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: 15QNZ

Calculation Name: 2IGB-B-Xray547

Preferred Name:

Target Type:

Ligand Name: uridine-5'-monophosphate | 1,2-ethanediol

Ligand 3-letter code: U5P | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IGB

Chain ID: B

ChEMBL ID:

UniProt ID: P41007

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1868941.864408
FMO2-HF: Nuclear repulsion 1799288.623411
FMO2-HF: Total energy -69653.240997
FMO2-MP2: Total energy -69857.341691


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.
-176.174-172.24319.994-12.041-11.883-0.125
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 : 0.791 / q_NPA : 0.885
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].
3A3LYS10.7970.8942.64032.08534.9881.138-1.789-2.252-0.015
4A4ALA00.006-0.0014.4195.5095.725-0.001-0.024-0.1910.000
177A177HIS00.014-0.0043.468-15.050-14.5190.005-0.215-0.321-0.001
178A178GLU-1-0.814-0.9052.936-25.821-24.5590.017-0.531-0.748-0.001
179A179LYS00.0850.0661.730-110.168-111.14918.835-9.482-8.371-0.108
5A5VAL00.0240.0207.749-1.768-1.7680.0000.0000.0000.000
6A6VAL0-0.054-0.03210.9291.3711.3710.0000.0000.0000.000
7A7MET0-0.057-0.03514.0671.7021.7020.0000.0000.0000.000
8A8ASP-1-0.792-0.88215.758-16.825-16.8250.0000.0000.0000.000
9A9GLU-1-0.833-0.92417.598-13.697-13.6970.0000.0000.0000.000
10A10GLN0-0.038-0.01820.5361.3911.3910.0000.0000.0000.000
11A11ALA0-0.039-0.02819.7990.6890.6890.0000.0000.0000.000
12A12ILE00.0250.01517.3170.5520.5520.0000.0000.0000.000
13A13ARG10.9640.98521.86412.15912.1590.0000.0000.0000.000
14A14ARG10.9150.95224.89212.40012.4000.0000.0000.0000.000
15A15ALA00.0010.01423.6890.4470.4470.0000.0000.0000.000
16A16LEU00.0470.01923.3490.3540.3540.0000.0000.0000.000
17A17THR00.0030.00426.9350.2800.2800.0000.0000.0000.000
18A18ARG10.7780.88525.84812.23512.2350.0000.0000.0000.000
19A19ILE00.0180.00625.3730.2480.2480.0000.0000.0000.000
20A20ALA00.0070.00829.8800.2480.2480.0000.0000.0000.000
21A21HIS00.0370.01932.5170.3600.3600.0000.0000.0000.000
22A22GLU-1-0.839-0.91330.100-10.767-10.7670.0000.0000.0000.000
23A23ILE0-0.035-0.01930.5380.1930.1930.0000.0000.0000.000
24A24ILE00.0340.03034.6140.1860.1860.0000.0000.0000.000
25A25GLU-1-0.966-0.98337.264-8.424-8.4240.0000.0000.0000.000
26A26ARG10.7510.86532.5479.8029.8020.0000.0000.0000.000
27A27ASN0-0.063-0.04236.0190.2030.2030.0000.0000.0000.000
28A28LYS10.8820.95039.9267.3597.3590.0000.0000.0000.000
29A29GLY00.0890.06741.2550.2420.2420.0000.0000.0000.000
30A30ILE00.022-0.01637.734-0.246-0.2460.0000.0000.0000.000
31A31ASP-1-0.856-0.92840.633-7.458-7.4580.0000.0000.0000.000
32A32GLY0-0.008-0.00742.278-0.094-0.0940.0000.0000.0000.000
33A33CYS0-0.0730.00037.278-0.147-0.1470.0000.0000.0000.000
34A34VAL00.0070.00335.6280.0800.0800.0000.0000.0000.000
35A35LEU0-0.0110.00730.072-0.200-0.2000.0000.0000.0000.000
36A36VAL00.006-0.00729.4720.1650.1650.0000.0000.0000.000
37A37GLY00.0170.01326.527-0.312-0.3120.0000.0000.0000.000
38A38ILE0-0.027-0.02522.7600.2220.2220.0000.0000.0000.000
39A39LYS10.8870.93318.00115.90615.9060.0000.0000.0000.000
40A40THR00.0140.00319.6240.2590.2590.0000.0000.0000.000
41A41ARG10.8400.89315.12720.54220.5420.0000.0000.0000.000
42A42GLY00.0550.03120.2690.3100.3100.0000.0000.0000.000
43A43ILE0-0.030-0.00122.7710.6020.6020.0000.0000.0000.000
44A44TYR00.0170.00621.7400.7180.7180.0000.0000.0000.000
45A45LEU0-0.027-0.01320.2390.3330.3330.0000.0000.0000.000
46A46ALA00.0180.00824.6060.4070.4070.0000.0000.0000.000
47A47ARG10.8840.93127.44811.74611.7460.0000.0000.0000.000
48A48ARG10.7230.78821.61314.39614.3960.0000.0000.0000.000
49A49LEU0-0.030-0.01527.1070.1530.1530.0000.0000.0000.000
50A50ALA00.0290.02130.1220.2970.2970.0000.0000.0000.000
51A51GLU-1-0.898-0.94331.185-9.388-9.3880.0000.0000.0000.000
52A52ARG10.7840.89026.74011.66511.6650.0000.0000.0000.000
53A53ILE00.0170.00033.3140.1900.1900.0000.0000.0000.000
54A54GLU-1-0.860-0.90435.919-8.105-8.1050.0000.0000.0000.000
55A55GLN0-0.097-0.05234.4400.1630.1630.0000.0000.0000.000
56A56ILE0-0.109-0.04534.9510.1200.1200.0000.0000.0000.000
57A57GLU-1-0.869-0.95639.058-7.673-7.6730.0000.0000.0000.000
58A58GLY0-0.050-0.00541.1480.2270.2270.0000.0000.0000.000
59A59ALA0-0.037-0.03041.4020.1760.1760.0000.0000.0000.000
60A60SER0-0.018-0.01438.715-0.129-0.1290.0000.0000.0000.000
61A61VAL0-0.034-0.01135.2760.1020.1020.0000.0000.0000.000
62A62PRO0-0.026-0.01335.958-0.196-0.1960.0000.0000.0000.000
63A63VAL00.0170.01030.343-0.184-0.1840.0000.0000.0000.000
64A64GLY0-0.009-0.00432.6870.1910.1910.0000.0000.0000.000
65A65GLU-1-0.890-0.94028.425-11.228-11.2280.0000.0000.0000.000
66A66LEU00.0210.00627.2430.3250.3250.0000.0000.0000.000
67A67ASP-1-0.860-0.92823.609-13.720-13.7200.0000.0000.0000.000
68A68ILE0-0.002-0.00423.2350.4020.4020.0000.0000.0000.000
69A69THR0-0.016-0.00721.205-0.660-0.6600.0000.0000.0000.000
70A70LEU0-0.032-0.01917.2730.4420.4420.0000.0000.0000.000
71A71TYR00.0490.01521.256-0.014-0.0140.0000.0000.0000.000
72A72ARG10.7930.88621.92813.67413.6740.0000.0000.0000.000
73A73ASP-1-0.842-0.91224.202-11.930-11.9300.0000.0000.0000.000
74A74ASP-1-0.824-0.88422.958-14.028-14.0280.0000.0000.0000.000
75A75LEU0-0.042-0.00720.009-0.236-0.2360.0000.0000.0000.000
76A76THR0-0.066-0.04918.314-1.082-1.0820.0000.0000.0000.000
77A77VAL00.0040.02115.1940.3500.3500.0000.0000.0000.000
78A78LYS10.8090.89816.11313.52713.5270.0000.0000.0000.000
79A79THR0-0.073-0.05718.046-0.371-0.3710.0000.0000.0000.000
80A80ASP-1-0.753-0.86519.805-14.347-14.3470.0000.0000.0000.000
81A81ASP-1-0.897-0.93719.600-14.672-14.6720.0000.0000.0000.000
82A82HIS0-0.047-0.04819.1700.3770.3770.0000.0000.0000.000
83A83GLU-1-0.823-0.91121.864-11.657-11.6570.0000.0000.0000.000
84A84PRO0-0.087-0.04522.341-0.262-0.2620.0000.0000.0000.000
85A85LEU00.0280.01123.9730.5730.5730.0000.0000.0000.000
86A86VAL00.005-0.00525.920-0.439-0.4390.0000.0000.0000.000
87A87LYS10.8650.92824.68712.74912.7490.0000.0000.0000.000
88A88GLY00.0120.00728.0910.1880.1880.0000.0000.0000.000
89A89THR0-0.034-0.02729.442-0.176-0.1760.0000.0000.0000.000
90A90ASN0-0.032-0.00631.8540.5640.5640.0000.0000.0000.000
91A91VAL00.0450.02133.320-0.211-0.2110.0000.0000.0000.000
92A92PRO0-0.0180.01635.5990.2380.2380.0000.0000.0000.000
93A93PHE00.004-0.01434.9670.2420.2420.0000.0000.0000.000
94A94PRO0-0.016-0.01439.923-0.095-0.0950.0000.0000.0000.000
95A95VAL00.0750.04036.808-0.050-0.0500.0000.0000.0000.000
96A96THR00.000-0.01739.842-0.097-0.0970.0000.0000.0000.000
97A97GLU-1-0.954-0.98143.019-6.733-6.7330.0000.0000.0000.000
98A98ARG10.8580.95539.4547.5267.5260.0000.0000.0000.000
99A99ASN00.010-0.01237.8330.0080.0080.0000.0000.0000.000
100A100VAL00.0240.00533.195-0.080-0.0800.0000.0000.0000.000
101A101ILE0-0.006-0.00230.222-0.183-0.1830.0000.0000.0000.000
102A102LEU00.0290.01227.589-0.176-0.1760.0000.0000.0000.000
103A103VAL00.0040.00024.259-0.116-0.1160.0000.0000.0000.000
104A104ASP-1-0.787-0.89520.379-15.735-15.7350.0000.0000.0000.000
105A105ASP-1-0.855-0.94916.621-18.634-18.6340.0000.0000.0000.000
106A106VAL0-0.049-0.03914.178-0.228-0.2280.0000.0000.0000.000
107A107LEU0-0.0260.00217.6150.3150.3150.0000.0000.0000.000
108A108PHE00.0480.00414.422-0.548-0.5480.0000.0000.0000.000
109A109THR00.0570.03318.0840.9180.9180.0000.0000.0000.000
110A110GLY00.0260.00620.4650.7450.7450.0000.0000.0000.000
111A111ARG10.8520.91721.64114.31114.3110.0000.0000.0000.000
112A112THR00.0370.00820.0060.4860.4860.0000.0000.0000.000
113A113VAL00.0180.01723.1430.3510.3510.0000.0000.0000.000
114A114ARG10.8260.91825.67511.33511.3350.0000.0000.0000.000
115A115ALA00.0120.01825.9310.3750.3750.0000.0000.0000.000
116A116ALA00.015-0.00226.7110.3120.3120.0000.0000.0000.000
117A117MET0-0.040-0.01928.6040.3520.3520.0000.0000.0000.000
118A118ASP-1-0.847-0.93531.269-9.704-9.7040.0000.0000.0000.000
119A119ALA00.0440.02731.3460.2980.2980.0000.0000.0000.000
120A120VAL0-0.024-0.01532.3060.2420.2420.0000.0000.0000.000
121A121MET0-0.090-0.05234.7350.2750.2750.0000.0000.0000.000
122A122ASP-1-0.953-0.96936.252-8.680-8.6800.0000.0000.0000.000
123A123LEU00.0110.01134.5250.1980.1980.0000.0000.0000.000
124A124GLY0-0.033-0.01638.3620.2280.2280.0000.0000.0000.000
125A125ARG10.8880.94040.4347.5357.5350.0000.0000.0000.000
126A126PRO00.0270.03537.6140.1860.1860.0000.0000.0000.000
127A127ALA0-0.0010.00340.5840.0960.0960.0000.0000.0000.000
128A128ARG10.8420.91537.1188.0738.0730.0000.0000.0000.000
129A129ILE00.0130.01932.158-0.038-0.0380.0000.0000.0000.000
130A130GLN0-0.042-0.02632.321-0.052-0.0520.0000.0000.0000.000
131A131LEU0-0.0130.00024.589-0.141-0.1410.0000.0000.0000.000
132A132ALA00.0360.02426.8680.0640.0640.0000.0000.0000.000
133A133VAL00.000-0.00921.189-0.222-0.2220.0000.0000.0000.000
134A134LEU00.0150.01918.0990.3270.3270.0000.0000.0000.000
135A135VAL0-0.001-0.01215.693-0.116-0.1160.0000.0000.0000.000
136A136ASP-1-0.757-0.83718.903-14.709-14.7090.0000.0000.0000.000
137A137ARG10.8300.91011.26424.92024.9200.0000.0000.0000.000
138A138GLY0-0.015-0.00317.128-0.447-0.4470.0000.0000.0000.000
139A139HIS0-0.067-0.06515.7170.4240.4240.0000.0000.0000.000
140A140ARG10.7440.84919.52014.17214.1720.0000.0000.0000.000
141A141GLU-1-0.787-0.87820.145-15.505-15.5050.0000.0000.0000.000
142A142LEU00.0250.01824.2010.4800.4800.0000.0000.0000.000
143A143PRO0-0.0100.00427.052-0.280-0.2800.0000.0000.0000.000
144A144ILE00.0040.00225.9680.2740.2740.0000.0000.0000.000
145A145ARG10.8160.86426.3319.9379.9370.0000.0000.0000.000
146A146ALA00.0230.02225.0380.2790.2790.0000.0000.0000.000
147A147ASP-1-0.820-0.87427.084-9.810-9.8100.0000.0000.0000.000
148A148PHE00.0460.02228.2930.2150.2150.0000.0000.0000.000
149A149VAL00.0320.01822.393-0.387-0.3870.0000.0000.0000.000
150A150GLY00.0140.02122.6760.3940.3940.0000.0000.0000.000
151A151LYS10.8800.93317.06617.17317.1730.0000.0000.0000.000
152A152ASN00.0430.02519.921-0.617-0.6170.0000.0000.0000.000
153A153VAL0-0.028-0.02813.8760.0600.0600.0000.0000.0000.000
154A154PRO00.006-0.00116.296-0.542-0.5420.0000.0000.0000.000
155A155THR00.0170.02812.162-1.116-1.1160.0000.0000.0000.000
156A156SER00.0010.01510.1271.9481.9480.0000.0000.0000.000
157A157ARG10.8340.88412.80618.10518.1050.0000.0000.0000.000
158A158SER0-0.033-0.0358.6131.5421.5420.0000.0000.0000.000
159A159GLU-1-0.818-0.8817.300-34.627-34.6270.0000.0000.0000.000
160A160LEU00.0250.0136.2254.3664.3660.0000.0000.0000.000
161A161ILE0-0.023-0.0148.455-1.548-1.5480.0000.0000.0000.000
162A162VAL0-0.017-0.0057.2050.2800.2800.0000.0000.0000.000
163A163VAL0-0.010-0.01110.3180.8140.8140.0000.0000.0000.000
164A164GLU-1-0.885-0.92010.898-27.564-27.5640.0000.0000.0000.000
165A165LEU0-0.016-0.02214.5100.8790.8790.0000.0000.0000.000
166A166SER00.018-0.00818.2530.1930.1930.0000.0000.0000.000
167A167GLU-1-0.809-0.87620.057-13.695-13.6950.0000.0000.0000.000
168A168VAL0-0.087-0.05118.1250.4380.4380.0000.0000.0000.000
169A169ASP-1-0.755-0.84014.338-20.813-20.8130.0000.0000.0000.000
170A170GLY0-0.0250.00315.671-0.612-0.6120.0000.0000.0000.000
171A171ILE0-0.024-0.01313.7600.6490.6490.0000.0000.0000.000
172A172ASP-1-0.747-0.82016.763-15.411-15.4110.0000.0000.0000.000
173A173GLN0-0.096-0.08310.8850.7440.7440.0000.0000.0000.000
174A174VAL00.0120.01113.409-0.210-0.2100.0000.0000.0000.000
175A175SER00.0430.0208.642-0.801-0.8010.0000.0000.0000.000
176A176ILE0-0.0160.0027.2320.3550.3550.0000.0000.0000.000