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: R98M8

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1590701.249945
FMO2-HF: Nuclear repulsion 1518552.134961
FMO2-HF: Total energy -72149.114984
FMO2-MP2: Total energy -72357.149445


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.
-13.599-6.5684.294-3.179-8.145-0.034
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 : 0.023 / q_NPA : 0.028
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].
3A3LEU00.0690.0423.576-1.580-0.9691.4650.287-2.3630.000
4A4PHE0-0.037-0.0504.692-0.1210.0150.001-0.025-0.1120.000
5A5GLY00.0350.0237.945-0.220-0.2200.0000.0000.0000.000
6A6TYR0-0.058-0.05010.7000.0220.0220.0000.0000.0000.000
7A7ALA00.007-0.00213.899-0.028-0.0280.0000.0000.0000.000
8A8ARG10.9621.02517.3680.0350.0350.0000.0000.0000.000
9A9VAL0-0.074-0.04720.568-0.003-0.0030.0000.0000.0000.000
10A10SER00.0620.03123.522-0.005-0.0050.0000.0000.0000.000
11A11THR00.002-0.00426.7620.0060.0060.0000.0000.0000.000
12A12SER00.038-0.00528.0450.0070.0070.0000.0000.0000.000
13A13GLN00.036-0.01626.138-0.004-0.0040.0000.0000.0000.000
14A14GLN00.1380.09726.2540.0060.0060.0000.0000.0000.000
15A15SER0-0.009-0.02126.0260.0010.0010.0000.0000.0000.000
16A16LEU0-0.059-0.03021.623-0.004-0.0040.0000.0000.0000.000
17A17ASP-1-0.858-0.93221.6190.1520.1520.0000.0000.0000.000
18A18ILE00.0520.02721.4680.0110.0110.0000.0000.0000.000
19A19GLN0-0.057-0.04218.744-0.017-0.0170.0000.0000.0000.000
20A20VAL00.0050.01317.1650.0080.0080.0000.0000.0000.000
21A21ARG10.9210.97317.070-0.137-0.1370.0000.0000.0000.000
22A22ALA00.0250.01017.2700.0170.0170.0000.0000.0000.000
23A23LEU00.0080.00111.8490.0030.0030.0000.0000.0000.000
24A24LYS10.9050.95512.611-0.266-0.2660.0000.0000.0000.000
25A25ASP-1-0.945-0.96914.3960.2070.2070.0000.0000.0000.000
26A26ALA0-0.050-0.01611.498-0.017-0.0170.0000.0000.0000.000
27A27GLY00.0340.02210.3560.0010.0010.0000.0000.0000.000
28A28VAL0-0.046-0.0108.6450.2200.2200.0000.0000.0000.000
29A29LYS10.9480.9739.710-1.002-1.0020.0000.0000.0000.000
30A30ALA00.051-0.00111.519-0.038-0.0380.0000.0000.0000.000
31A31ASN00.0230.00912.9900.0280.0280.0000.0000.0000.000
32A32ARG10.7860.9187.329-1.913-1.9130.0000.0000.0000.000
33A33ILE00.0370.02310.977-0.011-0.0110.0000.0000.0000.000
34A34PHE0-0.034-0.00511.9840.0050.0050.0000.0000.0000.000
35A35THR0-0.014-0.01615.572-0.047-0.0470.0000.0000.0000.000
36A36ASP-1-0.741-0.87218.6810.1060.1060.0000.0000.0000.000
37A37LYS10.8670.94021.517-0.128-0.1280.0000.0000.0000.000
38A38ALA0-0.021-0.01624.943-0.002-0.0020.0000.0000.0000.000
39A39SER00.0150.00726.095-0.004-0.0040.0000.0000.0000.000
40A40GLY0-0.0240.01728.278-0.003-0.0030.0000.0000.0000.000
41A41SER0-0.022-0.02430.181-0.004-0.0040.0000.0000.0000.000
42A42SER0-0.017-0.00130.025-0.003-0.0030.0000.0000.0000.000
43A43SER0-0.059-0.04327.153-0.004-0.0040.0000.0000.0000.000
44A44ASP-1-0.873-0.94725.8930.0620.0620.0000.0000.0000.000
45A45ARG10.9320.98421.167-0.011-0.0110.0000.0000.0000.000
46A46LYS11.0511.02821.076-0.159-0.1590.0000.0000.0000.000
47A47GLY00.0190.00918.9370.0210.0210.0000.0000.0000.000
48A48LEU0-0.009-0.01515.6290.0340.0340.0000.0000.0000.000
49A49ASP-1-0.888-0.94916.1760.0760.0760.0000.0000.0000.000
50A50LEU0-0.063-0.02015.6900.0280.0280.0000.0000.0000.000
51A51LEU0-0.026-0.01410.5870.0580.0580.0000.0000.0000.000
52A52ARG10.8470.90011.5200.0320.0320.0000.0000.0000.000
53A53MET0-0.0070.01712.955-0.020-0.0200.0000.0000.0000.000
54A54LYS10.8440.9268.897-0.947-0.9470.0000.0000.0000.000
55A55VAL0-0.072-0.0427.2080.2700.2700.0000.0000.0000.000
56A56GLU-1-0.945-0.9554.6703.1203.241-0.001-0.012-0.1070.000
57A57GLU-1-0.912-0.9655.463-1.066-1.0660.0000.0000.0000.000
58A58GLY00.0140.0143.9240.2120.5810.003-0.080-0.2920.000
59A59ASP-1-0.860-0.9352.736-8.946-3.8811.242-2.949-3.358-0.032
60A60VAL00.0250.0182.444-1.263-0.5991.585-0.394-1.855-0.002
61A61ILE0-0.046-0.0104.3641.1901.255-0.001-0.006-0.0580.000
62A62LEU00.0030.0036.342-0.171-0.1710.0000.0000.0000.000
63A63VAL0-0.002-0.0229.1700.1280.1280.0000.0000.0000.000
64A64LYS10.8480.93512.951-0.035-0.0350.0000.0000.0000.000
65A65LYS10.9891.01215.9070.0390.0390.0000.0000.0000.000
66A66LEU00.1130.05117.6910.0160.0160.0000.0000.0000.000
67A67ASP-1-0.880-0.93818.594-0.068-0.0680.0000.0000.0000.000
68A68ARG10.8530.91817.6390.0380.0380.0000.0000.0000.000
69A69LEU0-0.007-0.00814.6500.0300.0300.0000.0000.0000.000
70A70GLY00.0290.00617.5630.0070.0070.0000.0000.0000.000
71A71ARG10.8630.94620.9330.0450.0450.0000.0000.0000.000
72A72ASP-1-0.835-0.92824.708-0.080-0.0800.0000.0000.0000.000
73A73THR00.0480.01323.862-0.008-0.0080.0000.0000.0000.000
74A74ALA00.0230.00723.389-0.017-0.0170.0000.0000.0000.000
75A75ASP-1-0.973-0.99822.196-0.072-0.0720.0000.0000.0000.000
76A76MET0-0.0010.00919.466-0.015-0.0150.0000.0000.0000.000
77A77ILE00.0090.01119.006-0.029-0.0290.0000.0000.0000.000
78A78GLN00.011-0.01619.493-0.040-0.0400.0000.0000.0000.000
79A79LEU00.0260.03716.519-0.010-0.0100.0000.0000.0000.000
80A80ILE0-0.014-0.01514.452-0.016-0.0160.0000.0000.0000.000
81A81LYS10.9250.96314.8690.1800.1800.0000.0000.0000.000
82A82GLU-1-0.899-0.92115.158-0.093-0.0930.0000.0000.0000.000
83A83PHE0-0.026-0.03610.9880.0160.0160.0000.0000.0000.000
84A84ASP-1-0.809-0.91011.130-0.734-0.7340.0000.0000.0000.000
85A85ALA0-0.067-0.02112.477-0.073-0.0730.0000.0000.0000.000
86A86GLN0-0.061-0.0229.698-0.031-0.0310.0000.0000.0000.000
87A87GLY00.0620.0189.2730.0250.0250.0000.0000.0000.000
88A88VAL0-0.102-0.0346.897-0.433-0.4330.0000.0000.0000.000
89A89SER00.0350.0215.8680.0780.0780.0000.0000.0000.000
90A90ILE0-0.014-0.0287.4360.0290.0290.0000.0000.0000.000
91A91ARG10.9460.9698.3780.6010.6010.0000.0000.0000.000
92A92PHE0-0.008-0.01510.0210.1220.1220.0000.0000.0000.000
93A93ILE00.008-0.01710.458-0.002-0.0020.0000.0000.0000.000
94A94ASP-1-0.920-0.96213.611-0.071-0.0710.0000.0000.0000.000
95A95ASP-1-0.853-0.93316.068-0.169-0.1690.0000.0000.0000.000
96A96GLY0-0.100-0.01914.700-0.010-0.0100.0000.0000.0000.000
97A97ILE0-0.014-0.02314.056-0.076-0.0760.0000.0000.0000.000
98A98SER00.008-0.00110.089-0.059-0.0590.0000.0000.0000.000
99A99THR0-0.022-0.00710.9700.0120.0120.0000.0000.0000.000
100A100ASP-1-0.906-0.9698.641-1.626-1.6260.0000.0000.0000.000
101A101GLY00.0960.04110.0250.1410.1410.0000.0000.0000.000
102A102GLU-1-0.900-0.95611.793-0.440-0.4400.0000.0000.0000.000
103A103MET0-0.0260.00712.6950.0800.0800.0000.0000.0000.000
104A104GLY00.0590.03913.8700.0810.0810.0000.0000.0000.000
105A105LYS10.9130.95314.8510.6370.6370.0000.0000.0000.000
106A106MET00.0150.01818.1120.0640.0640.0000.0000.0000.000
107A107VAL0-0.003-0.00815.7770.0490.0490.0000.0000.0000.000
108A108VAL00.019-0.00217.9270.0520.0520.0000.0000.0000.000
109A109THR0-0.022-0.01220.4860.0410.0410.0000.0000.0000.000
110A110ILE00.0130.01222.4980.0300.0300.0000.0000.0000.000
111A111LEU0-0.0300.00219.9430.0280.0280.0000.0000.0000.000
112A112SER0-0.024-0.02724.0430.0240.0240.0000.0000.0000.000
113A113ALA0-0.0170.01126.4770.0130.0130.0000.0000.0000.000
114A114VAL00.005-0.02826.9780.0160.0160.0000.0000.0000.000
115A115ALA00.0260.02828.0710.0130.0130.0000.0000.0000.000
116A116GLN00.013-0.00629.8710.0130.0130.0000.0000.0000.000
117A117ALA0-0.0120.01031.8820.0080.0080.0000.0000.0000.000
118A118GLU-1-0.939-0.99932.598-0.072-0.0720.0000.0000.0000.000
119A119ARG10.9430.97633.6860.0820.0820.0000.0000.0000.000
120A120GLN00.0130.01035.9670.0070.0070.0000.0000.0000.000
121A121ARG10.9490.99333.3770.1010.1010.0000.0000.0000.000
122A122ILE0-0.002-0.00437.4840.0050.0050.0000.0000.0000.000
123A123LEU0-0.022-0.02340.3520.0040.0040.0000.0000.0000.000
124A124GLU-1-0.933-0.96341.836-0.062-0.0620.0000.0000.0000.000
125A125ARG10.9310.96640.9010.0590.0590.0000.0000.0000.000
126A126THR0-0.076-0.03744.3780.0030.0030.0000.0000.0000.000
127A127ASN00.0020.00246.3270.0040.0040.0000.0000.0000.000
128A128GLU-1-0.871-0.91748.025-0.038-0.0380.0000.0000.0000.000
129A129GLY00.0440.02150.8370.0020.0020.0000.0000.0000.000
130A130ARG10.8790.92646.6490.0360.0360.0000.0000.0000.000
131A131GLN00.0230.00650.9430.0020.0020.0000.0000.0000.000
132A132GLU-1-0.903-0.93353.472-0.029-0.0290.0000.0000.0000.000
133A133ALA0-0.001-0.01754.9700.0020.0020.0000.0000.0000.000
134A134MET0-0.056-0.03353.3800.0020.0020.0000.0000.0000.000
135A135ALA0-0.031-0.01256.3440.0010.0010.0000.0000.0000.000
136A136LYS10.9020.94159.0910.0270.0270.0000.0000.0000.000
137A137GLY00.0480.03659.9750.0010.0010.0000.0000.0000.000
138A138VAL0-0.077-0.02256.8080.0010.0010.0000.0000.0000.000
139A139VAL0-0.0020.00258.1280.0000.0000.0000.0000.0000.000
140A140PHE00.0070.01752.0050.0000.0000.0000.0000.0000.000
141A141GLY00.001-0.00152.1450.0010.0010.0000.0000.0000.000
142A142ARG10.9200.95652.1460.0080.0080.0000.0000.0000.000
143A143LYS11.0321.01653.7220.0110.0110.0000.0000.0000.000
144A144ARG10.9510.96956.9870.0110.0110.0000.0000.0000.000
145A145LYS10.9660.97256.1520.0020.0020.0000.0000.0000.000
146A146ILE0-0.030-0.01059.5490.0010.0010.0000.0000.0000.000
147A147ASP-1-0.816-0.90562.034-0.003-0.0030.0000.0000.0000.000
148A148ARG10.8690.90260.4040.0080.0080.0000.0000.0000.000
149A149ASP-1-0.827-0.88966.713-0.005-0.0050.0000.0000.0000.000
150A150ALA00.0240.01668.9710.0000.0000.0000.0000.0000.000
151A151VAL0-0.056-0.04565.3270.0000.0000.0000.0000.0000.000
152A152LEU00.0090.00068.6330.0000.0000.0000.0000.0000.000
153A153ASN00.0600.03770.9260.0000.0000.0000.0000.0000.000
154A154MET00.000-0.00169.7130.0010.0010.0000.0000.0000.000
155A155TRP0-0.017-0.01269.6630.0010.0010.0000.0000.0000.000
156A156GLN0-0.0070.00072.5300.0000.0000.0000.0000.0000.000
157A157GLN0-0.084-0.01875.5630.0000.0000.0000.0000.0000.000
158A158GLY00.0110.00375.7720.0000.0000.0000.0000.0000.000
159A159LEU0-0.061-0.02472.3870.0010.0010.0000.0000.0000.000
160A160GLY00.0770.02970.293-0.001-0.0010.0000.0000.0000.000
161A161ALA00.0640.00865.0460.0000.0000.0000.0000.0000.000
162A162SER0-0.020-0.02764.5700.0000.0000.0000.0000.0000.000
163A163HIS00.0190.03565.6210.0010.0010.0000.0000.0000.000
164A164ILE00.0360.02366.7470.0000.0000.0000.0000.0000.000
165A165SER0-0.046-0.04862.0270.0000.0000.0000.0000.0000.000
166A166LYS10.9400.98163.438-0.007-0.0070.0000.0000.0000.000
167A167THR0-0.015-0.02564.5990.0010.0010.0000.0000.0000.000
168A168MET0-0.0150.00665.1170.0000.0000.0000.0000.0000.000
169A169ASN0-0.0230.00160.4100.0000.0000.0000.0000.0000.000
170A170ILE0-0.0470.00959.8180.0000.0000.0000.0000.0000.000
171A171ALA00.0100.00056.6020.0010.0010.0000.0000.0000.000
172A172ARG11.0380.99358.620-0.004-0.0040.0000.0000.0000.000
173A173SER00.0200.01456.1450.0000.0000.0000.0000.0000.000
174A174THR0-0.014-0.01458.019-0.001-0.0010.0000.0000.0000.000
175A175VAL00.0330.03360.070-0.001-0.0010.0000.0000.0000.000
176A176TYR00.0610.01561.8490.0000.0000.0000.0000.0000.000
177A177LYS10.8950.97157.7900.0060.0060.0000.0000.0000.000
178A178VAL0-0.030-0.04761.703-0.001-0.0010.0000.0000.0000.000
179A179ILE00.0080.02164.1180.0000.0000.0000.0000.0000.000
180A180ASN0-0.017-0.02963.9030.0000.0000.0000.0000.0000.000
181A181GLU-1-0.925-0.96061.013-0.011-0.0110.0000.0000.0000.000
182A182SER0-0.036-0.01165.1340.0000.0000.0000.0000.0000.000
183A183ASN0-0.0200.02168.3570.0000.0000.0000.0000.0000.000