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: LQ4G9

Calculation Name: 1UCD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: uridine-5'-monophosphate | uracil

Ligand 3-letter code: U5P | URA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1UCD

Chain ID: A

ChEMBL ID:

UniProt ID: P23540

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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2129038.66963
FMO2-HF: Nuclear repulsion 2053932.896072
FMO2-HF: Total energy -75105.773558
FMO2-MP2: Total energy -75322.749858


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:PHE)


Summations of interaction energy for fragment #1(A:1:PHE)
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.
43.00362.18532.227-17.449-33.965-0.152
Interaction energy analysis for fragmet #1(A:1:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.757 / 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].
3A3SER0-0.037-0.0223.0579.61712.8390.126-1.416-1.932-0.005
4A4PHE00.0190.0062.636-13.395-9.6072.923-1.944-4.766-0.022
5A5TRP0-0.015-0.0164.9244.6814.722-0.001-0.003-0.0370.000
37A38PRO00.0630.0452.506-1.993-0.5811.851-0.929-2.3350.004
38A39GLN0-0.061-0.0442.7144.7295.7160.233-0.283-0.938-0.002
39A40GLN00.0440.0061.887-55.372-54.80814.335-7.501-7.399-0.091
40A41SER00.007-0.0023.6805.9456.0840.011-0.056-0.0950.000
44A45LEU0-0.025-0.0052.205-0.5520.1611.804-0.732-1.786-0.003
47A48CYS0-0.0520.0114.146-1.501-1.298-0.002-0.033-0.1680.000
90A92SER0-0.018-0.0292.477-16.842-13.3564.463-3.258-4.691-0.003
91A93GLU-1-0.809-0.8683.165-24.326-25.2200.0811.823-1.010-0.003
92A94SER0-0.022-0.0092.488-2.048-0.7260.440-0.628-1.134-0.006
93A95THR0-0.015-0.0102.480-3.238-1.6111.088-0.928-1.788-0.011
94A96PHE0-0.056-0.0212.4032.6123.9861.114-0.651-1.8370.001
169A171GLN00.000-0.0142.158-4.042-2.9412.896-1.689-2.3070.005
170A172ASP-1-0.732-0.8342.627-29.090-29.0790.8660.788-1.666-0.016
171A173GLY0-0.011-0.0014.6611.2151.301-0.001-0.009-0.0760.000
6A6PHE00.0250.0148.552-0.218-0.2180.0000.0000.0000.000
7A7VAL0-0.0090.00010.5581.4481.4480.0000.0000.0000.000
8A8GLN00.0280.00813.5810.9930.9930.0000.0000.0000.000
9A9GLN0-0.010-0.02916.9400.0610.0610.0000.0000.0000.000
10A10TRP00.0190.01220.1690.2670.2670.0000.0000.0000.000
11A11PRO0-0.0160.01323.8170.1330.1330.0000.0000.0000.000
12A12PRO00.0260.00925.7580.1290.1290.0000.0000.0000.000
13A13ALA00.0160.02526.1280.2000.2000.0000.0000.0000.000
14A14VAL0-0.025-0.00622.5790.0480.0480.0000.0000.0000.000
15A15CYS00.0010.00825.593-0.354-0.3540.0000.0000.0000.000
16A16SER0-0.035-0.00328.9460.2930.2930.0000.0000.0000.000
17A17PHE0-0.021-0.02627.0490.2090.2090.0000.0000.0000.000
18A18GLN0-0.049-0.02227.899-0.190-0.1900.0000.0000.0000.000
19A19LYS10.8400.91231.2889.2739.2730.0000.0000.0000.000
20A20SER00.0040.01434.4670.3040.3040.0000.0000.0000.000
21A21GLY00.0400.02634.323-0.248-0.2480.0000.0000.0000.000
22A22SER0-0.007-0.00434.325-0.014-0.0140.0000.0000.0000.000
23A24PRO00.0300.01628.9830.1440.1440.0000.0000.0000.000
24A25GLY00.037-0.00927.6980.0970.0970.0000.0000.0000.000
25A26SER0-0.030-0.03428.4610.0130.0130.0000.0000.0000.000
26A27GLY00.0110.01531.7500.2000.2000.0000.0000.0000.000
27A28LEU0-0.0250.00225.5110.0840.0840.0000.0000.0000.000
28A29ARG10.9180.95727.9988.9048.9040.0000.0000.0000.000
29A30THR00.020-0.01324.785-0.009-0.0090.0000.0000.0000.000
30A31PHE00.0320.00820.605-0.019-0.0190.0000.0000.0000.000
31A32THR00.0020.01620.5630.0230.0230.0000.0000.0000.000
32A33ILE00.0340.01514.552-0.297-0.2970.0000.0000.0000.000
33A34HIS0-0.084-0.02415.8370.8770.8770.0000.0000.0000.000
34A35GLY00.028-0.01113.0490.2600.2600.0000.0000.0000.000
35A36LEU0-0.0060.0296.5750.1980.1980.0000.0000.0000.000
36A37TRP0-0.049-0.0317.472-0.475-0.4750.0000.0000.0000.000
41A42GLY0-0.0040.0097.1253.7013.7010.0000.0000.0000.000
42A43THR0-0.050-0.0227.3673.8503.8500.0000.0000.0000.000
43A44SER00.0190.0086.357-5.706-5.7060.0000.0000.0000.000
45A46THR0-0.058-0.0616.1233.1603.1600.0000.0000.0000.000
46A47ASN0-0.032-0.0219.0150.7350.7350.0000.0000.0000.000
48A49PRO00.0260.0089.3941.2491.2490.0000.0000.0000.000
49A50GLY00.0250.0159.535-2.751-2.7510.0000.0000.0000.000
50A51SER0-0.065-0.06111.1482.2592.2590.0000.0000.0000.000
51A52PRO00.0090.00413.323-0.601-0.6010.0000.0000.0000.000
52A53PHE0-0.021-0.00315.601-0.047-0.0470.0000.0000.0000.000
53A54ASP-1-0.766-0.85416.509-13.209-13.2090.0000.0000.0000.000
54A55ILE00.0200.00718.057-0.430-0.4300.0000.0000.0000.000
55A56THR0-0.001-0.02220.5520.0530.0530.0000.0000.0000.000
56A57LYS10.8870.94014.58416.23916.2390.0000.0000.0000.000
57A58ILE0-0.012-0.01015.243-0.626-0.6260.0000.0000.0000.000
58A59SER00.0010.00517.8960.4050.4050.0000.0000.0000.000
59A60HIS00.0170.00916.2680.7720.7720.0000.0000.0000.000
60A61LEU0-0.012-0.01014.8630.1460.1460.0000.0000.0000.000
61A62GLN00.0120.01719.415-0.064-0.0640.0000.0000.0000.000
62A63SER00.0030.00021.9330.1170.1170.0000.0000.0000.000
63A64GLN00.0480.01919.846-0.070-0.0700.0000.0000.0000.000
64A65LEU00.0190.00816.334-0.099-0.0990.0000.0000.0000.000
65A66ASN0-0.010-0.01120.299-0.273-0.2730.0000.0000.0000.000
66A67THR0-0.0200.01223.3050.4070.4070.0000.0000.0000.000
67A68LEU0-0.033-0.01718.8110.0410.0410.0000.0000.0000.000
68A69TRP0-0.004-0.01112.720-0.587-0.5870.0000.0000.0000.000
69A70PRO00.0430.03819.600-0.100-0.1000.0000.0000.0000.000
70A71ASN0-0.033-0.03822.461-0.353-0.3530.0000.0000.0000.000
71A72VAL00.004-0.00423.1050.5410.5410.0000.0000.0000.000
72A73LEU00.0250.00423.4600.4370.4370.0000.0000.0000.000
73A74ARG10.9430.96624.06311.98811.9880.0000.0000.0000.000
74A75ALA00.0500.03927.091-0.373-0.3730.0000.0000.0000.000
75A76ASN00.0020.00025.590-0.157-0.1570.0000.0000.0000.000
76A77ASN00.0610.02222.855-0.341-0.3410.0000.0000.0000.000
77A78GLN00.0710.04021.650-0.706-0.7060.0000.0000.0000.000
78A79GLN00.0240.01220.968-0.492-0.4920.0000.0000.0000.000
79A80PHE0-0.049-0.01718.434-0.610-0.6100.0000.0000.0000.000
80A81TRP0-0.016-0.02317.125-0.739-0.7390.0000.0000.0000.000
81A82SER00.0470.02116.064-1.330-1.3300.0000.0000.0000.000
82A83HIS0-0.0170.00116.072-0.840-0.8400.0000.0000.0000.000
83A84GLU-1-0.811-0.92013.287-20.868-20.8680.0000.0000.0000.000
84A85TRP00.009-0.0118.661-2.073-2.0730.0000.0000.0000.000
85A86THR00.008-0.01111.156-1.711-1.7110.0000.0000.0000.000
86A87LYS10.9340.97711.83318.07118.0710.0000.0000.0000.000
87A88HIS10.8320.9127.87123.67423.6740.0000.0000.0000.000
88A89GLY00.0510.0326.791-3.482-3.4820.0000.0000.0000.000
89A90THR00.0440.0236.835-3.220-3.2200.0000.0000.0000.000
95A97ASN00.1010.0485.7090.7910.7910.0000.0000.0000.000
96A98GLN00.0340.0099.0420.0880.0880.0000.0000.0000.000
97A99ALA00.0220.01111.5130.2600.2600.0000.0000.0000.000
98A100ALA00.0060.0018.5520.5480.5480.0000.0000.0000.000
99A101TYR0-0.016-0.0146.9380.8530.8530.0000.0000.0000.000
100A102PHE0-0.009-0.0198.7910.2990.2990.0000.0000.0000.000
101A103LYS10.8370.90911.89416.26916.2690.0000.0000.0000.000
102A104LEU00.0200.0195.7110.7050.7050.0000.0000.0000.000
103A105ALA00.0110.00410.0520.6750.6750.0000.0000.0000.000
104A106VAL0-0.028-0.01211.8840.8890.8890.0000.0000.0000.000
105A107ASP-1-0.783-0.87312.712-15.243-15.2430.0000.0000.0000.000
106A108MET0-0.0250.0046.7620.4550.4550.0000.0000.0000.000
107A109ARG10.8190.89413.02513.87913.8790.0000.0000.0000.000
108A110ASN0-0.048-0.02416.3540.9850.9850.0000.0000.0000.000
109A111ASN0-0.022-0.01115.0731.0981.0980.0000.0000.0000.000
110A112TYR0-0.0010.00915.4510.2230.2230.0000.0000.0000.000
111A113ASP-1-0.812-0.91417.566-11.435-11.4350.0000.0000.0000.000
112A114ILE00.0140.00418.4870.3340.3340.0000.0000.0000.000
113A115ILE0-0.022-0.01422.2030.4030.4030.0000.0000.0000.000
114A116GLY0-0.027-0.02324.9410.4310.4310.0000.0000.0000.000
115A117ALA0-0.022-0.00822.8530.2690.2690.0000.0000.0000.000
116A118LEU0-0.020-0.00924.4130.2230.2230.0000.0000.0000.000
117A119ARG10.9340.97227.42510.02210.0220.0000.0000.0000.000
118A120PRO0-0.008-0.00628.9220.3040.3040.0000.0000.0000.000
119A121HIS00.0140.01828.0570.4150.4150.0000.0000.0000.000
120A122ALA00.0000.00732.1260.0670.0670.0000.0000.0000.000
121A123ALA0-0.0050.00329.0790.0470.0470.0000.0000.0000.000
122A124GLY00.0160.00428.800-0.345-0.3450.0000.0000.0000.000
123A125PRO0-0.0280.00028.0830.2230.2230.0000.0000.0000.000
124A126ASN00.005-0.03230.2830.0710.0710.0000.0000.0000.000
125A127GLY00.0180.01332.6930.2570.2570.0000.0000.0000.000
126A128ARG10.9400.97233.6837.9547.9540.0000.0000.0000.000
127A129THR00.008-0.00632.686-0.298-0.2980.0000.0000.0000.000
128A130LYS10.7960.91129.0679.6109.6100.0000.0000.0000.000
129A131SER00.0650.03529.674-0.205-0.2050.0000.0000.0000.000
130A132ARG10.9080.93522.58912.22812.2280.0000.0000.0000.000
131A133GLN0-0.003-0.00524.738-0.584-0.5840.0000.0000.0000.000
132A134ALA00.0260.02026.239-0.122-0.1220.0000.0000.0000.000
133A135ILE00.0150.00423.188-0.151-0.1510.0000.0000.0000.000
134A136LYS10.8330.89819.05514.48814.4880.0000.0000.0000.000
135A137GLY00.0380.02522.361-0.345-0.3450.0000.0000.0000.000
136A138PHE00.011-0.00724.897-0.037-0.0370.0000.0000.0000.000
137A139LEU0-0.006-0.00220.076-0.009-0.0090.0000.0000.0000.000
138A140LYS10.7760.88818.98114.09714.0970.0000.0000.0000.000
139A141ALA0-0.017-0.00821.494-0.090-0.0900.0000.0000.0000.000
140A142LYS10.9050.96622.06411.49011.4900.0000.0000.0000.000
141A143PHE00.005-0.01317.6350.0460.0460.0000.0000.0000.000
142A144GLY00.0640.05218.135-0.637-0.6370.0000.0000.0000.000
143A145LYS10.8410.92314.58717.08417.0840.0000.0000.0000.000
144A146PHE00.006-0.00617.3310.5310.5310.0000.0000.0000.000
145A147PRO00.0270.03315.716-1.008-1.0080.0000.0000.0000.000
146A148GLY00.0200.00815.4540.2770.2770.0000.0000.0000.000
147A149LEU0-0.045-0.02816.3890.1550.1550.0000.0000.0000.000
148A150ARG10.9480.95614.84817.44117.4410.0000.0000.0000.000
149A151CYS0-0.0790.00819.5110.9790.9790.0000.0000.0000.000
150A152ARG10.9420.98622.30411.50911.5090.0000.0000.0000.000
151A153THR00.0270.01024.8040.3100.3100.0000.0000.0000.000
152A154ASP-1-0.795-0.87628.271-9.072-9.0720.0000.0000.0000.000
153A155PRO0-0.002-0.00630.1290.1730.1730.0000.0000.0000.000
154A156GLN00.0030.00632.5300.0710.0710.0000.0000.0000.000
155A157THR00.003-0.02034.9610.1090.1090.0000.0000.0000.000
156A158LYS10.8820.93932.8579.0309.0300.0000.0000.0000.000
157A159VAL00.0240.02932.202-0.171-0.1710.0000.0000.0000.000
158A160SER0-0.0050.00227.218-0.358-0.3580.0000.0000.0000.000
159A161TYR00.0610.01827.5690.2820.2820.0000.0000.0000.000
160A162LEU00.006-0.00721.865-0.470-0.4700.0000.0000.0000.000
161A163VAL0-0.053-0.03121.1220.2160.2160.0000.0000.0000.000
162A164GLN0-0.006-0.01417.275-0.643-0.6430.0000.0000.0000.000
163A165VAL0-0.022-0.00117.4580.3290.3290.0000.0000.0000.000
164A166VAL0-0.032-0.00811.686-0.336-0.3360.0000.0000.0000.000
165A167ALA00.0530.03612.9360.7960.7960.0000.0000.0000.000
166A168CYS0-0.055-0.0149.386-2.496-2.4960.0000.0000.0000.000
167A169PHE00.0550.0236.7842.0352.0350.0000.0000.0000.000
168A170ALA00.0650.0286.038-3.348-3.3480.0000.0000.0000.000
172A174SER0-0.051-0.0425.7002.2352.2350.0000.0000.0000.000
173A175THR0-0.051-0.0538.4982.2882.2880.0000.0000.0000.000
174A176LEU0-0.033-0.0079.337-1.663-1.6630.0000.0000.0000.000
175A177ILE0-0.010-0.0238.1681.0021.0020.0000.0000.0000.000
176A178ASP-1-0.796-0.89012.014-15.809-15.8090.0000.0000.0000.000
177A180THR00.0250.00113.7651.0051.0050.0000.0000.0000.000
178A181ARG10.8990.95713.16319.96019.9600.0000.0000.0000.000
179A182ASP-1-0.761-0.86015.716-14.917-14.9170.0000.0000.0000.000
180A183THR0-0.045-0.03517.688-0.363-0.3630.0000.0000.0000.000
181A185GLY00.0940.04723.270-0.158-0.1580.0000.0000.0000.000
182A186ALA00.015-0.00826.207-0.153-0.1530.0000.0000.0000.000
183A187ASN0-0.015-0.01028.1690.0440.0440.0000.0000.0000.000
184A188PHE00.0130.00924.809-0.243-0.2430.0000.0000.0000.000
185A189ILE00.0130.01829.2920.1700.1700.0000.0000.0000.000
186A190PHE-1-0.778-0.87225.678-10.036-10.0360.0000.0000.0000.000