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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: 3Q27L

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1969242.223637
FMO2-HF: Nuclear repulsion 1895366.675294
FMO2-HF: Total energy -73875.548343
FMO2-MP2: Total energy -74085.299888


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.
-7.083-0.3914.315-2.677-8.331-0.022
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 : 0.007 / q_NPA : -0.013
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].
3A230PHE00.0510.0163.171-0.6700.8840.022-0.627-0.9500.002
4A231TRP00.016-0.0092.722-3.138-0.7730.791-1.233-1.923-0.009
5A232CYS0-0.034-0.0173.5470.7200.7750.0100.193-0.2580.000
6A233SER00.0350.0416.570-0.105-0.1050.0000.0000.0000.000
7A234ILE0-0.033-0.0349.3270.1090.1090.0000.0000.0000.000
8A235SER00.0130.02112.8480.0250.0250.0000.0000.0000.000
9A236TYR0-0.009-0.03616.0760.0150.0150.0000.0000.0000.000
10A237TYR00.014-0.00117.8360.0130.0130.0000.0000.0000.000
11A238GLU-1-0.708-0.81622.651-0.185-0.1850.0000.0000.0000.000
12A239LEU00.0080.00826.3440.0110.0110.0000.0000.0000.000
13A240ASN00.0010.00526.225-0.012-0.0120.0000.0000.0000.000
14A241GLN00.0130.01326.433-0.005-0.0050.0000.0000.0000.000
15A242ARG10.8500.92716.8500.3190.3190.0000.0000.0000.000
16A243VAL0-0.043-0.03222.1980.0130.0130.0000.0000.0000.000
17A244GLY00.0430.02121.278-0.022-0.0220.0000.0000.0000.000
18A245GLU-1-0.907-0.94817.516-0.316-0.3160.0000.0000.0000.000
19A246THR0-0.071-0.03612.1430.0220.0220.0000.0000.0000.000
20A247PHE0-0.0130.00911.856-0.017-0.0170.0000.0000.0000.000
21A248HIS00.0450.0168.602-0.177-0.1770.0000.0000.0000.000
22A249ALA00.0200.0077.9450.0690.0690.0000.0000.0000.000
23A250SER00.008-0.0066.667-0.516-0.5160.0000.0000.0000.000
24A251GLN00.0300.0287.973-0.118-0.1180.0000.0000.0000.000
25A252PRO00.0050.0137.899-0.088-0.0880.0000.0000.0000.000
26A253SER00.0000.0038.8810.1410.1410.0000.0000.0000.000
27A254MET0-0.0050.01711.280-0.061-0.0610.0000.0000.0000.000
28A255THR00.0070.00713.9330.0280.0280.0000.0000.0000.000
29A256VAL0-0.0140.00815.777-0.031-0.0310.0000.0000.0000.000
30A257ASP-1-0.803-0.89718.273-0.285-0.2850.0000.0000.0000.000
31A258GLY00.0310.00122.018-0.006-0.0060.0000.0000.0000.000
32A259PHE0-0.018-0.00624.3050.0230.0230.0000.0000.0000.000
33A260THR0-0.035-0.02725.354-0.012-0.0120.0000.0000.0000.000
34A261ASP-1-0.796-0.87624.350-0.219-0.2190.0000.0000.0000.000
35A262PRO0-0.007-0.00223.048-0.014-0.0140.0000.0000.0000.000
36A263SER00.0500.01917.826-0.014-0.0140.0000.0000.0000.000
37A264ASN00.010-0.00117.626-0.015-0.0150.0000.0000.0000.000
38A265SER00.0390.00512.948-0.008-0.0080.0000.0000.0000.000
39A266GLU-1-0.953-0.97712.928-0.595-0.5950.0000.0000.0000.000
40A267ARG10.7460.87615.1860.3470.3470.0000.0000.0000.000
41A268PHE00.0370.01715.554-0.002-0.0020.0000.0000.0000.000
42A269CYS0-0.056-0.04117.5710.0170.0170.0000.0000.0000.000
43A270LEU00.004-0.01419.5570.0090.0090.0000.0000.0000.000
44A271GLY00.0160.01322.9730.0210.0210.0000.0000.0000.000
45A272LEU0-0.014-0.01224.6760.0160.0160.0000.0000.0000.000
46A273LEU0-0.0340.00821.0510.0130.0130.0000.0000.0000.000
47A274SER00.0200.02025.6470.0090.0090.0000.0000.0000.000
48A275ASN0-0.005-0.03527.6980.0000.0000.0000.0000.0000.000
49A276VAL00.0400.02129.8840.0050.0050.0000.0000.0000.000
50A277ASN0-0.029-0.00632.0890.0040.0040.0000.0000.0000.000
51A278ARG10.8060.90127.8090.1710.1710.0000.0000.0000.000
52A279ASN00.0400.02532.9110.0050.0050.0000.0000.0000.000
53A280ALA00.1040.02634.594-0.006-0.0060.0000.0000.0000.000
54A281ALA00.0050.00934.713-0.003-0.0030.0000.0000.0000.000
55A282VAL0-0.003-0.00128.992-0.005-0.0050.0000.0000.0000.000
56A283GLU-1-0.848-0.91630.851-0.136-0.1360.0000.0000.0000.000
57A284LEU0-0.044-0.01232.862-0.003-0.0030.0000.0000.0000.000
58A285THR0-0.025-0.02928.5410.0000.0000.0000.0000.0000.000
59A286ARG10.8700.92025.7510.1950.1950.0000.0000.0000.000
60A287ARG10.8230.90928.9750.1220.1220.0000.0000.0000.000
61A288HIS0-0.034-0.01730.6580.0070.0070.0000.0000.0000.000
62A289ILE0-0.0280.01323.963-0.002-0.0020.0000.0000.0000.000
63A290GLY00.0560.03326.127-0.005-0.0050.0000.0000.0000.000
64A291ARG10.9480.94724.0540.1900.1900.0000.0000.0000.000
65A292GLY00.0060.01622.101-0.023-0.0230.0000.0000.0000.000
66A293VAL0-0.020-0.01017.3410.0210.0210.0000.0000.0000.000
67A294ARG10.9320.97515.7740.3990.3990.0000.0000.0000.000
68A295LEU0-0.043-0.02712.1200.0310.0310.0000.0000.0000.000
69A296TYR0-0.036-0.06111.827-0.061-0.0610.0000.0000.0000.000
70A297TYR00.0070.0132.793-0.5860.3280.078-0.278-0.714-0.001
71A298ILE00.018-0.0128.778-0.030-0.0300.0000.0000.0000.000
72A299GLY00.0360.0258.4500.0690.0690.0000.0000.0000.000
73A300GLY0-0.023-0.0106.2250.1280.1280.0000.0000.0000.000
74A301GLU-1-0.822-0.8987.172-0.112-0.1120.0000.0000.0000.000
75A302VAL00.0030.0038.351-0.121-0.1210.0000.0000.0000.000
76A303PHE0-0.009-0.01110.9040.0950.0950.0000.0000.0000.000
77A304ALA00.0110.00814.079-0.062-0.0620.0000.0000.0000.000
78A305GLU-1-0.832-0.90316.641-0.225-0.2250.0000.0000.0000.000
79A306CYS0-0.0440.00019.710-0.022-0.0220.0000.0000.0000.000
80A307LEU0-0.039-0.01420.6570.0210.0210.0000.0000.0000.000
81A308SER0-0.036-0.01423.8950.0190.0190.0000.0000.0000.000
82A309ASP-1-0.869-0.93726.253-0.143-0.1430.0000.0000.0000.000
83A310SER0-0.006-0.00628.5090.0150.0150.0000.0000.0000.000
84A311ALA0-0.043-0.03526.874-0.009-0.0090.0000.0000.0000.000
85A312ILE00.0180.00920.213-0.006-0.0060.0000.0000.0000.000
86A313PHE0-0.057-0.02523.3690.0170.0170.0000.0000.0000.000
87A314VAL00.0460.01617.337-0.019-0.0190.0000.0000.0000.000
88A315GLN0-0.003-0.00219.3260.0160.0160.0000.0000.0000.000
89A316SER00.026-0.01015.010-0.015-0.0150.0000.0000.0000.000
90A317PRO00.0410.02115.9850.0190.0190.0000.0000.0000.000
91A318ASN00.0160.01514.075-0.006-0.0060.0000.0000.0000.000
92A319CYS00.0170.01116.0520.0150.0150.0000.0000.0000.000
93A320ASN0-0.042-0.02918.0010.0100.0100.0000.0000.0000.000
94A321GLN0-0.0100.03818.5940.0090.0090.0000.0000.0000.000
95A322ARG10.9720.99920.3200.0370.0370.0000.0000.0000.000
96A323TYR0-0.042-0.05521.4470.0030.0030.0000.0000.0000.000
97A324GLY00.0170.03725.6370.0020.0020.0000.0000.0000.000
98A325TRP0-0.054-0.04223.656-0.002-0.0020.0000.0000.0000.000
99A326HIS0-0.005-0.01423.205-0.005-0.0050.0000.0000.0000.000
100A327PRO0-0.0320.00022.698-0.007-0.0070.0000.0000.0000.000
101A328ALA00.016-0.00422.756-0.007-0.0070.0000.0000.0000.000
102A329THR00.0100.01523.743-0.003-0.0030.0000.0000.0000.000
103A330VAL0-0.001-0.00322.895-0.011-0.0110.0000.0000.0000.000
104A331CYS0-0.0040.01121.6660.0130.0130.0000.0000.0000.000
105A332LYS10.9580.97923.3810.1030.1030.0000.0000.0000.000
106A333ILE00.0010.00519.7130.0080.0080.0000.0000.0000.000
107A334PRO0-0.015-0.02524.306-0.007-0.0070.0000.0000.0000.000
108A335PRO00.0450.00126.137-0.008-0.0080.0000.0000.0000.000
109A336GLY0-0.0050.00825.8340.0120.0120.0000.0000.0000.000
110A337CYS0-0.0560.00124.7840.0070.0070.0000.0000.0000.000
111A338ASN0-0.010-0.02119.640-0.016-0.0160.0000.0000.0000.000
112A339LEU00.0220.01118.8940.0240.0240.0000.0000.0000.000
113A340LYS10.8180.90614.2940.0780.0780.0000.0000.0000.000
114A341ILE0-0.013-0.01612.8910.0260.0260.0000.0000.0000.000
115A342PHE00.0270.0188.758-0.012-0.0120.0000.0000.0000.000
116A343ASN00.0260.00512.0870.0070.0070.0000.0000.0000.000
117A344ASN00.0830.0168.4200.0110.0110.0000.0000.0000.000
118A345GLN0-0.0150.00211.2760.0510.0510.0000.0000.0000.000
119A346GLU-1-0.881-0.96114.595-0.022-0.0220.0000.0000.0000.000
120A347PHE00.0300.0099.7850.0080.0080.0000.0000.0000.000
121A348ALA00.0180.01012.4590.0280.0280.0000.0000.0000.000
122A349ALA0-0.018-0.00213.7270.0190.0190.0000.0000.0000.000
123A350LEU00.004-0.00416.3710.0010.0010.0000.0000.0000.000
124A351LEU00.0110.02511.830-0.003-0.0030.0000.0000.0000.000
125A352ALA0-0.020-0.01415.8530.0090.0090.0000.0000.0000.000
126A353GLN0-0.029-0.00917.8020.0000.0000.0000.0000.0000.000
127A354SER00.031-0.01218.179-0.013-0.0130.0000.0000.0000.000
128A355VAL0-0.006-0.00517.391-0.004-0.0040.0000.0000.0000.000
129A356ASN0-0.062-0.03020.0240.0040.0040.0000.0000.0000.000
130A357GLN0-0.050-0.02522.880-0.008-0.0080.0000.0000.0000.000
131A358GLY00.0270.03022.861-0.012-0.0120.0000.0000.0000.000
132A359PHE00.026-0.00418.113-0.001-0.0010.0000.0000.0000.000
133A360GLU-1-0.857-0.94019.6040.0280.0280.0000.0000.0000.000
134A361ALA0-0.023-0.00920.613-0.014-0.0140.0000.0000.0000.000
135A362VAL00.0260.00815.438-0.008-0.0080.0000.0000.0000.000
136A363TYR00.0380.02415.365-0.015-0.0150.0000.0000.0000.000
137A364GLN00.0120.03016.421-0.050-0.0500.0000.0000.0000.000
138A365LEU00.0230.00913.826-0.030-0.0300.0000.0000.0000.000
139A366THR0-0.014-0.02612.433-0.043-0.0430.0000.0000.0000.000
140A367ARG10.9060.95513.2150.0060.0060.0000.0000.0000.000
141A368MET0-0.094-0.03313.459-0.019-0.0190.0000.0000.0000.000
142A369CYS0-0.067-0.0109.181-0.007-0.0070.0000.0000.0000.000
143A370THR00.0030.01410.457-0.095-0.0950.0000.0000.0000.000
144A371ILE0-0.031-0.01012.0650.0510.0510.0000.0000.0000.000
145A372ARG10.8330.91314.7960.1830.1830.0000.0000.0000.000
146A373MET0-0.011-0.01116.3840.0040.0040.0000.0000.0000.000
147A374SER0-0.007-0.01719.610-0.009-0.0090.0000.0000.0000.000
148A375PHE00.0510.01320.0040.0050.0050.0000.0000.0000.000
149A376VAL00.0210.02825.0740.0130.0130.0000.0000.0000.000
150A377LYS10.8980.95028.2690.1350.1350.0000.0000.0000.000
151A378GLY00.0530.04726.822-0.012-0.0120.0000.0000.0000.000
152A379TRP0-0.049-0.02521.2260.0060.0060.0000.0000.0000.000
153A387THR00.0570.02427.334-0.001-0.0010.0000.0000.0000.000
154A388VAL00.0170.00222.0620.0020.0020.0000.0000.0000.000
155A389THR00.001-0.00525.362-0.006-0.0060.0000.0000.0000.000
156A390SER0-0.061-0.01726.8790.0040.0040.0000.0000.0000.000
157A391THR0-0.0130.00725.2500.0060.0060.0000.0000.0000.000
158A392PRO0-0.001-0.03027.551-0.006-0.0060.0000.0000.0000.000
159A393CYS0-0.0090.01124.9140.0010.0010.0000.0000.0000.000
160A394TRP0-0.014-0.02419.687-0.004-0.0040.0000.0000.0000.000
161A395ILE00.0010.00316.167-0.006-0.0060.0000.0000.0000.000
162A396GLU-1-0.800-0.88314.976-0.259-0.2590.0000.0000.0000.000
163A397LEU0-0.014-0.00811.084-0.045-0.0450.0000.0000.0000.000
164A398HIS0-0.028-0.0259.4870.0510.0510.0000.0000.0000.000
165A399LEU00.009-0.0036.347-0.226-0.2260.0000.0000.0000.000
166A400ASN00.037-0.0063.0820.2580.7300.098-0.134-0.4360.000
167A401GLY0-0.0060.0152.418-1.835-0.3621.676-1.589-1.5600.001
168A402PRO00.005-0.0152.7592.5120.5160.2272.161-0.3930.000
169A403LEU00.0610.0306.3810.1750.1750.0000.0000.0000.000
170A404GLN00.0140.0092.506-3.091-1.2361.413-1.170-2.097-0.015
171A405TRP0-0.056-0.0155.9530.2580.2580.0000.0000.0000.000
172A406LEU00.035-0.0047.7220.0030.0030.0000.0000.0000.000
173A407ASP-1-0.929-0.9479.0040.4190.4190.0000.0000.0000.000
174A408LYS10.9330.9679.329-0.880-0.8800.0000.0000.0000.000
175A409VAL0-0.040-0.02811.259-0.044-0.0440.0000.0000.0000.000
176A410LEU00.009-0.00813.742-0.039-0.0390.0000.0000.0000.000
177A411THR0-0.004-0.00213.552-0.040-0.0400.0000.0000.0000.000
178A412GLN0-0.046-0.02714.3290.0580.0580.0000.0000.0000.000
179A413MET0-0.090-0.01417.412-0.025-0.0250.0000.0000.0000.000
180A414GLY00.0200.02619.786-0.031-0.0310.0000.0000.0000.000
181A415SER0-0.015-0.01921.493-0.004-0.0040.0000.0000.0000.000
182A416PRO00.0320.01625.217-0.002-0.0020.0000.0000.0000.000
183A417SER0-0.073-0.02427.247-0.017-0.0170.0000.0000.0000.000