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: 1NVJZ

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309815.00927
FMO2-HF: Nuclear repulsion 2230771.127147
FMO2-HF: Total energy -79043.882123
FMO2-MP2: Total energy -79274.647047


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.
-11.975-9.0735.96-3.807-5.0560.027
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 : 0.022 / 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-1-0.923-0.9702.066-9.256-6.7665.930-3.745-4.6750.025
4A278LEU0-0.035-0.0403.743-2.318-1.9060.030-0.062-0.3810.002
5A279TYR0-0.041-0.0144.863-0.140-0.1400.0000.0000.0000.000
6A280ARG10.9251.0026.007-0.676-0.6760.0000.0000.0000.000
7A281ALA00.0190.0189.404-0.159-0.1590.0000.0000.0000.000
8A282CYS0-0.014-0.00812.6500.0160.0160.0000.0000.0000.000
9A283LEU0-0.0130.00614.752-0.003-0.0030.0000.0000.0000.000
10A284TYR0-0.036-0.03118.132-0.020-0.0200.0000.0000.0000.000
11A285GLU-1-0.908-0.92920.399-0.025-0.0250.0000.0000.0000.000
12A286ARG10.9480.95724.0380.0040.0040.0000.0000.0000.000
13A287VAL0-0.0070.01525.3290.0010.0010.0000.0000.0000.000
14A288LEU0-0.028-0.02127.9980.0020.0020.0000.0000.0000.000
15A289LEU00.0150.00531.764-0.004-0.0040.0000.0000.0000.000
16A290ALA0-0.0140.00734.4330.0040.0040.0000.0000.0000.000
17A291LEU00.0110.00234.7460.0020.0020.0000.0000.0000.000
18A292HIS00.028-0.00236.5490.0010.0010.0000.0000.0000.000
19A293ASP-1-0.820-0.88436.904-0.045-0.0450.0000.0000.0000.000
20A294ARG10.9260.93738.8960.0190.0190.0000.0000.0000.000
21A295ALA0-0.0050.00841.5750.0020.0020.0000.0000.0000.000
22A296PRO0-0.037-0.02045.1670.0000.0000.0000.0000.0000.000
23A297GLN00.030-0.00246.6500.0020.0020.0000.0000.0000.000
24A298LEU0-0.059-0.00943.4490.0000.0000.0000.0000.0000.000
25A299LYS10.8830.95445.5580.0240.0240.0000.0000.0000.000
26A300ILE0-0.033-0.02339.066-0.002-0.0020.0000.0000.0000.000
27A301SER00.005-0.00638.9190.0020.0020.0000.0000.0000.000
28A302ASP-1-0.847-0.94139.305-0.011-0.0110.0000.0000.0000.000
29A303ASP-1-0.904-0.93634.953-0.028-0.0280.0000.0000.0000.000
30A304ARG10.8390.91634.4550.0200.0200.0000.0000.0000.000
31A305LEU00.0050.00432.087-0.006-0.0060.0000.0000.0000.000
32A306THR00.0350.02736.218-0.003-0.0030.0000.0000.0000.000
33A307VAL0-0.039-0.01739.9480.0030.0030.0000.0000.0000.000
34A308VAL00.0200.01442.580-0.001-0.0010.0000.0000.0000.000
35A309GLY00.0050.00246.3590.0010.0010.0000.0000.0000.000
36A310GLU-1-0.812-0.92348.473-0.019-0.0190.0000.0000.0000.000
37A311LYS10.8630.92451.5500.0200.0200.0000.0000.0000.000
38A312GLY00.0290.01653.076-0.001-0.0010.0000.0000.0000.000
39A313TYR0-0.029-0.02548.0450.0000.0000.0000.0000.0000.000
40A314SER0-0.0110.01547.4950.0010.0010.0000.0000.0000.000
41A315MET0-0.048-0.02441.229-0.002-0.0020.0000.0000.0000.000
42A316VAL00.0140.01038.2610.0030.0030.0000.0000.0000.000
43A317ARG10.8060.89235.6910.0470.0470.0000.0000.0000.000
44A318ALA0-0.004-0.00131.8140.0040.0040.0000.0000.0000.000
45A319SER0-0.011-0.04629.1350.0010.0010.0000.0000.0000.000
46A320HIS00.0130.03925.258-0.001-0.0010.0000.0000.0000.000
47A321GLY0-0.008-0.01028.5880.0000.0000.0000.0000.0000.000
48A322VAL0-0.022-0.01525.872-0.005-0.0050.0000.0000.0000.000
49A323ARG10.9240.95126.7180.1160.1160.0000.0000.0000.000
50A324LYS10.9831.00020.6630.2300.2300.0000.0000.0000.000
51A325GLY0-0.0030.01424.123-0.009-0.0090.0000.0000.0000.000
52A326ALA00.0160.00924.7360.0170.0170.0000.0000.0000.000
53A327TRP0-0.034-0.02721.437-0.013-0.0130.0000.0000.0000.000
54A328TYR00.0230.00227.1720.0100.0100.0000.0000.0000.000
55A329PHE0-0.022-0.01228.5600.0000.0000.0000.0000.0000.000
56A330GLU-1-0.755-0.87631.139-0.091-0.0910.0000.0000.0000.000
57A331ILE0-0.007-0.00734.0630.0040.0040.0000.0000.0000.000
58A332THR0-0.0140.00937.381-0.002-0.0020.0000.0000.0000.000
59A333VAL0-0.025-0.01039.7180.0030.0030.0000.0000.0000.000
60A334ASP-1-0.789-0.85641.813-0.041-0.0410.0000.0000.0000.000
61A335GLU-1-0.944-0.98044.411-0.026-0.0260.0000.0000.0000.000
62A336MET0-0.082-0.04247.299-0.002-0.0020.0000.0000.0000.000
63A337PRO00.0570.04350.1310.0000.0000.0000.0000.0000.000
64A338PRO00.0280.01353.872-0.001-0.0010.0000.0000.0000.000
65A339ASP-1-0.882-0.94256.619-0.026-0.0260.0000.0000.0000.000
66A340THR0-0.0010.00151.6310.0000.0000.0000.0000.0000.000
67A341ALA0-0.056-0.04350.260-0.001-0.0010.0000.0000.0000.000
68A342ALA00.0470.02844.8530.0010.0010.0000.0000.0000.000
69A343ARG10.8130.91745.2850.0450.0450.0000.0000.0000.000
70A344LEU00.0520.04140.1170.0010.0010.0000.0000.0000.000
71A345GLY00.0460.00138.329-0.001-0.0010.0000.0000.0000.000
72A346TRP00.0470.03930.4080.0000.0000.0000.0000.0000.000
73A347SER0-0.014-0.04836.4050.0050.0050.0000.0000.0000.000
74A348GLN00.0130.02335.998-0.002-0.0020.0000.0000.0000.000
75A349PRO00.0350.01234.8600.0040.0040.0000.0000.0000.000
76A350LEU0-0.014-0.00337.5980.0030.0030.0000.0000.0000.000
77A351GLY0-0.0180.01740.4200.0020.0020.0000.0000.0000.000
78A352ASN00.0350.02142.2380.0030.0030.0000.0000.0000.000
79A353LEU00.0320.00941.052-0.001-0.0010.0000.0000.0000.000
80A354GLN0-0.0190.00044.9960.0010.0010.0000.0000.0000.000
81A355ALA00.0210.01247.5240.0010.0010.0000.0000.0000.000
82A356PRO0-0.063-0.02647.087-0.001-0.0010.0000.0000.0000.000
83A357LEU00.0730.03740.163-0.001-0.0010.0000.0000.0000.000
84A358GLY0-0.0030.00144.0330.0000.0000.0000.0000.0000.000
85A359TYR0-0.042-0.01345.2380.0010.0010.0000.0000.0000.000
86A360ASP-1-0.756-0.87044.645-0.049-0.0490.0000.0000.0000.000
87A361LYS10.9260.95541.9060.0610.0610.0000.0000.0000.000
88A362PHE0-0.004-0.00140.734-0.004-0.0040.0000.0000.0000.000
89A363SER00.0420.03739.892-0.002-0.0020.0000.0000.0000.000
90A364TYR00.0210.03138.9070.0010.0010.0000.0000.0000.000
91A365SER0-0.054-0.04840.507-0.001-0.0010.0000.0000.0000.000
92A366TRP00.0540.03040.2200.0000.0000.0000.0000.0000.000
93A367ARG10.8360.91443.9700.0460.0460.0000.0000.0000.000
94A368SER00.0830.05847.210-0.001-0.0010.0000.0000.0000.000
95A369LYS10.9930.98448.0040.0360.0360.0000.0000.0000.000
96A370LYS10.8990.92251.1510.0390.0390.0000.0000.0000.000
97A371GLY00.1000.08647.467-0.001-0.0010.0000.0000.0000.000
98A372THR0-0.061-0.02247.682-0.001-0.0010.0000.0000.0000.000
99A373LYS10.9080.96644.6880.0700.0700.0000.0000.0000.000
100A374PHE0-0.035-0.03445.6490.0030.0030.0000.0000.0000.000
101A375HIS00.0310.01642.869-0.003-0.0030.0000.0000.0000.000
102A376GLN0-0.037-0.01045.6120.0040.0040.0000.0000.0000.000
103A377SER0-0.033-0.04348.1920.0020.0020.0000.0000.0000.000
104A378ILE0-0.035-0.00849.8130.0020.0020.0000.0000.0000.000
105A379GLY0-0.029-0.01549.547-0.002-0.0020.0000.0000.0000.000
106A380LYS10.9300.95348.4510.0600.0600.0000.0000.0000.000
107A381HIS00.0280.00049.5830.0010.0010.0000.0000.0000.000
108A382TYR0-0.047-0.05840.844-0.001-0.0010.0000.0000.0000.000
109A383SER00.0740.04645.240-0.002-0.0020.0000.0000.0000.000
110A384SER0-0.023-0.00447.3950.0020.0020.0000.0000.0000.000
111A385GLY0-0.009-0.01347.729-0.002-0.0020.0000.0000.0000.000
112A386TYR0-0.031-0.01044.3770.0000.0000.0000.0000.0000.000
113A387GLY0-0.001-0.02246.7160.0020.0020.0000.0000.0000.000
114A388GLN00.0550.02846.129-0.002-0.0020.0000.0000.0000.000
115A389GLY0-0.0030.00144.5320.0000.0000.0000.0000.0000.000
116A390ASP-1-0.851-0.91643.035-0.056-0.0560.0000.0000.0000.000
117A391VAL0-0.015-0.01136.4070.0010.0010.0000.0000.0000.000
118A392LEU0-0.061-0.03638.756-0.004-0.0040.0000.0000.0000.000
119A393GLY00.0520.01434.936-0.001-0.0010.0000.0000.0000.000
120A394PHE0-0.041-0.03533.9220.0040.0040.0000.0000.0000.000
121A395TYR00.0650.02928.782-0.002-0.0020.0000.0000.0000.000
122A396ILE0-0.037-0.00630.0350.0080.0080.0000.0000.0000.000
123A397ASN00.0530.01628.269-0.019-0.0190.0000.0000.0000.000
124A398LEU0-0.026-0.00728.6490.0110.0110.0000.0000.0000.000
125A399PRO00.001-0.00127.397-0.011-0.0110.0000.0000.0000.000
126A400GLU-1-0.851-0.93322.781-0.230-0.2300.0000.0000.0000.000
127A401ASP-1-0.897-0.95827.620-0.149-0.1490.0000.0000.0000.000
128A402THR0-0.056-0.02924.045-0.003-0.0030.0000.0000.0000.000
129A403ILE0-0.003-0.00120.544-0.008-0.0080.0000.0000.0000.000
130A404SER0-0.006-0.00823.865-0.010-0.0100.0000.0000.0000.000
131A405GLY00.0020.01827.1620.0070.0070.0000.0000.0000.000
132A406ARG10.9130.92529.4490.1850.1850.0000.0000.0000.000
133A443GLY0-0.0110.00331.070-0.011-0.0110.0000.0000.0000.000
134A444SER0-0.0470.00132.0750.0050.0050.0000.0000.0000.000
135A445SER00.0510.02732.981-0.003-0.0030.0000.0000.0000.000
136A446GLU-1-0.941-0.97333.560-0.116-0.1160.0000.0000.0000.000
137A447ILE0-0.021-0.00834.128-0.003-0.0030.0000.0000.0000.000
138A448ILE0-0.022-0.00734.1790.0050.0050.0000.0000.0000.000
139A449PHE0-0.0010.00636.034-0.001-0.0010.0000.0000.0000.000
140A450TYR0-0.024-0.01633.598-0.001-0.0010.0000.0000.0000.000
141A451LYS10.9050.94537.9950.0600.0600.0000.0000.0000.000
142A452ASN0-0.015-0.00238.973-0.001-0.0010.0000.0000.0000.000
143A453GLY00.0550.01835.8050.0000.0000.0000.0000.0000.000
144A454VAL0-0.050-0.01536.695-0.005-0.0050.0000.0000.0000.000
145A455ASN00.0210.02235.8340.0090.0090.0000.0000.0000.000
146A456GLN0-0.067-0.04738.3810.0070.0070.0000.0000.0000.000
147A457GLY00.0350.02939.7970.0040.0040.0000.0000.0000.000
148A458VAL00.0290.02637.6150.0010.0010.0000.0000.0000.000
149A459ALA0-0.053-0.01139.8730.0050.0050.0000.0000.0000.000
150A460TYR0-0.024-0.02839.8160.0070.0070.0000.0000.0000.000
151A461LYS10.9901.00138.2190.0900.0900.0000.0000.0000.000
152A462ASP-1-0.881-0.93737.556-0.096-0.0960.0000.0000.0000.000
153A463ILE0-0.051-0.01734.7370.0060.0060.0000.0000.0000.000
154A464PHE0-0.014-0.01737.467-0.001-0.0010.0000.0000.0000.000
155A465GLU-1-0.792-0.88032.277-0.114-0.1140.0000.0000.0000.000
156A466GLY0-0.027-0.01633.2600.0080.0080.0000.0000.0000.000
157A467VAL0-0.060-0.02629.659-0.007-0.0070.0000.0000.0000.000
158A468TYR0-0.027-0.05431.4010.0120.0120.0000.0000.0000.000
159A469PHE00.0090.00031.370-0.007-0.0070.0000.0000.0000.000
160A470PRO00.0190.02331.1940.0030.0030.0000.0000.0000.000
161A471ALA00.001-0.00934.1710.0050.0050.0000.0000.0000.000
162A472ILE00.0320.02037.834-0.002-0.0020.0000.0000.0000.000
163A473SER0-0.033-0.01140.7510.0030.0030.0000.0000.0000.000
164A474LEU00.0340.00144.060-0.002-0.0020.0000.0000.0000.000
165A475TYR0-0.049-0.02347.1220.0020.0020.0000.0000.0000.000
166A476LYS10.8840.91850.9240.0260.0260.0000.0000.0000.000
167A477SER0-0.045-0.01750.665-0.001-0.0010.0000.0000.0000.000
168A478CYS0-0.0330.01648.2630.0000.0000.0000.0000.0000.000
169A479THR00.0370.00344.0870.0010.0010.0000.0000.0000.000
170A480VAL0-0.057-0.02540.765-0.002-0.0020.0000.0000.0000.000
171A481SER00.054-0.00837.8500.0030.0030.0000.0000.0000.000
172A482ILE0-0.076-0.03233.540-0.004-0.0040.0000.0000.0000.000
173A483ASN00.0210.00730.2160.0020.0020.0000.0000.0000.000
174A484PHE00.033-0.01128.175-0.007-0.0070.0000.0000.0000.000
175A485GLY00.0320.04226.430-0.013-0.0130.0000.0000.0000.000
176A486PRO00.003-0.01922.5250.0100.0100.0000.0000.0000.000
177A487CYS0-0.028-0.01924.623-0.011-0.0110.0000.0000.0000.000
178A488PHE0-0.0150.00726.4610.0080.0080.0000.0000.0000.000
179A489LYS10.9350.96529.8850.0650.0650.0000.0000.0000.000
180A490TYR0-0.079-0.05233.1530.0030.0030.0000.0000.0000.000
181A491PRO00.0150.01828.005-0.002-0.0020.0000.0000.0000.000
182A492PRO0-0.0170.00029.2060.0020.0020.0000.0000.0000.000
183A493LYS10.9480.95829.2970.1000.1000.0000.0000.0000.000
184A494ASP-1-0.851-0.91930.029-0.134-0.1340.0000.0000.0000.000
185A495LEU0-0.0090.00729.111-0.003-0.0030.0000.0000.0000.000
186A496THR0-0.0060.00323.5250.0030.0030.0000.0000.0000.000
187A497TYR0-0.013-0.02124.1330.0110.0110.0000.0000.0000.000
188A498ARG10.9270.97917.2710.2440.2440.0000.0000.0000.000
189A499PRO00.0190.01321.7570.0170.0170.0000.0000.0000.000
190A500MET00.0240.00723.889-0.008-0.0080.0000.0000.0000.000
191A501SER00.0420.02723.1940.0020.0020.0000.0000.0000.000
192A502ASP-1-0.861-0.93519.741-0.207-0.2070.0000.0000.0000.000
193A503MET0-0.107-0.05820.318-0.014-0.0140.0000.0000.0000.000
194A504GLY00.0250.02822.3350.0060.0060.0000.0000.0000.000
195A505TRP0-0.067-0.02916.4980.0210.0210.0000.0000.0000.000
196A506GLY00.0310.01517.949-0.016-0.0160.0000.0000.0000.000
197A507ALA0-0.035-0.02015.642-0.013-0.0130.0000.0000.0000.000
198A508VAL00.007-0.0059.4490.0110.0110.0000.0000.0000.000
199A509VAL0-0.024-0.01212.882-0.011-0.0110.0000.0000.0000.000
200A510GLU-1-0.970-0.98411.1790.4390.4390.0000.0000.0000.000
201A511HIS0-0.010-0.0048.938-0.029-0.0290.0000.0000.0000.000