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: 3K4NL

Calculation Name: 1H2E-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | 1,2-ethanediol

Ligand 3-letter code: PO4 | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H2E

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ALU0

Base Structure: X-ray

Registration Date: 2025-09-03

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2538713.149125
FMO2-HF: Nuclear repulsion 2455994.66053
FMO2-HF: Total energy -82718.488594
FMO2-MP2: Total energy -82961.077703


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-339.843-338.17229.113-17.332-13.449-0.175
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.758 / q_NPA : 0.853
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].
3A4THR0-0.016-0.0153.8253.9225.214-0.023-0.563-0.7050.000
137A138VAL00.0380.0063.780-1.052-0.973-0.001-0.019-0.0590.000
141A142GLU-1-0.842-0.8891.743-137.503-140.77318.263-9.208-5.784-0.107
142A143GLY00.0020.0032.98210.80911.5930.038-0.272-0.550-0.001
143A144GLU-1-0.911-0.9374.048-22.481-22.2560.000-0.012-0.2130.000
185A186VAL0-0.021-0.0063.8473.6674.0110.000-0.129-0.2150.000
186A187ASP-1-0.846-0.9292.189-107.275-105.10610.823-7.141-5.850-0.067
187A188GLY0-0.014-0.0183.52410.00310.0510.0130.012-0.0730.000
4A5LEU0-0.021-0.0176.8603.7853.7850.0000.0000.0000.000
5A6TYR00.0380.0129.6442.0182.0180.0000.0000.0000.000
6A7LEU0-0.029-0.01812.3300.4910.4910.0000.0000.0000.000
7A8THR00.006-0.01915.4710.9880.9880.0000.0000.0000.000
8A9ARG10.7330.85919.26011.61111.6110.0000.0000.0000.000
9A10HIS0-0.019-0.03022.6540.0400.0400.0000.0000.0000.000
10A11GLY00.0480.01825.1870.0970.0970.0000.0000.0000.000
11A12GLU-1-0.732-0.82728.145-9.096-9.0960.0000.0000.0000.000
12A13THR00.007-0.00730.7150.1640.1640.0000.0000.0000.000
13A14LYS10.9340.96933.3317.8737.8730.0000.0000.0000.000
14A15TRP00.004-0.00735.2420.1240.1240.0000.0000.0000.000
15A16ASN00.0360.03630.766-0.045-0.0450.0000.0000.0000.000
16A17VAL00.0210.01434.5310.1370.1370.0000.0000.0000.000
17A18GLU-1-0.930-0.97637.542-7.652-7.6520.0000.0000.0000.000
18A19ARG10.9020.95136.4368.7698.7690.0000.0000.0000.000
19A20ARG10.8000.90637.6887.7417.7410.0000.0000.0000.000
20A21MET0-0.0140.00832.933-0.234-0.2340.0000.0000.0000.000
21A22GLN00.0220.03931.4230.2060.2060.0000.0000.0000.000
22A23GLY00.0500.02729.8150.1510.1510.0000.0000.0000.000
23A24TRP0-0.052-0.04527.162-0.098-0.0980.0000.0000.0000.000
24A25GLN0-0.0150.01530.4660.1270.1270.0000.0000.0000.000
25A26ASP-1-0.804-0.90230.613-10.875-10.8750.0000.0000.0000.000
26A27SER0-0.036-0.01632.8460.4270.4270.0000.0000.0000.000
27A28PRO00.0550.02333.013-0.264-0.2640.0000.0000.0000.000
28A29LEU0-0.0250.00228.9590.1270.1270.0000.0000.0000.000
29A30THR0-0.086-0.07333.1500.2820.2820.0000.0000.0000.000
30A31GLU-1-0.837-0.90634.481-9.071-9.0710.0000.0000.0000.000
31A32LYS10.7970.88831.4339.8809.8800.0000.0000.0000.000
32A33GLY00.0420.02131.012-0.274-0.2740.0000.0000.0000.000
33A34ARG10.8990.93929.9178.7328.7320.0000.0000.0000.000
34A35GLN0-0.003-0.02130.379-0.445-0.4450.0000.0000.0000.000
35A36ASP-1-0.801-0.87827.882-10.890-10.8900.0000.0000.0000.000
36A37ALA00.0270.00525.936-0.518-0.5180.0000.0000.0000.000
37A38MET0-0.040-0.01525.924-0.338-0.3380.0000.0000.0000.000
38A39ARG10.7790.88927.08010.06610.0660.0000.0000.0000.000
39A40LEU0-0.012-0.00319.925-0.338-0.3380.0000.0000.0000.000
40A41GLY00.0570.01722.139-0.639-0.6390.0000.0000.0000.000
41A42LYS10.7660.87922.98511.39211.3920.0000.0000.0000.000
42A43ARG10.7660.85519.15715.00815.0080.0000.0000.0000.000
43A44LEU00.0180.00516.697-0.707-0.7070.0000.0000.0000.000
44A45GLU-1-0.845-0.89918.881-12.920-12.9200.0000.0000.0000.000
45A46ALA0-0.045-0.02318.910-0.110-0.1100.0000.0000.0000.000
46A47VAL0-0.0110.01013.413-0.649-0.6490.0000.0000.0000.000
47A48GLU-1-0.939-0.96212.523-21.165-21.1650.0000.0000.0000.000
48A49LEU0-0.050-0.03412.584-1.963-1.9630.0000.0000.0000.000
49A50ALA00.0640.04511.4231.6421.6420.0000.0000.0000.000
50A51ALA0-0.035-0.03513.2721.4791.4790.0000.0000.0000.000
51A52ILE0-0.0180.00014.331-0.829-0.8290.0000.0000.0000.000
52A53TYR0-0.012-0.02012.7391.2701.2700.0000.0000.0000.000
53A54THR00.011-0.00216.8740.1510.1510.0000.0000.0000.000
54A55SER0-0.0200.01820.0840.1740.1740.0000.0000.0000.000
55A56THR0-0.004-0.02722.3840.1370.1370.0000.0000.0000.000
56A57SER0-0.049-0.01225.4870.3970.3970.0000.0000.0000.000
57A58GLY00.0590.02726.843-0.342-0.3420.0000.0000.0000.000
58A59ARG10.7930.87627.47910.87010.8700.0000.0000.0000.000
59A60ALA0-0.033-0.00923.177-0.151-0.1510.0000.0000.0000.000
60A61LEU00.0400.02824.086-0.499-0.4990.0000.0000.0000.000
61A62GLU-1-0.824-0.93225.504-10.254-10.2540.0000.0000.0000.000
62A63THR0-0.008-0.01823.6460.0820.0820.0000.0000.0000.000
63A64ALA00.0130.00621.512-0.257-0.2570.0000.0000.0000.000
64A65GLU-1-0.985-0.99322.902-11.967-11.9670.0000.0000.0000.000
65A66ILE0-0.051-0.02525.6290.0780.0780.0000.0000.0000.000
66A67VAL0-0.016-0.01320.6920.0080.0080.0000.0000.0000.000
67A68ARG10.8850.95221.89813.42513.4250.0000.0000.0000.000
68A69GLY00.0270.01823.064-0.011-0.0110.0000.0000.0000.000
69A70GLY0-0.053-0.03026.4650.2960.2960.0000.0000.0000.000
70A71ARG10.8530.92118.12916.20416.2040.0000.0000.0000.000
71A72LEU0-0.022-0.01621.693-0.018-0.0180.0000.0000.0000.000
72A73ILE00.0420.03017.294-0.549-0.5490.0000.0000.0000.000
73A74PRO0-0.0290.00116.8971.0841.0840.0000.0000.0000.000
74A75ILE00.016-0.00218.490-0.699-0.6990.0000.0000.0000.000
75A76TYR0-0.034-0.00915.6060.5960.5960.0000.0000.0000.000
76A77GLN00.004-0.02019.3680.1090.1090.0000.0000.0000.000
77A78ASP-1-0.759-0.85417.566-17.226-17.2260.0000.0000.0000.000
78A79GLU-1-0.831-0.91520.619-12.754-12.7540.0000.0000.0000.000
79A80ARG10.7370.83715.52519.01219.0120.0000.0000.0000.000
80A81LEU00.0380.03215.960-0.126-0.1260.0000.0000.0000.000
81A82ARG10.8730.93720.11812.35012.3500.0000.0000.0000.000
82A83GLU-1-0.744-0.87223.609-12.732-12.7320.0000.0000.0000.000
83A84ILE0-0.034-0.00625.6280.0670.0670.0000.0000.0000.000
84A85HIS10.7770.86827.36610.29210.2920.0000.0000.0000.000
85A86LEU00.0530.00630.3650.1060.1060.0000.0000.0000.000
86A87GLY0-0.0090.00633.4290.2670.2670.0000.0000.0000.000
87A88ASP-1-0.802-0.87236.083-7.798-7.7980.0000.0000.0000.000
88A89TRP0-0.051-0.05035.0410.1170.1170.0000.0000.0000.000
89A90GLU-1-0.755-0.84932.623-9.816-9.8160.0000.0000.0000.000
90A91GLY00.0300.01336.7360.2200.2200.0000.0000.0000.000
91A92LYS10.7650.87938.9237.8157.8150.0000.0000.0000.000
92A93THR00.014-0.02638.954-0.204-0.2040.0000.0000.0000.000
93A94HIS00.0430.00435.7940.2150.2150.0000.0000.0000.000
94A95ASP-1-0.855-0.90340.626-7.214-7.2140.0000.0000.0000.000
95A96GLU-1-0.828-0.89343.414-7.216-7.2160.0000.0000.0000.000
96A97ILE0-0.0030.00438.0460.0650.0650.0000.0000.0000.000
97A98ARG10.8430.89940.9607.6307.6300.0000.0000.0000.000
98A99GLN0-0.049-0.02244.1720.2240.2240.0000.0000.0000.000
99A100MET0-0.0390.01642.7540.0990.0990.0000.0000.0000.000
100A101ASP-1-0.809-0.89341.165-7.550-7.5500.0000.0000.0000.000
101A102PRO0-0.002-0.00741.563-0.225-0.2250.0000.0000.0000.000
102A103ILE0-0.007-0.00741.502-0.125-0.1250.0000.0000.0000.000
103A104ALA00.0250.01538.176-0.170-0.1700.0000.0000.0000.000
104A105PHE00.024-0.00936.985-0.291-0.2910.0000.0000.0000.000
105A106ASP-1-0.872-0.91937.239-8.294-8.2940.0000.0000.0000.000
106A107HIS00.0250.00335.775-0.302-0.3020.0000.0000.0000.000
107A108PHE0-0.022-0.01030.411-0.367-0.3670.0000.0000.0000.000
108A109TRP0-0.036-0.01631.058-0.520-0.5200.0000.0000.0000.000
109A110GLN0-0.022-0.03333.078-0.405-0.4050.0000.0000.0000.000
110A111ALA0-0.055-0.01633.619-0.058-0.0580.0000.0000.0000.000
111A112PRO00.0550.03029.1490.1010.1010.0000.0000.0000.000
112A113HIS00.000-0.00830.319-0.249-0.2490.0000.0000.0000.000
113A114LEU0-0.024-0.01531.4490.1520.1520.0000.0000.0000.000
114A115TYR0-0.063-0.01531.3340.2030.2030.0000.0000.0000.000
115A116ALA0-0.007-0.00632.855-0.295-0.2950.0000.0000.0000.000
116A117PRO0-0.0150.00833.2510.3330.3330.0000.0000.0000.000
117A118GLN00.005-0.00935.880-0.070-0.0700.0000.0000.0000.000
118A119ARG10.8050.87136.4827.8257.8250.0000.0000.0000.000
119A120GLY00.0210.01033.1940.1010.1010.0000.0000.0000.000
120A121GLU-1-0.800-0.85826.416-12.024-12.0240.0000.0000.0000.000
121A122ARG10.8580.88328.65510.87910.8790.0000.0000.0000.000
122A123PHE00.0420.00725.927-0.442-0.4420.0000.0000.0000.000
123A124CYS00.0240.01023.957-0.369-0.3690.0000.0000.0000.000
124A125ASP-1-0.769-0.83823.227-11.792-11.7920.0000.0000.0000.000
125A126VAL0-0.020-0.01322.143-0.471-0.4710.0000.0000.0000.000
126A127GLN0-0.003-0.01419.288-0.209-0.2090.0000.0000.0000.000
127A128GLN0-0.0190.00318.490-0.535-0.5350.0000.0000.0000.000
128A129ARG10.7660.83518.15412.63012.6300.0000.0000.0000.000
129A130ALA00.0200.01717.632-0.735-0.7350.0000.0000.0000.000
130A131LEU00.0250.00612.574-1.157-1.1570.0000.0000.0000.000
131A132GLU-1-0.885-0.92113.175-18.528-18.5280.0000.0000.0000.000
132A133ALA0-0.027-0.01513.781-1.155-1.1550.0000.0000.0000.000
133A134VAL00.0250.00910.072-1.251-1.2510.0000.0000.0000.000
134A135GLN0-0.052-0.0317.075-1.719-1.7190.0000.0000.0000.000
135A136SER0-0.027-0.0149.041-1.751-1.7510.0000.0000.0000.000
136A137ILE0-0.039-0.0219.5010.2920.2920.0000.0000.0000.000
138A139ASP-1-0.868-0.9285.979-37.740-37.7400.0000.0000.0000.000
139A140ARG10.7970.9007.98624.86924.8690.0000.0000.0000.000
140A141HIS00.0020.0127.3225.6155.6150.0000.0000.0000.000
144A145THR00.0130.0026.429-4.224-4.2240.0000.0000.0000.000
145A146VAL0-0.033-0.0119.0283.0243.0240.0000.0000.0000.000
146A147LEU0-0.0150.00111.534-0.028-0.0280.0000.0000.0000.000
147A148ILE0-0.010-0.00311.6170.5290.5290.0000.0000.0000.000
148A149VAL0-0.018-0.00815.6420.5160.5160.0000.0000.0000.000
149A150THR0-0.012-0.03318.4980.4340.4340.0000.0000.0000.000
150A151HIS00.004-0.01521.1760.8580.8580.0000.0000.0000.000
151A152GLY00.0530.03522.621-0.502-0.5020.0000.0000.0000.000
152A153VAL0-0.007-0.01623.893-0.274-0.2740.0000.0000.0000.000
153A154VAL0-0.0100.01618.966-0.338-0.3380.0000.0000.0000.000
154A155LEU0-0.0010.00418.023-0.693-0.6930.0000.0000.0000.000
155A156LYS10.8590.93219.39912.88412.8840.0000.0000.0000.000
156A157THR0-0.026-0.02920.854-0.373-0.3730.0000.0000.0000.000
157A158LEU00.0020.01514.530-0.368-0.3680.0000.0000.0000.000
158A159MET0-0.0100.00215.383-1.057-1.0570.0000.0000.0000.000
159A160ALA0-0.036-0.02017.886-0.034-0.0340.0000.0000.0000.000
160A161ALA0-0.0020.00316.0140.1250.1250.0000.0000.0000.000
161A162PHE00.009-0.02111.499-0.520-0.5200.0000.0000.0000.000
162A163LYS10.8110.89314.65815.08215.0820.0000.0000.0000.000
163A164ASP-1-0.916-0.93717.344-15.095-15.0950.0000.0000.0000.000
164A165THR0-0.067-0.03119.0731.0851.0850.0000.0000.0000.000
165A166PRO0-0.017-0.01322.160-0.010-0.0100.0000.0000.0000.000
166A167LEU00.0520.01123.1700.2280.2280.0000.0000.0000.000
167A168ASP-1-0.854-0.91426.087-10.607-10.6070.0000.0000.0000.000
168A169HIS10.8000.88826.55911.15811.1580.0000.0000.0000.000
169A170LEU00.0350.04223.474-0.304-0.3040.0000.0000.0000.000
170A171TRP0-0.044-0.03725.017-0.585-0.5850.0000.0000.0000.000
171A172SER0-0.035-0.01725.0700.4260.4260.0000.0000.0000.000
172A173PRO0-0.036-0.01525.217-0.424-0.4240.0000.0000.0000.000
173A174PRO00.0380.03722.140-0.195-0.1950.0000.0000.0000.000
174A175TYR00.0260.00224.779-0.238-0.2380.0000.0000.0000.000
175A176MET00.0060.01319.591-0.150-0.1500.0000.0000.0000.000
176A177TYR00.009-0.02424.3980.0990.0990.0000.0000.0000.000
177A178GLY00.0380.03724.796-0.578-0.5780.0000.0000.0000.000
178A179THR0-0.018-0.01223.2600.2140.2140.0000.0000.0000.000
179A180SER0-0.048-0.03122.187-0.487-0.4870.0000.0000.0000.000
180A181VAL0-0.013-0.00316.719-0.476-0.4760.0000.0000.0000.000
181A182THR00.001-0.00114.2340.8150.8150.0000.0000.0000.000
182A183ILE0-0.0120.00110.359-0.102-0.1020.0000.0000.0000.000
183A184ILE0-0.030-0.0158.6161.2611.2610.0000.0000.0000.000
184A185GLU-1-0.783-0.8595.682-40.345-40.3450.0000.0000.0000.000
188A189GLY0-0.027-0.0154.8025.9735.9730.0000.0000.0000.000
189A190THR0-0.037-0.0066.7305.6995.6990.0000.0000.0000.000
190A191PHE00.008-0.0016.696-5.245-5.2450.0000.0000.0000.000
191A192HIS0-0.014-0.0106.3636.8496.8490.0000.0000.0000.000
192A193VAL0-0.023-0.0189.784-0.813-0.8130.0000.0000.0000.000
193A194ALA00.0050.01910.6681.1001.1000.0000.0000.0000.000
194A195VAL0-0.032-0.02212.6631.7221.7220.0000.0000.0000.000
195A196GLU-1-0.795-0.89415.311-16.570-16.5700.0000.0000.0000.000
196A197GLY00.014-0.00218.0310.8090.8090.0000.0000.0000.000
197A198ASP-1-0.780-0.85419.870-13.339-13.3390.0000.0000.0000.000
198A199VAL00.017-0.00921.612-0.228-0.2280.0000.0000.0000.000
199A200SER0-0.029-0.02323.3630.6090.6090.0000.0000.0000.000
200A201HIS0-0.050-0.00622.6850.0670.0670.0000.0000.0000.000
201A202ILE0-0.048-0.01925.8000.2940.2940.0000.0000.0000.000
202A203GLU-1-0.833-0.89028.721-9.987-9.9870.0000.0000.0000.000
203A204GLU-1-0.970-0.98732.461-8.363-8.3630.0000.0000.0000.000
204A205VAL00.0150.00529.363-0.216-0.2160.0000.0000.0000.000
205A206LYS10.8550.89431.3909.3169.3160.0000.0000.0000.000
206A207GLU-1-0.844-0.90231.517-10.135-10.1350.0000.0000.0000.000
207A208VAL-1-0.860-0.89930.579-10.171-10.1710.0000.0000.0000.000