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: G6KV1

Calculation Name: 3DMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P8H7

Base Structure: X-ray

Registration Date: 2023-09-20

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 146
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1198661.732265
FMO2-HF: Nuclear repulsion 1143293.707276
FMO2-HF: Total energy -55368.024989
FMO2-MP2: Total energy -55530.061148


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-13.549-7.3281.755-4.197-3.78-0.029
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.016
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].
3A2ALA0-0.006-0.0063.104-2.0080.3160.027-1.229-1.1230.004
4A3ASP-1-0.874-0.9222.590-13.263-9.3701.729-2.962-2.660-0.033
5A4PRO00.024-0.0084.7100.6080.612-0.001-0.0060.0030.000
6A5LYS10.8230.8977.1121.2151.2150.0000.0000.0000.000
7A6GLU-1-0.828-0.9145.027-0.723-0.7230.0000.0000.0000.000
8A7LEU0-0.002-0.0077.0550.5300.5300.0000.0000.0000.000
9A8GLN00.0160.0089.3200.3210.3210.0000.0000.0000.000
10A9ASP-1-0.814-0.88910.187-0.708-0.7080.0000.0000.0000.000
11A10LYS10.8790.9408.2460.3070.3070.0000.0000.0000.000
12A11PHE00.0100.00912.4850.1070.1070.0000.0000.0000.000
13A12TRP00.0280.01115.0540.0800.0800.0000.0000.0000.000
14A13LYS10.9500.98214.8410.2160.2160.0000.0000.0000.000
15A14ALA00.0140.01016.6680.0390.0390.0000.0000.0000.000
16A15LEU0-0.0100.00018.3850.0270.0270.0000.0000.0000.000
17A16LYS10.8770.95620.3720.1710.1710.0000.0000.0000.000
18A17SER0-0.049-0.03021.3620.0100.0100.0000.0000.0000.000
19A18ASP-1-0.855-0.93421.338-0.030-0.0300.0000.0000.0000.000
20A19ARG10.9020.96623.6830.0950.0950.0000.0000.0000.000
21A20THR0-0.024-0.00925.506-0.004-0.0040.0000.0000.0000.000
22A21VAL00.0000.01424.199-0.002-0.0020.0000.0000.0000.000
23A22MET0-0.0280.00626.5650.0040.0040.0000.0000.0000.000
24A23LEU00.013-0.00628.091-0.004-0.0040.0000.0000.0000.000
25A24GLY00.0230.01929.8080.0080.0080.0000.0000.0000.000
26A25LEU0-0.032-0.02930.727-0.008-0.0080.0000.0000.0000.000
27A26ASP-1-0.902-0.95829.027-0.067-0.0670.0000.0000.0000.000
28A27GLY0-0.016-0.01331.6620.0000.0000.0000.0000.0000.000
29A28VAL0-0.106-0.04634.0860.0010.0010.0000.0000.0000.000
30A29GLU-1-0.908-0.94036.391-0.017-0.0170.0000.0000.0000.000
31A30ASP-1-0.881-0.94137.940-0.023-0.0230.0000.0000.0000.000
32A31GLY00.021-0.00634.694-0.004-0.0040.0000.0000.0000.000
33A32HIS0-0.049-0.03135.151-0.004-0.0040.0000.0000.0000.000
34A33ALA0-0.0110.00232.319-0.004-0.0040.0000.0000.0000.000
35A34ARG10.9360.94932.9170.0400.0400.0000.0000.0000.000
36A35PRO0-0.0130.00530.726-0.006-0.0060.0000.0000.0000.000
37A36MET0-0.023-0.00530.3050.0020.0020.0000.0000.0000.000
38A37THR00.011-0.00529.204-0.002-0.0020.0000.0000.0000.000
39A38ALA00.0140.01025.398-0.002-0.0020.0000.0000.0000.000
40A39GLN0-0.088-0.04727.0750.0090.0090.0000.0000.0000.000
41A40ILE00.0370.01821.208-0.001-0.0010.0000.0000.0000.000
42A41GLU-1-0.907-0.96025.638-0.116-0.1160.0000.0000.0000.000
43A42GLY00.0190.01623.708-0.014-0.0140.0000.0000.0000.000
44A43ASP-1-0.921-0.98919.579-0.177-0.1770.0000.0000.0000.000
45A44SER0-0.061-0.04117.134-0.008-0.0080.0000.0000.0000.000
46A45GLY00.0220.02218.7050.0170.0170.0000.0000.0000.000
47A46GLY00.0070.02020.3410.0210.0210.0000.0000.0000.000
48A47PRO0-0.012-0.02323.353-0.005-0.0050.0000.0000.0000.000
49A48ILE0-0.032-0.00721.993-0.003-0.0030.0000.0000.0000.000
50A49TRP00.0160.00326.1640.0100.0100.0000.0000.0000.000
51A50PHE00.0250.00026.8390.0000.0000.0000.0000.0000.000
52A51PHE00.0370.02531.9020.0010.0010.0000.0000.0000.000
53A52THR0-0.015-0.00835.2980.0040.0040.0000.0000.0000.000
54A53SER00.0810.05837.888-0.001-0.0010.0000.0000.0000.000
55A54LYS10.8470.90341.2770.0510.0510.0000.0000.0000.000
56A55ASP-1-0.889-0.94343.452-0.033-0.0330.0000.0000.0000.000
57A56ASN00.000-0.00136.5610.0050.0050.0000.0000.0000.000
58A57ALA00.022-0.00140.163-0.002-0.0020.0000.0000.0000.000
59A58LEU0-0.020-0.01134.310-0.001-0.0010.0000.0000.0000.000
60A59ILE00.0260.01938.356-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.014-0.00439.950-0.002-0.0020.0000.0000.0000.000
62A61MET0-0.054-0.01338.7630.0010.0010.0000.0000.0000.000
63A62LEU0-0.045-0.01335.199-0.002-0.0020.0000.0000.0000.000
64A63GLY00.0480.02737.838-0.003-0.0030.0000.0000.0000.000
65A64GLN0-0.050-0.02937.017-0.003-0.0030.0000.0000.0000.000
66A65GLY0-0.0060.00134.259-0.007-0.0070.0000.0000.0000.000
67A66ARG10.9040.97433.8950.0620.0620.0000.0000.0000.000
68A67ARG10.9170.96627.0300.0940.0940.0000.0000.0000.000
69A68VAL0-0.007-0.00527.7980.0100.0100.0000.0000.0000.000
70A69ILE00.0390.01724.155-0.013-0.0130.0000.0000.0000.000
71A70GLY0-0.009-0.01424.7960.0110.0110.0000.0000.0000.000
72A71ALA0-0.016-0.00423.460-0.011-0.0110.0000.0000.0000.000
73A72PHE00.010-0.00618.5630.0020.0020.0000.0000.0000.000
74A73SER0-0.011-0.00820.3030.0090.0090.0000.0000.0000.000
75A74SER0-0.005-0.02917.989-0.006-0.0060.0000.0000.0000.000
76A75LYS10.9210.93920.3040.0390.0390.0000.0000.0000.000
77A76GLY0-0.026-0.01320.8990.0090.0090.0000.0000.0000.000
78A77HIS0-0.047-0.01620.4750.0260.0260.0000.0000.0000.000
79A78ASP-1-0.845-0.88215.2630.0660.0660.0000.0000.0000.000
80A79LEU0-0.017-0.00712.9140.0240.0240.0000.0000.0000.000
81A80PHE00.0060.00415.974-0.009-0.0090.0000.0000.0000.000
82A81ALA0-0.003-0.00616.529-0.022-0.0220.0000.0000.0000.000
83A82SER0-0.0230.00818.3030.0190.0190.0000.0000.0000.000
84A83ILE0-0.008-0.01219.803-0.028-0.0280.0000.0000.0000.000
85A84SER00.0530.03921.6260.0280.0280.0000.0000.0000.000
86A85GLY00.0560.01123.205-0.023-0.0230.0000.0000.0000.000
87A86SER0-0.043-0.00625.9290.0180.0180.0000.0000.0000.000
88A87LEU00.0190.01929.522-0.006-0.0060.0000.0000.0000.000
89A88ARG10.9840.97831.8060.1140.1140.0000.0000.0000.000
90A89GLU-1-0.805-0.89034.504-0.062-0.0620.0000.0000.0000.000
91A90ASP-1-0.918-0.97434.791-0.096-0.0960.0000.0000.0000.000
92A91THR00.0160.00836.367-0.004-0.0040.0000.0000.0000.000
93A92ASP-1-0.860-0.92336.735-0.081-0.0810.0000.0000.0000.000
94A93PRO00.024-0.00438.157-0.002-0.0020.0000.0000.0000.000
95A94ALA00.0460.03137.7470.0010.0010.0000.0000.0000.000
96A95VAL0-0.025-0.01932.691-0.003-0.0030.0000.0000.0000.000
97A96VAL0-0.010-0.00534.983-0.001-0.0010.0000.0000.0000.000
98A97ASP-1-0.859-0.92737.048-0.062-0.0620.0000.0000.0000.000
99A98ARG10.8520.93832.1070.1140.1140.0000.0000.0000.000
100A99LEU0-0.023-0.00829.967-0.002-0.0020.0000.0000.0000.000
101A100TRP00.0060.01933.2250.0030.0030.0000.0000.0000.000
102A101ASN00.006-0.00732.4840.0030.0030.0000.0000.0000.000
103A102PRO00.0440.01035.9000.0020.0020.0000.0000.0000.000
104A103TYR0-0.015-0.00332.4080.0040.0040.0000.0000.0000.000
105A104VAL00.0000.00234.5120.0030.0030.0000.0000.0000.000
106A105ALA0-0.037-0.02837.0930.0020.0020.0000.0000.0000.000
107A106ALA0-0.008-0.00439.5730.0020.0020.0000.0000.0000.000
108A107TRP0-0.067-0.02236.2390.0040.0040.0000.0000.0000.000
109A108TYR0-0.054-0.03238.646-0.001-0.0010.0000.0000.0000.000
110A109GLU-1-0.895-0.94043.724-0.025-0.0250.0000.0000.0000.000
111A110GLY0-0.042-0.02247.2610.0000.0000.0000.0000.0000.000
112A111GLY0-0.023-0.00844.240-0.001-0.0010.0000.0000.0000.000
113A112LYS10.8260.87840.2000.0570.0570.0000.0000.0000.000
114A113ASP-1-0.915-0.94343.636-0.044-0.0440.0000.0000.0000.000
115A114ASP-1-0.894-0.93944.886-0.034-0.0340.0000.0000.0000.000
116A115PRO00.005-0.00845.707-0.002-0.0020.0000.0000.0000.000
117A116LYS10.7840.89345.9350.0300.0300.0000.0000.0000.000
118A117LEU00.0260.02239.3610.0000.0000.0000.0000.0000.000
119A118ALA0-0.064-0.03739.5170.0000.0000.0000.0000.0000.000
120A119LEU00.0050.01133.5520.0000.0000.0000.0000.0000.000
121A120LEU0-0.008-0.01033.223-0.001-0.0010.0000.0000.0000.000
122A121ARG10.8120.90129.5380.1240.1240.0000.0000.0000.000
123A122LEU00.0090.00525.5780.0050.0050.0000.0000.0000.000
124A123ASP-1-0.857-0.93026.545-0.158-0.1580.0000.0000.0000.000
125A124ALA0-0.038-0.03121.7900.0060.0060.0000.0000.0000.000
126A125ASP-1-0.870-0.91422.473-0.232-0.2320.0000.0000.0000.000
127A126HIS0-0.094-0.07217.798-0.025-0.0250.0000.0000.0000.000
128A127ALA00.0300.00216.5780.0360.0360.0000.0000.0000.000
129A128GLN0-0.0410.00815.399-0.050-0.0500.0000.0000.0000.000
130A129ILE0-0.008-0.01512.2810.0260.0260.0000.0000.0000.000
131A130TRP0-0.019-0.01012.7800.0050.0050.0000.0000.0000.000
132A131LEU0-0.006-0.0118.594-0.026-0.0260.0000.0000.0000.000
133A132ASN0-0.052-0.01213.1380.0770.0770.0000.0000.0000.000
134A133GLY00.0030.00513.7040.0370.0370.0000.0000.0000.000
135A134SER0-0.033-0.02614.409-0.077-0.0770.0000.0000.0000.000
136A135SER00.017-0.00415.9950.0560.0560.0000.0000.0000.000
137A136LEU0-0.0130.00818.580-0.045-0.0450.0000.0000.0000.000
138A137LEU00.0130.00620.522-0.004-0.0040.0000.0000.0000.000
139A138ALA00.0150.00923.9890.0110.0110.0000.0000.0000.000
140A139GLY00.0060.00426.197-0.009-0.0090.0000.0000.0000.000
141A140ILE00.005-0.00428.016-0.010-0.0100.0000.0000.0000.000
142A141LYS10.9170.95731.692-0.146-0.1460.0000.0000.0000.000
143A142VAL00.0330.02034.070-0.005-0.0050.0000.0000.0000.000
144A143LEU0-0.011-0.00436.7960.0020.0020.0000.0000.0000.000
145A144LEU00.0140.00235.7650.0000.0000.0000.0000.0000.000
146A145GLY00.0130.01640.151-0.005-0.0050.0000.0000.0000.000