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: Y95K2

Calculation Name: 1XTT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: uridine-5'-monophosphate | acetic acid

Ligand 3-letter code: U5P | ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XTT

Chain ID: A

ChEMBL ID:

UniProt ID: Q980Q4

Base Structure: X-ray

Registration Date: 2025-10-03

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2530328.19812
FMO2-HF: Nuclear repulsion 2447884.92159
FMO2-HF: Total energy -82443.276529
FMO2-MP2: Total energy -82689.144526


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-83.854-78.07825.45-13.896-17.329-0.161
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.751 / q_NPA : 0.861
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].
3A4TYR0-0.007-0.0012.4361.5224.7371.074-1.528-2.760-0.011
179A180LEU0-0.027-0.0162.854-2.981-2.2800.120-0.211-0.610-0.002
183A184PRO00.0670.0463.940-8.566-8.186-0.001-0.182-0.198-0.001
184A185PHE0-0.013-0.0211.890-37.682-37.7067.656-3.783-3.849-0.049
185A186ILE0-0.0030.0062.361-6.050-4.6413.075-1.812-2.672-0.025
186A187TYR00.0210.0071.791-42.598-42.55113.478-6.831-6.694-0.072
187A188LEU0-0.0050.0023.09913.86213.9100.0480.451-0.546-0.001
4A5VAL00.0470.0246.0101.9481.9480.0000.0000.0000.000
5A6ILE0-0.061-0.0309.1210.8690.8690.0000.0000.0000.000
6A7ASP-1-0.837-0.90512.164-19.273-19.2730.0000.0000.0000.000
7A8LYS10.8740.92312.46522.09322.0930.0000.0000.0000.000
8A9PRO00.0430.00917.1870.2640.2640.0000.0000.0000.000
9A10ILE00.0030.00619.6650.3410.3410.0000.0000.0000.000
10A11THR0-0.020-0.03715.9490.6720.6720.0000.0000.0000.000
11A12LEU00.0660.03917.6280.1630.1630.0000.0000.0000.000
12A13HIS00.0030.02420.3000.1950.1950.0000.0000.0000.000
13A14ILE00.000-0.01021.1630.4130.4130.0000.0000.0000.000
14A15LEU00.0050.00318.2250.3330.3330.0000.0000.0000.000
15A16THR0-0.029-0.02521.5140.2920.2920.0000.0000.0000.000
16A17GLN0-0.065-0.03224.7850.7570.7570.0000.0000.0000.000
17A18LEU0-0.035-0.00121.2440.3020.3020.0000.0000.0000.000
18A19ARG10.7890.84319.54615.34315.3430.0000.0000.0000.000
19A20ASP-1-0.862-0.91225.373-9.851-9.8510.0000.0000.0000.000
20A21LYS10.9590.98129.1579.2339.2330.0000.0000.0000.000
21A22TYR0-0.039-0.02931.0150.2230.2230.0000.0000.0000.000
22A23THR0-0.079-0.03128.6590.3550.3550.0000.0000.0000.000
23A24ASP-1-0.732-0.83531.006-9.772-9.7720.0000.0000.0000.000
24A25GLN00.0650.01230.332-0.097-0.0970.0000.0000.0000.000
25A26ILE0-0.055-0.01530.116-0.350-0.3500.0000.0000.0000.000
26A27ASN0-0.064-0.07030.380-0.447-0.4470.0000.0000.0000.000
27A28PHE00.0330.03623.408-0.460-0.4600.0000.0000.0000.000
28A29ARG10.9360.96125.9159.9629.9620.0000.0000.0000.000
29A30LYS10.8780.94825.7019.6989.6980.0000.0000.0000.000
30A31ASN0-0.013-0.02024.296-0.343-0.3430.0000.0000.0000.000
31A32LEU00.0530.03319.652-0.624-0.6240.0000.0000.0000.000
32A33VAL00.0250.01720.889-0.737-0.7370.0000.0000.0000.000
33A34ARG10.8480.91921.68711.36511.3650.0000.0000.0000.000
34A35LEU00.0430.01917.481-0.475-0.4750.0000.0000.0000.000
35A36GLY00.0290.02416.882-1.067-1.0670.0000.0000.0000.000
36A37ARG10.8990.95417.13212.27212.2720.0000.0000.0000.000
37A38ILE0-0.0110.00115.571-0.390-0.3900.0000.0000.0000.000
38A39LEU00.0240.00611.785-0.827-0.8270.0000.0000.0000.000
39A40GLY00.0460.02412.547-1.544-1.5440.0000.0000.0000.000
40A41TYR0-0.0080.00714.332-0.415-0.4150.0000.0000.0000.000
41A42GLU-1-0.846-0.92410.778-21.967-21.9670.0000.0000.0000.000
42A43ILE0-0.0080.0038.859-1.483-1.4830.0000.0000.0000.000
43A44SER00.000-0.01510.423-0.684-0.6840.0000.0000.0000.000
44A45ASN0-0.050-0.02011.8630.8110.8110.0000.0000.0000.000
45A46THR0-0.045-0.0196.480-2.435-2.4350.0000.0000.0000.000
46A47LEU0-0.047-0.0128.418-1.835-1.8350.0000.0000.0000.000
47A48ASP-1-0.816-0.90210.336-24.944-24.9440.0000.0000.0000.000
48A49TYR0-0.063-0.04112.3151.2351.2350.0000.0000.0000.000
49A50GLU-1-0.905-0.93615.871-14.135-14.1350.0000.0000.0000.000
50A51ILE0-0.046-0.03519.1040.2130.2130.0000.0000.0000.000
51A52VAL00.0090.01121.6120.2740.2740.0000.0000.0000.000
52A53GLU-1-0.955-0.97724.849-9.585-9.5850.0000.0000.0000.000
53A54VAL0-0.016-0.01227.628-0.024-0.0240.0000.0000.0000.000
54A55GLU-1-0.861-0.92630.370-8.122-8.1220.0000.0000.0000.000
55A56THR0-0.031-0.01633.252-0.029-0.0290.0000.0000.0000.000
56A57PRO00.008-0.02035.5330.1710.1710.0000.0000.0000.000
57A58LEU0-0.025-0.00438.0660.2100.2100.0000.0000.0000.000
58A59GLY00.0090.01939.6060.1310.1310.0000.0000.0000.000
59A60VAL0-0.0070.00836.1150.0320.0320.0000.0000.0000.000
60A61LYS10.9110.93533.2098.3698.3690.0000.0000.0000.000
61A62THR0-0.020-0.01129.6270.0280.0280.0000.0000.0000.000
62A63LYS10.9620.98125.42311.09811.0980.0000.0000.0000.000
63A64GLY00.0150.01124.8920.1290.1290.0000.0000.0000.000
64A65VAL0-0.037-0.02418.210-0.167-0.1670.0000.0000.0000.000
65A66ASP-1-0.880-0.93320.720-13.482-13.4820.0000.0000.0000.000
66A67ILE00.0180.00814.949-0.567-0.5670.0000.0000.0000.000
67A68THR00.0880.04617.162-0.280-0.2800.0000.0000.0000.000
68A69ASP-1-0.773-0.87513.143-20.635-20.6350.0000.0000.0000.000
69A70LEU0-0.011-0.00216.047-0.366-0.3660.0000.0000.0000.000
70A71ASN0-0.069-0.04217.6241.1691.1690.0000.0000.0000.000
71A72ASN0-0.047-0.00816.3011.3271.3270.0000.0000.0000.000
72A73ILE00.0590.03913.618-1.428-1.4280.0000.0000.0000.000
73A74VAL0-0.020-0.01115.0771.3791.3790.0000.0000.0000.000
74A75ILE00.0140.01414.888-1.377-1.3770.0000.0000.0000.000
75A76ILE0-0.036-0.02215.5291.1841.1840.0000.0000.0000.000
76A77ASN00.016-0.01616.667-1.083-1.0830.0000.0000.0000.000
77A78ILE00.0190.01515.7870.7090.7090.0000.0000.0000.000
78A79LEU0-0.0240.00319.7400.2630.2630.0000.0000.0000.000
79A80ARG10.8650.89823.44010.73110.7310.0000.0000.0000.000
80A81ALA00.0360.01420.8850.1050.1050.0000.0000.0000.000
81A82ALA00.007-0.00118.556-0.090-0.0900.0000.0000.0000.000
82A83VAL00.0120.02920.252-0.261-0.2610.0000.0000.0000.000
83A84PRO00.0450.01022.905-0.124-0.1240.0000.0000.0000.000
84A85LEU0-0.0100.00215.507-0.029-0.0290.0000.0000.0000.000
85A86VAL00.020-0.00818.027-0.634-0.6340.0000.0000.0000.000
86A87GLU-1-0.939-0.96619.835-11.977-11.9770.0000.0000.0000.000
87A88GLY0-0.039-0.02320.7170.3510.3510.0000.0000.0000.000
88A89LEU00.0190.00914.2520.0580.0580.0000.0000.0000.000
89A90LEU0-0.014-0.00918.036-0.087-0.0870.0000.0000.0000.000
90A91LYS10.8370.92120.73912.62412.6240.0000.0000.0000.000
91A92ALA00.0060.02317.1860.3960.3960.0000.0000.0000.000
92A93PHE0-0.008-0.00613.200-0.083-0.0830.0000.0000.0000.000
93A94PRO00.0050.00018.8080.1860.1860.0000.0000.0000.000
94A95LYS10.9020.94621.03813.46413.4640.0000.0000.0000.000
95A96ALA0-0.0200.01018.129-0.159-0.1590.0000.0000.0000.000
96A97ARG10.7850.86718.68616.13116.1310.0000.0000.0000.000
97A98GLN00.0390.01419.540-0.768-0.7680.0000.0000.0000.000
98A99GLY0-0.001-0.00419.8580.6330.6330.0000.0000.0000.000
99A100VAL0-0.030-0.00820.546-0.521-0.5210.0000.0000.0000.000
100A101ILE0-0.005-0.01818.2640.2840.2840.0000.0000.0000.000
101A102GLY00.0050.01222.109-0.217-0.2170.0000.0000.0000.000
102A103ALA0-0.002-0.00820.9300.1640.1640.0000.0000.0000.000
103A104SER00.005-0.00122.908-0.027-0.0270.0000.0000.0000.000
104A105ARG10.8880.93420.88013.79213.7920.0000.0000.0000.000
105A106VAL00.0050.00424.7460.4620.4620.0000.0000.0000.000
106A107GLU-1-0.956-0.97026.852-10.558-10.5580.0000.0000.0000.000
107A108VAL0-0.003-0.00526.1420.2030.2030.0000.0000.0000.000
108A109ASP-1-0.834-0.92029.328-9.844-9.8440.0000.0000.0000.000
109A110GLY00.0310.04429.7010.2740.2740.0000.0000.0000.000
110A111LYS10.8700.92230.7379.7439.7430.0000.0000.0000.000
111A112GLU-1-0.898-0.96327.855-10.567-10.5670.0000.0000.0000.000
112A113VAL00.0110.02122.5490.0370.0370.0000.0000.0000.000
113A114PRO0-0.019-0.00523.017-0.237-0.2370.0000.0000.0000.000
114A115LYS11.0041.00720.49112.76612.7660.0000.0000.0000.000
115A116ASP-1-0.778-0.88419.056-17.627-17.6270.0000.0000.0000.000
116A117MET0-0.023-0.00421.0900.3900.3900.0000.0000.0000.000
117A118ASP-1-0.871-0.91521.958-12.707-12.7070.0000.0000.0000.000
118A119VAL0-0.013-0.01120.0510.0450.0450.0000.0000.0000.000
119A120TYR00.0200.02123.236-0.018-0.0180.0000.0000.0000.000
120A121ILE0-0.019-0.02521.039-0.319-0.3190.0000.0000.0000.000
121A122TYR0-0.0060.01025.0440.4880.4880.0000.0000.0000.000
122A123TYR0-0.003-0.00826.2540.3140.3140.0000.0000.0000.000
123A124LYS10.9850.99521.12613.47613.4760.0000.0000.0000.000
124A125LYS10.9450.99324.54611.66311.6630.0000.0000.0000.000
125A126ILE00.010-0.00719.255-0.354-0.3540.0000.0000.0000.000
126A127PRO0-0.0200.00720.8030.5130.5130.0000.0000.0000.000
127A128ASP-1-0.873-0.94121.275-13.166-13.1660.0000.0000.0000.000
128A129ILE0-0.037-0.01415.669-0.273-0.2730.0000.0000.0000.000
129A130ARG10.8210.87318.58615.43215.4320.0000.0000.0000.000
130A131ALA00.0680.03216.096-0.922-0.9220.0000.0000.0000.000
131A132LYS10.8910.93414.02217.36317.3630.0000.0000.0000.000
132A133VAL0-0.0030.00815.075-0.164-0.1640.0000.0000.0000.000
133A134ASP-1-0.733-0.80515.224-16.816-16.8160.0000.0000.0000.000
134A135ASN0-0.036-0.03210.534-3.367-3.3670.0000.0000.0000.000
135A136VAL0-0.001-0.00711.0931.5961.5960.0000.0000.0000.000
136A137ILE00.0130.00610.386-2.875-2.8750.0000.0000.0000.000
137A138ILE0-0.005-0.00710.8222.3192.3190.0000.0000.0000.000
138A139ALA0-0.001-0.00212.197-1.657-1.6570.0000.0000.0000.000
139A140ASP-1-0.836-0.95614.511-16.188-16.1880.0000.0000.0000.000
140A141PRO0-0.028-0.00915.038-1.152-1.1520.0000.0000.0000.000
141A142MET00.0170.02616.753-0.424-0.4240.0000.0000.0000.000
142A143ILE00.0040.00810.5570.1520.1520.0000.0000.0000.000
143A144ALA00.0510.01614.598-0.254-0.2540.0000.0000.0000.000
144A145THR00.0280.00416.106-0.879-0.8790.0000.0000.0000.000
145A146ALA00.0060.01012.542-0.363-0.3630.0000.0000.0000.000
146A147SER0-0.0070.00914.424-0.535-0.5350.0000.0000.0000.000
147A148THR00.0320.01217.0320.2100.2100.0000.0000.0000.000
148A149MET00.0300.02410.896-0.141-0.1410.0000.0000.0000.000
149A150LEU0-0.008-0.01811.533-0.681-0.6810.0000.0000.0000.000
150A151LYS10.9130.96913.87413.96213.9620.0000.0000.0000.000
151A152VAL0-0.015-0.00214.6950.7370.7370.0000.0000.0000.000
152A153LEU0-0.018-0.0129.389-0.217-0.2170.0000.0000.0000.000
153A154GLU-1-0.933-0.95913.080-16.437-16.4370.0000.0000.0000.000
154A155GLU-1-0.888-0.94315.964-14.635-14.6350.0000.0000.0000.000
155A156VAL0-0.031-0.02712.2950.2040.2040.0000.0000.0000.000
156A157VAL0-0.012-0.01410.743-0.499-0.4990.0000.0000.0000.000
157A158LYS10.8440.92313.36515.92415.9240.0000.0000.0000.000
158A159ALA0-0.0110.00615.8920.7510.7510.0000.0000.0000.000
159A160ASN0-0.042-0.01913.483-0.807-0.8070.0000.0000.0000.000
160A161PRO00.0290.01810.8920.7760.7760.0000.0000.0000.000
161A162LYS10.7890.90011.16020.75920.7590.0000.0000.0000.000
162A163ARG10.8370.9175.89830.47230.4720.0000.0000.0000.000
163A164ILE0-0.0020.0056.7663.2253.2250.0000.0000.0000.000
164A165TYR0-0.005-0.0095.700-7.828-7.8280.0000.0000.0000.000
165A166ILE0-0.012-0.0087.0193.4263.4260.0000.0000.0000.000
166A167VAL0-0.0020.0038.713-1.926-1.9260.0000.0000.0000.000
167A168SER00.0040.01711.5031.5781.5780.0000.0000.0000.000
168A169ILE0-0.059-0.03413.494-0.213-0.2130.0000.0000.0000.000
169A170ILE00.0240.00815.692-0.003-0.0030.0000.0000.0000.000
170A171SER00.001-0.00311.766-0.710-0.7100.0000.0000.0000.000
171A172SER00.0170.01413.7930.3780.3780.0000.0000.0000.000
172A173GLU-1-0.864-0.94312.793-20.944-20.9440.0000.0000.0000.000
173A174TYR0-0.076-0.04912.500-1.746-1.7460.0000.0000.0000.000
174A175GLY00.0260.01012.896-0.844-0.8440.0000.0000.0000.000
175A176VAL00.018-0.0057.533-2.141-2.1410.0000.0000.0000.000
176A177ASN0-0.019-0.0058.251-2.857-2.8570.0000.0000.0000.000
177A178LYS10.8310.92510.07516.69116.6910.0000.0000.0000.000
178A179ILE0-0.012-0.0076.2600.3260.3260.0000.0000.0000.000
180A181SER0-0.043-0.0356.246-0.836-0.8360.0000.0000.0000.000
181A182LYS10.9230.9759.07024.02524.0250.0000.0000.0000.000
182A183TYR0-0.004-0.0177.1143.1423.1420.0000.0000.0000.000
188A189PHE00.0280.0035.407-0.794-0.7940.0000.0000.0000.000
189A190THR0-0.003-0.0088.3652.7872.7870.0000.0000.0000.000
190A191VAL0-0.006-0.00211.344-0.151-0.1510.0000.0000.0000.000
191A192ALA0-0.004-0.00414.2090.7940.7940.0000.0000.0000.000
192A193ILE0-0.027-0.0129.653-1.228-1.2280.0000.0000.0000.000
193A194ASP-1-0.722-0.81914.223-15.172-15.1720.0000.0000.0000.000
194A195PRO00.0380.02016.725-0.908-0.9080.0000.0000.0000.000
195A196GLU-1-0.958-0.97718.517-13.338-13.3380.0000.0000.0000.000
196A197LEU0-0.064-0.03518.355-0.343-0.3430.0000.0000.0000.000
197A198ASN00.0980.05022.1220.1390.1390.0000.0000.0000.000
198A199ASN00.019-0.00425.297-0.606-0.6060.0000.0000.0000.000
199A200LYS10.8260.90227.14910.34710.3470.0000.0000.0000.000
200A201GLY00.0410.01522.963-0.216-0.2160.0000.0000.0000.000
201A202TYR0-0.054-0.02721.907-0.783-0.7830.0000.0000.0000.000
202A203ILE0-0.012-0.01317.0560.1690.1690.0000.0000.0000.000
203A204LEU0-0.0230.01521.1030.7160.7160.0000.0000.0000.000
204A205PRO00.032-0.00721.611-0.510-0.5100.0000.0000.0000.000
205A206GLY00.0050.01321.0750.4140.4140.0000.0000.0000.000
206A207LEU0-0.007-0.01921.0080.0580.0580.0000.0000.0000.000
207A208GLY00.0150.01824.2550.5070.5070.0000.0000.0000.000
208A209ASP-1-0.778-0.89124.101-13.121-13.1210.0000.0000.0000.000
209A210ALA00.004-0.01421.6000.2060.2060.0000.0000.0000.000
210A211GLY0-0.023-0.00923.5910.0300.0300.0000.0000.0000.000
211A212ASP-1-0.826-0.92025.942-10.503-10.5030.0000.0000.0000.000
212A213ARG10.7560.86426.06611.81111.8110.0000.0000.0000.000
213A214ALA0-0.0060.00125.4740.1580.1580.0000.0000.0000.000
214A215PHE0-0.091-0.07525.7860.2300.2300.0000.0000.0000.000
215A216GLY-1-0.800-0.85530.525-9.612-9.6120.0000.0000.0000.000