Manual

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: MVLGZ

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 OptHSide
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 -2108284.127716
FMO2-HF: Nuclear repulsion 2031762.831439
FMO2-HF: Total energy -76521.296278
FMO2-MP2: Total energy -76738.093433


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.
-1.7390.249-0.008-1.017-0.9630.005
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 : 0.040 / q_NPA : 0.015
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].
3A380ASN00.011-0.0083.689-2.124-0.136-0.008-1.017-0.9630.005
4A381THR00.0680.0395.918-0.031-0.0310.0000.0000.0000.000
5A382ILE0-0.0710.0028.3830.2410.2410.0000.0000.0000.000
6A383GLN00.0670.02311.478-0.027-0.0270.0000.0000.0000.000
7A384GLN00.062-0.00214.4730.0870.0870.0000.0000.0000.000
8A385LEU00.0360.03716.9560.0280.0280.0000.0000.0000.000
9A386MET00.0350.02215.9430.0440.0440.0000.0000.0000.000
10A387MET0-0.029-0.00613.9960.0540.0540.0000.0000.0000.000
11A388ILE00.019-0.01116.0650.0420.0420.0000.0000.0000.000
12A389LEU00.0110.00219.6750.0280.0280.0000.0000.0000.000
13A390ASN0-0.051-0.02814.9710.0510.0510.0000.0000.0000.000
14A391SER0-0.068-0.02618.6540.0270.0270.0000.0000.0000.000
15A392ALA0-0.0070.01420.1900.0100.0100.0000.0000.0000.000
16A393SER0-0.002-0.00723.6180.0140.0140.0000.0000.0000.000
17A394ASP-1-0.808-0.89226.638-0.031-0.0310.0000.0000.0000.000
18A395GLN0-0.0140.00528.7410.0000.0000.0000.0000.0000.000
19A396PRO00.0030.00031.148-0.005-0.0050.0000.0000.0000.000
20A397SER00.003-0.03031.6410.0060.0060.0000.0000.0000.000
21A398GLU-1-0.861-0.93533.222-0.028-0.0280.0000.0000.0000.000
22A399ASN0-0.004-0.00434.8240.0050.0050.0000.0000.0000.000
23A400LEU0-0.007-0.00434.0750.0010.0010.0000.0000.0000.000
24A401ILE0-0.036-0.02736.7390.0030.0030.0000.0000.0000.000
25A402SER0-0.011-0.01539.1470.0030.0030.0000.0000.0000.000
26A403TYR0-0.015-0.02737.9200.0000.0000.0000.0000.0000.000
27A404PHE0-0.053-0.03637.4080.0010.0010.0000.0000.0000.000
28A405ASN0-0.005-0.03242.6810.0020.0020.0000.0000.0000.000
29A406ASN00.0000.01344.3170.0030.0030.0000.0000.0000.000
30A407CYS0-0.124-0.03544.736-0.001-0.0010.0000.0000.0000.000
31A408THR0-0.010-0.00747.6460.0010.0010.0000.0000.0000.000
32A409VAL0-0.0040.01149.4130.0020.0020.0000.0000.0000.000
33A410ASN00.0250.00044.808-0.003-0.0030.0000.0000.0000.000
34A411PRO00.0540.04242.6200.0020.0020.0000.0000.0000.000
35A412LYS10.9740.99139.4490.0210.0210.0000.0000.0000.000
36A413GLU-1-0.916-0.95241.214-0.017-0.0170.0000.0000.0000.000
37A414SER00.0250.00342.4690.0000.0000.0000.0000.0000.000
38A415ILE0-0.015-0.00137.731-0.001-0.0010.0000.0000.0000.000
39A416LEU0-0.027-0.02836.509-0.001-0.0010.0000.0000.0000.000
40A417LYS10.8190.90038.2600.0180.0180.0000.0000.0000.000
41A418ARG10.9550.98438.3190.0390.0390.0000.0000.0000.000
42A419VAL00.0500.03933.2180.0000.0000.0000.0000.0000.000
43A420LYS10.9430.98334.9970.0060.0060.0000.0000.0000.000
44A421ASP-1-0.841-0.90936.719-0.016-0.0160.0000.0000.0000.000
45A422ILE00.015-0.00234.2560.0020.0020.0000.0000.0000.000
46A423GLY00.025-0.00232.909-0.001-0.0010.0000.0000.0000.000
47A424TYR0-0.044-0.02933.2870.0030.0030.0000.0000.0000.000
48A425ILE00.0240.02335.8080.0020.0020.0000.0000.0000.000
49A426PHE00.0480.00527.3760.0010.0010.0000.0000.0000.000
50A427LYS10.9230.95729.6740.0070.0070.0000.0000.0000.000
51A428GLU-1-0.847-0.89532.160-0.009-0.0090.0000.0000.0000.000
52A429LYS10.8160.88533.7790.0220.0220.0000.0000.0000.000
53A430PHE00.0170.00724.320-0.001-0.0010.0000.0000.0000.000
54A431ALA00.0320.01630.0690.0010.0010.0000.0000.0000.000
55A432LYS10.9290.98031.6080.0180.0180.0000.0000.0000.000
56A433ALA0-0.047-0.01630.8350.0000.0000.0000.0000.0000.000
57A434VAL0-0.042-0.01725.736-0.002-0.0020.0000.0000.0000.000
58A435GLY0-0.0110.00128.6570.0050.0050.0000.0000.0000.000
59A436GLN0-0.014-0.03429.926-0.002-0.0020.0000.0000.0000.000
60A437GLY0-0.005-0.00128.2150.0000.0000.0000.0000.0000.000
61A438CYS00.0900.08024.9110.0060.0060.0000.0000.0000.000
62A439VAL0-0.026-0.02725.581-0.010-0.0100.0000.0000.0000.000
63A440GLU-1-0.866-0.93623.2310.0430.0430.0000.0000.0000.000
64A441ILE00.0190.00620.363-0.013-0.0130.0000.0000.0000.000
65A442GLY00.0360.01523.144-0.014-0.0140.0000.0000.0000.000
66A443SER0-0.056-0.04126.200-0.010-0.0100.0000.0000.0000.000
67A444GLN00.0330.02220.0320.0060.0060.0000.0000.0000.000
68A445ARG10.8960.94719.8910.0660.0660.0000.0000.0000.000
69A446TYR0-0.017-0.00923.984-0.010-0.0100.0000.0000.0000.000
70A447LYS10.8430.91424.6790.0070.0070.0000.0000.0000.000
71A448LEU0-0.006-0.00519.173-0.004-0.0040.0000.0000.0000.000
72A449GLY00.0290.01723.835-0.010-0.0100.0000.0000.0000.000
73A450VAL0-0.002-0.00926.723-0.002-0.0020.0000.0000.0000.000
74A451ARG10.8100.89821.7870.0540.0540.0000.0000.0000.000
75A452LEU00.0030.01724.654-0.003-0.0030.0000.0000.0000.000
76A453TYR0-0.018-0.02226.8760.0010.0010.0000.0000.0000.000
77A454TYR0-0.006-0.01530.2220.0020.0020.0000.0000.0000.000
78A455ARG10.8270.90224.3630.1560.1560.0000.0000.0000.000
79A456VAL00.029-0.00628.667-0.001-0.0010.0000.0000.0000.000
80A457MET0-0.0110.02131.1330.0050.0050.0000.0000.0000.000
81A458GLU-1-0.775-0.84732.523-0.070-0.0700.0000.0000.0000.000
82A459SER0-0.087-0.03731.1780.0040.0040.0000.0000.0000.000
83A460MET00.0210.01333.3120.0000.0000.0000.0000.0000.000
84A461LEU0-0.033-0.00936.2640.0030.0030.0000.0000.0000.000
85A462LYS10.9000.95032.3960.0840.0840.0000.0000.0000.000
86A463SER00.0160.01136.4850.0000.0000.0000.0000.0000.000
87A464GLU-1-0.837-0.88938.340-0.064-0.0640.0000.0000.0000.000
88A465GLU-1-0.851-0.90641.197-0.048-0.0480.0000.0000.0000.000
89A466GLU-1-0.950-0.96940.115-0.065-0.0650.0000.0000.0000.000
90A467ARG10.7600.84942.2760.0660.0660.0000.0000.0000.000
91A468LEU0-0.090-0.05043.9370.0020.0020.0000.0000.0000.000
92A469SER0-0.0090.00945.9640.0030.0030.0000.0000.0000.000
93A470ILE0-0.045-0.01546.4030.0030.0030.0000.0000.0000.000
94A471GLN00.0370.00044.9330.0000.0000.0000.0000.0000.000
95A472ASN0-0.0020.00045.2840.0000.0000.0000.0000.0000.000
96A473PHE00.0570.01443.1560.0000.0000.0000.0000.0000.000
97A474SER00.0240.01345.1220.0000.0000.0000.0000.0000.000
98A475LYS10.9540.97647.1810.0390.0390.0000.0000.0000.000
99A476LEU00.0320.01640.9870.0010.0010.0000.0000.0000.000
100A477LEU00.0360.01640.253-0.001-0.0010.0000.0000.0000.000
101A478ASN0-0.072-0.04443.1360.0030.0030.0000.0000.0000.000
102A479ASP-1-0.841-0.91244.343-0.043-0.0430.0000.0000.0000.000
103A480ASN00.0210.00042.918-0.003-0.0030.0000.0000.0000.000
104A481ILE00.0130.00941.604-0.002-0.0020.0000.0000.0000.000
105A482PHE00.0760.06138.109-0.004-0.0040.0000.0000.0000.000
106A483HIS00.0210.00438.009-0.007-0.0070.0000.0000.0000.000
107A484MET0-0.043-0.01736.861-0.003-0.0030.0000.0000.0000.000
108A485SER0-0.012-0.03936.482-0.003-0.0030.0000.0000.0000.000
109A486LEU00.0150.01633.155-0.006-0.0060.0000.0000.0000.000
110A487LEU0-0.039-0.02131.403-0.007-0.0070.0000.0000.0000.000
111A488ALA00.0070.00231.567-0.005-0.0050.0000.0000.0000.000
112A489CYS00.0220.01130.083-0.006-0.0060.0000.0000.0000.000
113A490ALA00.0130.01228.227-0.012-0.0120.0000.0000.0000.000
114A491LEU00.002-0.00726.798-0.008-0.0080.0000.0000.0000.000
115A492GLU-1-0.833-0.89526.709-0.113-0.1130.0000.0000.0000.000
116A493VAL00.0500.00123.250-0.011-0.0110.0000.0000.0000.000
117A494VAL0-0.057-0.00421.931-0.022-0.0220.0000.0000.0000.000
118A495MET0-0.066-0.04521.909-0.008-0.0080.0000.0000.0000.000
119A496ALA00.0170.02023.2890.0010.0010.0000.0000.0000.000
120A497THR0-0.041-0.03917.622-0.028-0.0280.0000.0000.0000.000
121A498TYR0-0.046-0.02518.041-0.024-0.0240.0000.0000.0000.000
122A499SER0-0.0100.00817.419-0.002-0.0020.0000.0000.0000.000
123A500ARG10.8740.93513.692-0.092-0.0920.0000.0000.0000.000
124A501SER0-0.027-0.02114.225-0.039-0.0390.0000.0000.0000.000
125A502THR0-0.016-0.00216.5490.0280.0280.0000.0000.0000.000
126A503SER00.0190.00416.966-0.015-0.0150.0000.0000.0000.000
127A504GLN00.001-0.00518.8680.0190.0190.0000.0000.0000.000
128A505ASN0-0.024-0.03817.8740.0240.0240.0000.0000.0000.000
129A506LEU0-0.0220.00915.1260.0130.0130.0000.0000.0000.000
130A507ASP-1-0.800-0.89719.5480.0500.0500.0000.0000.0000.000
131A508SER0-0.054-0.04420.955-0.017-0.0170.0000.0000.0000.000
132A509GLY0-0.0300.02020.985-0.021-0.0210.0000.0000.0000.000
133A510THR00.025-0.00721.907-0.005-0.0050.0000.0000.0000.000
134A511ASP-1-0.815-0.88024.505-0.118-0.1180.0000.0000.0000.000
135A512LEU0-0.051-0.03125.5900.0100.0100.0000.0000.0000.000
136A513SER0-0.016-0.00525.8590.0000.0000.0000.0000.0000.000
137A514PHE00.028-0.01727.7500.0110.0110.0000.0000.0000.000
138A515PRO0-0.046-0.01431.250-0.001-0.0010.0000.0000.0000.000
139A516TRP00.0560.02129.9470.0050.0050.0000.0000.0000.000
140A517ILE00.0410.01129.9150.0080.0080.0000.0000.0000.000
141A518LEU00.0200.02432.8470.0050.0050.0000.0000.0000.000
142A519ASN0-0.026-0.00235.8470.0030.0030.0000.0000.0000.000
143A520VAL0-0.086-0.03332.8590.0050.0050.0000.0000.0000.000
144A521LEU0-0.042-0.02134.1410.0040.0040.0000.0000.0000.000
145A522ASN0-0.062-0.02537.6690.0010.0010.0000.0000.0000.000
146A523LEU0-0.027-0.00436.7900.0010.0010.0000.0000.0000.000
147A524LYS10.9080.94039.8530.0420.0420.0000.0000.0000.000
148A525ALA00.0870.02838.905-0.003-0.0030.0000.0000.0000.000
149A526PHE00.0540.01639.314-0.003-0.0030.0000.0000.0000.000
150A527ASP-1-0.826-0.89341.337-0.051-0.0510.0000.0000.0000.000
151A528PHE00.0300.00531.514-0.002-0.0020.0000.0000.0000.000
152A529TYR0-0.034-0.05336.640-0.003-0.0030.0000.0000.0000.000
153A530LYS10.8240.90637.8000.0520.0520.0000.0000.0000.000
154A531VAL0-0.036-0.00534.3950.0000.0000.0000.0000.0000.000
155A532ILE00.0060.01332.287-0.005-0.0050.0000.0000.0000.000
156A533GLU-1-0.778-0.88233.386-0.103-0.1030.0000.0000.0000.000
157A534SER00.0470.00634.311-0.004-0.0040.0000.0000.0000.000
158A535PHE00.0350.02927.623-0.003-0.0030.0000.0000.0000.000
159A536ILE0-0.055-0.04029.189-0.009-0.0090.0000.0000.0000.000
160A537LYS10.7790.89130.2370.1040.1040.0000.0000.0000.000
161A538ALA0-0.0060.00632.034-0.002-0.0020.0000.0000.0000.000
162A539GLU-1-0.813-0.89225.492-0.168-0.1680.0000.0000.0000.000
163A540GLY00.0850.03426.707-0.011-0.0110.0000.0000.0000.000
164A541ASN0-0.103-0.04621.3630.0040.0040.0000.0000.0000.000
165A542LEU00.0080.00921.597-0.027-0.0270.0000.0000.0000.000
166A543THR00.0500.02617.9680.0040.0040.0000.0000.0000.000
167A544ARG10.9430.94921.2160.2210.2210.0000.0000.0000.000
168A545GLU-1-0.988-0.99618.448-0.329-0.3290.0000.0000.0000.000
169A546MET00.0260.03421.5510.0320.0320.0000.0000.0000.000
170A547ILE0-0.014-0.01223.5020.0200.0200.0000.0000.0000.000
171A548LYS10.9220.96123.3580.2530.2530.0000.0000.0000.000
172A549HIS0-0.030-0.00824.9820.0070.0070.0000.0000.0000.000
173A550LEU00.0200.00226.9930.0160.0160.0000.0000.0000.000
174A551GLU-1-0.758-0.87329.574-0.150-0.1500.0000.0000.0000.000
175A552ARG10.8560.92029.4310.1220.1220.0000.0000.0000.000
176A553CYS0-0.068-0.04529.8670.0110.0110.0000.0000.0000.000
177A554GLU-1-0.845-0.90532.802-0.093-0.0930.0000.0000.0000.000
178A555HIS00.0030.02434.6770.0010.0010.0000.0000.0000.000
179A556ARG10.9400.96331.4840.0990.0990.0000.0000.0000.000
180A557ILE0-0.036-0.01135.7030.0060.0060.0000.0000.0000.000
181A558MET0-0.0260.01138.7870.0060.0060.0000.0000.0000.000
182A559GLU-1-0.840-0.93539.092-0.075-0.0750.0000.0000.0000.000
183A560SER0-0.140-0.06740.5090.0040.0040.0000.0000.0000.000
184A561LEU0-0.093-0.04542.4290.0040.0040.0000.0000.0000.000
185A562ALA0-0.0090.00244.9860.0020.0020.0000.0000.0000.000