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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 94RJ2

Calculation Name: 1AD6-A-Xray372

Preferred Name: Retinoblastoma-associated protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1AD6

Chain ID: A

ChEMBL ID: CHEMBL5288

UniProt ID: P06400

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2108913.083705
FMO2-HF: Nuclear repulsion 2032393.855657
FMO2-HF: Total energy -76519.228048
FMO2-MP2: Total energy -76736.201138


3D Structure
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:378:VAL)


Summations of interaction energy for fragment #1(A:378:VAL)
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.
-0.9480.2840.063-0.335-0.9590.005
Interaction energy analysis for fragmet #1(A:378:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.013
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].
3A380ASN00.004-0.0103.268-1.1430.0890.063-0.335-0.9590.005
4A381THR00.0650.0346.043-0.071-0.0710.0000.0000.0000.000
5A382ILE0-0.0670.0158.3580.1910.1910.0000.0000.0000.000
6A383GLN00.0740.01511.500-0.066-0.0660.0000.0000.0000.000
7A384GLN00.051-0.00314.4240.1020.1020.0000.0000.0000.000
8A385LEU00.0460.04816.7730.0270.0270.0000.0000.0000.000
9A386MET00.0380.02316.0210.0430.0430.0000.0000.0000.000
10A387MET0-0.027-0.00714.0420.0530.0530.0000.0000.0000.000
11A388ILE00.007-0.00916.0720.0380.0380.0000.0000.0000.000
12A389LEU0-0.006-0.01419.6780.0250.0250.0000.0000.0000.000
13A390ASN0-0.043-0.02114.8880.0450.0450.0000.0000.0000.000
14A391SER0-0.060-0.02618.3470.0200.0200.0000.0000.0000.000
15A392ALA0-0.0210.01020.1880.0030.0030.0000.0000.0000.000
16A393SER00.005-0.00823.6200.0160.0160.0000.0000.0000.000
17A394ASP-1-0.844-0.93226.7620.0090.0090.0000.0000.0000.000
18A395GLN0-0.036-0.01028.7480.0010.0010.0000.0000.0000.000
19A396PRO00.0000.00231.152-0.004-0.0040.0000.0000.0000.000
20A397SER00.009-0.00931.6870.0050.0050.0000.0000.0000.000
21A398GLU-1-0.870-0.93533.221-0.018-0.0180.0000.0000.0000.000
22A399ASN00.0030.02734.5870.0040.0040.0000.0000.0000.000
23A400LEU0-0.0180.00333.8390.0000.0000.0000.0000.0000.000
24A401ILE0-0.032-0.03036.7420.0020.0020.0000.0000.0000.000
25A402SER0-0.038-0.05939.1480.0020.0020.0000.0000.0000.000
26A403TYR0-0.032-0.04537.8880.0000.0000.0000.0000.0000.000
27A404PHE0-0.068-0.04237.4990.0010.0010.0000.0000.0000.000
28A405ASN0-0.010-0.04042.6860.0030.0030.0000.0000.0000.000
29A406ASN00.0410.03744.7240.0030.0030.0000.0000.0000.000
30A407CYS0-0.138-0.03144.666-0.001-0.0010.0000.0000.0000.000
31A408THR0-0.008-0.00947.6520.0010.0010.0000.0000.0000.000
32A409VAL0-0.0130.00349.1300.0020.0020.0000.0000.0000.000
33A410ASN00.0220.00144.888-0.002-0.0020.0000.0000.0000.000
34A411PRO00.0950.05742.6870.0020.0020.0000.0000.0000.000
35A412LYS10.9680.99839.3410.0070.0070.0000.0000.0000.000
36A413GLU-1-0.916-0.95341.224-0.002-0.0020.0000.0000.0000.000
37A414SER0-0.002-0.01542.4810.0010.0010.0000.0000.0000.000
38A415ILE0-0.021-0.01337.7680.0000.0000.0000.0000.0000.000
39A416LEU0-0.027-0.02836.4770.0010.0010.0000.0000.0000.000
40A417LYS10.8700.93738.2740.0020.0020.0000.0000.0000.000
41A418ARG10.9671.00238.5240.0200.0200.0000.0000.0000.000
42A419VAL00.0480.04033.3390.0010.0010.0000.0000.0000.000
43A420LYS10.9440.99335.017-0.016-0.0160.0000.0000.0000.000
44A421ASP-1-0.855-0.92636.7380.0070.0070.0000.0000.0000.000
45A422ILE00.013-0.00634.3270.0020.0020.0000.0000.0000.000
46A423GLY00.029-0.01632.9460.0010.0010.0000.0000.0000.000
47A424TYR0-0.038-0.02633.3130.0050.0050.0000.0000.0000.000
48A425ILE00.0520.04735.8360.0030.0030.0000.0000.0000.000
49A426PHE00.003-0.01427.4460.0020.0020.0000.0000.0000.000
50A427LYS10.9230.95930.100-0.028-0.0280.0000.0000.0000.000
51A428GLU-1-0.928-0.94232.1890.0250.0250.0000.0000.0000.000
52A429LYS10.9080.93934.064-0.004-0.0040.0000.0000.0000.000
53A430PHE00.0320.00624.6240.0010.0010.0000.0000.0000.000
54A431ALA00.0260.02130.2810.0030.0030.0000.0000.0000.000
55A432LYS10.9310.97631.803-0.012-0.0120.0000.0000.0000.000
56A433ALA0-0.064-0.02330.968-0.001-0.0010.0000.0000.0000.000
57A434VAL0-0.020-0.01426.1170.0000.0000.0000.0000.0000.000
58A435GLY0-0.042-0.00628.8920.0070.0070.0000.0000.0000.000
59A436GLN00.001-0.02930.259-0.003-0.0030.0000.0000.0000.000
60A437GLY0-0.030-0.02028.3970.0040.0040.0000.0000.0000.000
61A438CYS00.1330.11525.0510.0100.0100.0000.0000.0000.000
62A439VAL0-0.019-0.03125.612-0.008-0.0080.0000.0000.0000.000
63A440GLU-1-0.873-0.93023.2400.1130.1130.0000.0000.0000.000
64A441ILE00.0220.01720.781-0.012-0.0120.0000.0000.0000.000
65A442GLY00.0020.00323.173-0.015-0.0150.0000.0000.0000.000
66A443SER0-0.058-0.05426.059-0.015-0.0150.0000.0000.0000.000
67A444GLN00.0220.01420.274-0.004-0.0040.0000.0000.0000.000
68A445ARG10.9080.95519.860-0.037-0.0370.0000.0000.0000.000
69A446TYR0-0.026-0.01724.011-0.013-0.0130.0000.0000.0000.000
70A447LYS10.8820.95324.647-0.045-0.0450.0000.0000.0000.000
71A448LEU0-0.0060.00019.416-0.006-0.0060.0000.0000.0000.000
72A449GLY00.0270.00223.854-0.013-0.0130.0000.0000.0000.000
73A450VAL00.006-0.00626.746-0.006-0.0060.0000.0000.0000.000
74A451ARG10.8380.92121.6930.0010.0010.0000.0000.0000.000
75A452LEU0-0.0010.01524.548-0.006-0.0060.0000.0000.0000.000
76A453TYR0-0.018-0.03326.892-0.003-0.0030.0000.0000.0000.000
77A454TYR00.001-0.01130.158-0.001-0.0010.0000.0000.0000.000
78A455ARG10.8500.92024.5370.1210.1210.0000.0000.0000.000
79A456VAL00.022-0.01428.729-0.003-0.0030.0000.0000.0000.000
80A457MET0-0.0180.01631.1460.0020.0020.0000.0000.0000.000
81A458GLU-1-0.795-0.89332.402-0.054-0.0540.0000.0000.0000.000
82A459SER0-0.119-0.05831.0850.0020.0020.0000.0000.0000.000
83A460MET00.0220.01833.240-0.001-0.0010.0000.0000.0000.000
84A461LEU0-0.0060.00036.2750.0020.0020.0000.0000.0000.000
85A462LYS10.9570.99131.6840.0740.0740.0000.0000.0000.000
86A463SER0-0.043-0.01135.8950.0000.0000.0000.0000.0000.000
87A464GLU-1-0.810-0.89737.873-0.053-0.0530.0000.0000.0000.000
88A465GLU-1-0.901-0.93040.896-0.042-0.0420.0000.0000.0000.000
89A466GLU-1-0.928-0.95339.596-0.059-0.0590.0000.0000.0000.000
90A467ARG10.7650.86941.8400.0540.0540.0000.0000.0000.000
91A468LEU0-0.098-0.05343.4120.0020.0020.0000.0000.0000.000
92A469SER00.0140.01345.4110.0030.0030.0000.0000.0000.000
93A470ILE0-0.060-0.02146.0100.0030.0030.0000.0000.0000.000
94A471GLN00.0730.02144.7800.0000.0000.0000.0000.0000.000
95A472ASN0-0.0110.00845.2880.0010.0010.0000.0000.0000.000
96A473PHE00.0640.01743.2380.0000.0000.0000.0000.0000.000
97A474SER00.0590.01945.1330.0010.0010.0000.0000.0000.000
98A475LYS10.9570.98447.1940.0290.0290.0000.0000.0000.000
99A476LEU00.0430.02240.9800.0010.0010.0000.0000.0000.000
100A477LEU00.0420.00940.0710.0000.0000.0000.0000.0000.000
101A478ASN0-0.082-0.03943.1500.0040.0040.0000.0000.0000.000
102A479ASP-1-0.893-0.93544.074-0.027-0.0270.0000.0000.0000.000
103A480ASN0-0.004-0.03142.938-0.001-0.0010.0000.0000.0000.000
104A481ILE00.0580.03441.6270.0000.0000.0000.0000.0000.000
105A482PHE00.0720.05737.769-0.003-0.0030.0000.0000.0000.000
106A483HIS00.0260.00438.030-0.004-0.0040.0000.0000.0000.000
107A484MET0-0.036-0.00636.884-0.001-0.0010.0000.0000.0000.000
108A485SER0-0.026-0.03336.555-0.001-0.0010.0000.0000.0000.000
109A486LEU00.0140.01033.359-0.004-0.0040.0000.0000.0000.000
110A487LEU0-0.042-0.01931.535-0.004-0.0040.0000.0000.0000.000
111A488ALA00.0010.00231.593-0.002-0.0020.0000.0000.0000.000
112A489CYS00.0330.01530.157-0.003-0.0030.0000.0000.0000.000
113A490ALA00.0120.01328.277-0.009-0.0090.0000.0000.0000.000
114A491LEU00.002-0.00126.862-0.003-0.0030.0000.0000.0000.000
115A492GLU-1-0.811-0.87726.800-0.064-0.0640.0000.0000.0000.000
116A493VAL00.046-0.00123.330-0.007-0.0070.0000.0000.0000.000
117A494VAL0-0.038-0.01121.912-0.014-0.0140.0000.0000.0000.000
118A495MET0-0.070-0.05022.0050.0030.0030.0000.0000.0000.000
119A496ALA00.0110.01023.3490.0040.0040.0000.0000.0000.000
120A497THR0-0.020-0.00317.631-0.024-0.0240.0000.0000.0000.000
121A498TYR0-0.0120.01718.118-0.008-0.0080.0000.0000.0000.000
122A499SER0-0.001-0.00917.5460.0080.0080.0000.0000.0000.000
123A500ARG10.8900.95412.918-0.317-0.3170.0000.0000.0000.000
124A501SER0-0.034-0.03314.401-0.002-0.0020.0000.0000.0000.000
125A502THR00.0010.00816.6950.0340.0340.0000.0000.0000.000
126A503SER00.002-0.00416.986-0.004-0.0040.0000.0000.0000.000
127A504GLN0-0.002-0.02119.0380.0160.0160.0000.0000.0000.000
128A505ASN0-0.041-0.04417.4170.0380.0380.0000.0000.0000.000
129A506LEU0-0.0100.01315.2700.0120.0120.0000.0000.0000.000
130A507ASP-1-0.814-0.89719.7920.1370.1370.0000.0000.0000.000
131A508SER0-0.044-0.04521.184-0.012-0.0120.0000.0000.0000.000
132A509GLY0-0.0570.00821.174-0.014-0.0140.0000.0000.0000.000
133A510THR00.042-0.00822.100-0.007-0.0070.0000.0000.0000.000
134A511ASP-1-0.856-0.89724.662-0.053-0.0530.0000.0000.0000.000
135A512LEU0-0.033-0.02925.7180.0050.0050.0000.0000.0000.000
136A513SER0-0.033-0.02225.904-0.004-0.0040.0000.0000.0000.000
137A514PHE00.011-0.02027.8330.0080.0080.0000.0000.0000.000
138A515PRO0-0.067-0.02731.3120.0000.0000.0000.0000.0000.000
139A516TRP00.0540.03829.4950.0040.0040.0000.0000.0000.000
140A517ILE00.0430.01330.6460.0060.0060.0000.0000.0000.000
141A518LEU00.0080.01732.9520.0030.0030.0000.0000.0000.000
142A519ASN0-0.0090.00035.9760.0010.0010.0000.0000.0000.000
143A520VAL0-0.085-0.03133.1700.0040.0040.0000.0000.0000.000
144A521LEU0-0.031-0.02133.8750.0030.0030.0000.0000.0000.000
145A522ASN0-0.061-0.01937.791-0.001-0.0010.0000.0000.0000.000
146A523LEU0-0.009-0.00437.2680.0000.0000.0000.0000.0000.000
147A524LYS10.9180.96239.9270.0250.0250.0000.0000.0000.000
148A525ALA00.0940.03238.940-0.002-0.0020.0000.0000.0000.000
149A526PHE00.0510.01239.335-0.003-0.0030.0000.0000.0000.000
150A527ASP-1-0.865-0.93041.358-0.034-0.0340.0000.0000.0000.000
151A528PHE00.0290.00031.656-0.002-0.0020.0000.0000.0000.000
152A529TYR00.024-0.00336.649-0.003-0.0030.0000.0000.0000.000
153A530LYS10.8600.93137.7790.0350.0350.0000.0000.0000.000
154A531VAL0-0.050-0.00834.406-0.001-0.0010.0000.0000.0000.000
155A532ILE00.0250.01532.109-0.005-0.0050.0000.0000.0000.000
156A533GLU-1-0.863-0.93333.342-0.083-0.0830.0000.0000.0000.000
157A534SER00.0560.00734.239-0.006-0.0060.0000.0000.0000.000
158A535PHE00.0300.02627.642-0.003-0.0030.0000.0000.0000.000
159A536ILE0-0.054-0.04328.994-0.008-0.0080.0000.0000.0000.000
160A537LYS10.8200.92830.1540.0940.0940.0000.0000.0000.000
161A538ALA0-0.0030.00631.702-0.003-0.0030.0000.0000.0000.000
162A539GLU-1-0.802-0.88225.199-0.140-0.1400.0000.0000.0000.000
163A540GLY00.0770.03326.288-0.010-0.0100.0000.0000.0000.000
164A541ASN0-0.100-0.05220.6820.0050.0050.0000.0000.0000.000
165A542LEU00.0100.00621.525-0.020-0.0200.0000.0000.0000.000
166A543THR00.0260.01917.932-0.002-0.0020.0000.0000.0000.000
167A544ARG11.0170.99721.1190.2120.2120.0000.0000.0000.000
168A545GLU-1-0.965-0.98718.569-0.241-0.2410.0000.0000.0000.000
169A546MET00.0120.02821.7110.0280.0280.0000.0000.0000.000
170A547ILE00.005-0.00623.4540.0170.0170.0000.0000.0000.000
171A548LYS10.8970.94123.8410.2060.2060.0000.0000.0000.000
172A549HIS0-0.015-0.00524.9480.0050.0050.0000.0000.0000.000
173A550LEU00.016-0.00826.9580.0140.0140.0000.0000.0000.000
174A551GLU-1-0.865-0.92229.545-0.120-0.1200.0000.0000.0000.000
175A552ARG10.8610.92829.3450.0920.0920.0000.0000.0000.000
176A553CYS0-0.067-0.04029.9220.0100.0100.0000.0000.0000.000
177A554GLU-1-0.872-0.94132.793-0.076-0.0760.0000.0000.0000.000
178A555HIS0-0.0180.00934.6890.0040.0040.0000.0000.0000.000
179A556ARG10.9530.96732.0030.0650.0650.0000.0000.0000.000
180A557ILE0-0.012-0.00835.6570.0050.0050.0000.0000.0000.000
181A558MET0-0.046-0.00138.7860.0050.0050.0000.0000.0000.000
182A559GLU-1-0.849-0.95739.185-0.055-0.0550.0000.0000.0000.000
183A560SER0-0.146-0.05140.4300.0040.0040.0000.0000.0000.000
184A561LEU0-0.107-0.04442.4350.0030.0030.0000.0000.0000.000
185A562ALA0-0.0010.00644.9650.0010.0010.0000.0000.0000.000