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: 7YK9K

Calculation Name: 1CJB-A-Xray547

Preferred Name: Hypoxanthine-guanine-xanthine phosphoribosyltransferase

Target Type: SINGLE PROTEIN

Ligand Name: (1s)-1(9-deazahypoxanthin-9yl)1,4-dideoxy-1,4-imino-d-ribitol-5-phosphate | pyrophosphate 2-

Ligand 3-letter code: IRP | POP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CJB

Chain ID: A

ChEMBL ID: CHEMBL3988608

UniProt ID: P20035

Base Structure: X-ray

Registration Date: 2025-09-02

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2900142.231441
FMO2-HF: Nuclear repulsion 2809566.15699
FMO2-HF: Total energy -90576.074452
FMO2-MP2: Total energy -90841.161655


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.
-37.517-35.0440.041-1.012-1.5-0.004
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 : 0.852 / q_NPA : 0.904
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].
3A4PRO00.0220.0163.236-4.682-2.7210.044-0.927-1.077-0.004
11A12ASN0-0.057-0.0354.679-1.246-1.027-0.001-0.017-0.2010.000
63A64VAL0-0.049-0.0104.048-3.439-3.212-0.001-0.053-0.1730.000
64A65TYR00.019-0.0024.426-7.387-7.321-0.001-0.015-0.0490.000
4A5ASN00.0200.0085.7615.2425.2420.0000.0000.0000.000
5A6ASN0-0.017-0.0047.7983.9613.9610.0000.0000.0000.000
6A7PRO00.0340.00510.3170.3800.3800.0000.0000.0000.000
7A8GLY00.0170.01013.0851.2241.2240.0000.0000.0000.000
8A9ALA0-0.019-0.00910.9071.0561.0560.0000.0000.0000.000
9A10GLY00.0090.00710.4550.6020.6020.0000.0000.0000.000
10A11GLU-1-0.906-0.9506.605-36.459-36.4590.0000.0000.0000.000
12A13ALA00.0140.0237.108-1.706-1.7060.0000.0000.0000.000
13A14PHE0-0.097-0.0427.7420.8120.8120.0000.0000.0000.000
14A15ASP-1-0.856-0.92111.504-18.563-18.5630.0000.0000.0000.000
15A16PRO0-0.075-0.03115.2510.0460.0460.0000.0000.0000.000
16A17VAL0-0.012-0.01517.7860.4580.4580.0000.0000.0000.000
17A18PHE00.013-0.00620.9840.0330.0330.0000.0000.0000.000
18A19VAL0-0.0070.01623.2750.3600.3600.0000.0000.0000.000
19A20ASN00.011-0.01926.645-0.348-0.3480.0000.0000.0000.000
20A21ASP-1-0.830-0.92529.236-10.520-10.5200.0000.0000.0000.000
21A22ASP-1-0.907-0.95231.854-8.692-8.6920.0000.0000.0000.000
22A23ASP-1-0.839-0.89429.469-10.339-10.3390.0000.0000.0000.000
23A24GLY0-0.030-0.02232.6070.0050.0050.0000.0000.0000.000
24A25TYR0-0.036-0.02731.4100.0060.0060.0000.0000.0000.000
25A26ASP-1-0.829-0.90536.647-7.748-7.7480.0000.0000.0000.000
26A27LEU0-0.049-0.03838.735-0.104-0.1040.0000.0000.0000.000
27A28ASP-1-0.875-0.92840.787-7.108-7.1080.0000.0000.0000.000
28A29SER0-0.026-0.00338.9250.0800.0800.0000.0000.0000.000
29A30PHE0-0.028-0.02334.636-0.204-0.2040.0000.0000.0000.000
30A31MET00.0050.00838.4940.2210.2210.0000.0000.0000.000
31A32ILE00.0310.02437.260-0.259-0.2590.0000.0000.0000.000
32A33PRO00.0070.00239.2490.2320.2320.0000.0000.0000.000
33A34ALA00.0450.01842.4010.0100.0100.0000.0000.0000.000
34A35HIS00.0010.00342.4880.2050.2050.0000.0000.0000.000
35A36TYR0-0.020-0.06338.9470.1320.1320.0000.0000.0000.000
36A37LYS10.8960.95442.4967.0427.0420.0000.0000.0000.000
37A38LYS10.9250.95543.5986.7436.7430.0000.0000.0000.000
38A39TYR0-0.0220.00342.3990.0910.0910.0000.0000.0000.000
39A40LEU00.0210.01837.260-0.203-0.2030.0000.0000.0000.000
40A41THR0-0.016-0.01438.3180.1710.1710.0000.0000.0000.000
41A42LYS10.9120.95934.5699.2419.2410.0000.0000.0000.000
42A43VAL0-0.010-0.01232.912-0.188-0.1880.0000.0000.0000.000
43A44LEU0-0.012-0.00528.8660.0400.0400.0000.0000.0000.000
44A45VAL00.028-0.00525.995-0.191-0.1910.0000.0000.0000.000
45A46PRO00.0330.02129.388-0.003-0.0030.0000.0000.0000.000
46A47ASN0-0.021-0.02428.975-0.643-0.6430.0000.0000.0000.000
47A48GLY00.0190.00327.979-0.386-0.3860.0000.0000.0000.000
48A49VAL00.0370.01725.408-0.419-0.4190.0000.0000.0000.000
49A50ILE00.0040.00524.165-0.684-0.6840.0000.0000.0000.000
50A51LYS10.8660.91723.05710.41110.4110.0000.0000.0000.000
51A52ASN00.0410.01722.944-0.476-0.4760.0000.0000.0000.000
52A53ARG10.7820.90515.74017.45317.4530.0000.0000.0000.000
53A54ILE0-0.001-0.00318.422-1.047-1.0470.0000.0000.0000.000
54A55GLU-1-0.863-0.91218.165-14.756-14.7560.0000.0000.0000.000
55A56LYS10.8360.90713.36420.67120.6710.0000.0000.0000.000
56A57LEU00.0210.00314.033-1.449-1.4490.0000.0000.0000.000
57A58ALA00.0220.01513.326-1.749-1.7490.0000.0000.0000.000
58A59TYR00.0320.01313.553-1.814-1.8140.0000.0000.0000.000
59A60ASP-1-0.791-0.88710.182-26.035-26.0350.0000.0000.0000.000
60A61ILE00.0190.0158.951-3.513-3.5130.0000.0000.0000.000
61A62LYS10.8380.9039.22119.52219.5220.0000.0000.0000.000
62A63LYS10.7860.8907.82727.70827.7080.0000.0000.0000.000
65A66ASN0-0.0160.0007.0083.7993.7990.0000.0000.0000.000
66A67ASN0-0.001-0.0128.6833.3533.3530.0000.0000.0000.000
67A68GLU-1-0.952-0.9617.775-26.660-26.6600.0000.0000.0000.000
68A69GLU-1-0.783-0.85610.048-18.114-18.1140.0000.0000.0000.000
69A70PHE0-0.026-0.02010.938-0.786-0.7860.0000.0000.0000.000
70A71HIS0-0.008-0.02213.0472.0582.0580.0000.0000.0000.000
71A72ILE0-0.009-0.00215.743-0.600-0.6000.0000.0000.0000.000
72A73LEU00.007-0.01017.3631.1181.1180.0000.0000.0000.000
73A74CYS0-0.058-0.00919.530-0.047-0.0470.0000.0000.0000.000
74A75LEU00.0570.03420.8630.5340.5340.0000.0000.0000.000
75A76LEU0-0.0280.01724.0160.3390.3390.0000.0000.0000.000
76A77LYS10.8360.87727.6899.3829.3820.0000.0000.0000.000
77A78GLY00.0550.03327.5090.0330.0330.0000.0000.0000.000
78A79SER00.0230.00322.357-0.040-0.0400.0000.0000.0000.000
79A80ARG10.9800.99824.01010.20510.2050.0000.0000.0000.000
80A81GLY00.0100.01226.115-0.040-0.0400.0000.0000.0000.000
81A82PHE00.004-0.00616.871-0.029-0.0290.0000.0000.0000.000
82A83PHE00.0790.02220.752-0.380-0.3800.0000.0000.0000.000
83A84THR0-0.018-0.02122.103-0.146-0.1460.0000.0000.0000.000
84A85ALA0-0.040-0.01523.3120.0360.0360.0000.0000.0000.000
85A86LEU00.0160.00715.857-0.212-0.2120.0000.0000.0000.000
86A87LEU00.0600.03319.182-0.617-0.6170.0000.0000.0000.000
87A88LYS10.9120.98220.86011.80311.8030.0000.0000.0000.000
88A89HIS0-0.047-0.01919.5990.0920.0920.0000.0000.0000.000
89A90LEU00.0110.00514.081-0.314-0.3140.0000.0000.0000.000
90A91SER0-0.012-0.01717.561-0.291-0.2910.0000.0000.0000.000
91A92ARG10.8350.92120.13213.35813.3580.0000.0000.0000.000
92A93ILE00.007-0.00415.8800.1160.1160.0000.0000.0000.000
93A94HIS00.0040.02314.935-1.239-1.2390.0000.0000.0000.000
94A95ASN00.020-0.01317.228-0.159-0.1590.0000.0000.0000.000
95A96TYR0-0.050-0.03220.7490.6850.6850.0000.0000.0000.000
96A97SER0-0.060-0.03016.765-0.115-0.1150.0000.0000.0000.000
97A98ALA0-0.0410.00718.395-0.433-0.4330.0000.0000.0000.000
98A99VAL00.0260.00119.7330.6660.6660.0000.0000.0000.000
99A100GLU-1-0.943-0.97321.829-11.779-11.7790.0000.0000.0000.000
100A101THR00.0390.02121.411-0.232-0.2320.0000.0000.0000.000
101A102SER0-0.058-0.02118.042-0.624-0.6240.0000.0000.0000.000
102A103LYS10.9530.97116.92216.08416.0840.0000.0000.0000.000
103A104PRO00.0330.01017.720-0.520-0.5200.0000.0000.0000.000
104A105LEU0-0.0080.01511.529-0.447-0.4470.0000.0000.0000.000
105A106PHE00.000-0.01414.053-1.277-1.2770.0000.0000.0000.000
106A107GLY00.0200.02716.3201.1061.1060.0000.0000.0000.000
107A108GLU-1-0.922-0.95718.395-14.013-14.0130.0000.0000.0000.000
108A109HIS10.8370.88819.60514.94714.9470.0000.0000.0000.000
109A110TYR0-0.037-0.02422.623-0.291-0.2910.0000.0000.0000.000
110A111VAL00.0280.00822.8930.3210.3210.0000.0000.0000.000
111A112ARG10.8620.94425.72310.00910.0090.0000.0000.0000.000
112A113VAL00.0450.02124.7020.1590.1590.0000.0000.0000.000
113A114LYS10.8750.95128.1329.4079.4070.0000.0000.0000.000
114A115SER00.1100.04928.657-0.080-0.0800.0000.0000.0000.000
115A116TYR00.0120.02228.7030.0890.0890.0000.0000.0000.000
116A117CYS0-0.044-0.02133.2010.1840.1840.0000.0000.0000.000
117A118ASN00.0360.02136.9660.1510.1510.0000.0000.0000.000
118A119ASP-1-0.830-0.90934.999-8.763-8.7630.0000.0000.0000.000
119A120GLN0-0.0030.00133.658-0.392-0.3920.0000.0000.0000.000
120A121SER0-0.0130.00330.3970.0430.0430.0000.0000.0000.000
121A122THR00.012-0.00932.5080.1010.1010.0000.0000.0000.000
122A123GLY0-0.042-0.01531.7910.1610.1610.0000.0000.0000.000
123A124THR0-0.029-0.02031.745-0.270-0.2700.0000.0000.0000.000
124A125LEU0-0.036-0.04725.863-0.359-0.3590.0000.0000.0000.000
125A126GLU-1-0.929-0.94130.435-9.189-9.1890.0000.0000.0000.000
126A127ILE0-0.006-0.02025.388-0.362-0.3620.0000.0000.0000.000
127A128VAL0-0.0050.00129.1340.3120.3120.0000.0000.0000.000
128A129SER0-0.051-0.04426.149-0.319-0.3190.0000.0000.0000.000
129A130GLU-1-0.808-0.87524.820-12.135-12.1350.0000.0000.0000.000
130A131ASP-1-0.808-0.86526.310-11.736-11.7360.0000.0000.0000.000
131A132LEU00.0290.00621.583-0.352-0.3520.0000.0000.0000.000
132A133SER0-0.044-0.04421.340-0.730-0.7300.0000.0000.0000.000
133A134CYS0-0.060-0.03221.896-0.504-0.5040.0000.0000.0000.000
134A135LEU0-0.011-0.01417.368-0.474-0.4740.0000.0000.0000.000
135A136LYS10.8740.94516.74612.77912.7790.0000.0000.0000.000
136A137GLY0-0.020-0.01415.1670.1780.1780.0000.0000.0000.000
137A138LYS10.7900.88314.14115.94915.9490.0000.0000.0000.000
138A139HIS00.0340.0097.557-0.622-0.6220.0000.0000.0000.000
139A140VAL0-0.001-0.01211.3871.5541.5540.0000.0000.0000.000
140A141LEU0-0.025-0.01011.475-1.906-1.9060.0000.0000.0000.000
141A142ILE0-0.0070.00013.6341.7821.7820.0000.0000.0000.000
142A143VAL0-0.023-0.01015.936-0.837-0.8370.0000.0000.0000.000
143A144GLU-1-0.833-0.94118.484-12.996-12.9960.0000.0000.0000.000
144A145ASP-1-0.827-0.93020.511-12.891-12.8910.0000.0000.0000.000
145A146ILE0-0.030-0.03622.544-0.274-0.2740.0000.0000.0000.000
146A147ILE0-0.0150.00517.8240.1640.1640.0000.0000.0000.000
147A148ASP-1-0.786-0.89622.314-10.981-10.9810.0000.0000.0000.000
148A149THR00.029-0.00324.897-0.366-0.3660.0000.0000.0000.000
149A150GLY00.0310.02822.536-0.152-0.1520.0000.0000.0000.000
150A151LYS10.9260.95422.64710.10810.1080.0000.0000.0000.000
151A152THR00.0200.00824.0400.1780.1780.0000.0000.0000.000
152A153LEU00.0710.03617.984-0.050-0.0500.0000.0000.0000.000
153A154VAL00.0170.02819.761-0.421-0.4210.0000.0000.0000.000
154A155LYS10.8940.95220.81411.01411.0140.0000.0000.0000.000
155A156PHE00.0300.01219.5620.1420.1420.0000.0000.0000.000
156A157CYS00.000-0.00316.864-0.526-0.5260.0000.0000.0000.000
157A158GLU-1-0.819-0.89718.577-14.934-14.9340.0000.0000.0000.000
158A159TYR0-0.065-0.03920.9430.4710.4710.0000.0000.0000.000
159A160LEU00.0430.00816.7860.1460.1460.0000.0000.0000.000
160A161LYS10.8210.90916.82715.68615.6860.0000.0000.0000.000
161A162LYS10.9030.96318.43612.73412.7340.0000.0000.0000.000
162A163PHE0-0.0080.00019.8200.5670.5670.0000.0000.0000.000
163A164GLU-1-0.917-0.95217.482-14.005-14.0050.0000.0000.0000.000
164A165ILE00.0050.01213.263-0.145-0.1450.0000.0000.0000.000
165A166LYS10.9250.9839.29124.49824.4980.0000.0000.0000.000
166A167THR0-0.037-0.0287.030-2.008-2.0080.0000.0000.0000.000
167A168VAL0-0.002-0.0039.6001.8471.8470.0000.0000.0000.000
168A169ALA00.0200.0288.767-1.637-1.6370.0000.0000.0000.000
169A170ILE0-0.047-0.02910.7362.6792.6790.0000.0000.0000.000
170A171ALA00.0260.01212.620-1.357-1.3570.0000.0000.0000.000
171A172CYS0-0.050-0.02414.6501.3661.3660.0000.0000.0000.000
172A173LEU0-0.0190.01317.868-0.356-0.3560.0000.0000.0000.000
173A174PHE00.009-0.01720.3700.1300.1300.0000.0000.0000.000
174A175ILE00.0230.01619.226-0.413-0.4130.0000.0000.0000.000
175A176LYS10.8240.92021.61211.03011.0300.0000.0000.0000.000
176A177ARG10.7610.86224.64711.65411.6540.0000.0000.0000.000
177A178THR0-0.032-0.02326.3190.4630.4630.0000.0000.0000.000
178A179PRO0-0.014-0.01027.257-0.398-0.3980.0000.0000.0000.000
179A180LEU0-0.017-0.01429.1600.0530.0530.0000.0000.0000.000
180A181TRP0-0.055-0.01118.658-0.131-0.1310.0000.0000.0000.000
181A182ASN0-0.035-0.02522.077-0.417-0.4170.0000.0000.0000.000
182A183GLY00.0420.02620.699-0.211-0.2110.0000.0000.0000.000
183A184PHE0-0.0240.00716.303-1.059-1.0590.0000.0000.0000.000
184A185LYS10.8960.93914.20719.32519.3250.0000.0000.0000.000
185A186ALA0-0.017-0.01314.116-0.339-0.3390.0000.0000.0000.000
186A187ASP-1-0.797-0.9098.500-31.235-31.2350.0000.0000.0000.000
187A188PHE0-0.010-0.0157.727-1.447-1.4470.0000.0000.0000.000
188A189VAL00.0540.02412.1381.4901.4900.0000.0000.0000.000
189A190GLY00.0230.01815.666-0.053-0.0530.0000.0000.0000.000
190A191PHE0-0.016-0.01318.616-0.045-0.0450.0000.0000.0000.000
191A192SER00.0140.02421.0040.0280.0280.0000.0000.0000.000
192A193ILE0-0.006-0.00922.4200.3930.3930.0000.0000.0000.000
193A194PRO00.0560.03026.074-0.181-0.1810.0000.0000.0000.000
194A195ASP-1-0.846-0.92229.176-10.318-10.3180.0000.0000.0000.000
195A196HIS00.0400.02230.9380.4950.4950.0000.0000.0000.000
196A197PHE0-0.058-0.03531.428-0.310-0.3100.0000.0000.0000.000
197A198VAL00.0250.01328.2280.2360.2360.0000.0000.0000.000
198A199VAL0-0.017-0.01331.696-0.032-0.0320.0000.0000.0000.000
199A200GLY00.0600.03332.4040.0140.0140.0000.0000.0000.000
200A201TYR0-0.029-0.02924.790-0.331-0.3310.0000.0000.0000.000
201A202SER0-0.070-0.03628.034-0.376-0.3760.0000.0000.0000.000
202A203LEU00.0230.03326.3440.0570.0570.0000.0000.0000.000
203A204ASP-1-0.840-0.90930.220-9.460-9.4600.0000.0000.0000.000
204A205TYR00.0240.00733.599-0.181-0.1810.0000.0000.0000.000
205A206ASN0-0.032-0.03136.4270.0100.0100.0000.0000.0000.000
206A207GLU-1-0.811-0.91835.420-9.115-9.1150.0000.0000.0000.000
207A208ILE0-0.0210.00737.1620.0070.0070.0000.0000.0000.000
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