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: VN6R1

Calculation Name: 4RN3-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: 4RN3

Chain ID: B

ChEMBL ID:

UniProt ID: Q74BH2

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2320937.288135
FMO2-HF: Nuclear repulsion 2238310.890188
FMO2-HF: Total energy -82626.397947
FMO2-MP2: Total energy -82860.486766


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:ALA)


Summations of interaction energy for fragment #1(A:9: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.
-267.853-264.91517.809-12.765-7.984-0.152
Interaction energy analysis for fragmet #1(A:9:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.699 / q_NPA : 0.817
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].
3A11LYS10.8290.9063.57640.31841.556-0.004-0.633-0.602-0.001
159A167GLU-1-0.832-0.8834.304-47.174-46.918-0.001-0.038-0.2170.000
160A168ALA00.0220.0165.366-1.358-1.350-0.001-0.004-0.0040.000
203A211LEU-1-0.781-0.8511.708-151.005-149.56917.815-12.090-7.161-0.151
4A12ALA00.0000.0046.2985.2915.2910.0000.0000.0000.000
5A13VAL00.0130.0138.701-2.067-2.0670.0000.0000.0000.000
6A14ILE0-0.044-0.02110.8712.4082.4080.0000.0000.0000.000
7A15TYR00.0700.03213.790-0.434-0.4340.0000.0000.0000.000
8A16ASP-1-0.730-0.87017.145-13.374-13.3740.0000.0000.0000.000
9A17CYS0-0.049-0.03520.452-0.098-0.0980.0000.0000.0000.000
10A18ASP-1-0.754-0.82323.493-11.350-11.3500.0000.0000.0000.000
11A19GLY00.0650.04424.521-0.228-0.2280.0000.0000.0000.000
12A20VAL0-0.057-0.01618.773-0.454-0.4540.0000.0000.0000.000
13A21MET0-0.073-0.03320.458-0.419-0.4190.0000.0000.0000.000
14A22PHE00.001-0.02222.5120.2120.2120.0000.0000.0000.000
15A23ASP-1-0.763-0.85926.244-10.474-10.4740.0000.0000.0000.000
16A24SER0-0.006-0.04628.8750.2820.2820.0000.0000.0000.000
17A25PHE0-0.0240.00331.2230.4050.4050.0000.0000.0000.000
18A26GLU-1-0.722-0.83434.010-8.090-8.0900.0000.0000.0000.000
19A27ALA00.0130.01433.7100.2610.2610.0000.0000.0000.000
20A28ASN0-0.029-0.02432.0160.1970.1970.0000.0000.0000.000
21A29LEU0-0.0060.00836.0700.3120.3120.0000.0000.0000.000
22A30ALA0-0.013-0.01639.1610.2620.2620.0000.0000.0000.000
23A31PHE0-0.009-0.00738.0700.2140.2140.0000.0000.0000.000
24A32TYR00.0480.00335.7500.2480.2480.0000.0000.0000.000
25A33GLN0-0.030-0.01941.6810.3550.3550.0000.0000.0000.000
26A34ARG10.8630.91242.5687.6327.6320.0000.0000.0000.000
27A35ILE0-0.0040.00241.3140.1620.1620.0000.0000.0000.000
28A36MET0-0.055-0.02544.3800.1970.1970.0000.0000.0000.000
29A37GLU-1-0.960-0.97047.831-6.406-6.4060.0000.0000.0000.000
30A38MET0-0.045-0.02847.2210.0950.0950.0000.0000.0000.000
31A39MET0-0.047-0.01648.1520.0830.0830.0000.0000.0000.000
32A40GLY0-0.0120.01051.1320.0970.0970.0000.0000.0000.000
33A41ARG10.8060.89849.3146.5126.5120.0000.0000.0000.000
34A42PRO0-0.013-0.01050.775-0.005-0.0050.0000.0000.0000.000
35A43ARG10.9480.97245.8776.8256.8250.0000.0000.0000.000
36A44LEU00.0170.01242.3770.0560.0560.0000.0000.0000.000
37A45SER00.0000.00045.729-0.044-0.0440.0000.0000.0000.000
38A46ARG10.8360.84939.4207.8477.8470.0000.0000.0000.000
39A47ASP-1-0.881-0.93642.038-7.151-7.1510.0000.0000.0000.000
40A48ASN0-0.066-0.02643.900-0.087-0.0870.0000.0000.0000.000
41A49GLU-1-0.755-0.86636.651-8.846-8.8460.0000.0000.0000.000
42A50GLU-1-0.943-0.95638.955-7.654-7.6540.0000.0000.0000.000
43A51GLN00.012-0.01439.399-0.161-0.1610.0000.0000.0000.000
44A52MET0-0.042-0.00737.992-0.184-0.1840.0000.0000.0000.000
45A53ARG10.8650.91232.6789.0699.0690.0000.0000.0000.000
46A54ILE00.0370.02934.426-0.314-0.3140.0000.0000.0000.000
47A55LEU0-0.067-0.03635.176-0.209-0.2090.0000.0000.0000.000
48A56HIS0-0.050-0.04230.975-0.014-0.0140.0000.0000.0000.000
49A57THR0-0.017-0.00129.285-0.390-0.3900.0000.0000.0000.000
50A58TYR-1-0.909-0.95729.842-10.401-10.4010.0000.0000.0000.000
51A59ALA0-0.043-0.01532.0720.0290.0290.0000.0000.0000.000
52A60ASN0-0.044-0.02033.8420.3410.3410.0000.0000.0000.000
53A61ARG10.8180.90636.4198.3218.3210.0000.0000.0000.000
54A62GLU-1-0.788-0.87639.810-7.666-7.6660.0000.0000.0000.000
55A63VAL0-0.040-0.03041.7640.1610.1610.0000.0000.0000.000
56A64LEU00.0200.01844.6110.1010.1010.0000.0000.0000.000
57A65ALA00.004-0.01047.2490.1180.1180.0000.0000.0000.000
58A66HIS0-0.072-0.03849.1010.1740.1740.0000.0000.0000.000
59A67PHE00.0250.00652.8210.0570.0570.0000.0000.0000.000
60A68PHE00.0100.01851.9980.0020.0020.0000.0000.0000.000
61A69PRO0-0.0020.00447.380-0.061-0.0610.0000.0000.0000.000
62A70SER0-0.001-0.01848.009-0.107-0.1070.0000.0000.0000.000
63A71PRO0-0.018-0.00146.9270.0780.0780.0000.0000.0000.000
64A72GLY00.0470.03949.8570.1020.1020.0000.0000.0000.000
65A73ASP-1-0.862-0.92249.583-6.632-6.6320.0000.0000.0000.000
66A74TRP0-0.018-0.03240.8560.0010.0010.0000.0000.0000.000
67A75GLU-1-0.813-0.87745.364-6.707-6.7070.0000.0000.0000.000
68A76GLU00.002-0.00446.966-0.029-0.0290.0000.0000.0000.000
69A77ALA00.1080.04245.186-0.054-0.0540.0000.0000.0000.000
70A78VAL0-0.044-0.00841.391-0.198-0.1980.0000.0000.0000.000
71A79ARG10.7870.86343.2366.5366.5360.0000.0000.0000.000
72A80CYS0-0.028-0.01945.7390.0160.0160.0000.0000.0000.000
73A81ALA00.0250.00240.745-0.060-0.0600.0000.0000.0000.000
74A82GLY0-0.0220.00241.371-0.164-0.1640.0000.0000.0000.000
75A83ALA0-0.035-0.01342.420-0.003-0.0030.0000.0000.0000.000
76A84ILE0-0.035-0.00441.2010.0830.0830.0000.0000.0000.000
77A85ASP-1-0.793-0.89239.796-8.417-8.4170.0000.0000.0000.000
78A86TYR00.0420.01532.859-0.144-0.1440.0000.0000.0000.000
79A87ARG10.8650.91636.5348.2478.2470.0000.0000.0000.000
80A88GLU-1-0.866-0.91437.581-7.522-7.5220.0000.0000.0000.000
81A89LEU0-0.039-0.02137.0160.0820.0820.0000.0000.0000.000
82A90VAL00.0070.00531.529-0.159-0.1590.0000.0000.0000.000
83A91PRO0-0.041-0.02733.203-0.224-0.2240.0000.0000.0000.000
84A92LEU0-0.028-0.00135.4410.0930.0930.0000.0000.0000.000
85A93MET0-0.070-0.01428.5520.0870.0870.0000.0000.0000.000
86A94ILE00.0110.00529.6640.0350.0350.0000.0000.0000.000
87A95MET0-0.051-0.01524.529-0.398-0.3980.0000.0000.0000.000
88A96GLU-1-0.829-0.88522.696-12.703-12.7030.0000.0000.0000.000
89A97GLU-1-0.857-0.94023.075-13.291-13.2910.0000.0000.0000.000
90A98GLY0-0.026-0.01921.398-0.621-0.6210.0000.0000.0000.000
91A99PHE00.0390.01717.584-0.749-0.7490.0000.0000.0000.000
92A100ARG10.9020.95418.99912.47712.4770.0000.0000.0000.000
93A101GLU-1-0.852-0.93419.631-14.501-14.5010.0000.0000.0000.000
94A102ALA00.0120.02815.353-0.861-0.8610.0000.0000.0000.000
95A103LEU0-0.009-0.00214.937-1.622-1.6220.0000.0000.0000.000
96A104ASP-1-0.862-0.91615.779-16.086-16.0860.0000.0000.0000.000
97A105THR0-0.092-0.05112.990-0.274-0.2740.0000.0000.0000.000
98A106LEU00.000-0.0069.697-1.720-1.7200.0000.0000.0000.000
99A107LYS10.9460.98211.58414.57014.5700.0000.0000.0000.000
100A108GLY0-0.056-0.02213.1650.6340.6340.0000.0000.0000.000
101A109ARG10.8730.9448.35725.76225.7620.0000.0000.0000.000
102A110VAL0-0.0060.0076.599-4.808-4.8080.0000.0000.0000.000
103A111GLY0-0.0200.0029.1563.4363.4360.0000.0000.0000.000
104A112LEU00.0070.00211.437-1.461-1.4610.0000.0000.0000.000
105A113GLY00.025-0.00514.2011.2671.2670.0000.0000.0000.000
106A114VAL0-0.018-0.00516.695-0.253-0.2530.0000.0000.0000.000
107A115CYS0-0.035-0.00418.4190.5380.5380.0000.0000.0000.000
108A116THR00.0440.03020.2590.3000.3000.0000.0000.0000.000
109A117ASN00.018-0.01423.642-0.194-0.1940.0000.0000.0000.000
110A118ARG10.7930.86526.65211.59011.5900.0000.0000.0000.000
111A119SER00.0330.01828.409-0.225-0.2250.0000.0000.0000.000
112A120THR00.0200.00530.641-0.193-0.1930.0000.0000.0000.000
113A121SER00.0060.01031.600-0.199-0.1990.0000.0000.0000.000
114A122MET00.0590.04623.6910.1580.1580.0000.0000.0000.000
115A123ASP-1-0.748-0.84627.186-12.050-12.0500.0000.0000.0000.000
116A124MET0-0.098-0.03728.1850.1690.1690.0000.0000.0000.000
117A125VAL00.0400.01727.0270.1960.1960.0000.0000.0000.000
118A126LEU00.0020.00522.6800.0320.0320.0000.0000.0000.000
119A127ARG10.9680.98826.4839.9009.9000.0000.0000.0000.000
120A128LEU0-0.080-0.04329.1370.2270.2270.0000.0000.0000.000
121A129PHE00.0220.01727.4280.1740.1740.0000.0000.0000.000
122A130SER0-0.074-0.02427.381-0.159-0.1590.0000.0000.0000.000
123A131LEU00.043-0.00522.314-0.340-0.3400.0000.0000.0000.000
124A132ASP-1-0.897-0.95622.304-12.855-12.8550.0000.0000.0000.000
125A133SER0-0.023-0.01522.484-0.685-0.6850.0000.0000.0000.000
126A134TYR0-0.121-0.09417.959-0.041-0.0410.0000.0000.0000.000
127A135PHE0-0.0140.00417.315-1.074-1.0740.0000.0000.0000.000
128A136SER0-0.028-0.02416.6430.4940.4940.0000.0000.0000.000
129A137ILE0-0.021-0.00717.2760.7880.7880.0000.0000.0000.000
130A138VAL00.0310.01119.667-0.467-0.4670.0000.0000.0000.000
131A139MET0-0.0170.00620.8661.0451.0450.0000.0000.0000.000
132A140THR00.0030.00222.931-0.103-0.1030.0000.0000.0000.000
133A141ALA00.0610.01926.1580.0260.0260.0000.0000.0000.000
134A142SER0-0.059-0.04828.3790.3880.3880.0000.0000.0000.000
135A143ARG10.7100.82625.78512.30412.3040.0000.0000.0000.000
136A144VAL0-0.036-0.01723.963-0.438-0.4380.0000.0000.0000.000
137A145THR0-0.087-0.05927.1400.4820.4820.0000.0000.0000.000
138A146ASN0-0.047-0.02226.4870.6170.6170.0000.0000.0000.000
139A147PRO00.0290.01325.725-0.515-0.5150.0000.0000.0000.000
140A148LYS10.7770.88720.73814.58114.5810.0000.0000.0000.000
141A149PRO00.0280.01323.1400.5050.5050.0000.0000.0000.000
142A150HIS00.0290.01822.816-0.720-0.7200.0000.0000.0000.000
143A151PRO00.0730.04018.961-0.298-0.2980.0000.0000.0000.000
144A152GLU-1-0.750-0.84419.482-12.645-12.6450.0000.0000.0000.000
145A153PRO0-0.017-0.01520.863-0.365-0.3650.0000.0000.0000.000
146A154LEU00.0290.00815.351-0.633-0.6330.0000.0000.0000.000
147A155LEU0-0.009-0.00916.104-0.983-0.9830.0000.0000.0000.000
148A156LYS10.8980.93117.32612.24312.2430.0000.0000.0000.000
149A157VAL0-0.0100.00014.4620.0080.0080.0000.0000.0000.000
150A158LEU0-0.026-0.00811.062-0.978-0.9780.0000.0000.0000.000
151A159GLU-1-0.968-0.98114.126-15.336-15.3360.0000.0000.0000.000
152A160HIS0-0.044-0.00716.181-0.430-0.4300.0000.0000.0000.000
153A161PHE0-0.011-0.01112.230-0.203-0.2030.0000.0000.0000.000
154A162GLY0-0.0100.01613.428-0.523-0.5230.0000.0000.0000.000
155A163ILE0-0.080-0.0408.243-1.543-1.5430.0000.0000.0000.000
156A164GLY00.0360.0158.8752.0292.0290.0000.0000.0000.000
157A165PRO00.028-0.0078.473-2.796-2.7960.0000.0000.0000.000
158A166ARG10.9580.9575.57725.78225.7820.0000.0000.0000.000
161A169LEU00.0130.0156.6630.2650.2650.0000.0000.0000.000
162A170PHE0-0.044-0.0329.4071.6651.6650.0000.0000.0000.000
163A171VAL0-0.008-0.00213.1610.2390.2390.0000.0000.0000.000
164A172GLY00.028-0.00415.2660.8010.8010.0000.0000.0000.000
165A173ASP-1-0.818-0.89818.628-13.618-13.6180.0000.0000.0000.000
166A174SER00.008-0.00921.6930.7270.7270.0000.0000.0000.000
167A175GLU-1-0.802-0.89121.787-13.591-13.5910.0000.0000.0000.000
168A176VAL0-0.023-0.02222.589-0.338-0.3380.0000.0000.0000.000
169A177ASP-1-0.748-0.87918.817-15.053-15.0530.0000.0000.0000.000
170A178ARG10.7620.86417.81513.48813.4880.0000.0000.0000.000
171A179LEU0-0.010-0.00918.286-0.498-0.4980.0000.0000.0000.000
172A180SER0-0.025-0.01419.483-0.323-0.3230.0000.0000.0000.000
173A181ALA0-0.001-0.01514.326-0.419-0.4190.0000.0000.0000.000
174A182GLU-1-0.896-0.93915.223-15.934-15.9340.0000.0000.0000.000
175A183ALA0-0.030-0.01917.111-0.092-0.0920.0000.0000.0000.000
176A184ALA0-0.021-0.01015.3850.2990.2990.0000.0000.0000.000
177A185GLY0-0.045-0.01313.399-0.784-0.7840.0000.0000.0000.000
178A186VAL0-0.073-0.03610.441-1.894-1.8940.0000.0000.0000.000
179A187PRO0-0.042-0.0236.7221.7511.7510.0000.0000.0000.000
180A188PHE00.0470.0299.859-0.685-0.6850.0000.0000.0000.000
181A189VAL00.011-0.00810.939-0.804-0.8040.0000.0000.0000.000
182A190ALA00.0290.02213.5710.8990.8990.0000.0000.0000.000
183A191TYR0-0.038-0.06017.238-0.641-0.6410.0000.0000.0000.000
184A192LYS10.8380.91318.94414.31614.3160.0000.0000.0000.000
185A193ALA00.0560.05721.2210.7340.7340.0000.0000.0000.000
186A194PRO0-0.072-0.03821.670-0.597-0.5970.0000.0000.0000.000
187A195LEU00.0100.00919.8150.2860.2860.0000.0000.0000.000
188A196PRO0-0.042-0.02419.027-0.575-0.5750.0000.0000.0000.000
189A197ALA00.007-0.00314.668-0.042-0.0420.0000.0000.0000.000
190A198ALA0-0.063-0.0179.7760.2300.2300.0000.0000.0000.000
191A199TYR00.006-0.0016.235-1.999-1.9990.0000.0000.0000.000
192A200ARG10.8680.92812.39016.48316.4830.0000.0000.0000.000
193A201MET0-0.0250.00913.792-1.517-1.5170.0000.0000.0000.000
194A202GLU-1-0.909-0.95616.544-12.820-12.8200.0000.0000.0000.000
195A203HIS0-0.038-0.02518.4990.0380.0380.0000.0000.0000.000
196A204HIS00.0660.03116.657-2.056-2.0560.0000.0000.0000.000
197A205ARG10.9110.95715.39314.39114.3910.0000.0000.0000.000
198A206GLU-1-0.811-0.91413.874-19.141-19.1410.0000.0000.0000.000
199A207ILE00.0240.00210.084-2.117-2.1170.0000.0000.0000.000
200A208ILE0-0.086-0.0359.087-3.291-3.2910.0000.0000.0000.000
201A209ASP-1-0.938-0.9688.243-28.667-28.6670.0000.0000.0000.000
202A210LEU0-0.085-0.0387.052-0.818-0.8180.0000.0000.0000.000