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: L6LQ9

Calculation Name: 2PB7-A-Xray549

Preferred Name: E3 ubiquitin-protein ligase UHRF1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PB7

Chain ID: A

ChEMBL ID: CHEMBL2424510

UniProt ID: Q96T88

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2357024.632789
FMO2-HF: Nuclear repulsion 2276393.509019
FMO2-HF: Total energy -80631.12377
FMO2-MP2: Total energy -80868.067208


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:409:GLU)


Summations of interaction energy for fragment #1(A:409:GLU)
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.
-93.546-89.1915.805-9.797-10.360.071
Interaction energy analysis for fragmet #1(A:409:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.008
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].
3A411THR00.0270.0022.6729.17611.5160.760-1.213-1.887-0.012
4A412ILE00.0210.0214.8251.8602.005-0.001-0.010-0.1340.000
7A415SER00.018-0.0113.336-5.278-4.1880.032-0.516-0.6060.004
8A416ASN0-0.048-0.0225.124-1.022-1.007-0.001-0.002-0.0110.000
29A437SER0-0.037-0.0234.772-0.1120.071-0.001-0.012-0.1680.000
30A438GLU-1-0.961-0.9992.388-31.770-30.3110.757-0.862-1.354-0.008
31A439SER00.0200.0043.772-0.702-0.7260.000-0.0080.0330.000
35A443ARG10.8310.9201.788-48.410-49.26214.259-7.174-6.2330.087
5A413VAL00.0110.0106.7040.4510.4510.0000.0000.0000.000
6A414PRO00.0330.0235.8912.4762.4760.0000.0000.0000.000
9A417HIS00.0230.0138.349-1.177-1.1770.0000.0000.0000.000
10A418TYR00.003-0.02010.319-0.237-0.2370.0000.0000.0000.000
11A419GLY00.0500.03113.748-0.307-0.3070.0000.0000.0000.000
12A420PRO00.0320.00713.5920.3290.3290.0000.0000.0000.000
13A421ILE0-0.0030.0168.5840.6290.6290.0000.0000.0000.000
14A422PRO00.005-0.00711.010-0.437-0.4370.0000.0000.0000.000
15A423GLY00.0420.02112.612-0.589-0.5890.0000.0000.0000.000
16A424ILE0-0.073-0.02810.922-0.473-0.4730.0000.0000.0000.000
17A425PRO00.0430.04014.3770.4460.4460.0000.0000.0000.000
18A426VAL0-0.042-0.02117.379-0.203-0.2030.0000.0000.0000.000
19A427GLY0-0.031-0.02919.322-0.044-0.0440.0000.0000.0000.000
20A428THR0-0.051-0.02414.086-0.208-0.2080.0000.0000.0000.000
21A429MET0-0.023-0.01716.4950.2520.2520.0000.0000.0000.000
22A430TRP00.0470.02111.1390.0900.0900.0000.0000.0000.000
23A431ARG10.9540.98714.1612.7692.7690.0000.0000.0000.000
24A432PHE0-0.035-0.02012.0960.6360.6360.0000.0000.0000.000
25A433ARG10.8400.89611.075-0.592-0.5920.0000.0000.0000.000
26A434VAL00.0530.0366.5730.4890.4890.0000.0000.0000.000
27A435GLN00.0770.0166.405-1.985-1.9850.0000.0000.0000.000
28A436VAL0-0.0110.0097.688-0.544-0.5440.0000.0000.0000.000
32A440GLY0-0.023-0.0314.8512.2352.2350.0000.0000.0000.000
33A441VAL0-0.0160.0035.6823.1463.1460.0000.0000.0000.000
34A442HIS0-0.0190.0028.3591.6141.6140.0000.0000.0000.000
36A444PRO0-0.0050.0226.107-1.368-1.3680.0000.0000.0000.000
37A445HIS00.0960.0485.414-0.479-0.4790.0000.0000.0000.000
38A446VAL00.0200.0159.935-0.413-0.4130.0000.0000.0000.000
39A447ALA00.0300.01412.894-0.203-0.2030.0000.0000.0000.000
40A448GLY00.0620.03013.6510.0280.0280.0000.0000.0000.000
41A449ILE00.007-0.00414.688-0.151-0.1510.0000.0000.0000.000
42A450HIS0-0.025-0.0136.977-0.940-0.9400.0000.0000.0000.000
43A451GLY00.0440.00711.436-0.535-0.5350.0000.0000.0000.000
44A452ARG10.9060.9667.661-10.627-10.6270.0000.0000.0000.000
45A453SER00.0190.01213.979-0.233-0.2330.0000.0000.0000.000
46A454ASN0-0.006-0.00615.338-0.071-0.0710.0000.0000.0000.000
47A455ASP-1-0.791-0.85913.6525.1245.1240.0000.0000.0000.000
48A456GLY00.0640.04415.390-0.533-0.5330.0000.0000.0000.000
49A457ALA0-0.005-0.00614.1950.6810.6810.0000.0000.0000.000
50A458TYR0-0.044-0.03310.1600.3310.3310.0000.0000.0000.000
51A459SER0-0.016-0.02811.075-0.083-0.0830.0000.0000.0000.000
52A460LEU0-0.029-0.01013.3910.3710.3710.0000.0000.0000.000
53A461VAL0-0.007-0.00513.554-0.391-0.3910.0000.0000.0000.000
54A462LEU00.0150.01116.5020.0600.0600.0000.0000.0000.000
55A463ALA00.000-0.00618.563-0.220-0.2200.0000.0000.0000.000
56A464GLY0-0.0100.00220.624-0.035-0.0350.0000.0000.0000.000
57A465GLY0-0.0120.00024.1950.0550.0550.0000.0000.0000.000
58A466TYR0-0.036-0.03323.174-0.144-0.1440.0000.0000.0000.000
59A467GLU-1-0.823-0.93428.3580.6040.6040.0000.0000.0000.000
60A468ASP-1-0.815-0.87831.9810.3850.3850.0000.0000.0000.000
61A469ASP-1-0.808-0.87726.4470.6650.6650.0000.0000.0000.000
62A470VAL0-0.022-0.01429.295-0.090-0.0900.0000.0000.0000.000
63A471ASP-1-0.749-0.82725.6350.1240.1240.0000.0000.0000.000
64A472HIS00.0300.00828.515-0.100-0.1000.0000.0000.0000.000
65A473GLY00.0240.02126.496-0.028-0.0280.0000.0000.0000.000
66A474ASN0-0.005-0.01025.8580.0320.0320.0000.0000.0000.000
67A475PHE0-0.015-0.01026.9830.0830.0830.0000.0000.0000.000
68A476PHE00.0060.00621.236-0.083-0.0830.0000.0000.0000.000
69A477THR00.0320.03427.0800.0770.0770.0000.0000.0000.000
70A478TYR0-0.030-0.02119.311-0.061-0.0610.0000.0000.0000.000
71A479THR00.0580.01625.1440.0650.0650.0000.0000.0000.000
72A480GLY0-0.0230.00122.9050.0990.0990.0000.0000.0000.000
73A481SER0-0.082-0.05720.239-0.044-0.0440.0000.0000.0000.000
74A482GLY00.012-0.00222.3020.0750.0750.0000.0000.0000.000
75A483GLY00.1100.04123.988-0.104-0.1040.0000.0000.0000.000
76A484ARG00.0470.05023.7870.1490.1490.0000.0000.0000.000
77A485ASP-1-0.790-0.87727.2920.7980.7980.0000.0000.0000.000
78A486LEU00.0130.00426.462-0.053-0.0530.0000.0000.0000.000
79A487SER0-0.041-0.02325.143-0.015-0.0150.0000.0000.0000.000
80A488GLY00.0190.01526.092-0.028-0.0280.0000.0000.0000.000
81A489ASN0-0.037-0.03724.897-0.158-0.1580.0000.0000.0000.000
82A490LYS10.9780.99427.785-0.347-0.3470.0000.0000.0000.000
83A491ARG10.8480.89430.327-0.707-0.7070.0000.0000.0000.000
84A492THR0-0.053-0.02625.303-0.044-0.0440.0000.0000.0000.000
85A493ALA0-0.026-0.01527.511-0.013-0.0130.0000.0000.0000.000
86A494GLU-1-0.870-0.93730.0480.3970.3970.0000.0000.0000.000
87A495GLN0-0.081-0.04429.777-0.008-0.0080.0000.0000.0000.000
88A496SER00.003-0.01030.984-0.041-0.0410.0000.0000.0000.000
89A497CYS0-0.0600.01130.2800.0370.0370.0000.0000.0000.000
90A498ASP-1-0.769-0.87130.7830.8200.8200.0000.0000.0000.000
91A499GLN0-0.056-0.02025.7670.1100.1100.0000.0000.0000.000
92A500LYS0-0.020-0.01625.784-0.013-0.0130.0000.0000.0000.000
93A501LEU00.0330.03724.3230.1360.1360.0000.0000.0000.000
94A502THR0-0.017-0.04422.1080.1160.1160.0000.0000.0000.000
95A503ASN00.000-0.01717.5340.1130.1130.0000.0000.0000.000
96A504THR00.0630.01714.7800.1350.1350.0000.0000.0000.000
97A505ASN00.0470.04917.321-0.016-0.0160.0000.0000.0000.000
98A506ARG10.8920.95320.199-2.110-2.1100.0000.0000.0000.000
99A507ALA0-0.046-0.01115.739-0.048-0.0480.0000.0000.0000.000
100A508LEU00.0300.00717.833-0.027-0.0270.0000.0000.0000.000
101A509ALA00.0310.01719.610-0.165-0.1650.0000.0000.0000.000
102A510LEU0-0.038-0.01019.064-0.136-0.1360.0000.0000.0000.000
103A511ASN0-0.053-0.02617.0430.2350.2350.0000.0000.0000.000
104A512CYS0-0.073-0.01320.985-0.193-0.1930.0000.0000.0000.000
105A513PHE00.0190.01124.7880.0550.0550.0000.0000.0000.000
106A514ALA0-0.014-0.02626.943-0.136-0.1360.0000.0000.0000.000
107A515PRO0-0.005-0.00327.6170.1100.1100.0000.0000.0000.000
108A516ILE0-0.036-0.01323.677-0.028-0.0280.0000.0000.0000.000
109A517ASN00.0430.02027.629-0.016-0.0160.0000.0000.0000.000
110A518ASP-1-0.889-0.96028.1231.3761.3760.0000.0000.0000.000
111A519GLN0-0.053-0.03029.883-0.087-0.0870.0000.0000.0000.000
112A520GLU-1-0.933-0.97433.3150.7660.7660.0000.0000.0000.000
113A521GLY0-0.015-0.00429.874-0.019-0.0190.0000.0000.0000.000
114A522ALA0-0.038-0.01729.441-0.019-0.0190.0000.0000.0000.000
115A523GLU-1-0.828-0.92030.1100.7100.7100.0000.0000.0000.000
116A524ALA0-0.0320.00328.454-0.010-0.0100.0000.0000.0000.000
117A525LYS10.9490.95730.537-0.714-0.7140.0000.0000.0000.000
118A526ASP-1-0.817-0.88630.4010.8610.8610.0000.0000.0000.000
119A527TRP00.047-0.00127.0620.0830.0830.0000.0000.0000.000
120A528ARG10.8650.92326.336-0.540-0.5400.0000.0000.0000.000
121A529SER0-0.005-0.01125.4680.0780.0780.0000.0000.0000.000
122A530GLY0-0.0170.01423.8650.1270.1270.0000.0000.0000.000
123A531LYS10.8380.91117.267-3.240-3.2400.0000.0000.0000.000
124A532PRO0-0.030-0.01516.961-0.089-0.0890.0000.0000.0000.000
125A533VAL00.0020.00416.0580.3870.3870.0000.0000.0000.000
126A534ARG10.7670.8689.820-4.039-4.0390.0000.0000.0000.000
127A535VAL00.0000.00315.1550.1960.1960.0000.0000.0000.000
128A536VAL0-0.002-0.00213.114-0.313-0.3130.0000.0000.0000.000
129A537ARG10.7370.83716.5830.1900.1900.0000.0000.0000.000
130A538ASN00.005-0.03016.811-0.117-0.1170.0000.0000.0000.000
131A539VAL00.0480.03819.2110.1740.1740.0000.0000.0000.000
132A540LYS10.8750.94421.4310.1390.1390.0000.0000.0000.000
133A541GLY0-0.012-0.01922.7000.1220.1220.0000.0000.0000.000
134A542GLY00.014-0.00224.3080.0670.0670.0000.0000.0000.000
135A543LYS10.9120.95827.1150.1860.1860.0000.0000.0000.000
136A544ASN0-0.044-0.02628.3160.0080.0080.0000.0000.0000.000
137A545SER00.002-0.02426.3350.0350.0350.0000.0000.0000.000
138A546LYS10.9440.97728.5640.0300.0300.0000.0000.0000.000
139A547TYR0-0.0040.01526.009-0.051-0.0510.0000.0000.0000.000
140A548ALA00.0040.01523.231-0.048-0.0480.0000.0000.0000.000
141A549PRO0-0.066-0.01519.7180.0080.0080.0000.0000.0000.000
142A550ALA00.0410.00222.9890.0180.0180.0000.0000.0000.000
143A551GLU-1-0.812-0.90420.291-1.957-1.9570.0000.0000.0000.000
144A552GLY0-0.0100.00517.993-0.055-0.0550.0000.0000.0000.000
145A553ASN0-0.070-0.04014.4880.6970.6970.0000.0000.0000.000
146A554ARG10.8360.89416.6060.4400.4400.0000.0000.0000.000
147A555TYR00.0210.02614.5150.4420.4420.0000.0000.0000.000
148A556ASP-1-0.726-0.84116.536-0.543-0.5430.0000.0000.0000.000
149A557GLY00.0360.01918.2400.0260.0260.0000.0000.0000.000
150A558ILE0-0.040-0.02916.3620.2160.2160.0000.0000.0000.000
151A559TYR0-0.036-0.04319.585-0.220-0.2200.0000.0000.0000.000
152A560LYS10.8060.89420.758-0.981-0.9810.0000.0000.0000.000
153A561VAL00.0270.00921.654-0.139-0.1390.0000.0000.0000.000
154A562VAL0-0.020-0.00524.3850.0050.0050.0000.0000.0000.000
155A563LYS10.8770.91627.975-0.693-0.6930.0000.0000.0000.000
156A564TYR00.0050.00725.8940.0500.0500.0000.0000.0000.000
157A565TRP0-0.018-0.01627.9920.0220.0220.0000.0000.0000.000
158A566PRO00.0110.02829.8780.0240.0240.0000.0000.0000.000
159A567GLU-1-0.809-0.89231.7090.5670.5670.0000.0000.0000.000
160A568LYS10.9140.95633.272-0.505-0.5050.0000.0000.0000.000
161A569GLY00.1170.07432.748-0.031-0.0310.0000.0000.0000.000
162A570LYS10.8530.91332.374-0.403-0.4030.0000.0000.0000.000
163A571SER0-0.051-0.01932.668-0.037-0.0370.0000.0000.0000.000
164A572GLY0-0.0210.00135.495-0.010-0.0100.0000.0000.0000.000
165A573PHE0-0.027-0.01633.2440.0120.0120.0000.0000.0000.000
166A574LEU0-0.016-0.00530.366-0.015-0.0150.0000.0000.0000.000
167A575VAL0-0.010-0.00128.7810.0700.0700.0000.0000.0000.000
168A576TRP00.016-0.00425.8650.0310.0310.0000.0000.0000.000
169A577ARG10.7560.85026.959-0.619-0.6190.0000.0000.0000.000
170A578TYR0-0.022-0.03923.0900.0800.0800.0000.0000.0000.000
171A579LEU0-0.0070.00626.355-0.105-0.1050.0000.0000.0000.000
172A580LEU0-0.014-0.00421.2490.0990.0990.0000.0000.0000.000
173A581ARG10.9240.95925.242-0.734-0.7340.0000.0000.0000.000
174A582ARG10.7990.89822.2060.0310.0310.0000.0000.0000.000
175A583ASP-1-0.836-0.90623.6430.7540.7540.0000.0000.0000.000
176A584ASP-1-0.791-0.89120.5920.3110.3110.0000.0000.0000.000
177A585ASP-1-0.880-0.93023.7510.2550.2550.0000.0000.0000.000
178A586GLU-1-0.912-0.95120.001-0.597-0.5970.0000.0000.0000.000
179A587PRO0-0.011-0.01124.4940.0450.0450.0000.0000.0000.000
180A588GLY00.0690.04824.505-0.076-0.0760.0000.0000.0000.000
181A589PRO00.0170.01021.935-0.011-0.0110.0000.0000.0000.000
182A590TRP0-0.0030.00523.732-0.083-0.0830.0000.0000.0000.000
183A591THR0-0.033-0.03528.2730.0040.0040.0000.0000.0000.000
184A592LYS10.8540.90329.9400.4150.4150.0000.0000.0000.000
185A593GLU-1-0.872-0.94730.309-0.279-0.2790.0000.0000.0000.000
186A594GLY00.0250.02426.451-0.058-0.0580.0000.0000.0000.000
187A595LYS10.8920.95026.2400.3740.3740.0000.0000.0000.000
188A596ASP-1-0.844-0.90328.110-0.634-0.6340.0000.0000.0000.000
189A597ARG10.9380.96824.5200.3820.3820.0000.0000.0000.000
190A598ILE00.0400.02122.475-0.086-0.0860.0000.0000.0000.000
191A599LYS10.9450.97624.2530.7120.7120.0000.0000.0000.000
192A600LYS10.9070.94126.7380.5720.5720.0000.0000.0000.000
193A601LEU0-0.0100.00221.7290.0040.0040.0000.0000.0000.000
194A602GLY00.0140.02221.973-0.162-0.1620.0000.0000.0000.000
195A603LEU0-0.049-0.01918.141-0.195-0.1950.0000.0000.0000.000
196A604THR00.002-0.00719.2060.1130.1130.0000.0000.0000.000
197A605MET0-0.052-0.01717.725-0.304-0.3040.0000.0000.0000.000
198A606GLN00.0520.03912.150-0.794-0.7940.0000.0000.0000.000
199A607TYR0-0.009-0.01814.276-0.061-0.0610.0000.0000.0000.000
200A608PRO0-0.049-0.03510.655-0.422-0.4220.0000.0000.0000.000
201A609GLU-1-0.828-0.90510.809-4.577-4.5770.0000.0000.0000.000
202A610GLY00.0310.01312.655-0.234-0.2340.0000.0000.0000.000
203A611TYR0-0.049-0.04814.8010.4840.4840.0000.0000.0000.000
204A612LEU0-0.064-0.02516.5430.3050.3050.0000.0000.0000.000
205A613GLU-1-0.978-0.97718.866-3.141-3.1410.0000.0000.0000.000
206A614ALA0-0.049-0.03519.4600.2450.2450.0000.0000.0000.000
207A615LEU-1-0.959-0.96021.184-2.187-2.1870.0000.0000.0000.000