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: KV9K3

Calculation Name: 1U3E-M-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-2-hydroxymethyl-propane-1,3-diol | 1,2-ethanediol | manganese (ii) ion | strontium ion

Ligand 3-letter code: TRS | EDO | MN | SR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1U3E

Chain ID: M

ChEMBL ID:

UniProt ID: P34081

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1491469.153425
FMO2-HF: Nuclear repulsion 1422439.39945
FMO2-HF: Total energy -69029.753975
FMO2-MP2: Total energy -69232.066857


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.
119.399130.19110.551-7.237-14.104-0.064
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 : 0.757 / q_NPA : 0.891
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].
3A3TRP00.0380.0042.8766.2989.2671.808-1.251-3.526-0.003
4A4LYS10.8900.9445.36429.70029.722-0.001-0.002-0.0190.000
16A16SER00.0770.0392.492-5.453-4.1721.670-0.998-1.953-0.002
17A17ASN00.0250.0042.639-8.407-6.0801.175-1.492-2.010-0.017
18A18THR00.011-0.0072.1921.5722.6883.141-1.248-3.009-0.009
19A19GLY00.0290.0104.6523.8933.967-0.001-0.011-0.0610.000
20A20GLU-1-0.923-0.9602.653-43.409-40.4062.759-2.235-3.526-0.033
5A5ASP-1-0.808-0.8978.973-21.576-21.5760.0000.0000.0000.000
6A6ILE0-0.069-0.02411.6630.0920.0920.0000.0000.0000.000
7A7LYS10.9450.95913.52519.59819.5980.0000.0000.0000.000
8A8GLY0-0.039-0.01616.7260.4930.4930.0000.0000.0000.000
9A9TYR0-0.049-0.03916.3921.1081.1080.0000.0000.0000.000
10A10GLU-1-0.712-0.85115.515-16.398-16.3980.0000.0000.0000.000
11A11GLY00.0110.01315.2740.9580.9580.0000.0000.0000.000
12A12HIS0-0.080-0.02816.7100.3440.3440.0000.0000.0000.000
13A13TYR0-0.039-0.04213.4250.2210.2210.0000.0000.0000.000
14A14GLN00.0090.0068.912-0.921-0.9210.0000.0000.0000.000
15A15VAL0-0.021-0.0147.8410.7810.7810.0000.0000.0000.000
21A21VAL0-0.001-0.0145.912-0.109-0.1090.0000.0000.0000.000
22A22TYR0-0.0020.0078.0250.7000.7000.0000.0000.0000.000
23A23SER0-0.033-0.0129.9390.9370.9370.0000.0000.0000.000
24A24ILE00.0580.02912.907-0.073-0.0730.0000.0000.0000.000
25A25LYS10.9580.98214.66313.08213.0820.0000.0000.0000.000
26A26SER0-0.036-0.02915.6880.5750.5750.0000.0000.0000.000
27A27GLY00.0460.04014.6710.3100.3100.0000.0000.0000.000
28A28LYS10.9570.98311.79113.83313.8330.0000.0000.0000.000
29A29THR00.0500.0126.732-0.060-0.0600.0000.0000.0000.000
30A30LEU0-0.081-0.04010.0141.2501.2500.0000.0000.0000.000
31A31LYS10.9890.99311.21113.66213.6620.0000.0000.0000.000
32A32HIS10.8220.8958.59822.65922.6590.0000.0000.0000.000
33A33GLN00.0090.00513.4190.2220.2220.0000.0000.0000.000
34A34ILE00.0410.01314.149-0.532-0.5320.0000.0000.0000.000
35A35PRO0-0.014-0.00117.9790.5250.5250.0000.0000.0000.000
36A36LYS11.0100.99221.5179.3749.3740.0000.0000.0000.000
37A37ASP-1-0.796-0.87821.331-12.373-12.3730.0000.0000.0000.000
38A38GLY00.0360.01419.449-0.151-0.1510.0000.0000.0000.000
39A39TYR0-0.031-0.01517.254-0.843-0.8430.0000.0000.0000.000
40A40HIS00.0190.01311.884-0.710-0.7100.0000.0000.0000.000
41A41ARG10.8340.90114.77712.61312.6130.0000.0000.0000.000
42A42ILE00.0140.02112.749-0.277-0.2770.0000.0000.0000.000
43A43GLY00.0200.01115.8850.4970.4970.0000.0000.0000.000
44A44LEU0-0.0150.00414.594-0.488-0.4880.0000.0000.0000.000
45A45PHE00.016-0.00618.6320.6490.6490.0000.0000.0000.000
46A46LYS10.8980.93320.81912.44012.4400.0000.0000.0000.000
47A47GLY00.0300.02223.3370.3560.3560.0000.0000.0000.000
48A48GLY00.0090.00525.8400.3490.3490.0000.0000.0000.000
49A49LYS10.9520.97526.5449.6459.6450.0000.0000.0000.000
50A50GLY00.0360.03222.956-0.430-0.4300.0000.0000.0000.000
51A51LYS10.9310.96422.06212.57112.5710.0000.0000.0000.000
52A52THR00.001-0.00319.912-0.550-0.5500.0000.0000.0000.000
53A53PHE0-0.003-0.00316.7830.2590.2590.0000.0000.0000.000
54A54GLN00.013-0.00116.522-0.164-0.1640.0000.0000.0000.000
55A55VAL00.0150.0089.969-0.223-0.2230.0000.0000.0000.000
56A56HIS00.0440.01811.993-1.458-1.4580.0000.0000.0000.000
57A57ARG10.9400.97713.32514.02714.0270.0000.0000.0000.000
58A58LEU0-0.0020.01112.147-0.142-0.1420.0000.0000.0000.000
59A59VAL00.0270.0348.304-0.626-0.6260.0000.0000.0000.000
60A60ALA00.0460.00910.507-0.788-0.7880.0000.0000.0000.000
61A61ILE0-0.008-0.00313.4980.3730.3730.0000.0000.0000.000
62A62HIS0-0.044-0.02410.3141.5351.5350.0000.0000.0000.000
63A63PHE0-0.010-0.0166.280-1.472-1.4720.0000.0000.0000.000
64A64CYS0-0.056-0.00610.393-0.839-0.8390.0000.0000.0000.000
65A65GLU-1-0.856-0.92313.458-18.903-18.9030.0000.0000.0000.000
66A66GLY00.0170.00116.3640.2590.2590.0000.0000.0000.000
67A67TYR0-0.088-0.04518.8030.3680.3680.0000.0000.0000.000
68A68GLU-1-0.838-0.93020.539-12.031-12.0310.0000.0000.0000.000
69A69GLU-1-0.937-0.96624.238-10.530-10.5300.0000.0000.0000.000
70A70GLY0-0.025-0.01026.5500.1910.1910.0000.0000.0000.000
71A71LEU0-0.076-0.01122.7750.0550.0550.0000.0000.0000.000
72A72VAL0-0.044-0.03722.233-0.228-0.2280.0000.0000.0000.000
73A73VAL0-0.014-0.00815.590-0.296-0.2960.0000.0000.0000.000
74A74ASP-1-0.799-0.88118.910-14.277-14.2770.0000.0000.0000.000
75A75HIS10.7840.87714.07916.41316.4130.0000.0000.0000.000
76A76LYS10.9100.95714.60820.17920.1790.0000.0000.0000.000
77A77ASP-1-0.744-0.84715.726-16.955-16.9550.0000.0000.0000.000
78A78GLY0-0.036-0.01018.8600.5700.5700.0000.0000.0000.000
79A79ASN0-0.025-0.01314.7370.6230.6230.0000.0000.0000.000
80A80LYS10.8910.94015.39512.28712.2870.0000.0000.0000.000
81A81ASP-1-0.816-0.89712.894-16.798-16.7980.0000.0000.0000.000
82A82ASN0-0.055-0.03210.916-3.288-3.2880.0000.0000.0000.000
83A83ASN0-0.036-0.0309.3301.3971.3970.0000.0000.0000.000
84A84LEU00.0720.0506.078-1.883-1.8830.0000.0000.0000.000
85A85SER00.021-0.0067.5621.2341.2340.0000.0000.0000.000
86A86THR00.0170.0148.3631.9561.9560.0000.0000.0000.000
87A87ASN0-0.029-0.02610.8182.7802.7800.0000.0000.0000.000
88A88LEU0-0.044-0.00911.4531.7911.7910.0000.0000.0000.000
89A89ARG10.8500.89814.17414.07414.0740.0000.0000.0000.000
90A90TRP0-0.0320.00216.3521.0251.0250.0000.0000.0000.000
91A91VAL0-0.004-0.00819.6260.3180.3180.0000.0000.0000.000
92A92THR00.0700.04122.9720.1850.1850.0000.0000.0000.000
93A93GLN00.047-0.00326.550-0.012-0.0120.0000.0000.0000.000
94A94LYS10.8870.94327.9489.1289.1280.0000.0000.0000.000
95A95ILE00.0960.04225.6610.0440.0440.0000.0000.0000.000
96A96ASN0-0.021-0.00423.678-0.275-0.2750.0000.0000.0000.000
97A97VAL00.0150.00926.1900.0700.0700.0000.0000.0000.000
98A98GLU-1-0.833-0.92029.688-9.566-9.5660.0000.0000.0000.000
99A99ASN00.0190.02424.943-0.033-0.0330.0000.0000.0000.000
100A100GLN0-0.021-0.01427.0450.0300.0300.0000.0000.0000.000
101A101MET0-0.032-0.01828.8790.2870.2870.0000.0000.0000.000
102A102SER0-0.0100.00429.7890.2210.2210.0000.0000.0000.000
103A103ARG10.9030.94024.49911.75911.7590.0000.0000.0000.000
104A104GLY00.0360.03729.9290.0670.0670.0000.0000.0000.000
105A105THR0-0.086-0.04928.047-0.059-0.0590.0000.0000.0000.000
106A106LEU0-0.0130.00030.398-0.120-0.1200.0000.0000.0000.000
107A107ASN0-0.0030.00132.3940.3990.3990.0000.0000.0000.000
108A108VAL00.0900.03635.129-0.024-0.0240.0000.0000.0000.000
109A109SER00.0480.02738.2400.1260.1260.0000.0000.0000.000
110A110LYS10.9220.94837.9917.4767.4760.0000.0000.0000.000
111A111ALA00.0160.00938.7170.1190.1190.0000.0000.0000.000
112A112GLN00.0280.00340.6010.2020.2020.0000.0000.0000.000
113A113GLN00.0270.02043.0520.0230.0230.0000.0000.0000.000
114A114ILE00.000-0.00540.7930.1460.1460.0000.0000.0000.000
115A115ALA00.0060.01844.5540.1220.1220.0000.0000.0000.000
116A116LYS10.9640.98046.1796.1486.1480.0000.0000.0000.000
117A117ILE0-0.0020.00947.3810.1430.1430.0000.0000.0000.000
118A118LYS10.9890.97343.1496.8986.8980.0000.0000.0000.000
119A119ASN0-0.047-0.02047.150-0.029-0.0290.0000.0000.0000.000
120A120GLN0-0.064-0.01550.4910.2060.2060.0000.0000.0000.000
121A121LYS10.9570.97453.1085.6865.6860.0000.0000.0000.000
122A122PRO00.0620.03455.8310.0650.0650.0000.0000.0000.000
123A123ILE0-0.053-0.02259.048-0.004-0.0040.0000.0000.0000.000
124A124ILE00.0440.02662.519-0.003-0.0030.0000.0000.0000.000
125A125VAL0-0.050-0.02766.110-0.011-0.0110.0000.0000.0000.000
126A126ILE00.0400.01668.7480.0130.0130.0000.0000.0000.000
127A127SER0-0.020-0.02272.305-0.030-0.0300.0000.0000.0000.000
128A128PRO0-0.040-0.02775.1450.0190.0190.0000.0000.0000.000
129A129ASP-1-0.858-0.93278.404-3.997-3.9970.0000.0000.0000.000
130A130GLY00.0090.01177.4840.0370.0370.0000.0000.0000.000
131A131ILE0-0.0110.01074.314-0.042-0.0420.0000.0000.0000.000
132A132GLU-1-0.940-0.97270.874-4.376-4.3760.0000.0000.0000.000
133A133LYS10.9230.96366.6294.6154.6150.0000.0000.0000.000
134A134GLU-1-0.842-0.89661.670-4.983-4.9830.0000.0000.0000.000
135A135TYR00.026-0.00762.8630.0030.0030.0000.0000.0000.000
136A136PRO00.0420.00857.547-0.045-0.0450.0000.0000.0000.000
137A137SER0-0.010-0.02456.907-0.074-0.0740.0000.0000.0000.000
138A138THR00.0430.02058.9470.0570.0570.0000.0000.0000.000
139A139LYS10.9070.95156.6435.4785.4780.0000.0000.0000.000
140A140CYS00.0230.03159.8980.0640.0640.0000.0000.0000.000
141A141ALA00.0960.04961.5710.0620.0620.0000.0000.0000.000
142A142CYS0-0.102-0.04463.4730.0690.0690.0000.0000.0000.000
143A143GLU-1-0.967-0.96961.551-5.016-5.0160.0000.0000.0000.000
144A144GLU-1-0.918-0.96864.805-4.687-4.6870.0000.0000.0000.000
145A145LEU0-0.022-0.00567.3010.0720.0720.0000.0000.0000.000
146A146GLY00.0430.05468.7390.0540.0540.0000.0000.0000.000
147A147LEU0-0.080-0.03667.3270.0480.0480.0000.0000.0000.000
148A148THR00.002-0.01366.149-0.045-0.0450.0000.0000.0000.000
149A149ARG11.0100.97556.7905.3385.3380.0000.0000.0000.000
150A150GLY00.0060.02062.654-0.031-0.0310.0000.0000.0000.000
151A151LYS10.8710.94363.5994.7204.7200.0000.0000.0000.000
152A152VAL00.0560.03064.3490.0160.0160.0000.0000.0000.000
153A153THR0-0.042-0.03959.860-0.043-0.0430.0000.0000.0000.000
154A154ASP-1-0.857-0.94162.936-4.837-4.8370.0000.0000.0000.000
155A155VAL0-0.067-0.02465.4400.0160.0160.0000.0000.0000.000
156A156LEU0-0.049-0.01061.5270.0080.0080.0000.0000.0000.000
157A157LYS10.8400.91957.4375.2785.2780.0000.0000.0000.000
158A158GLY00.0500.04663.679-0.003-0.0030.0000.0000.0000.000
159A159HIS00.0070.00862.1660.0940.0940.0000.0000.0000.000
160A160ARG10.8870.93667.6024.5284.5280.0000.0000.0000.000
161A161ILE00.1110.05669.929-0.050-0.0500.0000.0000.0000.000
162A162HIS00.0060.01472.3870.0350.0350.0000.0000.0000.000
163A163HIS0-0.019-0.02569.554-0.047-0.0470.0000.0000.0000.000
164A164LYS10.8740.92770.4694.4284.4280.0000.0000.0000.000
165A165GLY00.0640.04474.8120.0230.0230.0000.0000.0000.000
166A166TYR00.0770.05271.8010.0130.0130.0000.0000.0000.000
167A167THR0-0.027-0.04171.215-0.043-0.0430.0000.0000.0000.000
168A168PHE00.0450.01266.178-0.021-0.0210.0000.0000.0000.000
169A169ARG10.9330.96865.5854.5314.5310.0000.0000.0000.000
170A170TYR00.016-0.00459.152-0.053-0.0530.0000.0000.0000.000
171A171LYS10.8770.93760.3295.0515.0510.0000.0000.0000.000
172A172LEU0-0.037-0.01759.419-0.108-0.1080.0000.0000.0000.000
173A173ASN0-0.056-0.03757.5610.0750.0750.0000.0000.0000.000
174A174GLY-1-0.892-0.93154.150-5.589-5.5890.0000.0000.0000.000