049-0.0490.0000.0000.0000.000
84A90ILE0-0.035-0.02937.854-0.004-0.0040.0000.0000.0000.000
85A91VAL00.005-0.00237.715-0.004-0.0040.0000.0000.0000.000
86A92GLU-1-0.898-0.93237.217-0.053-0.0530.0000.0000.0000.000
87A93ILE0-0.034-0.01935.602-0.004-0.0040.0000.0000.0000.000
88A94LEU0-0.007-0.01532.529-0.006-0.0060.0000.0000.0000.000
89A95LEU00.0510.03432.520-0.005-0.0050.0000.0000.0000.000
90A96PHE00.0160.03532.845-0.005-0.0050.0000.0000.0000.000
91A97ALA0-0.012-0.02430.451-0.007-0.0070.0000.0000.0000.000
92A98SER0-0.035-0.01828.481-0.008-0.0080.0000.0000.0000.000
93A99ASP-1-0.760-0.84927.824-0.086-0.0860.0000.0000.0000.000
94A100THR0-0.044-0.01928.000-0.005-0.0050.0000.0000.0000.000
95A101LEU0-0.037-0.03024.574-0.011-0.0110.0000.0000.0000.000
96A102ARG10.9230.95023.4900.0860.0860.0000.0000.0000.000
97A103ALA00.0510.03323.419-0.010-0.0100.0000.0000.0000.000
98A104MET0-0.073-0.03222.486-0.014-0.0140.0000.0000.0000.000
99A105LEU0-0.0340.00817.656-0.026-0.0260.0000.0000.0000.000
100A106GLU-1-0.928-0.97118.580-0.157-0.1570.0000.0000.0000.000
101A107GLU-1-0.843-0.90319.279-0.211-0.2110.0000.0000.0000.000
102A108THR0-0.013-0.00917.133-0.029-0.0290.0000.0000.0000.000
103A109ALA0-0.025-0.00114.519-0.067-0.0670.0000.0000.0000.000
104A110ALA0-0.0130.01213.909-0.060-0.0600.0000.0000.0000.000
105A111SER0-0.021-0.00915.494-0.030-0.0300.0000.0000.0000.000
106A112ARG10.8100.9027.1530.8400.8400.0000.0000.0000.000
107A113ALA0-0.0080.00413.315-0.061-0.0610.0000.0000.0000.000
108A114ASP-1-0.697-0.84816.004-0.224-0.2240.0000.0000.0000.000
109A115VAL0-0.0090.02719.0480.0060.0060.0000.0000.0000.000
110A116GLU-1-0.881-0.93322.258-0.161-0.1610.0000.0000.0000.000
111A117GLY0-0.006-0.01825.5030.0050.0050.0000.0000.0000.000
112A118THR00.0400.01227.8600.0060.0060.0000.0000.0000.000
113A119GLY00.0020.01229.7220.0080.0080.0000.0000.0000.000
114A120SER00.0090.00528.2480.0060.0060.0000.0000.0000.000
115A121GLU-1-0.848-0.91230.917-0.093-0.0930.0000.0000.0000.000
116A122ALA00.0410.02933.4480.0050.0050.0000.0000.0000.000
117A123LEU00.0560.03030.3430.0040.0040.0000.0000.0000.000
118A124MET0-0.046-0.01130.5980.0020.0020.0000.0000.0000.000
119A125ASP-1-0.880-0.92933.943-0.069-0.0690.0000.0000.0000.000
120A126GLN0-0.060-0.02837.1180.0040.0040.0000.0000.0000.000
121A127LEU00.0530.02132.2330.0040.0040.0000.0000.0000.000
122A128ARG10.9620.99132.7950.0910.0910.0000.0000.0000.000
123A129SER00.0210.02238.1310.0050.0050.0000.0000.0000.000
124A130LYS10.8300.90539.5320.0500.0500.0000.0000.0000.000
125A131ILE0-0.0040.00135.4880.0040.0040.0000.0000.0000.000
126A132ALA0-0.016-0.00940.1320.0030.0030.0000.0000.0000.000
127A133ARG10.7040.82043.0540.0520.0520.0000.0000.0000.000
128A134CYS0-0.073-0.03642.0770.0030.0030.0000.0000.0000.000
129A135SER00.0200.01542.4460.0010.0010.0000.0000.0000.000
130A136ARG10.8660.95944.6080.0400.0400.0000.0000.0000.000
131A137NME00.0190.01947.4760.0010.0010.0000.0000.0000.000
132A144NA+10.6690.94345.7400.0300.0300.0000.0000.0000.000
133A145HOH0-0.056-0.05138.4410.0000.0000.0000.0000.0000.000
134A148HOH0-0.032-0.02340.4070.0000.0000.0000.0000.0000.000
135A151HOH0-0.037-0.02439.9170.0000.0000.0000.0000.0000.000
136A154HOH0-0.027-0.01836.0220.0010.0010.0000.0000.0000.000
137A155HOH00.0190.00521.8570.0010.0010.0000.0000.0000.000
138A156HOH0-0.003-0.00231.002-0.002-0.0020.0000.0000.0000.000
139A157HOH0-0.029-0.0368.387-0.009-0.0090.0000.0000.0000.000
140A160HOH0-0.055-0.04044.4540.0000.0000.0000.0000.0000.000
141A161HOH0-0.046-0.04420.095-0.008-0.0080.0000.0000.0000.000
142A166HOH0-0.029-0.01216.7460.0080.0080.0000.0000.0000.000
143A167HOH0-0.028-0.03147.3800.0010.0010.0000.0000.0000.000
144A168HOH0-0.062-0.05933.901-0.001-0.0010.0000.0000.0000.000
145A169HOH0-0.069-0.04516.8190.0020.0020.0000.0000.0000.000
146A170HOH0-0.050-0.03830.513-0.003-0.0030.0000.0000.0000.000
147A171HOH0-0.017-0.01518.4870.0000.0000.0000.0000.0000.000
148A172HOH0-0.040-0.03016.5580.0090.0090.0000.0000.0000.000
149A176HOH00.0070.01526.9930.0030.0030.0000.0000.0000.000
150A179HOH0-0.040-0.02842.8400.0010.0010.0000.0000.0000.000
151A180HOH0-0.026-0.01723.767-0.003-0.0030.0000.0000.0000.000
152A185HOH0-0.024-0.02012.4330.0150.0150.0000.0000.0000.000
153A186HOH0-0.013-0.01518.921-0.013-0.0130.0000.0000.0000.000
154A187HOH0-0.053-0.05424.2710.0030.0030.0000.0000.0000.000
155A188HOH0-0.057-0.03225.2590.0030.0030.0000.0000.0000.000
156A189HOH0-0.032-0.01641.3190.0010.0010.0000.0000.0000.000
157A190HOH0-0.028-0.02219.4270.0050.0050.0000.0000.0000.000
158A191HOH0-0.005-0.00427.8850.0020.0020.0000.0000.0000.000
159A192HOH0-0.009-0.01037.001-0.001-0.0010.0000.0000.0000.000
160A193HOH0-0.009-0.00327.6340.0050.0050.0000.0000.0000.000
161A194HOH0-0.036-0.02618.1130.0070.0070.0000.0000.0000.000
162A195HOH0-0.033-0.02440.5020.0010.0010.0000.0000.0000.000
163A196HOH0-0.034-0.02243.1730.0000.0000.0000.0000.0000.000
164A197HOH00.0180.00017.541-0.006-0.0060.0000.0000.0000.000
165A198HOH0-0.045-0.03528.2060.0040.0040.0000.0000.0000.000
166A199HOH00.0160.03817.7550.0080.0080.0000.0000.0000.000
167A200HOH0-0.043-0.07641.883-0.001-0.0010.0000.0000.0000.000
168A201HOH0-0.046-0.0259.296-0.024-0.0240.0000.0000.0000.000
169A202HOH00.0220.01726.1150.0030.0030.0000.0000.0000.000
170A203HOH0-0.0030.02440.5690.0000.0000.0000.0000.0000.000
171A204HOH0-0.012-0.00824.6500.0000.0000.0000.0000.0000.000
172A205HOH0-0.024-0.01835.1800.0020.0020.0000.0000.0000.000
173A206HOH0-0.016-0.01329.395-0.001-0.0010.0000.0000.0000.000
174A207HOH0-0.059-0.05333.4870.0010.0010.0000.0000.0000.000
175A209HOH0-0.059-0.03930.5560.0030.0030.0000.0000.0000.000
176A212HOH0-0.039-0.03530.250-0.001-0.0010.0000.0000.0000.000
177A214HOH0-0.064-0.05213.6270.0180.0180.0000.0000.0000.000
178A215HOH00.0100.00828.5760.0030.0030.0000.0000.0000.000
179A216HOH0-0.080-0.08019.1930.0030.0030.0000.0000.0000.000
180A220HOH0-0.003-0.01133.1270.0020.0020.0000.0000.0000.000
181A221HOH0-0.018-0.02519.392-0.003-0.0030.0000.0000.0000.000
182A223HOH00.0260.01031.5490.0000.0000.0000.0000.0000.000
183A224HOH00.0540.04616.3250.0130.0130.0000.0000.0000.000
184A225HOH0-0.065-0.05043.3320.0000.0000.0000.0000.0000.000
185A228HOH0-0.063-0.05436.534-0.001-0.0010.0000.0000.0000.000
186A229HOH0-0.033-0.01937.9420.0000.0000.0000.0000.0000.000
187A230HOH0-0.008-0.01512.085-0.033-0.0330.0000.0000.0000.000
188A231HOH0-0.030-0.0209.2130.0170.0170.0000.0000.0000.000
189A233HOH0-0.029-0.02223.7100.0030.0030.0000.0000.0000.000
190A234HOH0-0.046-0.0284.0340.1660.2750.001-0.056-0.0530.000
191A238HOH00.0090.00634.0940.0010.0010.0000.0000.0000.000
192A239HOH0-0.0040.01022.5110.0080.0080.0000.0000.0000.000
193A241HOH0-0.0080.01020.827-0.003-0.0030.0000.0000.0000.000
194A243HOH0-0.028-0.02128.378-0.001-0.0010.0000.0000.0000.000
195A245HOH0-0.022-0.01238.6980.0010.0010.0000.0000.0000.000
196A247HOH00.0120.00727.5390.0020.0020.0000.0000.0000.000
197A248HOH0-0.066-0.05024.1400.0060.0060.0000.0000.0000.000
198A250HOH0-0.036-0.02019.982-0.009-0.0090.0000.0000.0000.000
199A254HOH00.0370.0282.4520.391-2.1455.027-1.491-1.000-0.012
200A256HOH0-0.026-0.0209.548-0.031-0.0310.0000.0000.0000.000
201A258HOH0-0.018-0.01431.422-0.001-0.0010.0000.0000.0000.000
202A259HOH0-0.026-0.01532.736-0.002-0.0020.0000.0000.0000.000
203A260HOH0-0.034-0.01836.1300.0000.0000.0000.0000.0000.000
204A266HOH0-0.017-0.01423.6740.0040.0040.0000.0000.0000.000
205A268HOH0-0.052-0.03832.8750.0010.0010.0000.0000.0000.000
206A269HOH0-0.059-0.04934.8350.0010.0010.0000.0000.0000.000
207A270HOH0-0.031-0.02239.550-0.001-0.0010.0000.0000.0000.000
208A273HOH0-0.060-0.05335.497-0.002-0.0020.0000.0000.0000.000
209A274HOH00.0280.01547.012-0.001-0.0010.0000.0000.0000.000
210A277HOH00.0270.01646.029-0.001-0.0010.0000.0000.0000.000
211A279HOH0-0.076-0.06018.121-0.007-0.0070.0000.0000.0000.000
212A282HOH0-0.052-0.03713.350-0.007-0.0070.0000.0000.0000.000
213A283HOH0-0.018-0.01318.558-0.002-0.0020.0000.0000.0000.000
214A284HOH0-0.041-0.03019.4760.0090.0090.0000.0000.0000.000
215A285HOH00.0220.01747.970-0.001-0.0010.0000.0000.0000.000
216A289HOH0-0.054-0.04320.4350.0010.0010.0000.0000.0000.000
217A290HOH0-0.033-0.02214.507-0.020-0.0200.0000.0000.0000.000