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

tag_button

FMODB ID: GNJ11

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:

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. 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 -2564140.169567
FMO2-HF: Nuclear repulsion 2479218.951664
FMO2-HF: Total energy -84921.217903
FMO2-MP2: Total energy -85174.200947


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.
-15.488-4.8865.632-4.895-11.34-0.024
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 : -0.011
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].
3A3SER00.0270.0123.7750.7362.731-0.036-0.971-0.9880.002
4A4LYS10.9720.9976.935-0.074-0.0740.0000.0000.0000.000
5A5ARG10.8690.9459.7370.3050.3050.0000.0000.0000.000
6A6LEU00.017-0.0057.0910.0540.0540.0000.0000.0000.000
7A7GLU-1-0.831-0.8895.499-0.723-0.7230.0000.0000.0000.000
8A8LEU00.003-0.0128.5290.0670.0670.0000.0000.0000.000
9A9VAL0-0.0180.00911.2820.0370.0370.0000.0000.0000.000
10A10ALA00.0310.0048.9480.0700.0700.0000.0000.0000.000
11A11SER0-0.081-0.04011.0580.0730.0730.0000.0000.0000.000
12A12PHE0-0.006-0.00313.3050.0580.0580.0000.0000.0000.000
13A13VAL0-0.052-0.01712.0610.0440.0440.0000.0000.0000.000
14A14SER00.0450.03014.902-0.018-0.0180.0000.0000.0000.000
15A15GLN00.0250.00515.580-0.027-0.0270.0000.0000.0000.000
16A16GLY0-0.058-0.03916.2170.0220.0220.0000.0000.0000.000
17A17ALA0-0.0040.01515.7630.0220.0220.0000.0000.0000.000
18A18ILE0-0.0020.01116.1710.0120.0120.0000.0000.0000.000
19A19LEU0-0.012-0.00910.636-0.011-0.0110.0000.0000.0000.000
20A20LEU00.0010.00014.5850.0410.0410.0000.0000.0000.000
21A21ASP-1-0.777-0.8619.542-0.564-0.5640.0000.0000.0000.000
22A22VAL0-0.009-0.03112.8390.0450.0450.0000.0000.0000.000
23A23GLY0-0.041-0.01514.417-0.029-0.0290.0000.0000.0000.000
24A24SER0-0.036-0.0169.000-0.028-0.0280.0000.0000.0000.000
25A25ASP-1-0.855-0.8927.822-0.891-0.8910.0000.0000.0000.000
26A26HIS10.8280.8875.7410.3610.3610.0000.0000.0000.000
27A27ALA00.0570.0276.0960.4030.4030.0000.0000.0000.000
28A28TYR0-0.018-0.0162.115-3.244-0.8363.160-1.249-4.319-0.007
29A29LEU00.0640.0403.147-1.800-0.8610.112-0.243-0.808-0.005
30A30PRO00.0170.0025.393-0.0660.024-0.001-0.007-0.0820.000
31A31ILE0-0.033-0.0193.298-0.796-0.0860.945-0.322-1.334-0.001
32A32GLU-1-0.811-0.9062.693-8.774-5.8870.318-1.420-1.785-0.013
33A33LEU0-0.017-0.0094.2340.3540.4680.001-0.024-0.0920.000
34A34VAL0-0.051-0.0317.9490.1260.1260.0000.0000.0000.000
35A35GLU-1-0.872-0.9164.8112.3452.7020.004-0.074-0.2870.000
36A36ARG10.7270.8536.1451.2551.2550.0000.0000.0000.000
37A37GLY0-0.0150.0049.4440.0410.0410.0000.0000.0000.000
38A38GLN0-0.004-0.00310.804-0.060-0.0600.0000.0000.0000.000
39A39ILE0-0.016-0.00410.8770.0240.0240.0000.0000.0000.000
40A40LYS10.9400.98513.642-0.027-0.0270.0000.0000.0000.000
41A41SER0-0.057-0.06513.7580.0510.0510.0000.0000.0000.000
42A42ALA00.0070.01711.471-0.052-0.0520.0000.0000.0000.000
43A43ILE0-0.0140.00813.5840.0600.0600.0000.0000.0000.000
44A44ALA00.0190.01510.707-0.051-0.0510.0000.0000.0000.000
45A45GLY00.0110.00112.7540.0370.0370.0000.0000.0000.000
46A46GLH0-0.080-0.10211.536-0.039-0.0390.0000.0000.0000.000
47A47VAL00.0500.02816.2040.0200.0200.0000.0000.0000.000
48A48VAL0-0.019-0.00517.4410.0120.0120.0000.0000.0000.000
49A49GLU-1-0.842-0.93117.1980.0000.0000.0000.0000.0000.000
50A50GLY00.001-0.00216.1820.0150.0150.0000.0000.0000.000
51A51PRO00.009-0.01112.5450.0160.0160.0000.0000.0000.000
52A52TYR00.0540.02312.3470.0290.0290.0000.0000.0000.000
53A53GLN00.0260.01413.5700.0680.0680.0000.0000.0000.000
54A54SER0-0.057-0.0038.6540.0040.0040.0000.0000.0000.000
55A55ALA00.0210.0198.8080.1110.1110.0000.0000.0000.000
56A56VAL00.0440.0199.4210.1770.1770.0000.0000.0000.000
57A57LYS10.9320.9649.874-0.055-0.0550.0000.0000.0000.000
58A58ASN0-0.019-0.0124.709-0.0600.042-0.001-0.005-0.0950.000
59A59VAL00.0460.0296.1670.4500.4500.0000.0000.0000.000
60A60GLU-1-0.980-1.0098.3500.2950.2950.0000.0000.0000.000
61A61ALA0-0.059-0.0266.309-0.034-0.0340.0000.0000.0000.000
62A62HIS10.7980.8712.366-4.660-3.6601.130-0.580-1.5500.000
63A63GLY00.0110.0307.310-0.106-0.1060.0000.0000.0000.000
64A64LEU0-0.014-0.0137.148-0.129-0.1290.0000.0000.0000.000
65A65LYS10.9820.98611.118-0.392-0.3920.0000.0000.0000.000
66A66GLU-1-0.925-0.95313.8690.1370.1370.0000.0000.0000.000
67A67LYS10.8340.91912.270-0.240-0.2400.0000.0000.0000.000
68A68ILE00.0180.0168.521-0.038-0.0380.0000.0000.0000.000
69A69GLN00.0300.03212.6010.0270.0270.0000.0000.0000.000
70A70VAL00.0080.00711.976-0.019-0.0190.0000.0000.0000.000
71A71ARG10.7470.84914.911-0.021-0.0210.0000.0000.0000.000
72A72LEU00.0040.01417.515-0.020-0.0200.0000.0000.0000.000
73A73ALA00.014-0.01119.6960.0040.0040.0000.0000.0000.000
74A74ASN00.005-0.01020.090-0.023-0.0230.0000.0000.0000.000
75A75GLY00.0180.01020.0580.0060.0060.0000.0000.0000.000
76A76LEU00.0620.03020.2690.0020.0020.0000.0000.0000.000
77A77ALA0-0.049-0.01922.2660.0090.0090.0000.0000.0000.000
78A78ALA0-0.039-0.00718.3120.0100.0100.0000.0000.0000.000
79A79PHE00.008-0.00719.9990.0110.0110.0000.0000.0000.000
80A80GLU-1-0.861-0.92121.871-0.026-0.0260.0000.0000.0000.000
81A81GLU-1-0.864-0.93824.381-0.041-0.0410.0000.0000.0000.000
82A82THR0-0.038-0.02025.4820.0010.0010.0000.0000.0000.000
83A83ASP-1-0.807-0.89420.8210.0070.0070.0000.0000.0000.000
84A84GLN0-0.055-0.02421.687-0.002-0.0020.0000.0000.0000.000
85A85VAL0-0.024-0.01218.391-0.003-0.0030.0000.0000.0000.000
86A86SER00.0710.04519.392-0.002-0.0020.0000.0000.0000.000
87A87VAL00.000-0.00615.935-0.012-0.0120.0000.0000.0000.000
88A88ILE00.0000.01016.4900.0030.0030.0000.0000.0000.000
89A89THR0-0.004-0.00112.2610.0020.0020.0000.0000.0000.000
90A90ILE00.0320.00514.8660.0130.0130.0000.0000.0000.000
91A91ALA00.047-0.03512.5330.0140.0140.0000.0000.0000.000
92A92GLY00.004-0.01514.468-0.011-0.0110.0000.0000.0000.000
93A93MET0-0.0240.01215.3730.0230.0230.0000.0000.0000.000
94A94GLY0-0.0020.00718.8370.0030.0030.0000.0000.0000.000
95A95GLY00.1010.04122.421-0.002-0.0020.0000.0000.0000.000
96A96ARG10.9100.94923.9310.0840.0840.0000.0000.0000.000
97A97LEU0-0.044-0.01020.7480.0070.0070.0000.0000.0000.000
98A98ILE00.0240.00818.9740.0030.0030.0000.0000.0000.000
99A99ALA00.0460.02422.4270.0050.0050.0000.0000.0000.000
100A100ARG10.9480.97625.9120.0820.0820.0000.0000.0000.000
101A101ILE0-0.011-0.00919.8870.0060.0060.0000.0000.0000.000
102A102LEU0-0.008-0.00922.1530.0050.0050.0000.0000.0000.000
103A103GLU-1-0.919-0.97025.006-0.056-0.0560.0000.0000.0000.000
104A104GLU-1-0.979-0.99526.853-0.060-0.0600.0000.0000.0000.000
105A105GLY0-0.020-0.00625.8560.0060.0060.0000.0000.0000.000
106A106LEU00.0250.00726.9000.0000.0000.0000.0000.0000.000
107A107GLY0-0.061-0.04328.8380.0000.0000.0000.0000.0000.000
108A108LYS10.8600.93325.0590.0480.0480.0000.0000.0000.000
109A109LEU0-0.017-0.01123.518-0.003-0.0030.0000.0000.0000.000
110A110ALA0-0.0210.00326.304-0.003-0.0030.0000.0000.0000.000
111A111ASN0-0.006-0.00326.959-0.002-0.0020.0000.0000.0000.000
112A112VAL0-0.059-0.01021.203-0.002-0.0020.0000.0000.0000.000
113A113GLU-1-0.951-0.97022.440-0.094-0.0940.0000.0000.0000.000
114A114ARG10.8110.88919.0890.1580.1580.0000.0000.0000.000
115A115LEU0-0.021-0.00319.464-0.009-0.0090.0000.0000.0000.000
116A116ILE0-0.044-0.01915.1130.0020.0020.0000.0000.0000.000
117A117LEU00.013-0.00616.765-0.024-0.0240.0000.0000.0000.000
118A118GLN00.0110.09014.571-0.046-0.0460.0000.0000.0000.000
119A119PRO00.0150.02517.495-0.019-0.0190.0000.0000.0000.000
120A120ASN0-0.029-0.04717.483-0.012-0.0120.0000.0000.0000.000
121A121ASN0-0.007-0.00920.5500.0150.0150.0000.0000.0000.000
122A122ARG10.7800.86924.3390.0810.0810.0000.0000.0000.000
123A123GLU-1-0.799-0.91423.694-0.119-0.1190.0000.0000.0000.000
124A124ASP-1-0.819-0.88526.063-0.080-0.0800.0000.0000.0000.000
125A125ASP-1-0.813-0.92129.313-0.077-0.0770.0000.0000.0000.000
126A126LEU0-0.025-0.01322.7060.0010.0010.0000.0000.0000.000
127A127ARG10.8020.89725.7330.1050.1050.0000.0000.0000.000
128A128ILE0-0.0190.00128.8850.0040.0040.0000.0000.0000.000
129A129TRP0-0.0110.00527.0030.0000.0000.0000.0000.0000.000
130A130LEU00.001-0.01724.9450.0030.0030.0000.0000.0000.000
131A131GLN00.0690.04529.1240.0030.0030.0000.0000.0000.000
132A132ASP-1-0.969-0.98932.361-0.055-0.0550.0000.0000.0000.000
133A133HIS10.7740.89330.5620.0680.0680.0000.0000.0000.000
134A134GLY00.0010.01331.527-0.001-0.0010.0000.0000.0000.000
135A135PHE0-0.0100.00726.788-0.002-0.0020.0000.0000.0000.000
136A136GLN0-0.019-0.01428.6750.0050.0050.0000.0000.0000.000
137A137ILE0-0.009-0.02025.134-0.007-0.0070.0000.0000.0000.000
138A138VAL0-0.008-0.00524.0370.0080.0080.0000.0000.0000.000
139A139ALA0-0.001-0.00522.0960.0020.0020.0000.0000.0000.000
140A140GLU-1-0.750-0.87522.012-0.111-0.1110.0000.0000.0000.000
141A141SER0-0.039-0.01818.1410.0020.0020.0000.0000.0000.000
142A142ILE00.0220.02119.705-0.013-0.0130.0000.0000.0000.000
143A143LEU0-0.040-0.00113.6630.0170.0170.0000.0000.0000.000
144A144GLU-1-0.867-0.95317.704-0.057-0.0570.0000.0000.0000.000
145A145GLU-1-0.920-1.00311.283-0.267-0.2670.0000.0000.0000.000
146A146ALA0-0.007-0.00314.721-0.017-0.0170.0000.0000.0000.000
147A147GLY00.0250.02616.474-0.008-0.0080.0000.0000.0000.000
148A148LYS10.8890.94718.3740.1250.1250.0000.0000.0000.000
149A149PHE00.0500.02318.715-0.001-0.0010.0000.0000.0000.000
150A150TYR0-0.028-0.01816.231-0.021-0.0210.0000.0000.0000.000
151A151GLU-1-0.755-0.85318.844-0.111-0.1110.0000.0000.0000.000
152A152ILE0-0.014-0.02114.798-0.026-0.0260.0000.0000.0000.000
153A153LEU0-0.010-0.01718.9220.0200.0200.0000.0000.0000.000
154A154VAL00.0140.01519.114-0.020-0.0200.0000.0000.0000.000
155A155VAL0-0.021-0.00721.3690.0170.0170.0000.0000.0000.000
156A156GLU-1-0.778-0.88823.264-0.119-0.1190.0000.0000.0000.000
157A157ALA00.0320.02525.8810.0030.0030.0000.0000.0000.000
158A158GLY0-0.002-0.01929.1020.0020.0020.0000.0000.0000.000
159A159GLN0-0.041-0.01832.146-0.001-0.0010.0000.0000.0000.000
160A160MET00.0320.04530.412-0.002-0.0020.0000.0000.0000.000
161A161LYS10.8740.92134.2540.0490.0490.0000.0000.0000.000
162A162LEU00.0340.01230.8080.0010.0010.0000.0000.0000.000
163A163SER00.0520.03735.4300.0020.0020.0000.0000.0000.000
164A164ALA00.0530.00435.833-0.003-0.0030.0000.0000.0000.000
165A165SER00.0530.01735.110-0.002-0.0020.0000.0000.0000.000
166A166ASP-1-0.851-0.93032.587-0.064-0.0640.0000.0000.0000.000
167A167VAL0-0.057-0.01831.255-0.006-0.0060.0000.0000.0000.000
168A168ARG10.8340.90128.4720.0750.0750.0000.0000.0000.000
169A169PHE00.0090.00429.767-0.005-0.0050.0000.0000.0000.000
170A170GLY00.0660.04027.736-0.005-0.0050.0000.0000.0000.000
171A171PRO0-0.041-0.00528.4300.0050.0050.0000.0000.0000.000
172A172PHE0-0.023-0.02625.8890.0040.0040.0000.0000.0000.000
173A173LEU0-0.020-0.03122.7360.0030.0030.0000.0000.0000.000
174A174SER00.014-0.00226.7210.0070.0070.0000.0000.0000.000
175A175LYS10.9540.98229.8310.0600.0600.0000.0000.0000.000
176A176GLU-1-0.955-0.94824.071-0.079-0.0790.0000.0000.0000.000
177A177VAL00.0130.01128.3580.0050.0050.0000.0000.0000.000
178A178SER0-0.028-0.01723.8520.0060.0060.0000.0000.0000.000
179A179PRO00.028-0.01024.2560.0000.0000.0000.0000.0000.000
180A180VAL00.0100.00720.0800.0010.0010.0000.0000.0000.000
181A181PHE00.0040.01423.504-0.004-0.0040.0000.0000.0000.000
182A182VAL00.0360.01625.8390.0010.0010.0000.0000.0000.000
183A183GLN0-0.055-0.02122.8710.0040.0040.0000.0000.0000.000
184A184LYS10.8140.91024.1030.1050.1050.0000.0000.0000.000
185A185TRP00.0360.00226.3930.0010.0010.0000.0000.0000.000
186A186GLN00.0800.04129.9460.0000.0000.0000.0000.0000.000
187A187LYS10.9640.98726.4180.0520.0520.0000.0000.0000.000
188A188GLU-1-0.978-0.99429.677-0.066-0.0660.0000.0000.0000.000
189A189ALA00.0240.00631.2200.0020.0020.0000.0000.0000.000
190A190GLU-1-0.905-0.94532.191-0.036-0.0360.0000.0000.0000.000
191A191LYS10.8830.93727.2710.0700.0700.0000.0000.0000.000
192A192LEU0-0.025-0.01434.1410.0020.0020.0000.0000.0000.000
193A193GLU-1-0.878-0.95836.761-0.031-0.0310.0000.0000.0000.000
194A194PHE0-0.045-0.00336.9500.0020.0020.0000.0000.0000.000
195A195ALA0-0.043-0.02537.5260.0010.0010.0000.0000.0000.000
196A196LEU0-0.005-0.03739.3990.0010.0010.0000.0000.0000.000
197A197GLY0-0.0050.00041.6910.0020.0020.0000.0000.0000.000
198A198GLN0-0.076-0.03739.2170.0010.0010.0000.0000.0000.000
199A199ILE00.0320.03942.8710.0020.0020.0000.0000.0000.000
200A200PRO0-0.0370.04545.5650.0000.0000.0000.0000.0000.000
201A201GLU-1-0.900-0.99549.114-0.023-0.0230.0000.0000.0000.000
202A202LYS10.8350.90551.3200.0210.0210.0000.0000.0000.000
203A203ASN00.0610.02748.4000.0000.0000.0000.0000.0000.000
204A204LEU00.0250.01649.584-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.890-0.94648.599-0.027-0.0270.0000.0000.0000.000
206A206GLU-1-0.931-0.96644.499-0.035-0.0350.0000.0000.0000.000
207A207ARG10.9310.94544.3280.0260.0260.0000.0000.0000.000
208A208GLN0-0.050-0.02544.5710.0000.0000.0000.0000.0000.000
209A209VAL00.0200.02040.376-0.002-0.0020.0000.0000.0000.000
210A210LEU0-0.037-0.03439.297-0.003-0.0030.0000.0000.0000.000
211A211VAL00.0030.01340.362-0.001-0.0010.0000.0000.0000.000
212A212ASP-1-0.841-0.92142.050-0.036-0.0360.0000.0000.0000.000
213A213LYS10.8630.93435.7890.0520.0520.0000.0000.0000.000
214A214ILE00.0180.01737.286-0.002-0.0020.0000.0000.0000.000
215A215GLN00.006-0.00138.7230.0000.0000.0000.0000.0000.000
216A216ALA00.0290.03237.2190.0000.0000.0000.0000.0000.000
217A217ILE0-0.042-0.02433.438-0.001-0.0010.0000.0000.0000.000
218A218LYS10.8790.94135.7330.0330.0330.0000.0000.0000.000
219A219GLU-1-0.963-0.98938.193-0.036-0.0360.0000.0000.0000.000
220A220VAL0-0.066-0.02332.9150.0000.0000.0000.0000.0000.000
221A221LEU0-0.047-0.01831.344-0.002-0.0020.0000.0000.0000.000
222A222HIS0-0.077-0.01534.7320.0020.0020.0000.0000.0000.000