FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: N3RNQ

Calculation Name: 3KR9-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KR9

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2566353.729746
FMO2-HF: Nuclear repulsion 2481413.448342
FMO2-HF: Total energy -84940.281404
FMO2-MP2: Total energy -85193.353192


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:1:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-15.417-4.8235.647-4.908-11.332-0.024
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.010
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].
3A3SER 00.0310.0133.7750.8322.780-0.026-0.955-0.9660.002
4A4LYS 10.9720.9976.935-0.093-0.0930.0000.0000.0000.000
5A5ARG 10.8690.9469.7370.2760.2760.0000.0000.0000.000
6A6LEU 00.019-0.0057.0910.0430.0430.0000.0000.0000.000
7A7GLU -1-0.831-0.8895.499-0.700-0.7000.0000.0000.0000.000
8A8LEU 00.003-0.0128.5290.0650.0650.0000.0000.0000.000
9A9VAL 0-0.0190.00911.2820.0330.0330.0000.0000.0000.000
10A10ALA 00.0310.0038.9480.0650.0650.0000.0000.0000.000
11A11SER 0-0.082-0.03911.0580.0740.0740.0000.0000.0000.000
12A12PHE 0-0.003-0.00213.3060.0580.0580.0000.0000.0000.000
13A13VAL 0-0.051-0.01712.0610.0430.0430.0000.0000.0000.000
14A14SER 00.0460.03014.902-0.017-0.0170.0000.0000.0000.000
15A15GLN 00.0230.00515.580-0.027-0.0270.0000.0000.0000.000
16A16GLY 0-0.059-0.03916.2170.0240.0240.0000.0000.0000.000
17A17ALA 0-0.0080.01415.7630.0220.0220.0000.0000.0000.000
18A18ILE 00.0000.01316.1710.0110.0110.0000.0000.0000.000
19A19LEU 0-0.013-0.00910.636-0.011-0.0110.0000.0000.0000.000
20A20LEU 00.0030.00114.5850.0400.0400.0000.0000.0000.000
21A21ASP -1-0.779-0.8629.542-0.559-0.5590.0000.0000.0000.000
22A22VAL 0-0.013-0.03212.8390.0450.0450.0000.0000.0000.000
23A23GLY 0-0.037-0.01414.417-0.029-0.0290.0000.0000.0000.000
24A24SER 0-0.036-0.0159.000-0.030-0.0300.0000.0000.0000.000
25A25ASP -1-0.854-0.8937.822-0.873-0.8730.0000.0000.0000.000
26A26HIS 10.8290.8885.7400.3610.3610.0000.0000.0000.000
27A27ALA 00.0580.0276.0950.4000.4000.0000.0000.0000.000
28A28TYR 0-0.017-0.0152.115-3.258-0.8493.161-1.256-4.315-0.007
29A29LEU 00.0530.0353.147-1.842-0.8990.113-0.254-0.802-0.005
30A30PRO 00.0250.0055.393-0.0500.0400.000-0.007-0.0830.000
31A31ILE 0-0.032-0.0193.298-0.782-0.0710.945-0.324-1.332-0.001
32A32GLU -1-0.813-0.9062.693-8.881-5.9630.319-1.426-1.811-0.013
33A33LEU 0-0.016-0.0094.2340.3830.5020.002-0.023-0.0970.000
34A34VAL 0-0.053-0.0317.9490.1390.1390.0000.0000.0000.000
35A35GLU -1-0.870-0.9154.8112.2742.6270.005-0.075-0.2820.000
36A36ARG 10.7250.8526.1461.2461.2460.0000.0000.0000.000
37A37GLY 0-0.0150.0049.4440.0480.0480.0000.0000.0000.000
38A38GLN 0-0.004-0.00310.804-0.059-0.0590.0000.0000.0000.000
39A39ILE 0-0.014-0.00310.8770.0270.0270.0000.0000.0000.000
40A40LYS 10.9350.98413.642-0.017-0.0170.0000.0000.0000.000
41A41SER 0-0.054-0.06413.7580.0520.0520.0000.0000.0000.000
42A42ALA 0-0.0010.01411.471-0.051-0.0510.0000.0000.0000.000
43A43ILE 0-0.0060.01013.5840.0590.0590.0000.0000.0000.000
44A44ALA 00.0220.01510.707-0.051-0.0510.0000.0000.0000.000
45A45GLY 00.006-0.00112.7540.0360.0360.0000.0000.0000.000
46A46GLH 0-0.083-0.10111.535-0.038-0.0380.0000.0000.0000.000
47A47VAL 00.0540.02916.2040.0200.0200.0000.0000.0000.000
48A48VAL 0-0.021-0.00617.4410.0120.0120.0000.0000.0000.000
49A49GLU -1-0.841-0.93117.198-0.004-0.0040.0000.0000.0000.000
50A50GLY 00.001-0.00116.1820.0140.0140.0000.0000.0000.000
51A51PRO 00.009-0.01112.5440.0140.0140.0000.0000.0000.000
52A52TYR 00.0480.02012.3460.0290.0290.0000.0000.0000.000
53A53GLN 00.0320.01613.5690.0660.0660.0000.0000.0000.000
54A54SER 0-0.057-0.0038.6540.0030.0030.0000.0000.0000.000
55A55ALA 00.0230.0198.8080.1080.1080.0000.0000.0000.000
56A56VAL 00.0380.0189.4210.1750.1750.0000.0000.0000.000
57A57LYS 10.9370.9669.874-0.044-0.0440.0000.0000.0000.000
58A58ASN 0-0.020-0.0124.709-0.0670.0360.000-0.006-0.0970.000
59A59VAL 00.0430.0286.1670.4460.4460.0000.0000.0000.000
60A60GLU -1-0.978-1.0088.3500.2740.2740.0000.0000.0000.000
61A61ALA 0-0.057-0.0256.309-0.029-0.0290.0000.0000.0000.000
62A62HIS 10.7990.8722.366-4.520-3.5201.128-0.582-1.5470.000
63A63GLY 00.0080.0297.310-0.113-0.1130.0000.0000.0000.000
64A64LEU 0-0.014-0.0147.148-0.127-0.1270.0000.0000.0000.000
65A65LYS 10.9810.98711.118-0.378-0.3780.0000.0000.0000.000
66A66GLU -1-0.922-0.95213.8690.1260.1260.0000.0000.0000.000
67A67LYS 10.8320.91812.270-0.226-0.2260.0000.0000.0000.000
68A68ILE 00.0160.0148.521-0.037-0.0370.0000.0000.0000.000
69A69GLN 00.0320.03212.6010.0260.0260.0000.0000.0000.000
70A70VAL 00.0090.00811.976-0.019-0.0190.0000.0000.0000.000
71A71ARG 10.7480.84914.911-0.017-0.0170.0000.0000.0000.000
72A72LEU 00.0010.01317.515-0.020-0.0200.0000.0000.0000.000
73A73ALA 00.017-0.01119.6950.0040.0040.0000.0000.0000.000
74A74ASN 00.002-0.01120.090-0.023-0.0230.0000.0000.0000.000
75A75GLY 00.0190.01020.0580.0050.0050.0000.0000.0000.000
76A76LEU 00.0630.03020.2690.0020.0020.0000.0000.0000.000
77A77ALA 0-0.049-0.01822.2660.0090.0090.0000.0000.0000.000
78A78ALA 0-0.039-0.00718.3120.0100.0100.0000.0000.0000.000
79A79PHE 00.005-0.00719.9990.0100.0100.0000.0000.0000.000
80A80GLU -1-0.856-0.92121.871-0.027-0.0270.0000.0000.0000.000
81A81GLU -1-0.865-0.93824.381-0.042-0.0420.0000.0000.0000.000
82A82THR 0-0.040-0.02025.4830.0010.0010.0000.0000.0000.000
83A83ASP -1-0.807-0.89420.8210.0020.0020.0000.0000.0000.000
84A84GLN 0-0.054-0.02421.687-0.002-0.0020.0000.0000.0000.000
85A85VAL 0-0.029-0.01418.391-0.004-0.0040.0000.0000.0000.000
86A86SER 00.0740.04619.392-0.003-0.0030.0000.0000.0000.000
87A87VAL 0-0.003-0.00715.935-0.012-0.0120.0000.0000.0000.000
88A88ILE 00.0070.01216.4900.0020.0020.0000.0000.0000.000
89A89THR 0-0.008-0.00212.2610.0010.0010.0000.0000.0000.000
90A90ILE 00.0310.00514.8660.0120.0120.0000.0000.0000.000
91A91ALA 00.051-0.03512.5330.0140.0140.0000.0000.0000.000
92A92GLY 00.001-0.01614.468-0.011-0.0110.0000.0000.0000.000
93A93MET 0-0.0220.01215.3730.0240.0240.0000.0000.0000.000
94A94GLY 0-0.0030.00618.8370.0040.0040.0000.0000.0000.000
95A95GLY 00.1040.04222.421-0.002-0.0020.0000.0000.0000.000
96A96ARG 10.9100.94923.9310.0810.0810.0000.0000.0000.000
97A97LEU 0-0.045-0.01120.7470.0070.0070.0000.0000.0000.000
98A98ILE 00.0200.00718.9740.0020.0020.0000.0000.0000.000
99A99ALA 00.0510.02722.4270.0060.0060.0000.0000.0000.000
100A100ARG 10.9470.97525.9120.0800.0800.0000.0000.0000.000
101A101ILE 0-0.012-0.00919.8860.0060.0060.0000.0000.0000.000
102A102LEU 0-0.009-0.00922.1530.0050.0050.0000.0000.0000.000
103A103GLU -1-0.918-0.97025.006-0.054-0.0540.0000.0000.0000.000
104A104GLU -1-0.978-0.99426.853-0.059-0.0590.0000.0000.0000.000
105A105GLY 0-0.021-0.00725.8560.0060.0060.0000.0000.0000.000
106A106LEU 00.0240.00626.9000.0000.0000.0000.0000.0000.000
107A107GLY 0-0.059-0.04228.8380.0000.0000.0000.0000.0000.000
108A108LYS 10.8570.93125.0590.0490.0490.0000.0000.0000.000
109A109LEU 0-0.016-0.01123.518-0.003-0.0030.0000.0000.0000.000
110A110ALA 0-0.0210.00426.304-0.003-0.0030.0000.0000.0000.000
111A111ASN 0-0.005-0.00326.959-0.002-0.0020.0000.0000.0000.000
112A112VAL 0-0.058-0.01021.204-0.002-0.0020.0000.0000.0000.000
113A113GLU -1-0.953-0.97022.440-0.095-0.0950.0000.0000.0000.000
114A114ARG 10.8100.88919.0890.1560.1560.0000.0000.0000.000
115A115LEU 0-0.020-0.00319.464-0.010-0.0100.0000.0000.0000.000
116A116ILE 0-0.040-0.01815.1130.0010.0010.0000.0000.0000.000
117A117LEU 00.010-0.00716.765-0.024-0.0240.0000.0000.0000.000
118A118GLN 00.0140.09014.571-0.044-0.0440.0000.0000.0000.000
119A119PRO 00.0060.02217.495-0.018-0.0180.0000.0000.0000.000
120A120ASN 0-0.025-0.04517.483-0.010-0.0100.0000.0000.0000.000
121A121ASN 0-0.006-0.01020.5500.0160.0160.0000.0000.0000.000
122A122ARG 10.7820.87024.3390.0780.0780.0000.0000.0000.000
123A123GLU -1-0.797-0.91423.694-0.113-0.1130.0000.0000.0000.000
124A124ASP -1-0.822-0.88526.063-0.077-0.0770.0000.0000.0000.000
125A125ASP -1-0.817-0.92329.313-0.074-0.0740.0000.0000.0000.000
126A126LEU 0-0.019-0.01222.7060.0010.0010.0000.0000.0000.000
127A127ARG 10.8000.89725.7330.1000.1000.0000.0000.0000.000
128A128ILE 0-0.0220.00028.8850.0040.0040.0000.0000.0000.000
129A129TRP 0-0.0090.00627.0030.0000.0000.0000.0000.0000.000
130A130LEU 00.001-0.01824.9450.0030.0030.0000.0000.0000.000
131A131GLN 00.0680.04629.1240.0030.0030.0000.0000.0000.000
132A132ASP -1-0.968-0.98832.361-0.053-0.0530.0000.0000.0000.000
133A133HIS 10.7740.89230.5620.0670.0670.0000.0000.0000.000
134A134GLY 00.0000.01331.527-0.001-0.0010.0000.0000.0000.000
135A135PHE 0-0.0060.00826.788-0.002-0.0020.0000.0000.0000.000
136A136GLN 0-0.020-0.01528.6750.0050.0050.0000.0000.0000.000
137A137ILE 0-0.009-0.02025.134-0.007-0.0070.0000.0000.0000.000
138A138VAL 0-0.011-0.00524.0370.0080.0080.0000.0000.0000.000
139A139ALA 0-0.001-0.00522.0960.0010.0010.0000.0000.0000.000
140A140GLU -1-0.753-0.87622.012-0.107-0.1070.0000.0000.0000.000
141A141SER 0-0.036-0.01718.1410.0020.0020.0000.0000.0000.000
142A142ILE 00.0220.02119.704-0.012-0.0120.0000.0000.0000.000
143A143LEU 0-0.037-0.00213.6630.0170.0170.0000.0000.0000.000
144A144GLU -1-0.872-0.95417.703-0.047-0.0470.0000.0000.0000.000
145A145GLU -1-0.919-1.00311.283-0.235-0.2350.0000.0000.0000.000
146A146ALA 0-0.005-0.00214.721-0.018-0.0180.0000.0000.0000.000
147A147GLY 00.0250.02716.474-0.009-0.0090.0000.0000.0000.000
148A148LYS 10.8900.94718.3740.1140.1140.0000.0000.0000.000
149A149PHE 00.0500.02318.7150.0000.0000.0000.0000.0000.000
150A150TYR 0-0.026-0.01716.230-0.022-0.0220.0000.0000.0000.000
151A151GLU -1-0.754-0.85318.844-0.105-0.1050.0000.0000.0000.000
152A152ILE 0-0.016-0.02114.798-0.026-0.0260.0000.0000.0000.000
153A153LEU 0-0.008-0.01718.9220.0200.0200.0000.0000.0000.000
154A154VAL 00.0080.01319.114-0.020-0.0200.0000.0000.0000.000
155A155VAL 0-0.016-0.00621.3690.0170.0170.0000.0000.0000.000
156A156GLU -1-0.778-0.88923.264-0.118-0.1180.0000.0000.0000.000
157A157ALA 00.0320.02625.8810.0040.0040.0000.0000.0000.000
158A158GLY 0-0.002-0.01929.1020.0020.0020.0000.0000.0000.000
159A159GLN 0-0.043-0.01832.146-0.001-0.0010.0000.0000.0000.000
160A160MET 00.0330.04530.414-0.002-0.0020.0000.0000.0000.000
161A161LYS 10.8740.92234.2540.0470.0470.0000.0000.0000.000
162A162LEU 00.0330.01030.8050.0010.0010.0000.0000.0000.000
163A163SER 00.0510.03635.4300.0020.0020.0000.0000.0000.000
164A164ALA 00.0540.00535.833-0.003-0.0030.0000.0000.0000.000
165A165SER 00.0500.01735.124-0.002-0.0020.0000.0000.0000.000
166A166ASP -1-0.847-0.92932.587-0.061-0.0610.0000.0000.0000.000
167A167VAL 0-0.056-0.01831.255-0.006-0.0060.0000.0000.0000.000
168A168ARG 10.8340.90228.4720.0710.0710.0000.0000.0000.000
169A169PHE 00.0060.00429.767-0.005-0.0050.0000.0000.0000.000
170A170GLY 00.0710.04027.736-0.005-0.0050.0000.0000.0000.000
171A171PRO 0-0.044-0.00628.4300.0050.0050.0000.0000.0000.000
172A172PHE 0-0.024-0.02725.8890.0030.0030.0000.0000.0000.000
173A173LEU 0-0.021-0.03222.7360.0030.0030.0000.0000.0000.000
174A174SER 00.0170.00026.7210.0070.0070.0000.0000.0000.000
175A175LYS 10.9530.98229.8310.0570.0570.0000.0000.0000.000
176A176GLU -1-0.954-0.94824.071-0.074-0.0740.0000.0000.0000.000
177A177VAL 00.0170.01328.3580.0050.0050.0000.0000.0000.000
178A178SER 0-0.031-0.01923.8520.0060.0060.0000.0000.0000.000
179A179PRO 00.028-0.01024.2550.0000.0000.0000.0000.0000.000
180A180VAL 00.0080.00720.0800.0010.0010.0000.0000.0000.000
181A181PHE 00.0070.01523.504-0.004-0.0040.0000.0000.0000.000
182A182VAL 00.0350.01525.8380.0010.0010.0000.0000.0000.000
183A183GLN 0-0.054-0.02122.8710.0040.0040.0000.0000.0000.000
184A184LYS 10.8140.91024.1030.0990.0990.0000.0000.0000.000
185A185TRP 00.0320.00026.3930.0010.0010.0000.0000.0000.000
186A186GLN 00.0830.04229.9460.0000.0000.0000.0000.0000.000
187A187LYS 10.9660.98926.4180.0460.0460.0000.0000.0000.000
188A188GLU -1-0.976-0.99429.677-0.062-0.0620.0000.0000.0000.000
189A189ALA 00.0210.00531.2200.0020.0020.0000.0000.0000.000
190A190GLU -1-0.905-0.94532.191-0.032-0.0320.0000.0000.0000.000
191A191LYS 10.8830.93727.2710.0650.0650.0000.0000.0000.000
192A192LEU 0-0.024-0.01334.1410.0020.0020.0000.0000.0000.000
193A193GLU -1-0.880-0.95836.761-0.028-0.0280.0000.0000.0000.000
194A194PHE 0-0.045-0.00336.9500.0020.0020.0000.0000.0000.000
195A195ALA 0-0.043-0.02537.5260.0010.0010.0000.0000.0000.000
196A196LEU 0-0.008-0.03839.3990.0010.0010.0000.0000.0000.000
197A197GLY 0-0.0020.00241.6910.0020.0020.0000.0000.0000.000
198A198GLN 0-0.078-0.03939.2170.0010.0010.0000.0000.0000.000
199A199ILE 00.0320.04042.8710.0020.0020.0000.0000.0000.000
200A200PRO 0-0.0370.04645.5650.0000.0000.0000.0000.0000.000
201A201GLU -1-0.900-0.99849.114-0.021-0.0210.0000.0000.0000.000
202A202LYS 10.8360.90751.3200.0190.0190.0000.0000.0000.000
203A203ASN 00.0610.02748.4010.0000.0000.0000.0000.0000.000
204A204LEU 00.0270.01749.584-0.001-0.0010.0000.0000.0000.000
205A205GLU -1-0.890-0.94648.599-0.026-0.0260.0000.0000.0000.000
206A206GLU -1-0.931-0.96644.499-0.033-0.0330.0000.0000.0000.000
207A207ARG 10.9280.94344.3280.0240.0240.0000.0000.0000.000
208A208GLN 0-0.045-0.02344.5710.0000.0000.0000.0000.0000.000
209A209VAL 00.0180.01940.376-0.002-0.0020.0000.0000.0000.000
210A210LEU 0-0.038-0.03539.297-0.003-0.0030.0000.0000.0000.000
211A211VAL 00.0060.01440.362-0.001-0.0010.0000.0000.0000.000
212A212ASP -1-0.842-0.92242.050-0.034-0.0340.0000.0000.0000.000
213A213LYS 10.8630.93535.7890.0490.0490.0000.0000.0000.000
214A214ILE 00.0160.01637.286-0.002-0.0020.0000.0000.0000.000
215A215GLN 00.008-0.00138.7230.0000.0000.0000.0000.0000.000
216A216ALA 00.0260.03237.2190.0000.0000.0000.0000.0000.000
217A217ILE 0-0.044-0.02533.438-0.001-0.0010.0000.0000.0000.000
218A218LYS 10.8810.94135.7330.0310.0310.0000.0000.0000.000
219A219GLU -1-0.964-0.99038.193-0.034-0.0340.0000.0000.0000.000
220A220VAL 0-0.063-0.02132.9140.0000.0000.0000.0000.0000.000
221A221LEU 0-0.044-0.02231.344-0.001-0.0010.0000.0000.0000.000
222A222HIS 0-0.070-0.00934.7310.0020.0020.0000.0000.0000.000
223A223NME 0-0.016-0.00436.5830.0000.0000.0000.0000.0000.000