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: 98422

Calculation Name: 2XLF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XLF

Chain ID: A

ChEMBL ID:

UniProt ID: P73600

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3019450.111701
FMO2-HF: Nuclear repulsion 2926978.212124
FMO2-HF: Total energy -92471.899577
FMO2-MP2: Total energy -92739.905204


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:36:HIS)


Summations of interaction energy for fragment #1(A:36:HIS)
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.
-61.092-49.23215.26-11.464-15.657-0.066
Interaction energy analysis for fragmet #1(A:36:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.030
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].
3A38PHE00.0320.0143.829-2.6320.730-0.017-1.786-1.5590.006
4A39ASP-1-0.837-0.9146.148-0.600-0.6000.0000.0000.0000.000
5A40ASP-1-0.829-0.9319.785-1.355-1.3550.0000.0000.0000.000
6A41ILE0-0.0240.0098.262-0.359-0.3590.0000.0000.0000.000
7A42PRO00.0620.04911.9510.2340.2340.0000.0000.0000.000
8A43MET00.0070.02415.656-0.185-0.1850.0000.0000.0000.000
9A44PRO0-0.001-0.01418.0010.0820.0820.0000.0000.0000.000
10A45LYS10.8540.93420.8470.7460.7460.0000.0000.0000.000
11A46LEU0-0.015-0.01024.1750.0370.0370.0000.0000.0000.000
12A47ALA0-0.010-0.01026.7920.0090.0090.0000.0000.0000.000
13A48ASP-1-0.925-0.95929.893-0.407-0.4070.0000.0000.0000.000
14A49PRO0-0.032-0.01025.953-0.017-0.0170.0000.0000.0000.000
15A50LEU0-0.042-0.00625.6730.0560.0560.0000.0000.0000.000
16A51LEU00.0200.01125.139-0.051-0.0510.0000.0000.0000.000
17A52ILE0-0.025-0.02325.0340.0490.0490.0000.0000.0000.000
18A53TYR00.0180.00625.122-0.045-0.0450.0000.0000.0000.000
19A54THR0-0.035-0.05822.3620.0600.0600.0000.0000.0000.000
20A55PRO00.003-0.02425.5680.0200.0200.0000.0000.0000.000
21A56ALA0-0.047-0.00222.4860.0390.0390.0000.0000.0000.000
22A57ASN0-0.024-0.00523.4670.0040.0040.0000.0000.0000.000
23A58GLU-1-0.755-0.85019.095-0.836-0.8360.0000.0000.0000.000
24A59ILE0-0.0130.00122.2890.0360.0360.0000.0000.0000.000
25A60PHE0-0.004-0.02018.937-0.085-0.0850.0000.0000.0000.000
26A61ASP-1-0.851-0.92020.917-0.745-0.7450.0000.0000.0000.000
27A62ILE0-0.025-0.02120.165-0.105-0.1050.0000.0000.0000.000
28A63ALA0-0.024-0.00720.5580.0830.0830.0000.0000.0000.000
29A64SER0-0.032-0.04020.260-0.076-0.0760.0000.0000.0000.000
30A65CYS00.0210.01118.680-0.029-0.0290.0000.0000.0000.000
31A66SER0-0.006-0.00219.943-0.023-0.0230.0000.0000.0000.000
32A67ALA00.0240.01420.0710.0440.0440.0000.0000.0000.000
33A68LYS10.8800.91820.9500.7870.7870.0000.0000.0000.000
34A69ASP-1-0.812-0.86617.997-0.996-0.9960.0000.0000.0000.000
35A70ILE00.0250.01913.998-0.031-0.0310.0000.0000.0000.000
36A71GLY00.0210.00318.2180.0850.0850.0000.0000.0000.000
37A72PHE00.0170.01515.606-0.070-0.0700.0000.0000.0000.000
38A73ALA0-0.0110.00417.3370.1290.1290.0000.0000.0000.000
39A74ILE0-0.023-0.00713.939-0.169-0.1690.0000.0000.0000.000
40A75ALA00.0280.01215.9080.1820.1820.0000.0000.0000.000
41A76HIS10.8110.89515.1661.3531.3530.0000.0000.0000.000
42A77ALA0-0.003-0.00616.6640.1320.1320.0000.0000.0000.000
43A78GLN00.0140.00617.895-0.031-0.0310.0000.0000.0000.000
44A79ILE00.0030.01117.4060.0440.0440.0000.0000.0000.000
45A80PRO00.0310.01420.5260.0190.0190.0000.0000.0000.000
46A81PRO00.0320.00822.425-0.023-0.0230.0000.0000.0000.000
47A82GLY0-0.021-0.00722.4330.0140.0140.0000.0000.0000.000
48A83GLY0-0.037-0.00322.7000.0110.0110.0000.0000.0000.000
49A84GLY00.034-0.00519.916-0.029-0.0290.0000.0000.0000.000
50A85PRO0-0.073-0.01818.5160.0710.0710.0000.0000.0000.000
51A86MET00.0070.00820.4190.0150.0150.0000.0000.0000.000
52A87PRO0-0.020-0.00319.830-0.049-0.0490.0000.0000.0000.000
53A88HIS0-0.0040.00117.822-0.044-0.0440.0000.0000.0000.000
54A89ILE0-0.029-0.00218.901-0.023-0.0230.0000.0000.0000.000
55A90HIS00.0320.02117.1580.0120.0120.0000.0000.0000.000
56A91TYR00.005-0.02919.3290.0140.0140.0000.0000.0000.000
57A92PHE00.0000.01120.9110.0190.0190.0000.0000.0000.000
58A93ILE0-0.035-0.00815.238-0.034-0.0340.0000.0000.0000.000
59A94ASN00.0050.02012.2490.1510.1510.0000.0000.0000.000
60A95GLU-1-0.777-0.90611.678-1.404-1.4040.0000.0000.0000.000
61A96TRP0-0.047-0.0265.7730.4550.4550.0000.0000.0000.000
62A97PHE00.0060.0027.5380.5410.5410.0000.0000.0000.000
63A98TRP0-0.028-0.0226.533-0.709-0.7090.0000.0000.0000.000
64A99THR00.0810.0438.5490.4450.4450.0000.0000.0000.000
65A100PRO0-0.021-0.0099.9840.0370.0370.0000.0000.0000.000
66A101GLU-1-0.861-0.95212.095-0.568-0.5680.0000.0000.0000.000
67A102GLY00.0050.02510.2620.1630.1630.0000.0000.0000.000
68A103GLY00.0140.00311.0660.0130.0130.0000.0000.0000.000
69A104ILE0-0.043-0.01812.5960.1080.1080.0000.0000.0000.000
70A105GLU-1-0.776-0.84711.976-0.199-0.1990.0000.0000.0000.000
71A106LEU0-0.041-0.0269.614-0.068-0.0680.0000.0000.0000.000
72A107PHE00.014-0.00713.0840.1890.1890.0000.0000.0000.000
73A108HIS0-0.001-0.00111.055-0.336-0.3360.0000.0000.0000.000
74A109SER00.0220.01114.0930.1150.1150.0000.0000.0000.000
75A110THR00.006-0.00714.511-0.018-0.0180.0000.0000.0000.000
76A111LYS10.9180.97316.1570.0080.0080.0000.0000.0000.000
77A112GLN00.0040.01616.669-0.121-0.1210.0000.0000.0000.000
78A113TYR00.020-0.01219.7290.0760.0760.0000.0000.0000.000
79A114PRO00.0240.01122.608-0.047-0.0470.0000.0000.0000.000
80A115ASN0-0.026-0.02523.610-0.047-0.0470.0000.0000.0000.000
81A116MET0-0.0120.01225.421-0.003-0.0030.0000.0000.0000.000
82A117ASP-1-0.902-0.94226.980-0.218-0.2180.0000.0000.0000.000
83A118GLU-1-0.970-0.96028.719-0.080-0.0800.0000.0000.0000.000
84A119LEU0-0.003-0.00127.640-0.014-0.0140.0000.0000.0000.000
85A120PRO0-0.009-0.00424.2310.0270.0270.0000.0000.0000.000
86A121VAL00.0510.01227.2400.0030.0030.0000.0000.0000.000
87A122VAL0-0.013-0.02230.1830.0140.0140.0000.0000.0000.000
88A123GLY0-0.043-0.00832.7530.0150.0150.0000.0000.0000.000
89A124GLY0-0.014-0.00834.106-0.008-0.0080.0000.0000.0000.000
90A125ALA00.0560.03829.288-0.012-0.0120.0000.0000.0000.000
91A126GLY0-0.050-0.02428.9370.0190.0190.0000.0000.0000.000
92A127ARG10.8690.94826.4690.0330.0330.0000.0000.0000.000
93A128GLY0-0.011-0.00422.6990.0280.0280.0000.0000.0000.000
94A129ASP-1-0.844-0.90120.9780.1200.1200.0000.0000.0000.000
95A130LEU0-0.041-0.02417.184-0.006-0.0060.0000.0000.0000.000
96A131TYR0-0.028-0.02713.9710.1190.1190.0000.0000.0000.000
97A132SER0-0.039-0.02713.898-0.064-0.0640.0000.0000.0000.000
98A133ILE0-0.056-0.0297.4030.2070.2070.0000.0000.0000.000
99A134GLN0-0.024-0.01810.338-0.295-0.2950.0000.0000.0000.000
100A135SER0-0.049-0.0337.6430.0450.0450.0000.0000.0000.000
101A136GLU-1-0.879-0.9556.0660.1310.1310.0000.0000.0000.000
102A137PRO0-0.008-0.0167.719-0.572-0.5720.0000.0000.0000.000
103A138LYS10.7520.8647.3651.4061.4060.0000.0000.0000.000
104A139GLN0-0.0030.0103.097-0.893-0.3060.017-0.158-0.4460.000
105A140LEU0-0.028-0.0112.426-0.2781.4140.940-0.748-1.8840.002
106A141ILE0-0.023-0.0072.524-6.149-3.7730.818-1.318-1.876-0.021
107A142TYR00.0090.0035.213-0.0400.033-0.001-0.003-0.0690.000
108A143SER0-0.014-0.0366.6420.8760.8760.0000.0000.0000.000
109A144PRO0-0.014-0.00810.032-0.025-0.0250.0000.0000.0000.000
110A145ASN00.0490.02912.8090.0510.0510.0000.0000.0000.000
111A146HIS0-0.021-0.02116.4130.0740.0740.0000.0000.0000.000
112A147TYR0-0.0060.01013.9210.1640.1640.0000.0000.0000.000
113A148MET0-0.050-0.01416.609-0.075-0.0750.0000.0000.0000.000
114A149HIS10.8740.93914.0501.0091.0090.0000.0000.0000.000
115A150GLY00.0270.01215.5490.0260.0260.0000.0000.0000.000
116A151PHE0-0.020-0.01114.691-0.065-0.0650.0000.0000.0000.000
117A152VAL00.0310.02416.5730.0380.0380.0000.0000.0000.000
118A153ASN00.0140.00616.839-0.016-0.0160.0000.0000.0000.000
119A154PRO0-0.020-0.00616.9710.0430.0430.0000.0000.0000.000
120A155THR0-0.040-0.02617.8580.0560.0560.0000.0000.0000.000
121A156ASP-1-0.902-0.95420.754-0.224-0.2240.0000.0000.0000.000
122A157LYS10.8390.92218.5230.5240.5240.0000.0000.0000.000
123A158THR0-0.009-0.00921.043-0.017-0.0170.0000.0000.0000.000
124A159LEU0-0.0190.01715.5630.0240.0240.0000.0000.0000.000
125A160PRO0-0.0020.01815.408-0.020-0.0200.0000.0000.0000.000
126A161ILE0-0.012-0.01611.935-0.101-0.1010.0000.0000.0000.000
127A162VAL0-0.047-0.01611.6760.1690.1690.0000.0000.0000.000
128A163PHE00.0350.03111.273-0.341-0.3410.0000.0000.0000.000
129A164VAL00.009-0.00810.8350.1580.1580.0000.0000.0000.000
130A165TRP0-0.009-0.02212.395-0.110-0.1100.0000.0000.0000.000
131A166MET00.009-0.00213.2000.0180.0180.0000.0000.0000.000
132A167ARG10.8850.93915.1770.8880.8880.0000.0000.0000.000
133A168ASN0-0.047-0.03417.473-0.047-0.0470.0000.0000.0000.000
134A169GLU-1-0.904-0.97318.689-0.661-0.6610.0000.0000.0000.000
135A170VAL0-0.042-0.01821.5780.0530.0530.0000.0000.0000.000
136A171ALA0-0.0380.00521.8420.0370.0370.0000.0000.0000.000
137A172PRO0-0.0120.00323.8610.0130.0130.0000.0000.0000.000
138A173ASP-1-0.860-0.90925.657-0.597-0.5970.0000.0000.0000.000
139A174PHE00.0160.01525.1840.0360.0360.0000.0000.0000.000
140A175PRO00.0170.00727.548-0.020-0.0200.0000.0000.0000.000
141A176TYR0-0.018-0.01924.7020.0080.0080.0000.0000.0000.000
142A177HIS10.7880.87324.2510.5150.5150.0000.0000.0000.000
143A178ASP-1-0.719-0.81620.532-0.829-0.8290.0000.0000.0000.000
144A179GLY00.0350.01719.847-0.090-0.0900.0000.0000.0000.000
145A180GLY00.0100.01221.6420.0330.0330.0000.0000.0000.000
146A181MET00.0120.01518.3610.0670.0670.0000.0000.0000.000
147A182ARG10.8760.91121.6020.7060.7060.0000.0000.0000.000
148A183GLH0-0.053-0.08823.2200.0620.0620.0000.0000.0000.000
149A184TYR0-0.009-0.00122.7160.0340.0340.0000.0000.0000.000
150A185PHE00.0400.00119.7360.0490.0490.0000.0000.0000.000
151A186GLN0-0.0070.00225.3220.0020.0020.0000.0000.0000.000
152A187ALA0-0.045-0.00628.1490.0350.0350.0000.0000.0000.000
153A188VAL0-0.028-0.01727.1300.0320.0320.0000.0000.0000.000
154A189GLY00.0030.00128.0930.0220.0220.0000.0000.0000.000
155A190PRO0-0.054-0.00629.0870.0070.0070.0000.0000.0000.000
156A191ARG10.9690.97529.7220.4420.4420.0000.0000.0000.000
157A192ILE0-0.022-0.00426.7700.0300.0300.0000.0000.0000.000
158A193THR0-0.023-0.02630.784-0.013-0.0130.0000.0000.0000.000
159A194ASP-1-0.839-0.93632.994-0.318-0.3180.0000.0000.0000.000
160A195LEU0-0.010-0.00126.8720.0000.0000.0000.0000.0000.000
161A196ASN0-0.089-0.04130.440-0.006-0.0060.0000.0000.0000.000
162A197ASN0-0.058-0.02233.0780.0270.0270.0000.0000.0000.000
163A198LEU00.0000.01128.413-0.008-0.0080.0000.0000.0000.000
164A199PRO0-0.0110.00730.7870.0210.0210.0000.0000.0000.000
165A200GLU-1-0.926-0.96532.521-0.247-0.2470.0000.0000.0000.000
166A201LEU0-0.060-0.01328.7490.0030.0030.0000.0000.0000.000
167A202THR00.000-0.01533.3560.0250.0250.0000.0000.0000.000
168A203ASN00.023-0.02634.323-0.021-0.0210.0000.0000.0000.000
169A204ALA00.0020.01335.163-0.003-0.0030.0000.0000.0000.000
170A205GLN00.0920.06031.5870.0040.0040.0000.0000.0000.000
171A206ARG10.9740.98930.3540.2650.2650.0000.0000.0000.000
172A207ALA0-0.012-0.00730.635-0.008-0.0080.0000.0000.0000.000
173A208ALA00.0130.00732.079-0.003-0.0030.0000.0000.0000.000
174A209PHE00.0310.02222.631-0.009-0.0090.0000.0000.0000.000
175A210ALA00.0490.02927.142-0.027-0.0270.0000.0000.0000.000
176A211SER0-0.017-0.02028.842-0.001-0.0010.0000.0000.0000.000
177A212GLU-1-0.822-0.90429.894-0.339-0.3390.0000.0000.0000.000
178A213ALA0-0.0290.00025.306-0.018-0.0180.0000.0000.0000.000
179A214PRO00.0560.02226.210-0.033-0.0330.0000.0000.0000.000
180A215LYS10.7890.88828.0410.3410.3410.0000.0000.0000.000
181A216TYR0-0.055-0.04124.765-0.013-0.0130.0000.0000.0000.000
182A217GLY00.0420.03423.673-0.054-0.0540.0000.0000.0000.000
183A218ILE0-0.022-0.02521.058-0.049-0.0490.0000.0000.0000.000
184A219ASN0-0.013-0.00223.1800.0330.0330.0000.0000.0000.000
185A220GLN0-0.010-0.02222.653-0.074-0.0740.0000.0000.0000.000
186A221SER0-0.033-0.01124.0360.0320.0320.0000.0000.0000.000
187A222SER0-0.039-0.04926.364-0.024-0.0240.0000.0000.0000.000
188A223TYR0-0.002-0.01228.5630.0120.0120.0000.0000.0000.000
189A224PHE00.0750.01820.1460.0080.0080.0000.0000.0000.000
190A225MET0-0.023-0.01324.917-0.002-0.0020.0000.0000.0000.000
191A226GLU-1-0.837-0.88827.240-0.197-0.1970.0000.0000.0000.000
192A227TYR00.0510.00123.3180.0100.0100.0000.0000.0000.000
193A228VAL0-0.021-0.00522.2880.0170.0170.0000.0000.0000.000
194A229ASN0-0.119-0.05624.221-0.011-0.0110.0000.0000.0000.000
195A230THR0-0.053-0.05722.8120.0220.0220.0000.0000.0000.000
196A231ILE00.0340.01418.409-0.023-0.0230.0000.0000.0000.000
197A232SER0-0.0240.00318.2830.0350.0350.0000.0000.0000.000
198A233ASP-1-0.737-0.86915.2160.4320.4320.0000.0000.0000.000
199A234LYS10.7840.88314.199-0.520-0.5200.0000.0000.0000.000
200A235LEU00.0310.0198.083-0.023-0.0230.0000.0000.0000.000
201A236PRO00.0060.00911.8150.3010.3010.0000.0000.0000.000
202A237ALA00.0650.01310.0010.0770.0770.0000.0000.0000.000
203A238GLN0-0.005-0.0029.2670.7380.7380.0000.0000.0000.000
204A239ILE00.0220.0099.5060.0470.0470.0000.0000.0000.000
205A240ALA00.0390.0356.621-0.216-0.2160.0000.0000.0000.000
206A241LYS10.8330.9104.865-1.324-1.115-0.001-0.006-0.2020.000
207A242LEU0-0.0150.0156.2760.1080.1080.0000.0000.0000.000
208A243LYS10.8810.9322.499-15.803-13.2764.408-2.008-4.9280.022
209A244ASN0-0.025-0.0304.6360.8590.939-0.001-0.005-0.0740.000
210A245ASP-1-0.789-0.8961.865-36.555-35.6489.098-5.421-4.585-0.075
211A246LYS10.8980.9624.9052.8012.848-0.001-0.011-0.0340.000
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