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: J4YZ9

Calculation Name: 3TGO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | glycerol | chloride ion | potassium ion

Ligand 3-letter code: PO4 | GOL | CL | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TGO

Chain ID: A

ChEMBL ID:

UniProt ID: P0A903

Base Structure: X-ray

Registration Date: 2025-09-02

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2409571.236156
FMO2-HF: Nuclear repulsion 2322063.69157
FMO2-HF: Total energy -87507.544586
FMO2-MP2: Total energy -87762.843191


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:26:GLU)


Summations of interaction energy for fragment #1(A:26:GLU)
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.
3.9026.5550.178-1.022-1.809-0.004
Interaction energy analysis for fragmet #1(A:26:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.114 / q_NPA : -0.065
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].
3A28PRO00.0530.0323.0465.3627.7050.181-0.986-1.539-0.004
4A29ASP-1-0.896-0.9434.7432.5582.673-0.001-0.003-0.1100.000
28A53THR0-0.069-0.0483.912-1.270-1.181-0.001-0.026-0.0630.000
36A61ARG10.8110.8984.291-0.234-0.128-0.001-0.007-0.0970.000
5A30ASN0-0.038-0.0077.302-0.361-0.3610.0000.0000.0000.000
6A31PRO00.0420.00910.207-0.117-0.1170.0000.0000.0000.000
7A32PRO00.0210.00813.040-0.488-0.4880.0000.0000.0000.000
8A33ASN00.0480.02414.214-0.478-0.4780.0000.0000.0000.000
9A34GLU-1-0.850-0.91113.159-0.493-0.4930.0000.0000.0000.000
10A35ILE0-0.0050.0198.901-0.555-0.5550.0000.0000.0000.000
11A36TYR0-0.041-0.04811.952-0.585-0.5850.0000.0000.0000.000
12A37ALA00.0200.01215.055-0.126-0.1260.0000.0000.0000.000
13A38THR0-0.041-0.03210.396-0.129-0.1290.0000.0000.0000.000
14A39ALA0-0.033-0.02612.210-0.440-0.4400.0000.0000.0000.000
15A40GLN0-0.010-0.00113.044-0.008-0.0080.0000.0000.0000.000
16A41GLN00.0030.00515.5170.2230.2230.0000.0000.0000.000
17A42LYS10.8950.95210.8135.6095.6090.0000.0000.0000.000
18A43LEU0-0.035-0.01914.094-0.087-0.0870.0000.0000.0000.000
19A44GLN0-0.063-0.03616.3470.3040.3040.0000.0000.0000.000
20A45ASP-1-0.936-0.96216.079-3.095-3.0950.0000.0000.0000.000
21A46GLY0-0.011-0.00518.1020.0350.0350.0000.0000.0000.000
22A47ASN0-0.048-0.01912.202-0.895-0.8950.0000.0000.0000.000
23A48TRP00.0550.02012.490-0.865-0.8650.0000.0000.0000.000
24A49ARG10.9190.9498.1596.8616.8610.0000.0000.0000.000
25A50GLN00.0280.0217.949-1.568-1.5680.0000.0000.0000.000
26A51ALA00.0320.0198.849-0.752-0.7520.0000.0000.0000.000
27A52ILE00.0120.0059.701-0.114-0.1140.0000.0000.0000.000
29A54GLN0-0.001-0.0046.805-0.258-0.2580.0000.0000.0000.000
30A55LEU00.0070.0008.5671.0631.0630.0000.0000.0000.000
31A56GLU-1-0.837-0.8978.088-4.369-4.3690.0000.0000.0000.000
32A57ALA0-0.024-0.0045.7871.0981.0980.0000.0000.0000.000
33A58LEU0-0.029-0.0057.7771.6021.6020.0000.0000.0000.000
34A59ASP-1-0.896-0.96011.261-1.150-1.1500.0000.0000.0000.000
35A60ASN0-0.077-0.0589.6461.0271.0270.0000.0000.0000.000
37A62TYR0-0.039-0.01711.1670.5960.5960.0000.0000.0000.000
38A63PRO00.0750.04514.795-0.154-0.1540.0000.0000.0000.000
39A64PHE0-0.061-0.04117.355-0.073-0.0730.0000.0000.0000.000
40A65GLY00.0250.02218.5240.0980.0980.0000.0000.0000.000
41A66PRO0-0.041-0.03119.427-0.065-0.0650.0000.0000.0000.000
42A67TYR0-0.028-0.03017.148-0.051-0.0510.0000.0000.0000.000
43A68SER00.0400.03318.242-0.211-0.2110.0000.0000.0000.000
44A69GLN00.0390.01219.067-0.218-0.2180.0000.0000.0000.000
45A70GLN00.0590.01520.702-0.092-0.0920.0000.0000.0000.000
46A71VAL00.0230.02414.342-0.205-0.2050.0000.0000.0000.000
47A72GLN00.0200.00416.758-0.205-0.2050.0000.0000.0000.000
48A73LEU0-0.041-0.01818.524-0.084-0.0840.0000.0000.0000.000
49A74ASP-1-0.784-0.88216.893-2.365-2.3650.0000.0000.0000.000
50A75LEU0-0.016-0.00412.412-0.272-0.2720.0000.0000.0000.000
51A76ILE0-0.041-0.01016.238-0.090-0.0900.0000.0000.0000.000
52A77TYR0-0.020-0.00719.4880.0410.0410.0000.0000.0000.000
53A78ALA00.0320.00614.816-0.010-0.0100.0000.0000.0000.000
54A79TYR0-0.046-0.06912.6900.1420.1420.0000.0000.0000.000
55A80TYR0-0.031-0.01716.8500.0670.0670.0000.0000.0000.000
56A81LYS10.8800.94918.6632.2082.2080.0000.0000.0000.000
57A82ASN0-0.056-0.04313.988-0.214-0.2140.0000.0000.0000.000
58A83ALA00.0030.01717.086-0.034-0.0340.0000.0000.0000.000
59A84ASP-1-0.758-0.83613.773-4.620-4.6200.0000.0000.0000.000
60A85LEU0-0.016-0.01617.4890.0940.0940.0000.0000.0000.000
61A86PRO00.011-0.01819.5990.1170.1170.0000.0000.0000.000
62A87LEU00.0050.00913.8790.1920.1920.0000.0000.0000.000
63A88ALA00.0460.02917.9610.0810.0810.0000.0000.0000.000
64A89GLN00.0190.00720.0250.2500.2500.0000.0000.0000.000
65A90ALA0-0.0020.01318.7690.1500.1500.0000.0000.0000.000
66A91ALA00.0420.01417.8110.1660.1660.0000.0000.0000.000
67A92ILE00.0130.00319.7460.1820.1820.0000.0000.0000.000
68A93ASP-1-0.835-0.91623.448-1.007-1.0070.0000.0000.0000.000
69A94ARG10.8590.93619.7141.3171.3170.0000.0000.0000.000
70A95PHE00.0430.02822.2570.1480.1480.0000.0000.0000.000
71A96ILE00.015-0.00924.0080.1130.1130.0000.0000.0000.000
72A97ARG10.8690.94525.9210.6330.6330.0000.0000.0000.000
73A98LEU0-0.002-0.00822.4810.0990.0990.0000.0000.0000.000
74A99ASN0-0.0210.00823.8980.1200.1200.0000.0000.0000.000
75A100PRO00.0150.00528.132-0.029-0.0290.0000.0000.0000.000
76A101THR0-0.021-0.01531.415-0.002-0.0020.0000.0000.0000.000
77A102HIS00.0000.00726.7870.0070.0070.0000.0000.0000.000
78A103PRO00.007-0.01030.492-0.012-0.0120.0000.0000.0000.000
79A104ASN00.0180.02427.2050.0360.0360.0000.0000.0000.000
80A105ILE0-0.001-0.00428.867-0.093-0.0930.0000.0000.0000.000
81A106ASP-1-0.782-0.86330.340-0.901-0.9010.0000.0000.0000.000
82A107TYR00.013-0.00423.980-0.054-0.0540.0000.0000.0000.000
83A108VAL00.0000.00525.057-0.080-0.0800.0000.0000.0000.000
84A109MET0-0.019-0.01027.237-0.024-0.0240.0000.0000.0000.000
85A110TYR0-0.064-0.05829.297-0.026-0.0260.0000.0000.0000.000
86A111MET00.0180.01023.1210.0010.0010.0000.0000.0000.000
87A112ARG10.7720.90826.1511.0941.0940.0000.0000.0000.000
88A113GLY00.0480.01327.522-0.016-0.0160.0000.0000.0000.000
89A114LEU0-0.006-0.01227.3800.0090.0090.0000.0000.0000.000
90A115THR0-0.045-0.03123.585-0.106-0.1060.0000.0000.0000.000
91A116ASN0-0.025-0.01625.919-0.060-0.0600.0000.0000.0000.000
92A117MET00.0140.02628.6880.0350.0350.0000.0000.0000.000
93A118ALA00.0090.01425.9250.0250.0250.0000.0000.0000.000
94A119LEU00.0200.00824.065-0.041-0.0410.0000.0000.0000.000
95A120ASP-1-0.853-0.92427.602-0.892-0.8920.0000.0000.0000.000
96A121ASP-1-0.858-0.92830.378-1.052-1.0520.0000.0000.0000.000
97A122SER0-0.051-0.03426.8750.0130.0130.0000.0000.0000.000
98A123ALA0-0.0020.00528.8250.0100.0100.0000.0000.0000.000
99A124LEU0-0.036-0.02130.8100.0510.0510.0000.0000.0000.000
100A125GLN0-0.038-0.02429.010-0.017-0.0170.0000.0000.0000.000
101A126GLY0-0.015-0.00630.5050.0160.0160.0000.0000.0000.000
102A127PHE0-0.0060.00331.1540.0180.0180.0000.0000.0000.000
103A128PHE00.0050.00634.5810.0690.0690.0000.0000.0000.000
104A129GLY0-0.022-0.01236.580-0.001-0.0010.0000.0000.0000.000
105A130VAL0-0.080-0.04336.7190.0410.0410.0000.0000.0000.000
106A131ASP-1-0.793-0.88137.938-0.801-0.8010.0000.0000.0000.000
107A132ARG10.8200.89339.4670.5840.5840.0000.0000.0000.000
108A133SER00.0300.02140.906-0.026-0.0260.0000.0000.0000.000
109A134ASP-1-0.833-0.91143.146-0.545-0.5450.0000.0000.0000.000
110A135ARG10.8660.92535.1160.8490.8490.0000.0000.0000.000
111A136ASP-1-0.796-0.88237.899-0.675-0.6750.0000.0000.0000.000
112A137PRO0-0.0180.01635.738-0.052-0.0520.0000.0000.0000.000
113A138GLN00.000-0.02930.7870.0480.0480.0000.0000.0000.000
114A139HIS0-0.038-0.01129.0980.0080.0080.0000.0000.0000.000
115A140ALA00.0500.02732.179-0.017-0.0170.0000.0000.0000.000
116A141ARG10.8480.90034.9970.6650.6650.0000.0000.0000.000
117A142ALA0-0.024-0.00731.4860.0280.0280.0000.0000.0000.000
118A143ALA00.0460.01131.9880.0090.0090.0000.0000.0000.000
119A144PHE00.0040.00833.0350.0190.0190.0000.0000.0000.000
120A145SER0-0.0100.00634.8010.0380.0380.0000.0000.0000.000
121A146ASP-1-0.835-0.92830.652-0.955-0.9550.0000.0000.0000.000
122A147PHE00.028-0.00531.7550.0140.0140.0000.0000.0000.000
123A148SER0-0.040-0.02835.2770.0480.0480.0000.0000.0000.000
124A149LYS10.8370.92532.7900.8250.8250.0000.0000.0000.000
125A150LEU00.0060.01633.1020.0280.0280.0000.0000.0000.000
126A151VAL0-0.005-0.00635.8940.0290.0290.0000.0000.0000.000
127A152ARG10.9050.95739.3680.5700.5700.0000.0000.0000.000
128A153GLY0-0.0050.01038.5010.0310.0310.0000.0000.0000.000
129A154TYR00.009-0.00834.8180.0220.0220.0000.0000.0000.000
130A155PRO00.0400.03238.788-0.033-0.0330.0000.0000.0000.000
131A156ASN0-0.026-0.02841.300-0.006-0.0060.0000.0000.0000.000
132A157SER0-0.035-0.03534.781-0.019-0.0190.0000.0000.0000.000
133A158GLN00.004-0.00132.4530.0290.0290.0000.0000.0000.000
134A159TYR00.0260.00530.523-0.036-0.0360.0000.0000.0000.000
135A160THR00.0030.00334.911-0.023-0.0230.0000.0000.0000.000
136A161THR00.0190.01838.0150.0200.0200.0000.0000.0000.000
137A162ASP-1-0.793-0.85234.167-0.966-0.9660.0000.0000.0000.000
138A163ALA00.0400.01535.200-0.002-0.0020.0000.0000.0000.000
139A164THR0-0.008-0.02036.5640.0230.0230.0000.0000.0000.000
140A165LYS10.9150.95739.0840.6490.6490.0000.0000.0000.000
141A166ARG10.8610.89832.3101.0621.0620.0000.0000.0000.000
142A167LEU0-0.0110.00137.7200.0080.0080.0000.0000.0000.000
143A168VAL0-0.0030.00039.7330.0190.0190.0000.0000.0000.000
144A169PHE00.0090.00536.4840.0160.0160.0000.0000.0000.000
145A170LEU0-0.019-0.01134.9690.0010.0010.0000.0000.0000.000
146A171LYS10.8380.91039.1480.5080.5080.0000.0000.0000.000
147A172ASP-1-0.820-0.89242.607-0.573-0.5730.0000.0000.0000.000
148A173ARG10.8640.92334.9540.8990.8990.0000.0000.0000.000
149A174LEU0-0.052-0.03038.4630.0100.0100.0000.0000.0000.000
150A175ALA00.0410.02341.9220.0170.0170.0000.0000.0000.000
151A176LYS10.8570.90343.7920.6030.6030.0000.0000.0000.000
152A177TYR00.0010.03041.6800.0150.0150.0000.0000.0000.000
153A178GLU-1-0.808-0.88043.825-0.474-0.4740.0000.0000.0000.000
154A179TYR0-0.060-0.05446.6610.0230.0230.0000.0000.0000.000
155A180SER00.022-0.00545.6090.0170.0170.0000.0000.0000.000
156A181VAL0-0.033-0.01045.4170.0140.0140.0000.0000.0000.000
157A182ALA0-0.008-0.00148.2100.0210.0210.0000.0000.0000.000
158A183GLU-1-0.858-0.89950.398-0.425-0.4250.0000.0000.0000.000
159A184TYR00.0350.01948.3260.0170.0170.0000.0000.0000.000
160A185TYR0-0.011-0.02348.8540.0120.0120.0000.0000.0000.000
161A186THR0-0.031-0.02953.4330.0230.0230.0000.0000.0000.000
162A187GLU-1-0.903-0.94552.305-0.395-0.3950.0000.0000.0000.000
163A188ARG10.7730.87251.3760.3980.3980.0000.0000.0000.000
164A189GLY00.0210.02156.4950.0090.0090.0000.0000.0000.000
165A190ALA0-0.0100.00755.1640.0110.0110.0000.0000.0000.000
166A191TRP00.037-0.00256.587-0.013-0.0130.0000.0000.0000.000
167A192VAL00.0450.01357.117-0.004-0.0040.0000.0000.0000.000
168A193ALA0-0.019-0.00252.772-0.005-0.0050.0000.0000.0000.000
169A194VAL0-0.0140.00453.321-0.015-0.0150.0000.0000.0000.000
170A195VAL0-0.007-0.00754.744-0.010-0.0100.0000.0000.0000.000
171A196ASN00.0220.00253.5640.0010.0010.0000.0000.0000.000
172A197ARG10.7940.88444.6170.4590.4590.0000.0000.0000.000
173A198VAL00.0200.00051.424-0.013-0.0130.0000.0000.0000.000
174A199GLU-1-0.953-0.97453.772-0.304-0.3040.0000.0000.0000.000
175A200GLY0-0.013-0.00650.461-0.001-0.0010.0000.0000.0000.000
176A201MET0-0.055-0.02148.646-0.007-0.0070.0000.0000.0000.000
177A202LEU0-0.006-0.01250.843-0.006-0.0060.0000.0000.0000.000
178A203ARG10.8040.90148.5900.3950.3950.0000.0000.0000.000
179A204ASP-1-0.842-0.90146.675-0.432-0.4320.0000.0000.0000.000
180A205TYR0-0.029-0.02842.602-0.023-0.0230.0000.0000.0000.000
181A206PRO00.0560.06048.939-0.005-0.0050.0000.0000.0000.000
182A207ASP-1-0.854-0.90248.771-0.466-0.4660.0000.0000.0000.000
183A208THR0-0.049-0.03046.743-0.011-0.0110.0000.0000.0000.000
184A209GLN0-0.024-0.02449.4620.0160.0160.0000.0000.0000.000
185A210ALA00.0380.02048.1290.0150.0150.0000.0000.0000.000
186A211THR0-0.001-0.03150.1620.0090.0090.0000.0000.0000.000
187A212ARG10.8590.92652.3430.4100.4100.0000.0000.0000.000
188A213ASP-1-0.796-0.89251.839-0.426-0.4260.0000.0000.0000.000
189A214ALA00.0190.00852.5300.0090.0090.0000.0000.0000.000
190A215LEU0-0.0020.00354.6160.0150.0150.0000.0000.0000.000
191A216PRO00.0360.00457.7190.0140.0140.0000.0000.0000.000
192A217LEU00.0000.01554.0600.0130.0130.0000.0000.0000.000
193A218MET0-0.027-0.00157.5580.0090.0090.0000.0000.0000.000
194A219GLU-1-0.812-0.90459.162-0.255-0.2550.0000.0000.0000.000
195A220ASN00.0160.01360.6150.0200.0200.0000.0000.0000.000
196A221ALA00.0010.00759.3580.0100.0100.0000.0000.0000.000
197A222TYR00.020-0.01061.1850.0080.0080.0000.0000.0000.000
198A223ARG10.7790.87664.2020.2520.2520.0000.0000.0000.000
199A224GLN0-0.039-0.00963.2330.0150.0150.0000.0000.0000.000
200A225MET0-0.069-0.02761.4650.0080.0080.0000.0000.0000.000
201A226GLN0-0.033-0.01066.2350.0110.0110.0000.0000.0000.000
202A227MET0-0.027-0.00564.7550.0050.0050.0000.0000.0000.000
203A228ASN00.0400.00567.735-0.012-0.0120.0000.0000.0000.000
204A229ALA00.0230.01669.677-0.004-0.0040.0000.0000.0000.000
205A230GLN0-0.005-0.00864.740-0.001-0.0010.0000.0000.0000.000
206A231ALA00.0580.02865.111-0.008-0.0080.0000.0000.0000.000
207A232GLU-1-0.877-0.95566.025-0.222-0.2220.0000.0000.0000.000
208A233LYS10.8490.93565.4490.2270.2270.0000.0000.0000.000
209A234VAL00.0330.02160.808-0.005-0.0050.0000.0000.0000.000
210A235ALA00.0530.03563.402-0.007-0.0070.0000.0000.0000.000
211A236LYS10.9040.94765.8410.2250.2250.0000.0000.0000.000
212A237ILE0-0.0030.00460.091-0.001-0.0010.0000.0000.0000.000
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