FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VZGZ1

Calculation Name: 1GDT-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1GDT

Chain ID: A

ChEMBL ID:

UniProt ID: P03012

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1588162.381497
FMO2-HF: Nuclear repulsion 1516011.025709
FMO2-HF: Total energy -72151.355788
FMO2-MP2: Total energy -72358.966498


3D Structure Molmil
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.
-101.41-93.4819.739-6.724-10.945-0.077
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 : 1 / q_Mulliken : 0.870 / q_NPA : 0.950
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].
3A3LEU00.0570.0443.200-1.0290.0510.2780.530-1.888-0.002
4A4PHE0-0.030-0.0404.3463.7883.9170.000-0.017-0.1130.000
56A56GLU-1-0.937-0.9593.414-61.948-60.7030.007-0.711-0.542-0.006
57A57GLU-1-0.894-0.9525.173-37.343-37.280-0.001-0.008-0.0540.000
58A58GLY00.0140.0073.502-10.918-10.3540.012-0.172-0.404-0.001
59A59ASP-1-0.843-0.9292.151-95.861-91.5697.466-5.903-5.855-0.062
60A60VAL00.0150.0062.4017.2387.7591.977-0.446-2.052-0.006
61A61ILE0-0.043-0.0144.1111.3581.3930.0000.003-0.0370.000
5A5GLY00.0460.0227.6190.3570.3570.0000.0000.0000.000
6A6TYR0-0.088-0.06710.3980.4030.4030.0000.0000.0000.000
7A7ALA00.0190.00013.8060.4880.4880.0000.0000.0000.000
8A8ARG10.8570.94417.32014.20114.2010.0000.0000.0000.000
9A9VAL0-0.046-0.03220.5680.2380.2380.0000.0000.0000.000
10A10SER00.0460.02523.3490.1240.1240.0000.0000.0000.000
11A11THR00.004-0.00226.703-0.004-0.0040.0000.0000.0000.000
12A12SER00.0310.01228.248-0.132-0.1320.0000.0000.0000.000
13A13GLN00.031-0.00226.192-0.223-0.2230.0000.0000.0000.000
14A14GLN00.0920.04526.353-0.441-0.4410.0000.0000.0000.000
15A15SER00.008-0.00925.6880.0630.0630.0000.0000.0000.000
16A16LEU0-0.049-0.01721.418-0.329-0.3290.0000.0000.0000.000
17A17ASP-1-0.861-0.93721.333-12.573-12.5730.0000.0000.0000.000
18A18ILE00.0140.00921.625-0.341-0.3410.0000.0000.0000.000
19A19GLN0-0.032-0.02118.647-0.493-0.4930.0000.0000.0000.000
20A20VAL00.0250.01017.084-0.755-0.7550.0000.0000.0000.000
21A21ARG10.7950.89116.88212.46512.4650.0000.0000.0000.000
22A22ALA00.0520.01917.562-0.323-0.3230.0000.0000.0000.000
23A23LEU0-0.008-0.00212.077-0.500-0.5000.0000.0000.0000.000
24A24LYS10.9240.95912.61314.02514.0250.0000.0000.0000.000
25A25ASP-1-0.847-0.90014.252-13.960-13.9600.0000.0000.0000.000
26A26ALA0-0.033-0.00511.616-0.013-0.0130.0000.0000.0000.000
27A27GLY00.0260.02210.527-1.010-1.0100.0000.0000.0000.000
28A28VAL0-0.040-0.0098.505-1.487-1.4870.0000.0000.0000.000
29A29LYS10.9540.9669.44123.15623.1560.0000.0000.0000.000
30A30ALA00.042-0.00511.477-0.304-0.3040.0000.0000.0000.000
31A31ASN0-0.0060.00013.315-0.114-0.1140.0000.0000.0000.000
32A32ARG10.8560.9436.74535.94135.9410.0000.0000.0000.000
33A33ILE00.0150.02110.840-0.991-0.9910.0000.0000.0000.000
34A34PHE0-0.0240.00111.5870.6490.6490.0000.0000.0000.000
35A35THR0-0.017-0.02715.4180.5410.5410.0000.0000.0000.000
36A36ASP-1-0.742-0.83618.636-14.689-14.6890.0000.0000.0000.000
37A37LYS10.9160.96021.57011.62911.6290.0000.0000.0000.000
38A38ALA0-0.011-0.01124.998-0.127-0.1270.0000.0000.0000.000
39A39SER0-0.007-0.02326.0900.3290.3290.0000.0000.0000.000
40A40GLY0-0.0130.01828.2940.3710.3710.0000.0000.0000.000
41A41SER0-0.018-0.01530.2420.0780.0780.0000.0000.0000.000
42A42SER0-0.036-0.03329.4460.2780.2780.0000.0000.0000.000
43A43SER0-0.032-0.02126.737-0.276-0.2760.0000.0000.0000.000
44A44ASP-1-0.784-0.85525.577-11.813-11.8130.0000.0000.0000.000
45A45ARG10.8330.91620.87613.32213.3220.0000.0000.0000.000
46A46LYS11.0361.01120.56812.34312.3430.0000.0000.0000.000
47A47GLY0-0.018-0.01018.704-0.521-0.5210.0000.0000.0000.000
48A48LEU00.011-0.00915.091-1.120-1.1200.0000.0000.0000.000
49A49ASP-1-0.819-0.89915.751-16.320-16.3200.0000.0000.0000.000
50A50LEU0-0.042-0.01915.677-0.628-0.6280.0000.0000.0000.000
51A51LEU0-0.062-0.0229.828-1.296-1.2960.0000.0000.0000.000
52A52ARG10.7610.81111.21715.01615.0160.0000.0000.0000.000
53A53MET0-0.0010.02112.363-0.324-0.3240.0000.0000.0000.000
54A54LYS10.8730.9459.10226.23426.2340.0000.0000.0000.000
55A55VAL0-0.069-0.0336.707-3.919-3.9190.0000.0000.0000.000
62A62LEU00.0140.0036.4011.5601.5600.0000.0000.0000.000
63A63VAL0-0.014-0.0049.3270.6900.6900.0000.0000.0000.000
64A64LYS10.8240.91313.09714.24414.2440.0000.0000.0000.000
65A65LYS10.9230.94715.98212.11512.1150.0000.0000.0000.000
66A66LEU00.0690.02917.932-0.238-0.2380.0000.0000.0000.000
67A67ASP-1-0.851-0.90519.144-12.401-12.4010.0000.0000.0000.000
68A68ARG10.8290.92217.77712.69812.6980.0000.0000.0000.000
69A69LEU00.0560.03414.543-0.416-0.4160.0000.0000.0000.000
70A70GLY00.0560.02717.626-0.131-0.1310.0000.0000.0000.000
71A71ARG10.8060.88620.72012.08712.0870.0000.0000.0000.000
72A72ASP-1-0.804-0.89724.478-10.306-10.3060.0000.0000.0000.000
73A73THR00.014-0.00723.949-0.475-0.4750.0000.0000.0000.000
74A74ALA00.0190.00023.626-0.476-0.4760.0000.0000.0000.000
75A75ASP-1-0.872-0.92022.351-13.468-13.4680.0000.0000.0000.000
76A76MET0-0.007-0.00119.452-0.734-0.7340.0000.0000.0000.000
77A77ILE0-0.0100.00918.985-0.717-0.7170.0000.0000.0000.000
78A78GLN0-0.003-0.01919.873-0.562-0.5620.0000.0000.0000.000
79A79LEU00.0250.02116.136-0.586-0.5860.0000.0000.0000.000
80A80ILE0-0.005-0.00614.559-1.090-1.0900.0000.0000.0000.000
81A81LYS10.9230.96514.92113.37213.3720.0000.0000.0000.000
82A82GLU-1-0.822-0.85214.998-18.237-18.2370.0000.0000.0000.000
83A83PHE0-0.016-0.02110.902-0.762-0.7620.0000.0000.0000.000
84A84ASP-1-0.768-0.89111.253-22.664-22.6640.0000.0000.0000.000
85A85ALA0-0.068-0.02912.533-0.692-0.6920.0000.0000.0000.000
86A86GLN0-0.047-0.0169.1351.0891.0890.0000.0000.0000.000
87A87GLY00.0580.0289.082-3.015-3.0150.0000.0000.0000.000
88A88VAL0-0.092-0.0356.711-4.428-4.4280.0000.0000.0000.000
89A89SER00.0170.0115.6143.8353.8350.0000.0000.0000.000
90A90ILE0-0.015-0.0197.189-1.392-1.3920.0000.0000.0000.000
91A91ARG10.9310.9688.66020.76020.7600.0000.0000.0000.000
92A92PHE00.005-0.00910.3010.1010.1010.0000.0000.0000.000
93A93ILE0-0.044-0.03110.5540.2830.2830.0000.0000.0000.000
94A94ASP-1-0.847-0.93214.053-13.502-13.5020.0000.0000.0000.000
95A95ASP-1-0.818-0.91516.803-13.048-13.0480.0000.0000.0000.000
96A96GLY0-0.043-0.00815.0740.2850.2850.0000.0000.0000.000
97A97ILE0-0.001-0.00914.509-0.783-0.7830.0000.0000.0000.000
98A98SER0-0.012-0.0209.912-1.197-1.1970.0000.0000.0000.000
99A99THR0-0.034-0.02711.3700.6290.6290.0000.0000.0000.000
100A100ASP-1-0.892-0.9598.838-26.069-26.0690.0000.0000.0000.000
101A101GLY00.0950.05210.3691.7471.7470.0000.0000.0000.000
102A102GLU-1-0.836-0.91112.365-16.787-16.7870.0000.0000.0000.000
103A103MET0-0.065-0.01112.5161.1681.1680.0000.0000.0000.000
104A104GLY00.0550.02114.3360.9500.9500.0000.0000.0000.000
105A105LYS10.8390.91115.42119.24219.2420.0000.0000.0000.000
106A106MET00.0170.03018.5441.0631.0630.0000.0000.0000.000
107A107VAL00.0030.00116.4220.7750.7750.0000.0000.0000.000
108A108VAL00.003-0.00918.1660.7420.7420.0000.0000.0000.000
109A109THR0-0.012-0.00920.8050.7810.7810.0000.0000.0000.000
110A110ILE0-0.005-0.00622.7420.6310.6310.0000.0000.0000.000
111A111LEU0-0.020-0.01020.1340.5400.5400.0000.0000.0000.000
112A112SER00.002-0.01324.3050.4460.4460.0000.0000.0000.000
113A113ALA0-0.024-0.00326.5920.4470.4470.0000.0000.0000.000
114A114VAL00.000-0.00727.5400.4500.4500.0000.0000.0000.000
115A115ALA00.0200.01528.0860.3710.3710.0000.0000.0000.000
116A116GLN00.0190.00729.9700.4120.4120.0000.0000.0000.000
117A117ALA00.0240.01632.1740.3370.3370.0000.0000.0000.000
118A118GLU-1-0.880-0.94933.118-8.167-8.1670.0000.0000.0000.000
119A119ARG10.8980.94133.7388.9598.9590.0000.0000.0000.000
120A120GLN00.0210.02436.2430.1260.1260.0000.0000.0000.000
121A121ARG10.9170.96233.5988.7748.7740.0000.0000.0000.000
122A122ILE0-0.021-0.01137.2450.2460.2460.0000.0000.0000.000
123A123LEU0-0.0040.00540.4870.1920.1920.0000.0000.0000.000
124A124GLU-1-0.943-0.97242.108-6.874-6.8740.0000.0000.0000.000
125A125ARG10.9270.96140.7787.4217.4210.0000.0000.0000.000
126A126THR0-0.069-0.04644.2480.1550.1550.0000.0000.0000.000
127A127ASN0-0.020-0.01446.5200.1590.1590.0000.0000.0000.000
128A128GLU-1-0.842-0.90948.221-5.756-5.7560.0000.0000.0000.000
129A129GLY00.0340.01750.9840.1030.1030.0000.0000.0000.000
130A130ARG10.8540.93346.9556.5166.5160.0000.0000.0000.000
131A131GLN00.0260.00051.0080.0380.0380.0000.0000.0000.000
132A132GLU-1-0.827-0.88153.553-5.340-5.3400.0000.0000.0000.000
133A133ALA00.011-0.01054.9160.1150.1150.0000.0000.0000.000
134A134MET0-0.049-0.02953.7930.0770.0770.0000.0000.0000.000
135A135ALA0-0.009-0.00156.5410.0780.0780.0000.0000.0000.000
136A136LYS10.8180.88559.2725.3125.3120.0000.0000.0000.000
137A137GLY00.0190.03560.1870.0910.0910.0000.0000.0000.000
138A138VAL0-0.051-0.02356.9620.0400.0400.0000.0000.0000.000
139A139VAL0-0.015-0.01057.860-0.063-0.0630.0000.0000.0000.000
140A140PHE00.0160.01051.601-0.112-0.1120.0000.0000.0000.000
141A141GLY0-0.0040.00251.5700.0150.0150.0000.0000.0000.000
142A142ARG10.9070.94951.5646.1336.1330.0000.0000.0000.000
143A143LYS11.0391.01453.4455.6255.6250.0000.0000.0000.000
144A144ARG10.9130.95056.8585.0955.0950.0000.0000.0000.000
145A145LYS10.9510.96655.7395.5265.5260.0000.0000.0000.000
146A146ILE0-0.050-0.01558.886-0.023-0.0230.0000.0000.0000.000
147A147ASP-1-0.814-0.89861.885-4.698-4.6980.0000.0000.0000.000
148A148ARG10.8400.87360.5115.1385.1380.0000.0000.0000.000
149A149ASP-1-0.828-0.89366.670-4.548-4.5480.0000.0000.0000.000
150A150ALA00.0120.00568.4090.0550.0550.0000.0000.0000.000
151A151VAL0-0.051-0.03964.8140.0140.0140.0000.0000.0000.000
152A152LEU00.0130.00568.2710.0210.0210.0000.0000.0000.000
153A153ASN00.0240.01970.7130.0850.0850.0000.0000.0000.000
154A154MET0-0.024-0.01769.1020.0190.0190.0000.0000.0000.000
155A155TRP00.000-0.00869.263-0.009-0.0090.0000.0000.0000.000
156A156GLN00.0030.00772.0380.0450.0450.0000.0000.0000.000
157A157GLN0-0.065-0.02075.3990.0750.0750.0000.0000.0000.000
158A158GLY00.0260.01975.4520.0440.0440.0000.0000.0000.000
159A159LEU0-0.053-0.02072.127-0.030-0.0300.0000.0000.0000.000
160A160GLY00.0710.02769.943-0.051-0.0510.0000.0000.0000.000
161A161ALA00.0770.01864.768-0.033-0.0330.0000.0000.0000.000
162A162SER0-0.016-0.02264.085-0.082-0.0820.0000.0000.0000.000
163A163HIS00.0300.03265.141-0.063-0.0630.0000.0000.0000.000
164A164ILE00.0480.02966.059-0.035-0.0350.0000.0000.0000.000
165A165SER0-0.061-0.05461.399-0.033-0.0330.0000.0000.0000.000
166A166LYS10.9010.96462.6884.7064.7060.0000.0000.0000.000
167A167THR0-0.021-0.02264.0320.0090.0090.0000.0000.0000.000
168A168MET0-0.0210.00064.5050.0460.0460.0000.0000.0000.000
169A169ASN0-0.0290.00159.866-0.048-0.0480.0000.0000.0000.000
170A170ILE0-0.0220.00159.305-0.115-0.1150.0000.0000.0000.000
171A171ALA00.0270.00655.9760.0130.0130.0000.0000.0000.000
172A172ARG11.0080.98957.9815.3295.3290.0000.0000.0000.000
173A173SER00.0100.00855.4470.0880.0880.0000.0000.0000.000
174A174THR0-0.033-0.02657.2440.0130.0130.0000.0000.0000.000
175A175VAL00.0270.03259.6280.0470.0470.0000.0000.0000.000
176A176TYR00.0600.02061.6360.0300.0300.0000.0000.0000.000
177A177LYS10.9050.98156.9985.5925.5920.0000.0000.0000.000
178A178VAL0-0.044-0.03861.6420.0190.0190.0000.0000.0000.000
179A179ILE00.0060.02163.9470.0430.0430.0000.0000.0000.000
180A180ASN00.014-0.00963.6800.0540.0540.0000.0000.0000.000
181A181GLU-1-0.855-0.90760.960-5.302-5.3020.0000.0000.0000.000
182A182SER0-0.056-0.04164.9180.0180.0180.0000.0000.0000.000
183A183ASN-1-0.938-0.94068.301-4.511-4.5110.0000.0000.0000.000