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: 98KK2

Calculation Name: 3L7N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DTU5

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:

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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3060998.09048
FMO2-HF: Nuclear repulsion 2967442.708531
FMO2-HF: Total energy -93555.381949
FMO2-MP2: Total energy -93824.614764


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.
-7.7350.4367.434-7.208-8.397-0.039
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 : 0.059 / q_NPA : 0.031
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].
3A3ILE00.0210.0163.343-0.6431.0660.007-0.759-0.9570.003
4A4HIS00.0190.0195.4560.7000.7000.0000.0000.0000.000
5A5PHE00.012-0.0109.0920.1280.1280.0000.0000.0000.000
6A6ILE0-0.013-0.00711.9380.0460.0460.0000.0000.0000.000
7A7LEU00.000-0.01815.1370.0290.0290.0000.0000.0000.000
8A8HIS10.7670.83918.0450.2600.2600.0000.0000.0000.000
9A9GLU-1-0.794-0.92121.555-0.120-0.1200.0000.0000.0000.000
10A10THR0-0.136-0.05021.905-0.012-0.0120.0000.0000.0000.000
11A11PHE00.0630.01722.939-0.004-0.0040.0000.0000.0000.000
12A12GLU-1-0.892-0.92520.932-0.140-0.1400.0000.0000.0000.000
13A13ALA0-0.048-0.02418.890-0.034-0.0340.0000.0000.0000.000
14A14PRO00.014-0.00313.6500.0040.0040.0000.0000.0000.000
15A15GLY00.0350.00314.8780.0030.0030.0000.0000.0000.000
16A16ALA00.0430.00914.922-0.020-0.0200.0000.0000.0000.000
17A17TYR00.0490.03210.9370.0150.0150.0000.0000.0000.000
18A18LEU0-0.037-0.01110.159-0.068-0.0680.0000.0000.0000.000
19A19ALA00.0220.00510.9010.0150.0150.0000.0000.0000.000
20A20TRP0-0.0100.0035.094-0.015-0.0150.0000.0000.0000.000
21A21ALA00.013-0.0026.9670.1240.1240.0000.0000.0000.000
22A22ALA0-0.026-0.0157.0160.1880.1880.0000.0000.0000.000
23A23LEU0-0.068-0.0389.3610.1640.1640.0000.0000.0000.000
24A24ARG10.7370.8526.577-0.333-0.3330.0000.0000.0000.000
25A25GLY0-0.0050.0135.1830.2350.371-0.001-0.009-0.1260.000
26A26HIS0-0.011-0.0032.305-0.9671.0066.837-4.119-4.692-0.029
27A27ASP-1-0.961-0.9883.550-1.931-0.6540.006-0.586-0.6960.002
28A28VAL00.0160.0055.623-0.701-0.7010.0000.0000.0000.000
29A29SER0-0.0080.0058.1850.2960.2960.0000.0000.0000.000
30A30MET0-0.048-0.04010.984-0.006-0.0060.0000.0000.0000.000
31A31THR0-0.0020.00513.8280.0490.0490.0000.0000.0000.000
32A32LYS10.9110.93916.8580.2670.2670.0000.0000.0000.000
33A33VAL00.0480.02519.7040.0290.0290.0000.0000.0000.000
34A34TYR00.0700.04020.6820.0210.0210.0000.0000.0000.000
35A35ARG10.8450.92522.6550.1780.1780.0000.0000.0000.000
36A36TYR0-0.059-0.03925.0810.0060.0060.0000.0000.0000.000
37A37GLU-1-0.879-0.91119.471-0.283-0.2830.0000.0000.0000.000
38A38LYS10.9100.93821.3410.1880.1880.0000.0000.0000.000
39A39LEU00.0630.02717.673-0.023-0.0230.0000.0000.0000.000
40A40PRO00.0240.03213.7530.0430.0430.0000.0000.0000.000
41A41LYS10.9230.94816.2980.2870.2870.0000.0000.0000.000
42A42ASP-1-0.916-0.93914.697-0.307-0.3070.0000.0000.0000.000
43A43ILE0-0.089-0.05111.802-0.068-0.0680.0000.0000.0000.000
44A44ASP-1-0.881-0.95010.396-0.534-0.5340.0000.0000.0000.000
45A45ASP-1-0.924-0.9579.900-0.664-0.6640.0000.0000.0000.000
46A46PHE0-0.043-0.0256.463-0.119-0.1190.0000.0000.0000.000
47A47ASP-1-0.822-0.9042.561-6.721-3.8300.586-1.724-1.753-0.015
48A48MET0-0.033-0.0194.5050.5660.751-0.001-0.011-0.1730.000
49A49LEU0-0.0400.0045.998-0.171-0.1710.0000.0000.0000.000
50A50ILE00.0070.0047.7460.1610.1610.0000.0000.0000.000
51A51LEU0-0.038-0.02311.066-0.007-0.0070.0000.0000.0000.000
52A52MET00.0460.01413.3940.0430.0430.0000.0000.0000.000
53A53GLY00.0750.04016.9570.0050.0050.0000.0000.0000.000
54A54GLY0-0.001-0.02520.700-0.022-0.0220.0000.0000.0000.000
55A55PRO00.0280.04223.6630.0080.0080.0000.0000.0000.000
56A56GLN0-0.040-0.01225.1310.0040.0040.0000.0000.0000.000
57A57SER00.1440.07426.767-0.003-0.0030.0000.0000.0000.000
58A58PRO0-0.041-0.03224.916-0.008-0.0080.0000.0000.0000.000
59A59SER0-0.046-0.02526.6440.0020.0020.0000.0000.0000.000
60A60SER00.0270.04228.9570.0030.0030.0000.0000.0000.000
61A61THR0-0.0100.00730.140-0.009-0.0090.0000.0000.0000.000
62A62LYS10.9070.93828.1920.1430.1430.0000.0000.0000.000
63A63LYS10.9150.95132.2310.0770.0770.0000.0000.0000.000
64A64GLU-1-0.831-0.92132.902-0.090-0.0900.0000.0000.0000.000
65A65PHE00.0440.03328.818-0.002-0.0020.0000.0000.0000.000
66A66PRO0-0.028-0.01529.790-0.009-0.0090.0000.0000.0000.000
67A67TYR0-0.039-0.01525.158-0.003-0.0030.0000.0000.0000.000
68A68TYR0-0.048-0.02023.443-0.022-0.0220.0000.0000.0000.000
69A69ASP-1-0.888-0.96924.590-0.155-0.1550.0000.0000.0000.000
70A70ALA00.1180.05823.872-0.017-0.0170.0000.0000.0000.000
71A71GLN0-0.0010.00423.666-0.014-0.0140.0000.0000.0000.000
72A72ALA0-0.037-0.01222.190-0.008-0.0080.0000.0000.0000.000
73A73GLU-1-0.784-0.88319.395-0.289-0.2890.0000.0000.0000.000
74A74VAL00.0080.01518.903-0.026-0.0260.0000.0000.0000.000
75A75LYS10.9240.95720.0260.1520.1520.0000.0000.0000.000
76A76LEU00.0150.02014.204-0.003-0.0030.0000.0000.0000.000
77A77ILE00.0480.01815.466-0.037-0.0370.0000.0000.0000.000
78A78GLN0-0.027-0.01215.992-0.010-0.0100.0000.0000.0000.000
79A79LYS10.8040.91016.3920.3230.3230.0000.0000.0000.000
80A80ALA00.0620.02711.846-0.002-0.0020.0000.0000.0000.000
81A81ALA00.0280.00412.9800.0080.0080.0000.0000.0000.000
82A82LYS10.8760.95014.9310.2300.2300.0000.0000.0000.000
83A83SER0-0.052-0.03212.6350.0180.0180.0000.0000.0000.000
84A84GLU-1-0.967-0.98412.033-0.064-0.0640.0000.0000.0000.000
85A85LYS10.8270.9427.9700.8480.8480.0000.0000.0000.000
86A86ILE00.0550.0325.4410.1280.1280.0000.0000.0000.000
87A87ILE0-0.049-0.0288.611-0.203-0.2030.0000.0000.0000.000
88A88VAL00.0270.01210.1960.0930.0930.0000.0000.0000.000
89A89GLY0-0.0010.00412.427-0.060-0.0600.0000.0000.0000.000
90A90VAL00.006-0.00715.3350.0310.0310.0000.0000.0000.000
91A91CYM-1-0.722-0.79017.955-0.149-0.1490.0000.0000.0000.000
92A92LEU0-0.070-0.07421.684-0.007-0.0070.0000.0000.0000.000
93A93GLY0-0.019-0.02017.954-0.005-0.0050.0000.0000.0000.000
94A94ALA0-0.039-0.04518.678-0.009-0.0090.0000.0000.0000.000
95A95GLN0-0.064-0.04419.8380.0080.0080.0000.0000.0000.000
96A96LEU0-0.010-0.00120.1030.0080.0080.0000.0000.0000.000
97A97MET0-0.0160.01015.255-0.005-0.0050.0000.0000.0000.000
98A98GLY00.0410.01919.7200.0120.0120.0000.0000.0000.000
99A99VAL0-0.004-0.00123.1170.0070.0070.0000.0000.0000.000
100A100ALA0-0.059-0.02320.1800.0050.0050.0000.0000.0000.000
101A101TYR0-0.044-0.03016.9480.0010.0010.0000.0000.0000.000
102A102GLY0-0.013-0.00822.8080.0140.0140.0000.0000.0000.000
103A103ALA0-0.042-0.01726.0040.0090.0090.0000.0000.0000.000
104A104ASP-1-0.867-0.92626.941-0.105-0.1050.0000.0000.0000.000
105A105TYR0-0.098-0.05827.1550.0050.0050.0000.0000.0000.000
106A106LEU0-0.013-0.01828.7390.0060.0060.0000.0000.0000.000
107A107HIS0-0.014-0.01430.440-0.001-0.0010.0000.0000.0000.000
108A108SER0-0.047-0.03230.6700.0020.0020.0000.0000.0000.000
109A109PRO0-0.039-0.02132.3970.0020.0020.0000.0000.0000.000
110A110LYS10.8980.95134.2240.0360.0360.0000.0000.0000.000
111A111LYS10.9410.98632.4270.0530.0530.0000.0000.0000.000
112A112GLU-1-0.803-0.87029.445-0.042-0.0420.0000.0000.0000.000
113A113ILE00.0130.00529.642-0.007-0.0070.0000.0000.0000.000
114A114GLY00.0600.02829.0210.0050.0050.0000.0000.0000.000
115A115ASN0-0.024-0.02326.775-0.008-0.0080.0000.0000.0000.000
116A116TYR00.0220.00728.2550.0040.0040.0000.0000.0000.000
117A117LEU0-0.004-0.00227.899-0.001-0.0010.0000.0000.0000.000
118A118ILE0-0.057-0.01322.932-0.006-0.0060.0000.0000.0000.000
119A119SER00.040-0.01327.2700.0040.0040.0000.0000.0000.000
120A120LEU0-0.079-0.03323.100-0.005-0.0050.0000.0000.0000.000
121A121THR0-0.029-0.00726.1510.0010.0010.0000.0000.0000.000
122A122GLU-1-0.917-0.96727.1310.0170.0170.0000.0000.0000.000
123A123ALA00.004-0.00824.9700.0050.0050.0000.0000.0000.000
124A124GLY00.021-0.00722.8170.0050.0050.0000.0000.0000.000
125A125LYS10.9100.97222.947-0.009-0.0090.0000.0000.0000.000
126A126MET0-0.048-0.01624.4060.0070.0070.0000.0000.0000.000
127A127ASP-1-0.833-0.89317.9350.0580.0580.0000.0000.0000.000
128A128SER00.0560.02417.1740.0060.0060.0000.0000.0000.000
129A129TYR0-0.042-0.00813.2200.0170.0170.0000.0000.0000.000
130A130LEU00.006-0.00615.833-0.005-0.0050.0000.0000.0000.000
131A131SER0-0.030-0.03418.737-0.008-0.0080.0000.0000.0000.000
132A132ASP-1-0.873-0.92018.1610.1230.1230.0000.0000.0000.000
133A133PHE0-0.054-0.02117.172-0.012-0.0120.0000.0000.0000.000
134A134SER0-0.026-0.02922.1320.0010.0010.0000.0000.0000.000
135A135ASP-1-0.899-0.95925.5340.0190.0190.0000.0000.0000.000
136A136ASP-1-0.868-0.91627.789-0.005-0.0050.0000.0000.0000.000
137A137LEU0-0.024-0.00722.0320.0050.0050.0000.0000.0000.000
138A138LEU00.0190.00926.431-0.005-0.0050.0000.0000.0000.000
139A139VAL0-0.034-0.02122.2680.0020.0020.0000.0000.0000.000
140A140GLY00.0920.03923.3330.0010.0010.0000.0000.0000.000
141A141HIS0-0.108-0.04524.316-0.013-0.0130.0000.0000.0000.000
142A142TRP00.064-0.00125.8840.0030.0030.0000.0000.0000.000
143A143HIS10.7780.88826.4600.0620.0620.0000.0000.0000.000
144A144GLY00.0680.02328.3750.0070.0070.0000.0000.0000.000
145A145ASP-1-0.803-0.88028.620-0.077-0.0770.0000.0000.0000.000
146A146MET0-0.047-0.01326.5020.0030.0030.0000.0000.0000.000
147A147PRO00.0430.02322.888-0.001-0.0010.0000.0000.0000.000
148A148GLY00.0490.02825.6090.0110.0110.0000.0000.0000.000
149A149LEU0-0.050-0.03424.948-0.006-0.0060.0000.0000.0000.000
150A150PRO0-0.0170.00223.9880.0060.0060.0000.0000.0000.000
151A151ASP-1-0.862-0.94026.705-0.045-0.0450.0000.0000.0000.000
152A152LYS10.8250.91122.8130.0950.0950.0000.0000.0000.000
153A153ALA0-0.071-0.01322.8770.0020.0020.0000.0000.0000.000
154A154GLN0-0.005-0.00622.6790.0130.0130.0000.0000.0000.000
155A155VAL00.0500.02222.989-0.007-0.0070.0000.0000.0000.000
156A156LEU0-0.056-0.03919.2930.0080.0080.0000.0000.0000.000
157A157ALA00.0510.01323.4400.0070.0070.0000.0000.0000.000
158A158ILE0-0.0310.01925.157-0.009-0.0090.0000.0000.0000.000
159A159SER00.045-0.00628.0480.0030.0030.0000.0000.0000.000
160A160GLN0-0.009-0.01629.8400.0000.0000.0000.0000.0000.000
161A161GLY00.0140.02532.4330.0000.0000.0000.0000.0000.000
162A162CYS0-0.041-0.00828.532-0.005-0.0050.0000.0000.0000.000
163A163PRO00.0360.01429.5670.0020.0020.0000.0000.0000.000
164A164ARG10.8740.91125.8190.0630.0630.0000.0000.0000.000
165A165GLN00.0230.01223.939-0.016-0.0160.0000.0000.0000.000
166A166ILE00.0560.03418.819-0.012-0.0120.0000.0000.0000.000
167A167ILE0-0.052-0.01619.8020.0100.0100.0000.0000.0000.000
168A168LYS10.8850.95617.121-0.040-0.0400.0000.0000.0000.000
169A169PHE00.004-0.00918.0010.0080.0080.0000.0000.0000.000
170A170GLY00.0150.00416.950-0.001-0.0010.0000.0000.0000.000
171A171PRO0-0.018-0.02114.7520.0080.0080.0000.0000.0000.000
172A172LYS10.9450.9758.786-0.457-0.4570.0000.0000.0000.000
173A173GLN00.0150.02111.426-0.014-0.0140.0000.0000.0000.000
174A174TYR0-0.032-0.04513.5150.0370.0370.0000.0000.0000.000
175A175ALA0-0.002-0.00815.084-0.044-0.0440.0000.0000.0000.000
176A176PHE00.0020.01614.5760.0220.0220.0000.0000.0000.000
177A177GLN00.0950.04918.933-0.021-0.0210.0000.0000.0000.000
178A178CYS0-0.0290.00921.887-0.004-0.0040.0000.0000.0000.000
179A179HIS10.8140.87619.8610.1130.1130.0000.0000.0000.000
180A180LEU00.0290.00517.7720.0120.0120.0000.0000.0000.000
181A181GLU-1-0.792-0.88916.191-0.126-0.1260.0000.0000.0000.000
182A182PHE00.0440.01117.804-0.004-0.0040.0000.0000.0000.000
183A183THR00.0310.01820.1070.0070.0070.0000.0000.0000.000
184A184PRO00.0790.03222.837-0.008-0.0080.0000.0000.0000.000
185A185GLU-1-0.892-0.95124.188-0.041-0.0410.0000.0000.0000.000
186A186LEU0-0.063-0.02419.227-0.010-0.0100.0000.0000.0000.000
187A187VAL00.0250.01923.881-0.004-0.0040.0000.0000.0000.000
188A188ALA0-0.0090.00226.7290.0010.0010.0000.0000.0000.000
189A189ALA0-0.039-0.02025.8640.0000.0000.0000.0000.0000.000
190A190LEU0-0.005-0.00224.247-0.001-0.0010.0000.0000.0000.000
191A191ILE0-0.032-0.02528.2780.0020.0020.0000.0000.0000.000
192A192ALA0-0.082-0.02731.1830.0020.0020.0000.0000.0000.000
193A193GLN0-0.028-0.01629.8260.0020.0020.0000.0000.0000.000
194A194GLU-1-0.966-0.97231.975-0.068-0.0680.0000.0000.0000.000
195A195ASP-1-0.878-0.93533.734-0.053-0.0530.0000.0000.0000.000
196A196ASP-1-0.966-0.99437.305-0.037-0.0370.0000.0000.0000.000
197A197LEU00.0390.01433.8060.0000.0000.0000.0000.0000.000
198A198ASP-1-0.938-0.97737.322-0.028-0.0280.0000.0000.0000.000
199A199THR0-0.022-0.00740.7170.0010.0010.0000.0000.0000.000
200A200GLN0-0.052-0.05135.9150.0010.0010.0000.0000.0000.000
201A201SER00.0010.00438.0670.0010.0010.0000.0000.0000.000
202A202GLN0-0.034-0.01139.5330.0010.0010.0000.0000.0000.000
203A203THR0-0.077-0.02442.2510.0000.0000.0000.0000.0000.000
204A204GLU-1-0.932-0.96037.274-0.040-0.0400.0000.0000.0000.000
205A205THR0-0.048-0.02337.9380.0000.0000.0000.0000.0000.000
206A206TYR0-0.046-0.03533.6380.0020.0020.0000.0000.0000.000
207A207VAL00.0620.04033.636-0.004-0.0040.0000.0000.0000.000
208A208GLN00.0270.02032.4520.0010.0010.0000.0000.0000.000
209A209THR00.0670.03535.320-0.003-0.0030.0000.0000.0000.000
210A210ALA00.030-0.00834.1900.0000.0000.0000.0000.0000.000
211A211GLU-1-0.938-0.96034.044-0.018-0.0180.0000.0000.0000.000
212A212GLU-1-0.889-0.94634.487-0.020-0.0200.0000.0000.0000.000
213A213MET0-0.0200.00030.0190.0000.0000.0000.0000.0000.000
214A214GLN0-0.046-0.01029.528-0.002-0.0020.0000.0000.0000.000
215A215THR0-0.082-0.05430.9450.0020.0020.0000.0000.0000.000
216A216PHE0-0.034-0.00126.6090.0040.0040.0000.0000.0000.000
217A217ASP-1-0.783-0.83026.4080.0070.0070.0000.0000.0000.000
218A218TYR0-0.049-0.06422.852-0.001-0.0010.0000.0000.0000.000
219A219SER0-0.021-0.07321.9960.0000.0000.0000.0000.0000.000
220A220SER0-0.035-0.02221.4000.0110.0110.0000.0000.0000.000
221A221MET0-0.0110.03720.7920.0030.0030.0000.0000.0000.000
222A222ASN0-0.029-0.01317.6440.0060.0060.0000.0000.0000.000
223A223GLN00.0200.01516.5300.0070.0070.0000.0000.0000.000
224A224ALA00.0700.03217.1840.0190.0190.0000.0000.0000.000
225A225LEU0-0.0090.03813.4910.0190.0190.0000.0000.0000.000
226A226TYR0-0.059-0.03212.5310.0100.0100.0000.0000.0000.000
227A227SER0-0.078-0.06912.3990.0450.0450.0000.0000.0000.000
228A228PHE00.0590.01912.1040.0380.0380.0000.0000.0000.000
229A229LEU0-0.046-0.0188.5120.0250.0250.0000.0000.0000.000
230A230ASP-1-0.737-0.8668.5280.5930.5930.0000.0000.0000.000
231A231ARG10.8290.9129.769-0.046-0.0460.0000.0000.0000.000
232A232LEU0-0.088-0.0248.7930.0310.0310.0000.0000.0000.000
233A233THR0-0.136-0.0944.9390.0680.0680.0000.0000.0000.000
234A234GLU-1-0.991-0.9666.7780.9220.9220.0000.0000.0000.000