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: KVJQ3

Calculation Name: 3RYK-A-Xray547

Preferred Name:

Target Type:

Ligand Name: thymidine-5'-diphosphate | pyrophosphate 2-

Ligand 3-letter code: TYD | POP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RYK

Chain ID: A

ChEMBL ID:

UniProt ID: A0A1S0

Base Structure: X-ray

Registration Date: 2025-10-05

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1880511.245023
FMO2-HF: Nuclear repulsion 1811422.075961
FMO2-HF: Total energy -69089.169061
FMO2-MP2: Total energy -69293.287273


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
21.34123.5413.14-1.952-3.387-0.016
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.914
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].
3A2LYS10.9380.9713.31238.67540.2490.047-0.873-0.748-0.003
18A17ARG10.8670.9222.80944.87945.8130.112-0.333-0.713-0.004
19A18LEU00.0440.0434.9232.0362.164-0.001-0.010-0.1170.000
32A31ASN0-0.035-0.0334.7422.9953.067-0.001-0.004-0.0670.000
35A34VAL0-0.036-0.0102.245-2.838-3.3512.984-0.725-1.746-0.009
36A35LEU00.0250.0204.7550.4580.463-0.001-0.0070.0040.000
4A3VAL00.0420.0236.0472.8602.8600.0000.0000.0000.000
5A4ILE0-0.070-0.0209.551-0.360-0.3600.0000.0000.0000.000
6A5GLU-1-0.788-0.88012.563-15.557-15.5570.0000.0000.0000.000
7A6THR0-0.036-0.03314.126-1.230-1.2300.0000.0000.0000.000
8A7ASN0-0.0020.00316.3510.1610.1610.0000.0000.0000.000
9A8PHE00.0380.00819.940-0.341-0.3410.0000.0000.0000.000
10A9THR00.0020.02120.3510.2280.2280.0000.0000.0000.000
11A10ASP-1-0.842-0.92417.840-15.398-15.3980.0000.0000.0000.000
12A11ALA0-0.0160.00316.776-0.893-0.8930.0000.0000.0000.000
13A12LYS10.8970.95411.92820.73720.7370.0000.0000.0000.000
14A13LEU00.0160.03414.247-0.158-0.1580.0000.0000.0000.000
15A14LEU0-0.009-0.0189.024-1.673-1.6730.0000.0000.0000.000
16A15GLU-1-0.858-0.9408.409-26.397-26.3970.0000.0000.0000.000
17A16PRO00.0010.0135.836-8.209-8.2090.0000.0000.0000.000
20A19PHE0-0.058-0.0315.024-4.341-4.3410.0000.0000.0000.000
21A20GLY00.0230.0129.6251.6111.6110.0000.0000.0000.000
22A21ASP-1-0.830-0.90413.099-18.892-18.8920.0000.0000.0000.000
23A22ASP-1-0.904-0.94616.315-14.651-14.6510.0000.0000.0000.000
24A23ARG10.8330.89918.57516.41416.4140.0000.0000.0000.000
25A24GLY00.0160.01717.8840.4290.4290.0000.0000.0000.000
26A25PHE0-0.037-0.03011.878-0.859-0.8590.0000.0000.0000.000
27A26PHE00.0520.0398.0060.7610.7610.0000.0000.0000.000
28A27THR0-0.047-0.0696.907-2.186-2.1860.0000.0000.0000.000
29A28GLU-1-0.876-0.9094.929-42.774-42.7740.0000.0000.0000.000
30A29SER0-0.009-0.0066.500-3.302-3.3020.0000.0000.0000.000
31A30TYR00.0550.0188.5461.1801.1800.0000.0000.0000.000
33A32LYS10.9440.9796.50216.66916.6690.0000.0000.0000.000
34A33LYS11.0301.0166.29934.37134.3710.0000.0000.0000.000
37A36GLU-1-0.896-0.9437.641-20.116-20.1160.0000.0000.0000.000
38A37THR0-0.088-0.0575.854-0.546-0.5460.0000.0000.0000.000
39A38LEU0-0.064-0.0255.1590.2430.2430.0000.0000.0000.000
40A39GLY00.0210.0088.5241.7761.7760.0000.0000.0000.000
41A40VAL0-0.071-0.03210.4161.5821.5820.0000.0000.0000.000
42A41THR00.0240.00511.682-0.965-0.9650.0000.0000.0000.000
43A42HIS00.0320.01713.3780.4370.4370.0000.0000.0000.000
44A43SER0-0.037-0.02514.146-1.224-1.2240.0000.0000.0000.000
45A44PHE00.002-0.01212.8860.5500.5500.0000.0000.0000.000
46A45VAL0-0.0070.00617.422-0.119-0.1190.0000.0000.0000.000
47A46GLN00.0190.00020.5030.6980.6980.0000.0000.0000.000
48A47ASP-1-0.845-0.90417.489-17.581-17.5810.0000.0000.0000.000
49A48ASN0-0.0130.00920.3571.1521.1520.0000.0000.0000.000
50A49VAL00.004-0.01321.257-0.737-0.7370.0000.0000.0000.000
51A50SER0-0.025-0.00623.4650.7050.7050.0000.0000.0000.000
52A51TYR00.028-0.00325.455-0.277-0.2770.0000.0000.0000.000
53A52SER0-0.017-0.01927.6630.4370.4370.0000.0000.0000.000
54A53ALA00.0360.03229.660-0.216-0.2160.0000.0000.0000.000
55A54GLU-1-0.874-0.92632.227-8.648-8.6480.0000.0000.0000.000
56A55ALA0-0.0150.00731.085-0.295-0.2950.0000.0000.0000.000
57A56GLY00.0530.01031.4890.3330.3330.0000.0000.0000.000
58A57THR0-0.043-0.02230.9020.3390.3390.0000.0000.0000.000
59A58ILE0-0.023-0.01530.583-0.413-0.4130.0000.0000.0000.000
60A59ARG10.8460.92927.94210.52310.5230.0000.0000.0000.000
61A60GLY00.0050.01028.810-0.442-0.4420.0000.0000.0000.000
62A61LEU0-0.011-0.00328.2390.1800.1800.0000.0000.0000.000
63A62HIS00.0300.03027.171-0.080-0.0800.0000.0000.0000.000
64A63PHE00.027-0.01427.662-0.318-0.3180.0000.0000.0000.000
65A64GLN0-0.064-0.02227.6550.4420.4420.0000.0000.0000.000
66A65LYS10.8750.92728.9398.6728.6720.0000.0000.0000.000
67A66ASN00.0390.00628.514-0.213-0.2130.0000.0000.0000.000
68A67PRO0-0.037-0.02431.3320.2820.2820.0000.0000.0000.000
69A68LYS10.9310.98328.6788.9988.9980.0000.0000.0000.000
70A69ALA00.0330.03226.572-0.171-0.1710.0000.0000.0000.000
71A70GLN0-0.051-0.03622.845-0.274-0.2740.0000.0000.0000.000
72A71THR0-0.059-0.03617.2220.1290.1290.0000.0000.0000.000
73A72LYS10.8280.89818.88812.73212.7320.0000.0000.0000.000
74A73LEU0-0.013-0.00111.144-0.612-0.6120.0000.0000.0000.000
75A74ILE0-0.0060.00315.6990.2320.2320.0000.0000.0000.000
76A75GLN00.0380.00413.188-2.558-2.5580.0000.0000.0000.000
77A76VAL0-0.017-0.00316.3741.1401.1400.0000.0000.0000.000
78A77MET0-0.037-0.01315.500-1.131-1.1310.0000.0000.0000.000
79A78GLN0-0.008-0.01818.831-0.114-0.1140.0000.0000.0000.000
80A79GLY00.0560.03821.9510.2670.2670.0000.0000.0000.000
81A80ALA00.002-0.01921.765-0.845-0.8450.0000.0000.0000.000
82A81ILE0-0.022-0.00321.1110.7320.7320.0000.0000.0000.000
83A82TYR00.0330.01722.967-0.724-0.7240.0000.0000.0000.000
84A83ASP-1-0.812-0.91621.417-13.889-13.8890.0000.0000.0000.000
85A84VAL00.0300.01223.550-0.212-0.2120.0000.0000.0000.000
86A85ILE0-0.026-0.01220.6270.0090.0090.0000.0000.0000.000
87A86VAL00.0330.00624.6750.0770.0770.0000.0000.0000.000
88A87ASP-1-0.723-0.80726.003-11.818-11.8180.0000.0000.0000.000
89A88LEU00.004-0.00727.3280.4440.4440.0000.0000.0000.000
90A89ARG10.7570.84022.99712.91412.9140.0000.0000.0000.000
91A90LYS10.9810.98229.9358.1098.1090.0000.0000.0000.000
92A91ASP-1-0.923-0.96031.218-9.258-9.2580.0000.0000.0000.000
93A92SER0-0.072-0.03927.159-0.112-0.1120.0000.0000.0000.000
94A93PRO0-0.004-0.00527.6020.2670.2670.0000.0000.0000.000
95A94THR0-0.053-0.04025.780-0.050-0.0500.0000.0000.0000.000
96A95PHE00.0170.01228.6220.0080.0080.0000.0000.0000.000
97A96LYS10.8880.95630.8838.8258.8250.0000.0000.0000.000
98A97GLN0-0.0180.00728.054-0.330-0.3300.0000.0000.0000.000
99A98TRP00.011-0.00426.861-0.473-0.4730.0000.0000.0000.000
100A99ARG10.7960.87320.38814.94614.9460.0000.0000.0000.000
101A100GLY00.0430.02924.324-0.031-0.0310.0000.0000.0000.000
102A101TYR0-0.021-0.02319.129-0.505-0.5050.0000.0000.0000.000
103A102ILE00.0130.00720.7780.3810.3810.0000.0000.0000.000
104A103LEU0-0.0230.00416.442-1.069-1.0690.0000.0000.0000.000
105A104SER00.010-0.01817.6721.0761.0760.0000.0000.0000.000
106A105ALA00.0430.03017.013-1.142-1.1420.0000.0000.0000.000
107A106ASP-1-0.916-0.95816.514-16.814-16.8140.0000.0000.0000.000
108A107ASN0-0.037-0.03214.921-1.465-1.4650.0000.0000.0000.000
109A108HIS10.8770.94411.55920.13720.1370.0000.0000.0000.000
110A109ARG10.9000.97112.09020.94820.9480.0000.0000.0000.000
111A110GLN0-0.037-0.04610.6960.7680.7680.0000.0000.0000.000
112A111LEU0-0.0180.00413.636-0.619-0.6190.0000.0000.0000.000
113A112LEU0-0.032-0.00513.2450.3660.3660.0000.0000.0000.000
114A113VAL00.020-0.00215.3020.4150.4150.0000.0000.0000.000
115A114PRO00.0200.01019.0100.0260.0260.0000.0000.0000.000
116A115LYS10.9000.94620.40713.41713.4170.0000.0000.0000.000
117A116GLY0-0.005-0.01023.5720.0220.0220.0000.0000.0000.000
118A117PHE0-0.009-0.00523.1210.1100.1100.0000.0000.0000.000
119A118ALA0-0.0110.01225.8770.1370.1370.0000.0000.0000.000
120A119HIS0-0.058-0.05722.267-0.070-0.0700.0000.0000.0000.000
121A120GLY00.0540.02625.3950.4120.4120.0000.0000.0000.000
122A121PHE0-0.033-0.00624.204-0.309-0.3090.0000.0000.0000.000
123A122CYS00.0190.01926.5370.6020.6020.0000.0000.0000.000
124A123THR0-0.037-0.02527.008-0.439-0.4390.0000.0000.0000.000
125A124LEU0-0.008-0.00224.7920.3950.3950.0000.0000.0000.000
126A125VAL0-0.0100.00126.2040.2670.2670.0000.0000.0000.000
127A126PRO00.0190.00528.807-0.155-0.1550.0000.0000.0000.000
128A127HIS0-0.0090.01628.750-0.476-0.4760.0000.0000.0000.000
129A128THR00.0260.01523.902-0.574-0.5740.0000.0000.0000.000
130A129ILE0-0.047-0.02622.2520.3950.3950.0000.0000.0000.000
131A130VAL00.0380.02420.839-0.791-0.7910.0000.0000.0000.000
132A131MET0-0.0060.00117.2050.0530.0530.0000.0000.0000.000
133A132TYR00.003-0.01017.776-0.560-0.5600.0000.0000.0000.000
134A133LYS10.8600.93713.21019.48019.4800.0000.0000.0000.000
135A134VAL00.003-0.00517.885-0.107-0.1070.0000.0000.0000.000
136A135ASP-1-0.799-0.89518.520-14.281-14.2810.0000.0000.0000.000
137A136GLU-1-0.853-0.91720.192-10.831-10.8310.0000.0000.0000.000
138A137TYR00.0120.00624.016-0.144-0.1440.0000.0000.0000.000
139A138TYR0-0.103-0.06526.2140.2430.2430.0000.0000.0000.000
140A139SER0-0.002-0.01028.3660.3310.3310.0000.0000.0000.000
141A140ALA00.016-0.00431.8430.0260.0260.0000.0000.0000.000
142A141ASP-1-0.926-0.95234.543-8.122-8.1220.0000.0000.0000.000
143A142HIS00.0110.00932.205-0.085-0.0850.0000.0000.0000.000
144A143ASP-1-0.815-0.88431.648-10.000-10.0000.0000.0000.0000.000
145A144SER0-0.002-0.01032.0450.4140.4140.0000.0000.0000.000
146A145GLY00.0310.00031.809-0.366-0.3660.0000.0000.0000.000
147A146VAL0-0.0160.00332.6300.1800.1800.0000.0000.0000.000
148A147LEU0-0.0200.00333.639-0.244-0.2440.0000.0000.0000.000
149A148TRP00.0480.01433.463-0.136-0.1360.0000.0000.0000.000
150A149ASN0-0.024-0.00734.489-0.210-0.2100.0000.0000.0000.000
151A150ASP-1-0.738-0.87435.764-8.271-8.2710.0000.0000.0000.000
152A151LYS10.9230.94137.1957.1617.1610.0000.0000.0000.000
153A152GLU-1-0.912-0.94937.344-8.075-8.0750.0000.0000.0000.000
154A153LEU0-0.046-0.02031.830-0.200-0.2000.0000.0000.0000.000
155A154ALA0-0.036-0.01734.044-0.169-0.1690.0000.0000.0000.000
156A155ILE0-0.0010.01330.394-0.134-0.1340.0000.0000.0000.000
157A156PRO0-0.025-0.00331.0440.2110.2110.0000.0000.0000.000
158A157TRP0-0.024-0.03128.218-0.491-0.4910.0000.0000.0000.000
159A158PRO0-0.031-0.01529.4580.2760.2760.0000.0000.0000.000
160A159VAL0-0.009-0.01832.6450.0930.0930.0000.0000.0000.000
161A160THR00.0030.01135.608-0.009-0.0090.0000.0000.0000.000
162A161SER0-0.040-0.03338.9740.2110.2110.0000.0000.0000.000
163A162PRO00.0170.02835.2880.0330.0330.0000.0000.0000.000
164A163ILE00.0140.01435.3260.2510.2510.0000.0000.0000.000
165A164LEU00.0070.00234.267-0.292-0.2920.0000.0000.0000.000
166A165SER0-0.060-0.06435.5830.3140.3140.0000.0000.0000.000
167A166ASP-1-0.834-0.93937.423-7.572-7.5720.0000.0000.0000.000
168A167LYS10.9170.95834.5878.9588.9580.0000.0000.0000.000
169A168ASP-1-0.808-0.88732.895-9.471-9.4710.0000.0000.0000.000
170A169ARG10.8490.92836.1307.9997.9990.0000.0000.0000.000
171A170ILE0-0.0100.00139.3500.1810.1810.0000.0000.0000.000
172A171LEU0-0.0580.00433.6160.0300.0300.0000.0000.0000.000
173A172PRO0-0.016-0.00136.7010.1530.1530.0000.0000.0000.000
174A173LEU0-0.023-0.02237.556-0.181-0.1810.0000.0000.0000.000
175A174LEU-1-0.959-0.96733.515-8.545-8.5450.0000.0000.0000.000