Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K9G83

Calculation Name: 1GDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GDT

Chain ID: A

ChEMBL ID:

UniProt ID: P03012

Base Structure: X-ray

Registration Date: 2023-06-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1589495.802484
FMO2-HF: Nuclear repulsion 1517343.954773
FMO2-HF: Total energy -72151.847712
FMO2-MP2: Total energy -72359.550847


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.
-16.846-8.966.279-4.584-9.582-0.037
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 : 0.045 / q_NPA : 0.049
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].
3A3LEU00.0250.0252.846-5.076-2.3190.912-0.972-2.696-0.001
4A4PHE0-0.051-0.0453.7290.4830.6390.0080.016-0.1810.000
5A5GLY00.0370.0137.008-0.036-0.0360.0000.0000.0000.000
6A6TYR0-0.096-0.0799.9130.0410.0410.0000.0000.0000.000
7A7ALA00.0290.00613.3630.0220.0220.0000.0000.0000.000
8A8ARG10.8480.93816.9520.3050.3050.0000.0000.0000.000
9A9VAL0-0.044-0.02520.1120.0110.0110.0000.0000.0000.000
10A10SER00.0440.02622.9120.0020.0020.0000.0000.0000.000
11A11THR0-0.0010.00126.3080.0040.0040.0000.0000.0000.000
12A12SER00.0380.01327.705-0.003-0.0030.0000.0000.0000.000
13A13GLN00.035-0.00225.693-0.008-0.0080.0000.0000.0000.000
14A14GLN00.0650.02925.908-0.007-0.0070.0000.0000.0000.000
15A15SER00.0250.00125.1460.0070.0070.0000.0000.0000.000
16A16LEU0-0.052-0.01520.686-0.008-0.0080.0000.0000.0000.000
17A17ASP-1-0.857-0.93620.952-0.089-0.0890.0000.0000.0000.000
18A18ILE00.0140.01421.3170.0060.0060.0000.0000.0000.000
19A19GLN0-0.020-0.00818.422-0.014-0.0140.0000.0000.0000.000
20A20VAL00.0370.01116.719-0.010-0.0100.0000.0000.0000.000
21A21ARG10.7700.87116.6020.0130.0130.0000.0000.0000.000
22A22ALA00.0560.02417.4720.0180.0180.0000.0000.0000.000
23A23LEU0-0.021-0.00911.9340.0010.0010.0000.0000.0000.000
24A24LYS10.9270.96312.3840.0070.0070.0000.0000.0000.000
25A25ASP-1-0.834-0.89113.9740.0550.0550.0000.0000.0000.000
26A26ALA0-0.045-0.01111.5690.0230.0230.0000.0000.0000.000
27A27GLY00.0340.02410.2260.0080.0080.0000.0000.0000.000
28A28VAL0-0.038-0.0068.1900.1310.1310.0000.0000.0000.000
29A29LYS10.9700.9759.103-0.374-0.3740.0000.0000.0000.000
30A30ALA00.035-0.01111.141-0.083-0.0830.0000.0000.0000.000
31A31ASN0-0.025-0.00412.691-0.002-0.0020.0000.0000.0000.000
32A32ARG10.8980.9586.8630.3160.3160.0000.0000.0000.000
33A33ILE00.0160.02610.251-0.108-0.1080.0000.0000.0000.000
34A34PHE0-0.0170.00311.3950.0330.0330.0000.0000.0000.000
35A35THR0-0.006-0.02214.9880.0020.0020.0000.0000.0000.000
36A36ASP-1-0.771-0.84518.206-0.256-0.2560.0000.0000.0000.000
37A37LYS10.9270.96721.2040.1200.1200.0000.0000.0000.000
38A38ALA0-0.002-0.00624.522-0.004-0.0040.0000.0000.0000.000
39A39SER0-0.006-0.03125.7090.0100.0100.0000.0000.0000.000
40A40GLY0-0.0030.02528.0330.0100.0100.0000.0000.0000.000
41A41SER0-0.031-0.02729.9820.0010.0010.0000.0000.0000.000
42A42SER0-0.040-0.03129.1710.0080.0080.0000.0000.0000.000
43A43SER0-0.018-0.01226.318-0.010-0.0100.0000.0000.0000.000
44A44ASP-1-0.791-0.84625.315-0.173-0.1730.0000.0000.0000.000
45A45ARG10.7980.87720.3480.2420.2420.0000.0000.0000.000
46A46LYS11.0150.99920.0960.1320.1320.0000.0000.0000.000
47A47GLY0-0.019-0.01118.465-0.004-0.0040.0000.0000.0000.000
48A48LEU00.020-0.00514.699-0.033-0.0330.0000.0000.0000.000
49A49ASP-1-0.780-0.86715.424-0.351-0.3510.0000.0000.0000.000
50A50LEU0-0.031-0.01016.295-0.004-0.0040.0000.0000.0000.000
51A51LEU0-0.050-0.0159.464-0.018-0.0180.0000.0000.0000.000
52A52ARG10.7640.81711.6440.2880.2880.0000.0000.0000.000
53A53MET0-0.0110.01312.730-0.006-0.0060.0000.0000.0000.000
54A54LYS10.8860.9539.5200.4340.4340.0000.0000.0000.000
55A55VAL0-0.051-0.0197.114-0.139-0.1390.0000.0000.0000.000
56A56GLU-1-0.803-0.8804.8430.0460.0460.0000.0000.0000.000
57A57GLU-1-0.910-0.9555.758-0.820-0.8200.0000.0000.0000.000
58A58GLY00.0220.0113.2040.2680.7830.039-0.130-0.4250.000
59A59ASP-1-0.808-0.9142.342-13.374-8.7552.887-3.380-4.125-0.031
60A60VAL00.005-0.0042.2911.1230.9152.434-0.123-2.104-0.005
61A61ILE0-0.050-0.0164.2590.5940.641-0.0010.005-0.0510.000
62A62LEU00.008-0.0016.1860.1220.1220.0000.0000.0000.000
63A63VAL0-0.010-0.0079.1530.0810.0810.0000.0000.0000.000
64A64LYS10.7720.87412.9260.1850.1850.0000.0000.0000.000
65A65LYS10.9090.94115.9140.1910.1910.0000.0000.0000.000
66A66LEU00.0700.03217.725-0.014-0.0140.0000.0000.0000.000
67A67ASP-1-0.819-0.89318.996-0.212-0.2120.0000.0000.0000.000
68A68ARG10.7910.89117.5870.1990.1990.0000.0000.0000.000
69A69LEU00.0570.03914.502-0.013-0.0130.0000.0000.0000.000
70A70GLY00.0230.01217.379-0.005-0.0050.0000.0000.0000.000
71A71ARG10.7550.83520.6910.2240.2240.0000.0000.0000.000
72A72ASP-1-0.782-0.89324.363-0.165-0.1650.0000.0000.0000.000
73A73THR0-0.014-0.01623.830-0.021-0.0210.0000.0000.0000.000
74A74ALA00.0220.01023.560-0.021-0.0210.0000.0000.0000.000
75A75ASP-1-0.809-0.87722.579-0.265-0.2650.0000.0000.0000.000
76A76MET0-0.0120.00119.342-0.031-0.0310.0000.0000.0000.000
77A77ILE0-0.0170.00618.870-0.038-0.0380.0000.0000.0000.000
78A78GLN0-0.018-0.02919.787-0.023-0.0230.0000.0000.0000.000
79A79LEU00.0160.01715.763-0.018-0.0180.0000.0000.0000.000
80A80ILE0-0.006-0.00714.590-0.057-0.0570.0000.0000.0000.000
81A81LYS10.9170.96014.8540.2410.2410.0000.0000.0000.000
82A82GLU-1-0.828-0.85515.319-0.416-0.4160.0000.0000.0000.000
83A83PHE0-0.003-0.01910.760-0.008-0.0080.0000.0000.0000.000
84A84ASP-1-0.748-0.88011.158-0.854-0.8540.0000.0000.0000.000
85A85ALA0-0.073-0.02912.5230.0020.0020.0000.0000.0000.000
86A86GLN0-0.061-0.0269.7350.1280.1280.0000.0000.0000.000
87A87GLY00.0550.0279.224-0.021-0.0210.0000.0000.0000.000
88A88VAL0-0.076-0.0206.566-0.395-0.3950.0000.0000.0000.000
89A89SER00.0080.0065.6600.3770.3770.0000.0000.0000.000
90A90ILE0-0.003-0.0087.412-0.150-0.1500.0000.0000.0000.000
91A91ARG10.8610.9118.7930.5190.5190.0000.0000.0000.000
92A92PHE0-0.001-0.00510.4030.0320.0320.0000.0000.0000.000
93A93ILE0-0.024-0.02310.7260.0420.0420.0000.0000.0000.000
94A94ASP-1-0.806-0.89614.215-0.143-0.1430.0000.0000.0000.000
95A95ASP-1-0.801-0.90617.069-0.243-0.2430.0000.0000.0000.000
96A96GLY0-0.0250.00215.6130.0110.0110.0000.0000.0000.000
97A97ILE00.0280.01114.977-0.033-0.0330.0000.0000.0000.000
98A98SER0-0.005-0.0179.8870.0000.0000.0000.0000.0000.000
99A99THR0-0.063-0.04511.1280.0330.0330.0000.0000.0000.000
100A100ASP-1-0.863-0.9379.126-0.971-0.9710.0000.0000.0000.000
101A101GLY00.0960.05010.3010.1730.1730.0000.0000.0000.000
102A102GLU-1-0.835-0.89712.323-0.336-0.3360.0000.0000.0000.000
103A103MET0-0.056-0.01412.6380.0540.0540.0000.0000.0000.000
104A104GLY00.0420.01814.1360.0450.0450.0000.0000.0000.000
105A105LYS10.8350.90315.2440.4810.4810.0000.0000.0000.000
106A106MET00.0150.03018.3760.0460.0460.0000.0000.0000.000
107A107VAL00.0030.00016.3280.0350.0350.0000.0000.0000.000
108A108VAL00.002-0.00818.2130.0350.0350.0000.0000.0000.000
109A109THR0-0.014-0.01120.7920.0350.0350.0000.0000.0000.000
110A110ILE0-0.005-0.00722.6040.0240.0240.0000.0000.0000.000
111A111LEU0-0.017-0.00920.2200.0210.0210.0000.0000.0000.000
112A112SER00.007-0.00924.2980.0180.0180.0000.0000.0000.000
113A113ALA0-0.029-0.00726.6400.0160.0160.0000.0000.0000.000
114A114VAL00.002-0.00527.3050.0150.0150.0000.0000.0000.000
115A115ALA00.0150.01428.1050.0120.0120.0000.0000.0000.000
116A116GLN00.0220.00630.0080.0170.0170.0000.0000.0000.000
117A117ALA00.0060.01132.1690.0100.0100.0000.0000.0000.000
118A118GLU-1-0.855-0.92033.022-0.100-0.1000.0000.0000.0000.000
119A119ARG10.9110.94333.4110.1230.1230.0000.0000.0000.000
120A120GLN0-0.008-0.00736.1820.0030.0030.0000.0000.0000.000
121A121ARG10.8880.93433.0800.1160.1160.0000.0000.0000.000
122A122ILE0-0.044-0.00537.0990.0060.0060.0000.0000.0000.000
123A123LEU00.0040.01040.4570.0050.0050.0000.0000.0000.000
124A124GLU-1-0.864-0.92842.208-0.070-0.0700.0000.0000.0000.000
125A125ARG10.8960.93740.1340.0820.0820.0000.0000.0000.000
126A126THR0-0.066-0.04444.2190.0030.0030.0000.0000.0000.000
127A127ASN0-0.019-0.01246.5340.0030.0030.0000.0000.0000.000
128A128GLU-1-0.849-0.91148.212-0.048-0.0480.0000.0000.0000.000
129A129GLY00.0120.00450.8400.0020.0020.0000.0000.0000.000
130A130ARG10.8650.93547.2950.0630.0630.0000.0000.0000.000
131A131GLN00.0330.00551.1010.0010.0010.0000.0000.0000.000
132A132GLU-1-0.795-0.86353.643-0.040-0.0400.0000.0000.0000.000
133A133ALA00.0430.00554.9310.0020.0020.0000.0000.0000.000
134A134MET0-0.058-0.03254.4940.0010.0010.0000.0000.0000.000
135A135ALA0-0.015-0.00356.5770.0010.0010.0000.0000.0000.000
136A136LYS10.7630.87259.3030.0420.0420.0000.0000.0000.000
137A137GLY00.0370.03360.0990.0010.0010.0000.0000.0000.000
138A138VAL0-0.057-0.02756.7270.0010.0010.0000.0000.0000.000
139A139VAL0-0.003-0.00757.772-0.001-0.0010.0000.0000.0000.000
140A140PHE00.0010.00451.511-0.002-0.0020.0000.0000.0000.000
141A141GLY00.012-0.00152.4840.0000.0000.0000.0000.0000.000
142A142ARG10.9050.95550.7060.0540.0540.0000.0000.0000.000
143A143LYS11.0191.00353.3210.0460.0460.0000.0000.0000.000
144A144ARG10.8760.92656.6320.0400.0400.0000.0000.0000.000
145A145LYS10.9650.97355.6760.0420.0420.0000.0000.0000.000
146A146ILE0-0.052-0.01758.4060.0000.0000.0000.0000.0000.000
147A147ASP-1-0.799-0.89461.745-0.031-0.0310.0000.0000.0000.000
148A148ARG10.8380.87760.4840.0380.0380.0000.0000.0000.000
149A149ASP-1-0.826-0.89566.471-0.030-0.0300.0000.0000.0000.000
150A150ALA00.0180.01368.3840.0010.0010.0000.0000.0000.000
151A151VAL0-0.053-0.04064.6770.0000.0000.0000.0000.0000.000
152A152LEU0-0.005-0.00168.1420.0000.0000.0000.0000.0000.000
153A153ASN00.0410.02070.5810.0010.0010.0000.0000.0000.000
154A154MET0-0.038-0.02168.9150.0000.0000.0000.0000.0000.000
155A155TRP0-0.005-0.01069.0660.0000.0000.0000.0000.0000.000
156A156GLN0-0.012-0.00171.9320.0010.0010.0000.0000.0000.000
157A157GLN0-0.048-0.01375.3010.0010.0010.0000.0000.0000.000
158A158GLY00.0310.02375.2800.0010.0010.0000.0000.0000.000
159A159LEU0-0.061-0.02271.6640.0000.0000.0000.0000.0000.000
160A160GLY00.0820.03070.043-0.001-0.0010.0000.0000.0000.000
161A161ALA00.0650.00964.6180.0000.0000.0000.0000.0000.000
162A162SER0-0.005-0.01064.239-0.001-0.0010.0000.0000.0000.000
163A163HIS00.0830.07465.3060.0000.0000.0000.0000.0000.000
164A164ILE00.0330.02565.6870.0000.0000.0000.0000.0000.000
165A165SER0-0.039-0.04561.3460.0000.0000.0000.0000.0000.000
166A166LYS10.8780.94362.5140.0280.0280.0000.0000.0000.000
167A167THR0-0.032-0.03463.9450.0000.0000.0000.0000.0000.000
168A168MET0-0.0190.00064.1630.0010.0010.0000.0000.0000.000
169A169ASN0-0.041-0.00159.752-0.001-0.0010.0000.0000.0000.000
170A170ILE0-0.025-0.00358.993-0.002-0.0020.0000.0000.0000.000
171A171ALA00.0250.00155.6890.0000.0000.0000.0000.0000.000
172A172ARG10.9840.97157.6940.0360.0360.0000.0000.0000.000
173A173SER00.0130.01055.3840.0010.0010.0000.0000.0000.000
174A174THR00.004-0.00856.7080.0000.0000.0000.0000.0000.000
175A175VAL00.0370.03959.2490.0010.0010.0000.0000.0000.000
176A176TYR00.0710.03161.5890.0000.0000.0000.0000.0000.000
177A177LYS10.8880.96356.4290.0450.0450.0000.0000.0000.000
178A178VAL0-0.035-0.02861.4190.0000.0000.0000.0000.0000.000
179A179ILE00.0130.02363.6470.0010.0010.0000.0000.0000.000
180A180ASN0-0.006-0.02363.5830.0010.0010.0000.0000.0000.000
181A181GLU-1-0.810-0.86460.810-0.040-0.0400.0000.0000.0000.000
182A182SER0-0.002-0.01364.6190.0000.0000.0000.0000.0000.000
183A183ASN0-0.0400.00168.1680.0020.0020.0000.0000.0000.000