FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: L7779

Calculation Name: 3WJA-A-Xray372

Preferred Name: NADP-dependent malic enzyme

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3WJA

Chain ID: A

ChEMBL ID: CHEMBL3495

UniProt ID: P48163

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 562
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12035045.924017
FMO2-HF: Nuclear repulsion 11813990.050779
FMO2-HF: Total energy -221055.873238
FMO2-MP2: Total energy -221700.555609


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:18:ARG)


Summations of interaction energy for fragment #1(A:18:ARG)
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.
-121.714-115.1597.661-5.671-8.543-0.014
Interaction energy analysis for fragmet #1(A:18:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.982 / q_NPA : 0.974
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].
3A20HIS00.0370.0353.613-1.7390.275-0.023-1.095-0.8960.001
4A21THR00.015-0.0066.2282.1002.1000.0000.0000.0000.000
5A22HIS00.0180.0019.7230.7000.7000.0000.0000.0000.000
6A23GLN00.0310.02712.9160.4850.4850.0000.0000.0000.000
7A24ARG10.9210.95711.07418.69518.6950.0000.0000.0000.000
8A25GLY00.0390.02616.0700.7240.7240.0000.0000.0000.000
9A26TYR00.0450.00718.330-0.582-0.5820.0000.0000.0000.000
10A27LEU00.0510.03019.395-0.273-0.2730.0000.0000.0000.000
11A28LEU0-0.0220.01512.182-0.219-0.2190.0000.0000.0000.000
12A29THR0-0.059-0.06015.355-0.357-0.3570.0000.0000.0000.000
13A30ARG10.9070.95717.35912.88212.8820.0000.0000.0000.000
14A31ASN00.0240.02813.5410.0400.0400.0000.0000.0000.000
15A32PRO00.0850.04114.254-1.248-1.2480.0000.0000.0000.000
16A33HIS10.8460.90610.78118.10718.1070.0000.0000.0000.000
17A34LEU0-0.073-0.0338.547-2.277-2.2770.0000.0000.0000.000
18A35ASN0-0.052-0.02510.620-1.253-1.2530.0000.0000.0000.000
19A36LYS10.8780.9395.99134.99034.9900.0000.0000.0000.000
20A37ASP-1-0.814-0.90812.494-16.364-16.3640.0000.0000.0000.000
21A38LEU0-0.033-0.03815.357-0.288-0.2880.0000.0000.0000.000
22A39ALA0-0.0230.00010.8170.1990.1990.0000.0000.0000.000
23A40PHE0-0.056-0.00410.747-1.524-1.5240.0000.0000.0000.000
24A41THR00.0700.0269.9212.4602.4600.0000.0000.0000.000
25A42LEU00.007-0.00612.7410.4140.4140.0000.0000.0000.000
26A43GLU-1-0.886-0.93711.578-23.319-23.3190.0000.0000.0000.000
27A44GLU-1-0.777-0.8938.292-29.552-29.5520.0000.0000.0000.000
28A45ARG10.8000.88412.57417.89417.8940.0000.0000.0000.000
29A46GLN0-0.015-0.01815.8540.3800.3800.0000.0000.0000.000
30A47GLN00.0210.01612.5880.2170.2170.0000.0000.0000.000
31A48LEU0-0.034-0.01610.9280.3450.3450.0000.0000.0000.000
32A49ASN0-0.041-0.01914.9260.3610.3610.0000.0000.0000.000
33A50ILE00.0230.01415.2740.6170.6170.0000.0000.0000.000
34A51HIS0-0.013-0.00519.534-0.215-0.2150.0000.0000.0000.000
35A52GLY00.0160.01020.5160.5240.5240.0000.0000.0000.000
36A53LEU0-0.038-0.01320.8600.4440.4440.0000.0000.0000.000
37A54LEU0-0.023-0.00617.039-0.070-0.0700.0000.0000.0000.000
38A55PRO00.0230.01321.3870.2390.2390.0000.0000.0000.000
39A56PRO00.0210.02620.857-0.774-0.7740.0000.0000.0000.000
40A57SER0-0.033-0.01120.2560.0490.0490.0000.0000.0000.000
41A58PHE00.0340.00314.872-0.246-0.2460.0000.0000.0000.000
42A59ASN0-0.058-0.03015.4080.8470.8470.0000.0000.0000.000
43A60SER00.1120.06112.209-0.838-0.8380.0000.0000.0000.000
44A61GLN00.062-0.01110.1981.1551.1550.0000.0000.0000.000
45A62GLU-1-0.884-0.94912.851-20.780-20.7800.0000.0000.0000.000
46A63ILE0-0.029-0.00715.7491.1711.1710.0000.0000.0000.000
47A64GLN0-0.0060.00213.533-0.094-0.0940.0000.0000.0000.000
48A65VAL00.0460.02216.1320.7820.7820.0000.0000.0000.000
49A66LEU0-0.0080.01218.6720.8480.8480.0000.0000.0000.000
50A67ARG10.8960.95319.48214.76314.7630.0000.0000.0000.000
51A68VAL00.0150.01919.8860.6560.6560.0000.0000.0000.000
52A69VAL00.0360.00822.1440.5290.5290.0000.0000.0000.000
53A70LYS10.9790.98924.57811.45011.4500.0000.0000.0000.000
54A71ASN0-0.080-0.05025.6010.6500.6500.0000.0000.0000.000
55A72PHE00.0290.00126.1710.3770.3770.0000.0000.0000.000
56A73GLU-1-0.973-0.99728.165-10.335-10.3350.0000.0000.0000.000
57A74HIS0-0.055-0.02430.6440.3650.3650.0000.0000.0000.000
58A75LEU0-0.0320.01229.7870.2820.2820.0000.0000.0000.000
59A76ASN00.013-0.00933.5640.0400.0400.0000.0000.0000.000
60A77SER0-0.019-0.00735.1530.1580.1580.0000.0000.0000.000
61A78ASP-1-0.832-0.93432.548-9.637-9.6370.0000.0000.0000.000
62A79PHE00.0130.01431.694-0.342-0.3420.0000.0000.0000.000
63A80ASP-1-0.832-0.92431.884-9.140-9.1400.0000.0000.0000.000
64A81ARG10.8660.94329.0839.3259.3250.0000.0000.0000.000
65A82TYR00.007-0.01027.638-0.420-0.4200.0000.0000.0000.000
66A83LEU0-0.024-0.01327.135-0.424-0.4240.0000.0000.0000.000
67A84LEU0-0.0010.02025.239-0.359-0.3590.0000.0000.0000.000
68A85LEU0-0.032-0.02822.303-0.588-0.5880.0000.0000.0000.000
69A86MET00.0210.01522.271-0.690-0.6900.0000.0000.0000.000
70A87ASP-1-0.841-0.91122.854-11.655-11.6550.0000.0000.0000.000
71A88LEU0-0.079-0.04218.208-0.436-0.4360.0000.0000.0000.000
72A89GLN0-0.0150.00518.328-0.469-0.4690.0000.0000.0000.000
73A90ASP-1-0.911-0.96517.987-13.830-13.8300.0000.0000.0000.000
74A91ARG10.9120.97118.74914.41314.4130.0000.0000.0000.000
75A92ASN0-0.040-0.04913.534-1.544-1.5440.0000.0000.0000.000
76A93GLU-1-0.768-0.87712.487-19.939-19.9390.0000.0000.0000.000
77A94LYS10.8210.9086.25335.89735.8970.0000.0000.0000.000
78A95LEU0-0.027-0.00611.8570.1970.1970.0000.0000.0000.000
79A96PHE00.0340.01014.5760.7050.7050.0000.0000.0000.000
80A97TYR00.0580.02313.8480.8480.8480.0000.0000.0000.000
81A98ARG10.9200.98612.44721.74321.7430.0000.0000.0000.000
82A99VAL0-0.007-0.00815.0170.5480.5480.0000.0000.0000.000
83A100LEU00.0030.02618.5960.6030.6030.0000.0000.0000.000
84A101THR0-0.060-0.05315.7980.2940.2940.0000.0000.0000.000
85A102SER0-0.152-0.07918.4780.1690.1690.0000.0000.0000.000
86A103ASP-1-0.860-0.94819.611-11.781-11.7810.0000.0000.0000.000
87A104ILE00.0240.01620.6660.3770.3770.0000.0000.0000.000
88A105GLU-1-0.941-0.97423.300-10.331-10.3310.0000.0000.0000.000
89A106LYS10.9400.99326.15711.76011.7600.0000.0000.0000.000
90A107PHE0-0.021-0.03122.8710.3380.3380.0000.0000.0000.000
91A108MET0-0.0020.00524.225-0.040-0.0400.0000.0000.0000.000
92A109PRO00.0020.01626.0390.1160.1160.0000.0000.0000.000
93A110ILE0-0.0400.03227.0040.3180.3180.0000.0000.0000.000
94A111VAL00.004-0.01723.0450.1410.1410.0000.0000.0000.000
95A112TYR00.0590.03026.2970.0090.0090.0000.0000.0000.000
96A113THR0-0.0350.00328.0950.2390.2390.0000.0000.0000.000
97A114PRO00.012-0.01131.179-0.165-0.1650.0000.0000.0000.000
98A115THR00.002-0.04031.0160.3170.3170.0000.0000.0000.000
99A116VAL0-0.0010.01229.0750.1760.1760.0000.0000.0000.000
100A117GLY00.0470.01831.5230.1090.1090.0000.0000.0000.000
101A118LEU0-0.0070.00334.9180.1850.1850.0000.0000.0000.000
102A119ALA00.018-0.00831.8180.1330.1330.0000.0000.0000.000
103A120CYS0-0.053-0.01232.6910.0360.0360.0000.0000.0000.000
104A121GLN0-0.013-0.01634.7690.0770.0770.0000.0000.0000.000
105A122GLN0-0.0070.00336.2050.2200.2200.0000.0000.0000.000
106A123TYR0-0.0260.00828.343-0.080-0.0800.0000.0000.0000.000
107A124SER0-0.010-0.03034.474-0.083-0.0830.0000.0000.0000.000
108A125LEU0-0.0250.02237.0120.0390.0390.0000.0000.0000.000
109A126VAL0-0.065-0.04332.678-0.044-0.0440.0000.0000.0000.000
110A127PHE00.0310.02730.089-0.412-0.4120.0000.0000.0000.000
111A128ARG10.8950.93629.3899.9919.9910.0000.0000.0000.000
112A129LYS10.8070.90424.35011.65111.6510.0000.0000.0000.000
113A130PRO00.0100.02326.137-0.122-0.1220.0000.0000.0000.000
114A131ARG10.9180.95618.27613.53113.5310.0000.0000.0000.000
115A132GLY00.0250.00223.0030.3460.3460.0000.0000.0000.000
116A133LEU0-0.0020.00424.3080.0820.0820.0000.0000.0000.000
117A134PHE00.006-0.02026.5220.1320.1320.0000.0000.0000.000
118A135ILE0-0.0030.00928.4320.0180.0180.0000.0000.0000.000
119A136THR0-0.024-0.01232.3210.1940.1940.0000.0000.0000.000
120A137ILE00.0340.00436.111-0.047-0.0470.0000.0000.0000.000
121A138HIS0-0.046-0.04238.9760.1100.1100.0000.0000.0000.000
122A139ASP-1-0.866-0.91234.682-8.356-8.3560.0000.0000.0000.000
123A140ARG10.8740.92136.1477.2797.2790.0000.0000.0000.000
124A141GLY0-0.049-0.03637.1960.1570.1570.0000.0000.0000.000
125A142HIS0-0.034-0.01534.845-0.142-0.1420.0000.0000.0000.000
126A143ILE00.0650.04430.236-0.303-0.3030.0000.0000.0000.000
127A144ALA00.015-0.00329.251-0.324-0.3240.0000.0000.0000.000
128A145SER0-0.100-0.05528.415-0.315-0.3150.0000.0000.0000.000
129A146VAL00.0550.02528.755-0.258-0.2580.0000.0000.0000.000
130A147LEU0-0.003-0.01525.155-0.372-0.3720.0000.0000.0000.000
131A148ASN0-0.040-0.00324.041-0.768-0.7680.0000.0000.0000.000
132A149ALA0-0.0070.01224.417-0.173-0.1730.0000.0000.0000.000
133A150TRP0-0.037-0.00918.383-0.007-0.0070.0000.0000.0000.000
134A151PRO0-0.050-0.02118.094-0.077-0.0770.0000.0000.0000.000
135A152GLU-1-0.968-0.98213.537-19.159-19.1590.0000.0000.0000.000
136A153ASP-1-0.886-0.94816.189-13.532-13.5320.0000.0000.0000.000
137A154VAL0-0.075-0.03813.4940.3820.3820.0000.0000.0000.000
138A155ILE0-0.0120.00115.377-0.519-0.5190.0000.0000.0000.000
139A156LYS10.8770.93012.51319.11019.1100.0000.0000.0000.000
140A157ALA00.0170.00118.1390.4120.4120.0000.0000.0000.000
141A158ILE00.0050.01620.206-0.224-0.2240.0000.0000.0000.000
142A159VAL0-0.0300.00523.1340.2060.2060.0000.0000.0000.000
143A160VAL00.0040.00225.650-0.050-0.0500.0000.0000.0000.000
144A161THR00.0370.01328.8630.2120.2120.0000.0000.0000.000
145A162ASP-1-0.754-0.89532.152-8.072-8.0720.0000.0000.0000.000
146A163GLY00.0290.02835.0460.2010.2010.0000.0000.0000.000
147A164GLU-1-0.877-0.92536.316-6.938-6.9380.0000.0000.0000.000
148A165ARG10.8090.90536.7388.2838.2830.0000.0000.0000.000
149A166ILE00.0320.03234.227-0.180-0.1800.0000.0000.0000.000
150A167LEU00.0250.00735.6820.2950.2950.0000.0000.0000.000
151A168GLY0-0.053-0.02737.798-0.039-0.0390.0000.0000.0000.000
152A169LEU0-0.084-0.04637.2950.1250.1250.0000.0000.0000.000
153A170GLY0-0.0300.00640.8080.1450.1450.0000.0000.0000.000
154A171ASP-1-0.713-0.82239.928-7.524-7.5240.0000.0000.0000.000
155A172LEU0-0.023-0.02136.8360.1140.1140.0000.0000.0000.000
156A173GLY00.0650.03338.311-0.074-0.0740.0000.0000.0000.000
157A174CYS00.0080.01134.438-0.328-0.3280.0000.0000.0000.000
158A175ASN00.0540.03833.695-0.375-0.3750.0000.0000.0000.000
159A176GLY00.001-0.00633.726-0.169-0.1690.0000.0000.0000.000
160A177MET0-0.0120.01227.099-0.295-0.2950.0000.0000.0000.000
161A178GLY00.005-0.01028.302-0.405-0.4050.0000.0000.0000.000
162A179ILE0-0.022-0.01528.132-0.397-0.3970.0000.0000.0000.000
163A180PRO00.0210.01326.298-0.390-0.3900.0000.0000.0000.000
164A181VAL00.0060.00723.002-0.582-0.5820.0000.0000.0000.000
165A182GLY00.0270.01423.059-0.564-0.5640.0000.0000.0000.000
166A183LYS10.7870.89924.02710.12410.1240.0000.0000.0000.000
167A184LEU00.0260.00220.002-0.463-0.4630.0000.0000.0000.000
168A185ALA0-0.0090.01019.478-0.849-0.8490.0000.0000.0000.000
169A186LEU00.019-0.01419.350-0.765-0.7650.0000.0000.0000.000
170A187TYR0-0.017-0.02418.896-0.371-0.3710.0000.0000.0000.000
171A188THR0-0.036-0.00713.948-0.224-0.2240.0000.0000.0000.000
172A189ALA0-0.059-0.03315.675-0.914-0.9140.0000.0000.0000.000
173A190CYS0-0.048-0.03317.595-0.282-0.2820.0000.0000.0000.000
174A191GLY00.0590.02417.9250.1210.1210.0000.0000.0000.000
175A192GLY0-0.038-0.00613.688-0.406-0.4060.0000.0000.0000.000
176A193MET00.0620.05612.863-1.361-1.3610.0000.0000.0000.000
177A194ASN00.0320.0048.757-0.263-0.2630.0000.0000.0000.000
178A195PRO00.0110.01511.5350.8400.8400.0000.0000.0000.000
179A196GLN00.008-0.0018.9691.1211.1210.0000.0000.0000.000
180A197GLU-1-0.869-0.92611.284-19.835-19.8350.0000.0000.0000.000
181A198CYS0-0.052-0.02414.7750.8780.8780.0000.0000.0000.000
182A199LEU00.0230.01217.804-0.058-0.0580.0000.0000.0000.000
183A200PRO0-0.019-0.01620.8340.4130.4130.0000.0000.0000.000
184A201VAL0-0.0010.00323.9940.0320.0320.0000.0000.0000.000
185A202ILE0-0.0050.00727.2470.1290.1290.0000.0000.0000.000
186A203LEU0-0.019-0.01330.8630.0200.0200.0000.0000.0000.000
187A204ASP-1-0.794-0.90633.736-7.724-7.7240.0000.0000.0000.000
188A205VAL00.026-0.00536.5860.0840.0840.0000.0000.0000.000
189A206GLY00.0210.01539.8780.2340.2340.0000.0000.0000.000
190A207THR0-0.061-0.07040.977-0.097-0.0970.0000.0000.0000.000
191A208GLU-1-0.833-0.94343.100-6.253-6.2530.0000.0000.0000.000
192A209ASN0-0.0280.00542.8750.2500.2500.0000.0000.0000.000
193A210GLU-1-0.803-0.91345.596-6.134-6.1340.0000.0000.0000.000
194A211GLU-1-0.935-0.96645.838-6.267-6.2670.0000.0000.0000.000
195A212LEU0-0.028-0.01040.431-0.028-0.0280.0000.0000.0000.000
196A213LEU0-0.043-0.01444.239-0.015-0.0150.0000.0000.0000.000
197A214LYS10.8920.95146.5246.1196.1190.0000.0000.0000.000
198A215ASP-1-0.842-0.90743.274-7.055-7.0550.0000.0000.0000.000
199A216PRO0-0.051-0.02644.493-0.088-0.0880.0000.0000.0000.000
200A217LEU0-0.027-0.02640.410-0.074-0.0740.0000.0000.0000.000
201A218TYR0-0.034-0.00238.823-0.307-0.3070.0000.0000.0000.000
202A219ILE00.003-0.01333.6910.0520.0520.0000.0000.0000.000
203A220GLY0-0.008-0.00637.021-0.143-0.1430.0000.0000.0000.000
204A221LEU0-0.053-0.01738.2970.1870.1870.0000.0000.0000.000
205A222ARG10.8490.92740.8726.8916.8910.0000.0000.0000.000
206A223GLN0-0.0170.00343.3980.1600.1600.0000.0000.0000.000
207A224ARG10.8310.89944.7576.0676.0670.0000.0000.0000.000
208A225ARG10.7410.86838.6697.4497.4490.0000.0000.0000.000
209A226VAL00.0270.02743.0000.1650.1650.0000.0000.0000.000
210A227ARG10.7990.87543.6516.5956.5950.0000.0000.0000.000
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