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

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FMODB ID: 4JQ8N

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646179.26253
FMO2-HF: Nuclear repulsion 2560411.770027
FMO2-HF: Total energy -85767.492503
FMO2-MP2: Total energy -86012.80947


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.
-11.673-1.4464.985-4.998-10.213-0.026
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 : -0.014 / 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].
3A5SER00.0240.0033.815-1.0260.870-0.024-0.900-0.9720.002
4A6ALA0-0.0290.0025.9360.1440.1440.0000.0000.0000.000
5A7VAL00.020-0.0029.684-0.046-0.0460.0000.0000.0000.000
6A8ILE0-0.010-0.00712.1340.0470.0470.0000.0000.0000.000
7A9LEU0-0.036-0.02315.686-0.011-0.0110.0000.0000.0000.000
8A10ALA00.0400.00318.6910.0150.0150.0000.0000.0000.000
9A11GLY00.0700.03022.3160.0100.0100.0000.0000.0000.000
10A12CYS0-0.101-0.05522.800-0.013-0.0130.0000.0000.0000.000
11A13GLY00.0360.02324.8620.0060.0060.0000.0000.0000.000
12A14HIS00.0480.02225.811-0.001-0.0010.0000.0000.0000.000
13A15MET0-0.038-0.03026.8050.0010.0010.0000.0000.0000.000
14A16ASP-1-0.855-0.93328.880-0.051-0.0510.0000.0000.0000.000
15A17GLY00.0390.03125.4810.0050.0050.0000.0000.0000.000
16A18SER00.0210.02020.107-0.001-0.0010.0000.0000.0000.000
17A19GLU-1-0.835-0.93721.612-0.115-0.1150.0000.0000.0000.000
18A20ILE00.0080.00220.805-0.013-0.0130.0000.0000.0000.000
19A21ARG10.8890.93620.5120.0940.0940.0000.0000.0000.000
20A22GLU-1-0.764-0.91318.248-0.164-0.1640.0000.0000.0000.000
21A23ALA00.0230.01716.323-0.027-0.0270.0000.0000.0000.000
22A24VAL0-0.008-0.01315.481-0.027-0.0270.0000.0000.0000.000
23A25LEU0-0.044-0.02415.695-0.026-0.0260.0000.0000.0000.000
24A26VAL00.0420.01611.221-0.032-0.0320.0000.0000.0000.000
25A27MET0-0.054-0.01411.306-0.056-0.0560.0000.0000.0000.000
26A28LEU0-0.0320.00111.183-0.052-0.0520.0000.0000.0000.000
27A29GLU-1-0.770-0.88510.305-0.411-0.4110.0000.0000.0000.000
28A30LEU0-0.009-0.0026.078-0.073-0.0730.0000.0000.0000.000
29A31ASP-1-0.895-0.9476.875-0.647-0.6470.0000.0000.0000.000
30A32ARG10.8460.9418.8580.3060.3060.0000.0000.0000.000
31A33HIS0-0.066-0.0304.671-0.085-0.001-0.001-0.002-0.0810.000
32A34ASN0-0.077-0.0304.608-0.440-0.259-0.001-0.010-0.1700.000
33A35VAL0-0.038-0.0092.307-2.629-1.6472.706-0.935-2.753-0.003
34A36ASN00.0180.0093.6360.3330.8800.007-0.049-0.5040.000
35A37PHE00.022-0.0045.673-0.317-0.3170.0000.0000.0000.000
36A38LYS10.9540.9888.308-0.040-0.0400.0000.0000.0000.000
37A39CYS0-0.032-0.00611.505-0.047-0.0470.0000.0000.0000.000
38A40PHE00.0290.00812.0760.0410.0410.0000.0000.0000.000
39A41ALA00.0440.01716.694-0.020-0.0200.0000.0000.0000.000
40A42PRO00.0490.03220.1180.0140.0140.0000.0000.0000.000
41A43ASN00.0260.01623.158-0.009-0.0090.0000.0000.0000.000
42A44LYS10.7920.87325.7550.0070.0070.0000.0000.0000.000
43A45ASN0-0.004-0.00528.364-0.004-0.0040.0000.0000.0000.000
44A46GLN0-0.039-0.01828.008-0.002-0.0020.0000.0000.0000.000
45A47LYS10.9060.95530.1960.0330.0330.0000.0000.0000.000
46A48GLN00.0100.00332.2220.0050.0050.0000.0000.0000.000
47A49VAL00.0340.02832.229-0.003-0.0030.0000.0000.0000.000
48A50VAL0-0.036-0.02332.8380.0020.0020.0000.0000.0000.000
49A51ASP-1-0.781-0.86633.769-0.041-0.0410.0000.0000.0000.000
50A52HIS0-0.021-0.03330.184-0.005-0.0050.0000.0000.0000.000
51A53LYS10.8860.95634.4380.0400.0400.0000.0000.0000.000
52A54LYS10.7820.86437.5260.0310.0310.0000.0000.0000.000
53A55LYS10.9100.96235.1020.0550.0550.0000.0000.0000.000
54A56GLU-1-0.809-0.89037.628-0.031-0.0310.0000.0000.0000.000
55A57SER0-0.0170.00137.0230.0000.0000.0000.0000.0000.000
56A58VAL00.0330.00737.4180.0020.0020.0000.0000.0000.000
57A59GLY0-0.011-0.00138.6950.0000.0000.0000.0000.0000.000
58A60GLU-1-0.928-0.97036.967-0.027-0.0270.0000.0000.0000.000
59A61VAL0-0.005-0.00834.652-0.001-0.0010.0000.0000.0000.000
60A62ARG10.9390.98330.7570.0390.0390.0000.0000.0000.000
61A63ASN00.0400.01527.418-0.003-0.0030.0000.0000.0000.000
62A64ILE00.0470.02123.497-0.004-0.0040.0000.0000.0000.000
63A65LEU0-0.0120.01721.533-0.009-0.0090.0000.0000.0000.000
64A66VAL00.002-0.00823.612-0.004-0.0040.0000.0000.0000.000
65A67GLU-1-0.884-0.96125.720-0.043-0.0430.0000.0000.0000.000
66A68SER0-0.021-0.01520.393-0.011-0.0110.0000.0000.0000.000
67A69ALA00.0070.00520.893-0.013-0.0130.0000.0000.0000.000
68A70ARG10.8800.94222.1480.0430.0430.0000.0000.0000.000
69A71ILE00.002-0.00117.985-0.004-0.0040.0000.0000.0000.000
70A72ALA0-0.0090.00317.232-0.015-0.0150.0000.0000.0000.000
71A73ARG10.9330.96718.3980.0810.0810.0000.0000.0000.000
72A74GLY0-0.003-0.00320.9040.0100.0100.0000.0000.0000.000
73A75SER0-0.046-0.01316.2180.0220.0220.0000.0000.0000.000
74A76VAL0-0.028-0.01116.601-0.026-0.0260.0000.0000.0000.000
75A77TYR0-0.025-0.01115.4200.0230.0230.0000.0000.0000.000
76A78ASP-1-0.817-0.92918.965-0.004-0.0040.0000.0000.0000.000
77A79ILE0-0.012-0.01517.4960.0090.0090.0000.0000.0000.000
78A80GLU-1-0.896-0.94018.8540.0230.0230.0000.0000.0000.000
79A81GLN0-0.072-0.03918.7130.0180.0180.0000.0000.0000.000
80A82ILE0-0.064-0.01412.7420.0190.0190.0000.0000.0000.000
81A83ARG10.8680.91313.275-0.336-0.3360.0000.0000.0000.000
82A84VAL00.0400.02611.5490.0360.0360.0000.0000.0000.000
83A85GLU-1-0.905-0.97010.1840.2280.2280.0000.0000.0000.000
84A86GLU-1-0.908-0.9398.6800.5330.5330.0000.0000.0000.000
85A87PHE0-0.043-0.0205.9500.1640.1640.0000.0000.0000.000
86A88ASP-1-0.810-0.9202.672-3.7750.1511.564-2.524-2.965-0.026
87A89MET0-0.044-0.0214.458-0.4000.0030.005-0.055-0.3540.000
88A90LEU0-0.0060.0166.770-0.011-0.0110.0000.0000.0000.000
89A91VAL00.0200.0098.8580.0070.0070.0000.0000.0000.000
90A92ILE0-0.024-0.02111.4840.0240.0240.0000.0000.0000.000
91A93PRO00.015-0.00114.3330.0050.0050.0000.0000.0000.000
92A94GLY00.0900.05917.0860.0140.0140.0000.0000.0000.000
93A95GLY00.0020.00020.6440.0000.0000.0000.0000.0000.000
94A96TYR0-0.003-0.00323.9390.0010.0010.0000.0000.0000.000
95A97GLY00.0220.01725.9040.0060.0060.0000.0000.0000.000
96A98VAL0-0.014-0.00220.6750.0070.0070.0000.0000.0000.000
97A99ALA00.0070.01023.5190.0040.0040.0000.0000.0000.000
98A100LYS10.7800.89626.3810.0460.0460.0000.0000.0000.000
99A101ASN0-0.035-0.04525.9110.0110.0110.0000.0000.0000.000
100A102PHE0-0.036-0.01320.3280.0060.0060.0000.0000.0000.000
101A103SER0-0.038-0.01725.8410.0030.0030.0000.0000.0000.000
102A104ASN00.003-0.00228.438-0.003-0.0030.0000.0000.0000.000
103A105LEU00.0190.00727.0620.0000.0000.0000.0000.0000.000
104A106PHE0-0.039-0.03227.436-0.002-0.0020.0000.0000.0000.000
105A107ASP-1-0.847-0.90232.547-0.036-0.0360.0000.0000.0000.000
106A108GLU-1-0.866-0.91035.535-0.029-0.0290.0000.0000.0000.000
107A109ASP-1-0.843-0.94639.125-0.022-0.0220.0000.0000.0000.000
108A110LYS10.7440.85537.8520.0250.0250.0000.0000.0000.000
109A111GLU-1-0.896-0.91136.376-0.030-0.0300.0000.0000.0000.000
110A112ASN0-0.078-0.03835.4820.0020.0020.0000.0000.0000.000
111A113ASP-1-0.969-0.98330.930-0.035-0.0350.0000.0000.0000.000
112A114TYR00.014-0.00629.8380.0050.0050.0000.0000.0000.000
113A115ILE0-0.020-0.00924.192-0.005-0.0050.0000.0000.0000.000
114A116LEU0-0.048-0.02124.2020.0040.0040.0000.0000.0000.000
115A117PRO00.0260.01124.645-0.004-0.0040.0000.0000.0000.000
116A118GLU-1-0.768-0.88522.739-0.011-0.0110.0000.0000.0000.000
117A119PHE0-0.0030.00518.327-0.002-0.0020.0000.0000.0000.000
118A120LYS10.9570.97019.9100.0180.0180.0000.0000.0000.000
119A121ASN0-0.005-0.02220.553-0.007-0.0070.0000.0000.0000.000
120A122ALA00.0570.04616.3690.0050.0050.0000.0000.0000.000
121A123VAL00.0230.00015.661-0.006-0.0060.0000.0000.0000.000
122A124ARG10.8640.91715.8930.0240.0240.0000.0000.0000.000
123A125GLU-1-0.919-0.94715.2660.0670.0670.0000.0000.0000.000
124A126PHE0-0.004-0.0108.8170.0170.0170.0000.0000.0000.000
125A127TYR0-0.017-0.01812.4890.0030.0030.0000.0000.0000.000
126A128ASN00.0160.00214.862-0.004-0.0040.0000.0000.0000.000
127A129ALA0-0.062-0.02411.9970.0160.0160.0000.0000.0000.000
128A130LYS10.8140.90611.497-0.010-0.0100.0000.0000.0000.000
129A131LYS10.8650.9577.661-0.180-0.1800.0000.0000.0000.000
130A132PRO0-0.002-0.0016.6350.0180.0180.0000.0000.0000.000
131A133ILE00.0040.0139.316-0.028-0.0280.0000.0000.0000.000
132A134GLY00.0160.00211.2590.0090.0090.0000.0000.0000.000
133A135ALA0-0.035-0.01612.1300.0080.0080.0000.0000.0000.000
134A136VAL00.025-0.00415.229-0.002-0.0020.0000.0000.0000.000
135A137CYS0-0.044-0.01717.6730.0170.0170.0000.0000.0000.000
136A138ILE00.0650.02621.4630.0030.0030.0000.0000.0000.000
137A139SER0-0.051-0.03218.6840.0130.0130.0000.0000.0000.000
138A140PRO00.0360.02918.4720.0040.0040.0000.0000.0000.000
139A141ALA00.0060.01120.0870.0070.0070.0000.0000.0000.000
140A142VAL00.0010.00321.9000.0080.0080.0000.0000.0000.000
141A143VAL0-0.006-0.01117.0900.0070.0070.0000.0000.0000.000
142A144VAL0-0.017-0.00220.3280.0080.0080.0000.0000.0000.000
143A145ALA00.0240.01522.7500.0070.0070.0000.0000.0000.000
144A146LEU0-0.042-0.01519.4330.0080.0080.0000.0000.0000.000
145A147LEU0-0.035-0.02217.9030.0090.0090.0000.0000.0000.000
146A148LYS10.9861.02722.4080.0450.0450.0000.0000.0000.000
147A149ASP-1-0.967-0.98725.844-0.024-0.0240.0000.0000.0000.000
148A150ILE0-0.115-0.06520.5240.0050.0050.0000.0000.0000.000
149A151ALA0-0.019-0.00321.4900.0000.0000.0000.0000.0000.000
150A152LYS10.9641.00623.3840.0490.0490.0000.0000.0000.000
151A153VAL0-0.028-0.00919.374-0.003-0.0030.0000.0000.0000.000
152A154LYS10.9210.96020.4120.1130.1130.0000.0000.0000.000
153A155VAL0-0.013-0.00518.569-0.013-0.0130.0000.0000.0000.000
154A156THR00.0160.01319.3350.0090.0090.0000.0000.0000.000
155A157ILE0-0.020-0.02820.884-0.009-0.0090.0000.0000.0000.000
156A158GLY0-0.032-0.03123.4110.0040.0040.0000.0000.0000.000
157A159GLU-1-0.832-0.89724.832-0.083-0.0830.0000.0000.0000.000
158A160ASP-1-0.860-0.95727.627-0.074-0.0740.0000.0000.0000.000
159A161SER00.0140.00929.6460.0040.0040.0000.0000.0000.000
160A162ASN0-0.076-0.03432.4620.0040.0040.0000.0000.0000.000
161A163GLY00.0930.05730.997-0.003-0.0030.0000.0000.0000.000
162A164LEU0-0.014-0.01628.9590.0020.0020.0000.0000.0000.000
163A165ILE00.008-0.00424.2600.0010.0010.0000.0000.0000.000
164A166ASP-1-0.919-0.95027.339-0.050-0.0500.0000.0000.0000.000
165A167LYS10.9350.97830.1370.0450.0450.0000.0000.0000.000
166A168MET0-0.052-0.03127.0210.0040.0040.0000.0000.0000.000
167A169GLY00.0070.00627.7140.0010.0010.0000.0000.0000.000
168A170GLY0-0.007-0.02124.840-0.001-0.0010.0000.0000.0000.000
169A171VAL0-0.054-0.04224.3450.0050.0050.0000.0000.0000.000
170A172HIS00.0550.03423.852-0.014-0.0140.0000.0000.0000.000
171A173VAL0-0.040-0.01522.0300.0040.0040.0000.0000.0000.000
172A174ASP-1-0.849-0.92523.482-0.093-0.0930.0000.0000.0000.000
173A175CYS0-0.039-0.01620.655-0.009-0.0090.0000.0000.0000.000
174A176PRO00.0230.01022.7440.0040.0040.0000.0000.0000.000
175A177THR0-0.033-0.02421.811-0.010-0.0100.0000.0000.0000.000
176A178ILE00.0050.01520.666-0.011-0.0110.0000.0000.0000.000
177A179LYS10.7580.86917.4910.1910.1910.0000.0000.0000.000
178A180SER0-0.048-0.03714.766-0.004-0.0040.0000.0000.0000.000
179A181VAL00.0330.01316.6790.0070.0070.0000.0000.0000.000
180A182LYS10.9700.98512.2910.2210.2210.0000.0000.0000.000
181A183ASP-1-0.861-0.92415.370-0.096-0.0960.0000.0000.0000.000
182A184ASP-1-0.947-0.99414.748-0.169-0.1690.0000.0000.0000.000
183A185VAL00.0020.00715.3180.0000.0000.0000.0000.0000.000
184A186ASN0-0.054-0.03616.6160.0150.0150.0000.0000.0000.000
185A187ARG10.9320.97610.7170.1250.1250.0000.0000.0000.000
186A188ILE00.0230.02112.501-0.015-0.0150.0000.0000.0000.000
187A189PHE0-0.001-0.00210.173-0.005-0.0050.0000.0000.0000.000
188A190SER00.0260.00813.4600.0090.0090.0000.0000.0000.000
189A191CYS00.0240.00715.677-0.004-0.0040.0000.0000.0000.000
190A192SER00.0480.03717.8730.0050.0050.0000.0000.0000.000
191A193ALA00.0510.01419.6090.0070.0070.0000.0000.0000.000
192A194TYR00.003-0.00721.6080.0060.0060.0000.0000.0000.000
193A195MET0-0.0020.01523.9210.0090.0090.0000.0000.0000.000
194A196ARG10.7710.88824.6820.1110.1110.0000.0000.0000.000
195A197ASN0-0.044-0.02527.382-0.005-0.0050.0000.0000.0000.000
196A198ASP-1-0.782-0.89326.110-0.103-0.1030.0000.0000.0000.000
197A199SER0-0.061-0.03126.940-0.002-0.0020.0000.0000.0000.000
198A200LEU00.030-0.00522.606-0.005-0.0050.0000.0000.0000.000
199A201TYR00.0270.00820.768-0.009-0.0090.0000.0000.0000.000
200A202ASN00.0340.01021.695-0.016-0.0160.0000.0000.0000.000
201A203VAL0-0.005-0.00220.320-0.010-0.0100.0000.0000.0000.000
202A204TYR0-0.091-0.08814.8490.0000.0000.0000.0000.0000.000
203A205LEU00.0030.02017.005-0.021-0.0210.0000.0000.0000.000
204A206GLY00.0400.02916.970-0.017-0.0170.0000.0000.0000.000
205A207ILE0-0.002-0.01113.750-0.012-0.0120.0000.0000.0000.000
206A208GLN0-0.019-0.00212.770-0.010-0.0100.0000.0000.0000.000
207A209ASP-1-0.820-0.88411.986-0.289-0.2890.0000.0000.0000.000
208A210MET00.0070.02111.386-0.011-0.0110.0000.0000.0000.000
209A211ILE00.0010.0017.172-0.020-0.0200.0000.0000.0000.000
210A212SER00.0120.0037.308-0.083-0.0830.0000.0000.0000.000
211A213SER0-0.046-0.0228.258-0.031-0.0310.0000.0000.0000.000
212A214MET0-0.087-0.0266.331-0.003-0.0030.0000.0000.0000.000
213A215VAL00.0330.0113.097-0.772-0.0540.132-0.160-0.6900.001
214A216ASN0-0.053-0.0264.265-0.445-0.275-0.001-0.023-0.1470.000
215A217TYR0-0.095-0.0297.0160.0520.0520.0000.0000.0000.000
216A218LEU0-0.0040.0122.523-1.494-0.1740.598-0.340-1.5770.000