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: 89KJY

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2315007.797555
FMO2-HF: Nuclear repulsion 2235963.336803
FMO2-HF: Total energy -79044.460753
FMO2-MP2: Total energy -79275.430561


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.
-32.792-33.43321.704-12.293-8.769-0.026
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 : 0.027 / q_NPA : -0.005
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-1-0.845-0.9161.694-34.027-35.60921.663-11.999-8.083-0.028
4A278LEU0-0.020-0.0183.612-0.5180.2060.042-0.270-0.4950.002
5A279TYR0-0.031-0.0074.6540.2940.511-0.001-0.024-0.1910.000
6A280ARG10.8410.9435.2851.6881.6880.0000.0000.0000.000
7A281ALA00.0180.0179.365-0.106-0.1060.0000.0000.0000.000
8A282CYS0-0.020-0.01612.363-0.029-0.0290.0000.0000.0000.000
9A283LEU0-0.0130.00614.6020.0420.0420.0000.0000.0000.000
10A284TYR0-0.041-0.03517.969-0.023-0.0230.0000.0000.0000.000
11A285GLU-1-0.904-0.92520.464-0.179-0.1790.0000.0000.0000.000
12A286ARG10.9430.96224.1620.1540.1540.0000.0000.0000.000
13A287VAL00.0010.01625.2460.0100.0100.0000.0000.0000.000
14A288LEU0-0.032-0.02127.9760.0030.0030.0000.0000.0000.000
15A289LEU00.0050.00131.7320.0000.0000.0000.0000.0000.000
16A290ALA0-0.0150.00134.7170.0000.0000.0000.0000.0000.000
17A291LEU00.0350.02134.7100.0050.0050.0000.0000.0000.000
18A292HIS00.021-0.00136.7600.0070.0070.0000.0000.0000.000
19A293ASP-1-0.785-0.84137.009-0.097-0.0970.0000.0000.0000.000
20A294ARG10.8980.91339.0000.0800.0800.0000.0000.0000.000
21A295ALA00.0110.01041.7520.0030.0030.0000.0000.0000.000
22A296PRO0-0.037-0.01545.179-0.002-0.0020.0000.0000.0000.000
23A297GLN00.0410.00846.892-0.001-0.0010.0000.0000.0000.000
24A298LEU0-0.057-0.01943.7360.0010.0010.0000.0000.0000.000
25A299LYS10.8450.91545.0200.0610.0610.0000.0000.0000.000
26A300ILE0-0.020-0.02239.073-0.001-0.0010.0000.0000.0000.000
27A301SER00.007-0.01738.4040.0020.0020.0000.0000.0000.000
28A302ASP-1-0.869-0.94539.271-0.087-0.0870.0000.0000.0000.000
29A303ASP-1-0.863-0.91334.821-0.116-0.1160.0000.0000.0000.000
30A304ARG10.8030.90634.2080.0930.0930.0000.0000.0000.000
31A305LEU00.0120.00831.812-0.007-0.0070.0000.0000.0000.000
32A306THR00.0190.00635.9670.0000.0000.0000.0000.0000.000
33A307VAL0-0.044-0.03139.7560.0020.0020.0000.0000.0000.000
34A308VAL00.0260.02042.4780.0010.0010.0000.0000.0000.000
35A309GLY00.0270.01546.3000.0000.0000.0000.0000.0000.000
36A310GLU-1-0.833-0.89348.500-0.053-0.0530.0000.0000.0000.000
37A311LYS10.9050.93551.5390.0500.0500.0000.0000.0000.000
38A312GLY00.0400.03053.6550.0000.0000.0000.0000.0000.000
39A313TYR0-0.045-0.04048.0530.0000.0000.0000.0000.0000.000
40A314SER0-0.0190.01447.8510.0000.0000.0000.0000.0000.000
41A315MET0-0.061-0.02841.522-0.003-0.0030.0000.0000.0000.000
42A316VAL00.0180.01038.6520.0020.0020.0000.0000.0000.000
43A317ARG10.7940.86135.7530.0970.0970.0000.0000.0000.000
44A318ALA00.0200.00831.7260.0020.0020.0000.0000.0000.000
45A319SER0-0.034-0.04029.3460.0060.0060.0000.0000.0000.000
46A320HIS00.0150.01326.0540.0040.0040.0000.0000.0000.000
47A321GLY00.003-0.01328.6020.0070.0070.0000.0000.0000.000
48A322VAL0-0.019-0.00626.018-0.011-0.0110.0000.0000.0000.000
49A323ARG10.8740.90427.0910.1560.1560.0000.0000.0000.000
50A324LYS10.8440.90621.9110.2470.2470.0000.0000.0000.000
51A325GLY00.0390.03324.083-0.018-0.0180.0000.0000.0000.000
52A326ALA0-0.0010.00224.6550.0170.0170.0000.0000.0000.000
53A327TRP0-0.009-0.02022.028-0.026-0.0260.0000.0000.0000.000
54A328TYR00.011-0.00227.0000.0200.0200.0000.0000.0000.000
55A329PHE0-0.019-0.01128.253-0.013-0.0130.0000.0000.0000.000
56A330GLU-1-0.727-0.86130.884-0.135-0.1350.0000.0000.0000.000
57A331ILE0-0.007-0.01333.937-0.001-0.0010.0000.0000.0000.000
58A332THR00.0000.01737.2440.0020.0020.0000.0000.0000.000
59A333VAL0-0.033-0.01739.6760.0010.0010.0000.0000.0000.000
60A334ASP-1-0.762-0.86941.549-0.089-0.0890.0000.0000.0000.000
61A335GLU-1-0.929-0.97844.348-0.060-0.0600.0000.0000.0000.000
62A336MET0-0.052-0.02546.885-0.002-0.0020.0000.0000.0000.000
63A337PRO00.0740.05450.1010.0020.0020.0000.0000.0000.000
64A338PRO00.0240.01153.867-0.001-0.0010.0000.0000.0000.000
65A339ASP-1-0.809-0.88256.680-0.048-0.0480.0000.0000.0000.000
66A340THR00.006-0.00251.622-0.001-0.0010.0000.0000.0000.000
67A341ALA0-0.051-0.03850.2120.0000.0000.0000.0000.0000.000
68A342ALA00.0640.03244.940-0.001-0.0010.0000.0000.0000.000
69A343ARG10.7810.89245.1740.0690.0690.0000.0000.0000.000
70A344LEU00.0480.05140.083-0.001-0.0010.0000.0000.0000.000
71A345GLY00.0460.00038.0950.0030.0030.0000.0000.0000.000
72A346TRP00.0430.03030.330-0.006-0.0060.0000.0000.0000.000
73A347SER0-0.007-0.03336.4660.0100.0100.0000.0000.0000.000
74A348GLN00.0240.02636.142-0.001-0.0010.0000.0000.0000.000
75A349PRO00.0330.01335.1360.0050.0050.0000.0000.0000.000
76A350LEU0-0.016-0.00237.8650.0030.0030.0000.0000.0000.000
77A351GLY0-0.0300.00840.7020.0040.0040.0000.0000.0000.000
78A352ASN00.0290.00542.536-0.002-0.0020.0000.0000.0000.000
79A353LEU00.0340.01741.0280.0010.0010.0000.0000.0000.000
80A354GLN0-0.045-0.01845.0030.0030.0030.0000.0000.0000.000
81A355ALA00.0240.02147.7350.0030.0030.0000.0000.0000.000
82A356PRO0-0.048-0.01947.324-0.003-0.0030.0000.0000.0000.000
83A357LEU00.0740.03240.1660.0010.0010.0000.0000.0000.000
84A358GLY00.0270.03144.2150.0020.0020.0000.0000.0000.000
85A359TYR0-0.027-0.01045.3400.0030.0030.0000.0000.0000.000
86A360ASP-1-0.751-0.85644.383-0.074-0.0740.0000.0000.0000.000
87A361LYS10.8700.94140.3240.0820.0820.0000.0000.0000.000
88A362PHE0-0.006-0.00440.917-0.003-0.0030.0000.0000.0000.000
89A363SER00.008-0.00740.083-0.005-0.0050.0000.0000.0000.000
90A364TYR00.0050.01939.1310.0040.0040.0000.0000.0000.000
91A365SER0-0.061-0.05140.316-0.004-0.0040.0000.0000.0000.000
92A366TRP00.0700.02940.3400.0030.0030.0000.0000.0000.000
93A367ARG10.8460.92043.9630.0580.0580.0000.0000.0000.000
94A368SER00.0360.03647.1610.0010.0010.0000.0000.0000.000
95A369LYS10.9960.98047.9930.0520.0520.0000.0000.0000.000
96A370LYS10.9370.95151.3180.0480.0480.0000.0000.0000.000
97A371GLY00.0990.07647.3680.0010.0010.0000.0000.0000.000
98A372THR0-0.071-0.01547.2600.0000.0000.0000.0000.0000.000
99A373LYS10.8820.96044.2910.0710.0710.0000.0000.0000.000
100A374PHE0-0.034-0.02945.3660.0050.0050.0000.0000.0000.000
101A375HIS0-0.0020.00242.903-0.003-0.0030.0000.0000.0000.000
102A376GLN0-0.042-0.01645.8320.0060.0060.0000.0000.0000.000
103A377SER0-0.010-0.02148.4640.0030.0030.0000.0000.0000.000
104A378ILE0-0.048-0.00850.2700.0020.0020.0000.0000.0000.000
105A379GLY00.013-0.00149.493-0.003-0.0030.0000.0000.0000.000
106A380LYS10.9090.94148.4750.0620.0620.0000.0000.0000.000
107A381HIS00.0460.01249.271-0.002-0.0020.0000.0000.0000.000
108A382TYR0-0.042-0.05440.398-0.001-0.0010.0000.0000.0000.000
109A383SER00.0810.05145.119-0.001-0.0010.0000.0000.0000.000
110A384SER00.0110.00947.2670.0030.0030.0000.0000.0000.000
111A385GLY0-0.032-0.01847.589-0.003-0.0030.0000.0000.0000.000
112A386TYR0-0.036-0.02344.246-0.001-0.0010.0000.0000.0000.000
113A387GLY00.025-0.00546.8710.0020.0020.0000.0000.0000.000
114A388GLN00.0320.02446.342-0.001-0.0010.0000.0000.0000.000
115A389GLY00.0060.01244.9050.0020.0020.0000.0000.0000.000
116A390ASP-1-0.784-0.87843.178-0.078-0.0780.0000.0000.0000.000
117A391VAL0-0.024-0.01636.712-0.002-0.0020.0000.0000.0000.000
118A392LEU0-0.054-0.02438.6890.0020.0020.0000.0000.0000.000
119A393GLY00.0530.02534.853-0.006-0.0060.0000.0000.0000.000
120A394PHE0-0.043-0.03233.7290.0100.0100.0000.0000.0000.000
121A395TYR00.0310.00528.310-0.006-0.0060.0000.0000.0000.000
122A396ILE0-0.030-0.00530.0210.0110.0110.0000.0000.0000.000
123A397ASN00.0280.00228.823-0.022-0.0220.0000.0000.0000.000
124A398LEU0-0.0080.00728.7150.0140.0140.0000.0000.0000.000
125A399PRO0-0.004-0.00427.691-0.013-0.0130.0000.0000.0000.000
126A400GLU-1-0.783-0.86823.933-0.218-0.2180.0000.0000.0000.000
127A401ASP-1-0.884-0.95027.872-0.116-0.1160.0000.0000.0000.000
128A402THR0-0.022-0.01524.4720.0050.0050.0000.0000.0000.000
129A403ILE0-0.012-0.00320.7560.0030.0030.0000.0000.0000.000
130A404SER0-0.006-0.00524.135-0.001-0.0010.0000.0000.0000.000
131A405GLY00.0030.01827.3000.0110.0110.0000.0000.0000.000
132A406ARG10.9010.92529.8150.1090.1090.0000.0000.0000.000
133A443GLY0-0.0160.00531.162-0.008-0.0080.0000.0000.0000.000
134A444SER0-0.031-0.03532.5540.0060.0060.0000.0000.0000.000
135A445SER00.0310.02633.117-0.004-0.0040.0000.0000.0000.000
136A446GLU-1-0.891-0.96633.606-0.091-0.0910.0000.0000.0000.000
137A447ILE0-0.027-0.01034.086-0.007-0.0070.0000.0000.0000.000
138A448ILE0-0.0110.00334.1040.0080.0080.0000.0000.0000.000
139A449PHE00.0110.00435.829-0.006-0.0060.0000.0000.0000.000
140A450TYR0-0.018-0.02633.5700.0020.0020.0000.0000.0000.000
141A451LYS10.7860.88037.9150.0740.0740.0000.0000.0000.000
142A452ASN0-0.029-0.02739.284-0.001-0.0010.0000.0000.0000.000
143A453GLY00.0440.02336.0940.0010.0010.0000.0000.0000.000
144A454VAL0-0.036-0.00736.829-0.002-0.0020.0000.0000.0000.000
145A455ASN00.0230.00735.7320.0040.0040.0000.0000.0000.000
146A456GLN0-0.063-0.04538.3700.0090.0090.0000.0000.0000.000
147A457GLY00.0410.03339.6420.0050.0050.0000.0000.0000.000
148A458VAL00.0200.01737.687-0.003-0.0030.0000.0000.0000.000
149A459ALA0-0.074-0.01939.6280.0060.0060.0000.0000.0000.000
150A460TYR0-0.019-0.02939.7030.0080.0080.0000.0000.0000.000
151A461LYS10.8440.90838.1630.0780.0780.0000.0000.0000.000
152A462ASP-1-0.816-0.85837.790-0.080-0.0800.0000.0000.0000.000
153A463ILE0-0.0200.00834.7450.0040.0040.0000.0000.0000.000
154A464PHE00.008-0.00837.468-0.002-0.0020.0000.0000.0000.000
155A465GLU-1-0.692-0.82032.613-0.133-0.1330.0000.0000.0000.000
156A466GLY0-0.040-0.02133.5850.0080.0080.0000.0000.0000.000
157A467VAL0-0.040-0.01429.715-0.005-0.0050.0000.0000.0000.000
158A468TYR0-0.025-0.05131.7190.0130.0130.0000.0000.0000.000
159A469PHE00.0240.00931.503-0.012-0.0120.0000.0000.0000.000
160A470PRO00.0090.01331.1770.0090.0090.0000.0000.0000.000
161A471ALA0-0.018-0.01434.1870.0020.0020.0000.0000.0000.000
162A472ILE00.0290.01637.8150.0020.0020.0000.0000.0000.000
163A473SER0-0.025-0.01040.7600.0030.0030.0000.0000.0000.000
164A474LEU00.0330.00844.0310.0000.0000.0000.0000.0000.000
165A475TYR0-0.099-0.05347.2670.0020.0020.0000.0000.0000.000
166A476LYS10.8390.88851.0970.0490.0490.0000.0000.0000.000
167A477SER0-0.049-0.02450.597-0.002-0.0020.0000.0000.0000.000
168A478CYS0-0.0510.00548.0220.0000.0000.0000.0000.0000.000
169A479THR00.008-0.00944.3230.0000.0000.0000.0000.0000.000
170A480VAL0-0.055-0.02141.0540.0000.0000.0000.0000.0000.000
171A481SER00.0590.01037.849-0.001-0.0010.0000.0000.0000.000
172A482ILE0-0.079-0.02833.4030.0000.0000.0000.0000.0000.000
173A483ASN0-0.018-0.02430.191-0.009-0.0090.0000.0000.0000.000
174A484PHE00.0410.00827.9700.0010.0010.0000.0000.0000.000
175A485GLY00.0300.04426.255-0.013-0.0130.0000.0000.0000.000
176A486PRO00.008-0.02022.0610.0040.0040.0000.0000.0000.000
177A487CYS0-0.030-0.01924.3700.0000.0000.0000.0000.0000.000
178A488PHE00.0080.02126.2500.0070.0070.0000.0000.0000.000
179A489LYS10.9110.96029.8860.1070.1070.0000.0000.0000.000
180A490TYR0-0.039-0.04033.1730.0080.0080.0000.0000.0000.000
181A491PRO00.0380.02128.1490.0010.0010.0000.0000.0000.000
182A492PRO0-0.0340.00329.6110.0070.0070.0000.0000.0000.000
183A493LYS10.9430.96329.3210.1050.1050.0000.0000.0000.000
184A494ASP-1-0.819-0.88530.531-0.118-0.1180.0000.0000.0000.000
185A495LEU00.0050.01129.5760.0040.0040.0000.0000.0000.000
186A496THR00.0190.01423.950-0.005-0.0050.0000.0000.0000.000
187A497TYR0-0.063-0.04224.4850.0060.0060.0000.0000.0000.000
188A498ARG10.8810.95017.7090.3660.3660.0000.0000.0000.000
189A499PRO00.0260.00821.6350.0250.0250.0000.0000.0000.000
190A500MET00.0220.00423.872-0.014-0.0140.0000.0000.0000.000
191A501SER00.0350.01622.6930.0000.0000.0000.0000.0000.000
192A502ASP-1-0.832-0.89518.530-0.419-0.4190.0000.0000.0000.000
193A503MET0-0.093-0.04520.481-0.028-0.0280.0000.0000.0000.000
194A504GLY00.0280.02722.5920.0070.0070.0000.0000.0000.000
195A505TRP0-0.086-0.04616.754-0.011-0.0110.0000.0000.0000.000
196A506GLY00.0320.01518.0560.0130.0130.0000.0000.0000.000
197A507ALA0-0.029-0.01815.353-0.053-0.0530.0000.0000.0000.000
198A508VAL00.0190.0078.9940.0200.0200.0000.0000.0000.000
199A509VAL0-0.028-0.01512.3490.0570.0570.0000.0000.0000.000
200A510GLU-1-0.940-0.9699.728-0.273-0.2730.0000.0000.0000.000
201A511HIS0-0.018-0.0099.689-0.028-0.0280.0000.0000.0000.000