FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9MMM2

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:


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 562
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12038717.473246
FMO2-HF: Nuclear repulsion 11817659.141182
FMO2-HF: Total energy -221058.332064
FMO2-MP2: Total energy -221703.07478


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.
-141.193-131.7358.859-7.315-11.002-0.028
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 : 0.959 / q_NPA : 0.968
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].
3A20HIS00.0380.0313.798-0.2331.453-0.026-0.913-0.7480.002
4A21THR00.0370.0026.5081.7141.7140.0000.0000.0000.000
5A22HIS00.0280.01910.0720.7020.7020.0000.0000.0000.000
6A23GLN00.0300.03813.3100.2350.2350.0000.0000.0000.000
7A24ARG10.9000.93411.30618.25318.2530.0000.0000.0000.000
8A25GLY00.0440.02716.4940.6840.6840.0000.0000.0000.000
9A26TYR00.0400.00218.476-0.625-0.6250.0000.0000.0000.000
10A27LEU00.0380.01519.404-0.300-0.3000.0000.0000.0000.000
11A28LEU0-0.0030.01812.140-0.249-0.2490.0000.0000.0000.000
12A29THR0-0.058-0.04515.435-0.456-0.4560.0000.0000.0000.000
13A30ARG10.9080.95617.46813.02213.0220.0000.0000.0000.000
14A31ASN00.0210.01613.4370.0060.0060.0000.0000.0000.000
15A32PRO00.0800.03814.277-1.272-1.2720.0000.0000.0000.000
16A33HIS10.7920.88710.61618.42718.4270.0000.0000.0000.000
17A34LEU0-0.074-0.0348.755-2.501-2.5010.0000.0000.0000.000
18A35ASN0-0.049-0.03010.669-1.215-1.2150.0000.0000.0000.000
19A36LYS10.8850.9376.49134.21234.2120.0000.0000.0000.000
20A37ASP-1-0.774-0.85612.579-16.850-16.8500.0000.0000.0000.000
21A38LEU0-0.026-0.02415.915-0.215-0.2150.0000.0000.0000.000
22A39ALA0-0.0160.00011.1320.2510.2510.0000.0000.0000.000
23A40PHE0-0.0430.00511.008-1.499-1.4990.0000.0000.0000.000
24A41THR00.0590.00611.7452.2972.2970.0000.0000.0000.000
25A42LEU0-0.010-0.01014.3150.3840.3840.0000.0000.0000.000
26A43GLU-1-0.871-0.93113.094-22.045-22.0450.0000.0000.0000.000
27A44GLU-1-0.770-0.8679.128-28.598-28.5980.0000.0000.0000.000
28A45ARG10.7870.87313.01417.89317.8930.0000.0000.0000.000
29A46GLN0-0.010-0.01916.2690.2920.2920.0000.0000.0000.000
30A47GLN00.0350.02512.9081.5611.5610.0000.0000.0000.000
31A48LEU0-0.052-0.02411.2800.3030.3030.0000.0000.0000.000
32A49ASN0-0.033-0.01815.3360.3380.3380.0000.0000.0000.000
33A50ILE00.0200.01415.5080.5830.5830.0000.0000.0000.000
34A51HIS0-0.017-0.00519.612-0.274-0.2740.0000.0000.0000.000
35A52GLY00.0220.01220.9440.5300.5300.0000.0000.0000.000
36A53LEU0-0.039-0.01420.9650.4330.4330.0000.0000.0000.000
37A54LEU0-0.026-0.00817.593-0.114-0.1140.0000.0000.0000.000
38A55PRO00.0280.01222.0230.2360.2360.0000.0000.0000.000
39A56PRO00.0170.02121.884-0.763-0.7630.0000.0000.0000.000
40A57SER0-0.034-0.01021.2460.0350.0350.0000.0000.0000.000
41A58PHE00.0410.00816.134-0.271-0.2710.0000.0000.0000.000
42A59ASN0-0.035-0.00716.0430.8350.8350.0000.0000.0000.000
43A60SER00.0800.01812.432-0.659-0.6590.0000.0000.0000.000
44A61GLN00.0690.0038.8301.1361.1360.0000.0000.0000.000
45A62GLU-1-0.807-0.88111.797-22.278-22.2780.0000.0000.0000.000
46A63ILE0-0.019-0.00514.9221.2201.2200.0000.0000.0000.000
47A64GLN0-0.0060.01513.199-0.201-0.2010.0000.0000.0000.000
48A65VAL00.0500.02514.8430.8060.8060.0000.0000.0000.000
49A66LEU0-0.0070.01017.5070.9170.9170.0000.0000.0000.000
50A67ARG10.8680.93019.15015.26115.2610.0000.0000.0000.000
51A68VAL00.0210.01618.8960.6740.6740.0000.0000.0000.000
52A69VAL00.0260.00620.6890.5500.5500.0000.0000.0000.000
53A70LYS10.9690.99123.22911.73311.7330.0000.0000.0000.000
54A71ASN0-0.072-0.04624.9280.6800.6800.0000.0000.0000.000
55A72PHE00.0290.00324.7350.3690.3690.0000.0000.0000.000
56A73GLU-1-0.945-0.98826.734-10.690-10.6900.0000.0000.0000.000
57A74HIS0-0.068-0.02529.2050.4660.4660.0000.0000.0000.000
58A75LEU0-0.0370.00728.6860.3030.3030.0000.0000.0000.000
59A76ASN00.003-0.01132.2300.1040.1040.0000.0000.0000.000
60A77SER0-0.025-0.03433.9230.1900.1900.0000.0000.0000.000
61A78ASP-1-0.790-0.90231.303-9.913-9.9130.0000.0000.0000.000
62A79PHE00.0210.01730.642-0.372-0.3720.0000.0000.0000.000
63A80ASP-1-0.819-0.88730.979-9.314-9.3140.0000.0000.0000.000
64A81ARG10.8200.89927.7879.4619.4610.0000.0000.0000.000
65A82TYR00.008-0.01026.634-0.415-0.4150.0000.0000.0000.000
66A83LEU0-0.024-0.01326.293-0.459-0.4590.0000.0000.0000.000
67A84LEU0-0.0010.01724.278-0.381-0.3810.0000.0000.0000.000
68A85LEU0-0.020-0.02221.089-0.629-0.6290.0000.0000.0000.000
69A86MET00.0120.01121.481-0.755-0.7550.0000.0000.0000.000
70A87ASP-1-0.813-0.90022.545-11.949-11.9490.0000.0000.0000.000
71A88LEU0-0.048-0.03117.834-0.450-0.4500.0000.0000.0000.000
72A89GLN0-0.0010.01217.833-0.689-0.6890.0000.0000.0000.000
73A90ASP-1-0.878-0.93317.924-14.083-14.0830.0000.0000.0000.000
74A91ARG10.8160.89918.15715.63515.6350.0000.0000.0000.000
75A92ASN0-0.044-0.05313.078-1.684-1.6840.0000.0000.0000.000
76A93GLU-1-0.756-0.87511.952-21.309-21.3090.0000.0000.0000.000
77A94LYS10.8070.8935.50641.14741.1470.0000.0000.0000.000
78A95LEU0-0.023-0.00611.0390.1680.1680.0000.0000.0000.000
79A96PHE00.0450.01713.5610.8420.8420.0000.0000.0000.000
80A97TYR00.0600.02512.7740.8800.8800.0000.0000.0000.000
81A98ARG10.8830.96110.63923.62623.6260.0000.0000.0000.000
82A99VAL0-0.016-0.01013.3020.6600.6600.0000.0000.0000.000
83A100LEU00.0080.02516.9510.6850.6850.0000.0000.0000.000
84A101THR0-0.047-0.04914.1320.2950.2950.0000.0000.0000.000
85A102SER0-0.143-0.07116.4950.1870.1870.0000.0000.0000.000
86A103ASP-1-0.870-0.95617.503-12.121-12.1210.0000.0000.0000.000
87A104ILE00.0310.01619.0460.4120.4120.0000.0000.0000.000
88A105GLU-1-0.890-0.95321.414-10.849-10.8490.0000.0000.0000.000
89A106LYS10.9400.99924.18012.40312.4030.0000.0000.0000.000
90A107PHE0-0.022-0.03020.7720.3850.3850.0000.0000.0000.000
91A108MET0-0.0010.00622.917-0.086-0.0860.0000.0000.0000.000
92A109PRO0-0.0040.01124.7890.1290.1290.0000.0000.0000.000
93A110ILE0-0.0420.00725.8440.3470.3470.0000.0000.0000.000
94A111VAL00.002-0.01622.1080.1370.1370.0000.0000.0000.000
95A112TYR00.0440.02225.305-0.007-0.0070.0000.0000.0000.000
96A113THR0-0.0260.01027.3300.2550.2550.0000.0000.0000.000
97A114PRO00.003-0.01830.260-0.184-0.1840.0000.0000.0000.000
98A115THR0-0.005-0.02230.0000.3530.3530.0000.0000.0000.000
99A116VAL00.0090.01428.3980.1940.1940.0000.0000.0000.000
100A117GLY00.0570.02730.7330.1200.1200.0000.0000.0000.000
101A118LEU0-0.006-0.00134.3100.2040.2040.0000.0000.0000.000
102A119ALA00.008-0.00631.3530.1430.1430.0000.0000.0000.000
103A120CYS0-0.045-0.01532.4470.0270.0270.0000.0000.0000.000
104A121GLN0-0.023-0.02034.5900.1090.1090.0000.0000.0000.000
105A122GLN0-0.017-0.00135.7580.2370.2370.0000.0000.0000.000
106A123TYR0-0.0250.00928.207-0.059-0.0590.0000.0000.0000.000
107A124SER00.021-0.02434.357-0.078-0.0780.0000.0000.0000.000
108A125LEU0-0.0330.01536.8910.0460.0460.0000.0000.0000.000
109A126VAL0-0.062-0.04132.549-0.043-0.0430.0000.0000.0000.000
110A127PHE00.0180.02530.448-0.421-0.4210.0000.0000.0000.000
111A128ARG10.8550.91528.23610.47610.4760.0000.0000.0000.000
112A129LYS10.7930.90423.50912.49612.4960.0000.0000.0000.000
113A130PRO00.0170.02726.130-0.156-0.1560.0000.0000.0000.000
114A131ARG10.8580.90418.12613.86913.8690.0000.0000.0000.000
115A132GLY00.0300.00422.9250.3640.3640.0000.0000.0000.000
116A133LEU0-0.0070.00224.3360.0970.0970.0000.0000.0000.000
117A134PHE00.005-0.02026.6470.1390.1390.0000.0000.0000.000
118A135ILE0-0.0070.00328.6040.0270.0270.0000.0000.0000.000
119A136THR0-0.024-0.03632.5740.1910.1910.0000.0000.0000.000
120A137ILE00.0270.00736.354-0.036-0.0360.0000.0000.0000.000
121A138HIS0-0.037-0.03539.2240.1290.1290.0000.0000.0000.000
122A139ASP-1-0.865-0.89334.955-8.418-8.4180.0000.0000.0000.000
123A140ARG10.8160.88036.3957.3287.3280.0000.0000.0000.000
124A141GLY0-0.045-0.03437.4240.1600.1600.0000.0000.0000.000
125A142HIS0-0.035-0.01435.101-0.129-0.1290.0000.0000.0000.000
126A143ILE00.0600.04030.557-0.316-0.3160.0000.0000.0000.000
127A144ALA00.015-0.00129.464-0.330-0.3300.0000.0000.0000.000
128A145SER0-0.100-0.05828.654-0.305-0.3050.0000.0000.0000.000
129A146VAL00.0490.02229.085-0.258-0.2580.0000.0000.0000.000
130A147LEU00.015-0.00625.415-0.356-0.3560.0000.0000.0000.000
131A148ASN0-0.043-0.01524.309-0.804-0.8040.0000.0000.0000.000
132A149ALA0-0.0120.01024.601-0.172-0.1720.0000.0000.0000.000
133A150TRP0-0.028-0.00718.650-0.091-0.0910.0000.0000.0000.000
134A151PRO0-0.046-0.02118.066-0.083-0.0830.0000.0000.0000.000
135A152GLU-1-0.883-0.92514.009-19.103-19.1030.0000.0000.0000.000
136A153ASP-1-0.832-0.93316.424-12.966-12.9660.0000.0000.0000.000
137A154VAL0-0.073-0.02813.5280.3860.3860.0000.0000.0000.000
138A155ILE0-0.021-0.00515.561-0.594-0.5940.0000.0000.0000.000
139A156LYS10.8350.89912.07519.83519.8350.0000.0000.0000.000
140A157ALA00.0130.00118.2210.4160.4160.0000.0000.0000.000
141A158ILE00.0120.01820.313-0.250-0.2500.0000.0000.0000.000
142A159VAL0-0.0310.00423.2860.2220.2220.0000.0000.0000.000
143A160VAL00.0070.00325.811-0.040-0.0400.0000.0000.0000.000
144A161THR00.020-0.01029.0450.2230.2230.0000.0000.0000.000
145A162ASP-1-0.751-0.86832.345-8.099-8.0990.0000.0000.0000.000
146A163GLY00.0370.02835.2580.2040.2040.0000.0000.0000.000
147A164GLU-1-0.848-0.90036.536-6.974-6.9740.0000.0000.0000.000
148A165ARG10.6430.79336.4828.5918.5910.0000.0000.0000.000
149A166ILE00.0380.04834.484-0.188-0.1880.0000.0000.0000.000
150A167LEU00.0340.01235.5260.2950.2950.0000.0000.0000.000
151A168GLY0-0.058-0.02837.727-0.042-0.0420.0000.0000.0000.000
152A169LEU0-0.083-0.04136.9350.1250.1250.0000.0000.0000.000
153A170GLY0-0.0250.00740.8710.1510.1510.0000.0000.0000.000
154A171ASP-1-0.717-0.80640.094-7.649-7.6490.0000.0000.0000.000
155A172LEU0-0.016-0.01137.0260.1200.1200.0000.0000.0000.000
156A173GLY00.0680.03438.321-0.077-0.0770.0000.0000.0000.000
157A174CYS0-0.0050.00934.566-0.343-0.3430.0000.0000.0000.000
158A175ASN00.0590.04333.686-0.422-0.4220.0000.0000.0000.000
159A176GLY0-0.002-0.00533.715-0.179-0.1790.0000.0000.0000.000
160A177MET0-0.0260.01226.979-0.286-0.2860.0000.0000.0000.000
161A178GLY00.009-0.00928.324-0.424-0.4240.0000.0000.0000.000
162A179ILE0-0.027-0.01828.114-0.414-0.4140.0000.0000.0000.000
163A180PRO00.0220.01626.427-0.418-0.4180.0000.0000.0000.000
164A181VAL00.0090.00722.950-0.596-0.5960.0000.0000.0000.000
165A182GLY00.0210.01423.084-0.614-0.6140.0000.0000.0000.000
166A183LYS10.7440.84323.63210.33310.3330.0000.0000.0000.000
167A184LEU00.0230.00420.268-0.514-0.5140.0000.0000.0000.000
168A185ALA0-0.0150.00419.165-0.933-0.9330.0000.0000.0000.000
169A186LEU00.013-0.01418.834-0.862-0.8620.0000.0000.0000.000
170A187TYR0-0.010-0.02119.052-0.421-0.4210.0000.0000.0000.000
171A188THR0-0.034-0.01413.798-0.266-0.2660.0000.0000.0000.000
172A189ALA0-0.049-0.02915.386-1.063-1.0630.0000.0000.0000.000
173A190CYS0-0.039-0.02716.903-0.479-0.4790.0000.0000.0000.000
174A191GLY00.0630.02918.0700.1550.1550.0000.0000.0000.000
175A192GLY0-0.042-0.00813.713-0.394-0.3940.0000.0000.0000.000
176A193MET00.0750.06213.101-1.511-1.5110.0000.0000.0000.000
177A194ASN00.0420.0159.440-0.884-0.8840.0000.0000.0000.000
178A195PRO00.0200.01611.7360.9850.9850.0000.0000.0000.000
179A196GLN0-0.024-0.0179.1530.3320.3320.0000.0000.0000.000
180A197GLU-1-0.831-0.89911.655-20.086-20.0860.0000.0000.0000.000
181A198CYS0-0.056-0.02514.9540.8560.8560.0000.0000.0000.000
182A199LEU00.0280.01117.996-0.078-0.0780.0000.0000.0000.000
183A200PRO0-0.016-0.00621.0740.4140.4140.0000.0000.0000.000
184A201VAL00.0060.00124.2290.0510.0510.0000.0000.0000.000
185A202ILE0-0.0130.00027.4840.1350.1350.0000.0000.0000.000
186A203LEU0-0.021-0.01231.0960.0300.0300.0000.0000.0000.000
187A204ASP-1-0.788-0.89733.971-7.805-7.8050.0000.0000.0000.000
188A205VAL00.026-0.00536.7980.0940.0940.0000.0000.0000.000
189A206GLY00.0230.01440.0840.2440.2440.0000.0000.0000.000
190A207THR0-0.072-0.07841.169-0.112-0.1120.0000.0000.0000.000
191A208GLU-1-0.815-0.92043.249-6.337-6.3370.0000.0000.0000.000
192A209ASN0-0.056-0.02542.9050.2470.2470.0000.0000.0000.000
193A210GLU-1-0.762-0.87545.643-6.174-6.1740.0000.0000.0000.000
194A211GLU-1-0.908-0.96445.876-6.319-6.3190.0000.0000.0000.000
195A212LEU0-0.0090.00440.313-0.030-0.0300.0000.0000.0000.000
196A213LEU0-0.033-0.01144.127-0.014-0.0140.0000.0000.0000.000
197A214LYS10.8200.91546.4516.2616.2610.0000.0000.0000.000
198A215ASP-1-0.834-0.90042.309-7.233-7.2330.0000.0000.0000.000
199A216PRO0-0.053-0.02144.361-0.091-0.0910.0000.0000.0000.000
200A217LEU0-0.034-0.02840.330-0.066-0.0660.0000.0000.0000.000
201A218TYR0-0.0140.00338.545-0.321-0.3210.0000.0000.0000.000
202A219ILE0-0.003-0.01333.4280.0530.0530.0000.0000.0000.000
203A220GLY0-0.018-0.01536.890-0.146-0.1460.0000.0000.0000.000
204A221LEU0-0.058-0.02238.2450.1930.1930.0000.0000.0000.000
205A222ARG10.8210.90340.8947.0027.0020.0000.0000.0000.000
206A223GLN0-0.0160.00443.4450.1890.1890.0000.0000.0000.000
207A224ARG10.8220.88544.8796.1416.1410.0000.0000.0000.000
208A225ARG10.7300.85238.9127.5797.5790.0000.0000.0000.000
209A226VAL00.0190.02343.2010.1680.1680.0000.0000.0000.000
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