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: G57Q1

Calculation Name: 3TOJ-A-Xray372

Preferred Name: MLL1/ASH2L/RBBP5/WDR5 complex

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 3TOJ

Chain ID: A

ChEMBL ID: CHEMBL3137282

UniProt ID: Q9UBL3

Base Structure: X-ray

Registration Date: 2023-09-23

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2311309.918712
FMO2-HF: Nuclear repulsion 2232265.586147
FMO2-HF: Total energy -79044.332565
FMO2-MP2: Total energy -79275.214252


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:275:SER)


Summations of interaction energy for fragment #1(A:275:SER)
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.
-14.115-8.2465.066-5.329-5.6060.03
Interaction energy analysis for fragmet #1(A:275:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.029
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].
3A277ASP-1-0.868-0.9342.105-12.015-6.6195.042-5.193-5.2450.029
4A278LEU0-0.020-0.0253.845-1.960-1.4870.024-0.136-0.3610.001
5A279TYR0-0.044-0.0164.832-0.013-0.0130.0000.0000.0000.000
6A280ARG10.8530.9505.838-0.448-0.4480.0000.0000.0000.000
7A281ALA00.0070.0139.462-0.116-0.1160.0000.0000.0000.000
8A282CYS0-0.011-0.00912.7240.0300.0300.0000.0000.0000.000
9A283LEU0-0.0160.00514.849-0.009-0.0090.0000.0000.0000.000
10A284TYR0-0.041-0.03018.266-0.012-0.0120.0000.0000.0000.000
11A285GLU-1-0.900-0.92220.548-0.042-0.0420.0000.0000.0000.000
12A286ARG10.9480.96124.1940.0540.0540.0000.0000.0000.000
13A287VAL0-0.0040.01425.5690.0040.0040.0000.0000.0000.000
14A288LEU0-0.032-0.02528.223-0.001-0.0010.0000.0000.0000.000
15A289LEU00.0150.00431.9860.0000.0000.0000.0000.0000.000
16A290ALA0-0.0100.01034.6230.0010.0010.0000.0000.0000.000
17A291LEU00.0180.01134.8030.0010.0010.0000.0000.0000.000
18A292HIS00.0370.00136.7070.0010.0010.0000.0000.0000.000
19A293ASP-1-0.812-0.85737.088-0.034-0.0340.0000.0000.0000.000
20A294ARG10.9110.92739.0720.0260.0260.0000.0000.0000.000
21A295ALA0-0.0060.00941.7700.0020.0020.0000.0000.0000.000
22A296PRO0-0.031-0.01645.367-0.001-0.0010.0000.0000.0000.000
23A297GLN00.0410.00746.8340.0000.0000.0000.0000.0000.000
24A298LEU0-0.058-0.01043.8600.0000.0000.0000.0000.0000.000
25A299LYS10.8360.90445.7640.0280.0280.0000.0000.0000.000
26A300ILE0-0.042-0.03039.276-0.001-0.0010.0000.0000.0000.000
27A301SER00.005-0.01338.9740.0020.0020.0000.0000.0000.000
28A302ASP-1-0.857-0.94639.580-0.033-0.0330.0000.0000.0000.000
29A303ASP-1-0.880-0.91835.191-0.050-0.0500.0000.0000.0000.000
30A304ARG10.8340.91234.6790.0350.0350.0000.0000.0000.000
31A305LEU00.0020.00232.166-0.002-0.0020.0000.0000.0000.000
32A306THR00.0220.01536.331-0.001-0.0010.0000.0000.0000.000
33A307VAL0-0.039-0.01840.0110.0020.0020.0000.0000.0000.000
34A308VAL00.0250.01642.7640.0000.0000.0000.0000.0000.000
35A309GLY00.0220.01146.5260.0010.0010.0000.0000.0000.000
36A310GLU-1-0.813-0.89748.726-0.023-0.0230.0000.0000.0000.000
37A311LYS10.8870.93451.7900.0220.0220.0000.0000.0000.000
38A312GLY00.0360.02253.332-0.001-0.0010.0000.0000.0000.000
39A313TYR0-0.026-0.02848.3070.0000.0000.0000.0000.0000.000
40A314SER0-0.0070.01447.6420.0010.0010.0000.0000.0000.000
41A315MET0-0.058-0.02741.456-0.002-0.0020.0000.0000.0000.000
42A316VAL00.0200.01338.5470.0020.0020.0000.0000.0000.000
43A317ARG10.8080.87435.9540.0340.0340.0000.0000.0000.000
44A318ALA0-0.002-0.00432.0820.0010.0010.0000.0000.0000.000
45A319SER0-0.010-0.02829.4170.0020.0020.0000.0000.0000.000
46A320HIS00.0160.01925.8510.0000.0000.0000.0000.0000.000
47A321GLY0-0.008-0.00928.8100.0000.0000.0000.0000.0000.000
48A322VAL0-0.024-0.01626.000-0.003-0.0030.0000.0000.0000.000
49A323ARG10.8870.91926.9590.0580.0580.0000.0000.0000.000
50A324LYS10.8690.92921.7470.1140.1140.0000.0000.0000.000
51A325GLY00.0220.02324.433-0.008-0.0080.0000.0000.0000.000
52A326ALA00.0010.00024.9180.0090.0090.0000.0000.0000.000
53A327TRP0-0.020-0.02521.828-0.012-0.0120.0000.0000.0000.000
54A328TYR00.0300.00327.2670.0090.0090.0000.0000.0000.000
55A329PHE0-0.018-0.00928.518-0.004-0.0040.0000.0000.0000.000
56A330GLU-1-0.751-0.87231.099-0.078-0.0780.0000.0000.0000.000
57A331ILE0-0.007-0.00834.0360.0010.0010.0000.0000.0000.000
58A332THR0-0.0070.01137.3460.0000.0000.0000.0000.0000.000
59A333VAL0-0.020-0.00739.6950.0020.0020.0000.0000.0000.000
60A334ASP-1-0.784-0.86341.661-0.047-0.0470.0000.0000.0000.000
61A335GLU-1-0.951-0.98444.384-0.031-0.0310.0000.0000.0000.000
62A336MET0-0.063-0.03647.0240.0000.0000.0000.0000.0000.000
63A337PRO00.0700.05050.0960.0000.0000.0000.0000.0000.000
64A338PRO00.0340.01753.8360.0000.0000.0000.0000.0000.000
65A339ASP-1-0.849-0.91356.583-0.023-0.0230.0000.0000.0000.000
66A340THR00.006-0.00151.6910.0000.0000.0000.0000.0000.000
67A341ALA0-0.049-0.03850.2560.0000.0000.0000.0000.0000.000
68A342ALA00.0550.03344.9700.0000.0000.0000.0000.0000.000
69A343ARG10.7960.90645.4650.0320.0320.0000.0000.0000.000
70A344LEU00.0480.04240.2470.0000.0000.0000.0000.0000.000
71A345GLY00.0520.00338.5060.0000.0000.0000.0000.0000.000
72A346TRP00.0430.03630.519-0.001-0.0010.0000.0000.0000.000
73A347SER0-0.014-0.03836.6660.0040.0040.0000.0000.0000.000
74A348GLN00.0070.01936.2290.0010.0010.0000.0000.0000.000
75A349PRO00.0430.01535.0520.0020.0020.0000.0000.0000.000
76A350LEU0-0.017-0.00537.7990.0020.0020.0000.0000.0000.000
77A351GLY0-0.0260.01140.6400.0010.0010.0000.0000.0000.000
78A352ASN00.0290.01342.4630.0000.0000.0000.0000.0000.000
79A353LEU00.0390.01641.259-0.001-0.0010.0000.0000.0000.000
80A354GLN0-0.030-0.00945.2120.0000.0000.0000.0000.0000.000
81A355ALA00.0180.01247.7600.0010.0010.0000.0000.0000.000
82A356PRO0-0.057-0.02247.338-0.001-0.0010.0000.0000.0000.000
83A357LEU00.0760.03640.5160.0010.0010.0000.0000.0000.000
84A358GLY00.0090.01944.3150.0000.0000.0000.0000.0000.000
85A359TYR0-0.043-0.01345.5180.0010.0010.0000.0000.0000.000
86A360ASP-1-0.739-0.86644.720-0.030-0.0300.0000.0000.0000.000
87A361LYS10.8870.94340.8460.0320.0320.0000.0000.0000.000
88A362PHE0-0.012-0.01241.103-0.001-0.0010.0000.0000.0000.000
89A363SER00.0260.02840.144-0.002-0.0020.0000.0000.0000.000
90A364TYR00.0020.02139.2570.0010.0010.0000.0000.0000.000
91A365SER0-0.056-0.05440.806-0.002-0.0020.0000.0000.0000.000
92A366TRP00.0640.03040.1320.0010.0010.0000.0000.0000.000
93A367ARG10.8290.91144.0320.0300.0300.0000.0000.0000.000
94A368SER00.0640.04447.1450.0000.0000.0000.0000.0000.000
95A369LYS11.0000.98647.9700.0270.0270.0000.0000.0000.000
96A370LYS10.9110.92851.1170.0270.0270.0000.0000.0000.000
97A371GLY00.0990.08747.4410.0000.0000.0000.0000.0000.000
98A372THR0-0.068-0.01847.6580.0000.0000.0000.0000.0000.000
99A373LYS10.8900.96744.7060.0380.0380.0000.0000.0000.000
100A374PHE0-0.018-0.02445.8570.0020.0020.0000.0000.0000.000
101A375HIS00.0140.00542.995-0.001-0.0010.0000.0000.0000.000
102A376GLN0-0.030-0.00345.8110.0020.0020.0000.0000.0000.000
103A377SER0-0.025-0.03448.4650.0010.0010.0000.0000.0000.000
104A378ILE0-0.043-0.01250.1000.0010.0010.0000.0000.0000.000
105A379GLY0-0.020-0.01049.854-0.001-0.0010.0000.0000.0000.000
106A380LYS10.9310.95448.8450.0310.0310.0000.0000.0000.000
107A381HIS00.0330.00449.6250.0000.0000.0000.0000.0000.000
108A382TYR0-0.033-0.05440.7990.0000.0000.0000.0000.0000.000
109A383SER00.0690.05145.227-0.001-0.0010.0000.0000.0000.000
110A384SER0-0.017-0.00247.3900.0010.0010.0000.0000.0000.000
111A385GLY0-0.008-0.01347.722-0.001-0.0010.0000.0000.0000.000
112A386TYR0-0.030-0.01944.346-0.001-0.0010.0000.0000.0000.000
113A387GLY00.010-0.01546.6830.0020.0020.0000.0000.0000.000
114A388GLN00.0490.02946.116-0.001-0.0010.0000.0000.0000.000
115A389GLY00.0030.00544.5290.0010.0010.0000.0000.0000.000
116A390ASP-1-0.806-0.89442.952-0.047-0.0470.0000.0000.0000.000
117A391VAL0-0.024-0.02036.4380.0000.0000.0000.0000.0000.000
118A392LEU0-0.061-0.03138.743-0.001-0.0010.0000.0000.0000.000
119A393GLY00.0470.01534.917-0.003-0.0030.0000.0000.0000.000
120A394PHE0-0.032-0.02833.8840.0050.0050.0000.0000.0000.000
121A395TYR00.0580.02828.624-0.002-0.0020.0000.0000.0000.000
122A396ILE0-0.037-0.00830.3110.0060.0060.0000.0000.0000.000
123A397ASN00.0410.01028.765-0.012-0.0120.0000.0000.0000.000
124A398LEU0-0.015-0.00328.9620.0070.0070.0000.0000.0000.000
125A399PRO00.0090.00527.696-0.005-0.0050.0000.0000.0000.000
126A400GLU-1-0.806-0.89123.461-0.105-0.1050.0000.0000.0000.000
127A401ASP-1-0.885-0.94627.883-0.056-0.0560.0000.0000.0000.000
128A402THR0-0.029-0.02124.3740.0000.0000.0000.0000.0000.000
129A403ILE0-0.020-0.01020.6700.0000.0000.0000.0000.0000.000
130A404SER00.002-0.00524.096-0.005-0.0050.0000.0000.0000.000
131A405GLY00.0050.01827.4160.0050.0050.0000.0000.0000.000
132A406ARG10.9130.92929.9090.0690.0690.0000.0000.0000.000
133A443GLY00.0000.00531.299-0.005-0.0050.0000.0000.0000.000
134A444SER0-0.058-0.03132.3790.0020.0020.0000.0000.0000.000
135A445SER00.0530.02433.304-0.002-0.0020.0000.0000.0000.000
136A446GLU-1-0.914-0.96433.824-0.055-0.0550.0000.0000.0000.000
137A447ILE0-0.034-0.01134.314-0.003-0.0030.0000.0000.0000.000
138A448ILE0-0.025-0.00834.0690.0040.0040.0000.0000.0000.000
139A449PHE00.0070.00436.011-0.002-0.0020.0000.0000.0000.000
140A450TYR0-0.021-0.03233.6210.0010.0010.0000.0000.0000.000
141A451LYS10.8370.92637.9970.0440.0440.0000.0000.0000.000
142A452ASN0-0.025-0.02138.970-0.001-0.0010.0000.0000.0000.000
143A453GLY00.0520.01635.8330.0000.0000.0000.0000.0000.000
144A454VAL0-0.055-0.01436.733-0.002-0.0020.0000.0000.0000.000
145A455ASN00.0140.00335.7740.0050.0050.0000.0000.0000.000
146A456GLN0-0.072-0.04838.4030.0050.0050.0000.0000.0000.000
147A457GLY00.0370.03339.7980.0030.0030.0000.0000.0000.000
148A458VAL00.0200.02137.537-0.001-0.0010.0000.0000.0000.000
149A459ALA0-0.072-0.02039.8600.0030.0030.0000.0000.0000.000
150A460TYR0-0.005-0.02140.0130.0040.0040.0000.0000.0000.000
151A461LYS10.8950.93238.4770.0430.0430.0000.0000.0000.000
152A462ASP-1-0.832-0.86437.811-0.043-0.0430.0000.0000.0000.000
153A463ILE0-0.0130.00835.0130.0030.0030.0000.0000.0000.000
154A464PHE00.007-0.01137.7400.0000.0000.0000.0000.0000.000
155A465GLU-1-0.738-0.84732.478-0.055-0.0550.0000.0000.0000.000
156A466GLY0-0.039-0.02833.5020.0040.0040.0000.0000.0000.000
157A467VAL0-0.047-0.01729.844-0.004-0.0040.0000.0000.0000.000
158A468TYR0-0.032-0.05731.6430.0050.0050.0000.0000.0000.000
159A469PHE00.0180.00431.628-0.005-0.0050.0000.0000.0000.000
160A470PRO00.0180.02331.4630.0030.0030.0000.0000.0000.000
161A471ALA0-0.006-0.00934.4460.0030.0030.0000.0000.0000.000
162A472ILE00.0270.01837.974-0.001-0.0010.0000.0000.0000.000
163A473SER0-0.029-0.00941.0240.0030.0030.0000.0000.0000.000
164A474LEU00.0320.00544.138-0.001-0.0010.0000.0000.0000.000
165A475TYR0-0.066-0.03047.3700.0020.0020.0000.0000.0000.000
166A476LYS10.8270.87851.1640.0230.0230.0000.0000.0000.000
167A477SER0-0.031-0.00750.837-0.001-0.0010.0000.0000.0000.000
168A478CYS0-0.0490.00948.2290.0000.0000.0000.0000.0000.000
169A479THR00.0340.00144.1190.0010.0010.0000.0000.0000.000
170A480VAL0-0.063-0.02940.900-0.001-0.0010.0000.0000.0000.000
171A481SER00.0710.01137.8740.0010.0010.0000.0000.0000.000
172A482ILE0-0.077-0.03233.600-0.001-0.0010.0000.0000.0000.000
173A483ASN00.003-0.00230.293-0.003-0.0030.0000.0000.0000.000
174A484PHE00.030-0.00728.304-0.001-0.0010.0000.0000.0000.000
175A485GLY00.0270.04026.400-0.006-0.0060.0000.0000.0000.000
176A486PRO00.004-0.01922.4470.0060.0060.0000.0000.0000.000
177A487CYS0-0.034-0.02424.604-0.008-0.0080.0000.0000.0000.000
178A488PHE0-0.0050.01326.4050.0070.0070.0000.0000.0000.000
179A489LYS10.9330.96629.8940.0640.0640.0000.0000.0000.000
180A490TYR0-0.063-0.04633.1760.0010.0010.0000.0000.0000.000
181A491PRO00.0200.01228.0030.0020.0020.0000.0000.0000.000
182A492PRO0-0.0140.00729.5080.0020.0020.0000.0000.0000.000
183A493LYS10.9500.96129.3400.0740.0740.0000.0000.0000.000
184A494ASP-1-0.835-0.88630.092-0.079-0.0790.0000.0000.0000.000
185A495LEU00.0000.01129.1580.0010.0010.0000.0000.0000.000
186A496THR00.0190.01823.621-0.004-0.0040.0000.0000.0000.000
187A497TYR0-0.046-0.04024.1440.0070.0070.0000.0000.0000.000
188A498ARG10.8860.94917.7480.1600.1600.0000.0000.0000.000
189A499PRO00.0290.01421.7340.0130.0130.0000.0000.0000.000
190A500MET00.0300.00823.954-0.004-0.0040.0000.0000.0000.000
191A501SER00.0390.02622.9800.0020.0020.0000.0000.0000.000
192A502ASP-1-0.833-0.90218.932-0.183-0.1830.0000.0000.0000.000
193A503MET0-0.101-0.05220.577-0.006-0.0060.0000.0000.0000.000
194A504GLY00.0230.02622.5450.0060.0060.0000.0000.0000.000
195A505TRP0-0.088-0.04416.7230.0080.0080.0000.0000.0000.000
196A506GLY00.0340.01718.085-0.001-0.0010.0000.0000.0000.000
197A507ALA0-0.037-0.02015.712-0.010-0.0100.0000.0000.0000.000
198A508VAL00.013-0.0039.432-0.003-0.0030.0000.0000.0000.000
199A509VAL0-0.030-0.01612.9110.0050.0050.0000.0000.0000.000
200A510GLU-1-0.954-0.97510.8140.3400.3400.0000.0000.0000.000
201A511HIS0-0.010-0.0069.369-0.010-0.0100.0000.0000.0000.000