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: 72KLK

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 OptAll
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 -2107022.776622
FMO2-HF: Nuclear repulsion 2030500.555444
FMO2-HF: Total energy -76522.221177
FMO2-MP2: Total energy -76738.831403


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.
-1.6390.161-0.007-1.005-0.7890.004
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 : 0.033 / 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].
3A380ASN00.003-0.0053.898-2.015-0.215-0.007-1.005-0.7890.004
4A381THR00.0540.0246.195-0.029-0.0290.0000.0000.0000.000
5A382ILE0-0.064-0.0088.8230.2070.2070.0000.0000.0000.000
6A383GLN00.0900.04111.7510.0140.0140.0000.0000.0000.000
7A384GLN00.0500.01315.0350.0770.0770.0000.0000.0000.000
8A385LEU00.0360.02917.2930.0280.0280.0000.0000.0000.000
9A386MET00.0330.02115.9950.0400.0400.0000.0000.0000.000
10A387MET00.0010.01014.4580.0500.0500.0000.0000.0000.000
11A388ILE00.0230.01216.3540.0410.0410.0000.0000.0000.000
12A389LEU0-0.005-0.00320.0670.0260.0260.0000.0000.0000.000
13A390ASN0-0.045-0.04016.7230.0500.0500.0000.0000.0000.000
14A391SER0-0.048-0.02419.0260.0240.0240.0000.0000.0000.000
15A392ALA0-0.0150.01020.6410.0120.0120.0000.0000.0000.000
16A393SER0-0.0010.00024.1810.0080.0080.0000.0000.0000.000
17A394ASP-1-0.824-0.89826.937-0.026-0.0260.0000.0000.0000.000
18A395GLN00.0080.01328.823-0.001-0.0010.0000.0000.0000.000
19A396PRO00.0080.00531.365-0.004-0.0040.0000.0000.0000.000
20A397SER00.000-0.03032.1050.0060.0060.0000.0000.0000.000
21A398GLU-1-0.872-0.94833.649-0.023-0.0230.0000.0000.0000.000
22A399ASN0-0.0080.00635.3290.0040.0040.0000.0000.0000.000
23A400LEU0-0.011-0.00834.3030.0010.0010.0000.0000.0000.000
24A401ILE0-0.018-0.02337.1370.0030.0030.0000.0000.0000.000
25A402SER0-0.006-0.01339.5440.0030.0030.0000.0000.0000.000
26A403TYR0-0.016-0.02138.2300.0010.0010.0000.0000.0000.000
27A404PHE0-0.037-0.03537.6430.0010.0010.0000.0000.0000.000
28A405ASN0-0.001-0.02143.0130.0020.0020.0000.0000.0000.000
29A406ASN0-0.0060.00444.8590.0020.0020.0000.0000.0000.000
30A407CYS0-0.117-0.03645.018-0.001-0.0010.0000.0000.0000.000
31A408THR0-0.003-0.01247.8720.0010.0010.0000.0000.0000.000
32A409VAL0-0.0010.01149.6810.0020.0020.0000.0000.0000.000
33A410ASN00.0420.01744.870-0.003-0.0030.0000.0000.0000.000
34A411PRO00.0380.04142.7460.0020.0020.0000.0000.0000.000
35A412LYS10.9670.99039.6910.0190.0190.0000.0000.0000.000
36A413GLU-1-0.934-0.96441.301-0.016-0.0160.0000.0000.0000.000
37A414SER00.006-0.00742.582-0.001-0.0010.0000.0000.0000.000
38A415ILE0-0.014-0.00637.630-0.001-0.0010.0000.0000.0000.000
39A416LEU00.0060.00236.661-0.001-0.0010.0000.0000.0000.000
40A417LYS10.8320.90438.2900.0170.0170.0000.0000.0000.000
41A418ARG10.9190.96638.5570.0360.0360.0000.0000.0000.000
42A419VAL00.0340.02133.396-0.001-0.0010.0000.0000.0000.000
43A420LYS10.9460.98235.2080.0050.0050.0000.0000.0000.000
44A421ASP-1-0.847-0.91337.050-0.016-0.0160.0000.0000.0000.000
45A422ILE00.0210.00134.4940.0020.0020.0000.0000.0000.000
46A423GLY00.0330.01733.198-0.002-0.0020.0000.0000.0000.000
47A424TYR0-0.057-0.03033.5230.0030.0030.0000.0000.0000.000
48A425ILE00.0060.00635.6600.0010.0010.0000.0000.0000.000
49A426PHE00.0370.00627.5680.0000.0000.0000.0000.0000.000
50A427LYS10.9100.94929.7100.0070.0070.0000.0000.0000.000
51A428GLU-1-0.808-0.88032.386-0.014-0.0140.0000.0000.0000.000
52A429LYS10.8050.88434.3530.0220.0220.0000.0000.0000.000
53A430PHE00.0180.00724.702-0.002-0.0020.0000.0000.0000.000
54A431ALA00.0220.00930.4100.0010.0010.0000.0000.0000.000
55A432LYS10.9180.95931.9140.0190.0190.0000.0000.0000.000
56A433ALA0-0.0170.00130.8160.0000.0000.0000.0000.0000.000
57A434VAL0-0.004-0.00125.760-0.006-0.0060.0000.0000.0000.000
58A435GLY0-0.0120.01028.6400.0050.0050.0000.0000.0000.000
59A436GLN00.002-0.01730.045-0.001-0.0010.0000.0000.0000.000
60A437GLY0-0.015-0.00128.221-0.001-0.0010.0000.0000.0000.000
61A438CYS00.0780.05225.3100.0040.0040.0000.0000.0000.000
62A439VAL00.001-0.00226.107-0.011-0.0110.0000.0000.0000.000
63A440GLU-1-0.863-0.92723.6210.0350.0350.0000.0000.0000.000
64A441ILE00.0160.00620.287-0.010-0.0100.0000.0000.0000.000
65A442GLY00.0440.02723.209-0.014-0.0140.0000.0000.0000.000
66A443SER0-0.068-0.05726.260-0.008-0.0080.0000.0000.0000.000
67A444GLN00.0270.01719.5950.0050.0050.0000.0000.0000.000
68A445ARG10.8600.91120.0610.0820.0820.0000.0000.0000.000
69A446TYR0-0.017-0.01624.090-0.010-0.0100.0000.0000.0000.000
70A447LYS10.8460.92524.5950.0050.0050.0000.0000.0000.000
71A448LEU0-0.023-0.00819.329-0.005-0.0050.0000.0000.0000.000
72A449GLY00.0540.02723.863-0.009-0.0090.0000.0000.0000.000
73A450VAL0-0.003-0.00726.866-0.001-0.0010.0000.0000.0000.000
74A451ARG10.7930.87522.1360.0450.0450.0000.0000.0000.000
75A452LEU0-0.0190.00524.969-0.002-0.0020.0000.0000.0000.000
76A453TYR0-0.020-0.03127.3000.0010.0010.0000.0000.0000.000
77A454TYR0-0.001-0.01530.6170.0030.0030.0000.0000.0000.000
78A455ARG10.8330.90224.4810.1450.1450.0000.0000.0000.000
79A456VAL00.0490.01329.0880.0000.0000.0000.0000.0000.000
80A457MET0-0.0190.01131.4400.0050.0050.0000.0000.0000.000
81A458GLU-1-0.753-0.83732.914-0.061-0.0610.0000.0000.0000.000
82A459SER0-0.097-0.04231.3600.0030.0030.0000.0000.0000.000
83A460MET00.0180.00133.4670.0020.0020.0000.0000.0000.000
84A461LEU0-0.036-0.01036.4900.0030.0030.0000.0000.0000.000
85A462LYS10.8800.93133.1170.0770.0770.0000.0000.0000.000
86A463SER0-0.0050.00636.9520.0000.0000.0000.0000.0000.000
87A464GLU-1-0.836-0.89338.754-0.062-0.0620.0000.0000.0000.000
88A465GLU-1-0.847-0.89941.461-0.045-0.0450.0000.0000.0000.000
89A466GLU-1-0.953-0.97540.614-0.062-0.0620.0000.0000.0000.000
90A467ARG10.7690.85642.4260.0640.0640.0000.0000.0000.000
91A468LEU0-0.072-0.04444.3240.0020.0020.0000.0000.0000.000
92A469SER0-0.0140.00646.2780.0030.0030.0000.0000.0000.000
93A470ILE0-0.055-0.01846.6120.0030.0030.0000.0000.0000.000
94A471GLN00.040-0.00244.857-0.001-0.0010.0000.0000.0000.000
95A472ASN00.0330.00645.3450.0000.0000.0000.0000.0000.000
96A473PHE00.0490.01642.7600.0000.0000.0000.0000.0000.000
97A474SER0-0.0050.00145.5780.0000.0000.0000.0000.0000.000
98A475LYS10.9520.98247.8070.0390.0390.0000.0000.0000.000
99A476LEU00.0230.01441.3050.0010.0010.0000.0000.0000.000
100A477LEU00.0250.00840.213-0.001-0.0010.0000.0000.0000.000
101A478ASN0-0.042-0.03143.2640.0030.0030.0000.0000.0000.000
102A479ASP-1-0.831-0.89244.586-0.042-0.0420.0000.0000.0000.000
103A480ASN00.0340.00843.192-0.002-0.0020.0000.0000.0000.000
104A481ILE0-0.032-0.01542.023-0.002-0.0020.0000.0000.0000.000
105A482PHE00.0570.03338.448-0.004-0.0040.0000.0000.0000.000
106A483HIS0-0.0040.00138.302-0.006-0.0060.0000.0000.0000.000
107A484MET0-0.018-0.01037.109-0.003-0.0030.0000.0000.0000.000
108A485SER00.007-0.01936.719-0.003-0.0030.0000.0000.0000.000
109A486LEU00.0100.01133.495-0.006-0.0060.0000.0000.0000.000
110A487LEU0-0.025-0.00831.721-0.007-0.0070.0000.0000.0000.000
111A488ALA00.0130.00431.820-0.004-0.0040.0000.0000.0000.000
112A489CYS0-0.006-0.00430.416-0.007-0.0070.0000.0000.0000.000
113A490ALA0-0.009-0.00728.552-0.011-0.0110.0000.0000.0000.000
114A491LEU0-0.010-0.01427.102-0.007-0.0070.0000.0000.0000.000
115A492GLU-1-0.785-0.87226.803-0.117-0.1170.0000.0000.0000.000
116A493VAL00.0460.01423.399-0.012-0.0120.0000.0000.0000.000
117A494VAL0-0.051-0.00921.904-0.023-0.0230.0000.0000.0000.000
118A495MET0-0.060-0.02821.992-0.007-0.0070.0000.0000.0000.000
119A496ALA00.0330.02223.194-0.001-0.0010.0000.0000.0000.000
120A497THR0-0.032-0.03117.781-0.029-0.0290.0000.0000.0000.000
121A498TYR0-0.030-0.02318.187-0.030-0.0300.0000.0000.0000.000
122A499SER0-0.033-0.00917.8580.0330.0330.0000.0000.0000.000
123A500ARG10.7950.87013.759-0.057-0.0570.0000.0000.0000.000
124A501SER0-0.008-0.00213.742-0.047-0.0470.0000.0000.0000.000
125A502THR0-0.0100.00916.4000.0310.0310.0000.0000.0000.000
126A503SER00.010-0.00617.103-0.020-0.0200.0000.0000.0000.000
127A504GLN00.016-0.00919.0920.0200.0200.0000.0000.0000.000
128A505ASN0-0.035-0.03017.6110.0110.0110.0000.0000.0000.000
129A506LEU0-0.0080.02215.3930.0200.0200.0000.0000.0000.000
130A507ASP-1-0.744-0.85519.3580.0500.0500.0000.0000.0000.000
131A508SER0-0.069-0.04920.705-0.018-0.0180.0000.0000.0000.000
132A509GLY0-0.0080.01621.426-0.019-0.0190.0000.0000.0000.000
133A510THR0-0.017-0.00722.378-0.005-0.0050.0000.0000.0000.000
134A511ASP-1-0.803-0.87224.358-0.125-0.1250.0000.0000.0000.000
135A512LEU0-0.048-0.03225.7110.0120.0120.0000.0000.0000.000
136A513SER0-0.029-0.00726.1440.0020.0020.0000.0000.0000.000
137A514PHE00.0160.00528.0300.0110.0110.0000.0000.0000.000
138A515PRO0-0.006-0.01231.413-0.004-0.0040.0000.0000.0000.000
139A516TRP00.0370.01530.3810.0040.0040.0000.0000.0000.000
140A517ILE00.0320.00029.9560.0080.0080.0000.0000.0000.000
141A518LEU00.0080.01032.8760.0040.0040.0000.0000.0000.000
142A519ASN0-0.032-0.01636.1550.0020.0020.0000.0000.0000.000
143A520VAL0-0.059-0.02433.1130.0050.0050.0000.0000.0000.000
144A521LEU0-0.025-0.01134.2170.0040.0040.0000.0000.0000.000
145A522ASN0-0.067-0.02538.0830.0010.0010.0000.0000.0000.000
146A523LEU0-0.0210.01337.0760.0010.0010.0000.0000.0000.000
147A524LYS10.9130.93940.2760.0420.0420.0000.0000.0000.000
148A525ALA00.0730.02339.270-0.003-0.0030.0000.0000.0000.000
149A526PHE00.0530.01839.547-0.003-0.0030.0000.0000.0000.000
150A527ASP-1-0.829-0.90041.463-0.050-0.0500.0000.0000.0000.000
151A528PHE00.0470.01631.572-0.002-0.0020.0000.0000.0000.000
152A529TYR0-0.042-0.05336.809-0.002-0.0020.0000.0000.0000.000
153A530LYS10.8230.89638.0990.0510.0510.0000.0000.0000.000
154A531VAL0-0.0210.00734.7610.0010.0010.0000.0000.0000.000
155A532ILE00.0040.01632.373-0.005-0.0050.0000.0000.0000.000
156A533GLU-1-0.772-0.85433.580-0.100-0.1000.0000.0000.0000.000
157A534SER00.014-0.01335.132-0.004-0.0040.0000.0000.0000.000
158A535PHE0-0.003-0.00927.868-0.003-0.0030.0000.0000.0000.000
159A536ILE0-0.041-0.03429.568-0.008-0.0080.0000.0000.0000.000
160A537LYS10.7770.87530.3220.1000.1000.0000.0000.0000.000
161A538ALA00.0180.03332.0430.0020.0020.0000.0000.0000.000
162A539GLU-1-0.809-0.88425.421-0.156-0.1560.0000.0000.0000.000
163A540GLY00.0750.02926.836-0.011-0.0110.0000.0000.0000.000
164A541ASN0-0.050-0.02621.3710.0060.0060.0000.0000.0000.000
165A542LEU0-0.011-0.00121.586-0.029-0.0290.0000.0000.0000.000
166A543THR00.0340.01318.0700.0070.0070.0000.0000.0000.000
167A544ARG10.8920.91121.4750.2070.2070.0000.0000.0000.000
168A545GLU-1-0.981-0.97818.348-0.349-0.3490.0000.0000.0000.000
169A546MET00.0410.03721.9530.0330.0330.0000.0000.0000.000
170A547ILE0-0.018-0.00523.6870.0190.0190.0000.0000.0000.000
171A548LYS10.9320.96123.2080.2600.2600.0000.0000.0000.000
172A549HIS0-0.033-0.01725.0520.0060.0060.0000.0000.0000.000
173A550LEU00.0260.01627.0660.0160.0160.0000.0000.0000.000
174A551GLU-1-0.764-0.86829.502-0.153-0.1530.0000.0000.0000.000
175A552ARG10.8140.90130.0110.1180.1180.0000.0000.0000.000
176A553CYS0-0.038-0.02329.9470.0110.0110.0000.0000.0000.000
177A554GLU-1-0.850-0.91232.937-0.092-0.0920.0000.0000.0000.000
178A555HIS0-0.016-0.00334.9650.0020.0020.0000.0000.0000.000
179A556ARG10.9130.94331.1780.1050.1050.0000.0000.0000.000
180A557ILE0-0.045-0.00636.3350.0060.0060.0000.0000.0000.000
181A558MET0-0.0140.01239.0040.0060.0060.0000.0000.0000.000
182A559GLU-1-0.812-0.92437.810-0.084-0.0840.0000.0000.0000.000
183A560SER0-0.115-0.06140.7890.0040.0040.0000.0000.0000.000
184A561LEU0-0.075-0.03142.6050.0040.0040.0000.0000.0000.000
185A562ALA0-0.0180.00044.9740.0020.0020.0000.0000.0000.000