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: ZZL6N

Calculation Name: 2IDE-C-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IDE

Chain ID: C

ChEMBL ID:

UniProt ID: Q5SHE1

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 147
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1220926.020915
FMO2-HF: Nuclear repulsion 1165743.994727
FMO2-HF: Total energy -55182.026188
FMO2-MP2: Total energy -55341.692397


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:9:GLY)


Summations of interaction energy for fragment #1(A:9:GLY)
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.
36.21637.337-0.01-0.399-0.7120
Interaction energy analysis for fragmet #1(A:9:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.880 / q_NPA : 0.923
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].
3A11PRO00.0750.0263.822-2.355-1.340-0.009-0.382-0.6240.000
4A12ARG10.8920.9414.01245.19845.304-0.001-0.017-0.0880.000
5A13MET00.0950.0678.761-0.010-0.0100.0000.0000.0000.000
6A14VAL0-0.044-0.03110.217-0.904-0.9040.0000.0000.0000.000
7A15ASP-1-0.786-0.87012.094-17.029-17.0290.0000.0000.0000.000
8A16VAL0-0.093-0.06114.220-0.060-0.0600.0000.0000.0000.000
9A17THR00.0360.01217.7080.9320.9320.0000.0000.0000.000
10A18GLU-1-0.940-0.95919.370-14.730-14.7300.0000.0000.0000.000
11A19LYS10.7970.89616.24017.61217.6120.0000.0000.0000.000
12A20PRO00.0290.01922.2640.1310.1310.0000.0000.0000.000
13A21GLU-1-0.908-0.95125.078-11.436-11.4360.0000.0000.0000.000
14A22THR0-0.058-0.03526.2740.3510.3510.0000.0000.0000.000
15A23PHE0-0.026-0.02927.722-0.138-0.1380.0000.0000.0000.000
16A24ARG10.8170.92021.47712.87812.8780.0000.0000.0000.000
17A25THR0-0.004-0.01727.6240.4560.4560.0000.0000.0000.000
18A26ALA0-0.0160.00325.025-0.331-0.3310.0000.0000.0000.000
19A27THR00.0320.02927.0540.1780.1780.0000.0000.0000.000
20A28ALA0-0.0080.00326.339-0.308-0.3080.0000.0000.0000.000
21A29GLU-1-0.679-0.83628.414-9.162-9.1620.0000.0000.0000.000
22A30ALA00.005-0.00729.027-0.501-0.5010.0000.0000.0000.000
23A31PHE0-0.039-0.00330.9090.3780.3780.0000.0000.0000.000
24A32VAL0-0.018-0.00432.748-0.280-0.2800.0000.0000.0000.000
25A33GLU-1-0.794-0.88035.027-8.607-8.6070.0000.0000.0000.000
26A34LEU0-0.038-0.02237.609-0.025-0.0250.0000.0000.0000.000
27A35THR00.016-0.01841.0560.0800.0800.0000.0000.0000.000
28A36GLU-1-0.844-0.94143.419-6.679-6.6790.0000.0000.0000.000
29A37GLU-1-0.850-0.89145.409-6.990-6.9900.0000.0000.0000.000
30A38ALA0-0.015-0.01242.6930.0290.0290.0000.0000.0000.000
31A39LEU0-0.0090.00244.755-0.041-0.0410.0000.0000.0000.000
32A40SER00.0400.00146.0170.0750.0750.0000.0000.0000.000
33A41ALA0-0.081-0.04346.3430.1040.1040.0000.0000.0000.000
34A42LEU00.002-0.00642.6160.0060.0060.0000.0000.0000.000
35A43GLU-1-0.941-0.97846.204-6.399-6.3990.0000.0000.0000.000
36A44LYS10.8410.94149.2586.5916.5910.0000.0000.0000.000
37A45GLY00.0310.02348.4440.0750.0750.0000.0000.0000.000
38A46GLY0-0.0010.00545.807-0.079-0.0790.0000.0000.0000.000
39A47VAL0-0.087-0.05643.8500.1690.1690.0000.0000.0000.000
40A48GLY00.0290.02146.8650.0500.0500.0000.0000.0000.000
41A49LYS10.7720.86639.4148.0748.0740.0000.0000.0000.000
42A50GLY00.0450.03544.805-0.076-0.0760.0000.0000.0000.000
43A51ASP-1-0.812-0.91044.107-7.258-7.2580.0000.0000.0000.000
44A52PRO00.012-0.02141.027-0.160-0.1600.0000.0000.0000.000
45A53LEU0-0.0100.00039.721-0.271-0.2710.0000.0000.0000.000
46A54VAL00.0100.00139.745-0.200-0.2000.0000.0000.0000.000
47A55VAL0-0.004-0.00238.386-0.159-0.1590.0000.0000.0000.000
48A56ALA00.0120.00335.943-0.237-0.2370.0000.0000.0000.000
49A57GLN0-0.026-0.02335.249-0.267-0.2670.0000.0000.0000.000
50A58LEU00.0460.02035.807-0.225-0.2250.0000.0000.0000.000
51A59ALA0-0.010-0.00733.557-0.218-0.2180.0000.0000.0000.000
52A60GLY00.0490.02731.253-0.352-0.3520.0000.0000.0000.000
53A61ILE00.001-0.00430.860-0.373-0.3730.0000.0000.0000.000
54A62LEU0-0.085-0.04931.799-0.252-0.2520.0000.0000.0000.000
55A63ALA0-0.021-0.00327.933-0.248-0.2480.0000.0000.0000.000
56A64ALA00.0580.03726.898-0.460-0.4600.0000.0000.0000.000
57A65LYS10.9440.96026.2339.0489.0480.0000.0000.0000.000
58A66LYS10.9370.98226.03010.48110.4810.0000.0000.0000.000
59A67THR00.0200.00620.782-0.386-0.3860.0000.0000.0000.000
60A68ALA0-0.030-0.02419.986-0.574-0.5740.0000.0000.0000.000
61A69ASP-1-0.982-0.96620.202-13.470-13.4700.0000.0000.0000.000
62A70LEU0-0.003-0.00821.126-0.351-0.3510.0000.0000.0000.000
63A71ILE0-0.031-0.01116.080-0.788-0.7880.0000.0000.0000.000
64A72PRO00.011-0.00813.937-0.484-0.4840.0000.0000.0000.000
65A73LEU0-0.075-0.0369.444-1.342-1.3420.0000.0000.0000.000
66A74CYS0-0.0180.00213.624-0.329-0.3290.0000.0000.0000.000
67A75HIS00.011-0.00414.8530.4250.4250.0000.0000.0000.000
68A76PRO00.0270.01318.7860.4840.4840.0000.0000.0000.000
69A77LEU00.0090.00721.3470.2010.2010.0000.0000.0000.000
70A78PRO00.0310.02524.4340.3070.3070.0000.0000.0000.000
71A79LEU0-0.0050.00425.8040.0970.0970.0000.0000.0000.000
72A80THR0-0.037-0.03029.4350.2450.2450.0000.0000.0000.000
73A81GLY0-0.001-0.00331.7470.3800.3800.0000.0000.0000.000
74A82VAL0-0.052-0.02630.425-0.403-0.4030.0000.0000.0000.000
75A83GLU-1-0.897-0.93232.894-8.020-8.0200.0000.0000.0000.000
76A84VAL0-0.022-0.02132.739-0.337-0.3370.0000.0000.0000.000
77A85ARG10.8740.94535.2848.3268.3260.0000.0000.0000.000
78A86VAL00.0250.00136.290-0.260-0.2600.0000.0000.0000.000
79A87GLU-1-0.838-0.89738.542-7.705-7.7050.0000.0000.0000.000
80A88LEU00.0470.02340.385-0.160-0.1600.0000.0000.0000.000
81A89LEU0-0.045-0.01538.8870.1980.1980.0000.0000.0000.000
82A90LYS10.9700.97142.8366.8816.8810.0000.0000.0000.000
83A91ALA00.002-0.00745.9440.0130.0130.0000.0000.0000.000
84A92GLU-1-0.840-0.90739.822-7.944-7.9440.0000.0000.0000.000
85A93LYS10.9160.97141.7776.9156.9150.0000.0000.0000.000
86A94ARG10.8250.92235.0288.4488.4480.0000.0000.0000.000
87A95VAL0-0.018-0.00637.6350.2100.2100.0000.0000.0000.000
88A96ARG10.7530.85434.4748.5668.5660.0000.0000.0000.000
89A97ILE0-0.0130.00032.5540.1860.1860.0000.0000.0000.000
90A98GLU-1-0.836-0.90432.739-9.023-9.0230.0000.0000.0000.000
91A99ALA00.0020.00029.9210.1820.1820.0000.0000.0000.000
92A100THR0-0.023-0.02030.202-0.216-0.2160.0000.0000.0000.000
93A101VAL0-0.010-0.00227.1160.1960.1960.0000.0000.0000.000
94A102LYS10.9610.97328.5949.1019.1010.0000.0000.0000.000
95A103THR00.019-0.00925.130-0.073-0.0730.0000.0000.0000.000
96A104LYS10.8830.94428.6199.6139.6130.0000.0000.0000.000
97A105ALA00.0930.06123.691-0.006-0.0060.0000.0000.0000.000
98A106GLU-1-0.822-0.90220.965-13.358-13.3580.0000.0000.0000.000
99A107THR0-0.073-0.03517.476-0.873-0.8730.0000.0000.0000.000
100A108GLY0-0.061-0.03219.7750.6980.6980.0000.0000.0000.000
101A109VAL00.0700.02921.277-0.205-0.2050.0000.0000.0000.000
102A110GLU-1-0.794-0.90919.684-14.516-14.5160.0000.0000.0000.000
103A111MET00.0010.01017.7490.1210.1210.0000.0000.0000.000
104A112GLU-1-0.816-0.90421.041-13.618-13.6180.0000.0000.0000.000
105A113ALA0-0.0010.00624.4320.4380.4380.0000.0000.0000.000
106A114MET00.005-0.00421.8970.5430.5430.0000.0000.0000.000
107A115THR0-0.017-0.01822.6440.1290.1290.0000.0000.0000.000
108A116ALA0-0.024-0.00424.9940.3390.3390.0000.0000.0000.000
109A117CYS0-0.033-0.01427.7570.4470.4470.0000.0000.0000.000
110A118ALA00.0230.00825.6510.3000.3000.0000.0000.0000.000
111A119VAL0-0.002-0.00426.8490.2420.2420.0000.0000.0000.000
112A120ALA00.0410.04029.3890.3400.3400.0000.0000.0000.000
113A121ALA00.0250.00230.4700.3270.3270.0000.0000.0000.000
114A122LEU0-0.002-0.01527.3320.2680.2680.0000.0000.0000.000
115A123THR0-0.033-0.01431.8940.2470.2470.0000.0000.0000.000
116A124VAL00.0180.00034.9320.2870.2870.0000.0000.0000.000
117A125TYR0-0.038-0.01634.1240.2050.2050.0000.0000.0000.000
118A126ASP-1-0.828-0.91635.299-8.335-8.3350.0000.0000.0000.000
119A127MET0-0.058-0.00637.0750.2150.2150.0000.0000.0000.000
120A128LEU00.0350.01339.6450.2680.2680.0000.0000.0000.000
121A129LYS10.8450.93136.6578.7018.7010.0000.0000.0000.000
122A130ALA0-0.032-0.01840.0430.0350.0350.0000.0000.0000.000
123A131ALA0-0.0030.00943.5450.1050.1050.0000.0000.0000.000
124A132SER0-0.003-0.01341.5560.0560.0560.0000.0000.0000.000
125A133LYS10.9260.96438.5407.3777.3770.0000.0000.0000.000
126A134GLY00.0030.01136.792-0.276-0.2760.0000.0000.0000.000
127A135LEU0-0.0140.01037.2790.0160.0160.0000.0000.0000.000
128A136VAL00.0160.00532.163-0.251-0.2510.0000.0000.0000.000
129A137ILE00.0030.01029.1180.1840.1840.0000.0000.0000.000
130A138SER0-0.035-0.04730.336-0.320-0.3200.0000.0000.0000.000
131A139GLN0-0.019-0.00828.120-0.547-0.5470.0000.0000.0000.000
132A140VAL00.0480.02225.4170.3320.3320.0000.0000.0000.000
133A141ARG10.7510.84225.1179.5859.5850.0000.0000.0000.000
134A142LEU00.0400.01822.1040.3220.3220.0000.0000.0000.000
135A143LEU0-0.052-0.01625.6300.0540.0540.0000.0000.0000.000
136A144HIS0-0.033-0.03728.0260.0440.0440.0000.0000.0000.000
137A145LYS10.8820.93919.93414.22114.2210.0000.0000.0000.000
138A146ALA00.0130.01226.4810.2060.2060.0000.0000.0000.000
139A147GLY00.0760.03227.116-0.112-0.1120.0000.0000.0000.000
140A148GLY0-0.0030.01122.920-0.151-0.1510.0000.0000.0000.000
141A149LYS10.9580.95817.80216.23016.2300.0000.0000.0000.000
142A150SER0-0.023-0.00521.0520.0290.0290.0000.0000.0000.000
143A151GLY00.0240.02423.0890.2000.2000.0000.0000.0000.000
144A152GLU-1-0.850-0.90725.944-9.866-9.8660.0000.0000.0000.000
145A153TRP0-0.038-0.01524.419-0.203-0.2030.0000.0000.0000.000
146A154ARG10.8610.90226.6939.5429.5420.0000.0000.0000.000
147A155ARG00.0200.02924.9501.0151.0150.0000.0000.0000.000