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: 5JR8Z

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2648803.608038
FMO2-HF: Nuclear repulsion 2563035.195904
FMO2-HF: Total energy -85768.412135
FMO2-MP2: Total energy -86013.752572


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.
-12.203-2.5565.856-5.26-10.241-0.029
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 : -0.011 / q_NPA : -0.006
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].
3A5SER00.0240.0083.815-1.1140.841-0.024-0.938-0.9930.003
4A6ALA0-0.0250.0015.9930.1470.1470.0000.0000.0000.000
5A7VAL00.018-0.0059.746-0.044-0.0440.0000.0000.0000.000
6A8ILE0-0.012-0.00612.1750.0450.0450.0000.0000.0000.000
7A9LEU0-0.028-0.01715.732-0.010-0.0100.0000.0000.0000.000
8A10ALA00.0480.00518.7280.0140.0140.0000.0000.0000.000
9A11GLY00.0630.03122.3520.0090.0090.0000.0000.0000.000
10A12CYS0-0.106-0.06422.824-0.012-0.0120.0000.0000.0000.000
11A13GLY00.0440.03224.8710.0060.0060.0000.0000.0000.000
12A14HIS00.0420.02125.815-0.001-0.0010.0000.0000.0000.000
13A15MET0-0.036-0.03026.8120.0000.0000.0000.0000.0000.000
14A16ASP-1-0.831-0.92328.890-0.046-0.0460.0000.0000.0000.000
15A17GLY00.0270.02625.5090.0040.0040.0000.0000.0000.000
16A18SER00.0210.01720.146-0.001-0.0010.0000.0000.0000.000
17A19GLU-1-0.812-0.94121.706-0.106-0.1060.0000.0000.0000.000
18A20ILE00.0000.00820.804-0.013-0.0130.0000.0000.0000.000
19A21ARG10.9070.94620.5020.0850.0850.0000.0000.0000.000
20A22GLU-1-0.779-0.91918.478-0.152-0.1520.0000.0000.0000.000
21A23ALA00.0270.01416.320-0.026-0.0260.0000.0000.0000.000
22A24VAL0-0.015-0.01515.472-0.026-0.0260.0000.0000.0000.000
23A25LEU0-0.035-0.01715.734-0.024-0.0240.0000.0000.0000.000
24A26VAL00.0370.01111.234-0.030-0.0300.0000.0000.0000.000
25A27MET0-0.061-0.01711.277-0.054-0.0540.0000.0000.0000.000
26A28LEU0-0.0200.00611.214-0.050-0.0500.0000.0000.0000.000
27A29GLU-1-0.738-0.84810.665-0.371-0.3710.0000.0000.0000.000
28A30LEU0-0.012-0.0015.991-0.067-0.0670.0000.0000.0000.000
29A31ASP-1-0.906-0.9526.888-0.592-0.5920.0000.0000.0000.000
30A32ARG10.8500.9258.8440.2850.2850.0000.0000.0000.000
31A33HIS0-0.063-0.0334.8440.0040.0040.0000.0000.0000.000
32A34ASN0-0.093-0.0394.496-0.453-0.250-0.001-0.015-0.1870.000
33A35VAL0-0.034-0.0022.344-2.756-1.5722.304-0.855-2.632-0.001
34A36ASN00.0060.0043.6530.3280.9150.006-0.062-0.5320.000
35A37PHE00.028-0.0045.706-0.342-0.3420.0000.0000.0000.000
36A38LYS10.8970.9668.342-0.106-0.1060.0000.0000.0000.000
37A39CYS0-0.022-0.00511.556-0.048-0.0480.0000.0000.0000.000
38A40PHE00.0290.00812.2380.0390.0390.0000.0000.0000.000
39A41ALA00.0380.01416.753-0.019-0.0190.0000.0000.0000.000
40A42PRO00.0480.03420.1750.0130.0130.0000.0000.0000.000
41A43ASN00.0100.01523.221-0.008-0.0080.0000.0000.0000.000
42A44LYS10.8040.87625.7920.0050.0050.0000.0000.0000.000
43A45ASN00.0080.00528.418-0.004-0.0040.0000.0000.0000.000
44A46GLN0-0.032-0.01828.105-0.002-0.0020.0000.0000.0000.000
45A47LYS10.8430.92330.2400.0300.0300.0000.0000.0000.000
46A48GLN00.0220.00832.2620.0040.0040.0000.0000.0000.000
47A49VAL00.0220.02432.263-0.002-0.0020.0000.0000.0000.000
48A50VAL0-0.025-0.02032.8360.0020.0020.0000.0000.0000.000
49A51ASP-1-0.777-0.86333.785-0.037-0.0370.0000.0000.0000.000
50A52HIS0-0.026-0.03729.996-0.005-0.0050.0000.0000.0000.000
51A53LYS10.8830.95334.4430.0370.0370.0000.0000.0000.000
52A54LYS10.7710.85537.5250.0280.0280.0000.0000.0000.000
53A55LYS10.9060.96135.3860.0500.0500.0000.0000.0000.000
54A56GLU-1-0.802-0.87937.634-0.028-0.0280.0000.0000.0000.000
55A57SER00.0080.00937.038-0.001-0.0010.0000.0000.0000.000
56A58VAL0-0.002-0.01237.4850.0020.0020.0000.0000.0000.000
57A59GLY0-0.0020.00538.7260.0000.0000.0000.0000.0000.000
58A60GLU-1-0.852-0.91636.361-0.025-0.0250.0000.0000.0000.000
59A61VAL0-0.009-0.01334.732-0.001-0.0010.0000.0000.0000.000
60A62ARG10.8410.91930.7840.0340.0340.0000.0000.0000.000
61A63ASN00.021-0.00127.503-0.004-0.0040.0000.0000.0000.000
62A64ILE00.0410.01923.625-0.003-0.0030.0000.0000.0000.000
63A65LEU00.0050.03421.585-0.009-0.0090.0000.0000.0000.000
64A66VAL00.004-0.00723.656-0.003-0.0030.0000.0000.0000.000
65A67GLU-1-0.779-0.88525.755-0.039-0.0390.0000.0000.0000.000
66A68SER0-0.024-0.02620.427-0.010-0.0100.0000.0000.0000.000
67A69ALA00.0040.00120.920-0.012-0.0120.0000.0000.0000.000
68A70ARG10.8070.88822.1720.0380.0380.0000.0000.0000.000
69A71ILE0-0.004-0.00418.076-0.003-0.0030.0000.0000.0000.000
70A72ALA0-0.015-0.00317.354-0.014-0.0140.0000.0000.0000.000
71A73ARG10.9270.96718.4180.0750.0750.0000.0000.0000.000
72A74GLY00.0080.00520.9360.0100.0100.0000.0000.0000.000
73A75SER0-0.047-0.01416.1610.0120.0120.0000.0000.0000.000
74A76VAL0-0.028-0.01016.640-0.025-0.0250.0000.0000.0000.000
75A77TYR0-0.010-0.00515.2120.0210.0210.0000.0000.0000.000
76A78ASP-1-0.801-0.93518.965-0.006-0.0060.0000.0000.0000.000
77A79ILE0-0.020-0.01017.5020.0090.0090.0000.0000.0000.000
78A80GLU-1-0.884-0.93518.8780.0220.0220.0000.0000.0000.000
79A81GLN0-0.072-0.03518.8130.0180.0180.0000.0000.0000.000
80A82ILE0-0.062-0.01112.8950.0190.0190.0000.0000.0000.000
81A83ARG10.8690.91513.284-0.324-0.3240.0000.0000.0000.000
82A84VAL00.0460.02011.6640.0320.0320.0000.0000.0000.000
83A85GLU-1-0.867-0.93710.2030.2100.2100.0000.0000.0000.000
84A86GLU-1-0.890-0.9318.7180.4690.4690.0000.0000.0000.000
85A87PHE0-0.026-0.0115.9780.1540.1540.0000.0000.0000.000
86A88ASP-1-0.801-0.9022.426-4.405-1.1023.020-2.869-3.453-0.031
87A89MET0-0.046-0.0244.256-0.3420.0350.002-0.047-0.3310.000
88A90LEU00.0000.0186.649-0.027-0.0270.0000.0000.0000.000
89A91VAL00.0180.0068.8350.0110.0110.0000.0000.0000.000
90A92ILE0-0.015-0.01511.5090.0210.0210.0000.0000.0000.000
91A93PRO00.0240.00514.4650.0060.0060.0000.0000.0000.000
92A94GLY00.0710.05917.0960.0140.0140.0000.0000.0000.000
93A95GLY00.004-0.00120.7490.0000.0000.0000.0000.0000.000
94A96TYR00.003-0.00123.9520.0000.0000.0000.0000.0000.000
95A97GLY00.0190.01425.9340.0050.0050.0000.0000.0000.000
96A98VAL0-0.021-0.00920.6820.0060.0060.0000.0000.0000.000
97A99ALA00.0010.01223.5530.0040.0040.0000.0000.0000.000
98A100LYS10.7680.88826.4150.0420.0420.0000.0000.0000.000
99A101ASN0-0.035-0.03626.0130.0110.0110.0000.0000.0000.000
100A102PHE0-0.020-0.00820.2380.0060.0060.0000.0000.0000.000
101A103SER0-0.039-0.02525.8920.0020.0020.0000.0000.0000.000
102A104ASN00.010-0.00428.487-0.002-0.0020.0000.0000.0000.000
103A105LEU00.0170.01227.2350.0000.0000.0000.0000.0000.000
104A106PHE0-0.033-0.02827.725-0.002-0.0020.0000.0000.0000.000
105A107ASP-1-0.845-0.90132.692-0.033-0.0330.0000.0000.0000.000
106A108GLU-1-0.853-0.90535.572-0.027-0.0270.0000.0000.0000.000
107A109ASP-1-0.845-0.94839.185-0.020-0.0200.0000.0000.0000.000
108A110LYS10.7460.86237.8960.0230.0230.0000.0000.0000.000
109A111GLU-1-0.880-0.90136.131-0.027-0.0270.0000.0000.0000.000
110A112ASN0-0.084-0.04835.3720.0020.0020.0000.0000.0000.000
111A113ASP-1-0.906-0.95830.649-0.032-0.0320.0000.0000.0000.000
112A114TYR00.0030.00130.3480.0030.0030.0000.0000.0000.000
113A115ILE0-0.021-0.01724.187-0.004-0.0040.0000.0000.0000.000
114A116LEU0-0.024-0.00324.5080.0040.0040.0000.0000.0000.000
115A117PRO00.0190.00624.713-0.003-0.0030.0000.0000.0000.000
116A118GLU-1-0.773-0.88622.776-0.010-0.0100.0000.0000.0000.000
117A119PHE0-0.0070.00118.320-0.003-0.0030.0000.0000.0000.000
118A120LYS10.8740.93319.9250.0200.0200.0000.0000.0000.000
119A121ASN0-0.010-0.02720.508-0.006-0.0060.0000.0000.0000.000
120A122ALA00.0610.04616.5460.0040.0040.0000.0000.0000.000
121A123VAL00.014-0.00215.591-0.007-0.0070.0000.0000.0000.000
122A124ARG10.8050.87715.8420.0220.0220.0000.0000.0000.000
123A125GLU-1-0.913-0.94315.3630.0540.0540.0000.0000.0000.000
124A126PHE0-0.003-0.0118.5860.0160.0160.0000.0000.0000.000
125A127TYR0-0.008-0.01112.4980.0030.0030.0000.0000.0000.000
126A128ASN0-0.008-0.00814.833-0.003-0.0030.0000.0000.0000.000
127A129ALA0-0.053-0.02112.1130.0140.0140.0000.0000.0000.000
128A130LYS10.8200.90711.600-0.004-0.0040.0000.0000.0000.000
129A131LYS10.8490.9358.077-0.144-0.1440.0000.0000.0000.000
130A132PRO0-0.010-0.0056.5730.0100.0100.0000.0000.0000.000
131A133ILE0-0.0070.0099.157-0.030-0.0300.0000.0000.0000.000
132A134GLY00.0200.00511.6840.0100.0100.0000.0000.0000.000
133A135ALA0-0.038-0.01812.5100.0060.0060.0000.0000.0000.000
134A136VAL00.035-0.00415.507-0.001-0.0010.0000.0000.0000.000
135A137CYS0-0.024-0.01417.9730.0160.0160.0000.0000.0000.000
136A138ILE00.0580.02621.7540.0030.0030.0000.0000.0000.000
137A139SER0-0.048-0.02718.9090.0120.0120.0000.0000.0000.000
138A140PRO00.0280.02118.6330.0050.0050.0000.0000.0000.000
139A141ALA00.0100.01620.4690.0070.0070.0000.0000.0000.000
140A142VAL0-0.003-0.00322.0900.0070.0070.0000.0000.0000.000
141A143VAL0-0.008-0.01117.3420.0060.0060.0000.0000.0000.000
142A144VAL0-0.016-0.00720.4010.0070.0070.0000.0000.0000.000
143A145ALA00.0290.01422.8250.0070.0070.0000.0000.0000.000
144A146LEU0-0.037-0.00919.3550.0070.0070.0000.0000.0000.000
145A147LEU0-0.007-0.00817.7990.0080.0080.0000.0000.0000.000
146A148LYS10.9050.98522.3100.0400.0400.0000.0000.0000.000
147A149ASP-1-0.852-0.92725.734-0.024-0.0240.0000.0000.0000.000
148A150ILE0-0.089-0.04720.5220.0050.0050.0000.0000.0000.000
149A151ALA0-0.0200.00221.4070.0000.0000.0000.0000.0000.000
150A152LYS10.8880.96423.3000.0500.0500.0000.0000.0000.000
151A153VAL0-0.046-0.01719.150-0.003-0.0030.0000.0000.0000.000
152A154LYS10.8680.92920.6340.0970.0970.0000.0000.0000.000
153A155VAL0-0.011-0.00718.758-0.012-0.0120.0000.0000.0000.000
154A156THR00.0230.00419.5760.0080.0080.0000.0000.0000.000
155A157ILE0-0.029-0.03421.169-0.008-0.0080.0000.0000.0000.000
156A158GLY0-0.022-0.02623.6640.0030.0030.0000.0000.0000.000
157A159GLU-1-0.832-0.89425.039-0.076-0.0760.0000.0000.0000.000
158A160ASP-1-0.866-0.96028.065-0.067-0.0670.0000.0000.0000.000
159A161SER00.0090.00530.0260.0030.0030.0000.0000.0000.000
160A162ASN0-0.068-0.02832.7410.0030.0030.0000.0000.0000.000
161A163GLY00.0940.06131.267-0.003-0.0030.0000.0000.0000.000
162A164LEU0-0.021-0.02729.1870.0020.0020.0000.0000.0000.000
163A165ILE00.0040.00024.5230.0010.0010.0000.0000.0000.000
164A166ASP-1-0.908-0.94727.701-0.046-0.0460.0000.0000.0000.000
165A167LYS10.9490.97930.4980.0400.0400.0000.0000.0000.000
166A168MET0-0.054-0.02327.1600.0040.0040.0000.0000.0000.000
167A169GLY00.0280.01627.7110.0010.0010.0000.0000.0000.000
168A170GLY00.009-0.00925.081-0.001-0.0010.0000.0000.0000.000
169A171VAL0-0.038-0.03324.6550.0050.0050.0000.0000.0000.000
170A172HIS00.0680.05224.160-0.014-0.0140.0000.0000.0000.000
171A173VAL0-0.033-0.01022.3230.0030.0030.0000.0000.0000.000
172A174ASP-1-0.858-0.92323.696-0.084-0.0840.0000.0000.0000.000
173A175CYS0-0.040-0.01520.763-0.008-0.0080.0000.0000.0000.000
174A176PRO00.0240.01722.7510.0040.0040.0000.0000.0000.000
175A177THR0-0.029-0.04021.901-0.009-0.0090.0000.0000.0000.000
176A178ILE00.0030.01020.718-0.010-0.0100.0000.0000.0000.000
177A179LYS10.7510.86417.5340.1710.1710.0000.0000.0000.000
178A180SER0-0.039-0.03414.860-0.005-0.0050.0000.0000.0000.000
179A181VAL00.0220.00316.8650.0070.0070.0000.0000.0000.000
180A182LYS10.8950.93612.5630.1810.1810.0000.0000.0000.000
181A183ASP-1-0.817-0.90415.571-0.083-0.0830.0000.0000.0000.000
182A184ASP-1-0.829-0.92814.951-0.164-0.1640.0000.0000.0000.000
183A185VAL0-0.022-0.00215.2010.0010.0010.0000.0000.0000.000
184A186ASN0-0.045-0.03516.5400.0140.0140.0000.0000.0000.000
185A187ARG10.9420.99610.8050.1110.1110.0000.0000.0000.000
186A188ILE00.0280.02112.426-0.013-0.0130.0000.0000.0000.000
187A189PHE00.0040.00210.287-0.003-0.0030.0000.0000.0000.000
188A190SER00.0200.00513.7560.0070.0070.0000.0000.0000.000
189A191CYS00.007-0.00815.688-0.004-0.0040.0000.0000.0000.000
190A192SER00.0570.03918.0830.0040.0040.0000.0000.0000.000
191A193ALA00.0280.00219.7440.0060.0060.0000.0000.0000.000
192A194TYR0-0.014-0.01621.7850.0060.0060.0000.0000.0000.000
193A195MET0-0.0080.01524.2250.0080.0080.0000.0000.0000.000
194A196ARG10.7650.88524.6990.1020.1020.0000.0000.0000.000
195A197ASN0-0.041-0.02827.550-0.005-0.0050.0000.0000.0000.000
196A198ASP-1-0.756-0.83726.200-0.097-0.0970.0000.0000.0000.000
197A199SER0-0.040-0.03127.042-0.002-0.0020.0000.0000.0000.000
198A200LEU00.021-0.00922.766-0.005-0.0050.0000.0000.0000.000
199A201TYR00.0240.00621.046-0.007-0.0070.0000.0000.0000.000
200A202ASN00.006-0.01521.904-0.014-0.0140.0000.0000.0000.000
201A203VAL0-0.011-0.00220.607-0.009-0.0090.0000.0000.0000.000
202A204TYR0-0.080-0.07115.2390.0010.0010.0000.0000.0000.000
203A205LEU00.0060.02117.137-0.020-0.0200.0000.0000.0000.000
204A206GLY00.0410.03117.014-0.015-0.0150.0000.0000.0000.000
205A207ILE0-0.002-0.01313.787-0.011-0.0110.0000.0000.0000.000
206A208GLN0-0.050-0.03512.883-0.009-0.0090.0000.0000.0000.000
207A209ASP-1-0.802-0.84912.048-0.250-0.2500.0000.0000.0000.000
208A210MET00.0260.04011.641-0.007-0.0070.0000.0000.0000.000
209A211ILE0-0.006-0.0037.374-0.018-0.0180.0000.0000.0000.000
210A212SER00.006-0.0107.320-0.066-0.0660.0000.0000.0000.000
211A213SER0-0.043-0.0248.268-0.020-0.0200.0000.0000.0000.000
212A214MET0-0.078-0.0216.6010.0020.0020.0000.0000.0000.000
213A215VAL00.0500.0203.204-0.712-0.0340.093-0.142-0.6290.000
214A216ASN0-0.065-0.0244.439-0.331-0.187-0.001-0.011-0.1320.000
215A217TYR0-0.105-0.0437.1700.0240.0240.0000.0000.0000.000
216A218LEU0-0.046-0.0212.565-1.386-0.1700.457-0.321-1.3520.000