FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: LNV39

Calculation Name: 3DHN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DHN

Chain ID: A

ChEMBL ID:

UniProt ID: Q89Z24

Base Structure: X-ray

Registration Date: 2023-09-23

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2665616.50778
FMO2-HF: Nuclear repulsion 2579369.669189
FMO2-HF: Total energy -86246.83859
FMO2-MP2: Total energy -86498.422936


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.
-138.351-134.07912.482-8.552-8.202-0.085
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 : 0.938 / q_NPA : 0.963
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].
3A5LYS10.8640.9211.7561.7732.31511.766-6.770-5.538-0.064
4A6LYS10.8150.8874.16934.96135.2310.000-0.071-0.1990.000
5A7ILE00.0320.0236.5940.2390.2390.0000.0000.0000.000
6A8VAL0-0.004-0.0039.3771.7201.7200.0000.0000.0000.000
7A9LEU0-0.0050.00413.037-0.315-0.3150.0000.0000.0000.000
8A10ILE00.0360.00414.6811.1591.1590.0000.0000.0000.000
9A11GLY00.0290.02118.2680.1340.1340.0000.0000.0000.000
10A12ALA0-0.0010.01517.270-0.032-0.0320.0000.0000.0000.000
11A13SER0-0.017-0.03018.8150.4500.4500.0000.0000.0000.000
12A14GLY00.0360.01921.898-0.063-0.0630.0000.0000.0000.000
13A15PHE00.0400.01622.084-0.578-0.5780.0000.0000.0000.000
14A16VAL00.0710.02618.478-0.557-0.5570.0000.0000.0000.000
15A17GLY00.0600.03917.927-1.006-1.0060.0000.0000.0000.000
16A18SER0-0.042-0.04417.162-0.967-0.9670.0000.0000.0000.000
17A19ALA00.0010.01117.146-0.802-0.8020.0000.0000.0000.000
18A20LEU0-0.0060.00013.113-1.141-1.1410.0000.0000.0000.000
19A21LEU0-0.0080.00112.405-1.990-1.9900.0000.0000.0000.000
20A22ASN0-0.040-0.04212.967-1.214-1.2140.0000.0000.0000.000
21A23GLU-1-0.762-0.83910.337-26.602-26.6020.0000.0000.0000.000
22A24ALA00.0210.0098.308-2.489-2.4890.0000.0000.0000.000
23A25LEU0-0.032-0.0198.108-3.451-3.4510.0000.0000.0000.000
24A26ASN0-0.035-0.0229.908-0.713-0.7130.0000.0000.0000.000
25A27ARG10.7350.8466.22338.32738.3270.0000.0000.0000.000
26A28GLY0-0.0110.0075.365-7.775-7.7750.0000.0000.0000.000
27A29PHE0-0.036-0.0122.944-11.087-9.4200.197-0.976-0.888-0.013
28A30GLU-1-0.898-0.9516.310-27.023-27.0230.0000.0000.0000.000
29A31VAL00.0080.0019.070-0.621-0.6210.0000.0000.0000.000
30A32THR0-0.021-0.01311.3352.6632.6630.0000.0000.0000.000
31A33ALA00.0260.01414.528-0.176-0.1760.0000.0000.0000.000
32A34VAL00.0290.01316.7670.9420.9420.0000.0000.0000.000
33A35VAL0-0.0070.00019.7960.1310.1310.0000.0000.0000.000
34A36ARG11.0341.00122.87811.29511.2950.0000.0000.0000.000
35A37HIS0-0.058-0.04526.1400.4670.4670.0000.0000.0000.000
36A38PRO00.0570.02024.288-0.206-0.2060.0000.0000.0000.000
37A39GLU-1-0.815-0.89325.187-11.332-11.3320.0000.0000.0000.000
38A40LYS10.8980.94726.00411.08711.0870.0000.0000.0000.000
39A41ILE0-0.0060.01219.953-0.117-0.1170.0000.0000.0000.000
40A42LYS10.8740.92423.41211.84211.8420.0000.0000.0000.000
41A43ILE0-0.0040.00716.9910.1440.1440.0000.0000.0000.000
42A44GLU-1-0.917-0.94720.029-13.788-13.7880.0000.0000.0000.000
43A45ASN00.039-0.00712.857-0.937-0.9370.0000.0000.0000.000
44A46GLU-1-0.863-0.92614.090-20.674-20.6740.0000.0000.0000.000
45A47HIS10.8010.91410.48425.90325.9030.0000.0000.0000.000
46A48LEU00.0050.01012.292-1.660-1.6600.0000.0000.0000.000
47A49LYS10.9230.97014.75321.98721.9870.0000.0000.0000.000
48A50VAL00.0350.01817.118-0.510-0.5100.0000.0000.0000.000
49A51LYS10.9240.96117.59518.17618.1760.0000.0000.0000.000
50A52LYS10.9020.95321.64111.13311.1330.0000.0000.0000.000
51A53ALA00.0220.00322.763-0.118-0.1180.0000.0000.0000.000
52A54ASP-1-0.836-0.87724.764-10.898-10.8980.0000.0000.0000.000
53A55VAL0-0.050-0.03422.992-0.043-0.0430.0000.0000.0000.000
54A56SER0-0.060-0.04625.498-0.012-0.0120.0000.0000.0000.000
55A57SER0-0.042-0.02327.8050.3200.3200.0000.0000.0000.000
56A58LEU00.0380.00124.924-0.470-0.4700.0000.0000.0000.000
57A59ASP-1-0.903-0.95924.890-11.592-11.5920.0000.0000.0000.000
58A60GLU-1-0.840-0.91724.993-11.856-11.8560.0000.0000.0000.000
59A61VAL0-0.053-0.01820.722-0.774-0.7740.0000.0000.0000.000
60A62CYS0-0.0440.00120.363-0.831-0.8310.0000.0000.0000.000
61A63GLU-1-0.814-0.89519.813-14.306-14.3060.0000.0000.0000.000
62A64VAL0-0.063-0.03318.083-0.640-0.6400.0000.0000.0000.000
63A65CYS0-0.049-0.02516.023-1.362-1.3620.0000.0000.0000.000
64A66LYS10.8640.92614.95412.57812.5780.0000.0000.0000.000
65A67GLY0-0.020-0.00512.785-0.185-0.1850.0000.0000.0000.000
66A68ALA0-0.065-0.02010.973-2.233-2.2330.0000.0000.0000.000
67A69ASP-1-0.756-0.8595.847-41.647-41.6470.0000.0000.0000.000
68A70ALA0-0.024-0.0118.0580.4820.4820.0000.0000.0000.000
69A71VAL0-0.007-0.00310.0900.0170.0170.0000.0000.0000.000
70A72ILE00.0410.0289.6340.3460.3460.0000.0000.0000.000
71A73SER0-0.008-0.01113.8680.7910.7910.0000.0000.0000.000
72A74ALA00.005-0.01317.5520.1030.1030.0000.0000.0000.000
73A75PHE0-0.035-0.01619.2910.6260.6260.0000.0000.0000.000
74A76ASN00.0080.01922.6390.2690.2690.0000.0000.0000.000
75A77PRO00.0100.01325.817-0.058-0.0580.0000.0000.0000.000
76A78GLY00.043-0.01228.4980.2530.2530.0000.0000.0000.000
77A79TRP0-0.057-0.06030.2940.1090.1090.0000.0000.0000.000
78A80ASN00.0520.04832.9360.0030.0030.0000.0000.0000.000
79A81ASN0-0.058-0.05734.941-0.039-0.0390.0000.0000.0000.000
80A82PRO0-0.056-0.01835.5340.1700.1700.0000.0000.0000.000
81A83ASP-1-0.900-0.94238.204-8.116-8.1160.0000.0000.0000.000
82A84ILE0-0.0150.01138.2070.1810.1810.0000.0000.0000.000
83A85TYR0-0.035-0.03834.471-0.258-0.2580.0000.0000.0000.000
84A86ASP-1-0.844-0.90135.526-8.550-8.5500.0000.0000.0000.000
85A87GLU-1-0.786-0.89733.130-9.925-9.9250.0000.0000.0000.000
86A88THR0-0.0140.00329.626-0.195-0.1950.0000.0000.0000.000
87A89ILE0-0.030-0.00229.715-0.415-0.4150.0000.0000.0000.000
88A90LYS10.8860.92829.5749.6469.6460.0000.0000.0000.000
89A91VAL0-0.029-0.01326.578-0.264-0.2640.0000.0000.0000.000
90A92TYR0-0.029-0.02124.630-0.291-0.2910.0000.0000.0000.000
91A93LEU00.0240.01024.581-0.571-0.5710.0000.0000.0000.000
92A94THR0-0.025-0.00325.086-0.204-0.2040.0000.0000.0000.000
93A95ILE0-0.026-0.00220.502-0.482-0.4820.0000.0000.0000.000
94A96ILE0-0.0030.00319.289-0.687-0.6870.0000.0000.0000.000
95A97ASP-1-0.838-0.93220.458-12.829-12.8290.0000.0000.0000.000
96A98GLY0-0.021-0.02022.0700.0420.0420.0000.0000.0000.000
97A99VAL0-0.044-0.03915.894-0.481-0.4810.0000.0000.0000.000
98A100LYS10.8340.91016.96512.57212.5720.0000.0000.0000.000
99A101LYS10.9090.96418.31811.98411.9840.0000.0000.0000.000
100A102ALA0-0.027-0.02116.9510.3050.3050.0000.0000.0000.000
101A103GLY0-0.019-0.00415.318-0.423-0.4230.0000.0000.0000.000
102A104VAL0-0.049-0.00811.733-0.981-0.9810.0000.0000.0000.000
103A105ASN00.017-0.0049.9471.8961.8960.0000.0000.0000.000
104A106ARG10.7650.8598.49827.80127.8010.0000.0000.0000.000
105A107PHE00.016-0.00111.193-0.640-0.6400.0000.0000.0000.000
106A108LEU00.0110.01010.6750.3760.3760.0000.0000.0000.000
107A109MET0-0.016-0.00814.5620.2440.2440.0000.0000.0000.000
108A110VAL00.0010.00417.397-0.019-0.0190.0000.0000.0000.000
109A111GLY00.0170.01119.1050.6350.6350.0000.0000.0000.000
110A112GLY00.039-0.00922.1540.1250.1250.0000.0000.0000.000
111A113ALA00.0210.01425.272-0.187-0.1870.0000.0000.0000.000
112A114GLY00.0430.01627.3640.2640.2640.0000.0000.0000.000
113A115SER00.0740.02226.7930.2380.2380.0000.0000.0000.000
114A116LEU0-0.0460.00924.922-0.018-0.0180.0000.0000.0000.000
115A117PHE0-0.020-0.00628.9130.3810.3810.0000.0000.0000.000
116A118ILE00.0310.00831.330-0.252-0.2520.0000.0000.0000.000
117A119ALA00.0080.00333.9050.1960.1960.0000.0000.0000.000
118A120PRO00.017-0.00335.714-0.174-0.1740.0000.0000.0000.000
119A121GLY0-0.014-0.00135.9240.2070.2070.0000.0000.0000.000
120A122LEU00.0110.01636.4760.1230.1230.0000.0000.0000.000
121A123ARG10.9240.95330.15510.01210.0120.0000.0000.0000.000
122A124LEU00.0310.01930.8410.2430.2430.0000.0000.0000.000
123A125MET0-0.0330.00932.0200.0360.0360.0000.0000.0000.000
124A126ASP-1-0.913-0.94734.756-8.553-8.5530.0000.0000.0000.000
125A127SER0-0.031-0.01936.6440.2270.2270.0000.0000.0000.000
126A128GLY00.0000.00738.8470.2010.2010.0000.0000.0000.000
127A129GLU-1-0.933-0.96336.558-8.186-8.1860.0000.0000.0000.000
128A130VAL0-0.093-0.03834.032-0.207-0.2070.0000.0000.0000.000
129A131PRO00.0300.00835.1060.2270.2270.0000.0000.0000.000
130A132GLU-1-0.876-0.94737.635-7.463-7.4630.0000.0000.0000.000
131A133ASN0-0.038-0.02636.605-0.109-0.1090.0000.0000.0000.000
132A134ILE0-0.024-0.01432.170-0.131-0.1310.0000.0000.0000.000
133A135LEU00.0220.02234.207-0.297-0.2970.0000.0000.0000.000
134A136PRO00.0180.00435.200-0.210-0.2100.0000.0000.0000.000
135A137GLY00.0610.03132.300-0.129-0.1290.0000.0000.0000.000
136A138VAL0-0.059-0.02830.552-0.407-0.4070.0000.0000.0000.000
137A139LYS10.8820.92931.0068.4068.4060.0000.0000.0000.000
138A140ALA00.0370.02931.742-0.121-0.1210.0000.0000.0000.000
139A141LEU0-0.030-0.01524.380-0.233-0.2330.0000.0000.0000.000
140A142GLY00.004-0.02027.607-0.377-0.3770.0000.0000.0000.000
141A143GLU-1-0.847-0.94329.462-9.595-9.5950.0000.0000.0000.000
142A144PHE0-0.026-0.01023.356-0.027-0.0270.0000.0000.0000.000
143A145TYR00.0550.00523.627-0.069-0.0690.0000.0000.0000.000
144A146LEU00.0180.00026.277-0.068-0.0680.0000.0000.0000.000
145A147ASN0-0.090-0.04029.0980.3360.3360.0000.0000.0000.000
146A148PHE00.0180.01126.8590.2790.2790.0000.0000.0000.000
147A149LEU00.0330.03221.204-0.128-0.1280.0000.0000.0000.000
148A150MET0-0.0240.00123.193-0.469-0.4690.0000.0000.0000.000
149A151LYS10.8000.88625.37110.32210.3220.0000.0000.0000.000
150A152GLU-1-0.807-0.87420.180-13.334-13.3340.0000.0000.0000.000
151A153LYS10.9160.93920.31411.64611.6460.0000.0000.0000.000
152A154GLU-1-0.944-0.95119.372-12.838-12.8380.0000.0000.0000.000
153A155ILE00.0140.01014.723-0.542-0.5420.0000.0000.0000.000
154A156ASP-1-0.817-0.87711.432-21.389-21.3890.0000.0000.0000.000
155A157TRP0-0.021-0.01213.489-1.584-1.5840.0000.0000.0000.000
156A158VAL00.0230.00813.5380.2150.2150.0000.0000.0000.000
157A159PHE0-0.0210.00016.512-0.219-0.2190.0000.0000.0000.000
158A160PHE00.0210.00215.4650.3640.3640.0000.0000.0000.000
159A161SER00.0090.00518.6540.2050.2050.0000.0000.0000.000
160A162PRO0-0.0160.02021.432-0.142-0.1420.0000.0000.0000.000
161A163ALA00.0150.01422.3750.4370.4370.0000.0000.0000.000
162A164ALA0-0.011-0.02325.368-0.024-0.0240.0000.0000.0000.000
163A165ASP-1-0.862-0.90228.400-10.368-10.3680.0000.0000.0000.000
164A166MET0-0.025-0.00521.533-0.505-0.5050.0000.0000.0000.000
165A167ARG10.8600.91325.65210.32410.3240.0000.0000.0000.000
166A168PRO0-0.023-0.01823.898-0.411-0.4110.0000.0000.0000.000
167A169GLY0-0.005-0.01323.5980.6110.6110.0000.0000.0000.000
168A170VAL0-0.0050.00022.754-0.147-0.1470.0000.0000.0000.000
169A171ARG10.8380.91012.28722.02522.0250.0000.0000.0000.000
170A172THR0-0.031-0.04919.592-0.016-0.0160.0000.0000.0000.000
171A173GLY0-0.051-0.02417.109-0.105-0.1050.0000.0000.0000.000
172A174ARG10.7850.85618.00012.53212.5320.0000.0000.0000.000
173A175TYR00.0390.00715.0620.5040.5040.0000.0000.0000.000
174A176ARG10.9020.96120.89012.37612.3760.0000.0000.0000.000
175A177LEU00.0380.01415.872-0.059-0.0590.0000.0000.0000.000
176A178GLY0-0.013-0.00920.3960.5520.5520.0000.0000.0000.000
177A179LYS10.8770.92721.29913.38213.3820.0000.0000.0000.000
178A180ASP-1-0.800-0.90823.377-12.572-12.5720.0000.0000.0000.000
179A181ASP-1-0.933-0.94726.472-10.371-10.3710.0000.0000.0000.000
180A182MET0-0.025-0.01427.062-0.383-0.3830.0000.0000.0000.000
181A183ILE0-0.030-0.00224.2930.2660.2660.0000.0000.0000.000
182A184VAL00.0110.01027.581-0.062-0.0620.0000.0000.0000.000
183A185ASP-1-0.731-0.84230.074-9.911-9.9110.0000.0000.0000.000
184A186ILE0-0.029-0.02531.2820.2340.2340.0000.0000.0000.000
185A187VAL0-0.065-0.03334.4820.2850.2850.0000.0000.0000.000
186A188GLY00.0300.03434.5810.2370.2370.0000.0000.0000.000
187A189ASN0-0.056-0.02432.6470.0380.0380.0000.0000.0000.000
188A190SER00.023-0.00128.085-0.332-0.3320.0000.0000.0000.000
189A191HIS0-0.054-0.04927.341-0.185-0.1850.0000.0000.0000.000
190A192ILE0-0.015-0.01420.769-0.277-0.2770.0000.0000.0000.000
191A193SER00.0390.02521.4550.0900.0900.0000.0000.0000.000
192A194VAL00.009-0.01219.979-0.621-0.6210.0000.0000.0000.000
193A195GLU-1-0.810-0.91717.960-15.447-15.4470.0000.0000.0000.000
194A196ASP-1-0.732-0.82316.550-17.326-17.3260.0000.0000.0000.000
195A197TYR0-0.022-0.01416.442-1.178-1.1780.0000.0000.0000.000
196A198ALA0-0.010-0.01714.272-1.076-1.0760.0000.0000.0000.000
197A199ALA0-0.015-0.01312.159-2.017-2.0170.0000.0000.0000.000
198A200ALA00.0310.03011.364-2.000-2.0000.0000.0000.0000.000
199A201MET0-0.017-0.00411.839-1.572-1.5720.0000.0000.0000.000
200A202ILE0-0.048-0.0306.694-2.001-2.0010.0000.0000.0000.000
201A203ASP-1-0.797-0.8726.910-35.537-35.5370.0000.0000.0000.000
202A204GLU-1-0.733-0.8278.168-27.539-27.5390.0000.0000.0000.000
203A205LEU0-0.054-0.0215.706-0.250-0.2500.0000.0000.0000.000
204A206GLU-1-0.911-0.9472.277-65.150-63.8370.518-0.620-1.211-0.007
205A207HIS0-0.071-0.0393.951-1.817-1.3370.001-0.115-0.366-0.001
206A208PRO0-0.0170.0046.1185.2085.2080.0000.0000.0000.000
207A209LYS10.7730.8739.25628.33328.3330.0000.0000.0000.000
208A210HIS0-0.057-0.02212.7642.8102.8100.0000.0000.0000.000
209A211HIS10.8170.8719.81720.59520.5950.0000.0000.0000.000
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