Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 82RLY

Calculation Name: 3KR9-A-Xray372

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: 2023-06-19

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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2564526.850021
FMO2-HF: Nuclear repulsion 2479603.394834
FMO2-HF: Total energy -84923.455187
FMO2-MP2: Total energy -85176.297751


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.
-16.027-7.61510.654-5.246-13.815-0.031
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 : -0.008
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].
3A3SER00.001-0.0023.7750.7242.741-0.036-0.980-1.0000.002
4A4LYS10.9580.9756.935-0.163-0.1630.0000.0000.0000.000
5A5ARG10.8730.9379.7780.3040.3040.0000.0000.0000.000
6A6LEU00.005-0.0087.4220.0340.0340.0000.0000.0000.000
7A7GLU-1-0.794-0.8716.209-0.894-0.8940.0000.0000.0000.000
8A8LEU00.012-0.0038.5650.0520.0520.0000.0000.0000.000
9A9VAL0-0.035-0.00611.4380.0300.0300.0000.0000.0000.000
10A10ALA00.0410.0088.8230.0630.0630.0000.0000.0000.000
11A11SER0-0.067-0.02310.9370.0760.0760.0000.0000.0000.000
12A12PHE0-0.011-0.00813.3320.0610.0610.0000.0000.0000.000
13A13VAL0-0.053-0.02011.9920.0380.0380.0000.0000.0000.000
14A14SER00.0400.02814.816-0.006-0.0060.0000.0000.0000.000
15A15GLN00.0270.00015.664-0.039-0.0390.0000.0000.0000.000
16A16GLY0-0.059-0.03616.3640.0220.0220.0000.0000.0000.000
17A17ALA00.0060.01715.6540.0160.0160.0000.0000.0000.000
18A18ILE0-0.0230.00116.0310.0020.0020.0000.0000.0000.000
19A19LEU00.002-0.00110.880-0.006-0.0060.0000.0000.0000.000
20A20LEU00.0020.00314.4210.0090.0090.0000.0000.0000.000
21A21ASP-1-0.781-0.8449.623-0.968-0.9680.0000.0000.0000.000
22A22VAL0-0.001-0.02512.8310.0110.0110.0000.0000.0000.000
23A23GLY0-0.048-0.01614.055-0.014-0.0140.0000.0000.0000.000
24A24SER0-0.033-0.0308.537-0.121-0.1210.0000.0000.0000.000
25A25ASP-1-0.823-0.9048.198-1.170-1.1700.0000.0000.0000.000
26A26HIS10.7960.8945.3880.7420.7420.0000.0000.0000.000
27A27ALA00.0540.0255.223-0.025-0.0250.0000.0000.0000.000
28A28TYR0-0.032-0.0242.158-2.081-1.0585.705-1.821-4.906-0.007
29A29LEU00.0600.0412.9560.146-0.2090.0081.068-0.720-0.005
30A30PRO00.0220.0045.6400.2260.2260.0000.0000.0000.000
31A31ILE0-0.026-0.0172.732-1.079-0.2331.127-0.356-1.616-0.002
32A32GLU-1-0.824-0.9042.609-10.295-6.5020.665-1.883-2.575-0.019
33A33LEU0-0.010-0.0034.4050.1100.2570.002-0.021-0.1290.000
34A34VAL0-0.047-0.0287.9800.1430.1430.0000.0000.0000.000
35A35GLU-1-0.855-0.9064.4323.4224.0760.022-0.182-0.494-0.001
36A36ARG10.6860.8195.9851.1761.1760.0000.0000.0000.000
37A37GLY0-0.0060.0139.3960.0190.0190.0000.0000.0000.000
38A38GLN00.0030.00111.104-0.076-0.0760.0000.0000.0000.000
39A39ILE0-0.0180.00210.6050.0100.0100.0000.0000.0000.000
40A40LYS10.9050.95213.7550.0940.0940.0000.0000.0000.000
41A41SER0-0.033-0.03913.5390.0660.0660.0000.0000.0000.000
42A42ALA00.0050.01511.030-0.041-0.0410.0000.0000.0000.000
43A43ILE0-0.0160.00613.1820.0510.0510.0000.0000.0000.000
44A44ALA00.0220.0149.864-0.061-0.0610.0000.0000.0000.000
45A45GLY00.0130.00511.9320.0550.0550.0000.0000.0000.000
46A46GLH0-0.079-0.07610.480-0.044-0.0440.0000.0000.0000.000
47A47VAL00.0490.02815.1890.0370.0370.0000.0000.0000.000
48A48VAL0-0.018-0.00616.5810.0290.0290.0000.0000.0000.000
49A49GLU-1-0.771-0.89416.572-0.190-0.1900.0000.0000.0000.000
50A50GLY00.0010.00416.059-0.002-0.0020.0000.0000.0000.000
51A51PRO00.014-0.00712.255-0.012-0.0120.0000.0000.0000.000
52A52TYR00.0340.01711.745-0.052-0.0520.0000.0000.0000.000
53A53GLN0-0.009-0.01812.5910.0080.0080.0000.0000.0000.000
54A54SER0-0.044-0.0149.142-0.044-0.0440.0000.0000.0000.000
55A55ALA00.0210.0217.809-0.036-0.0360.0000.0000.0000.000
56A56VAL00.0360.0158.2480.0460.0460.0000.0000.0000.000
57A57LYS10.9050.9589.5580.1630.1630.0000.0000.0000.000
58A58ASN0-0.020-0.0163.943-0.1060.0950.000-0.019-0.1810.000
59A59VAL00.0410.0275.3760.2470.2470.0000.0000.0000.000
60A60GLU-1-0.893-0.9487.1840.1940.1940.0000.0000.0000.000
61A61ALA0-0.061-0.0266.3120.0680.0680.0000.0000.0000.000
62A62HIS10.8010.8712.505-6.051-5.9653.161-1.052-2.1940.001
63A63GLY00.0160.0336.8680.0050.0050.0000.0000.0000.000
64A64LEU0-0.025-0.0206.625-0.085-0.0850.0000.0000.0000.000
65A65LYS10.8990.92810.287-0.182-0.1820.0000.0000.0000.000
66A66GLU-1-0.935-0.95912.6840.0260.0260.0000.0000.0000.000
67A67LYS10.8600.92811.891-0.132-0.1320.0000.0000.0000.000
68A68ILE00.0090.0117.774-0.052-0.0520.0000.0000.0000.000
69A69GLN00.0520.04911.7590.0180.0180.0000.0000.0000.000
70A70VAL00.0020.00210.495-0.053-0.0530.0000.0000.0000.000
71A71ARG10.7210.81613.5090.1940.1940.0000.0000.0000.000
72A72LEU00.0010.00916.318-0.036-0.0360.0000.0000.0000.000
73A73ALA00.012-0.00618.5120.0240.0240.0000.0000.0000.000
74A74ASN00.003-0.01319.210-0.042-0.0420.0000.0000.0000.000
75A75GLY00.0240.00819.7100.0150.0150.0000.0000.0000.000
76A76LEU00.0370.01919.786-0.013-0.0130.0000.0000.0000.000
77A77ALA0-0.037-0.01221.9190.0110.0110.0000.0000.0000.000
78A78ALA0-0.045-0.01117.5580.0080.0080.0000.0000.0000.000
79A79PHE00.015-0.00219.234-0.006-0.0060.0000.0000.0000.000
80A80GLU-1-0.791-0.88121.271-0.111-0.1110.0000.0000.0000.000
81A81GLU-1-0.840-0.92823.934-0.116-0.1160.0000.0000.0000.000
82A82THR0-0.042-0.02224.8470.0040.0040.0000.0000.0000.000
83A83ASP-1-0.798-0.87420.341-0.131-0.1310.0000.0000.0000.000
84A84GLN0-0.069-0.03021.3270.0000.0000.0000.0000.0000.000
85A85VAL0-0.013-0.00218.266-0.004-0.0040.0000.0000.0000.000
86A86SER00.0630.03919.4280.0010.0010.0000.0000.0000.000
87A87VAL0-0.004-0.01016.169-0.003-0.0030.0000.0000.0000.000
88A88ILE00.0040.01016.718-0.018-0.0180.0000.0000.0000.000
89A89THR0-0.003-0.01412.4870.0230.0230.0000.0000.0000.000
90A90ILE00.020-0.00115.144-0.009-0.0090.0000.0000.0000.000
91A91ALA00.0150.00012.9410.0390.0390.0000.0000.0000.000
92A92GLY00.0300.02514.922-0.029-0.0290.0000.0000.0000.000
93A93MET0-0.0170.00015.8760.0240.0240.0000.0000.0000.000
94A94GLY00.0110.01419.2620.0110.0110.0000.0000.0000.000
95A95GLY00.0950.03622.935-0.008-0.0080.0000.0000.0000.000
96A96ARG10.8860.92124.3980.1170.1170.0000.0000.0000.000
97A97LEU0-0.024-0.00521.2870.0080.0080.0000.0000.0000.000
98A98ILE00.0130.00619.517-0.003-0.0030.0000.0000.0000.000
99A99ALA00.0410.01922.8080.0030.0030.0000.0000.0000.000
100A100ARG10.7870.87825.9450.1520.1520.0000.0000.0000.000
101A101ILE0-0.012-0.01020.1970.0040.0040.0000.0000.0000.000
102A102LEU0-0.005-0.00222.3040.0030.0030.0000.0000.0000.000
103A103GLU-1-0.856-0.92825.205-0.105-0.1050.0000.0000.0000.000
104A104GLU-1-0.836-0.90626.651-0.137-0.1370.0000.0000.0000.000
105A105GLY0-0.0110.00325.6780.0050.0050.0000.0000.0000.000
106A106LEU00.0300.01526.7380.0000.0000.0000.0000.0000.000
107A107GLY0-0.059-0.04328.9130.0020.0020.0000.0000.0000.000
108A108LYS10.7910.88524.9890.1410.1410.0000.0000.0000.000
109A109LEU00.005-0.00123.542-0.006-0.0060.0000.0000.0000.000
110A110ALA0-0.028-0.00226.504-0.002-0.0020.0000.0000.0000.000
111A111ASN0-0.030-0.01227.0270.0050.0050.0000.0000.0000.000
112A112VAL0-0.053-0.00621.323-0.006-0.0060.0000.0000.0000.000
113A113GLU-1-0.940-0.96322.318-0.147-0.1470.0000.0000.0000.000
114A114ARG10.7880.86818.9730.2050.2050.0000.0000.0000.000
115A115LEU0-0.026-0.00419.637-0.021-0.0210.0000.0000.0000.000
116A116ILE0-0.040-0.02315.2490.0120.0120.0000.0000.0000.000
117A117LEU00.016-0.00117.022-0.040-0.0400.0000.0000.0000.000
118A118GLN00.0080.01614.958-0.009-0.0090.0000.0000.0000.000
119A119PRO00.0190.02117.874-0.024-0.0240.0000.0000.0000.000
120A120ASN0-0.068-0.05818.051-0.009-0.0090.0000.0000.0000.000
121A121ASN0-0.013-0.01620.7150.0170.0170.0000.0000.0000.000
122A122ARG10.7380.84424.5110.1020.1020.0000.0000.0000.000
123A123GLU-1-0.731-0.85724.117-0.139-0.1390.0000.0000.0000.000
124A124ASP-1-0.730-0.85426.418-0.108-0.1080.0000.0000.0000.000
125A125ASP-1-0.773-0.86529.576-0.108-0.1080.0000.0000.0000.000
126A126LEU0-0.020-0.01423.1530.0000.0000.0000.0000.0000.000
127A127ARG10.8060.90025.8010.1280.1280.0000.0000.0000.000
128A128ILE0-0.027-0.00529.1750.0040.0040.0000.0000.0000.000
129A129TRP0-0.047-0.03027.247-0.001-0.0010.0000.0000.0000.000
130A130LEU00.004-0.01025.0940.0020.0020.0000.0000.0000.000
131A131GLN00.0300.01729.4130.0080.0080.0000.0000.0000.000
132A132ASP-1-0.934-0.96332.608-0.082-0.0820.0000.0000.0000.000
133A133HIS10.7800.89430.9700.1120.1120.0000.0000.0000.000
134A134GLY0-0.0010.01731.791-0.003-0.0030.0000.0000.0000.000
135A135PHE0-0.0200.00026.800-0.004-0.0040.0000.0000.0000.000
136A136GLN0-0.024-0.02728.8050.0100.0100.0000.0000.0000.000
137A137ILE0-0.005-0.01825.150-0.009-0.0090.0000.0000.0000.000
138A138VAL0-0.006-0.00623.9640.0110.0110.0000.0000.0000.000
139A139ALA00.0150.00422.1260.0050.0050.0000.0000.0000.000
140A140GLU-1-0.741-0.86922.029-0.138-0.1380.0000.0000.0000.000
141A141SER0-0.039-0.01818.2660.0100.0100.0000.0000.0000.000
142A142ILE00.0210.01519.738-0.018-0.0180.0000.0000.0000.000
143A143LEU0-0.0290.00613.7940.0200.0200.0000.0000.0000.000
144A144GLU-1-0.831-0.93017.665-0.035-0.0350.0000.0000.0000.000
145A145GLU-1-0.892-0.97311.184-0.199-0.1990.0000.0000.0000.000
146A146ALA0-0.003-0.00114.656-0.024-0.0240.0000.0000.0000.000
147A147GLY00.0390.02616.458-0.013-0.0130.0000.0000.0000.000
148A148LYS10.8900.95518.2410.1280.1280.0000.0000.0000.000
149A149PHE00.0610.02718.7000.0020.0020.0000.0000.0000.000
150A150TYR0-0.044-0.02816.252-0.027-0.0270.0000.0000.0000.000
151A151GLU-1-0.757-0.85018.844-0.123-0.1230.0000.0000.0000.000
152A152ILE0-0.002-0.01314.837-0.034-0.0340.0000.0000.0000.000
153A153LEU0-0.014-0.01419.0920.0260.0260.0000.0000.0000.000
154A154VAL00.0120.01419.060-0.030-0.0300.0000.0000.0000.000
155A155VAL0-0.019-0.01221.4480.0230.0230.0000.0000.0000.000
156A156GLU-1-0.757-0.86323.355-0.164-0.1640.0000.0000.0000.000
157A157ALA00.0430.02925.9540.0060.0060.0000.0000.0000.000
158A158GLY00.002-0.01129.2090.0050.0050.0000.0000.0000.000
159A159GLN0-0.038-0.01632.280-0.001-0.0010.0000.0000.0000.000
160A160MET00.0310.04030.076-0.002-0.0020.0000.0000.0000.000
161A161LYS10.8480.90134.3790.0730.0730.0000.0000.0000.000
162A162LEU0-0.0140.01730.9120.0020.0020.0000.0000.0000.000
163A163SER00.000-0.02235.5990.0030.0030.0000.0000.0000.000
164A164ALA00.046-0.00536.036-0.005-0.0050.0000.0000.0000.000
165A165SER00.0580.02535.296-0.003-0.0030.0000.0000.0000.000
166A166ASP-1-0.788-0.87132.639-0.075-0.0750.0000.0000.0000.000
167A167VAL0-0.047-0.01631.405-0.008-0.0080.0000.0000.0000.000
168A168ARG10.7640.85827.9260.0960.0960.0000.0000.0000.000
169A169PHE0-0.009-0.00529.804-0.005-0.0050.0000.0000.0000.000
170A170GLY00.0700.04327.774-0.004-0.0040.0000.0000.0000.000
171A171PRO0-0.0350.00428.5520.0070.0070.0000.0000.0000.000
172A172PHE0-0.028-0.02225.9980.0060.0060.0000.0000.0000.000
173A173LEU0-0.022-0.02222.8140.0060.0060.0000.0000.0000.000
174A174SER0-0.020-0.02126.7600.0100.0100.0000.0000.0000.000
175A175LYS10.9390.97629.8680.0630.0630.0000.0000.0000.000
176A176GLU-1-0.884-0.91823.950-0.073-0.0730.0000.0000.0000.000
177A177VAL0-0.0090.00528.3960.0070.0070.0000.0000.0000.000
178A178SER0-0.035-0.03923.8470.0090.0090.0000.0000.0000.000
179A179PRO00.017-0.01624.1740.0000.0000.0000.0000.0000.000
180A180VAL00.0010.00420.1930.0010.0010.0000.0000.0000.000
181A181PHE00.0280.02423.546-0.006-0.0060.0000.0000.0000.000
182A182VAL00.0310.01225.8800.0000.0000.0000.0000.0000.000
183A183GLN0-0.082-0.03722.7020.0020.0020.0000.0000.0000.000
184A184LYS10.7830.88423.7580.1210.1210.0000.0000.0000.000
185A185TRP00.031-0.00126.393-0.001-0.0010.0000.0000.0000.000
186A186GLN00.0570.04029.9460.0000.0000.0000.0000.0000.000
187A187LYS10.8580.92026.6490.0390.0390.0000.0000.0000.000
188A188GLU-1-0.865-0.91829.426-0.077-0.0770.0000.0000.0000.000
189A189ALA00.0370.01031.2070.0010.0010.0000.0000.0000.000
190A190GLU-1-0.825-0.89431.571-0.031-0.0310.0000.0000.0000.000
191A191LYS10.7800.87027.4680.0780.0780.0000.0000.0000.000
192A192LEU0-0.026-0.01734.1290.0010.0010.0000.0000.0000.000
193A193GLU-1-0.830-0.91536.750-0.031-0.0310.0000.0000.0000.000
194A194PHE0-0.0330.00236.9060.0030.0030.0000.0000.0000.000
195A195ALA0-0.052-0.03137.4590.0010.0010.0000.0000.0000.000
196A196LEU0-0.002-0.02139.3900.0010.0010.0000.0000.0000.000
197A197GLY0-0.0010.00141.6810.0020.0020.0000.0000.0000.000
198A198GLN0-0.080-0.03839.1010.0020.0020.0000.0000.0000.000
199A199ILE00.0100.02542.9200.0020.0020.0000.0000.0000.000
200A200PRO0-0.0160.05145.5580.0000.0000.0000.0000.0000.000
201A201GLU-1-0.812-0.95149.106-0.027-0.0270.0000.0000.0000.000
202A202LYS10.8230.89851.3120.0250.0250.0000.0000.0000.000
203A203ASN00.0180.00248.4820.0000.0000.0000.0000.0000.000
204A204LEU00.0400.02449.578-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.860-0.94348.599-0.035-0.0350.0000.0000.0000.000
206A206GLU-1-0.925-0.94544.643-0.044-0.0440.0000.0000.0000.000
207A207ARG10.8360.89444.3210.0290.0290.0000.0000.0000.000
208A208GLN0-0.064-0.03244.5640.0010.0010.0000.0000.0000.000
209A209VAL00.0330.01940.250-0.002-0.0020.0000.0000.0000.000
210A210LEU0-0.046-0.03439.132-0.003-0.0030.0000.0000.0000.000
211A211VAL00.0090.01040.3620.0000.0000.0000.0000.0000.000
212A212ASP-1-0.835-0.90941.908-0.044-0.0440.0000.0000.0000.000
213A213LYS10.8670.93736.2670.0630.0630.0000.0000.0000.000
214A214ILE00.0090.01037.286-0.002-0.0020.0000.0000.0000.000
215A215GLN0-0.039-0.02538.7230.0020.0020.0000.0000.0000.000
216A216ALA00.0200.02837.3160.0000.0000.0000.0000.0000.000
217A217ILE0-0.038-0.02133.415-0.001-0.0010.0000.0000.0000.000
218A218LYS10.8380.89935.7750.0350.0350.0000.0000.0000.000
219A219GLU-1-0.903-0.95638.235-0.040-0.0400.0000.0000.0000.000
220A220VAL0-0.069-0.02532.9820.0010.0010.0000.0000.0000.000
221A221LEU0-0.041-0.02331.239-0.001-0.0010.0000.0000.0000.000
222A222HIS0-0.070-0.00934.7730.0040.0040.0000.0000.0000.000