FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YYQ72

Calculation Name: 4XPU-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XPU

Chain ID: A

ChEMBL ID:

UniProt ID: P68739

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2435504.753288
FMO2-HF: Nuclear repulsion 2354520.273835
FMO2-HF: Total energy -80984.479453
FMO2-MP2: Total energy -81219.662877


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:0:ACE )


Summations of interaction energy for fragment #1(A:0: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.
1.8862.758-0.004-0.38-0.487-0.001
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.004
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].
3A2ASP -1-0.812-0.8913.868-0.1630.709-0.004-0.380-0.487-0.001
4A3LEU 00.0430.0106.5620.2360.2360.0000.0000.0000.000
5A4ALA 0-0.028-0.0286.6340.2640.2640.0000.0000.0000.000
6A5SER 0-0.010-0.0097.1760.3280.3280.0000.0000.0000.000
7A6LEU 00.0570.0339.0230.1460.1460.0000.0000.0000.000
8A7ARG 10.8920.94811.4920.3920.3920.0000.0000.0000.000
9A8ALA 0-0.0020.00211.3370.0630.0630.0000.0000.0000.000
10A9GLN 00.0940.03512.7690.0640.0640.0000.0000.0000.000
11A10GLN 0-0.0200.01014.9810.0070.0070.0000.0000.0000.000
12A11ILE 0-0.071-0.04616.5530.0230.0230.0000.0000.0000.000
13A12GLU -1-0.891-0.93116.523-0.057-0.0570.0000.0000.0000.000
14A13LEU 00.0260.00218.8230.0140.0140.0000.0000.0000.000
15A14ALA 0-0.032-0.03021.0000.0100.0100.0000.0000.0000.000
16A15SER 0-0.046-0.03121.9050.0120.0120.0000.0000.0000.000
17A16SER 0-0.033-0.00322.7150.0120.0120.0000.0000.0000.000
18A17VAL 0-0.053-0.00625.1990.0060.0060.0000.0000.0000.000
19A18ILE 0-0.0200.01327.5840.0020.0020.0000.0000.0000.000
20A19ARG 10.8650.91327.6890.0690.0690.0000.0000.0000.000
21A20GLU -1-0.791-0.87233.452-0.026-0.0260.0000.0000.0000.000
22A21ASP -1-0.729-0.80736.270-0.032-0.0320.0000.0000.0000.000
23A22ARG 10.8260.88832.9340.0280.0280.0000.0000.0000.000
24A23LEU 00.0150.01037.6100.0000.0000.0000.0000.0000.000
25A24ASP -1-0.842-0.91838.186-0.015-0.0150.0000.0000.0000.000
26A25LYS 10.8060.88941.0970.0150.0150.0000.0000.0000.000
27A26ASP -1-0.914-0.92543.909-0.022-0.0220.0000.0000.0000.000
28A27PRO 0-0.033-0.04145.7970.0010.0010.0000.0000.0000.000
29A28PRO 0-0.008-0.00643.1180.0010.0010.0000.0000.0000.000
30A29ASP -1-0.833-0.90345.124-0.013-0.0130.0000.0000.0000.000
31A30LEU 0-0.070-0.04242.6500.0000.0000.0000.0000.0000.000
32A31ILE 0-0.028-0.00141.083-0.001-0.0010.0000.0000.0000.000
33A32ALA 00.0520.00537.4010.0010.0010.0000.0000.0000.000
34A33GLY 0-0.055-0.01637.862-0.002-0.0020.0000.0000.0000.000
35A34ALA 0-0.021-0.01932.7630.0010.0010.0000.0000.0000.000
36A35ASP -1-0.836-0.92133.411-0.057-0.0570.0000.0000.0000.000
37A36VAL 0-0.012-0.01327.3030.0010.0010.0000.0000.0000.000
38A37GLY 0-0.0110.00229.254-0.003-0.0030.0000.0000.0000.000
39A38PHE 0-0.074-0.03723.444-0.002-0.0020.0000.0000.0000.000
40A39GLU -1-0.767-0.87728.624-0.043-0.0430.0000.0000.0000.000
41A40GLN 00.005-0.01328.537-0.005-0.0050.0000.0000.0000.000
42A41GLY 00.0060.00627.836-0.004-0.0040.0000.0000.0000.000
43A42GLY 0-0.031-0.01324.741-0.009-0.0090.0000.0000.0000.000
44A43GLU -1-0.898-0.93523.434-0.095-0.0950.0000.0000.0000.000
45A44VAL 0-0.0140.00225.0310.0060.0060.0000.0000.0000.000
46A45THR 0-0.051-0.01724.447-0.008-0.0080.0000.0000.0000.000
47A46ARG 0-0.024-0.02726.8240.0070.0070.0000.0000.0000.000
48A47ALA 00.0190.00129.392-0.005-0.0050.0000.0000.0000.000
49A48ALA 00.0060.02331.3620.0050.0050.0000.0000.0000.000
50A49MET 0-0.036-0.02031.798-0.002-0.0020.0000.0000.0000.000
51A50VAL 0-0.016-0.01436.2260.0030.0030.0000.0000.0000.000
52A51LEU 00.0340.02139.402-0.001-0.0010.0000.0000.0000.000
53A52LEU 0-0.035-0.02141.8250.0000.0000.0000.0000.0000.000
54A53LYS 10.9430.99344.7910.0140.0140.0000.0000.0000.000
55A54TYR 0-0.0310.02246.097-0.002-0.0020.0000.0000.0000.000
56A55PRO 00.040-0.00648.0890.0010.0010.0000.0000.0000.000
57A56SER 0-0.066-0.03550.482-0.001-0.0010.0000.0000.0000.000
58A57LEU 0-0.024-0.02846.710-0.001-0.0010.0000.0000.0000.000
59A58GLU -1-0.901-0.94748.312-0.016-0.0160.0000.0000.0000.000
60A59LEU 0-0.011-0.00444.0870.0000.0000.0000.0000.0000.000
61A60VAL 0-0.022-0.01244.9730.0010.0010.0000.0000.0000.000
62A61GLU -1-0.796-0.86740.704-0.015-0.0150.0000.0000.0000.000
63A62TYR 0-0.0040.00040.274-0.002-0.0020.0000.0000.0000.000
64A63LYS 10.8680.94636.6810.0180.0180.0000.0000.0000.000
65A64VAL 00.0300.01634.652-0.003-0.0030.0000.0000.0000.000
66A65ALA 00.0210.02130.4980.0030.0030.0000.0000.0000.000
67A66ARG 10.8310.89330.0930.0340.0340.0000.0000.0000.000
68A67ILE 00.0010.00623.8430.0050.0050.0000.0000.0000.000
69A68ALA 00.0180.01323.672-0.005-0.0050.0000.0000.0000.000
70A69THR 0-0.056-0.04520.3400.0010.0010.0000.0000.0000.000
71A70THR 00.0130.01017.308-0.007-0.0070.0000.0000.0000.000
72A71MET 00.0080.01814.401-0.009-0.0090.0000.0000.0000.000
73A72PRO 00.0700.04114.5300.0230.0230.0000.0000.0000.000
74A73TYR 0-0.003-0.02416.973-0.019-0.0190.0000.0000.0000.000
75A74ILE 00.0500.03412.798-0.020-0.0200.0000.0000.0000.000
76A75PRO 00.0220.00217.0740.0220.0220.0000.0000.0000.000
77A76GLY 0-0.040-0.02317.781-0.029-0.0290.0000.0000.0000.000
78A77PHE 00.018-0.00714.3820.0010.0010.0000.0000.0000.000
79A78LEU 0-0.0080.01218.4060.0040.0040.0000.0000.0000.000
80A79SER 00.020-0.03321.2110.0030.0030.0000.0000.0000.000
81A80PHE 00.011-0.00616.1330.0080.0080.0000.0000.0000.000
82A81ARG 10.8500.93418.7550.1580.1580.0000.0000.0000.000
83A82GLU -1-0.875-0.95220.595-0.095-0.0950.0000.0000.0000.000
84A83TYR 00.0420.01021.3750.0100.0100.0000.0000.0000.000
85A84PRO 00.004-0.00620.5740.0110.0110.0000.0000.0000.000
86A85ALA 00.0420.03323.4760.0090.0090.0000.0000.0000.000
87A86LEU 0-0.004-0.00726.6940.0060.0060.0000.0000.0000.000
88A87LEU 0-0.0070.00524.4530.0050.0050.0000.0000.0000.000
89A88ALA 00.0370.01427.3650.0050.0050.0000.0000.0000.000
90A89ALA 00.002-0.01128.9980.0040.0040.0000.0000.0000.000
91A90TRP 00.0300.00230.6450.0020.0020.0000.0000.0000.000
92A91GLU -1-0.969-0.99228.834-0.011-0.0110.0000.0000.0000.000
93A92MET 0-0.071-0.01232.6770.0020.0020.0000.0000.0000.000
94A93LEU 0-0.097-0.03735.3840.0010.0010.0000.0000.0000.000
95A94SER 0-0.093-0.08837.6250.0020.0020.0000.0000.0000.000
96A95GLN 00.006-0.01240.3060.0020.0020.0000.0000.0000.000
97A96LYS 10.8930.96234.0540.0130.0130.0000.0000.0000.000
98A97PRO 0-0.0360.00036.7300.0010.0010.0000.0000.0000.000
99A98ASP -1-0.762-0.89938.269-0.017-0.0170.0000.0000.0000.000
100A99LEU 0-0.054-0.03037.672-0.001-0.0010.0000.0000.0000.000
101A100VAL 0-0.0010.00333.6660.0010.0010.0000.0000.0000.000
102A101PHE 0-0.028-0.02036.140-0.003-0.0030.0000.0000.0000.000
103A102VAL 00.034-0.00430.4320.0000.0000.0000.0000.0000.000
104A103ASP -1-0.846-0.92033.918-0.059-0.0590.0000.0000.0000.000
105A104GLY 00.0210.00730.966-0.005-0.0050.0000.0000.0000.000
106A105HIS 10.7350.84429.0840.0850.0850.0000.0000.0000.000
107A106GLY 00.0940.06329.289-0.002-0.0020.0000.0000.0000.000
108A107ILE 00.0630.02828.123-0.010-0.0100.0000.0000.0000.000
109A108SER 0-0.0040.04128.886-0.007-0.0070.0000.0000.0000.000
110A109HIS 00.065-0.00322.2410.0020.0020.0000.0000.0000.000
111A110PRO 0-0.055-0.03223.7400.0000.0000.0000.0000.0000.000
112A111ARG 10.8120.89516.8900.2640.2640.0000.0000.0000.000
113A112ARG 10.8180.91222.7070.1000.1000.0000.0000.0000.000
114A113LEU 00.0610.02920.7050.0070.0070.0000.0000.0000.000
115A114GLY 0-0.054-0.01423.627-0.010-0.0100.0000.0000.0000.000
116A115VAL 00.0620.01925.3720.0020.0020.0000.0000.0000.000
117A116ALA 00.0130.01426.3780.0050.0050.0000.0000.0000.000
118A117SER 00.001-0.01126.5080.0040.0040.0000.0000.0000.000
119A118HIS 0-0.0080.05119.323-0.003-0.0030.0000.0000.0000.000
120A119PHE 00.026-0.00224.6940.0040.0040.0000.0000.0000.000
121A120GLY 00.0300.01426.9460.0050.0050.0000.0000.0000.000
122A121LEU 0-0.032-0.01223.6040.0050.0050.0000.0000.0000.000
123A122LEU 0-0.045-0.03021.0280.0030.0030.0000.0000.0000.000
124A123VAL 0-0.028-0.00625.4060.0070.0070.0000.0000.0000.000
125A124ASP -1-0.872-0.92528.805-0.019-0.0190.0000.0000.0000.000
126A125VAL 00.0120.00430.5070.0040.0040.0000.0000.0000.000
127A126PRO 00.0020.03933.039-0.005-0.0050.0000.0000.0000.000
128A127THR 0-0.019-0.03731.5870.0000.0000.0000.0000.0000.000
129A128ILE 0-0.033-0.00934.113-0.003-0.0030.0000.0000.0000.000
130A129GLY 00.0110.00833.183-0.001-0.0010.0000.0000.0000.000
131A130VAL 0-0.013-0.00933.9140.0020.0020.0000.0000.0000.000
132A131ALA 00.0250.02033.434-0.001-0.0010.0000.0000.0000.000
133A132LYS 10.8840.92935.3700.0570.0570.0000.0000.0000.000
134A133LYS 10.9440.96334.4370.0650.0650.0000.0000.0000.000
135A134ARG 10.9470.98733.2260.0790.0790.0000.0000.0000.000
136A135LEU 0-0.033-0.00527.088-0.002-0.0020.0000.0000.0000.000
137A136CYS 0-0.040-0.01528.422-0.005-0.0050.0000.0000.0000.000
138A137GLY 00.0940.05431.0110.0050.0050.0000.0000.0000.000
139A138LYS 10.8910.92733.5320.0680.0680.0000.0000.0000.000
140A139PHE 00.0370.01637.2080.0000.0000.0000.0000.0000.000
141A140GLU -1-0.883-0.93540.618-0.042-0.0420.0000.0000.0000.000
142A141PRO 0-0.068-0.03743.8800.0010.0010.0000.0000.0000.000
143A142LEU 00.0040.01444.2190.0020.0020.0000.0000.0000.000
144A143SER 00.0620.03747.4110.0000.0000.0000.0000.0000.000
145A144SER 0-0.045-0.03850.102-0.001-0.0010.0000.0000.0000.000
146A145GLU -1-0.816-0.91051.942-0.031-0.0310.0000.0000.0000.000
147A146PRO 0-0.063-0.04750.941-0.002-0.0020.0000.0000.0000.000
148A147GLY 00.004-0.00249.9060.0010.0010.0000.0000.0000.000
149A148ALA 00.0120.03248.8080.0000.0000.0000.0000.0000.000
150A149LEU 0-0.009-0.02344.471-0.002-0.0020.0000.0000.0000.000
151A150ALA 00.0300.02543.6180.0010.0010.0000.0000.0000.000
152A151PRO 00.0270.02040.500-0.002-0.0020.0000.0000.0000.000
153A152LEU 0-0.090-0.04234.030-0.002-0.0020.0000.0000.0000.000
154A153MET 00.0150.00936.468-0.002-0.0020.0000.0000.0000.000
155A154ASP -1-0.835-0.94330.020-0.101-0.1010.0000.0000.0000.000
156A155LYS 10.8650.94127.4090.1090.1090.0000.0000.0000.000
157A156GLY 00.0250.02132.7980.0010.0010.0000.0000.0000.000
158A157GLU -1-0.857-0.92130.755-0.071-0.0710.0000.0000.0000.000
159A158GLN 00.004-0.01034.811-0.001-0.0010.0000.0000.0000.000
160A159LEU 0-0.056-0.02730.591-0.001-0.0010.0000.0000.0000.000
161A160ALA 0-0.018-0.03033.936-0.001-0.0010.0000.0000.0000.000
162A161TRP 00.0000.00136.5530.0000.0000.0000.0000.0000.000
163A162VAL 0-0.053-0.01339.060-0.002-0.0020.0000.0000.0000.000
164A163TRP 00.1020.04041.2820.0020.0020.0000.0000.0000.000
165A164ARG 10.8020.90144.2130.0370.0370.0000.0000.0000.000
166A165SER 0-0.021-0.01645.6260.0020.0020.0000.0000.0000.000
167A166LYS 10.9170.94647.4530.0310.0310.0000.0000.0000.000
168A167ALA 00.0440.01849.509-0.001-0.0010.0000.0000.0000.000
169A168ARG 10.9470.96050.8730.0280.0280.0000.0000.0000.000
170A169CYS 0-0.0180.02446.2540.0000.0000.0000.0000.0000.000
171A170ASN 00.010-0.00242.3950.0000.0000.0000.0000.0000.000
172A171PRO 00.0240.02541.8220.0010.0010.0000.0000.0000.000
173A172LEU 0-0.029-0.00240.001-0.003-0.0030.0000.0000.0000.000
174A173PHE 0-0.029-0.02835.998-0.001-0.0010.0000.0000.0000.000
175A174ILE 00.0280.02636.316-0.003-0.0030.0000.0000.0000.000
176A175ALA 0-0.007-0.01133.3330.0000.0000.0000.0000.0000.000
177A176THR 00.0050.03432.6510.0000.0000.0000.0000.0000.000
178A177GLY 00.022-0.00530.852-0.007-0.0070.0000.0000.0000.000
179A178HIS 00.0450.00329.086-0.009-0.0090.0000.0000.0000.000
180A179ARG 10.8230.92531.4450.0270.0270.0000.0000.0000.000
181A180VAL 00.0190.02034.3500.0030.0030.0000.0000.0000.000
182A181SER 0-0.008-0.02535.673-0.004-0.0040.0000.0000.0000.000
183A182VAL 00.012-0.01636.693-0.001-0.0010.0000.0000.0000.000
184A183ASP -1-0.828-0.91038.135-0.037-0.0370.0000.0000.0000.000
185A184SER 0-0.025-0.07140.6640.0010.0010.0000.0000.0000.000
186A185ALA 0-0.033-0.00837.7620.0010.0010.0000.0000.0000.000
187A186LEU 0-0.033-0.01939.8120.0000.0000.0000.0000.0000.000
188A187ALA 00.0160.01742.5460.0010.0010.0000.0000.0000.000
189A188TRP 00.0500.01341.5450.0020.0020.0000.0000.0000.000
190A189VAL 00.001-0.01340.5450.0010.0010.0000.0000.0000.000
191A190GLN 0-0.033-0.03043.4090.0020.0020.0000.0000.0000.000
192A191ARG 10.9080.97446.5330.0260.0260.0000.0000.0000.000
193A192CYS 0-0.0110.00844.4670.0010.0010.0000.0000.0000.000
194A193MET 0-0.0480.00844.237-0.001-0.0010.0000.0000.0000.000
195A194LYS 11.0551.02848.3120.0230.0230.0000.0000.0000.000
196A195GLY 0-0.0060.00050.8600.0000.0000.0000.0000.0000.000
197A196TYR 0-0.063-0.03147.4230.0000.0000.0000.0000.0000.000
198A197ARG 10.8510.91440.3590.0470.0470.0000.0000.0000.000
199A198LEU 00.0130.03040.056-0.001-0.0010.0000.0000.0000.000
200A199PRO 00.0360.01841.3800.0020.0020.0000.0000.0000.000
201A200GLU -1-0.765-0.88543.068-0.028-0.0280.0000.0000.0000.000
202A201PRO 00.0490.03240.1440.0000.0000.0000.0000.0000.000
203A202THR 00.0410.00036.9820.0000.0000.0000.0000.0000.000
204A203ARG 10.7900.89739.5570.0280.0280.0000.0000.0000.000
205A204TRP 00.001-0.01442.3160.0000.0000.0000.0000.0000.000
206A205ALA 0-0.016-0.00736.9680.0010.0010.0000.0000.0000.000
207A206ASP -1-0.800-0.90837.468-0.048-0.0480.0000.0000.0000.000
208A207ALA 0-0.120-0.05339.0910.0000.0000.0000.0000.0000.000
209A208VAL 0-0.054-0.01638.7150.0010.0010.0000.0000.0000.000
210A209NME 0-0.0250.01637.3050.0010.0010.0000.0000.0000.000