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: M999Z

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 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 562
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12071187.795843
FMO2-HF: Nuclear repulsion 11850128.762667
FMO2-HF: Total energy -221059.033176
FMO2-MP2: Total energy -221703.818452


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.
-161.354-157.96721.674-10.122-14.939-0.098
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 : 0.901 / q_NPA : 0.930
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].
3A20HIS00.0310.0243.8670.2701.793-0.014-0.834-0.6750.001
4A21THR00.0390.0036.5241.2531.2530.0000.0000.0000.000
5A22HIS00.0220.01610.2520.6900.6900.0000.0000.0000.000
6A23GLN00.0380.04213.5560.1560.1560.0000.0000.0000.000
7A24ARG10.8780.93211.63718.16818.1680.0000.0000.0000.000
8A25GLY00.0530.03216.9840.6620.6620.0000.0000.0000.000
9A26TYR00.030-0.00118.815-0.678-0.6780.0000.0000.0000.000
10A27LEU00.0270.01919.597-0.314-0.3140.0000.0000.0000.000
11A28LEU0-0.0010.01512.512-0.211-0.2110.0000.0000.0000.000
12A29THR0-0.052-0.04915.596-0.550-0.5500.0000.0000.0000.000
13A30ARG10.8960.95217.61413.26313.2630.0000.0000.0000.000
14A31ASN00.0390.02413.661-0.010-0.0100.0000.0000.0000.000
15A32PRO00.0550.03414.195-1.431-1.4310.0000.0000.0000.000
16A33HIS10.7820.86210.57818.78518.7850.0000.0000.0000.000
17A34LEU0-0.073-0.0348.815-2.601-2.6010.0000.0000.0000.000
18A35ASN0-0.032-0.03510.797-1.066-1.0660.0000.0000.0000.000
19A36LYS10.8700.9286.38734.33334.3330.0000.0000.0000.000
20A37ASP-1-0.761-0.83612.671-17.099-17.0990.0000.0000.0000.000
21A38LEU0-0.021-0.02515.709-0.467-0.4670.0000.0000.0000.000
22A39ALA0-0.030-0.00411.7590.2670.2670.0000.0000.0000.000
23A40PHE0-0.0260.00910.866-1.697-1.6970.0000.0000.0000.000
24A41THR00.043-0.01011.2322.4302.4300.0000.0000.0000.000
25A42LEU0-0.014-0.01114.0460.4640.4640.0000.0000.0000.000
26A43GLU-1-0.832-0.91413.156-21.386-21.3860.0000.0000.0000.000
27A44GLU-1-0.782-0.8619.057-29.169-29.1690.0000.0000.0000.000
28A45ARG10.7900.87612.94017.97817.9780.0000.0000.0000.000
29A46GLN0-0.014-0.00316.4330.4320.4320.0000.0000.0000.000
30A47GLN00.0280.00913.3261.5741.5740.0000.0000.0000.000
31A48LEU0-0.031-0.01911.0970.1210.1210.0000.0000.0000.000
32A49ASN0-0.052-0.02915.3000.5410.5410.0000.0000.0000.000
33A50ILE00.0140.00615.1610.6980.6980.0000.0000.0000.000
34A51HIS00.0020.00219.439-0.273-0.2730.0000.0000.0000.000
35A52GLY00.0000.00320.8890.5070.5070.0000.0000.0000.000
36A53LEU0-0.033-0.01120.9830.4040.4040.0000.0000.0000.000
37A54LEU0-0.0030.00117.262-0.168-0.1680.0000.0000.0000.000
38A55PRO00.0320.01121.6170.1230.1230.0000.0000.0000.000
39A56PRO00.0090.02622.006-0.773-0.7730.0000.0000.0000.000
40A57SER0-0.042-0.02021.6170.1550.1550.0000.0000.0000.000
41A58PHE00.0630.02616.336-0.345-0.3450.0000.0000.0000.000
42A59ASN0-0.028-0.01115.9571.1941.1940.0000.0000.0000.000
43A60SER00.0650.01712.247-0.648-0.6480.0000.0000.0000.000
44A61GLN00.0470.0008.8441.0091.0090.0000.0000.0000.000
45A62GLU-1-0.784-0.85711.849-22.812-22.8120.0000.0000.0000.000
46A63ILE0-0.0030.00415.0991.2241.2240.0000.0000.0000.000
47A64GLN0-0.024-0.00313.596-0.223-0.2230.0000.0000.0000.000
48A65VAL00.0530.02714.7850.7730.7730.0000.0000.0000.000
49A66LEU0-0.0100.00717.4710.9000.9000.0000.0000.0000.000
50A67ARG10.8770.93119.13015.56115.5610.0000.0000.0000.000
51A68VAL00.0210.01918.8630.6550.6550.0000.0000.0000.000
52A69VAL00.002-0.00120.8220.5850.5850.0000.0000.0000.000
53A70LYS10.8540.91023.28911.64111.6410.0000.0000.0000.000
54A71ASN0-0.036-0.02124.8280.7510.7510.0000.0000.0000.000
55A72PHE00.030-0.00124.6900.3820.3820.0000.0000.0000.000
56A73GLU-1-0.850-0.92326.725-10.756-10.7560.0000.0000.0000.000
57A74HIS0-0.061-0.02129.2020.5560.5560.0000.0000.0000.000
58A75LEU0-0.039-0.00328.3620.3120.3120.0000.0000.0000.000
59A76ASN0-0.011-0.00631.8820.1460.1460.0000.0000.0000.000
60A77SER0-0.031-0.02433.8910.1640.1640.0000.0000.0000.000
61A78ASP-1-0.796-0.90930.737-10.063-10.0630.0000.0000.0000.000
62A79PHE00.0370.02030.149-0.382-0.3820.0000.0000.0000.000
63A80ASP-1-0.792-0.87830.748-9.459-9.4590.0000.0000.0000.000
64A81ARG10.8050.88327.2519.5539.5530.0000.0000.0000.000
65A82TYR00.0210.00026.087-0.434-0.4340.0000.0000.0000.000
66A83LEU0-0.0080.00225.976-0.494-0.4940.0000.0000.0000.000
67A84LEU00.0010.00724.021-0.391-0.3910.0000.0000.0000.000
68A85LEU0-0.025-0.02020.741-0.713-0.7130.0000.0000.0000.000
69A86MET0-0.0070.00121.326-0.800-0.8000.0000.0000.0000.000
70A87ASP-1-0.825-0.90622.303-12.125-12.1250.0000.0000.0000.000
71A88LEU0-0.072-0.02817.587-0.422-0.4220.0000.0000.0000.000
72A89GLN0-0.0020.00817.580-0.738-0.7380.0000.0000.0000.000
73A90ASP-1-0.822-0.89917.741-14.263-14.2630.0000.0000.0000.000
74A91ARG10.8270.89417.92015.95215.9520.0000.0000.0000.000
75A92ASN0-0.037-0.04612.932-1.837-1.8370.0000.0000.0000.000
76A93GLU-1-0.750-0.85711.867-21.956-21.9560.0000.0000.0000.000
77A94LYS10.8080.8954.97245.11445.1140.0000.0000.0000.000
78A95LEU0-0.012-0.00310.6950.1360.1360.0000.0000.0000.000
79A96PHE00.0340.01213.2880.8810.8810.0000.0000.0000.000
80A97TYR00.0670.03012.3190.9830.9830.0000.0000.0000.000
81A98ARG10.8760.94710.24324.13924.1390.0000.0000.0000.000
82A99VAL0-0.017-0.00912.9430.7580.7580.0000.0000.0000.000
83A100LEU00.0040.01916.7240.6050.6050.0000.0000.0000.000
84A101THR0-0.033-0.04913.6550.3560.3560.0000.0000.0000.000
85A102SER0-0.136-0.06616.0460.4320.4320.0000.0000.0000.000
86A103ASP-1-0.831-0.92517.146-12.256-12.2560.0000.0000.0000.000
87A104ILE00.0240.01718.6020.5480.5480.0000.0000.0000.000
88A105GLU-1-0.864-0.93120.855-11.080-11.0800.0000.0000.0000.000
89A106LYS10.8880.95923.84512.86312.8630.0000.0000.0000.000
90A107PHE0-0.006-0.01920.2610.3220.3220.0000.0000.0000.000
91A108MET0-0.0100.00222.5180.0180.0180.0000.0000.0000.000
92A109PRO00.0010.01224.4370.1440.1440.0000.0000.0000.000
93A110ILE0-0.0440.00225.5080.3630.3630.0000.0000.0000.000
94A111VAL00.001-0.02421.8120.1250.1250.0000.0000.0000.000
95A112TYR00.0300.01125.025-0.089-0.0890.0000.0000.0000.000
96A113THR0-0.0170.01627.1140.2880.2880.0000.0000.0000.000
97A114PRO0-0.003-0.01730.000-0.161-0.1610.0000.0000.0000.000
98A115THR0-0.009-0.02229.6950.3230.3230.0000.0000.0000.000
99A116VAL00.0080.01027.8610.1690.1690.0000.0000.0000.000
100A117GLY00.0570.02830.3700.1010.1010.0000.0000.0000.000
101A118LEU0-0.005-0.00333.9690.1930.1930.0000.0000.0000.000
102A119ALA00.000-0.00631.1260.1290.1290.0000.0000.0000.000
103A120CYS0-0.037-0.00632.0080.0200.0200.0000.0000.0000.000
104A121GLN0-0.026-0.02034.3070.1140.1140.0000.0000.0000.000
105A122GLN0-0.044-0.02635.5750.2660.2660.0000.0000.0000.000
106A123TYR0-0.0130.00628.1170.0100.0100.0000.0000.0000.000
107A124SER00.031-0.01334.067-0.085-0.0850.0000.0000.0000.000
108A125LEU0-0.0210.01136.6380.0050.0050.0000.0000.0000.000
109A126VAL0-0.057-0.02932.400-0.037-0.0370.0000.0000.0000.000
110A127PHE00.0010.01330.451-0.444-0.4440.0000.0000.0000.000
111A128ARG10.8090.88728.05410.75910.7590.0000.0000.0000.000
112A129LYS10.8080.89423.40312.69412.6940.0000.0000.0000.000
113A130PRO00.0160.03026.075-0.108-0.1080.0000.0000.0000.000
114A131ARG10.8390.89118.24514.08314.0830.0000.0000.0000.000
115A132GLY00.0370.01022.6090.3310.3310.0000.0000.0000.000
116A133LEU0-0.022-0.00223.8770.1010.1010.0000.0000.0000.000
117A134PHE00.004-0.01726.3120.1440.1440.0000.0000.0000.000
118A135ILE0-0.0030.00328.614-0.007-0.0070.0000.0000.0000.000
119A136THR0-0.048-0.05032.3970.1760.1760.0000.0000.0000.000
120A137ILE00.0260.00436.226-0.008-0.0080.0000.0000.0000.000
121A138HIS0-0.037-0.02939.3210.1330.1330.0000.0000.0000.000
122A139ASP-1-0.852-0.89434.949-8.539-8.5390.0000.0000.0000.000
123A140ARG10.7920.86436.6257.4277.4270.0000.0000.0000.000
124A141GLY0-0.039-0.03037.8060.1900.1900.0000.0000.0000.000
125A142HIS0-0.010-0.00335.316-0.145-0.1450.0000.0000.0000.000
126A143ILE00.0380.03730.919-0.331-0.3310.0000.0000.0000.000
127A144ALA00.021-0.00529.632-0.342-0.3420.0000.0000.0000.000
128A145SER0-0.113-0.06228.822-0.304-0.3040.0000.0000.0000.000
129A146VAL00.0450.02028.890-0.305-0.3050.0000.0000.0000.000
130A147LEU00.013-0.01125.735-0.376-0.3760.0000.0000.0000.000
131A148ASN0-0.035-0.00724.358-0.846-0.8460.0000.0000.0000.000
132A149ALA0-0.0050.00924.703-0.145-0.1450.0000.0000.0000.000
133A150TRP0-0.0250.00018.658-0.067-0.0670.0000.0000.0000.000
134A151PRO0-0.043-0.02017.910-0.008-0.0080.0000.0000.0000.000
135A152GLU-1-0.860-0.89814.169-18.925-18.9250.0000.0000.0000.000
136A153ASP-1-0.820-0.92517.157-13.065-13.0650.0000.0000.0000.000
137A154VAL0-0.074-0.03013.6540.3020.3020.0000.0000.0000.000
138A155ILE0-0.039-0.01115.653-0.679-0.6790.0000.0000.0000.000
139A156LYS10.8260.89711.98220.53920.5390.0000.0000.0000.000
140A157ALA00.0060.00018.0190.4820.4820.0000.0000.0000.000
141A158ILE00.0210.01920.207-0.264-0.2640.0000.0000.0000.000
142A159VAL0-0.0330.00023.2580.2000.2000.0000.0000.0000.000
143A160VAL00.0050.00325.821-0.066-0.0660.0000.0000.0000.000
144A161THR00.016-0.01229.0800.2610.2610.0000.0000.0000.000
145A162ASP-1-0.737-0.85232.590-8.186-8.1860.0000.0000.0000.000
146A163GLY00.0470.03035.4260.1740.1740.0000.0000.0000.000
147A164GLU-1-0.847-0.90436.560-7.023-7.0230.0000.0000.0000.000
148A165ARG10.6530.79036.2678.7068.7060.0000.0000.0000.000
149A166ILE00.0370.04934.461-0.194-0.1940.0000.0000.0000.000
150A167LEU00.0200.00834.7470.3020.3020.0000.0000.0000.000
151A168GLY0-0.051-0.02537.262-0.059-0.0590.0000.0000.0000.000
152A169LEU0-0.107-0.05036.5560.1490.1490.0000.0000.0000.000
153A170GLY0-0.0030.01340.4800.1560.1560.0000.0000.0000.000
154A171ASP-1-0.725-0.80640.004-7.754-7.7540.0000.0000.0000.000
155A172LEU0-0.019-0.01236.9580.0930.0930.0000.0000.0000.000
156A173GLY00.0490.01938.104-0.096-0.0960.0000.0000.0000.000
157A174CYS0-0.029-0.01134.471-0.355-0.3550.0000.0000.0000.000
158A175ASN00.0540.03833.588-0.460-0.4600.0000.0000.0000.000
159A176GLY00.005-0.00833.564-0.189-0.1890.0000.0000.0000.000
160A177MET0-0.0340.00626.490-0.246-0.2460.0000.0000.0000.000
161A178GLY00.015-0.00228.232-0.436-0.4360.0000.0000.0000.000
162A179ILE0-0.021-0.01027.587-0.472-0.4720.0000.0000.0000.000
163A180PRO00.0130.00626.590-0.430-0.4300.0000.0000.0000.000
164A181VAL00.0140.01022.863-0.624-0.6240.0000.0000.0000.000
165A182GLY00.0130.01022.701-0.661-0.6610.0000.0000.0000.000
166A183LYS10.7390.84023.30910.52810.5280.0000.0000.0000.000
167A184LEU00.0170.00420.131-0.531-0.5310.0000.0000.0000.000
168A185ALA0-0.0070.00618.747-0.945-0.9450.0000.0000.0000.000
169A186LEU00.002-0.01318.563-0.867-0.8670.0000.0000.0000.000
170A187TYR00.002-0.01818.934-0.445-0.4450.0000.0000.0000.000
171A188THR0-0.033-0.00713.257-0.405-0.4050.0000.0000.0000.000
172A189ALA0-0.042-0.03215.014-1.070-1.0700.0000.0000.0000.000
173A190CYS0-0.034-0.02616.398-0.528-0.5280.0000.0000.0000.000
174A191GLY00.0650.02517.9490.2090.2090.0000.0000.0000.000
175A192GLY0-0.042-0.00813.587-0.391-0.3910.0000.0000.0000.000
176A193MET00.0330.02913.227-1.596-1.5960.0000.0000.0000.000
177A194ASN00.011-0.0089.804-1.183-1.1830.0000.0000.0000.000
178A195PRO0-0.0070.00711.4521.1531.1530.0000.0000.0000.000
179A196GLN0-0.009-0.0248.8680.1950.1950.0000.0000.0000.000
180A197GLU-1-0.794-0.86911.805-20.883-20.8830.0000.0000.0000.000
181A198CYS0-0.038-0.01614.8290.8970.8970.0000.0000.0000.000
182A199LEU00.0230.01117.920-0.078-0.0780.0000.0000.0000.000
183A200PRO00.000-0.00320.9100.4380.4380.0000.0000.0000.000
184A201VAL0-0.001-0.00224.1040.0490.0490.0000.0000.0000.000
185A202ILE0-0.013-0.00627.4820.1350.1350.0000.0000.0000.000
186A203LEU0-0.023-0.00831.1030.0290.0290.0000.0000.0000.000
187A204ASP-1-0.777-0.89334.015-7.817-7.8170.0000.0000.0000.000
188A205VAL00.0420.00336.8100.0960.0960.0000.0000.0000.000
189A206GLY00.0090.00840.2110.2600.2600.0000.0000.0000.000
190A207THR0-0.054-0.05741.006-0.145-0.1450.0000.0000.0000.000
191A208GLU-1-0.776-0.90243.024-6.443-6.4430.0000.0000.0000.000
192A209ASN0-0.062-0.03942.8310.2490.2490.0000.0000.0000.000
193A210GLU-1-0.760-0.88145.208-6.237-6.2370.0000.0000.0000.000
194A211GLU-1-0.846-0.90846.157-6.297-6.2970.0000.0000.0000.000
195A212LEU0-0.0090.00540.043-0.041-0.0410.0000.0000.0000.000
196A213LEU0-0.031-0.00943.929-0.016-0.0160.0000.0000.0000.000
197A214LYS10.7330.86046.3796.3366.3360.0000.0000.0000.000
198A215ASP-1-0.835-0.91742.071-7.363-7.3630.0000.0000.0000.000
199A216PRO0-0.045-0.01844.203-0.100-0.1000.0000.0000.0000.000
200A217LEU0-0.035-0.02840.085-0.081-0.0810.0000.0000.0000.000
201A218TYR0-0.0030.01438.419-0.321-0.3210.0000.0000.0000.000
202A219ILE0-0.014-0.00933.3010.0820.0820.0000.0000.0000.000
203A220GLY00.012-0.00236.292-0.235-0.2350.0000.0000.0000.000
204A221LEU0-0.071-0.02638.3860.2100.2100.0000.0000.0000.000
205A222ARG10.8240.90841.1197.0907.0900.0000.0000.0000.000
206A223GLN0-0.027-0.00743.4320.1990.1990.0000.0000.0000.000
207A224ARG10.8400.89745.0416.2036.2030.0000.0000.0000.000
208A225ARG10.7080.84638.7857.7007.7000.0000.0000.0000.000
209A226VAL00.0470.02443.2430.1580.1580.0000.0000.0000.000
210A227ARG10.7490.84644.0916.7856.7850.0000.0000.0000.000
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