FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: G8Z91

Calculation Name: 1MJS-A-Xray547

Preferred Name: Mothers against decapentaplegic homolog 3

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MJS

Chain ID: A

ChEMBL ID: CHEMBL1293258

UniProt ID: P84022

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2125247.168592
FMO2-HF: Nuclear repulsion 2048468.916352
FMO2-HF: Total energy -76778.25224
FMO2-MP2: Total energy -76996.933136


3D Structure Molmil
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.
-83.435-73.489.561-7.137-12.381-0.081
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 : 1 / q_Mulliken : 0.842 / q_NPA : 0.908
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].
3A230PHE00.0690.0323.2735.5557.2790.007-0.768-0.964-0.001
4A231TRP0-0.009-0.0142.329-12.729-10.2642.765-2.275-2.955-0.021
5A232CYS0-0.030-0.0153.2592.5662.3830.0060.568-0.391-0.001
70A297TYR00.0020.0123.085-5.329-3.8200.157-0.590-1.076-0.004
173A400ASN00.024-0.0072.8733.1743.7360.372-0.343-0.591-0.001
174A401GLY0-0.041-0.0192.440-8.973-7.0201.659-1.482-2.130-0.009
175A402PRO00.0120.0052.8524.4083.0920.2891.401-0.375-0.002
177A404GLN00.015-0.0022.277-16.748-13.5074.306-3.648-3.899-0.042
6A233SER00.0310.0376.056-0.091-0.0910.0000.0000.0000.000
7A234ILE0-0.022-0.0238.8160.8410.8410.0000.0000.0000.000
8A235SER0-0.0080.00512.3620.7600.7600.0000.0000.0000.000
9A236TYR0-0.009-0.03915.7670.1280.1280.0000.0000.0000.000
10A237TYR00.0230.00917.6670.2770.2770.0000.0000.0000.000
11A238GLU-1-0.727-0.83022.476-10.928-10.9280.0000.0000.0000.000
12A239LEU00.0220.01226.1880.3210.3210.0000.0000.0000.000
13A240ASN0-0.0050.00326.154-0.319-0.3190.0000.0000.0000.000
14A241GLN00.0100.02625.977-0.432-0.4320.0000.0000.0000.000
15A242ARG10.8560.92416.55115.60515.6050.0000.0000.0000.000
16A243VAL0-0.068-0.04022.1740.4020.4020.0000.0000.0000.000
17A244GLY00.0400.01621.111-0.449-0.4490.0000.0000.0000.000
18A245GLU-1-0.900-0.94817.461-15.332-15.3320.0000.0000.0000.000
19A246THR0-0.060-0.02912.0580.5480.5480.0000.0000.0000.000
20A247PHE00.0080.02411.279-0.532-0.5320.0000.0000.0000.000
21A248HIS00.0330.0018.088-3.050-3.0500.0000.0000.0000.000
22A249ALA00.0330.0187.3081.1331.1330.0000.0000.0000.000
23A250SER0-0.003-0.0046.108-5.024-5.0240.0000.0000.0000.000
24A251GLN0-0.036-0.0107.549-3.768-3.7680.0000.0000.0000.000
25A252PRO00.0070.0097.764-0.803-0.8030.0000.0000.0000.000
26A253SER0-0.025-0.0228.7261.6031.6030.0000.0000.0000.000
27A254MET0-0.0320.00611.541-0.618-0.6180.0000.0000.0000.000
28A255THR0-0.020-0.02113.9380.1140.1140.0000.0000.0000.000
29A256VAL0-0.0080.00515.472-0.639-0.6390.0000.0000.0000.000
30A257ASP-1-0.783-0.88417.990-13.411-13.4110.0000.0000.0000.000
31A258GLY00.0790.01821.722-0.098-0.0980.0000.0000.0000.000
32A259PHE0-0.0160.00524.1240.6000.6000.0000.0000.0000.000
33A260THR0-0.045-0.02825.077-0.269-0.2690.0000.0000.0000.000
34A261ASP-1-0.828-0.90823.848-11.541-11.5410.0000.0000.0000.000
35A262PRO0-0.037-0.01522.854-0.338-0.3380.0000.0000.0000.000
36A263SER00.0650.02317.600-0.309-0.3090.0000.0000.0000.000
37A264ASN0-0.005-0.00417.143-0.441-0.4410.0000.0000.0000.000
38A265SER00.0570.01712.523-0.033-0.0330.0000.0000.0000.000
39A266GLU-1-0.895-0.94212.517-20.417-20.4170.0000.0000.0000.000
40A267ARG10.7790.89814.97814.22114.2210.0000.0000.0000.000
41A268PHE00.0310.00815.2140.0580.0580.0000.0000.0000.000
42A269CYS0-0.042-0.02917.2240.2470.2470.0000.0000.0000.000
43A270LEU00.0220.00319.1130.2420.2420.0000.0000.0000.000
44A271GLY00.0170.01922.5070.4690.4690.0000.0000.0000.000
45A272LEU0-0.037-0.03224.4720.4790.4790.0000.0000.0000.000
46A273LEU0-0.0300.01420.6340.2320.2320.0000.0000.0000.000
47A274SER00.0070.01025.2800.2240.2240.0000.0000.0000.000
48A275ASN00.021-0.02327.265-0.131-0.1310.0000.0000.0000.000
49A276VAL00.0080.00929.5390.2080.2080.0000.0000.0000.000
50A277ASN0-0.024-0.00831.8080.1610.1610.0000.0000.0000.000
51A278ARG10.7890.89827.51010.39110.3910.0000.0000.0000.000
52A279ASN00.0610.02332.4900.2880.2880.0000.0000.0000.000
53A280ALA00.0970.03034.050-0.218-0.2180.0000.0000.0000.000
54A281ALA00.0160.01934.544-0.057-0.0570.0000.0000.0000.000
55A282VAL00.0040.01328.708-0.201-0.2010.0000.0000.0000.000
56A283GLU-1-0.904-0.97030.466-9.095-9.0950.0000.0000.0000.000
57A284LEU0-0.048-0.01232.398-0.079-0.0790.0000.0000.0000.000
58A285THR00.019-0.00427.896-0.050-0.0500.0000.0000.0000.000
59A286ARG10.8560.90425.39810.99510.9950.0000.0000.0000.000
60A287ARG10.8500.93028.5888.7108.7100.0000.0000.0000.000
61A288HIS0-0.024-0.00430.3990.2750.2750.0000.0000.0000.000
62A289ILE0-0.0210.01123.625-0.200-0.2000.0000.0000.0000.000
63A290GLY00.0500.02626.037-0.201-0.2010.0000.0000.0000.000
64A291ARG10.9200.93124.27111.56611.5660.0000.0000.0000.000
65A292GLY0-0.0090.00922.237-0.549-0.5490.0000.0000.0000.000
66A293VAL0-0.016-0.00917.2150.3240.3240.0000.0000.0000.000
67A294ARG10.8940.95615.58316.90016.9000.0000.0000.0000.000
68A295LEU00.0030.00312.0540.0510.0510.0000.0000.0000.000
69A296TYR0-0.035-0.05211.597-0.370-0.3700.0000.0000.0000.000
71A298ILE00.027-0.0018.496-0.466-0.4660.0000.0000.0000.000
72A299GLY00.0290.0218.8380.7830.7830.0000.0000.0000.000
73A300GLY0-0.036-0.0185.6760.2100.2100.0000.0000.0000.000
74A301GLU-1-0.822-0.8966.700-20.066-20.0660.0000.0000.0000.000
75A302VAL0-0.031-0.0247.855-2.091-2.0910.0000.0000.0000.000
76A303PHE00.000-0.00410.3771.7231.7230.0000.0000.0000.000
77A304ALA00.0030.00213.667-0.931-0.9310.0000.0000.0000.000
78A305GLU-1-0.827-0.90016.278-13.970-13.9700.0000.0000.0000.000
79A306CYS0-0.0400.00919.649-0.205-0.2050.0000.0000.0000.000
80A307LEU0-0.028-0.01320.5690.5630.5630.0000.0000.0000.000
81A308SER0-0.0170.00623.8280.6180.6180.0000.0000.0000.000
82A309ASP-1-0.860-0.93426.472-9.873-9.8730.0000.0000.0000.000
83A310SER0-0.038-0.02428.8210.3780.3780.0000.0000.0000.000
84A311ALA0-0.044-0.03526.748-0.331-0.3310.0000.0000.0000.000
85A312ILE00.0060.00119.9440.0660.0660.0000.0000.0000.000
86A313PHE0-0.021-0.00622.8890.4510.4510.0000.0000.0000.000
87A314VAL00.0200.00816.915-0.569-0.5690.0000.0000.0000.000
88A315GLN00.0600.02417.9750.3230.3230.0000.0000.0000.000
89A316SER0-0.043-0.02714.451-0.949-0.9490.0000.0000.0000.000
90A317PRO00.0210.00815.6880.2290.2290.0000.0000.0000.000
91A318ASN0-0.010-0.01112.9130.8260.8260.0000.0000.0000.000
92A319CYS-1-0.843-0.89415.647-15.283-15.2830.0000.0000.0000.000
93A320ASN00.0450.00217.6680.3980.3980.0000.0000.0000.000
94A321GLN0-0.0050.00918.6961.1591.1590.0000.0000.0000.000
95A322ARG10.7180.85216.12516.33516.3350.0000.0000.0000.000
96A323TYR0-0.046-0.02322.1400.5080.5080.0000.0000.0000.000
97A324GLY0-0.038-0.01023.5960.4440.4440.0000.0000.0000.000
98A325TRP0-0.009-0.00923.7760.1970.1970.0000.0000.0000.000
99A326HIS00.0790.03918.7510.3610.3610.0000.0000.0000.000
100A327PRO0-0.056-0.04920.559-0.456-0.4560.0000.0000.0000.000
101A328ALA0-0.025-0.02222.6990.3060.3060.0000.0000.0000.000
102A329THR00.039-0.01224.8100.3890.3890.0000.0000.0000.000
103A330VAL0-0.111-0.05724.299-0.208-0.2080.0000.0000.0000.000
104A331CYS-1-0.857-0.90121.579-12.744-12.7440.0000.0000.0000.000
105A332LYS10.9090.95822.7219.7029.7020.0000.0000.0000.000
106A333ILE0-0.0100.00019.3860.1640.1640.0000.0000.0000.000
107A334PRO0-0.029-0.02924.0160.0960.0960.0000.0000.0000.000
108A335PRO00.040-0.00725.873-0.363-0.3630.0000.0000.0000.000
109A336GLY0-0.023-0.00125.6860.3000.3000.0000.0000.0000.000
110A337CYS0-0.0480.00024.5960.0280.0280.0000.0000.0000.000
111A338ASN0-0.041-0.03519.294-0.631-0.6310.0000.0000.0000.000
112A339LEU00.0800.04218.2750.4710.4710.0000.0000.0000.000
113A340LYS10.7920.88113.99117.69317.6930.0000.0000.0000.000
114A341ILE00.0720.03612.6760.1180.1180.0000.0000.0000.000
115A342PHE0-0.0220.0068.649-0.444-0.4440.0000.0000.0000.000
116A343ASN00.0470.01811.801-1.412-1.4120.0000.0000.0000.000
117A344ASN00.0450.0057.965-0.062-0.0620.0000.0000.0000.000
118A345GLN0-0.015-0.00311.1010.4990.4990.0000.0000.0000.000
119A346GLU-1-0.852-0.92614.517-16.334-16.3340.0000.0000.0000.000
120A347PHE00.0340.0069.6040.2320.2320.0000.0000.0000.000
121A348ALA00.0120.00412.6210.3060.3060.0000.0000.0000.000
122A349ALA0-0.020-0.00313.8240.6820.6820.0000.0000.0000.000
123A350LEU00.0280.00916.3090.7080.7080.0000.0000.0000.000
124A351LEU00.0130.02111.5350.6170.6170.0000.0000.0000.000
125A352ALA0-0.034-0.02315.5840.5060.5060.0000.0000.0000.000
126A353GLN0-0.029-0.00217.7440.8800.8800.0000.0000.0000.000
127A354SER00.014-0.02017.6570.6360.6360.0000.0000.0000.000
128A355VAL00.004-0.00717.1230.2960.2960.0000.0000.0000.000
129A356ASN0-0.057-0.03219.7450.4340.4340.0000.0000.0000.000
130A357GLN0-0.048-0.02022.4950.2790.2790.0000.0000.0000.000
131A358GLY00.0270.02322.5180.3590.3590.0000.0000.0000.000
132A359PHE00.017-0.00918.221-0.467-0.4670.0000.0000.0000.000
133A360GLU-1-0.868-0.94119.287-14.180-14.1800.0000.0000.0000.000
134A361ALA0-0.0220.00120.214-0.375-0.3750.0000.0000.0000.000
135A362VAL00.011-0.00314.753-0.646-0.6460.0000.0000.0000.000
136A363TYR00.0290.02015.526-1.154-1.1540.0000.0000.0000.000
137A364GLN00.0270.01916.176-1.042-1.0420.0000.0000.0000.000
138A365LEU0-0.0060.00613.581-0.072-0.0720.0000.0000.0000.000
139A366THR0-0.009-0.02312.370-1.201-1.2010.0000.0000.0000.000
140A367ARG10.9110.95213.36013.68513.6850.0000.0000.0000.000
141A368MET0-0.0160.00313.3320.3820.3820.0000.0000.0000.000
142A369CYS0-0.085-0.0219.165-1.497-1.4970.0000.0000.0000.000
143A370THR0-0.024-0.00410.204-1.552-1.5520.0000.0000.0000.000
144A371ILE00.0040.00611.6860.8920.8920.0000.0000.0000.000
145A372ARG10.7700.88014.40814.59014.5900.0000.0000.0000.000
146A373MET00.0100.00116.421-0.483-0.4830.0000.0000.0000.000
147A374SER0-0.018-0.03019.191-0.073-0.0730.0000.0000.0000.000
148A375PHE00.0430.01919.9540.0150.0150.0000.0000.0000.000
149A376VAL00.0000.01224.8960.3360.3360.0000.0000.0000.000
150A377LYS10.8690.93227.4139.5499.5490.0000.0000.0000.000
151A378GLY00.0930.09225.581-0.311-0.3110.0000.0000.0000.000
152A379TRP0-0.047-0.03726.4050.1540.1540.0000.0000.0000.000
153A380GLY00.0120.00528.4550.3850.3850.0000.0000.0000.000
154A381ALA0-0.034-0.03626.2480.0060.0060.0000.0000.0000.000
155A382GLU-1-0.655-0.84220.997-12.654-12.6540.0000.0000.0000.000
156A383TYR-1-0.852-0.87920.891-13.331-13.3310.0000.0000.0000.000
157A384ARG10.8160.91819.27514.27714.2770.0000.0000.0000.000
158A385ARG00.0070.01124.0870.4480.4480.0000.0000.0000.000
159A386GLN0-0.0430.00225.9300.5400.5400.0000.0000.0000.000
160A387THR0-0.062-0.04325.096-0.493-0.4930.0000.0000.0000.000
161A388VAL00.0630.01821.5930.2280.2280.0000.0000.0000.000
162A389THR0-0.036-0.02924.9480.1220.1220.0000.0000.0000.000
163A390SER-1-0.822-0.88527.373-9.984-9.9840.0000.0000.0000.000
164A391THR0-0.092-0.04425.3400.3930.3930.0000.0000.0000.000
165A392PRO0-0.027-0.02827.537-0.200-0.2000.0000.0000.0000.000
166A393CYS0-0.020-0.01024.7710.0950.0950.0000.0000.0000.000
167A394TRP0-0.033-0.03419.535-0.355-0.3550.0000.0000.0000.000
168A395ILE00.0180.00215.448-0.073-0.0730.0000.0000.0000.000
169A396GLU-1-0.805-0.88014.726-16.574-16.5740.0000.0000.0000.000
170A397LEU0-0.010-0.00510.919-0.523-0.5230.0000.0000.0000.000
171A398HIS0-0.022-0.0159.394-0.139-0.1390.0000.0000.0000.000
172A399LEU00.0160.0026.300-3.305-3.3050.0000.0000.0000.000
176A403LEU00.0640.0316.1632.4182.4180.0000.0000.0000.000
178A405TRP0-0.062-0.0186.0292.6192.6190.0000.0000.0000.000
179A406LEU00.0450.0047.4972.7012.7010.0000.0000.0000.000
180A407ASP-1-0.918-0.9419.128-24.360-24.3600.0000.0000.0000.000
181A408LYS10.9350.9729.37727.06627.0660.0000.0000.0000.000
182A409VAL0-0.035-0.02011.1111.8421.8420.0000.0000.0000.000
183A410LEU00.012-0.00813.5131.4471.4470.0000.0000.0000.000
184A411THR0-0.011-0.00913.7991.5291.5290.0000.0000.0000.000
185A412GLN0-0.063-0.03914.347-0.267-0.2670.0000.0000.0000.000
186A413MET0-0.068-0.00117.1490.6390.6390.0000.0000.0000.000
187A414GLY00.0110.01319.4750.6330.6330.0000.0000.0000.000
188A415SER0-0.040-0.02821.3200.3540.3540.0000.0000.0000.000
189A416PRO0-0.045-0.03224.8900.1470.1470.0000.0000.0000.000
190A417SER-1-0.956-0.94826.913-9.805-9.8050.0000.0000.0000.000