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: 13N6Z

Calculation Name: 3VU9-B-Xray549

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VU9

Chain ID: B

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2366129.567501
FMO2-HF: Nuclear repulsion 2285611.249517
FMO2-HF: Total energy -80518.317984
FMO2-MP2: Total energy -80755.485573


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(B:3:TYR)


Summations of interaction energy for fragment #1(B:3:TYR)
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.
-133.781-113.97826.919-17.939-28.785-0.105
Interaction energy analysis for fragmet #1(B:3:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.745 / q_NPA : 0.852
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].
3B5ASP-1-0.884-0.9261.964-98.523-92.2486.543-6.937-5.882-0.087
4B6LEU0-0.080-0.0312.9637.8639.9000.424-0.731-1.7300.004
5B7GLU-1-0.870-0.9335.210-28.275-28.236-0.001-0.004-0.0330.000
25B27ASN0-0.049-0.0263.277-16.593-14.9230.065-0.644-1.091-0.005
28B30LYS10.8750.9573.71551.53951.7860.000-0.035-0.2120.000
33B35THR0-0.022-0.0093.611-3.417-2.7870.041-0.180-0.4910.001
35B37LEU0-0.035-0.0095.144-3.467-3.391-0.001-0.003-0.0710.000
109B111LYS10.8460.9032.69842.56845.4944.075-1.593-5.4080.015
110B112ILE00.0140.0042.954-4.016-2.1790.462-0.524-1.7750.001
111B113ILE0-0.0070.0071.771-21.442-23.35511.969-4.980-5.077-0.047
112B114LEU0-0.0090.0023.9044.3804.5870.004-0.057-0.1540.000
156B158SER00.0050.0092.451-2.316-1.2251.285-0.749-1.6270.004
157B159ILE0-0.040-0.0192.477-1.648-0.0370.701-0.801-1.5110.002
158B160ARG10.8850.9582.74836.25139.1801.353-0.686-3.5970.007
159B161THR00.0180.0094.221-0.148-0.007-0.001-0.015-0.1260.000
6B8LEU0-0.063-0.0227.832-1.210-1.2100.0000.0000.0000.000
7B9ILE0-0.043-0.0308.4050.1180.1180.0000.0000.0000.000
8B10THR0-0.0110.0129.6750.5190.5190.0000.0000.0000.000
9B11ILE0-0.003-0.00411.7160.2620.2620.0000.0000.0000.000
10B12TRP0-0.027-0.01610.580-1.655-1.6550.0000.0000.0000.000
11B13PRO0-0.001-0.01014.3821.0451.0450.0000.0000.0000.000
12B14SER0-0.043-0.01518.1250.0450.0450.0000.0000.0000.000
13B15PRO00.0340.05414.9750.3990.3990.0000.0000.0000.000
14B16THR0-0.020-0.01817.0040.6610.6610.0000.0000.0000.000
15B17LYS11.0390.99117.06212.99512.9950.0000.0000.0000.000
16B18ASN00.0630.03016.558-0.614-0.6140.0000.0000.0000.000
17B19LYS10.9550.98714.15618.05818.0580.0000.0000.0000.000
18B20LEU00.0680.05811.313-1.716-1.7160.0000.0000.0000.000
19B21CYS0-0.035-0.02211.600-1.152-1.1520.0000.0000.0000.000
20B22GLN0-0.001-0.00112.103-0.979-0.9790.0000.0000.0000.000
21B23PHE00.0330.0165.196-0.936-0.9360.0000.0000.0000.000
22B24ILE00.0320.0187.434-3.553-3.5530.0000.0000.0000.000
23B25LYS10.9490.9878.19018.10718.1070.0000.0000.0000.000
24B26GLN0-0.028-0.0067.4041.4361.4360.0000.0000.0000.000
26B28LEU00.000-0.0125.4680.0040.0040.0000.0000.0000.000
27B29SER0-0.061-0.0427.7651.9031.9030.0000.0000.0000.000
29B31GLU-1-0.884-0.9367.653-19.684-19.6840.0000.0000.0000.000
30B32HIS00.003-0.0059.098-1.871-1.8710.0000.0000.0000.000
31B33VAL0-0.016-0.0095.533-1.800-1.8000.0000.0000.0000.000
32B34VAL00.0580.0508.643-0.049-0.0490.0000.0000.0000.000
34B36GLN0-0.044-0.0405.0113.0023.0020.0000.0000.0000.000
36B38PHE00.008-0.0047.5422.8182.8180.0000.0000.0000.000
37B39PHE00.003-0.0019.753-0.690-0.6900.0000.0000.0000.000
38B40ILE0-0.009-0.00711.9451.1721.1720.0000.0000.0000.000
39B41ASP-1-0.743-0.87114.589-14.189-14.1890.0000.0000.0000.000
40B42ALA00.0100.01917.6400.5320.5320.0000.0000.0000.000
41B43THR0-0.085-0.05720.8150.5790.5790.0000.0000.0000.000
42B44SER0-0.005-0.00420.4850.5350.5350.0000.0000.0000.000
43B45SER0-0.067-0.04020.460-0.005-0.0050.0000.0000.0000.000
44B46PHE00.0430.02713.098-0.211-0.2110.0000.0000.0000.000
45B47PRO0-0.021-0.00516.1200.8740.8740.0000.0000.0000.000
46B48LEU00.0320.00518.999-0.134-0.1340.0000.0000.0000.000
47B49SER00.0080.00720.0820.0150.0150.0000.0000.0000.000
48B50GLN0-0.017-0.02719.9250.7930.7930.0000.0000.0000.000
49B51PHE00.0430.00612.759-0.146-0.1460.0000.0000.0000.000
50B52GLN00.0310.00617.8850.0880.0880.0000.0000.0000.000
51B53LYS10.8640.94220.68712.50412.5040.0000.0000.0000.000
52B54LEU0-0.043-0.02317.1960.0040.0040.0000.0000.0000.000
53B55VAL0-0.015-0.00414.094-0.846-0.8460.0000.0000.0000.000
54B56PRO00.0410.03717.4550.2270.2270.0000.0000.0000.000
55B57PRO00.0090.00820.034-0.246-0.2460.0000.0000.0000.000
56B58THR0-0.031-0.01721.0110.0320.0320.0000.0000.0000.000
57B59LEU0-0.0260.00620.8450.4480.4480.0000.0000.0000.000
58B60PRO00.0280.01120.620-0.503-0.5030.0000.0000.0000.000
59B61GLU-1-0.857-0.94117.121-15.013-15.0130.0000.0000.0000.000
60B62ASN0-0.032-0.04015.915-1.978-1.9780.0000.0000.0000.000
61B63VAL0-0.0040.01216.205-0.523-0.5230.0000.0000.0000.000
62B64ARG10.9970.99410.39922.77222.7720.0000.0000.0000.000
63B65ILE0-0.026-0.00111.189-1.060-1.0600.0000.0000.0000.000
64B66TYR0-0.057-0.06212.644-0.292-0.2920.0000.0000.0000.000
65B67GLU-1-0.891-0.93614.967-15.186-15.1860.0000.0000.0000.000
66B68ASN0-0.029-0.0159.5900.0510.0510.0000.0000.0000.000
67B69ILE0-0.0100.0079.782-1.690-1.6900.0000.0000.0000.000
68B70ARG10.8410.91711.41419.09019.0900.0000.0000.0000.000
69B71ILE00.0070.00512.794-0.597-0.5970.0000.0000.0000.000
70B72ASN00.004-0.01315.4210.4570.4570.0000.0000.0000.000
71B73THR0-0.0370.00517.146-0.216-0.2160.0000.0000.0000.000
72B74CYS0-0.0080.00617.9720.2100.2100.0000.0000.0000.000
73B75LEU00.020-0.00319.997-0.077-0.0770.0000.0000.0000.000
74B76ASP-1-0.870-0.92122.218-10.365-10.3650.0000.0000.0000.000
75B77LEU00.0310.00620.050-0.555-0.5550.0000.0000.0000.000
76B78GLU-1-0.845-0.90020.411-10.829-10.8290.0000.0000.0000.000
77B79GLU-1-0.853-0.91920.531-11.571-11.5710.0000.0000.0000.000
78B80LEU00.0460.00814.349-0.434-0.4340.0000.0000.0000.000
79B81SER0-0.0090.01316.022-0.686-0.6860.0000.0000.0000.000
80B82ALA0-0.003-0.00517.266-0.262-0.2620.0000.0000.0000.000
81B83ILE0-0.019-0.01013.068-0.248-0.2480.0000.0000.0000.000
82B84THR00.009-0.00812.452-0.936-0.9360.0000.0000.0000.000
83B85VAL0-0.059-0.03113.346-0.307-0.3070.0000.0000.0000.000
84B86LYS10.9390.97414.72312.49612.4960.0000.0000.0000.000
85B87LEU00.0360.0228.195-0.174-0.1740.0000.0000.0000.000
86B88LEU00.0330.01910.334-0.530-0.5300.0000.0000.0000.000
87B89GLN0-0.021-0.01412.3040.1070.1070.0000.0000.0000.000
88B90ILE00.0030.0029.7500.2350.2350.0000.0000.0000.000
89B91LEU00.0200.0115.9690.1380.1380.0000.0000.0000.000
90B92SER0-0.020-0.02010.1350.1410.1410.0000.0000.0000.000
91B93MET0-0.037-0.02013.6540.6200.6200.0000.0000.0000.000
92B94ASN00.0140.01910.814-0.112-0.1120.0000.0000.0000.000
93B95LYS10.8730.9318.70120.67520.6750.0000.0000.0000.000
94B96ILE0-0.041-0.01913.2450.5330.5330.0000.0000.0000.000
95B97ASN0-0.074-0.06416.3650.7830.7830.0000.0000.0000.000
96B98ALA00.0330.03414.2520.4150.4150.0000.0000.0000.000
97B99GLN0-0.023-0.02115.8061.1271.1270.0000.0000.0000.000
98B100ARG10.8780.93217.44211.77311.7730.0000.0000.0000.000
99B101GLY00.0260.01919.8470.6160.6160.0000.0000.0000.000
100B102THR0-0.088-0.04420.0320.5260.5260.0000.0000.0000.000
101B103GLU-1-0.851-0.92418.572-12.925-12.9250.0000.0000.0000.000
102B104ASP-1-0.842-0.90614.764-15.968-15.9680.0000.0000.0000.000
103B105ALA0-0.053-0.01416.226-0.474-0.4740.0000.0000.0000.000
104B106VAL0-0.064-0.03217.9000.2180.2180.0000.0000.0000.000
105B107THR0-0.077-0.05313.162-0.189-0.1890.0000.0000.0000.000
106B108GLU-1-0.879-0.93711.004-23.021-23.0210.0000.0000.0000.000
107B109PRO0-0.0070.0177.4720.6960.6960.0000.0000.0000.000
108B110LEU0-0.028-0.0106.437-2.139-2.1390.0000.0000.0000.000
113B115TYR0-0.055-0.0677.209-1.487-1.4870.0000.0000.0000.000
114B116ILE00.0050.0039.7831.3911.3910.0000.0000.0000.000
115B117ASN00.0070.00613.383-0.029-0.0290.0000.0000.0000.000
116B118GLY00.0620.03116.5530.4930.4930.0000.0000.0000.000
117B119LEU00.0490.02015.8970.5300.5300.0000.0000.0000.000
118B120GLU-1-0.791-0.90619.255-12.459-12.4590.0000.0000.0000.000
119B121VAL0-0.074-0.04122.5770.7010.7010.0000.0000.0000.000
120B122MET0-0.0380.00117.1320.3260.3260.0000.0000.0000.000
121B123PHE00.0420.00922.4000.4210.4210.0000.0000.0000.000
122B124ARG10.9360.97423.87510.92310.9230.0000.0000.0000.000
123B125ASN0-0.048-0.03425.6440.6410.6410.0000.0000.0000.000
124B126SER00.044-0.01724.6910.1720.1720.0000.0000.0000.000
125B127GLN0-0.039-0.00526.9340.2410.2410.0000.0000.0000.000
126B128PHE0-0.075-0.04029.4010.2940.2940.0000.0000.0000.000
127B129LYS10.8510.93126.83710.20310.2030.0000.0000.0000.000
128B130SER0-0.008-0.00628.9840.1320.1320.0000.0000.0000.000
129B131SER00.006-0.00530.5320.1910.1910.0000.0000.0000.000
130B132PRO00.0630.02529.884-0.314-0.3140.0000.0000.0000.000
131B133GLN00.0270.03328.985-0.399-0.3990.0000.0000.0000.000
132B134ARG10.9480.96724.8929.8789.8780.0000.0000.0000.000
133B135SER00.0290.00825.497-0.350-0.3500.0000.0000.0000.000
134B136HIS0-0.047-0.04324.039-0.584-0.5840.0000.0000.0000.000
135B137GLU-1-0.920-0.93023.655-10.189-10.1890.0000.0000.0000.000
136B138LEU00.0170.01221.198-0.358-0.3580.0000.0000.0000.000
137B139LEU0-0.0010.01018.708-0.568-0.5680.0000.0000.0000.000
138B140ARG10.8710.91318.65910.49410.4940.0000.0000.0000.000
139B141ASP-1-0.836-0.90018.647-12.134-12.1340.0000.0000.0000.000
140B142THR0-0.072-0.04615.098-0.380-0.3800.0000.0000.0000.000
141B143LEU00.006-0.00214.219-0.921-0.9210.0000.0000.0000.000
142B144LEU00.018-0.00113.864-0.953-0.9530.0000.0000.0000.000
143B145LYS10.9260.98213.82113.52213.5220.0000.0000.0000.000
144B146LEU00.029-0.0049.338-0.515-0.5150.0000.0000.0000.000
145B147ARG10.7960.8759.53918.03018.0300.0000.0000.0000.000
146B148VAL00.005-0.00110.784-0.847-0.8470.0000.0000.0000.000
147B149MET0-0.081-0.0318.7810.0040.0040.0000.0000.0000.000
148B150GLY00.0100.0066.264-0.784-0.7840.0000.0000.0000.000
149B151ASN0-0.031-0.0256.904-2.508-2.5080.0000.0000.0000.000
150B152ASP-1-0.866-0.9099.596-17.969-17.9690.0000.0000.0000.000
151B153GLU-1-0.945-0.9628.335-19.133-19.1330.0000.0000.0000.000
152B154ASN0-0.049-0.0359.628-0.666-0.6660.0000.0000.0000.000
153B155GLU-1-0.906-0.9527.567-25.200-25.2000.0000.0000.0000.000
154B156ASN0-0.056-0.0287.649-1.982-1.9820.0000.0000.0000.000
155B157ALA0-0.031-0.0216.953-0.129-0.1290.0000.0000.0000.000
160B162LEU0-0.023-0.0037.273-0.041-0.0410.0000.0000.0000.000
161B163LEU0-0.014-0.0119.5671.4771.4770.0000.0000.0000.000
162B164GLU-1-0.821-0.88713.300-17.297-17.2970.0000.0000.0000.000
163B165PHE00.039-0.00115.5990.8270.8270.0000.0000.0000.000
164B166PRO0-0.0010.01119.261-0.425-0.4250.0000.0000.0000.000
165B167LYS10.9700.98421.42013.81213.8120.0000.0000.0000.000
166B168GLU-1-0.884-0.94523.259-11.879-11.8790.0000.0000.0000.000
167B169GLN0-0.062-0.04323.2160.1470.1470.0000.0000.0000.000
168B170LEU00.0230.02119.595-0.014-0.0140.0000.0000.0000.000
169B171LEU00.0130.00223.868-0.112-0.1120.0000.0000.0000.000
170B172ASP-1-0.803-0.87125.925-10.898-10.8980.0000.0000.0000.000
171B173TYR0-0.029-0.02719.3020.2050.2050.0000.0000.0000.000
172B174TYR0-0.002-0.02119.9970.0790.0790.0000.0000.0000.000
173B175LEU0-0.041-0.02325.1510.2910.2910.0000.0000.0000.000
174B176LYS10.8990.96125.52411.25811.2580.0000.0000.0000.000
175B177LYS10.8030.88620.73314.89514.8950.0000.0000.0000.000
176B178ASN-1-0.957-0.95825.335-10.717-10.7170.0000.0000.0000.000
177B192ARG10.8300.86929.16010.56610.5660.0000.0000.0000.000
178B193ILE00.0160.02035.7500.1040.1040.0000.0000.0000.000
179B194LYS10.7470.84729.27310.45110.4510.0000.0000.0000.000
180B195ASN0-0.013-0.00633.9860.4280.4280.0000.0000.0000.000
181B196GLY00.0310.02432.186-0.047-0.0470.0000.0000.0000.000
182B197ASP-1-0.832-0.90026.668-11.155-11.1550.0000.0000.0000.000
183B198SER0-0.027-0.03024.9860.0500.0500.0000.0000.0000.000
184B199LEU00.0440.01119.957-0.179-0.1790.0000.0000.0000.000
185B200ALA00.0360.02220.553-0.457-0.4570.0000.0000.0000.000
186B201GLU-1-0.768-0.87221.124-11.807-11.8070.0000.0000.0000.000
187B202TYR00.0170.00022.661-0.225-0.2250.0000.0000.0000.000
188B203ILE00.004-0.00516.834-0.174-0.1740.0000.0000.0000.000
189B204TRP0-0.006-0.01118.553-0.029-0.0290.0000.0000.0000.000
190B205LYS10.7870.89420.07711.35911.3590.0000.0000.0000.000
191B206TYR0-0.042-0.01921.2610.2050.2050.0000.0000.0000.000
192B207TYR0-0.026-0.01416.5020.2180.2180.0000.0000.0000.000
193B208ALA0-0.007-0.00614.541-0.848-0.8480.0000.0000.0000.000
194B209ASP-1-0.762-0.84912.375-21.293-21.2930.0000.0000.0000.000
195B210SER0-0.003-0.00111.2450.4260.4260.0000.0000.0000.000
196B211LEU0-0.031-0.02114.0630.3010.3010.0000.0000.0000.000
197B212PHE0-0.0070.00710.170-0.539-0.5390.0000.0000.0000.000
198B213GLU-2-1.677-1.81513.290-35.537-35.5370.0000.0000.0000.000