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: LNZ69

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3019069.832601
FMO2-HF: Nuclear repulsion 2926598.540431
FMO2-HF: Total energy -92471.29217
FMO2-MP2: Total energy -92739.228129


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.
-52.001-37.2086.969-9.016-12.745-0.071
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 : -0.097 / q_NPA : -0.052
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].
3A38PHE00.0420.0213.829-2.7850.2710.035-1.522-1.5690.001
4A39ASP-1-0.915-0.9626.1120.5360.5360.0000.0000.0000.000
5A40ASP-1-0.864-0.9609.558-0.766-0.7660.0000.0000.0000.000
6A41ILE0-0.0080.0128.288-0.442-0.4420.0000.0000.0000.000
7A42PRO00.0570.04411.9820.2260.2260.0000.0000.0000.000
8A43MET00.0000.00915.636-0.194-0.1940.0000.0000.0000.000
9A44PRO0-0.005-0.01317.8050.0800.0800.0000.0000.0000.000
10A45LYS10.8850.95320.8040.5740.5740.0000.0000.0000.000
11A46LEU0-0.011-0.01224.1570.0230.0230.0000.0000.0000.000
12A47ALA0-0.007-0.00926.7140.0170.0170.0000.0000.0000.000
13A48ASP-1-0.925-0.95629.764-0.317-0.3170.0000.0000.0000.000
14A49PRO0-0.032-0.01226.008-0.025-0.0250.0000.0000.0000.000
15A50LEU0-0.043-0.00625.5030.0460.0460.0000.0000.0000.000
16A51LEU00.0230.01125.252-0.044-0.0440.0000.0000.0000.000
17A52ILE0-0.026-0.01825.2330.0340.0340.0000.0000.0000.000
18A53TYR00.018-0.00125.393-0.027-0.0270.0000.0000.0000.000
19A54THR0-0.032-0.04622.4470.0470.0470.0000.0000.0000.000
20A55PRO00.006-0.02525.6990.0260.0260.0000.0000.0000.000
21A56ALA0-0.056-0.00422.5070.0320.0320.0000.0000.0000.000
22A57ASN0-0.034-0.00323.5200.0200.0200.0000.0000.0000.000
23A58GLU-1-0.759-0.85819.273-0.707-0.7070.0000.0000.0000.000
24A59ILE0-0.0020.00522.5500.0170.0170.0000.0000.0000.000
25A60PHE00.004-0.01519.111-0.056-0.0560.0000.0000.0000.000
26A61ASP-1-0.872-0.92521.300-0.559-0.5590.0000.0000.0000.000
27A62ILE0-0.026-0.02420.057-0.089-0.0890.0000.0000.0000.000
28A63ALA0-0.024-0.01420.3000.0780.0780.0000.0000.0000.000
29A64SER0-0.026-0.02520.005-0.072-0.0720.0000.0000.0000.000
30A65CYS00.0200.01718.538-0.022-0.0220.0000.0000.0000.000
31A66SER0-0.029-0.01019.759-0.040-0.0400.0000.0000.0000.000
32A67ALA00.0390.01520.0200.0590.0590.0000.0000.0000.000
33A68LYS10.8660.92920.5490.8360.8360.0000.0000.0000.000
34A69ASP-1-0.789-0.87617.880-1.070-1.0700.0000.0000.0000.000
35A70ILE00.0130.01813.866-0.052-0.0520.0000.0000.0000.000
36A71GLY00.0270.00517.9850.1100.1100.0000.0000.0000.000
37A72PHE00.0170.01715.318-0.095-0.0950.0000.0000.0000.000
38A73ALA0-0.0090.00716.9920.1460.1460.0000.0000.0000.000
39A74ILE0-0.014-0.00413.946-0.176-0.1760.0000.0000.0000.000
40A75ALA00.0220.01115.9320.1740.1740.0000.0000.0000.000
41A76HIS10.8230.90515.4530.9900.9900.0000.0000.0000.000
42A77ALA0-0.006-0.00617.0690.0990.0990.0000.0000.0000.000
43A78GLN00.001-0.00318.3020.0470.0470.0000.0000.0000.000
44A79ILE00.0050.01317.632-0.001-0.0010.0000.0000.0000.000
45A80PRO00.0390.01620.6750.0470.0470.0000.0000.0000.000
46A81PRO00.0330.00522.398-0.025-0.0250.0000.0000.0000.000
47A82GLY0-0.028-0.00722.413-0.005-0.0050.0000.0000.0000.000
48A83GLY0-0.034-0.00222.690-0.011-0.0110.0000.0000.0000.000
49A84GLY00.037-0.00419.937-0.010-0.0100.0000.0000.0000.000
50A85PRO0-0.073-0.01518.4490.0560.0560.0000.0000.0000.000
51A86MET00.0160.00920.2600.0130.0130.0000.0000.0000.000
52A87PRO0-0.017-0.00719.507-0.058-0.0580.0000.0000.0000.000
53A88HIS0-0.0060.01617.756-0.040-0.0400.0000.0000.0000.000
54A89ILE0-0.0170.00418.509-0.053-0.0530.0000.0000.0000.000
55A90HIS00.0340.02016.770-0.008-0.0080.0000.0000.0000.000
56A91TYR0-0.005-0.04719.011-0.016-0.0160.0000.0000.0000.000
57A92PHE0-0.0010.01520.6920.0130.0130.0000.0000.0000.000
58A93ILE0-0.028-0.00214.981-0.022-0.0220.0000.0000.0000.000
59A94ASN00.0040.01411.7620.1350.1350.0000.0000.0000.000
60A95GLU-1-0.808-0.93311.384-1.485-1.4850.0000.0000.0000.000
61A96TRP0-0.042-0.0195.3470.4030.4030.0000.0000.0000.000
62A97PHE00.001-0.0057.5760.6190.6190.0000.0000.0000.000
63A98TRP0-0.026-0.0187.148-0.766-0.7660.0000.0000.0000.000
64A99THR00.0770.0378.7190.2250.2250.0000.0000.0000.000
65A100PRO0-0.023-0.0079.9360.3190.3190.0000.0000.0000.000
66A101GLU-1-0.934-0.99012.0920.1330.1330.0000.0000.0000.000
67A102GLY00.0020.02710.2080.1480.1480.0000.0000.0000.000
68A103GLY00.0100.00111.018-0.131-0.1310.0000.0000.0000.000
69A104ILE0-0.043-0.02112.506-0.001-0.0010.0000.0000.0000.000
70A105GLU-1-0.841-0.92011.954-0.057-0.0570.0000.0000.0000.000
71A106LEU0-0.040-0.0269.856-0.104-0.1040.0000.0000.0000.000
72A107PHE00.000-0.00913.0880.1430.1430.0000.0000.0000.000
73A108HIS0-0.0080.00111.128-0.357-0.3570.0000.0000.0000.000
74A109SER00.0150.00014.1050.1030.1030.0000.0000.0000.000
75A110THR00.011-0.00514.409-0.082-0.0820.0000.0000.0000.000
76A111LYS10.9560.99016.1490.2190.2190.0000.0000.0000.000
77A112GLN00.0070.01916.288-0.135-0.1350.0000.0000.0000.000
78A113TYR00.019-0.01019.1000.0810.0810.0000.0000.0000.000
79A114PRO00.0190.02222.067-0.038-0.0380.0000.0000.0000.000
80A115ASN0-0.030-0.02223.061-0.029-0.0290.0000.0000.0000.000
81A116MET0-0.0060.01525.166-0.005-0.0050.0000.0000.0000.000
82A117ASP-1-0.899-0.94026.534-0.323-0.3230.0000.0000.0000.000
83A118GLU-1-0.983-0.96828.070-0.237-0.2370.0000.0000.0000.000
84A119LEU0-0.010-0.00827.048-0.025-0.0250.0000.0000.0000.000
85A120PRO00.0070.00523.7550.0270.0270.0000.0000.0000.000
86A121VAL00.0610.01426.7380.0080.0080.0000.0000.0000.000
87A122VAL0-0.023-0.02529.8080.0100.0100.0000.0000.0000.000
88A123GLY0-0.045-0.00832.5800.0140.0140.0000.0000.0000.000
89A124GLY0-0.014-0.00633.678-0.007-0.0070.0000.0000.0000.000
90A125ALA00.0450.03728.769-0.013-0.0130.0000.0000.0000.000
91A126GLY0-0.063-0.03328.5890.0030.0030.0000.0000.0000.000
92A127ARG10.8770.95126.3060.1280.1280.0000.0000.0000.000
93A128GLY0-0.013-0.00522.6280.0210.0210.0000.0000.0000.000
94A129ASP-1-0.860-0.92320.793-0.084-0.0840.0000.0000.0000.000
95A130LEU0-0.050-0.03317.059-0.047-0.0470.0000.0000.0000.000
96A131TYR0-0.028-0.02513.9810.1080.1080.0000.0000.0000.000
97A132SER00.0400.01813.911-0.102-0.1020.0000.0000.0000.000
98A133ILE0-0.074-0.0377.4710.0960.0960.0000.0000.0000.000
99A134GLN0-0.019-0.00810.294-0.162-0.1620.0000.0000.0000.000
100A135SER0-0.034-0.0077.6220.2090.2090.0000.0000.0000.000
101A136GLU-1-0.884-0.9536.0181.5641.5640.0000.0000.0000.000
102A137PRO00.004-0.0157.665-0.403-0.4030.0000.0000.0000.000
103A138LYS10.8440.9327.7280.6230.6230.0000.0000.0000.000
104A139GLN00.0100.0183.126-0.1370.4570.015-0.150-0.4580.000
105A140LEU0-0.036-0.0112.468-1.5180.3740.580-0.703-1.7690.004
106A141ILE0-0.018-0.0012.528-5.251-3.6800.952-0.956-1.567-0.013
107A142TYR00.001-0.0014.9800.2180.2180.0000.0000.0000.000
108A143SER0-0.015-0.0426.2830.7770.7770.0000.0000.0000.000
109A144PRO0-0.019-0.0089.4510.0810.0810.0000.0000.0000.000
110A145ASN00.0400.00512.3560.1330.1330.0000.0000.0000.000
111A146HIS0-0.012-0.00315.9970.0540.0540.0000.0000.0000.000
112A147TYR00.0010.01413.0620.1920.1920.0000.0000.0000.000
113A148MET0-0.057-0.01316.068-0.028-0.0280.0000.0000.0000.000
114A149HIS10.8750.93913.7511.1631.1630.0000.0000.0000.000
115A150GLY00.0280.01415.2590.0490.0490.0000.0000.0000.000
116A151PHE0-0.020-0.01114.582-0.072-0.0720.0000.0000.0000.000
117A152VAL00.0330.03116.5640.0230.0230.0000.0000.0000.000
118A153ASN00.0190.00716.8220.0400.0400.0000.0000.0000.000
119A154PRO0-0.018-0.00216.9610.0150.0150.0000.0000.0000.000
120A155THR0-0.042-0.03017.8650.0520.0520.0000.0000.0000.000
121A156ASP-1-0.916-0.96420.7180.0140.0140.0000.0000.0000.000
122A157LYS10.9250.97218.6360.0160.0160.0000.0000.0000.000
123A158THR0-0.004-0.00921.002-0.011-0.0110.0000.0000.0000.000
124A159LEU0-0.0360.00415.7880.0460.0460.0000.0000.0000.000
125A160PRO00.0010.01815.456-0.074-0.0740.0000.0000.0000.000
126A161ILE0-0.005-0.01311.977-0.013-0.0130.0000.0000.0000.000
127A162VAL0-0.046-0.01112.1020.0990.0990.0000.0000.0000.000
128A163PHE00.0240.02711.603-0.279-0.2790.0000.0000.0000.000
129A164VAL00.015-0.00410.5370.1650.1650.0000.0000.0000.000
130A165TRP00.0330.00612.182-0.176-0.1760.0000.0000.0000.000
131A166MET00.001-0.00812.8970.0550.0550.0000.0000.0000.000
132A167ARG10.8830.93714.8180.9450.9450.0000.0000.0000.000
133A168ASN0-0.044-0.02517.151-0.040-0.0400.0000.0000.0000.000
134A169GLU-1-0.913-0.98418.320-0.856-0.8560.0000.0000.0000.000
135A170VAL0-0.041-0.01521.2440.0680.0680.0000.0000.0000.000
136A171ALA0-0.0360.00321.4710.0500.0500.0000.0000.0000.000
137A172PRO0-0.0110.00723.4580.0190.0190.0000.0000.0000.000
138A173ASP-1-0.857-0.90725.291-0.625-0.6250.0000.0000.0000.000
139A174PHE00.0040.00725.0190.0420.0420.0000.0000.0000.000
140A175PRO00.0160.00927.244-0.018-0.0180.0000.0000.0000.000
141A176TYR0-0.012-0.01724.3810.0130.0130.0000.0000.0000.000
142A177HIS10.7880.86624.0040.5420.5420.0000.0000.0000.000
143A178ASP-1-0.710-0.83220.141-0.858-0.8580.0000.0000.0000.000
144A179GLY00.0330.01519.500-0.100-0.1000.0000.0000.0000.000
145A180GLY00.0080.01321.2580.0220.0220.0000.0000.0000.000
146A181MET00.0110.01318.3200.0740.0740.0000.0000.0000.000
147A182ARG10.8710.92921.4610.6600.6600.0000.0000.0000.000
148A183GLH0-0.043-0.07923.0400.0770.0770.0000.0000.0000.000
149A184TYR0-0.011-0.00622.7910.0380.0380.0000.0000.0000.000
150A185PHE00.0400.00119.8430.0560.0560.0000.0000.0000.000
151A186GLN0-0.0080.00025.4230.0140.0140.0000.0000.0000.000
152A187ALA0-0.046-0.01028.2550.0360.0360.0000.0000.0000.000
153A188VAL0-0.030-0.01226.9470.0330.0330.0000.0000.0000.000
154A189GLY00.000-0.00328.2320.0240.0240.0000.0000.0000.000
155A190PRO0-0.0590.00029.2150.0040.0040.0000.0000.0000.000
156A191ARG10.9800.97129.9560.3610.3610.0000.0000.0000.000
157A192ILE0-0.0120.00027.1750.0270.0270.0000.0000.0000.000
158A193THR0-0.032-0.03131.119-0.011-0.0110.0000.0000.0000.000
159A194ASP-1-0.872-0.94233.394-0.194-0.1940.0000.0000.0000.000
160A195LEU0-0.006-0.00527.271-0.001-0.0010.0000.0000.0000.000
161A196ASN0-0.058-0.02730.8410.0070.0070.0000.0000.0000.000
162A197ASN0-0.057-0.02033.4940.0210.0210.0000.0000.0000.000
163A198LEU00.0030.00928.798-0.013-0.0130.0000.0000.0000.000
164A199PRO0-0.0190.00431.0360.0140.0140.0000.0000.0000.000
165A200GLU-1-0.915-0.95732.738-0.181-0.1810.0000.0000.0000.000
166A201LEU0-0.058-0.02028.875-0.004-0.0040.0000.0000.0000.000
167A202THR00.0140.00733.4660.0170.0170.0000.0000.0000.000
168A203ASN00.027-0.01934.340-0.017-0.0170.0000.0000.0000.000
169A204ALA0-0.0090.00535.106-0.007-0.0070.0000.0000.0000.000
170A205GLN00.0770.03931.601-0.006-0.0060.0000.0000.0000.000
171A206ARG10.9810.99130.3140.2220.2220.0000.0000.0000.000
172A207ALA0-0.012-0.00830.540-0.014-0.0140.0000.0000.0000.000
173A208ALA00.0140.00931.940-0.010-0.0100.0000.0000.0000.000
174A209PHE00.0300.02022.635-0.014-0.0140.0000.0000.0000.000
175A210ALA00.0500.03527.010-0.034-0.0340.0000.0000.0000.000
176A211SER0-0.017-0.02528.659-0.009-0.0090.0000.0000.0000.000
177A212GLU-1-0.823-0.90329.830-0.359-0.3590.0000.0000.0000.000
178A213ALA0-0.0260.00325.113-0.020-0.0200.0000.0000.0000.000
179A214PRO00.0520.01926.017-0.039-0.0390.0000.0000.0000.000
180A215LYS10.7910.89427.8050.3580.3580.0000.0000.0000.000
181A216TYR0-0.061-0.04924.617-0.006-0.0060.0000.0000.0000.000
182A217GLY00.0430.03423.514-0.059-0.0590.0000.0000.0000.000
183A218ILE0-0.006-0.01620.971-0.070-0.0700.0000.0000.0000.000
184A219ASN0-0.020-0.01022.8380.0530.0530.0000.0000.0000.000
185A220GLN0-0.034-0.04322.312-0.082-0.0820.0000.0000.0000.000
186A221SER0-0.024-0.00223.7470.0430.0430.0000.0000.0000.000
187A222SER0-0.009-0.02626.122-0.010-0.0100.0000.0000.0000.000
188A223TYR0-0.005-0.00328.2240.0210.0210.0000.0000.0000.000
189A224PHE00.0660.01720.443-0.005-0.0050.0000.0000.0000.000
190A225MET0-0.025-0.01524.923-0.015-0.0150.0000.0000.0000.000
191A226GLU-1-0.887-0.92827.266-0.259-0.2590.0000.0000.0000.000
192A227TYR00.0640.00422.9700.0000.0000.0000.0000.0000.000
193A228VAL0-0.008-0.00322.186-0.005-0.0050.0000.0000.0000.000
194A229ASN0-0.099-0.03424.2290.0210.0210.0000.0000.0000.000
195A230THR0-0.050-0.04623.0180.0270.0270.0000.0000.0000.000
196A231ILE00.0360.01418.362-0.040-0.0400.0000.0000.0000.000
197A232SER0-0.0230.00218.3420.0550.0550.0000.0000.0000.000
198A233ASP-1-0.758-0.86215.2190.2510.2510.0000.0000.0000.000
199A234LYS10.7890.87714.251-0.317-0.3170.0000.0000.0000.000
200A235LEU00.0280.0168.194-0.051-0.0510.0000.0000.0000.000
201A236PRO00.0130.01311.7500.1640.1640.0000.0000.0000.000
202A237ALA00.0640.01210.005-0.055-0.0550.0000.0000.0000.000
203A238GLN0-0.014-0.0109.3300.2920.2920.0000.0000.0000.000
204A239ILE00.0400.0179.233-0.063-0.0630.0000.0000.0000.000
205A240ALA00.0320.0296.418-0.321-0.3210.0000.0000.0000.000
206A241LYS10.8270.9154.917-0.640-0.418-0.001-0.007-0.2140.000
207A242LEU0-0.0090.0116.3170.2250.2250.0000.0000.0000.000
208A243LYS10.8980.9413.288-8.636-5.7970.277-0.924-2.1920.010
209A244ASN0-0.053-0.0464.2831.3791.485-0.001-0.010-0.0940.000
210A245ASP-1-0.774-0.8932.249-37.852-33.3765.113-4.739-4.850-0.073
211A246LYS10.9050.9724.9943.2853.322-0.001-0.005-0.0320.000
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