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: VN6Z1

Calculation Name: 4W4L-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4W4L

Chain ID: B

ChEMBL ID:

UniProt ID: O53943

Base Structure: X-ray

Registration Date: 2025-10-04

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 -1523030.74471
FMO2-HF: Nuclear repulsion 1452113.854422
FMO2-HF: Total energy -70916.890287
FMO2-MP2: Total energy -71120.466194


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.
-178.306-172.0526.871-5.502-7.624-0.041
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 : 0.800 / q_NPA : 0.904
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].
3A3PHE00.0760.0292.988-15.625-9.1660.884-3.251-4.092-0.030
4A4GLU-1-0.636-0.7844.287-39.593-39.4420.000-0.033-0.1180.000
5A5ALA0-0.083-0.0255.2262.3862.497-0.001-0.009-0.1020.000
6A6TYR0-0.075-0.0522.3661.050-0.1435.837-1.961-2.683-0.009
154A154ARG10.9290.9642.84752.97053.6960.151-0.248-0.629-0.002
7A7PRO00.0600.0528.525-0.359-0.3590.0000.0000.0000.000
8A8PRO00.0660.03111.639-1.009-1.0090.0000.0000.0000.000
9A9GLU-1-0.818-0.90513.601-16.845-16.8450.0000.0000.0000.000
10A10VAL0-0.075-0.0368.8330.2390.2390.0000.0000.0000.000
11A11ASN0-0.019-0.0187.581-2.327-2.3270.0000.0000.0000.000
12A12SER00.048-0.00610.3180.4050.4050.0000.0000.0000.000
13A13ALA0-0.037-0.02113.9740.5390.5390.0000.0000.0000.000
14A14ASN0-0.072-0.0408.4811.7431.7430.0000.0000.0000.000
15A15ILE0-0.029-0.00211.6760.0010.0010.0000.0000.0000.000
16A16TYR0-0.029-0.01813.7931.4231.4230.0000.0000.0000.000
17A17ALA0-0.0380.00715.9911.1771.1770.0000.0000.0000.000
18A18GLY0-0.007-0.00816.959-0.676-0.6760.0000.0000.0000.000
19A19PRO0-0.061-0.04317.8680.5770.5770.0000.0000.0000.000
20A20GLY00.0710.05519.2760.6440.6440.0000.0000.0000.000
21A21PRO00.0390.00819.793-0.338-0.3380.0000.0000.0000.000
22A22ASP-1-0.858-0.93020.746-12.074-12.0740.0000.0000.0000.000
23A23SER0-0.039-0.02520.5660.3120.3120.0000.0000.0000.000
24A24MET00.0190.01315.2450.2540.2540.0000.0000.0000.000
25A25LEU00.0440.01921.5010.4340.4340.0000.0000.0000.000
26A26ALA0-0.077-0.04024.6660.5230.5230.0000.0000.0000.000
27A27ALA00.0200.00622.8210.3930.3930.0000.0000.0000.000
28A28ALA00.0210.02023.8380.2450.2450.0000.0000.0000.000
29A29ARG10.9650.97825.37811.43111.4310.0000.0000.0000.000
30A30ALA00.0020.02027.4760.3830.3830.0000.0000.0000.000
31A31TRP00.031-0.00423.0410.4270.4270.0000.0000.0000.000
32A32ARG10.9110.94327.63010.78010.7800.0000.0000.0000.000
33A33SER0-0.026-0.02529.9450.4470.4470.0000.0000.0000.000
34A34LEU0-0.005-0.00528.6640.3120.3120.0000.0000.0000.000
35A35ASP-1-0.889-0.94429.887-10.184-10.1840.0000.0000.0000.000
36A36VAL0-0.0110.00831.8440.2870.2870.0000.0000.0000.000
37A37GLU-1-0.902-0.95635.281-8.085-8.0850.0000.0000.0000.000
38A38MET0-0.018-0.01432.7630.3070.3070.0000.0000.0000.000
39A39THR0-0.006-0.00534.6470.2010.2010.0000.0000.0000.000
40A40ALA00.0070.00136.8360.2530.2530.0000.0000.0000.000
41A41VAL00.0150.01537.9750.2810.2810.0000.0000.0000.000
42A42GLN0-0.0010.01137.0370.4050.4050.0000.0000.0000.000
43A43ARG10.9270.95337.9968.4438.4430.0000.0000.0000.000
44A44SER0-0.011-0.01442.4010.2700.2700.0000.0000.0000.000
45A45PHE00.0050.01641.6950.2030.2030.0000.0000.0000.000
46A46ASN00.002-0.02140.5810.2270.2270.0000.0000.0000.000
47A47ARG10.9770.99144.5666.5326.5320.0000.0000.0000.000
48A48THR0-0.029-0.01047.0220.2220.2220.0000.0000.0000.000
49A49LEU0-0.024-0.01244.1400.1510.1510.0000.0000.0000.000
50A50LEU00.017-0.00447.7490.1350.1350.0000.0000.0000.000
51A51SER0-0.028-0.02550.4180.1620.1620.0000.0000.0000.000
52A52LEU0-0.022-0.00451.3370.1390.1390.0000.0000.0000.000
53A53MET0-0.035-0.02451.8540.0920.0920.0000.0000.0000.000
54A54ASP-1-0.946-0.97953.853-5.577-5.5770.0000.0000.0000.000
55A55ALA0-0.026-0.00756.3750.1140.1140.0000.0000.0000.000
56A56TRP0-0.050-0.03057.4130.0700.0700.0000.0000.0000.000
57A57ALA00.0120.00856.8650.0830.0830.0000.0000.0000.000
58A58GLY00.0220.02657.9270.0300.0300.0000.0000.0000.000
59A59PRO00.021-0.02356.531-0.109-0.1090.0000.0000.0000.000
60A60VAL00.0010.01055.014-0.097-0.0970.0000.0000.0000.000
61A61VAL00.0320.02352.735-0.122-0.1220.0000.0000.0000.000
62A62MET0-0.018-0.00451.704-0.100-0.1000.0000.0000.0000.000
63A63GLN00.0650.03349.257-0.067-0.0670.0000.0000.0000.000
64A64LEU00.0100.00549.010-0.159-0.1590.0000.0000.0000.000
65A65MET0-0.053-0.01747.370-0.215-0.2150.0000.0000.0000.000
66A66GLU-1-1.006-1.00745.782-6.726-6.7260.0000.0000.0000.000
67A67ALA00.0210.01744.543-0.199-0.1990.0000.0000.0000.000
68A68ALA00.0190.00843.139-0.206-0.2060.0000.0000.0000.000
69A69LYS10.9430.98341.3937.1517.1510.0000.0000.0000.000
70A70PRO0-0.027-0.02838.115-0.250-0.2500.0000.0000.0000.000
71A71PHE00.0570.02836.997-0.297-0.2970.0000.0000.0000.000
72A72VAL00.0140.00737.425-0.188-0.1880.0000.0000.0000.000
73A73ARG10.9050.96235.4208.2488.2480.0000.0000.0000.000
74A74TRP00.0440.01930.5500.0000.0000.0000.0000.0000.000
75A75LEU00.0260.01332.732-0.266-0.2660.0000.0000.0000.000
76A76THR0-0.023-0.01934.4220.0200.0200.0000.0000.0000.000
77A77ASP-1-0.931-0.96729.745-10.334-10.3340.0000.0000.0000.000
78A78LEU0-0.013-0.00128.885-0.405-0.4050.0000.0000.0000.000
79A79CYS0-0.040-0.02129.387-0.194-0.1940.0000.0000.0000.000
80A80VAL0-0.0080.00127.588-0.173-0.1730.0000.0000.0000.000
81A81GLN0-0.039-0.03223.9680.0740.0740.0000.0000.0000.000
82A82LEU0-0.019-0.01725.384-0.467-0.4670.0000.0000.0000.000
83A83SER0-0.032-0.00526.933-0.294-0.2940.0000.0000.0000.000
84A84GLU-1-0.861-0.91022.097-13.472-13.4720.0000.0000.0000.000
85A85VAL00.015-0.00321.540-0.565-0.5650.0000.0000.0000.000
86A86GLU-1-0.835-0.90022.020-12.497-12.4970.0000.0000.0000.000
87A87ARG10.8390.92623.11912.00212.0020.0000.0000.0000.000
88A88GLN00.018-0.01818.176-1.125-1.1250.0000.0000.0000.000
89A89ILE0-0.0100.00718.161-0.934-0.9340.0000.0000.0000.000
90A90HIS0-0.061-0.05719.289-0.245-0.2450.0000.0000.0000.000
91A91GLU-1-0.910-0.92217.555-15.894-15.8940.0000.0000.0000.000
92A92ILE0-0.021-0.01614.020-0.905-0.9050.0000.0000.0000.000
93A93VAL0-0.018-0.01115.751-0.631-0.6310.0000.0000.0000.000
94A94ARG10.9120.95118.17614.22014.2200.0000.0000.0000.000
95A95ALA0-0.031-0.01013.076-0.289-0.2890.0000.0000.0000.000
96A96TYR00.0040.00014.291-0.442-0.4420.0000.0000.0000.000
97A97GLU-1-0.928-0.97215.293-14.228-14.2280.0000.0000.0000.000
98A98TRP0-0.070-0.04716.4300.2890.2890.0000.0000.0000.000
99A99ALA00.0390.02212.570-0.008-0.0080.0000.0000.0000.000
100A100HIS0-0.042-0.02214.4420.0410.0410.0000.0000.0000.000
101A101HIS10.7980.88016.82915.30915.3090.0000.0000.0000.000
102A102ASP-1-0.874-0.92716.005-16.528-16.5280.0000.0000.0000.000
103A103MET0-0.0650.01410.657-0.756-0.7560.0000.0000.0000.000
104A104VAL00.0530.03115.3691.3131.3130.0000.0000.0000.000
105A105PRO0-0.026-0.00917.375-0.060-0.0600.0000.0000.0000.000
106A106LEU00.0130.00116.7420.3370.3370.0000.0000.0000.000
107A107ALA0-0.024-0.00819.8830.2910.2910.0000.0000.0000.000
108A108GLN00.0110.00421.6060.4460.4460.0000.0000.0000.000
109A109ILE00.0450.04316.5830.3660.3660.0000.0000.0000.000
110A110TYR0-0.026-0.03419.3920.3940.3940.0000.0000.0000.000
111A111ASN0-0.035-0.00723.3510.3850.3850.0000.0000.0000.000
112A112ASN00.0560.02722.6950.1620.1620.0000.0000.0000.000
113A113ARG10.8040.88220.55213.62813.6280.0000.0000.0000.000
114A114ALA0-0.028-0.01524.4310.3660.3660.0000.0000.0000.000
115A115GLU-1-0.928-0.97627.905-10.154-10.1540.0000.0000.0000.000
116A116ARG10.8540.90524.74411.92011.9200.0000.0000.0000.000
117A117GLN0-0.082-0.04628.265-0.061-0.0610.0000.0000.0000.000
118A118ILE00.0300.01329.9360.3570.3570.0000.0000.0000.000
119A119LEU0-0.0110.00230.8150.3700.3700.0000.0000.0000.000
120A120ILE0-0.034-0.02429.4820.2420.2420.0000.0000.0000.000
121A121ASP-1-0.885-0.93132.823-8.776-8.7760.0000.0000.0000.000
122A122ASN0-0.076-0.04535.5030.5040.5040.0000.0000.0000.000
123A123ASN0-0.049-0.02234.2350.3340.3340.0000.0000.0000.000
124A124ALA00.0050.00736.9260.0240.0240.0000.0000.0000.000
125A125LEU0-0.027-0.01739.9350.1510.1510.0000.0000.0000.000
126A126GLY0-0.0030.00137.3360.0860.0860.0000.0000.0000.000
127A127GLN0-0.056-0.02837.008-0.193-0.1930.0000.0000.0000.000
128A128PHE00.0420.02234.370-0.001-0.0010.0000.0000.0000.000
129A129THR0-0.029-0.03232.162-0.294-0.2940.0000.0000.0000.000
130A130ALA0-0.0120.00331.083-0.276-0.2760.0000.0000.0000.000
131A131GLN00.0700.03330.212-0.257-0.2570.0000.0000.0000.000
132A132ILE0-0.037-0.01428.255-0.272-0.2720.0000.0000.0000.000
133A133ALA0-0.0070.00026.490-0.389-0.3890.0000.0000.0000.000
134A134ASP-1-0.907-0.95225.495-10.852-10.8520.0000.0000.0000.000
135A135LEU00.0040.00325.128-0.420-0.4200.0000.0000.0000.000
136A136ASP-1-0.796-0.85622.263-12.866-12.8660.0000.0000.0000.000
137A137GLN0-0.043-0.02120.238-0.284-0.2840.0000.0000.0000.000
138A138GLU-1-0.842-0.91420.570-12.908-12.9080.0000.0000.0000.000
139A139TYR0-0.112-0.07516.672-0.774-0.7740.0000.0000.0000.000
140A140ASP-1-0.908-0.97216.422-17.083-17.0830.0000.0000.0000.000
141A141ASP-1-0.890-0.93315.853-16.024-16.0240.0000.0000.0000.000
142A142PHE0-0.002-0.01516.261-0.772-0.7720.0000.0000.0000.000
143A143TRP0-0.073-0.04510.144-0.512-0.5120.0000.0000.0000.000
144A144ASP-1-0.984-0.98711.413-24.169-24.1690.0000.0000.0000.000
145A145GLU-1-0.881-0.93912.001-18.671-18.6710.0000.0000.0000.000
146A146ASP-1-0.726-0.88610.797-22.219-22.2190.0000.0000.0000.000
147A147GLY0-0.038-0.0197.915-2.825-2.8250.0000.0000.0000.000
148A148GLU-1-0.852-0.9138.315-26.221-26.2210.0000.0000.0000.000
149A149VAL00.0330.02410.840-1.648-1.6480.0000.0000.0000.000
150A150MET0-0.018-0.0166.205-0.430-0.4300.0000.0000.0000.000
151A151ARG10.6330.7806.37520.87020.8700.0000.0000.0000.000
152A152ASP-1-0.797-0.8887.425-27.567-27.5670.0000.0000.0000.000
153A153TYR0-0.037-0.0099.1081.7941.7940.0000.0000.0000.000
155A155LEU0-0.071-0.0307.023-0.008-0.0080.0000.0000.0000.000
156A156ARG11.0491.0268.94122.73322.7330.0000.0000.0000.000
157A157VAL00.0210.0109.5151.7381.7380.0000.0000.0000.000
158A158SER0-0.045-0.0227.9530.1560.1560.0000.0000.0000.000
159A159ASP-1-0.928-0.96510.073-22.605-22.6050.0000.0000.0000.000
160A160ALA00.0020.01213.2121.6721.6720.0000.0000.0000.000
161A161LEU0-0.014-0.02111.1051.3271.3270.0000.0000.0000.000
162A162SER0-0.103-0.04813.4571.4591.4590.0000.0000.0000.000
163A163LYS10.9170.96515.05717.86617.8660.0000.0000.0000.000
164A164LEU0-0.0350.00317.7241.2031.2030.0000.0000.0000.000
165A165THR0-0.012-0.00318.604-0.168-0.1680.0000.0000.0000.000
166A166PRO00.002-0.00819.1310.3840.3840.0000.0000.0000.000
167A167TRP00.0300.03421.4770.6710.6710.0000.0000.0000.000
168A168LYS10.9600.98024.84511.63311.6330.0000.0000.0000.000
169A169ALA00.0280.02027.5630.1800.1800.0000.0000.0000.000
170A170PRO0-0.0040.00830.4090.0300.0300.0000.0000.0000.000
171A171PRO0-0.036-0.00933.8650.0510.0510.0000.0000.0000.000
172A172PRO0-0.003-0.01336.3180.0680.0680.0000.0000.0000.000
173A173ILE0-0.036-0.02239.847-0.035-0.0350.0000.0000.0000.000
174A174ALA-1-0.925-0.95442.907-7.000-7.0000.0000.0000.0000.000