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: MNV2Z

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 OptAll
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 -3021179.23273
FMO2-HF: Nuclear repulsion 2928707.072185
FMO2-HF: Total energy -92472.160545
FMO2-MP2: Total energy -92740.278203


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.
-57.065-50.36824.917-13.556-18.058-0.064
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 : -0.034 / q_NPA : -0.026
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].
3A38PHE00.0210.0103.787-2.9000.2820.014-1.680-1.5160.005
4A39ASP-1-0.824-0.9036.043-0.578-0.5780.0000.0000.0000.000
5A40ASP-1-0.829-0.9319.763-1.272-1.2720.0000.0000.0000.000
6A41ILE0-0.0170.0048.011-0.443-0.4430.0000.0000.0000.000
7A42PRO00.0520.04011.7840.2400.2400.0000.0000.0000.000
8A43MET00.0140.02815.536-0.167-0.1670.0000.0000.0000.000
9A44PRO00.000-0.00718.1960.0770.0770.0000.0000.0000.000
10A45LYS10.8470.92121.1010.7110.7110.0000.0000.0000.000
11A46LEU0-0.029-0.01924.0820.0430.0430.0000.0000.0000.000
12A47ALA0-0.007-0.00226.5410.0080.0080.0000.0000.0000.000
13A48ASP-1-0.917-0.95429.722-0.388-0.3880.0000.0000.0000.000
14A49PRO0-0.004-0.00425.979-0.010-0.0100.0000.0000.0000.000
15A50LEU0-0.034-0.00325.2660.0530.0530.0000.0000.0000.000
16A51LEU00.0180.00225.055-0.040-0.0400.0000.0000.0000.000
17A52ILE0-0.025-0.01324.7670.0440.0440.0000.0000.0000.000
18A53TYR00.0020.00824.909-0.039-0.0390.0000.0000.0000.000
19A54THR0-0.022-0.05422.0540.0530.0530.0000.0000.0000.000
20A55PRO0-0.001-0.02425.3000.0180.0180.0000.0000.0000.000
21A56ALA0-0.0250.01122.4760.0350.0350.0000.0000.0000.000
22A57ASN0-0.040-0.01923.6980.0130.0130.0000.0000.0000.000
23A58GLU-1-0.778-0.86118.847-0.731-0.7310.0000.0000.0000.000
24A59ILE0-0.0070.00522.1110.0220.0220.0000.0000.0000.000
25A60PHE0-0.008-0.02318.670-0.085-0.0850.0000.0000.0000.000
26A61ASP-1-0.837-0.92120.804-0.690-0.6900.0000.0000.0000.000
27A62ILE0-0.039-0.02019.872-0.107-0.1070.0000.0000.0000.000
28A63ALA0-0.021-0.00520.1890.0760.0760.0000.0000.0000.000
29A64SER0-0.020-0.03120.189-0.067-0.0670.0000.0000.0000.000
30A65CYS00.0060.01018.803-0.028-0.0280.0000.0000.0000.000
31A66SER0-0.0020.00320.291-0.007-0.0070.0000.0000.0000.000
32A67ALA00.0260.00920.4980.0250.0250.0000.0000.0000.000
33A68LYS10.8790.92221.2690.7250.7250.0000.0000.0000.000
34A69ASP-1-0.806-0.86018.345-0.911-0.9110.0000.0000.0000.000
35A70ILE00.0320.02314.074-0.013-0.0130.0000.0000.0000.000
36A71GLY00.005-0.01618.1730.0890.0890.0000.0000.0000.000
37A72PHE00.0060.01015.610-0.054-0.0540.0000.0000.0000.000
38A73ALA00.0010.01317.3750.1030.1030.0000.0000.0000.000
39A74ILE0-0.022-0.01314.034-0.162-0.1620.0000.0000.0000.000
40A75ALA00.0320.01715.6000.1680.1680.0000.0000.0000.000
41A76HIS10.8140.89815.0911.2781.2780.0000.0000.0000.000
42A77ALA00.0160.00516.7420.1210.1210.0000.0000.0000.000
43A78GLN00.004-0.00117.877-0.031-0.0310.0000.0000.0000.000
44A79ILE00.0130.01317.3650.0440.0440.0000.0000.0000.000
45A80PRO00.0380.02620.4310.0170.0170.0000.0000.0000.000
46A81PRO00.0270.00822.278-0.018-0.0180.0000.0000.0000.000
47A82GLY0-0.0140.00022.1620.0160.0160.0000.0000.0000.000
48A83GLY0-0.037-0.00522.6950.0110.0110.0000.0000.0000.000
49A84GLY00.024-0.00719.874-0.037-0.0370.0000.0000.0000.000
50A85PRO0-0.067-0.01618.1910.0640.0640.0000.0000.0000.000
51A86MET00.0080.01020.2200.0220.0220.0000.0000.0000.000
52A87PRO0-0.0210.01219.779-0.040-0.0400.0000.0000.0000.000
53A88HIS00.0160.00917.475-0.041-0.0410.0000.0000.0000.000
54A89ILE0-0.0150.00118.705-0.001-0.0010.0000.0000.0000.000
55A90HIS00.0410.02916.9010.0150.0150.0000.0000.0000.000
56A91TYR00.014-0.02019.0000.0130.0130.0000.0000.0000.000
57A92PHE00.0070.02220.6500.0190.0190.0000.0000.0000.000
58A93ILE0-0.039-0.00715.020-0.041-0.0410.0000.0000.0000.000
59A94ASN00.0040.01612.2660.1620.1620.0000.0000.0000.000
60A95GLU-1-0.788-0.90711.423-1.257-1.2570.0000.0000.0000.000
61A96TRP0-0.060-0.0355.7550.4310.4310.0000.0000.0000.000
62A97PHE00.0100.0027.1260.5400.5400.0000.0000.0000.000
63A98TRP0-0.022-0.0186.540-0.725-0.7250.0000.0000.0000.000
64A99THR00.0620.0288.3060.3980.3980.0000.0000.0000.000
65A100PRO0-0.034-0.01510.1860.1050.1050.0000.0000.0000.000
66A101GLU-1-0.825-0.93112.454-0.516-0.5160.0000.0000.0000.000
67A102GLY0-0.0260.01010.1390.1410.1410.0000.0000.0000.000
68A103GLY00.0200.00810.9800.0200.0200.0000.0000.0000.000
69A104ILE0-0.032-0.02012.3830.1040.1040.0000.0000.0000.000
70A105GLU-1-0.800-0.84811.928-0.103-0.1030.0000.0000.0000.000
71A106LEU0-0.019-0.0139.289-0.067-0.0670.0000.0000.0000.000
72A107PHE00.010-0.00912.6510.1970.1970.0000.0000.0000.000
73A108HIS00.0040.00610.771-0.288-0.2880.0000.0000.0000.000
74A109SER00.0210.00713.6700.1170.1170.0000.0000.0000.000
75A110THR0-0.011-0.01714.5350.0240.0240.0000.0000.0000.000
76A111LYS10.8680.94716.427-0.052-0.0520.0000.0000.0000.000
77A112GLN00.0040.02016.122-0.096-0.0960.0000.0000.0000.000
78A113TYR0-0.017-0.02919.7180.0570.0570.0000.0000.0000.000
79A114PRO00.0290.00922.326-0.042-0.0420.0000.0000.0000.000
80A115ASN0-0.019-0.02623.239-0.054-0.0540.0000.0000.0000.000
81A116MET0-0.0350.00024.961-0.011-0.0110.0000.0000.0000.000
82A117ASP-1-0.867-0.92726.789-0.169-0.1690.0000.0000.0000.000
83A118GLU-1-0.961-0.96128.252-0.039-0.0390.0000.0000.0000.000
84A119LEU0-0.0030.00127.292-0.003-0.0030.0000.0000.0000.000
85A120PRO00.0010.01324.0960.0250.0250.0000.0000.0000.000
86A121VAL00.0340.00226.6780.0070.0070.0000.0000.0000.000
87A122VAL0-0.002-0.02629.7430.0160.0160.0000.0000.0000.000
88A123GLY0-0.025-0.00232.2920.0110.0110.0000.0000.0000.000
89A124GLY00.0070.00332.873-0.001-0.0010.0000.0000.0000.000
90A125ALA00.0510.04228.745-0.009-0.0090.0000.0000.0000.000
91A126GLY0-0.040-0.01828.2590.0200.0200.0000.0000.0000.000
92A127ARG10.8850.94826.015-0.011-0.0110.0000.0000.0000.000
93A128GLY0-0.0060.00522.1830.0280.0280.0000.0000.0000.000
94A129ASP-1-0.852-0.89820.9090.1610.1610.0000.0000.0000.000
95A130LEU0-0.042-0.02116.7390.0010.0010.0000.0000.0000.000
96A131TYR0-0.036-0.03213.6940.0930.0930.0000.0000.0000.000
97A132SER0-0.055-0.04413.497-0.042-0.0420.0000.0000.0000.000
98A133ILE0-0.059-0.0367.2330.2330.2330.0000.0000.0000.000
99A134GLN00.000-0.00910.156-0.318-0.3180.0000.0000.0000.000
100A135SER0-0.052-0.0307.6280.0270.0270.0000.0000.0000.000
101A136GLU-1-0.874-0.9506.2580.0890.0890.0000.0000.0000.000
102A137PRO0-0.003-0.0157.979-0.518-0.5180.0000.0000.0000.000
103A138LYS10.7430.8727.8161.3171.3170.0000.0000.0000.000
104A139GLN00.0280.0263.024-0.6180.0610.026-0.205-0.5000.000
105A140LEU0-0.059-0.0322.282-0.9930.7752.241-1.275-2.7340.003
106A141ILE0-0.027-0.0142.710-5.482-2.6630.898-1.624-2.093-0.022
107A142TYR0-0.001-0.0084.861-0.275-0.200-0.001-0.004-0.0700.000
108A143SER0-0.008-0.0266.5010.8190.8190.0000.0000.0000.000
109A144PRO0-0.022-0.0139.985-0.086-0.0860.0000.0000.0000.000
110A145ASN00.0530.03412.7300.0260.0260.0000.0000.0000.000
111A146HIS0-0.029-0.01216.3920.0630.0630.0000.0000.0000.000
112A147TYR0-0.022-0.00413.5570.1590.1590.0000.0000.0000.000
113A148MET0-0.0390.00116.339-0.078-0.0780.0000.0000.0000.000
114A149HIS10.8620.93313.8110.8700.8700.0000.0000.0000.000
115A150GLY00.0270.01615.0610.0280.0280.0000.0000.0000.000
116A151PHE0-0.021-0.02114.236-0.061-0.0610.0000.0000.0000.000
117A152VAL00.0140.01216.1010.0420.0420.0000.0000.0000.000
118A153ASN00.0370.01916.473-0.023-0.0230.0000.0000.0000.000
119A154PRO0-0.028-0.00716.3080.0430.0430.0000.0000.0000.000
120A155THR0-0.057-0.04217.6700.0510.0510.0000.0000.0000.000
121A156ASP-1-0.889-0.95420.566-0.208-0.2080.0000.0000.0000.000
122A157LYS10.8180.90718.3980.4760.4760.0000.0000.0000.000
123A158THR00.009-0.00321.103-0.008-0.0080.0000.0000.0000.000
124A159LEU0-0.0190.01215.4170.0220.0220.0000.0000.0000.000
125A160PRO0-0.0160.01615.475-0.025-0.0250.0000.0000.0000.000
126A161ILE0-0.017-0.01311.868-0.094-0.0940.0000.0000.0000.000
127A162VAL0-0.053-0.02411.4930.1460.1460.0000.0000.0000.000
128A163PHE00.0310.02711.058-0.316-0.3160.0000.0000.0000.000
129A164VAL00.016-0.00910.6450.1160.1160.0000.0000.0000.000
130A165TRP0-0.003-0.01611.994-0.131-0.1310.0000.0000.0000.000
131A166MET00.0170.00313.2700.0440.0440.0000.0000.0000.000
132A167ARG10.8820.94315.1700.8290.8290.0000.0000.0000.000
133A168ASN0-0.038-0.03317.692-0.031-0.0310.0000.0000.0000.000
134A169GLU-1-0.909-0.97518.306-0.609-0.6090.0000.0000.0000.000
135A170VAL0-0.055-0.02121.4950.0550.0550.0000.0000.0000.000
136A171ALA0-0.0170.01221.9220.0310.0310.0000.0000.0000.000
137A172PRO0-0.0250.00023.9610.0150.0150.0000.0000.0000.000
138A173ASP-1-0.850-0.91426.066-0.541-0.5410.0000.0000.0000.000
139A174PHE0-0.0120.00724.6840.0290.0290.0000.0000.0000.000
140A175PRO00.010-0.00427.442-0.021-0.0210.0000.0000.0000.000
141A176TYR0-0.023-0.01424.6440.0090.0090.0000.0000.0000.000
142A177HIS10.7960.88024.0960.4680.4680.0000.0000.0000.000
143A178ASP-1-0.730-0.82320.509-0.761-0.7610.0000.0000.0000.000
144A179GLY00.0450.01819.769-0.080-0.0800.0000.0000.0000.000
145A180GLY00.0020.00921.5790.0270.0270.0000.0000.0000.000
146A181MET00.0150.01617.8840.0620.0620.0000.0000.0000.000
147A182ARG10.8980.92321.1640.6640.6640.0000.0000.0000.000
148A183GLH0-0.055-0.07622.7670.0560.0560.0000.0000.0000.000
149A184TYR00.000-0.00822.3930.0310.0310.0000.0000.0000.000
150A185PHE00.0370.00019.1970.0390.0390.0000.0000.0000.000
151A186GLN0-0.011-0.00324.828-0.001-0.0010.0000.0000.0000.000
152A187ALA0-0.0360.00027.7390.0320.0320.0000.0000.0000.000
153A188VAL0-0.046-0.02526.5870.0320.0320.0000.0000.0000.000
154A189GLY00.0170.00527.5810.0190.0190.0000.0000.0000.000
155A190PRO0-0.063-0.01228.6150.0000.0000.0000.0000.0000.000
156A191ARG10.9180.95429.3530.4200.4200.0000.0000.0000.000
157A192ILE0-0.045-0.01926.5770.0300.0300.0000.0000.0000.000
158A193THR0-0.004-0.01230.564-0.009-0.0090.0000.0000.0000.000
159A194ASP-1-0.830-0.91832.898-0.304-0.3040.0000.0000.0000.000
160A195LEU00.004-0.00226.544-0.002-0.0020.0000.0000.0000.000
161A196ASN0-0.106-0.05930.1980.0000.0000.0000.0000.0000.000
162A197ASN0-0.058-0.02632.9750.0240.0240.0000.0000.0000.000
163A198LEU00.0120.01828.218-0.006-0.0060.0000.0000.0000.000
164A199PRO0-0.0240.00130.7490.0200.0200.0000.0000.0000.000
165A200GLU-1-0.924-0.96732.170-0.225-0.2250.0000.0000.0000.000
166A201LEU0-0.065-0.00728.4100.0040.0040.0000.0000.0000.000
167A202THR00.001-0.02832.9160.0230.0230.0000.0000.0000.000
168A203ASN00.049-0.00534.060-0.019-0.0190.0000.0000.0000.000
169A204ALA0-0.0050.01034.9700.0000.0000.0000.0000.0000.000
170A205GLN00.0870.06331.2770.0080.0080.0000.0000.0000.000
171A206ARG10.9480.97330.2070.2290.2290.0000.0000.0000.000
172A207ALA0-0.0150.00030.414-0.004-0.0040.0000.0000.0000.000
173A208ALA00.0100.00731.518-0.004-0.0040.0000.0000.0000.000
174A209PHE00.0390.01522.264-0.010-0.0100.0000.0000.0000.000
175A210ALA00.0530.04026.592-0.025-0.0250.0000.0000.0000.000
176A211SER0-0.011-0.01828.490-0.001-0.0010.0000.0000.0000.000
177A212GLU-1-0.815-0.88629.417-0.309-0.3090.0000.0000.0000.000
178A213ALA0-0.0080.00324.870-0.013-0.0130.0000.0000.0000.000
179A214PRO00.0500.01825.822-0.029-0.0290.0000.0000.0000.000
180A215LYS10.7790.88327.4170.3030.3030.0000.0000.0000.000
181A216TYR0-0.061-0.05924.445-0.011-0.0110.0000.0000.0000.000
182A217GLY00.0260.02523.152-0.052-0.0520.0000.0000.0000.000
183A218ILE0-0.008-0.02520.695-0.043-0.0430.0000.0000.0000.000
184A219ASN0-0.033-0.01122.6980.0280.0280.0000.0000.0000.000
185A220GLN0-0.028-0.03922.389-0.068-0.0680.0000.0000.0000.000
186A221SER0-0.043-0.02123.8990.0240.0240.0000.0000.0000.000
187A222SER0-0.040-0.04826.291-0.023-0.0230.0000.0000.0000.000
188A223TYR0-0.004-0.02127.9850.0040.0040.0000.0000.0000.000
189A224PHE00.0860.02319.4730.0120.0120.0000.0000.0000.000
190A225MET0-0.035-0.01724.5790.0020.0020.0000.0000.0000.000
191A226GLU-1-0.824-0.87226.920-0.153-0.1530.0000.0000.0000.000
192A227TYR00.0540.00123.0420.0090.0090.0000.0000.0000.000
193A228VAL0-0.0060.00721.5410.0210.0210.0000.0000.0000.000
194A229ASN0-0.099-0.06023.776-0.021-0.0210.0000.0000.0000.000
195A230THR0-0.060-0.06322.6360.0160.0160.0000.0000.0000.000
196A231ILE00.0560.01718.168-0.019-0.0190.0000.0000.0000.000
197A232SER0-0.0130.00517.6610.0350.0350.0000.0000.0000.000
198A233ASP-1-0.761-0.87014.7600.4990.4990.0000.0000.0000.000
199A234LYS10.7870.87513.856-0.559-0.5590.0000.0000.0000.000
200A235LEU00.0450.0287.7080.0120.0120.0000.0000.0000.000
201A236PRO00.0120.01211.3580.3310.3310.0000.0000.0000.000
202A237ALA00.0580.0129.7490.0870.0870.0000.0000.0000.000
203A238GLN0-0.003-0.0019.1460.7570.7570.0000.0000.0000.000
204A239ILE00.0110.0109.0950.0880.0880.0000.0000.0000.000
205A240ALA00.0320.0246.192-0.141-0.1410.0000.0000.0000.000
206A241LYS10.8610.9254.389-0.797-0.536-0.001-0.014-0.2460.000
207A242LEU0-0.0110.0186.0880.4590.4590.0000.0000.0000.000
208A243LYS10.8380.9112.486-15.012-13.3067.123-2.413-6.4160.027
209A244ASN0-0.014-0.0264.8100.8820.8820.0000.0000.0000.000
210A245ASP-1-0.783-0.8791.734-34.528-38.38614.618-6.320-4.440-0.077
211A246LYS10.8900.9424.7862.7312.796-0.001-0.021-0.0430.000
212A247ASP-1-0.773-0.8658.565-1.396-1.3960.0000.0000.0000.000
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