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: LNQ89

Calculation Name: 2EQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EQ5

Chain ID: A

ChEMBL ID:

UniProt ID: O58781

Base Structure: X-ray

Registration Date: 2023-09-22

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456598.44725
FMO2-HF: Nuclear repulsion 2375954.36619
FMO2-HF: Total energy -80644.08106
FMO2-MP2: Total energy -80882.777123


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-159.193-150.36918.212-12.555-14.479-0.13
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.925
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].
3A5THR0-0.018-0.0252.803-10.215-7.0040.356-1.752-1.815-0.005
4A6ILE0-0.027-0.0085.2283.9453.996-0.001-0.002-0.0470.000
5A7GLY00.0550.0288.288-0.307-0.3070.0000.0000.0000.000
6A8LEU0-0.056-0.03111.6970.7410.7410.0000.0000.0000.000
7A9ILE00.0260.00513.7650.5220.5220.0000.0000.0000.000
8A10ARG10.8020.88616.57316.90416.9040.0000.0000.0000.000
9A11VAL00.017-0.01019.7580.3230.3230.0000.0000.0000.000
10A12ILE00.027-0.00122.7900.5630.5630.0000.0000.0000.000
11A13THR0-0.067-0.03923.012-0.447-0.4470.0000.0000.0000.000
12A14LEU0-0.021-0.02720.4910.1110.1110.0000.0000.0000.000
13A15GLU-1-0.863-0.93921.817-12.372-12.3720.0000.0000.0000.000
14A16ASP-1-0.874-0.91220.243-14.947-14.9470.0000.0000.0000.000
15A17LYS10.8850.90914.66417.98317.9830.0000.0000.0000.000
16A18GLU-1-0.791-0.88214.936-20.146-20.1460.0000.0000.0000.000
17A19ILE0-0.004-0.01216.304-0.992-0.9920.0000.0000.0000.000
18A20LEU0-0.0020.01516.564-0.499-0.4990.0000.0000.0000.000
19A21ASN0-0.015-0.02412.467-1.797-1.7970.0000.0000.0000.000
20A22LEU0-0.0320.00612.708-1.819-1.8190.0000.0000.0000.000
21A23HIS00.0380.00113.456-0.255-0.2550.0000.0000.0000.000
22A24GLY00.0660.02910.468-0.814-0.8140.0000.0000.0000.000
23A25ARG10.9540.9698.91019.77919.7790.0000.0000.0000.000
24A26ILE00.0000.0129.505-1.742-1.7420.0000.0000.0000.000
25A27ILE0-0.0010.0057.858-1.008-1.0080.0000.0000.0000.000
26A28GLU-1-0.809-0.8994.884-44.801-44.8010.0000.0000.0000.000
27A29SER0-0.051-0.0215.475-4.782-4.7820.0000.0000.0000.000
28A30ALA0-0.0180.0088.1120.6930.6930.0000.0000.0000.000
29A31PHE0-0.015-0.0097.2861.7881.7880.0000.0000.0000.000
30A32PRO00.0680.0313.485-6.771-5.9480.010-0.314-0.518-0.001
31A33GLU-1-0.827-0.8921.767-79.216-80.76312.024-5.559-4.918-0.069
32A34LEU0-0.025-0.0102.359-1.9490.0993.853-2.695-3.205-0.027
33A35LYS10.8060.8932.40719.46323.5871.964-2.201-3.888-0.028
34A36VAL0-0.032-0.0193.8745.4935.6070.006-0.032-0.0880.000
35A37VAL00.0000.0137.662-0.171-0.1710.0000.0000.0000.000
36A38SER00.001-0.00410.2861.1511.1510.0000.0000.0000.000
37A39ARG10.7720.85013.57918.58918.5890.0000.0000.0000.000
38A40CYS0-0.0190.00917.075-0.217-0.2170.0000.0000.0000.000
39A41ILE00.0000.01720.5660.0810.0810.0000.0000.0000.000
40A42GLU-1-0.731-0.82523.763-11.791-11.7910.0000.0000.0000.000
41A43ASP-1-0.900-0.95526.465-9.950-9.9500.0000.0000.0000.000
42A44GLN0-0.0060.00127.8740.1950.1950.0000.0000.0000.000
43A45PRO00.0430.00928.022-0.339-0.3390.0000.0000.0000.000
44A46LYS10.9020.95028.8768.8818.8810.0000.0000.0000.000
45A47GLY00.0270.00627.256-0.058-0.0580.0000.0000.0000.000
46A48ILE0-0.044-0.01226.0530.3600.3600.0000.0000.0000.000
47A49TYR00.0170.01228.920-0.115-0.1150.0000.0000.0000.000
48A50ASN0-0.028-0.02231.7420.0260.0260.0000.0000.0000.000
49A51GLU-1-0.779-0.87733.066-8.500-8.5000.0000.0000.0000.000
50A52GLU-1-0.900-0.91634.673-8.200-8.2000.0000.0000.0000.000
51A53THR00.0510.00431.280-0.257-0.2570.0000.0000.0000.000
52A54GLU-1-0.903-0.95628.658-10.888-10.8880.0000.0000.0000.000
53A55ARG10.8490.89029.4838.4688.4680.0000.0000.0000.000
54A56GLU-1-0.891-0.93031.581-9.798-9.7980.0000.0000.0000.000
55A57ALA00.0400.01526.270-0.189-0.1890.0000.0000.0000.000
56A58GLU-1-0.803-0.87726.391-10.780-10.7800.0000.0000.0000.000
57A59PRO0-0.002-0.00126.088-0.396-0.3960.0000.0000.0000.000
58A60LYS10.7840.88825.41110.27610.2760.0000.0000.0000.000
59A61ILE0-0.008-0.00621.111-0.602-0.6020.0000.0000.0000.000
60A62ILE0-0.020-0.01721.327-0.597-0.5970.0000.0000.0000.000
61A63ARG10.8160.88522.18711.46011.4600.0000.0000.0000.000
62A64LEU00.0180.00217.809-0.383-0.3830.0000.0000.0000.000
63A65ALA0-0.0020.00117.329-0.820-0.8200.0000.0000.0000.000
64A66LYS10.8640.93317.49911.87011.8700.0000.0000.0000.000
65A67GLU-1-0.865-0.91818.481-13.568-13.5680.0000.0000.0000.000
66A68PHE00.0180.00412.864-0.491-0.4910.0000.0000.0000.000
67A69GLU-1-0.795-0.90413.946-15.810-15.8100.0000.0000.0000.000
68A70ARG10.8010.88415.83612.81012.8100.0000.0000.0000.000
69A71GLU-1-0.832-0.87813.180-18.460-18.4600.0000.0000.0000.000
70A72GLY0-0.0220.00812.621-0.943-0.9430.0000.0000.0000.000
71A73VAL0-0.077-0.0349.282-1.662-1.6620.0000.0000.0000.000
72A74ASP-1-0.808-0.9116.798-30.469-30.4690.0000.0000.0000.000
73A75ALA0-0.019-0.0299.7861.7141.7140.0000.0000.0000.000
74A76ILE0-0.0010.00811.283-0.912-0.9120.0000.0000.0000.000
75A77ILE00.0120.00211.3120.4230.4230.0000.0000.0000.000
76A78ILE00.0130.01014.744-0.028-0.0280.0000.0000.0000.000
77A79SER00.0170.01515.9530.2230.2230.0000.0000.0000.000
78A80CYS0-0.027-0.01118.4830.5310.5310.0000.0000.0000.000
79A81ALA00.0390.01822.067-0.181-0.1810.0000.0000.0000.000
80A82ALA00.0440.00823.9320.3240.3240.0000.0000.0000.000
81A83ASP-1-0.790-0.86922.831-13.436-13.4360.0000.0000.0000.000
82A84PRO00.0730.05023.4110.2010.2010.0000.0000.0000.000
83A85ALA00.0820.02923.809-0.566-0.5660.0000.0000.0000.000
84A86VAL0-0.056-0.00320.722-0.081-0.0810.0000.0000.0000.000
85A87GLU-1-0.881-0.94222.871-10.530-10.5300.0000.0000.0000.000
86A88LYS10.7890.86625.65510.39210.3920.0000.0000.0000.000
87A89VAL00.0430.00819.6540.0450.0450.0000.0000.0000.000
88A90ARG10.8220.90319.76313.84713.8470.0000.0000.0000.000
89A91LYS10.8200.91922.41110.50110.5010.0000.0000.0000.000
90A92LEU0-0.044-0.01723.5540.4010.4010.0000.0000.0000.000
91A93LEU0-0.0100.01317.5770.0340.0340.0000.0000.0000.000
92A94SER0-0.036-0.02218.8440.5890.5890.0000.0000.0000.000
93A95ILE0-0.0480.00013.468-0.205-0.2050.0000.0000.0000.000
94A96PRO0-0.055-0.03213.3890.8260.8260.0000.0000.0000.000
95A97VAL00.0340.02014.953-0.743-0.7430.0000.0000.0000.000
96A98ILE0-0.032-0.00113.3440.9130.9130.0000.0000.0000.000
97A99GLY00.0590.03617.083-0.065-0.0650.0000.0000.0000.000
98A100ALA00.0110.01318.762-0.137-0.1370.0000.0000.0000.000
99A101GLY00.0790.04519.9090.1640.1640.0000.0000.0000.000
100A102SER0-0.059-0.06621.8010.0510.0510.0000.0000.0000.000
101A103SER0-0.064-0.04418.334-0.260-0.2600.0000.0000.0000.000
102A104VAL0-0.002-0.00120.3160.0330.0330.0000.0000.0000.000
103A105SER0-0.014-0.01922.1030.3440.3440.0000.0000.0000.000
104A106ALA00.008-0.00122.0470.3100.3100.0000.0000.0000.000
105A107LEU0-0.027-0.02417.422-0.005-0.0050.0000.0000.0000.000
106A108ALA00.0230.01822.0730.0980.0980.0000.0000.0000.000
107A109LEU00.003-0.00225.2820.3180.3180.0000.0000.0000.000
108A110ALA0-0.083-0.02622.8280.2890.2890.0000.0000.0000.000
109A111TYR0-0.036-0.02220.459-0.346-0.3460.0000.0000.0000.000
110A112GLY0-0.016-0.00426.3420.3360.3360.0000.0000.0000.000
111A113ARG10.9280.95329.6679.2589.2580.0000.0000.0000.000
112A114ARG10.8140.90032.4209.0419.0410.0000.0000.0000.000
113A115VAL00.0260.01628.933-0.145-0.1450.0000.0000.0000.000
114A116GLY00.0220.01830.7650.4030.4030.0000.0000.0000.000
115A117VAL0-0.045-0.02628.715-0.489-0.4890.0000.0000.0000.000
116A118LEU00.0030.00228.5910.3750.3750.0000.0000.0000.000
117A119ASN0-0.0010.00228.263-0.847-0.8470.0000.0000.0000.000
118A120LEU00.001-0.02128.1350.0720.0720.0000.0000.0000.000
119A121THR0-0.024-0.03830.4500.3240.3240.0000.0000.0000.000
120A122GLU-1-0.802-0.87828.788-10.506-10.5060.0000.0000.0000.000
121A123GLU-1-0.845-0.89933.187-8.818-8.8180.0000.0000.0000.000
122A124THR0-0.017-0.04730.354-0.437-0.4370.0000.0000.0000.000
123A125PRO0-0.0060.00627.5710.2010.2010.0000.0000.0000.000
124A126LYN00.0620.02428.632-0.056-0.0560.0000.0000.0000.000
125A127VAL0-0.0170.00825.7310.1280.1280.0000.0000.0000.000
126A128ILE00.0080.00925.586-0.070-0.0700.0000.0000.0000.000
127A129ARG10.8390.89128.8539.1189.1180.0000.0000.0000.000
128A130SER0-0.066-0.04030.8620.3090.3090.0000.0000.0000.000
129A131ILE0-0.056-0.02425.4460.1000.1000.0000.0000.0000.000
130A132LEU00.0060.01728.215-0.048-0.0480.0000.0000.0000.000
131A133GLY00.0460.03231.1670.2230.2230.0000.0000.0000.000
132A134ASN0-0.044-0.03834.719-0.176-0.1760.0000.0000.0000.000
133A135ASN0-0.025-0.01532.5660.1880.1880.0000.0000.0000.000
134A136LEU0-0.047-0.00832.125-0.189-0.1890.0000.0000.0000.000
135A137ILE0-0.032-0.00234.3760.2860.2860.0000.0000.0000.000
136A138ALA0-0.011-0.01235.3570.2750.2750.0000.0000.0000.000
137A139GLU-1-0.816-0.87833.966-9.474-9.4740.0000.0000.0000.000
138A140ASP-1-0.813-0.90633.784-8.291-8.2910.0000.0000.0000.000
139A141HIS00.0110.01532.964-0.353-0.3530.0000.0000.0000.000
140A142PRO0-0.0070.00531.3310.2450.2450.0000.0000.0000.000
141A143SER00.022-0.03134.3830.0720.0720.0000.0000.0000.000
142A144GLY0-0.035-0.01837.736-0.020-0.0200.0000.0000.0000.000
143A145VAL0-0.061-0.02031.8420.0140.0140.0000.0000.0000.000
144A146SER0-0.029-0.00834.5940.1360.1360.0000.0000.0000.000
145A147ASN0-0.026-0.01329.656-0.490-0.4900.0000.0000.0000.000
146A148THR00.0500.01724.4730.1660.1660.0000.0000.0000.000
147A149LEU0-0.004-0.01025.858-0.156-0.1560.0000.0000.0000.000
148A150ASP-1-0.741-0.86928.656-9.333-9.3330.0000.0000.0000.000
149A151LEU0-0.041-0.01027.3330.1970.1970.0000.0000.0000.000
150A152LEU0-0.030-0.01124.720-0.213-0.2130.0000.0000.0000.000
151A153THR0-0.065-0.03828.8350.2480.2480.0000.0000.0000.000
152A154ASP-1-0.874-0.94632.671-9.180-9.1800.0000.0000.0000.000
153A155TRP0-0.021-0.01734.7560.0320.0320.0000.0000.0000.000
154A156GLY00.0740.03433.4310.0590.0590.0000.0000.0000.000
155A157ARG10.9580.98628.84910.39110.3910.0000.0000.0000.000
156A158ARG10.8820.92831.7267.9387.9380.0000.0000.0000.000
157A159GLU-1-0.769-0.83934.883-8.203-8.2030.0000.0000.0000.000
158A160VAL0-0.0090.00128.6450.0440.0440.0000.0000.0000.000
159A161ILE00.0260.01030.675-0.073-0.0730.0000.0000.0000.000
160A162ASN0-0.067-0.04032.6240.0940.0940.0000.0000.0000.000
161A163ALA00.0040.01232.9740.1180.1180.0000.0000.0000.000
162A164ALA00.0350.01530.5390.0260.0260.0000.0000.0000.000
163A165LYS10.8200.90132.4109.0039.0030.0000.0000.0000.000
164A166ARG10.8030.89335.5758.6008.6000.0000.0000.0000.000
165A167LEU0-0.029-0.01331.5820.1580.1580.0000.0000.0000.000
166A168LYS10.8880.93933.4109.5009.5000.0000.0000.0000.000
167A169GLU-1-0.935-0.96235.437-7.676-7.6760.0000.0000.0000.000
168A170LYS10.7900.90437.6758.5658.5650.0000.0000.0000.000
169A171GLY00.0190.01438.1530.0140.0140.0000.0000.0000.000
170A172VAL0-0.041-0.02032.385-0.042-0.0420.0000.0000.0000.000
171A173GLU-1-0.837-0.91531.583-9.466-9.4660.0000.0000.0000.000
172A174VAL0-0.0120.00126.081-0.311-0.3110.0000.0000.0000.000
173A175ILE0-0.0120.00327.3960.3600.3600.0000.0000.0000.000
174A176ALA00.0140.01224.916-0.555-0.5550.0000.0000.0000.000
175A177LEU0-0.001-0.00622.7810.4910.4910.0000.0000.0000.000
176A178GLY00.012-0.00124.140-0.484-0.4840.0000.0000.0000.000
177A179CYS0-0.033-0.03425.186-0.027-0.0270.0000.0000.0000.000
178A180THR0-0.032-0.02519.7230.0420.0420.0000.0000.0000.000
179A181GLY00.0170.01020.572-0.561-0.5610.0000.0000.0000.000
180A182MET0-0.004-0.01522.502-0.221-0.2210.0000.0000.0000.000
181A183SER00.013-0.02017.4050.1770.1770.0000.0000.0000.000
182A184THR0-0.103-0.04418.380-0.770-0.7700.0000.0000.0000.000
183A185ILE0-0.047-0.01419.418-0.079-0.0790.0000.0000.0000.000
184A186GLY00.0030.01119.4840.2430.2430.0000.0000.0000.000
185A187ILE00.011-0.00220.1930.2160.2160.0000.0000.0000.000
186A188ALA00.0290.01520.7780.3710.3710.0000.0000.0000.000
187A189PRO00.0410.01820.1750.4300.4300.0000.0000.0000.000
188A190VAL0-0.017-0.00822.9580.4750.4750.0000.0000.0000.000
189A191LEU0-0.018-0.01225.9640.5400.5400.0000.0000.0000.000
190A192GLU-1-0.877-0.94223.564-13.343-13.3430.0000.0000.0000.000
191A193GLU-1-0.961-0.97526.708-11.267-11.2670.0000.0000.0000.000
192A194GLU-1-0.885-0.92528.440-8.999-8.9990.0000.0000.0000.000
193A195VAL0-0.048-0.02829.7780.4090.4090.0000.0000.0000.000
194A196GLY00.0030.01429.9360.2720.2720.0000.0000.0000.000
195A197ILE0-0.079-0.04929.1520.2190.2190.0000.0000.0000.000
196A198PRO00.0170.01424.118-0.130-0.1300.0000.0000.0000.000
197A199VAL0-0.013-0.00224.1390.4240.4240.0000.0000.0000.000
198A200ILE0-0.023-0.01120.647-0.753-0.7530.0000.0000.0000.000
199A201ASP-1-0.726-0.85317.583-16.898-16.8980.0000.0000.0000.000
200A202PRO00.0170.00318.532-0.807-0.8070.0000.0000.0000.000
201A203VAL0-0.0160.00213.785-0.530-0.5300.0000.0000.0000.000
202A204ILE00.0230.01412.960-1.596-1.5960.0000.0000.0000.000
203A205ALA00.0210.01014.236-1.024-1.0240.0000.0000.0000.000
204A206SER0-0.050-0.04714.764-0.507-0.5070.0000.0000.0000.000
205A207GLY00.0250.00511.305-0.718-0.7180.0000.0000.0000.000
206A208ALA00.0320.02211.070-1.516-1.5160.0000.0000.0000.000
207A209VAL0-0.040-0.01913.085-0.019-0.0190.0000.0000.0000.000
208A210ALA00.003-0.00410.6220.3590.3590.0000.0000.0000.000
209A211LEU00.0180.0136.593-0.459-0.4590.0000.0000.0000.000
210A212HIS00.0240.0109.543-0.075-0.0750.0000.0000.0000.000
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