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: 9L1N2

Calculation Name: 1VQ2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 3,4-dihydro-2'-deoxyuridine-5'-monophosphate | zinc ion

Ligand 3-letter code: DDN | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VQ2

Chain ID: A

ChEMBL ID:

UniProt ID: P16006

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1745306.463491
FMO2-HF: Nuclear repulsion 1677029.598204
FMO2-HF: Total energy -68276.865286
FMO2-MP2: Total energy -68471.281885


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.
-106.069-97.20923.537-14.542-17.854-0.163
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 : 0.779 / q_NPA : 0.892
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].
3A3ALA00.1030.0533.7840.1911.5210.002-0.490-0.8420.001
5A5THR0-0.060-0.0143.1353.4984.1450.054-0.140-0.5610.000
6A6VAL00.0390.0172.3061.7892.3982.632-0.899-2.342-0.003
7A7LEU00.0180.0174.8733.9284.014-0.001-0.015-0.0700.000
9A9ILE00.0070.0053.7531.1121.4420.010-0.055-0.2850.000
29A29GLU-1-0.795-0.9172.059-149.114-148.05916.789-9.698-8.147-0.124
32A32GLY0-0.038-0.0112.1880.7851.2731.204-0.909-0.782-0.003
33A33ARG10.9370.9542.51128.50531.9521.764-2.072-3.138-0.031
34A34ILE0-0.0010.0012.385-0.937-0.3911.084-0.183-1.447-0.003
35A35ILE0-0.026-0.0174.7872.8002.880-0.001-0.009-0.0700.000
106A126TYR0-0.038-0.0283.3312.4222.6640.000-0.072-0.1700.000
4A4SER00.0480.0196.0370.3950.3950.0000.0000.0000.000
8A8GLN00.008-0.0108.0714.7684.7680.0000.0000.0000.000
10A10ALA00.0040.0027.7512.0522.0520.0000.0000.0000.000
11A11TYR0-0.003-0.0599.9101.5481.5480.0000.0000.0000.000
12A12LEU0-0.0160.0149.6581.4551.4550.0000.0000.0000.000
13A13VAL00.0120.0059.6411.1381.1380.0000.0000.0000.000
14A14SER0-0.027-0.03212.4451.4081.4080.0000.0000.0000.000
15A15GLN0-0.042-0.03315.4721.6421.6420.0000.0000.0000.000
16A16GLU-1-0.908-0.93815.588-14.137-14.1370.0000.0000.0000.000
17A17SER0-0.035-0.01018.1090.9910.9910.0000.0000.0000.000
18A18LYS10.9090.94620.16612.77612.7760.0000.0000.0000.000
19A19CYS0-0.074-0.01423.0680.5790.5790.0000.0000.0000.000
20A20CYS0-0.028-0.02524.829-0.064-0.0640.0000.0000.0000.000
21A21SER00.0610.02726.7970.2000.2000.0000.0000.0000.000
22A22TRP00.031-0.02021.577-0.199-0.1990.0000.0000.0000.000
23A23LYS10.8070.91918.89812.63212.6320.0000.0000.0000.000
24A24VAL0-0.013-0.01516.490-0.580-0.5800.0000.0000.0000.000
25A25GLY00.0500.01113.6350.4300.4300.0000.0000.0000.000
26A26ALA0-0.046-0.02011.541-0.786-0.7860.0000.0000.0000.000
27A27VAL0-0.002-0.0055.319-0.045-0.0450.0000.0000.0000.000
28A28ILE00.0200.0168.392-1.186-1.1860.0000.0000.0000.000
30A30LYS10.9850.9936.08527.40627.4060.0000.0000.0000.000
31A31ASN00.0080.0036.613-2.882-2.8820.0000.0000.0000.000
36A36SER00.008-0.0058.4712.7882.7880.0000.0000.0000.000
37A37THR0-0.051-0.0297.966-2.818-2.8180.0000.0000.0000.000
38A38GLY00.0810.04410.6391.3201.3200.0000.0000.0000.000
39A39TYR00.0240.01013.703-0.863-0.8630.0000.0000.0000.000
40A40ASN00.0110.00316.375-0.120-0.1200.0000.0000.0000.000
41A41GLY00.0200.01120.0300.1370.1370.0000.0000.0000.000
42A42SER0-0.004-0.02022.829-0.195-0.1950.0000.0000.0000.000
43A43PRO00.0090.01524.311-0.352-0.3520.0000.0000.0000.000
44A44ALA00.0290.01125.4730.2350.2350.0000.0000.0000.000
45A45GLY0-0.019-0.01026.8710.2080.2080.0000.0000.0000.000
46A46GLY0-0.0220.00329.0650.3320.3320.0000.0000.0000.000
47A47VAL00.0160.01729.367-0.198-0.1980.0000.0000.0000.000
48A48ASN0-0.0060.00725.961-0.557-0.5570.0000.0000.0000.000
49A49CYS0-0.0100.03526.7980.2930.2930.0000.0000.0000.000
50A50CYS0-0.040-0.02427.5770.1410.1410.0000.0000.0000.000
51A51ASP-1-0.816-0.91029.354-9.546-9.5460.0000.0000.0000.000
52A52TYR00.0120.00031.7610.3320.3320.0000.0000.0000.000
53A53ALA00.021-0.00131.8180.2350.2350.0000.0000.0000.000
54A54ALA0-0.029-0.01433.6350.1950.1950.0000.0000.0000.000
55A55GLU-1-0.972-0.98535.543-7.963-7.9630.0000.0000.0000.000
56A56GLN0-0.074-0.03436.8280.3240.3240.0000.0000.0000.000
57A57GLY0-0.0190.00238.2980.1020.1020.0000.0000.0000.000
58A58TRP00.003-0.01332.311-0.172-0.1720.0000.0000.0000.000
59A59LEU0-0.053-0.02031.410-0.210-0.2100.0000.0000.0000.000
60A60LEU00.0530.03934.8650.2800.2800.0000.0000.0000.000
61A61ASN0-0.027-0.03534.403-0.481-0.4810.0000.0000.0000.000
62A62LYS-1-0.781-0.85333.208-9.028-9.0280.0000.0000.0000.000
63A83ARG21.5551.74230.21518.42618.4260.0000.0000.0000.000
64A84PHE00.0910.03330.0490.2060.2060.0000.0000.0000.000
65A85VAL00.0500.04529.620-0.368-0.3680.0000.0000.0000.000
66A86LEU0-0.036-0.01430.2120.3070.3070.0000.0000.0000.000
67A87ALA00.0360.02432.305-0.084-0.0840.0000.0000.0000.000
68A88LYS10.7990.85034.0629.0259.0250.0000.0000.0000.000
69A89GLU-1-0.939-0.96235.958-7.577-7.5770.0000.0000.0000.000
70A90HIS00.0320.01236.365-0.066-0.0660.0000.0000.0000.000
71A91ARG10.8220.89528.03410.47210.4720.0000.0000.0000.000
72A92SER0-0.054-0.02333.099-0.291-0.2910.0000.0000.0000.000
73A93ALA00.0730.03634.884-0.152-0.1520.0000.0000.0000.000
74A94HIS0-0.027-0.02227.433-0.001-0.0010.0000.0000.0000.000
75A95SER0-0.004-0.02230.489-0.348-0.3480.0000.0000.0000.000
76A96GLU-1-0.918-0.93731.502-8.534-8.5340.0000.0000.0000.000
77A97TRP0-0.0050.00628.721-0.115-0.1150.0000.0000.0000.000
78A98SER0-0.029-0.03627.130-0.219-0.2190.0000.0000.0000.000
79A99SER0-0.030-0.04128.388-0.372-0.3720.0000.0000.0000.000
80A100LYS10.8730.94629.6988.5818.5810.0000.0000.0000.000
81A101ASN0-0.063-0.03429.2740.3000.3000.0000.0000.0000.000
82A102GLU-1-0.748-0.85824.467-11.805-11.8050.0000.0000.0000.000
83A103ILE00.0160.02621.091-0.159-0.1590.0000.0000.0000.000
84A104HIS00.010-0.01320.103-0.270-0.2700.0000.0000.0000.000
85A105ALA00.0070.02215.260-0.194-0.1940.0000.0000.0000.000
86A106GLU-1-0.806-0.95014.873-17.745-17.7450.0000.0000.0000.000
87A107LEU00.000-0.00315.955-0.499-0.4990.0000.0000.0000.000
88A108ASN00.0330.00517.0330.3720.3720.0000.0000.0000.000
89A109ALA0-0.0140.01212.384-0.158-0.1580.0000.0000.0000.000
90A110ILE0-0.012-0.00114.363-0.578-0.5780.0000.0000.0000.000
91A111LEU0-0.004-0.00316.6500.3390.3390.0000.0000.0000.000
92A112PHE00.0470.03013.1180.1900.1900.0000.0000.0000.000
93A113ALA0-0.017-0.00914.210-0.010-0.0100.0000.0000.0000.000
94A114ALA0-0.045-0.02215.9100.3210.3210.0000.0000.0000.000
95A115GLU-1-0.982-0.98519.598-13.207-13.2070.0000.0000.0000.000
96A116ASN0-0.032-0.02015.2021.0581.0580.0000.0000.0000.000
97A117GLY00.0160.02118.294-0.112-0.1120.0000.0000.0000.000
98A118SER0-0.079-0.03413.508-0.580-0.5800.0000.0000.0000.000
99A119SER0-0.001-0.01415.096-0.936-0.9360.0000.0000.0000.000
100A120ILE00.0370.00312.245-1.840-1.8400.0000.0000.0000.000
101A121GLU-1-0.836-0.90413.557-19.950-19.9500.0000.0000.0000.000
102A122GLY0-0.026-0.01412.989-0.980-0.9800.0000.0000.0000.000
103A123ALA0-0.077-0.0249.383-2.814-2.8140.0000.0000.0000.000
104A124THR0-0.009-0.0096.2001.2911.2910.0000.0000.0000.000
105A125MET0-0.0140.0068.008-1.989-1.9890.0000.0000.0000.000
107A127VAL00.0200.0029.4160.8820.8820.0000.0000.0000.000
108A128THR00.0200.01712.464-0.192-0.1920.0000.0000.0000.000
109A129LEU00.0220.01914.3830.3630.3630.0000.0000.0000.000
110A130SER0-0.017-0.01217.161-0.282-0.2820.0000.0000.0000.000
111A131PRO00.0300.03116.8840.7400.7400.0000.0000.0000.000
112A132CYS0-0.0100.03019.6310.4540.4540.0000.0000.0000.000
113A133PRO00.0410.00322.783-0.413-0.4130.0000.0000.0000.000
114A134ASP-1-0.814-0.91524.779-11.729-11.7290.0000.0000.0000.000
115A135CYS00.0130.00619.310-0.226-0.2260.0000.0000.0000.000
116A136ALA0-0.014-0.00519.912-0.697-0.6970.0000.0000.0000.000
117A137LYS10.8560.92420.89811.26811.2680.0000.0000.0000.000
118A138ALA00.0070.01421.0060.0220.0220.0000.0000.0000.000
119A139ILE0-0.010-0.01915.552-0.430-0.4300.0000.0000.0000.000
120A140ALA0-0.0140.00918.099-0.575-0.5750.0000.0000.0000.000
121A141GLN00.0040.01120.2860.0820.0820.0000.0000.0000.000
122A142SER0-0.059-0.04616.844-0.348-0.3480.0000.0000.0000.000
123A143GLY00.0470.02317.448-0.336-0.3360.0000.0000.0000.000
124A144ILE0-0.060-0.03011.698-1.287-1.2870.0000.0000.0000.000
125A145LYS10.8850.93212.35420.44320.4430.0000.0000.0000.000
126A146LYS10.8040.9167.49934.95734.9570.0000.0000.0000.000
127A147LEU00.0150.01811.026-1.156-1.1560.0000.0000.0000.000
128A148VAL0-0.042-0.0258.0920.2480.2480.0000.0000.0000.000
129A149TYR00.0170.00611.005-0.480-0.4800.0000.0000.0000.000
130A150CYS0-0.097-0.02613.422-0.127-0.1270.0000.0000.0000.000
131A151GLU-1-0.793-0.89114.944-14.952-14.9520.0000.0000.0000.000
132A152THR0-0.019-0.02318.647-0.525-0.5250.0000.0000.0000.000
133A153TYR00.007-0.00521.3300.6040.6040.0000.0000.0000.000
134A154ASP-1-0.797-0.88223.177-10.675-10.6750.0000.0000.0000.000
135A155LYS10.9180.97626.26410.90010.9000.0000.0000.0000.000
136A156ASN0-0.026-0.02222.2990.5850.5850.0000.0000.0000.000
137A157LYS10.8890.95926.38811.57111.5710.0000.0000.0000.000
138A158PRO00.0490.00426.295-0.543-0.5430.0000.0000.0000.000
139A159GLY00.0980.05025.1500.3680.3680.0000.0000.0000.000
140A160TRP0-0.066-0.03317.5110.0030.0030.0000.0000.0000.000
141A161ASP-1-0.786-0.88919.544-15.489-15.4890.0000.0000.0000.000
142A162ASP-1-0.879-0.93621.283-12.808-12.8080.0000.0000.0000.000
143A163ILE0-0.046-0.03122.216-0.008-0.0080.0000.0000.0000.000
144A164LEU0-0.023-0.00316.950-0.186-0.1860.0000.0000.0000.000
145A165ARG10.8810.92219.60615.47615.4760.0000.0000.0000.000
146A166ASN0-0.021-0.01620.764-0.056-0.0560.0000.0000.0000.000
147A167ALA0-0.0160.01020.4160.4200.4200.0000.0000.0000.000
148A168GLY0-0.025-0.00919.717-0.380-0.3800.0000.0000.0000.000
149A169ILE0-0.069-0.01614.428-1.071-1.0710.0000.0000.0000.000
150A170GLU-1-0.842-0.92511.320-26.234-26.2340.0000.0000.0000.000
151A171VAL00.007-0.00813.805-1.116-1.1160.0000.0000.0000.000
152A172PHE0-0.041-0.01711.6230.4470.4470.0000.0000.0000.000
153A173ASN0-0.032-0.02113.634-0.050-0.0500.0000.0000.0000.000
154A174VAL0-0.023-0.01710.089-1.000-1.0000.0000.0000.0000.000
155A175PRO00.0630.04113.4500.3110.3110.0000.0000.0000.000
156A176LYS10.9140.93015.25215.80415.8040.0000.0000.0000.000
157A177LYS10.9590.98715.89315.47815.4780.0000.0000.0000.000
158A178ASN0-0.082-0.04612.4840.5770.5770.0000.0000.0000.000
159A179LEU0-0.054-0.01810.829-2.127-2.1270.0000.0000.0000.000
160A180ASN0-0.010-0.00212.6360.1310.1310.0000.0000.0000.000
161A181LYS10.9350.9578.83325.09925.0990.0000.0000.0000.000
162A182LEU0-0.0030.02112.0420.0000.0000.0000.0000.0000.000
163A183ASN00.0150.00014.9410.4490.4490.0000.0000.0000.000
164A184TRP00.017-0.02314.5350.0030.0030.0000.0000.0000.000
165A185GLU-1-0.889-0.92719.804-11.824-11.8240.0000.0000.0000.000
166A186ASN0-0.108-0.05720.1320.3210.3210.0000.0000.0000.000
167A187ILE0-0.066-0.01415.878-0.432-0.4320.0000.0000.0000.000
168A188ASN00.0030.00619.2100.6060.6060.0000.0000.0000.000
169A189GLU-1-0.718-0.84918.298-17.125-17.1250.0000.0000.0000.000
170A190PHE0-0.0070.02421.1060.1370.1370.0000.0000.0000.000
171A191CYS0-0.052-0.03124.022-0.053-0.0530.0000.0000.0000.000
172A192GLY00.0430.02726.8100.3370.3370.0000.0000.0000.000
173A193GLU-2-1.703-1.82130.139-18.097-18.0970.0000.0000.0000.000