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

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FMODB ID: LJ579

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970317.480823
FMO2-HF: Nuclear repulsion 1896441.688711
FMO2-HF: Total energy -73875.792112
FMO2-MP2: Total energy -74085.52555


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.
-8.044-1.1877.021-3.77-10.109-0.032
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 : 0.010 / q_NPA : -0.011
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].
3A230PHE00.0370.0103.257-0.5051.2850.005-0.797-0.9970.001
4A231TRP00.008-0.0012.179-2.846-0.9662.372-1.925-2.328-0.009
5A232CYS0-0.065-0.0303.1391.2210.765-0.0060.807-0.3450.000
6A233SER00.0370.0415.925-0.113-0.1130.0000.0000.0000.000
7A234ILE0-0.025-0.0268.8270.0870.0870.0000.0000.0000.000
8A235SER00.0040.01012.2850.0290.0290.0000.0000.0000.000
9A236TYR0-0.007-0.03715.7710.0040.0040.0000.0000.0000.000
10A237TYR00.0100.00717.5650.0160.0160.0000.0000.0000.000
11A238GLU-1-0.723-0.81622.577-0.157-0.1570.0000.0000.0000.000
12A239LEU00.0060.00326.2790.0110.0110.0000.0000.0000.000
13A240ASN00.0150.01226.442-0.009-0.0090.0000.0000.0000.000
14A241GLN00.0160.03426.367-0.003-0.0030.0000.0000.0000.000
15A242ARG10.8460.90616.7470.2470.2470.0000.0000.0000.000
16A243VAL0-0.062-0.03922.1500.0100.0100.0000.0000.0000.000
17A244GLY00.0490.02021.166-0.019-0.0190.0000.0000.0000.000
18A245GLU-1-0.890-0.93917.469-0.249-0.2490.0000.0000.0000.000
19A246THR0-0.072-0.03512.0920.0230.0230.0000.0000.0000.000
20A247PHE0-0.0060.01111.265-0.013-0.0130.0000.0000.0000.000
21A248HIS00.0470.0088.209-0.132-0.1320.0000.0000.0000.000
22A249ALA00.0240.0107.2120.0470.0470.0000.0000.0000.000
23A250SER0-0.0040.0006.201-0.499-0.4990.0000.0000.0000.000
24A251GLN00.0170.0257.705-0.218-0.2180.0000.0000.0000.000
25A252PRO00.0010.0097.861-0.083-0.0830.0000.0000.0000.000
26A253SER0-0.036-0.0318.7950.1610.1610.0000.0000.0000.000
27A254MET00.0090.02111.634-0.075-0.0750.0000.0000.0000.000
28A255THR0-0.032-0.03414.1730.0210.0210.0000.0000.0000.000
29A256VAL0-0.013-0.00115.399-0.033-0.0330.0000.0000.0000.000
30A257ASP-1-0.773-0.87017.954-0.272-0.2720.0000.0000.0000.000
31A258GLY00.0610.01321.681-0.002-0.0020.0000.0000.0000.000
32A259PHE0-0.0150.00223.9540.0200.0200.0000.0000.0000.000
33A260THR0-0.034-0.01725.138-0.009-0.0090.0000.0000.0000.000
34A261ASP-1-0.775-0.88024.084-0.195-0.1950.0000.0000.0000.000
35A262PRO0-0.024-0.00922.934-0.013-0.0130.0000.0000.0000.000
36A263SER00.0500.02017.690-0.017-0.0170.0000.0000.0000.000
37A264ASN00.0010.00017.163-0.018-0.0180.0000.0000.0000.000
38A265SER00.0470.01012.669-0.005-0.0050.0000.0000.0000.000
39A266GLU-1-0.839-0.91312.669-0.565-0.5650.0000.0000.0000.000
40A267ARG10.7210.86615.1600.3090.3090.0000.0000.0000.000
41A268PHE00.0310.00915.2300.0030.0030.0000.0000.0000.000
42A269CYS0-0.033-0.02717.2560.0150.0150.0000.0000.0000.000
43A270LEU00.0220.00218.9910.0160.0160.0000.0000.0000.000
44A271GLY00.0160.01922.3370.0200.0200.0000.0000.0000.000
45A272LEU0-0.024-0.02324.3920.0160.0160.0000.0000.0000.000
46A273LEU0-0.0350.01320.5700.0110.0110.0000.0000.0000.000
47A274SER00.0170.01825.2110.0060.0060.0000.0000.0000.000
48A275ASN00.008-0.02927.2310.0010.0010.0000.0000.0000.000
49A276VAL00.0140.01129.5240.0030.0030.0000.0000.0000.000
50A277ASN0-0.016-0.00331.7580.0030.0030.0000.0000.0000.000
51A278ARG10.7980.89627.4990.1440.1440.0000.0000.0000.000
52A279ASN00.0450.01932.4740.0050.0050.0000.0000.0000.000
53A280ALA00.0810.02234.180-0.006-0.0060.0000.0000.0000.000
54A281ALA00.0210.02334.373-0.003-0.0030.0000.0000.0000.000
55A282VAL0-0.0150.00928.747-0.005-0.0050.0000.0000.0000.000
56A283GLU-1-0.805-0.88830.662-0.123-0.1230.0000.0000.0000.000
57A284LEU0-0.0050.00032.362-0.005-0.0050.0000.0000.0000.000
58A285THR0-0.014-0.02028.0610.0000.0000.0000.0000.0000.000
59A286ARG10.8780.91425.3490.1650.1650.0000.0000.0000.000
60A287ARG10.7840.87128.5090.1050.1050.0000.0000.0000.000
61A288HIS0-0.020-0.00130.3530.0070.0070.0000.0000.0000.000
62A289ILE0-0.034-0.00223.625-0.004-0.0040.0000.0000.0000.000
63A290GLY00.0570.02826.011-0.007-0.0070.0000.0000.0000.000
64A291ARG10.9290.93624.7400.1840.1840.0000.0000.0000.000
65A292GLY0-0.0100.00622.196-0.020-0.0200.0000.0000.0000.000
66A293VAL0-0.049-0.02517.5830.0170.0170.0000.0000.0000.000
67A294ARG10.8240.91515.6460.4090.4090.0000.0000.0000.000
68A295LEU0-0.009-0.00612.2850.0270.0270.0000.0000.0000.000
69A296TYR0-0.031-0.04911.757-0.038-0.0380.0000.0000.0000.000
70A297TYR00.0000.0092.791-1.0780.1680.324-0.489-1.082-0.003
71A298ILE00.0360.0068.698-0.054-0.0540.0000.0000.0000.000
72A299GLY00.0230.0169.1930.0570.0570.0000.0000.0000.000
73A300GLY00.0010.0065.6910.1180.1180.0000.0000.0000.000
74A301GLU-1-0.840-0.9086.732-0.192-0.1920.0000.0000.0000.000
75A302VAL0-0.016-0.0108.079-0.118-0.1180.0000.0000.0000.000
76A303PHE0-0.022-0.01910.5890.0930.0930.0000.0000.0000.000
77A304ALA00.0060.00413.965-0.055-0.0550.0000.0000.0000.000
78A305GLU-1-0.823-0.89916.637-0.239-0.2390.0000.0000.0000.000
79A306CYS0-0.0280.00919.914-0.014-0.0140.0000.0000.0000.000
80A307LEU0-0.0120.00320.8600.0210.0210.0000.0000.0000.000
81A308SER0-0.0170.00924.0770.0180.0180.0000.0000.0000.000
82A309ASP-1-0.855-0.92126.678-0.139-0.1390.0000.0000.0000.000
83A310SER0-0.033-0.03228.9790.0120.0120.0000.0000.0000.000
84A311ALA0-0.059-0.03927.182-0.010-0.0100.0000.0000.0000.000
85A312ILE00.0410.02320.4710.0010.0010.0000.0000.0000.000
86A313PHE0-0.037-0.01623.2860.0170.0170.0000.0000.0000.000
87A314VAL00.0310.01417.516-0.018-0.0180.0000.0000.0000.000
88A315GLN0-0.009-0.00819.4010.0150.0150.0000.0000.0000.000
89A316SER00.0570.01314.896-0.013-0.0130.0000.0000.0000.000
90A317PRO00.0290.01116.0630.0140.0140.0000.0000.0000.000
91A318ASN00.0080.00013.805-0.016-0.0160.0000.0000.0000.000
92A319CYS0-0.0040.00216.3290.0070.0070.0000.0000.0000.000
93A320ASN0-0.041-0.02318.0200.0060.0060.0000.0000.0000.000
94A321GLN00.0070.03218.8240.0090.0090.0000.0000.0000.000
95A322ARG10.9690.99920.0400.0660.0660.0000.0000.0000.000
96A323TYR0-0.020-0.03521.3220.0010.0010.0000.0000.0000.000
97A324GLY00.0050.02125.2570.0040.0040.0000.0000.0000.000
98A325TRP0-0.044-0.02823.3120.0010.0010.0000.0000.0000.000
99A326HIS0-0.010-0.01523.094-0.003-0.0030.0000.0000.0000.000
100A327PRO0-0.029-0.00322.681-0.006-0.0060.0000.0000.0000.000
101A328ALA00.014-0.00623.207-0.005-0.0050.0000.0000.0000.000
102A329THR00.0090.02123.678-0.002-0.0020.0000.0000.0000.000
103A330VAL0-0.006-0.00223.056-0.011-0.0110.0000.0000.0000.000
104A331CYS00.0120.01821.4300.0100.0100.0000.0000.0000.000
105A332LYS10.9410.97223.0110.1020.1020.0000.0000.0000.000
106A333ILE0-0.008-0.00119.7600.0040.0040.0000.0000.0000.000
107A334PRO0-0.008-0.01724.379-0.004-0.0040.0000.0000.0000.000
108A335PRO00.0610.00326.221-0.009-0.0090.0000.0000.0000.000
109A336GLY0-0.0130.00725.9810.0100.0100.0000.0000.0000.000
110A337CYS0-0.053-0.00124.8930.0030.0030.0000.0000.0000.000
111A338ASN0-0.025-0.02819.560-0.015-0.0150.0000.0000.0000.000
112A339LEU00.0270.01218.5100.0220.0220.0000.0000.0000.000
113A340LYS10.8310.90214.3460.1410.1410.0000.0000.0000.000
114A341ILE0-0.0030.00212.9170.0250.0250.0000.0000.0000.000
115A342PHE00.0230.0188.270-0.005-0.0050.0000.0000.0000.000
116A343ASN00.0100.00412.074-0.012-0.0120.0000.0000.0000.000
117A344ASN00.0800.0118.6110.0480.0480.0000.0000.0000.000
118A345GLN0-0.0030.00811.0380.0470.0470.0000.0000.0000.000
119A346GLU-1-0.886-0.96014.344-0.044-0.0440.0000.0000.0000.000
120A347PHE00.0270.0099.8550.0110.0110.0000.0000.0000.000
121A348ALA00.0310.01512.3930.0350.0350.0000.0000.0000.000
122A349ALA0-0.0160.00113.6320.0270.0270.0000.0000.0000.000
123A350LEU00.005-0.00316.4130.0090.0090.0000.0000.0000.000
124A351LEU00.0140.02411.4960.0040.0040.0000.0000.0000.000
125A352ALA0-0.016-0.01615.6290.0170.0170.0000.0000.0000.000
126A353GLN0-0.0200.00017.5500.0090.0090.0000.0000.0000.000
127A354SER00.011-0.01717.781-0.006-0.0060.0000.0000.0000.000
128A355VAL00.002-0.00717.2150.0020.0020.0000.0000.0000.000
129A356ASN0-0.057-0.03419.7770.0080.0080.0000.0000.0000.000
130A357GLN0-0.051-0.02022.484-0.009-0.0090.0000.0000.0000.000
131A358GLY00.0330.02622.352-0.010-0.0100.0000.0000.0000.000
132A359PHE00.0300.00118.236-0.005-0.0050.0000.0000.0000.000
133A360GLU-1-0.809-0.91119.2490.0540.0540.0000.0000.0000.000
134A361ALA0-0.033-0.00820.456-0.017-0.0170.0000.0000.0000.000
135A362VAL00.0300.00014.823-0.013-0.0130.0000.0000.0000.000
136A363TYR00.0110.01415.417-0.011-0.0110.0000.0000.0000.000
137A364GLN00.0090.01816.120-0.047-0.0470.0000.0000.0000.000
138A365LEU00.0050.00713.510-0.031-0.0310.0000.0000.0000.000
139A366THR00.003-0.01612.275-0.047-0.0470.0000.0000.0000.000
140A367ARG10.8610.92613.353-0.016-0.0160.0000.0000.0000.000
141A368MET0-0.042-0.01713.677-0.022-0.0220.0000.0000.0000.000
142A369CYS0-0.077-0.0099.342-0.015-0.0150.0000.0000.0000.000
143A370THR0-0.0190.00210.501-0.096-0.0960.0000.0000.0000.000
144A371ILE0-0.027-0.01212.1090.0380.0380.0000.0000.0000.000
145A372ARG10.8320.90414.8670.1600.1600.0000.0000.0000.000
146A373MET0-0.019-0.00916.378-0.003-0.0030.0000.0000.0000.000
147A374SER0-0.022-0.02119.515-0.002-0.0020.0000.0000.0000.000
148A375PHE00.0800.03419.861-0.001-0.0010.0000.0000.0000.000
149A376VAL00.0080.02025.0150.0110.0110.0000.0000.0000.000
150A377LYS10.8530.92027.8300.1230.1230.0000.0000.0000.000
151A378GLY00.0530.05426.709-0.010-0.0100.0000.0000.0000.000
152A379TRP0-0.047-0.02521.3770.0070.0070.0000.0000.0000.000
153A387THR00.0670.03127.4120.0010.0010.0000.0000.0000.000
154A388VAL0-0.007-0.00621.7420.0010.0010.0000.0000.0000.000
155A389THR0-0.003-0.00625.088-0.003-0.0030.0000.0000.0000.000
156A390SER0-0.057-0.02626.7140.0040.0040.0000.0000.0000.000
157A391THR0-0.018-0.01025.3010.0040.0040.0000.0000.0000.000
158A392PRO0-0.023-0.03727.259-0.005-0.0050.0000.0000.0000.000
159A393CYS0-0.0200.00024.8230.0020.0020.0000.0000.0000.000
160A394TRP0-0.039-0.03619.492-0.006-0.0060.0000.0000.0000.000
161A395ILE00.0190.00415.813-0.003-0.0030.0000.0000.0000.000
162A396GLU-1-0.794-0.88314.593-0.205-0.2050.0000.0000.0000.000
163A397LEU00.0000.00010.912-0.035-0.0350.0000.0000.0000.000
164A398HIS00.0130.0009.2590.0300.0300.0000.0000.0000.000
165A399LEU00.0160.0036.571-0.211-0.2110.0000.0000.0000.000
166A400ASN00.0290.0032.9650.1550.6280.177-0.175-0.4740.000
167A401GLY00.0100.0122.353-1.553-0.3882.186-1.634-1.7170.002
168A402PRO00.000-0.0102.8142.7820.6790.2132.297-0.408-0.001
169A403LEU00.0470.0216.3340.1960.1960.0000.0000.0000.000
170A404GLN00.0310.0072.535-5.048-2.1861.750-1.854-2.758-0.022
171A405TRP0-0.059-0.0166.1640.2350.2350.0000.0000.0000.000
172A406LEU00.019-0.0087.557-0.007-0.0070.0000.0000.0000.000
173A407ASP-1-0.922-0.9429.1740.6460.6460.0000.0000.0000.000
174A408LYS10.9430.9709.143-0.894-0.8940.0000.0000.0000.000
175A409VAL0-0.035-0.02111.040-0.062-0.0620.0000.0000.0000.000
176A410LEU00.001-0.01413.495-0.043-0.0430.0000.0000.0000.000
177A411THR0-0.002-0.00513.694-0.046-0.0460.0000.0000.0000.000
178A412GLN0-0.042-0.02414.0570.0510.0510.0000.0000.0000.000
179A413MET0-0.073-0.00417.028-0.034-0.0340.0000.0000.0000.000
180A414GLY00.0170.01119.312-0.030-0.0300.0000.0000.0000.000
181A415SER0-0.013-0.00921.187-0.008-0.0080.0000.0000.0000.000
182A416PRO00.0300.02024.529-0.005-0.0050.0000.0000.0000.000
183A417SER0-0.088-0.03326.709-0.019-0.0190.0000.0000.0000.000