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: 64N6Z

Calculation Name: 1TE2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-phosphoglycolic acid | calcium ion

Ligand 3-letter code: PGA | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TE2

Chain ID: A

ChEMBL ID:

UniProt ID: P77247

Base Structure: X-ray

Registration Date: 2025-10-05

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 218
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2568041.466375
FMO2-HF: Nuclear repulsion 2483488.101581
FMO2-HF: Total energy -84553.364794
FMO2-MP2: Total energy -84797.406963


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:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-398.816-390.99729.499-15.944-21.373-0.197
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.637 / q_NPA : 1.797
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].
3A7ILE0-0.033-0.0122.454-14.648-11.9042.349-1.360-3.733-0.013
4A8LEU00.005-0.0034.3396.7056.768-0.001-0.026-0.0370.000
162A166LEU0-0.055-0.0362.433-13.460-12.4761.137-0.724-1.397-0.003
163A167THR0-0.075-0.0421.794-42.683-44.59713.098-5.620-5.564-0.078
164A168CYS00.0240.0363.97110.32010.479-0.001-0.042-0.1160.000
165A169VAL0-0.035-0.0144.138-16.179-15.8030.001-0.072-0.3050.000
178A182LYS10.8090.8993.62172.39872.6000.000-0.037-0.1650.000
181A185ARG10.8930.9473.99261.64162.323-0.001-0.338-0.343-0.001
182A186MET00.0160.0421.820-50.825-49.97911.118-6.551-5.413-0.092
183A187ARG10.7960.9002.86369.33572.4291.773-1.140-3.726-0.010
184A188SER0-0.023-0.0094.0828.6138.8450.0260.023-0.2810.000
202A206ASN0-0.088-0.0464.603-8.173-8.063-0.001-0.004-0.1040.000
218A222GLY-1-0.894-0.9194.168-86.707-86.4660.001-0.053-0.1890.000
5A9ALA00.0300.0177.2086.2486.2480.0000.0000.0000.000
6A10ALA00.0220.0127.590-6.985-6.9850.0000.0000.0000.000
7A11ILE0-0.041-0.0219.0893.9313.9310.0000.0000.0000.000
8A12PHE00.0290.00511.771-1.931-1.9310.0000.0000.0000.000
9A13ASP-1-0.779-0.89514.651-30.978-30.9780.0000.0000.0000.000
10A14MET0-0.047-0.03116.2080.6230.6230.0000.0000.0000.000
11A15ASP-1-0.733-0.80820.062-23.832-23.8320.0000.0000.0000.000
12A16GLY00.0900.06120.937-0.733-0.7330.0000.0000.0000.000
13A17LEU0-0.105-0.03416.301-0.358-0.3580.0000.0000.0000.000
14A18LEU0-0.049-0.03418.534-0.066-0.0660.0000.0000.0000.000
15A19ILE0-0.002-0.01621.6161.0471.0470.0000.0000.0000.000
16A20ASP-1-0.900-0.94224.739-22.076-22.0760.0000.0000.0000.000
17A21SER0-0.038-0.06825.2380.7130.7130.0000.0000.0000.000
18A22GLU-1-0.859-0.91924.040-23.021-23.0210.0000.0000.0000.000
19A23PRO00.0380.01527.2510.7540.7540.0000.0000.0000.000
20A24LEU0-0.074-0.03930.2820.8350.8350.0000.0000.0000.000
21A25TRP0-0.008-0.03925.8591.1771.1770.0000.0000.0000.000
22A26ASP-1-0.762-0.84630.428-18.551-18.5510.0000.0000.0000.000
23A27ARG10.8400.91532.27615.91215.9120.0000.0000.0000.000
24A28ALA00.003-0.00733.0400.5690.5690.0000.0000.0000.000
25A29GLU-1-0.790-0.86831.361-17.998-17.9980.0000.0000.0000.000
26A30LEU0-0.018-0.00634.5940.5100.5100.0000.0000.0000.000
27A31ASP-1-0.793-0.89237.564-14.869-14.8690.0000.0000.0000.000
28A32VAL0-0.065-0.02537.1570.4920.4920.0000.0000.0000.000
29A33MET00.0480.04234.8350.5320.5320.0000.0000.0000.000
30A34ALA00.0350.02039.3960.3550.3550.0000.0000.0000.000
31A35SER0-0.117-0.06142.2150.3620.3620.0000.0000.0000.000
32A36LEU0-0.030-0.01739.6210.2480.2480.0000.0000.0000.000
33A37GLY0-0.028-0.00943.6590.1310.1310.0000.0000.0000.000
34A38VAL0-0.037-0.00638.7660.1190.1190.0000.0000.0000.000
35A39ASP-1-0.841-0.90342.246-13.915-13.9150.0000.0000.0000.000
36A40ILE00.029-0.00638.424-0.316-0.3160.0000.0000.0000.000
37A41SER0-0.078-0.06038.795-0.345-0.3450.0000.0000.0000.000
38A42ARG10.8050.87539.15414.25314.2530.0000.0000.0000.000
39A43ARG10.7760.85331.35218.03018.0300.0000.0000.0000.000
40A44ASN0-0.019-0.01233.655-0.289-0.2890.0000.0000.0000.000
41A45GLU-1-0.816-0.87834.343-15.219-15.2190.0000.0000.0000.000
42A46LEU0-0.047-0.00630.431-0.134-0.1340.0000.0000.0000.000
43A47PRO0-0.040-0.01926.3120.0580.0580.0000.0000.0000.000
44A48ASP-1-0.851-0.93822.409-24.396-24.3960.0000.0000.0000.000
45A49THR0-0.006-0.01624.457-0.224-0.2240.0000.0000.0000.000
46A50LEU00.0590.04520.729-0.532-0.5320.0000.0000.0000.000
47A51GLY00.0420.02019.428-1.196-1.1960.0000.0000.0000.000
48A52LEU0-0.092-0.03219.871-0.843-0.8430.0000.0000.0000.000
49A53ARG10.7360.82422.11323.52423.5240.0000.0000.0000.000
50A54ILE00.0760.03123.8030.4660.4660.0000.0000.0000.000
51A55ASP-1-0.752-0.85826.261-21.173-21.1730.0000.0000.0000.000
52A56MET0-0.015-0.00524.1590.4110.4110.0000.0000.0000.000
53A57VAL00.0420.02726.9520.4310.4310.0000.0000.0000.000
54A58VAL0-0.025-0.00729.3420.7470.7470.0000.0000.0000.000
55A59ASP-1-0.840-0.93430.403-17.708-17.7080.0000.0000.0000.000
56A60LEU0-0.054-0.02827.3000.5390.5390.0000.0000.0000.000
57A61TRP00.008-0.01931.7560.6790.6790.0000.0000.0000.000
58A62TYR0-0.015-0.00434.9000.4450.4450.0000.0000.0000.000
59A63ALA0-0.050-0.02434.3680.3790.3790.0000.0000.0000.000
60A64ARG10.7820.89831.53617.77817.7780.0000.0000.0000.000
61A65GLN0-0.055-0.03138.1560.7850.7850.0000.0000.0000.000
62A66PRO0-0.0040.01540.212-0.117-0.1170.0000.0000.0000.000
63A67TRP00.0170.01536.1050.2450.2450.0000.0000.0000.000
64A68ASN0-0.039-0.03843.009-0.124-0.1240.0000.0000.0000.000
65A69GLY00.0190.00744.969-0.003-0.0030.0000.0000.0000.000
66A70PRO0-0.017-0.00941.190-0.046-0.0460.0000.0000.0000.000
67A71SER0-0.005-0.03139.005-0.296-0.2960.0000.0000.0000.000
68A72ARG10.8770.92334.05116.48616.4860.0000.0000.0000.000
69A73GLN00.0040.00330.930-0.379-0.3790.0000.0000.0000.000
70A74GLU-1-0.828-0.88434.943-14.748-14.7480.0000.0000.0000.000
71A75VAL0-0.037-0.01535.4550.0210.0210.0000.0000.0000.000
72A76VAL00.0120.01330.344-0.183-0.1830.0000.0000.0000.000
73A77GLU-1-0.845-0.92332.440-18.461-18.4610.0000.0000.0000.000
74A78ARG10.8510.92434.36914.69814.6980.0000.0000.0000.000
75A79VAL00.000-0.00431.6710.1050.1050.0000.0000.0000.000
76A80ILE00.0440.01829.347-0.296-0.2960.0000.0000.0000.000
77A81ALA0-0.018-0.00531.880-0.134-0.1340.0000.0000.0000.000
78A82ARG10.8220.92634.98915.78415.7840.0000.0000.0000.000
79A83ALA00.0770.03030.4300.1230.1230.0000.0000.0000.000
80A84ILE0-0.017-0.01530.164-0.224-0.2240.0000.0000.0000.000
81A85SER0-0.039-0.03032.1260.0950.0950.0000.0000.0000.000
82A86LEU0-0.0080.00233.8900.1990.1990.0000.0000.0000.000
83A87VAL00.0260.02728.679-0.072-0.0720.0000.0000.0000.000
84A88GLU-1-0.874-0.93331.902-17.679-17.6790.0000.0000.0000.000
85A89GLU-1-1.020-1.00234.258-15.513-15.5130.0000.0000.0000.000
86A90THR0-0.039-0.05133.5360.0040.0040.0000.0000.0000.000
87A91ARG10.8340.92331.85318.58118.5810.0000.0000.0000.000
88A92PRO00.0160.02428.896-0.239-0.2390.0000.0000.0000.000
89A93LEU0-0.028-0.01724.412-0.796-0.7960.0000.0000.0000.000
90A94LEU00.0150.01623.2350.6160.6160.0000.0000.0000.000
91A95PRO0-0.012-0.02624.489-0.302-0.3020.0000.0000.0000.000
92A96GLY00.0470.01921.604-0.934-0.9340.0000.0000.0000.000
93A97VAL0-0.0070.01520.291-1.491-1.4910.0000.0000.0000.000
94A98ARG10.8580.92020.29421.72321.7230.0000.0000.0000.000
95A99GLU-1-0.882-0.95221.104-25.685-25.6850.0000.0000.0000.000
96A100ALA00.0200.01616.380-1.209-1.2090.0000.0000.0000.000
97A101VAL00.0280.01316.170-2.083-2.0830.0000.0000.0000.000
98A102ALA0-0.0040.00017.288-0.890-0.8900.0000.0000.0000.000
99A103LEU0-0.016-0.00714.361-0.815-0.8150.0000.0000.0000.000
100A104CYS0-0.058-0.03912.855-2.969-2.9690.0000.0000.0000.000
101A105LYS10.8590.94413.39730.81430.8140.0000.0000.0000.000
102A106GLU-1-0.931-0.96415.980-29.711-29.7110.0000.0000.0000.000
103A107GLN0-0.129-0.06211.107-2.276-2.2760.0000.0000.0000.000
104A108GLY0-0.022-0.00811.344-3.385-3.3850.0000.0000.0000.000
105A109LEU0-0.082-0.0318.198-2.139-2.1390.0000.0000.0000.000
106A110LEU00.0000.00411.7083.2523.2520.0000.0000.0000.000
107A111VAL0-0.002-0.00812.098-3.266-3.2660.0000.0000.0000.000
108A112GLY00.0060.00213.4121.9531.9530.0000.0000.0000.000
109A113LEU00.005-0.00114.645-0.259-0.2590.0000.0000.0000.000
110A114ALA00.0140.00513.4950.3700.3700.0000.0000.0000.000
111A115SER00.0330.02815.521-0.290-0.2900.0000.0000.0000.000
112A116ALA00.028-0.00318.4000.1740.1740.0000.0000.0000.000
113A117SER00.001-0.01820.6471.2741.2740.0000.0000.0000.000
114A118PRO00.0370.04023.025-0.815-0.8150.0000.0000.0000.000
115A119LEU00.0040.00422.393-0.122-0.1220.0000.0000.0000.000
116A120HIS00.004-0.00224.890-0.232-0.2320.0000.0000.0000.000
117A121MET00.0220.02326.3450.4160.4160.0000.0000.0000.000
118A122LEU0-0.005-0.00620.306-0.169-0.1690.0000.0000.0000.000
119A123GLU-1-0.804-0.87724.139-23.796-23.7960.0000.0000.0000.000
120A124LYS10.8260.91926.30518.25118.2510.0000.0000.0000.000
121A125VAL00.002-0.00524.8200.4280.4280.0000.0000.0000.000
122A126LEU00.0310.01320.9490.1300.1300.0000.0000.0000.000
123A127THR0-0.035-0.03025.2190.1790.1790.0000.0000.0000.000
124A128MET0-0.051-0.00328.6360.5050.5050.0000.0000.0000.000
125A129PHE00.0170.01326.5940.5720.5720.0000.0000.0000.000
126A130ASP-1-0.896-0.93427.606-20.184-20.1840.0000.0000.0000.000
127A131LEU00.0160.00122.313-0.566-0.5660.0000.0000.0000.000
128A132ARG10.7760.85522.18324.12624.1260.0000.0000.0000.000
129A133ASP-1-0.869-0.92723.577-24.578-24.5780.0000.0000.0000.000
130A134SER0-0.046-0.02520.372-0.767-0.7670.0000.0000.0000.000
131A135PHE0-0.018-0.01917.125-1.864-1.8640.0000.0000.0000.000
132A136ASP-1-0.806-0.89116.401-32.287-32.2870.0000.0000.0000.000
133A137ALA0-0.032-0.02216.1210.9590.9590.0000.0000.0000.000
134A138LEU00.0030.00417.251-1.028-1.0280.0000.0000.0000.000
135A139ALA0-0.061-0.03116.0090.6730.6730.0000.0000.0000.000
136A140SER0-0.003-0.02918.092-0.031-0.0310.0000.0000.0000.000
137A141ALA00.024-0.01018.5500.0800.0800.0000.0000.0000.000
138A142GLU-1-0.904-0.94620.279-20.702-20.7020.0000.0000.0000.000
139A143LYS10.9320.95823.55522.44322.4430.0000.0000.0000.000
140A144LEU0-0.0060.02417.9330.2580.2580.0000.0000.0000.000
141A145PRO0-0.019-0.00921.2440.4220.4220.0000.0000.0000.000
142A146TYR0-0.0020.00119.3360.6370.6370.0000.0000.0000.000
143A147SER00.0430.02518.730-1.252-1.2520.0000.0000.0000.000
144A148LYS10.7870.88814.50034.34534.3450.0000.0000.0000.000
145A149PRO00.0350.01815.2301.4401.4400.0000.0000.0000.000
146A150HIS0-0.022-0.01814.246-2.755-2.7550.0000.0000.0000.000
147A151PRO00.026-0.00110.685-0.008-0.0080.0000.0000.0000.000
148A152GLN0-0.073-0.03912.071-1.638-1.6380.0000.0000.0000.000
149A153VAL00.0330.01614.089-0.884-0.8840.0000.0000.0000.000
150A154TYR0-0.005-0.0539.288-1.260-1.2600.0000.0000.0000.000
151A155LEU0-0.046-0.0198.865-2.713-2.7130.0000.0000.0000.000
152A156ASP-1-0.841-0.91711.210-32.155-32.1550.0000.0000.0000.000
153A157CYS0-0.078-0.04012.3000.4360.4360.0000.0000.0000.000
154A158ALA00.0370.0149.0380.2190.2190.0000.0000.0000.000
155A159ALA0-0.0030.00010.8610.7490.7490.0000.0000.0000.000
156A160LYS10.8620.92913.70630.83630.8360.0000.0000.0000.000
157A161LEU00.0000.00711.4451.3621.3620.0000.0000.0000.000
158A162GLY0-0.0170.00814.170-0.051-0.0510.0000.0000.0000.000
159A163VAL0-0.042-0.0249.020-0.801-0.8010.0000.0000.0000.000
160A164ASP-1-0.824-0.9106.602-66.845-66.8450.0000.0000.0000.000
161A165PRO00.0600.0255.937-5.767-5.7670.0000.0000.0000.000
166A170ALA00.0020.0036.2856.1186.1180.0000.0000.0000.000
167A171LEU0-0.021-0.0059.204-1.328-1.3280.0000.0000.0000.000
168A172GLU-1-0.725-0.84011.987-35.375-35.3750.0000.0000.0000.000
169A173ASP-1-0.742-0.88214.343-29.404-29.4040.0000.0000.0000.000
170A174SER00.0620.04516.3840.8200.8200.0000.0000.0000.000
171A175VAL0-0.008-0.01914.942-2.267-2.2670.0000.0000.0000.000
172A176ASN00.007-0.01214.363-2.319-2.3190.0000.0000.0000.000
173A177GLY00.0600.01414.250-1.199-1.1990.0000.0000.0000.000
174A178MET0-0.0390.02010.118-3.295-3.2950.0000.0000.0000.000
175A179ILE0-0.010-0.0039.613-4.544-4.5440.0000.0000.0000.000
176A180ALA0-0.0010.02010.351-2.363-2.3630.0000.0000.0000.000
177A181SER0-0.019-0.0237.735-3.714-3.7140.0000.0000.0000.000
179A183ALA0-0.018-0.0086.562-3.614-3.6140.0000.0000.0000.000
180A184ALA0-0.009-0.0027.3120.5230.5230.0000.0000.0000.000
185A189ILE00.0540.0207.444-0.806-0.8060.0000.0000.0000.000
186A190VAL0-0.034-0.01710.8841.3691.3690.0000.0000.0000.000
187A191VAL00.008-0.00413.8650.1560.1560.0000.0000.0000.000
188A192PRO0-0.074-0.03317.1910.9130.9130.0000.0000.0000.000
189A193ALA00.1100.07219.1980.9360.9360.0000.0000.0000.000
190A194PRO00.006-0.01822.325-0.053-0.0530.0000.0000.0000.000
191A195GLU-1-0.950-0.96825.038-21.547-21.5470.0000.0000.0000.000
192A196ALA00.0020.00920.3950.0650.0650.0000.0000.0000.000
193A197GLN00.0130.00521.223-0.888-0.8880.0000.0000.0000.000
194A198ASN0-0.109-0.06621.9880.0210.0210.0000.0000.0000.000
195A199ASP-1-0.745-0.83319.285-27.982-27.9820.0000.0000.0000.000
196A200PRO0-0.026-0.02218.754-1.367-1.3670.0000.0000.0000.000
197A201ARG10.8550.90015.98926.10626.1060.0000.0000.0000.000
198A202PHE00.018-0.00713.810-2.629-2.6290.0000.0000.0000.000
199A203VAL0-0.056-0.01412.804-2.174-2.1740.0000.0000.0000.000
200A204LEU0-0.033-0.0128.638-2.112-2.1120.0000.0000.0000.000
201A205ALA00.0200.0108.065-6.023-6.0230.0000.0000.0000.000
203A207VAL00.0210.0227.8010.5110.5110.0000.0000.0000.000
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