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: 98RV2

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 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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2678444.166947
FMO2-HF: Nuclear repulsion 2592196.65334
FMO2-HF: Total energy -86247.513608
FMO2-MP2: Total energy -86499.160139


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.
-146.443-142.56715.381-9.746-9.513-0.098
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 : 0.923 / q_NPA : 0.960
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].
3A5LYS10.8720.9331.7680.8260.88511.057-6.228-4.889-0.063
4A6LYS10.8180.8884.29134.24534.459-0.001-0.042-0.1710.000
5A7ILE00.0290.0156.8300.1490.1490.0000.0000.0000.000
6A8VAL00.003-0.0019.6061.8661.8660.0000.0000.0000.000
7A9LEU0-0.0010.00813.052-0.622-0.6220.0000.0000.0000.000
8A10ILE00.0330.00914.7421.1571.1570.0000.0000.0000.000
9A11GLY00.0400.01718.3360.2310.2310.0000.0000.0000.000
10A12ALA0-0.0160.00816.923-0.054-0.0540.0000.0000.0000.000
11A13SER0-0.011-0.02818.3070.4130.4130.0000.0000.0000.000
12A14GLY00.0360.02021.4790.0460.0460.0000.0000.0000.000
13A15PHE00.0250.01621.350-0.709-0.7090.0000.0000.0000.000
14A16VAL00.0880.04017.973-0.610-0.6100.0000.0000.0000.000
15A17GLY00.0510.03617.310-1.091-1.0910.0000.0000.0000.000
16A18SER0-0.028-0.04216.646-0.964-0.9640.0000.0000.0000.000
17A19ALA00.0080.01816.681-0.783-0.7830.0000.0000.0000.000
18A20LEU00.0010.00512.698-1.279-1.2790.0000.0000.0000.000
19A21LEU0-0.0090.00011.890-2.140-2.1400.0000.0000.0000.000
20A22ASN0-0.041-0.04112.527-1.254-1.2540.0000.0000.0000.000
21A23GLU-1-0.760-0.8269.706-27.913-27.9130.0000.0000.0000.000
22A24ALA00.0190.0057.754-2.790-2.7900.0000.0000.0000.000
23A25LEU0-0.035-0.0267.879-3.188-3.1880.0000.0000.0000.000
24A26ASN0-0.047-0.02910.1000.0670.0670.0000.0000.0000.000
25A27ARG10.7300.8415.62740.67740.6770.0000.0000.0000.000
26A28GLY0-0.0190.0035.067-8.536-8.521-0.0010.000-0.0140.000
27A29PHE0-0.019-0.0132.946-9.396-7.8520.182-0.887-0.839-0.012
28A30GLU-1-0.942-0.9746.322-24.963-24.9630.0000.0000.0000.000
29A31VAL00.0040.0049.204-0.291-0.2910.0000.0000.0000.000
30A32THR0-0.0120.00111.4822.7522.7520.0000.0000.0000.000
31A33ALA00.0230.01014.664-0.369-0.3690.0000.0000.0000.000
32A34VAL00.0200.01516.7791.0821.0820.0000.0000.0000.000
33A35VAL00.0150.00819.6730.1160.1160.0000.0000.0000.000
34A36ARG10.9490.94422.74911.33511.3350.0000.0000.0000.000
35A37HIS0-0.061-0.05325.5100.5430.5430.0000.0000.0000.000
36A38PRO00.0750.02823.952-0.211-0.2110.0000.0000.0000.000
37A39GLU-1-0.790-0.87824.997-11.418-11.4180.0000.0000.0000.000
38A40LYS10.8570.94026.01311.10611.1060.0000.0000.0000.000
39A41ILE00.0000.01719.727-0.131-0.1310.0000.0000.0000.000
40A42LYS10.8470.89522.58712.62512.6250.0000.0000.0000.000
41A43ILE00.0040.02116.6190.1810.1810.0000.0000.0000.000
42A44GLU-1-0.911-0.94719.741-14.003-14.0030.0000.0000.0000.000
43A45ASN00.0600.00912.536-0.946-0.9460.0000.0000.0000.000
44A46GLU-1-0.853-0.92413.945-21.192-21.1920.0000.0000.0000.000
45A47HIS10.8120.91010.41525.51925.5190.0000.0000.0000.000
46A48LEU0-0.0070.01112.268-1.648-1.6480.0000.0000.0000.000
47A49LYS10.9360.96313.26323.82723.8270.0000.0000.0000.000
48A50VAL00.0150.00816.999-0.189-0.1890.0000.0000.0000.000
49A51LYS10.9170.95616.99418.49918.4990.0000.0000.0000.000
50A52LYS10.8760.93721.54611.39211.3920.0000.0000.0000.000
51A53ALA00.0560.02622.979-0.095-0.0950.0000.0000.0000.000
52A54ASP-1-0.840-0.88124.966-11.224-11.2240.0000.0000.0000.000
53A55VAL0-0.008-0.01123.073-0.112-0.1120.0000.0000.0000.000
54A56SER0-0.042-0.03525.410-0.009-0.0090.0000.0000.0000.000
55A57SER0-0.035-0.03327.6620.3540.3540.0000.0000.0000.000
56A58LEU00.0490.00625.284-0.452-0.4520.0000.0000.0000.000
57A59ASP-1-0.840-0.91124.993-11.876-11.8760.0000.0000.0000.000
58A60GLU-1-0.814-0.88125.037-11.883-11.8830.0000.0000.0000.000
59A61VAL0-0.039-0.01321.000-0.776-0.7760.0000.0000.0000.000
60A62CYS0-0.0370.01020.489-0.794-0.7940.0000.0000.0000.000
61A63GLU-1-0.823-0.91120.324-14.193-14.1930.0000.0000.0000.000
62A64VAL0-0.082-0.04618.615-0.682-0.6820.0000.0000.0000.000
63A65CYS0-0.051-0.02716.124-1.394-1.3940.0000.0000.0000.000
64A66LYS10.8410.91715.62312.50812.5080.0000.0000.0000.000
65A67GLY00.0120.01713.169-0.151-0.1510.0000.0000.0000.000
66A68ALA0-0.063-0.02611.316-1.899-1.8990.0000.0000.0000.000
67A69ASP-1-0.760-0.8596.117-40.880-40.8800.0000.0000.0000.000
68A70ALA0-0.027-0.0108.1930.2340.2340.0000.0000.0000.000
69A71VAL0-0.020-0.0119.9110.1140.1140.0000.0000.0000.000
70A72ILE00.0300.0199.5910.1750.1750.0000.0000.0000.000
71A73SER0-0.008-0.00513.6560.9980.9980.0000.0000.0000.000
72A74ALA00.020-0.00517.382-0.140-0.1400.0000.0000.0000.000
73A75PHE0-0.022-0.00319.1250.5580.5580.0000.0000.0000.000
74A76ASN00.0300.01922.5000.2580.2580.0000.0000.0000.000
75A77PRO0-0.031-0.00625.529-0.046-0.0460.0000.0000.0000.000
76A78GLY00.041-0.00328.4810.0560.0560.0000.0000.0000.000
77A79TRP0-0.034-0.05030.3150.1820.1820.0000.0000.0000.000
78A80ASN00.0340.03332.6480.0120.0120.0000.0000.0000.000
79A81ASN0-0.056-0.05634.865-0.019-0.0190.0000.0000.0000.000
80A82PRO0-0.047-0.01635.3170.1780.1780.0000.0000.0000.000
81A83ASP-1-0.896-0.93637.884-8.144-8.1440.0000.0000.0000.000
82A84ILE0-0.0250.00237.8920.1620.1620.0000.0000.0000.000
83A85TYR0-0.002-0.01234.142-0.228-0.2280.0000.0000.0000.000
84A86ASP-1-0.820-0.89934.303-8.790-8.7900.0000.0000.0000.000
85A87GLU-1-0.816-0.91032.759-10.184-10.1840.0000.0000.0000.000
86A88THR0-0.032-0.00629.353-0.236-0.2360.0000.0000.0000.000
87A89ILE0-0.0190.00029.226-0.476-0.4760.0000.0000.0000.000
88A90LYS10.8920.93629.3399.7589.7580.0000.0000.0000.000
89A91VAL0-0.035-0.00226.250-0.316-0.3160.0000.0000.0000.000
90A92TYR0-0.023-0.02224.076-0.307-0.3070.0000.0000.0000.000
91A93LEU00.0110.00724.411-0.563-0.5630.0000.0000.0000.000
92A94THR0-0.036-0.02324.807-0.265-0.2650.0000.0000.0000.000
93A95ILE0-0.047-0.01620.230-0.464-0.4640.0000.0000.0000.000
94A96ILE00.0000.00819.150-0.654-0.6540.0000.0000.0000.000
95A97ASP-1-0.819-0.92420.367-12.875-12.8750.0000.0000.0000.000
96A98GLY0-0.001-0.00622.4100.0710.0710.0000.0000.0000.000
97A99VAL0-0.039-0.03616.012-0.424-0.4240.0000.0000.0000.000
98A100LYS10.7990.88917.37212.70012.7000.0000.0000.0000.000
99A101LYS10.8430.91918.82911.76411.7640.0000.0000.0000.000
100A102ALA0-0.045-0.02417.3580.2420.2420.0000.0000.0000.000
101A103GLY00.0050.00516.142-0.555-0.5550.0000.0000.0000.000
102A104VAL0-0.034-0.01011.961-0.889-0.8890.0000.0000.0000.000
103A105ASN0-0.017-0.01710.3331.2721.2720.0000.0000.0000.000
104A106ARG10.7440.8498.27728.02328.0230.0000.0000.0000.000
105A107PHE00.007-0.00811.015-0.626-0.6260.0000.0000.0000.000
106A108LEU00.0200.01310.3770.1090.1090.0000.0000.0000.000
107A109MET0-0.039-0.01314.2870.3430.3430.0000.0000.0000.000
108A110VAL00.0160.00217.1300.0840.0840.0000.0000.0000.000
109A111GLY00.0200.01918.8320.6060.6060.0000.0000.0000.000
110A112GLY00.033-0.01321.9210.0880.0880.0000.0000.0000.000
111A113ALA00.0120.01325.057-0.099-0.0990.0000.0000.0000.000
112A114GLY00.0460.01726.8900.2270.2270.0000.0000.0000.000
113A115SER00.0710.02626.5390.2720.2720.0000.0000.0000.000
114A116LEU0-0.0530.00524.590-0.067-0.0670.0000.0000.0000.000
115A117PHE0-0.043-0.02328.5730.3920.3920.0000.0000.0000.000
116A118ILE00.019-0.00530.966-0.277-0.2770.0000.0000.0000.000
117A119ALA00.0090.01133.6780.1830.1830.0000.0000.0000.000
118A120PRO00.000-0.01435.664-0.153-0.1530.0000.0000.0000.000
119A121GLY00.0060.01835.3450.2380.2380.0000.0000.0000.000
120A122LEU00.0090.01336.401-0.036-0.0360.0000.0000.0000.000
121A123ARG10.9390.95929.85510.13510.1350.0000.0000.0000.000
122A124LEU00.0320.02430.5200.2480.2480.0000.0000.0000.000
123A125MET0-0.051-0.00331.4390.0560.0560.0000.0000.0000.000
124A126ASP-1-0.873-0.91434.243-8.574-8.5740.0000.0000.0000.000
125A127SER0-0.050-0.02836.0960.2350.2350.0000.0000.0000.000
126A128GLY00.0140.01638.4420.2090.2090.0000.0000.0000.000
127A129GLU-1-0.939-0.96136.101-8.255-8.2550.0000.0000.0000.000
128A130VAL0-0.062-0.03933.910-0.307-0.3070.0000.0000.0000.000
129A131PRO00.0200.00834.9170.2090.2090.0000.0000.0000.000
130A132GLU-1-0.858-0.93437.090-7.593-7.5930.0000.0000.0000.000
131A133ASN0-0.022-0.01536.275-0.054-0.0540.0000.0000.0000.000
132A134ILE0-0.027-0.02231.793-0.205-0.2050.0000.0000.0000.000
133A135LEU00.0110.02633.719-0.292-0.2920.0000.0000.0000.000
134A136PRO00.0380.01334.800-0.202-0.2020.0000.0000.0000.000
135A137GLY00.0440.02931.957-0.140-0.1400.0000.0000.0000.000
136A138VAL0-0.052-0.02930.044-0.419-0.4190.0000.0000.0000.000
137A139LYS10.8240.89830.5628.6168.6160.0000.0000.0000.000
138A140ALA00.0220.02131.620-0.190-0.1900.0000.0000.0000.000
139A141LEU0-0.023-0.01523.938-0.210-0.2100.0000.0000.0000.000
140A142GLY00.021-0.00526.960-0.436-0.4360.0000.0000.0000.000
141A143GLU-1-0.846-0.95628.797-9.797-9.7970.0000.0000.0000.000
142A144PHE0-0.008-0.00523.054-0.015-0.0150.0000.0000.0000.000
143A145TYR00.0560.00723.700-0.029-0.0290.0000.0000.0000.000
144A146LEU0-0.024-0.01326.085-0.050-0.0500.0000.0000.0000.000
145A147ASN0-0.052-0.03128.9710.3480.3480.0000.0000.0000.000
146A148PHE00.0010.01026.9000.3270.3270.0000.0000.0000.000
147A149LEU00.0230.02821.078-0.134-0.1340.0000.0000.0000.000
148A150MET0-0.0030.00223.147-0.405-0.4050.0000.0000.0000.000
149A151LYS10.8360.90925.17910.20710.2070.0000.0000.0000.000
150A152GLU-1-0.731-0.83820.128-13.591-13.5910.0000.0000.0000.000
151A153LYS10.7720.86220.08212.47912.4790.0000.0000.0000.000
152A154GLU-1-0.923-0.93619.151-12.988-12.9880.0000.0000.0000.000
153A155ILE0-0.0080.00214.533-0.592-0.5920.0000.0000.0000.000
154A156ASP-1-0.816-0.88211.254-21.724-21.7240.0000.0000.0000.000
155A157TRP0-0.008-0.00113.306-1.744-1.7440.0000.0000.0000.000
156A158VAL0-0.002-0.00113.4700.2590.2590.0000.0000.0000.000
157A159PHE0-0.0150.00016.346-0.326-0.3260.0000.0000.0000.000
158A160PHE00.011-0.00115.5290.1830.1830.0000.0000.0000.000
159A161SER00.0160.01718.5010.1750.1750.0000.0000.0000.000
160A162PRO0-0.0260.01221.390-0.249-0.2490.0000.0000.0000.000
161A163ALA00.0280.01822.2110.4340.4340.0000.0000.0000.000
162A164ALA0-0.007-0.02125.200-0.027-0.0270.0000.0000.0000.000
163A165ASP-1-0.873-0.90528.052-10.608-10.6080.0000.0000.0000.000
164A166MET0-0.005-0.00721.320-0.658-0.6580.0000.0000.0000.000
165A167ARG10.8690.92424.91910.56010.5600.0000.0000.0000.000
166A168PRO0-0.010-0.01123.211-0.460-0.4600.0000.0000.0000.000
167A169GLY0-0.013-0.01023.0750.6580.6580.0000.0000.0000.000
168A170VAL00.000-0.00122.159-0.013-0.0130.0000.0000.0000.000
169A171ARG10.8260.90211.63023.11623.1160.0000.0000.0000.000
170A172THR0-0.035-0.04318.819-0.207-0.2070.0000.0000.0000.000
171A173GLY0-0.033-0.01716.7920.0210.0210.0000.0000.0000.000
172A174ARG10.7500.83117.68312.76612.7660.0000.0000.0000.000
173A175TYR00.0380.01314.4130.7160.7160.0000.0000.0000.000
174A176ARG10.8850.94420.66412.50712.5070.0000.0000.0000.000
175A177LEU00.0600.02515.4220.1400.1400.0000.0000.0000.000
176A178GLY0-0.011-0.01220.0470.7550.7550.0000.0000.0000.000
177A179LYS10.8540.94620.95713.45913.4590.0000.0000.0000.000
178A180ASP-1-0.755-0.89422.807-13.041-13.0410.0000.0000.0000.000
179A181ASP-1-0.915-0.94525.922-10.619-10.6190.0000.0000.0000.000
180A182MET0-0.025-0.01226.639-0.406-0.4060.0000.0000.0000.000
181A183ILE0-0.0280.00423.8230.3410.3410.0000.0000.0000.000
182A184VAL00.0070.00327.0910.0150.0150.0000.0000.0000.000
183A185ASP-1-0.722-0.83529.632-10.048-10.0480.0000.0000.0000.000
184A186ILE0-0.022-0.01630.8070.2400.2400.0000.0000.0000.000
185A187VAL0-0.065-0.02834.0380.3090.3090.0000.0000.0000.000
186A188GLY00.0120.01934.2370.2040.2040.0000.0000.0000.000
187A189ASN0-0.056-0.03332.3040.0260.0260.0000.0000.0000.000
188A190SER00.0330.01627.683-0.367-0.3670.0000.0000.0000.000
189A191HIS0-0.058-0.04827.009-0.179-0.1790.0000.0000.0000.000
190A192ILE0-0.019-0.01020.223-0.262-0.2620.0000.0000.0000.000
191A193SER00.0310.01520.7270.0860.0860.0000.0000.0000.000
192A194VAL00.013-0.01219.422-0.651-0.6510.0000.0000.0000.000
193A195GLU-1-0.809-0.91917.254-15.830-15.8300.0000.0000.0000.000
194A196ASP-1-0.732-0.82315.849-17.955-17.9550.0000.0000.0000.000
195A197TYR0-0.025-0.02215.804-1.254-1.2540.0000.0000.0000.000
196A198ALA0-0.011-0.02113.971-1.080-1.0800.0000.0000.0000.000
197A199ALA0-0.023-0.01411.660-2.032-2.0320.0000.0000.0000.000
198A200ALA00.0470.03110.848-2.370-2.3700.0000.0000.0000.000
199A201MET0-0.023-0.00311.597-1.362-1.3620.0000.0000.0000.000
200A202ILE0-0.035-0.0256.425-2.183-2.1830.0000.0000.0000.000
201A203ASP-1-0.827-0.8976.597-37.029-37.0290.0000.0000.0000.000
202A204GLU-1-0.736-0.8297.858-27.991-27.9910.0000.0000.0000.000
203A205LEU0-0.028-0.0095.5820.2890.2890.0000.0000.0000.000
204A206GLU-1-0.912-0.9381.794-73.328-73.0094.084-1.820-2.583-0.016
205A207HIS0-0.068-0.0393.207-4.855-3.1300.060-0.769-1.017-0.007
206A208PRO0-0.0290.0045.7775.8575.8570.0000.0000.0000.000
207A209LYS10.7680.8668.77728.94128.9410.0000.0000.0000.000
208A210HIS0-0.011-0.00712.3872.5822.5820.0000.0000.0000.000
209A211HIS10.8230.86810.00820.68920.6890.0000.0000.0000.000
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