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: YV9M2

Calculation Name: 3L3B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L3B

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GI86

Base Structure: X-ray

Registration Date: 2023-09-22

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655200.650056
FMO2-HF: Nuclear repulsion 2569431.806601
FMO2-HF: Total energy -85768.843455
FMO2-MP2: Total energy -86014.175461


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:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-13.268-3.4316.873-5.397-11.314-0.027
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.003
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].
3A5SER00.013-0.0073.866-0.8450.835-0.016-0.805-0.8580.002
4A6ALA0-0.0070.0116.1600.1300.1300.0000.0000.0000.000
5A7VAL00.010-0.0019.780-0.048-0.0480.0000.0000.0000.000
6A8ILE0-0.0110.00012.2070.0410.0410.0000.0000.0000.000
7A9LEU0-0.037-0.02415.889-0.009-0.0090.0000.0000.0000.000
8A10ALA00.0690.01918.9070.0130.0130.0000.0000.0000.000
9A11GLY00.0570.02622.6090.0100.0100.0000.0000.0000.000
10A12CYS0-0.107-0.05323.270-0.012-0.0120.0000.0000.0000.000
11A13GLY00.0660.04025.3470.0060.0060.0000.0000.0000.000
12A14HIS00.0250.01326.094-0.003-0.0030.0000.0000.0000.000
13A15MET0-0.039-0.02627.0940.0010.0010.0000.0000.0000.000
14A16ASP-1-0.827-0.91929.081-0.055-0.0550.0000.0000.0000.000
15A17GLY00.0190.01825.8400.0040.0040.0000.0000.0000.000
16A18SER00.0040.00820.509-0.001-0.0010.0000.0000.0000.000
17A19GLU-1-0.815-0.93921.855-0.113-0.1130.0000.0000.0000.000
18A20ILE0-0.0020.00420.852-0.013-0.0130.0000.0000.0000.000
19A21ARG10.8990.94720.5470.0880.0880.0000.0000.0000.000
20A22GLU-1-0.760-0.91518.632-0.155-0.1550.0000.0000.0000.000
21A23ALA00.0350.01716.396-0.026-0.0260.0000.0000.0000.000
22A24VAL0-0.025-0.01115.497-0.028-0.0280.0000.0000.0000.000
23A25LEU0-0.023-0.01515.586-0.025-0.0250.0000.0000.0000.000
24A26VAL00.0210.00511.334-0.031-0.0310.0000.0000.0000.000
25A27MET0-0.054-0.01711.231-0.053-0.0530.0000.0000.0000.000
26A28LEU0-0.0110.00610.981-0.057-0.0570.0000.0000.0000.000
27A29GLU-1-0.744-0.84710.533-0.373-0.3730.0000.0000.0000.000
28A30LEU0-0.022-0.0116.089-0.059-0.0590.0000.0000.0000.000
29A31ASP-1-0.925-0.9546.490-0.681-0.6810.0000.0000.0000.000
30A32ARG10.8800.9408.3800.2640.2640.0000.0000.0000.000
31A33HIS0-0.061-0.0404.486-0.119-0.019-0.001-0.004-0.0960.000
32A34ASN0-0.094-0.0403.975-0.657-0.2990.001-0.066-0.2930.000
33A35VAL0-0.044-0.0082.386-3.568-2.0962.769-1.244-2.998-0.002
34A36ASN00.0080.0003.3290.3861.0600.0200.016-0.7110.000
35A37PHE00.013-0.0155.824-0.212-0.2120.0000.0000.0000.000
36A38LYS10.8590.9298.5030.0100.0100.0000.0000.0000.000
37A39CYS0-0.026-0.00111.817-0.037-0.0370.0000.0000.0000.000
38A40PHE00.0230.00612.4240.0350.0350.0000.0000.0000.000
39A41ALA00.0420.01616.844-0.013-0.0130.0000.0000.0000.000
40A42PRO00.0090.01520.3720.0110.0110.0000.0000.0000.000
41A43ASN00.0120.01523.471-0.006-0.0060.0000.0000.0000.000
42A44LYS10.7770.86425.7330.0250.0250.0000.0000.0000.000
43A45ASN00.0090.00428.540-0.005-0.0050.0000.0000.0000.000
44A46GLN0-0.022-0.01428.203-0.004-0.0040.0000.0000.0000.000
45A47LYS10.8370.91530.1280.0410.0410.0000.0000.0000.000
46A48GLN00.0160.00732.2610.0040.0040.0000.0000.0000.000
47A49VAL00.0160.01632.373-0.003-0.0030.0000.0000.0000.000
48A50VAL0-0.011-0.00332.9850.0030.0030.0000.0000.0000.000
49A51ASP-1-0.773-0.86034.083-0.043-0.0430.0000.0000.0000.000
50A52HIS0-0.011-0.02630.155-0.004-0.0040.0000.0000.0000.000
51A53LYS10.8680.94634.5210.0410.0410.0000.0000.0000.000
52A54LYS10.7550.84337.5230.0330.0330.0000.0000.0000.000
53A55LYS10.8970.95535.2990.0540.0540.0000.0000.0000.000
54A56GLU-1-0.769-0.86137.741-0.032-0.0320.0000.0000.0000.000
55A57SER00.0120.01137.236-0.001-0.0010.0000.0000.0000.000
56A58VAL0-0.007-0.01637.3380.0020.0020.0000.0000.0000.000
57A59GLY0-0.0020.00838.8840.0000.0000.0000.0000.0000.000
58A60GLU-1-0.856-0.91535.948-0.034-0.0340.0000.0000.0000.000
59A61VAL0-0.005-0.01034.860-0.001-0.0010.0000.0000.0000.000
60A62ARG10.8100.89230.7720.0440.0440.0000.0000.0000.000
61A63ASN00.020-0.00227.446-0.005-0.0050.0000.0000.0000.000
62A64ILE00.0560.02923.693-0.004-0.0040.0000.0000.0000.000
63A65LEU0-0.0050.02821.621-0.009-0.0090.0000.0000.0000.000
64A66VAL00.007-0.00423.515-0.004-0.0040.0000.0000.0000.000
65A67GLU-1-0.771-0.86525.773-0.052-0.0520.0000.0000.0000.000
66A68SER0-0.015-0.02520.455-0.010-0.0100.0000.0000.0000.000
67A69ALA00.0050.00420.934-0.013-0.0130.0000.0000.0000.000
68A70ARG10.7980.86522.2330.0500.0500.0000.0000.0000.000
69A71ILE0-0.0050.00018.249-0.003-0.0030.0000.0000.0000.000
70A72ALA00.001-0.00117.406-0.014-0.0140.0000.0000.0000.000
71A73ARG10.9230.96218.4040.0990.0990.0000.0000.0000.000
72A74GLY00.0150.01220.8230.0100.0100.0000.0000.0000.000
73A75SER0-0.048-0.01115.9850.0120.0120.0000.0000.0000.000
74A76VAL0-0.038-0.02016.349-0.027-0.0270.0000.0000.0000.000
75A77TYR00.0050.00614.9860.0310.0310.0000.0000.0000.000
76A78ASP-1-0.768-0.91719.301-0.032-0.0320.0000.0000.0000.000
77A79ILE0-0.016-0.00317.9180.0040.0040.0000.0000.0000.000
78A80GLU-1-0.877-0.93019.366-0.001-0.0010.0000.0000.0000.000
79A81GLN0-0.073-0.03119.3200.0160.0160.0000.0000.0000.000
80A82ILE0-0.045-0.00713.4340.0090.0090.0000.0000.0000.000
81A83ARG10.8370.89413.487-0.216-0.2160.0000.0000.0000.000
82A84VAL00.0420.02711.9620.0080.0080.0000.0000.0000.000
83A85GLU-1-0.833-0.91610.9150.1290.1290.0000.0000.0000.000
84A86GLU-1-0.864-0.9098.9960.2860.2860.0000.0000.0000.000
85A87PHE0-0.010-0.0026.0440.1080.1080.0000.0000.0000.000
86A88ASP-1-0.805-0.8972.434-4.708-1.5503.113-2.786-3.485-0.029
87A89MET0-0.044-0.0204.396-0.2110.1100.000-0.036-0.2860.000
88A90LEU00.0110.0176.789-0.027-0.0270.0000.0000.0000.000
89A91VAL00.002-0.0018.8950.0170.0170.0000.0000.0000.000
90A92ILE00.000-0.00811.6050.0200.0200.0000.0000.0000.000
91A93PRO00.0360.00914.5640.0100.0100.0000.0000.0000.000
92A94GLY00.0800.08017.3310.0130.0130.0000.0000.0000.000
93A95GLY00.0020.00021.0450.0000.0000.0000.0000.0000.000
94A96TYR0-0.023-0.01624.3790.0010.0010.0000.0000.0000.000
95A97GLY00.0490.03026.3970.0050.0050.0000.0000.0000.000
96A98VAL0-0.030-0.01320.5690.0050.0050.0000.0000.0000.000
97A99ALA0-0.0090.01223.6460.0030.0030.0000.0000.0000.000
98A100LYS10.7680.88826.4150.0490.0490.0000.0000.0000.000
99A101ASN0-0.035-0.04126.1420.0110.0110.0000.0000.0000.000
100A102PHE0-0.024-0.01520.4420.0050.0050.0000.0000.0000.000
101A103SER0-0.049-0.02426.0810.0020.0020.0000.0000.0000.000
102A104ASN00.007-0.01128.834-0.002-0.0020.0000.0000.0000.000
103A105LEU00.006-0.00327.5530.0010.0010.0000.0000.0000.000
104A106PHE0-0.040-0.02227.700-0.002-0.0020.0000.0000.0000.000
105A107ASP-1-0.797-0.88432.703-0.041-0.0410.0000.0000.0000.000
106A108GLU-1-0.852-0.91235.686-0.029-0.0290.0000.0000.0000.000
107A109ASP-1-0.856-0.94839.356-0.023-0.0230.0000.0000.0000.000
108A110LYS10.7530.86638.3140.0260.0260.0000.0000.0000.000
109A111GLU-1-0.855-0.91336.061-0.034-0.0340.0000.0000.0000.000
110A112ASN0-0.099-0.04335.2920.0020.0020.0000.0000.0000.000
111A113ASP-1-0.857-0.91530.728-0.039-0.0390.0000.0000.0000.000
112A114TYR00.0160.00830.4050.0020.0020.0000.0000.0000.000
113A115ILE00.003-0.00924.753-0.005-0.0050.0000.0000.0000.000
114A116LEU0-0.036-0.00624.4260.0030.0030.0000.0000.0000.000
115A117PRO00.0220.00724.933-0.004-0.0040.0000.0000.0000.000
116A118GLU-1-0.785-0.89422.797-0.028-0.0280.0000.0000.0000.000
117A119PHE00.0110.00618.567-0.004-0.0040.0000.0000.0000.000
118A120LYS10.8580.91720.3060.0290.0290.0000.0000.0000.000
119A121ASN0-0.004-0.01420.996-0.004-0.0040.0000.0000.0000.000
120A122ALA00.0590.04017.0000.0000.0000.0000.0000.0000.000
121A123VAL0-0.007-0.01415.961-0.011-0.0110.0000.0000.0000.000
122A124ARG10.8110.88516.2310.0330.0330.0000.0000.0000.000
123A125GLU-1-0.921-0.95615.6650.0110.0110.0000.0000.0000.000
124A126PHE00.0090.0038.8450.0150.0150.0000.0000.0000.000
125A127TYR00.0070.00212.7980.0060.0060.0000.0000.0000.000
126A128ASN00.001-0.00315.1740.0020.0020.0000.0000.0000.000
127A129ALA0-0.050-0.02012.1190.0140.0140.0000.0000.0000.000
128A130LYS10.8140.90012.2540.0090.0090.0000.0000.0000.000
129A131LYS10.8150.9078.232-0.066-0.0660.0000.0000.0000.000
130A132PRO0-0.014-0.0096.8110.0040.0040.0000.0000.0000.000
131A133ILE00.0110.0159.238-0.038-0.0380.0000.0000.0000.000
132A134GLY00.0290.00611.6200.0140.0140.0000.0000.0000.000
133A135ALA0-0.033-0.02212.4490.0020.0020.0000.0000.0000.000
134A136VAL00.025-0.00815.6620.0000.0000.0000.0000.0000.000
135A137CYS0-0.015-0.00518.0840.0140.0140.0000.0000.0000.000
136A138ILE00.0560.01921.8550.0030.0030.0000.0000.0000.000
137A139SER0-0.054-0.03919.2670.0110.0110.0000.0000.0000.000
138A140PRO00.0090.00218.5630.0040.0040.0000.0000.0000.000
139A141ALA00.0350.02320.3810.0060.0060.0000.0000.0000.000
140A142VAL0-0.0010.00222.2940.0070.0070.0000.0000.0000.000
141A143VAL0-0.008-0.00617.4100.0050.0050.0000.0000.0000.000
142A144VAL0-0.0040.00220.5430.0060.0060.0000.0000.0000.000
143A145ALA00.0180.01722.9990.0060.0060.0000.0000.0000.000
144A146LEU0-0.050-0.01819.5490.0070.0070.0000.0000.0000.000
145A147LEU0-0.004-0.00417.9830.0070.0070.0000.0000.0000.000
146A148LYS10.9110.96122.4850.0470.0470.0000.0000.0000.000
147A149ASP-1-0.859-0.90526.013-0.032-0.0320.0000.0000.0000.000
148A150ILE0-0.079-0.03920.9370.0050.0050.0000.0000.0000.000
149A151ALA0-0.0110.00021.8730.0010.0010.0000.0000.0000.000
150A152LYS10.8360.94323.9410.0460.0460.0000.0000.0000.000
151A153VAL0-0.056-0.02019.533-0.001-0.0010.0000.0000.0000.000
152A154LYS10.8380.90220.8310.0800.0800.0000.0000.0000.000
153A155VAL0-0.016-0.00819.001-0.009-0.0090.0000.0000.0000.000
154A156THR0-0.001-0.02519.4410.0070.0070.0000.0000.0000.000
155A157ILE0-0.006-0.01521.056-0.008-0.0080.0000.0000.0000.000
156A158GLY0-0.023-0.03223.6320.0010.0010.0000.0000.0000.000
157A159GLU-1-0.843-0.91725.028-0.074-0.0740.0000.0000.0000.000
158A160ASP-1-0.850-0.94328.177-0.065-0.0650.0000.0000.0000.000
159A161SER00.0100.00730.0550.0030.0030.0000.0000.0000.000
160A162ASN0-0.063-0.02332.9160.0030.0030.0000.0000.0000.000
161A163GLY00.0900.06431.801-0.003-0.0030.0000.0000.0000.000
162A164LEU0-0.022-0.02929.4180.0010.0010.0000.0000.0000.000
163A165ILE0-0.002-0.00224.7570.0000.0000.0000.0000.0000.000
164A166ASP-1-0.884-0.93827.972-0.045-0.0450.0000.0000.0000.000
165A167LYS10.9050.95530.5470.0400.0400.0000.0000.0000.000
166A168MET0-0.051-0.02627.1910.0020.0020.0000.0000.0000.000
167A169GLY00.0410.01527.8550.0000.0000.0000.0000.0000.000
168A170GLY0-0.005-0.00925.3200.0010.0010.0000.0000.0000.000
169A171VAL0-0.017-0.01424.8300.0050.0050.0000.0000.0000.000
170A172HIS00.0650.05124.329-0.013-0.0130.0000.0000.0000.000
171A173VAL0-0.018-0.01222.5070.0040.0040.0000.0000.0000.000
172A174ASP-1-0.844-0.91623.671-0.080-0.0800.0000.0000.0000.000
173A175CYS0-0.041-0.01720.929-0.006-0.0060.0000.0000.0000.000
174A176PRO00.0030.01123.1060.0020.0020.0000.0000.0000.000
175A177THR0-0.012-0.03922.133-0.007-0.0070.0000.0000.0000.000
176A178ILE0-0.0040.01520.621-0.010-0.0100.0000.0000.0000.000
177A179LYS10.7530.85717.4030.1590.1590.0000.0000.0000.000
178A180SER0-0.037-0.02714.781-0.002-0.0020.0000.0000.0000.000
179A181VAL00.0080.00316.7940.0090.0090.0000.0000.0000.000
180A182LYS10.9000.94012.6350.1550.1550.0000.0000.0000.000
181A183ASP-1-0.763-0.85715.738-0.074-0.0740.0000.0000.0000.000
182A184ASP-1-0.817-0.90914.954-0.136-0.1360.0000.0000.0000.000
183A185VAL0-0.013-0.00615.3890.0030.0030.0000.0000.0000.000
184A186ASN0-0.030-0.02716.9370.0140.0140.0000.0000.0000.000
185A187ARG10.8910.96710.9840.0970.0970.0000.0000.0000.000
186A188ILE00.0410.03612.432-0.020-0.0200.0000.0000.0000.000
187A189PHE0-0.002-0.01210.2670.0010.0010.0000.0000.0000.000
188A190SER00.0030.00313.8420.0050.0050.0000.0000.0000.000
189A191CYS00.005-0.00415.680-0.003-0.0030.0000.0000.0000.000
190A192SER00.0530.04217.9030.0030.0030.0000.0000.0000.000
191A193ALA00.0200.00019.6140.0060.0060.0000.0000.0000.000
192A194TYR0-0.041-0.02521.6800.0060.0060.0000.0000.0000.000
193A195MET0-0.0060.02324.3180.0070.0070.0000.0000.0000.000
194A196ARG10.7520.87324.5290.1000.1000.0000.0000.0000.000
195A197ASN0-0.026-0.01827.560-0.006-0.0060.0000.0000.0000.000
196A198ASP-1-0.752-0.83726.136-0.095-0.0950.0000.0000.0000.000
197A199SER0-0.046-0.04126.591-0.003-0.0030.0000.0000.0000.000
198A200LEU00.024-0.00322.340-0.004-0.0040.0000.0000.0000.000
199A201TYR00.0220.01121.008-0.008-0.0080.0000.0000.0000.000
200A202ASN00.000-0.01921.560-0.014-0.0140.0000.0000.0000.000
201A203VAL00.0110.00220.473-0.008-0.0080.0000.0000.0000.000
202A204TYR0-0.095-0.06514.8560.0020.0020.0000.0000.0000.000
203A205LEU00.0160.01116.819-0.020-0.0200.0000.0000.0000.000
204A206GLY00.0360.03516.763-0.011-0.0110.0000.0000.0000.000
205A207ILE0-0.009-0.01813.525-0.010-0.0100.0000.0000.0000.000
206A208GLN0-0.047-0.03412.623-0.007-0.0070.0000.0000.0000.000
207A209ASP-1-0.792-0.84511.900-0.225-0.2250.0000.0000.0000.000
208A210MET00.0160.04111.6590.0000.0000.0000.0000.0000.000
209A211ILE0-0.007-0.0087.196-0.008-0.0080.0000.0000.0000.000
210A212SER00.011-0.0137.181-0.047-0.0470.0000.0000.0000.000
211A213SER0-0.066-0.0328.255-0.005-0.0050.0000.0000.0000.000
212A214MET0-0.076-0.0266.6310.0090.0090.0000.0000.0000.000
213A215VAL00.0390.0202.965-0.838-0.0570.268-0.177-0.8710.001
214A216ASN0-0.038-0.0184.381-0.306-0.158-0.001-0.012-0.1350.000
215A217TYR0-0.118-0.0517.0690.0330.0330.0000.0000.0000.000
216A218LEU0-0.063-0.0312.422-1.328-0.1830.720-0.283-1.5810.001