Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: J3829

Calculation Name: 1MJS-A-Xray372

Preferred Name: Mothers against decapentaplegic homolog 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1MJS

Chain ID: A

ChEMBL ID: CHEMBL1293258

UniProt ID: P84022

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1969211.853423
FMO2-HF: Nuclear repulsion 1895337.037813
FMO2-HF: Total energy -73874.81561
FMO2-MP2: Total energy -74084.64791


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:228:PRO)


Summations of interaction energy for fragment #1(A:228:PRO)
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.
-8.362-1.6176.443-3.847-9.342-0.032
Interaction energy analysis for fragmet #1(A:228:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.009
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].
3A230PHE00.0420.0123.169-0.6201.0070.019-0.667-0.9790.002
4A231TRP00.018-0.0082.629-3.252-0.8860.801-1.268-1.899-0.008
5A232CYS0-0.036-0.0173.4610.7550.7570.0120.249-0.2630.000
6A233SER00.0170.0326.617-0.098-0.0980.0000.0000.0000.000
7A234ILE00.011-0.0129.3490.1110.1110.0000.0000.0000.000
8A235SER0-0.0060.00912.8820.0210.0210.0000.0000.0000.000
9A236TYR0-0.016-0.03816.0930.0180.0180.0000.0000.0000.000
10A237TYR00.0270.00417.9920.0150.0150.0000.0000.0000.000
11A238GLU-1-0.712-0.82722.671-0.180-0.1800.0000.0000.0000.000
12A239LEU0-0.0080.00426.3670.0110.0110.0000.0000.0000.000
13A240ASN0-0.016-0.01126.234-0.009-0.0090.0000.0000.0000.000
14A241GLN00.0220.02126.424-0.002-0.0020.0000.0000.0000.000
15A242ARG10.8860.95216.6400.3160.3160.0000.0000.0000.000
16A243VAL0-0.036-0.02422.2140.0120.0120.0000.0000.0000.000
17A244GLY00.0200.00521.303-0.021-0.0210.0000.0000.0000.000
18A245GLU-1-0.930-0.95817.593-0.319-0.3190.0000.0000.0000.000
19A246THR0-0.052-0.02912.1530.0270.0270.0000.0000.0000.000
20A247PHE0-0.0100.01311.818-0.023-0.0230.0000.0000.0000.000
21A248HIS00.0420.0168.634-0.174-0.1740.0000.0000.0000.000
22A249ALA00.0170.0047.9010.0590.0590.0000.0000.0000.000
23A250SER00.011-0.0046.707-0.503-0.5030.0000.0000.0000.000
24A251GLN00.0150.0227.896-0.053-0.0530.0000.0000.0000.000
25A252PRO00.0100.0157.881-0.072-0.0720.0000.0000.0000.000
26A253SER00.0090.0008.8680.1490.1490.0000.0000.0000.000
27A254MET0-0.0140.01211.246-0.066-0.0660.0000.0000.0000.000
28A255THR0-0.007-0.00213.8780.0260.0260.0000.0000.0000.000
29A256VAL00.0050.01915.725-0.032-0.0320.0000.0000.0000.000
30A257ASP-1-0.822-0.91218.201-0.276-0.2760.0000.0000.0000.000
31A258GLY00.024-0.00321.946-0.006-0.0060.0000.0000.0000.000
32A259PHE0-0.021-0.00524.4390.0240.0240.0000.0000.0000.000
33A260THR0-0.043-0.02925.371-0.011-0.0110.0000.0000.0000.000
34A261ASP-1-0.894-0.93624.311-0.218-0.2180.0000.0000.0000.000
35A262PRO0-0.008-0.00623.145-0.014-0.0140.0000.0000.0000.000
36A263SER00.0570.02017.893-0.014-0.0140.0000.0000.0000.000
37A264ASN00.0090.00717.613-0.017-0.0170.0000.0000.0000.000
38A265SER00.036-0.00212.782-0.005-0.0050.0000.0000.0000.000
39A266GLU-1-0.950-0.97812.837-0.610-0.6100.0000.0000.0000.000
40A267ARG10.8550.93815.1060.3600.3600.0000.0000.0000.000
41A268PHE00.0240.01315.639-0.003-0.0030.0000.0000.0000.000
42A269CYS0-0.032-0.01917.6090.0160.0160.0000.0000.0000.000
43A270LEU0-0.009-0.02119.6520.0090.0090.0000.0000.0000.000
44A271GLY00.0110.01023.0350.0200.0200.0000.0000.0000.000
45A272LEU0-0.019-0.01724.7360.0160.0160.0000.0000.0000.000
46A273LEU0-0.0170.01521.2550.0120.0120.0000.0000.0000.000
47A274SER00.0000.00325.6890.0100.0100.0000.0000.0000.000
48A275ASN00.002-0.03427.7230.0000.0000.0000.0000.0000.000
49A276VAL00.0440.02329.9070.0050.0050.0000.0000.0000.000
50A277ASN0-0.030-0.01032.1230.0050.0050.0000.0000.0000.000
51A278ARG10.7850.90027.8660.1690.1690.0000.0000.0000.000
52A279ASN00.0660.04532.9370.0030.0030.0000.0000.0000.000
53A280ALA00.1220.02934.631-0.006-0.0060.0000.0000.0000.000
54A281ALA0-0.015-0.00134.606-0.003-0.0030.0000.0000.0000.000
55A282VAL0-0.010-0.01029.065-0.005-0.0050.0000.0000.0000.000
56A283GLU-1-0.938-0.97330.900-0.133-0.1330.0000.0000.0000.000
57A284LEU0-0.036-0.00732.912-0.003-0.0030.0000.0000.0000.000
58A285THR0-0.012-0.01828.3150.0000.0000.0000.0000.0000.000
59A286ARG10.8880.93325.8900.1910.1910.0000.0000.0000.000
60A287ARG10.9000.95928.9000.1200.1200.0000.0000.0000.000
61A288HIS0-0.037-0.01430.6000.0070.0070.0000.0000.0000.000
62A289ILE0-0.0300.00923.898-0.002-0.0020.0000.0000.0000.000
63A290GLY00.0570.03126.074-0.004-0.0040.0000.0000.0000.000
64A291ARG10.9850.96923.9390.1940.1940.0000.0000.0000.000
65A292GLY00.0050.01422.046-0.023-0.0230.0000.0000.0000.000
66A293VAL0-0.023-0.00617.1820.0210.0210.0000.0000.0000.000
67A294ARG10.9380.98115.9200.3820.3820.0000.0000.0000.000
68A295LEU0-0.040-0.02512.0890.0340.0340.0000.0000.0000.000
69A296TYR0-0.034-0.06611.846-0.063-0.0630.0000.0000.0000.000
70A297TYR00.0070.0142.947-0.6160.2640.061-0.284-0.657-0.001
71A298ILE00.018-0.0138.816-0.048-0.0480.0000.0000.0000.000
72A299GLY00.0280.0188.2950.0740.0740.0000.0000.0000.000
73A300GLY0-0.027-0.0076.2420.1340.1340.0000.0000.0000.000
74A301GLU-1-0.791-0.8877.189-0.070-0.0700.0000.0000.0000.000
75A302VAL00.0030.0058.407-0.123-0.1230.0000.0000.0000.000
76A303PHE0-0.016-0.01210.9110.0920.0920.0000.0000.0000.000
77A304ALA00.0120.00714.093-0.061-0.0610.0000.0000.0000.000
78A305GLU-1-0.856-0.90616.648-0.211-0.2110.0000.0000.0000.000
79A306CYS0-0.0440.00219.713-0.022-0.0220.0000.0000.0000.000
80A307LEU0-0.044-0.02020.5740.0190.0190.0000.0000.0000.000
81A308SER0-0.050-0.02023.8710.0180.0180.0000.0000.0000.000
82A309ASP-1-0.871-0.93726.218-0.139-0.1390.0000.0000.0000.000
83A310SER00.003-0.00228.4690.0150.0150.0000.0000.0000.000
84A311ALA0-0.047-0.03726.858-0.008-0.0080.0000.0000.0000.000
85A312ILE00.0180.01320.184-0.005-0.0050.0000.0000.0000.000
86A313PHE0-0.058-0.02823.3860.0170.0170.0000.0000.0000.000
87A314VAL00.0460.01617.298-0.018-0.0180.0000.0000.0000.000
88A315GLN0-0.0040.00919.3530.0150.0150.0000.0000.0000.000
89A316SER00.004-0.02715.090-0.014-0.0140.0000.0000.0000.000
90A317PRO00.0370.01716.0220.0180.0180.0000.0000.0000.000
91A318ASN00.0070.00113.5860.0010.0010.0000.0000.0000.000
92A319CYS0-0.0020.01116.1060.0130.0130.0000.0000.0000.000
93A320ASN0-0.013-0.01718.0440.0090.0090.0000.0000.0000.000
94A321GLN0-0.0040.04218.7360.0090.0090.0000.0000.0000.000
95A322ARG10.9761.01120.5690.0250.0250.0000.0000.0000.000
96A323TYR0-0.048-0.07221.8020.0020.0020.0000.0000.0000.000
97A324GLY00.0350.04325.6340.0010.0010.0000.0000.0000.000
98A325TRP0-0.082-0.05023.938-0.002-0.0020.0000.0000.0000.000
99A326HIS00.012-0.00723.390-0.006-0.0060.0000.0000.0000.000
100A327PRO0-0.038-0.00222.744-0.005-0.0050.0000.0000.0000.000
101A328ALA00.014-0.00622.728-0.007-0.0070.0000.0000.0000.000
102A329THR0-0.012-0.00323.687-0.003-0.0030.0000.0000.0000.000
103A330VAL0-0.003-0.00722.935-0.010-0.0100.0000.0000.0000.000
104A331CYS0-0.0150.00021.4410.0130.0130.0000.0000.0000.000
105A332LYS10.9690.99023.4020.0980.0980.0000.0000.0000.000
106A333ILE0-0.0070.00419.7780.0080.0080.0000.0000.0000.000
107A334PRO0-0.027-0.04224.314-0.007-0.0070.0000.0000.0000.000
108A335PRO00.0490.00126.140-0.008-0.0080.0000.0000.0000.000
109A336GLY00.0010.01125.8310.0110.0110.0000.0000.0000.000
110A337CYS0-0.0500.00924.8040.0070.0070.0000.0000.0000.000
111A338ASN0-0.001-0.01219.735-0.017-0.0170.0000.0000.0000.000
112A339LEU00.0270.00918.9490.0230.0230.0000.0000.0000.000
113A340LYS10.8390.92714.5000.0640.0640.0000.0000.0000.000
114A341ILE0-0.018-0.02112.9220.0260.0260.0000.0000.0000.000
115A342PHE00.0170.0228.714-0.008-0.0080.0000.0000.0000.000
116A343ASN00.0410.00812.1160.0050.0050.0000.0000.0000.000
117A344ASN00.0740.0158.365-0.003-0.0030.0000.0000.0000.000
118A345GLN0-0.025-0.00411.3220.0550.0550.0000.0000.0000.000
119A346GLU-1-0.875-0.95014.640-0.005-0.0050.0000.0000.0000.000
120A347PHE00.0240.0059.9010.0080.0080.0000.0000.0000.000
121A348ALA00.0230.00912.3180.0290.0290.0000.0000.0000.000
122A349ALA0-0.025-0.00213.6540.0170.0170.0000.0000.0000.000
123A350LEU00.010-0.00216.383-0.001-0.0010.0000.0000.0000.000
124A351LEU00.0140.02811.866-0.005-0.0050.0000.0000.0000.000
125A352ALA0-0.020-0.01515.8890.0080.0080.0000.0000.0000.000
126A353GLN0-0.052-0.02617.819-0.010-0.0100.0000.0000.0000.000
127A354SER00.026-0.01918.238-0.015-0.0150.0000.0000.0000.000
128A355VAL00.0090.00517.656-0.005-0.0050.0000.0000.0000.000
129A356ASN0-0.060-0.02520.1360.0020.0020.0000.0000.0000.000
130A357GLN0-0.044-0.02022.983-0.008-0.0080.0000.0000.0000.000
131A358GLY00.0220.02623.000-0.013-0.0130.0000.0000.0000.000
132A359PHE00.028-0.00418.0400.0030.0030.0000.0000.0000.000
133A360GLU-1-0.890-0.95519.5910.0520.0520.0000.0000.0000.000
134A361ALA0-0.0130.00320.609-0.012-0.0120.0000.0000.0000.000
135A362VAL00.0160.00215.464-0.006-0.0060.0000.0000.0000.000
136A363TYR00.0310.01915.589-0.010-0.0100.0000.0000.0000.000
137A364GLN00.0480.03016.433-0.024-0.0240.0000.0000.0000.000
138A365LEU0-0.016-0.01013.871-0.031-0.0310.0000.0000.0000.000
139A366THR0-0.024-0.01612.591-0.041-0.0410.0000.0000.0000.000
140A367ARG10.9520.97413.278-0.001-0.0010.0000.0000.0000.000
141A368MET0-0.082-0.03213.521-0.021-0.0210.0000.0000.0000.000
142A369CYS0-0.063-0.0099.301-0.002-0.0020.0000.0000.0000.000
143A370THR00.0160.02010.504-0.096-0.0960.0000.0000.0000.000
144A371ILE0-0.035-0.01212.0910.0490.0490.0000.0000.0000.000
145A372ARG10.8480.92814.8300.1620.1620.0000.0000.0000.000
146A373MET0-0.002-0.01216.9560.0080.0080.0000.0000.0000.000
147A374SER0-0.029-0.03219.624-0.009-0.0090.0000.0000.0000.000
148A375PHE00.0590.01619.9670.0050.0050.0000.0000.0000.000
149A376VAL00.0250.03225.0280.0120.0120.0000.0000.0000.000
150A377LYS10.9100.95128.2710.1280.1280.0000.0000.0000.000
151A378GLY00.0570.05626.840-0.012-0.0120.0000.0000.0000.000
152A379TRP0-0.032-0.02021.3310.0030.0030.0000.0000.0000.000
153A387THR00.0510.02227.3540.0000.0000.0000.0000.0000.000
154A388VAL00.0160.00322.1000.0010.0010.0000.0000.0000.000
155A389THR00.0170.00325.391-0.007-0.0070.0000.0000.0000.000
156A390SER0-0.058-0.02126.8840.0030.0030.0000.0000.0000.000
157A391THR0-0.0280.00625.1900.0050.0050.0000.0000.0000.000
158A392PRO00.003-0.02827.576-0.006-0.0060.0000.0000.0000.000
159A393CYS00.0030.01524.896-0.001-0.0010.0000.0000.0000.000
160A394TRP0-0.021-0.02219.635-0.003-0.0030.0000.0000.0000.000
161A395ILE00.0020.00416.157-0.007-0.0070.0000.0000.0000.000
162A396GLU-1-0.831-0.91215.060-0.236-0.2360.0000.0000.0000.000
163A397LEU0-0.013-0.01111.051-0.047-0.0470.0000.0000.0000.000
164A398HIS0-0.032-0.0109.6360.0610.0610.0000.0000.0000.000
165A399LEU00.012-0.0066.366-0.228-0.2280.0000.0000.0000.000
166A400ASN00.039-0.0083.0000.4220.8990.119-0.145-0.4520.000
167A401GLY0-0.0090.0132.487-1.617-0.1431.312-1.350-1.4360.001
168A402PRO00.004-0.0152.8341.9660.4660.1901.674-0.3640.000
169A403LEU00.0630.0306.4640.1610.1610.0000.0000.0000.000
170A404GLN00.0170.0092.302-4.099-2.6803.929-2.056-3.292-0.026
171A405TRP0-0.055-0.0155.9420.2420.2420.0000.0000.0000.000
172A406LEU00.0430.0007.901-0.018-0.0180.0000.0000.0000.000
173A407ASP-1-0.920-0.9439.0030.4900.4900.0000.0000.0000.000
174A408LYS10.9650.9969.206-1.024-1.0240.0000.0000.0000.000
175A409VAL0-0.042-0.02611.327-0.053-0.0530.0000.0000.0000.000
176A410LEU00.011-0.00813.806-0.046-0.0460.0000.0000.0000.000
177A411THR0-0.016-0.01413.429-0.045-0.0450.0000.0000.0000.000
178A412GLN0-0.070-0.04715.1710.0080.0080.0000.0000.0000.000
179A413MET0-0.102-0.02017.634-0.029-0.0290.0000.0000.0000.000
180A414GLY00.0180.02519.758-0.033-0.0330.0000.0000.0000.000
181A415SER0-0.037-0.03221.465-0.005-0.0050.0000.0000.0000.000
182A416PRO00.0150.00625.188-0.003-0.0030.0000.0000.0000.000
183A417SER0-0.0320.00227.312-0.012-0.0120.0000.0000.0000.000