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: MN9NZ

Calculation Name: 1NM8-A-Xray372

Preferred Name: Carnitine acetylase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NM8

Chain ID: A

ChEMBL ID: CHEMBL3184

UniProt ID: P43155

Base Structure: X-ray

Registration Date: 2023-09-22

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 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 591
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -13566488.784051
FMO2-HF: Nuclear repulsion 13330121.913235
FMO2-HF: Total energy -236366.870816
FMO2-MP2: Total energy -237052.242342


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:9:HIS)


Summations of interaction energy for fragment #1(A:9:HIS)
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.
0.00200000000000052.181-0.033-1.082-1.0630.001
Interaction energy analysis for fragmet #1(A:9:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.025
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].
3A11THR00.0110.0093.801-1.0071.172-0.033-1.082-1.0630.001
4A12ASP-1-0.914-0.9596.8781.2701.2700.0000.0000.0000.000
5A13PRO0-0.047-0.0179.261-0.150-0.1500.0000.0000.0000.000
6A14LEU00.0130.01411.553-0.114-0.1140.0000.0000.0000.000
7A15PRO0-0.0100.00714.8760.0530.0530.0000.0000.0000.000
8A16ARG10.9860.97517.971-0.574-0.5740.0000.0000.0000.000
9A17LEU0-0.019-0.00120.406-0.031-0.0310.0000.0000.0000.000
10A18PRO00.0130.01723.7100.0160.0160.0000.0000.0000.000
11A19VAL0-0.011-0.00226.171-0.004-0.0040.0000.0000.0000.000
12A20PRO00.0370.02129.6870.0020.0020.0000.0000.0000.000
13A21PRO00.0350.00531.9670.0030.0030.0000.0000.0000.000
14A22LEU00.0350.01234.837-0.005-0.0050.0000.0000.0000.000
15A23GLN00.0730.02137.941-0.004-0.0040.0000.0000.0000.000
16A24GLN0-0.0130.01833.561-0.001-0.0010.0000.0000.0000.000
17A25SER0-0.010-0.06335.573-0.007-0.0070.0000.0000.0000.000
18A26LEU0-0.0040.00738.093-0.004-0.0040.0000.0000.0000.000
19A27ASP-1-0.902-0.94141.5180.0630.0630.0000.0000.0000.000
20A28HIS0-0.078-0.05636.731-0.009-0.0090.0000.0000.0000.000
21A29TYR00.0110.01241.063-0.004-0.0040.0000.0000.0000.000
22A30LEU00.0600.02442.570-0.004-0.0040.0000.0000.0000.000
23A31LYS10.8870.94443.131-0.053-0.0530.0000.0000.0000.000
24A32ALA0-0.013-0.01042.263-0.004-0.0040.0000.0000.0000.000
25A33LEU00.0250.01544.409-0.002-0.0020.0000.0000.0000.000
26A34GLN0-0.045-0.01147.539-0.005-0.0050.0000.0000.0000.000
27A35PRO0-0.029-0.01547.286-0.002-0.0020.0000.0000.0000.000
28A36ILE0-0.053-0.02446.628-0.002-0.0020.0000.0000.0000.000
29A37VAL00.0080.01750.2450.0020.0020.0000.0000.0000.000
30A38SER0-0.013-0.01552.942-0.003-0.0030.0000.0000.0000.000
31A39GLU-1-0.928-0.98355.3970.0330.0330.0000.0000.0000.000
32A40GLU-1-0.929-0.97256.8750.0410.0410.0000.0000.0000.000
33A41GLU-1-0.860-0.92454.2180.0500.0500.0000.0000.0000.000
34A42TRP0-0.026-0.01949.0470.0030.0030.0000.0000.0000.000
35A43ALA0-0.022-0.01652.8200.0020.0020.0000.0000.0000.000
36A44HIS00.0170.02054.4680.0000.0000.0000.0000.0000.000
37A45THR00.008-0.02048.7960.0020.0020.0000.0000.0000.000
38A46LYS10.8980.95549.780-0.051-0.0510.0000.0000.0000.000
39A47GLN0-0.0240.00350.8100.0000.0000.0000.0000.0000.000
40A48LEU00.0230.01250.2050.0030.0030.0000.0000.0000.000
41A49VAL0-0.042-0.03145.4190.0050.0050.0000.0000.0000.000
42A50ASP-1-0.912-0.96647.0470.0680.0680.0000.0000.0000.000
43A51GLU-1-0.949-0.97248.9840.0730.0730.0000.0000.0000.000
44A52PHE0-0.075-0.03741.6390.0070.0070.0000.0000.0000.000
45A53GLN0-0.041-0.04943.7920.0100.0100.0000.0000.0000.000
46A54ALA00.0220.04245.1160.0000.0000.0000.0000.0000.000
47A55SER0-0.024-0.01645.7200.0040.0040.0000.0000.0000.000
48A56GLY0-0.031-0.02345.128-0.003-0.0030.0000.0000.0000.000
49A57GLY00.0090.01645.9820.0000.0000.0000.0000.0000.000
50A58VAL0-0.009-0.02643.9900.0070.0070.0000.0000.0000.000
51A59GLY00.0520.02942.0440.0080.0080.0000.0000.0000.000
52A60GLU-1-0.830-0.92440.1050.1180.1180.0000.0000.0000.000
53A61ARG10.8920.96139.232-0.130-0.1300.0000.0000.0000.000
54A62LEU0-0.043-0.02038.6890.0120.0120.0000.0000.0000.000
55A63GLN00.0300.01733.7940.0080.0080.0000.0000.0000.000
56A64LYN00.0240.02833.1270.0230.0230.0000.0000.0000.000
57A65GLY0-0.018-0.01933.9190.0170.0170.0000.0000.0000.000
58A66LEU00.0020.00131.9100.0200.0200.0000.0000.0000.000
59A67GLU-1-0.876-0.93929.9030.2060.2060.0000.0000.0000.000
60A68ARG10.8880.94728.957-0.190-0.1900.0000.0000.0000.000
61A69ARG10.8850.94928.761-0.234-0.2340.0000.0000.0000.000
62A70ALA00.0280.01625.7330.0300.0300.0000.0000.0000.000
63A71ARG10.8670.92824.316-0.236-0.2360.0000.0000.0000.000
64A72LYS10.8770.94024.423-0.273-0.2730.0000.0000.0000.000
65A73THR0-0.0080.00523.8810.0090.0090.0000.0000.0000.000
66A74GLU-1-0.858-0.91718.1850.7150.7150.0000.0000.0000.000
67A75ASN00.017-0.00620.721-0.031-0.0310.0000.0000.0000.000
68A76TRP0-0.010-0.01023.320-0.007-0.0070.0000.0000.0000.000
69A77LEU00.0220.01326.698-0.018-0.0180.0000.0000.0000.000
70A78SER0-0.026-0.00924.501-0.007-0.0070.0000.0000.0000.000
71A79GLU-1-0.906-0.95526.5970.3330.3330.0000.0000.0000.000
72A80TRP0-0.009-0.02528.663-0.015-0.0150.0000.0000.0000.000
73A81TRP00.0620.04629.122-0.013-0.0130.0000.0000.0000.000
74A82LEU00.0570.04027.430-0.014-0.0140.0000.0000.0000.000
75A83LYS10.9200.95730.556-0.211-0.2110.0000.0000.0000.000
76A84THR0-0.047-0.04533.521-0.014-0.0140.0000.0000.0000.000
77A85ALA00.0230.03433.309-0.011-0.0110.0000.0000.0000.000
78A86TYR00.0390.01630.546-0.002-0.0020.0000.0000.0000.000
79A87LEU0-0.064-0.02131.049-0.008-0.0080.0000.0000.0000.000
80A88GLN0-0.014-0.02835.184-0.006-0.0060.0000.0000.0000.000
81A89TYR00.0570.05137.940-0.008-0.0080.0000.0000.0000.000
82A90ARG10.8130.87539.805-0.128-0.1280.0000.0000.0000.000
83A91GLN00.0220.02942.494-0.002-0.0020.0000.0000.0000.000
84A92PRO0-0.016-0.01141.9170.0060.0060.0000.0000.0000.000
85A93VAL00.0310.00737.095-0.001-0.0010.0000.0000.0000.000
86A94VAL00.0100.01639.580-0.002-0.0020.0000.0000.0000.000
87A95ILE00.0280.02941.256-0.001-0.0010.0000.0000.0000.000
88A96TYR0-0.009-0.02241.6900.0000.0000.0000.0000.0000.000
89A97SER0-0.0300.00335.9850.0060.0060.0000.0000.0000.000
90A98SER0-0.021-0.03335.4200.0050.0050.0000.0000.0000.000
91A99PRO00.0230.03033.710-0.008-0.0080.0000.0000.0000.000
92A100GLY00.0050.00535.4710.0030.0030.0000.0000.0000.000
93A101VAL0-0.025-0.01833.057-0.003-0.0030.0000.0000.0000.000
94A102MET00.0020.00536.4380.0010.0010.0000.0000.0000.000
95A103LEU0-0.021-0.01633.738-0.004-0.0040.0000.0000.0000.000
96A104PRO00.0110.00537.2040.0020.0020.0000.0000.0000.000
97A105LYS10.8900.95340.1310.0070.0070.0000.0000.0000.000
98A106GLN0-0.036-0.02537.849-0.008-0.0080.0000.0000.0000.000
99A107ASP-1-0.926-0.96641.989-0.028-0.0280.0000.0000.0000.000
100A108PHE0-0.0460.00940.7420.0000.0000.0000.0000.0000.000
101A109VAL00.0230.00244.9060.0020.0020.0000.0000.0000.000
102A110ASP-1-0.860-0.91947.257-0.009-0.0090.0000.0000.0000.000
103A111LEU00.0360.00845.1740.0000.0000.0000.0000.0000.000
104A112GLN00.0380.03943.399-0.001-0.0010.0000.0000.0000.000
105A113GLY00.038-0.01642.817-0.001-0.0010.0000.0000.0000.000
106A114GLN00.0400.02841.543-0.002-0.0020.0000.0000.0000.000
107A115LEU0-0.011-0.02740.2360.0020.0020.0000.0000.0000.000
108A116ARG10.8490.93438.5810.0160.0160.0000.0000.0000.000
109A117PHE00.0470.02635.801-0.001-0.0010.0000.0000.0000.000
110A118ALA00.0150.00335.5180.0010.0010.0000.0000.0000.000
111A119ALA0-0.017-0.01334.4470.0050.0050.0000.0000.0000.000
112A120LYS10.9430.97731.3720.0480.0480.0000.0000.0000.000
113A121LEU00.0120.01430.885-0.003-0.0030.0000.0000.0000.000
114A122ILE0-0.043-0.02829.8290.0050.0050.0000.0000.0000.000
115A123GLU-1-0.870-0.94927.8750.0060.0060.0000.0000.0000.000
116A124GLY00.0360.01026.583-0.004-0.0040.0000.0000.0000.000
117A125VAL0-0.048-0.02025.094-0.001-0.0010.0000.0000.0000.000
118A126LEU0-0.052-0.02923.8800.0170.0170.0000.0000.0000.000
119A127ASP-1-0.846-0.89022.356-0.075-0.0750.0000.0000.0000.000
120A128PHE00.007-0.00120.448-0.004-0.0040.0000.0000.0000.000
121A129LYS10.7950.85919.203-0.158-0.1580.0000.0000.0000.000
122A130VAL00.0000.02316.4130.0390.0390.0000.0000.0000.000
123A131MET00.0120.00914.7990.0040.0040.0000.0000.0000.000
124A132ILE0-0.050-0.01314.2730.0510.0510.0000.0000.0000.000
125A133ASP-1-0.850-0.91615.2630.3000.3000.0000.0000.0000.000
126A134ASN0-0.078-0.03312.0320.0870.0870.0000.0000.0000.000
127A135GLU-1-0.968-0.97710.1441.0661.0660.0000.0000.0000.000
128A136THR0-0.048-0.0279.463-0.014-0.0140.0000.0000.0000.000
129A137LEU0-0.034-0.00911.283-0.103-0.1030.0000.0000.0000.000
130A138PRO0-0.020-0.00712.640-0.009-0.0090.0000.0000.0000.000
131A139VAL00.0280.00011.0550.0760.0760.0000.0000.0000.000
132A140GLU-1-0.785-0.87813.822-0.055-0.0550.0000.0000.0000.000
133A141TYR0-0.010-0.02211.8150.0120.0120.0000.0000.0000.000
134A142LEU00.0110.00518.073-0.005-0.0050.0000.0000.0000.000
135A143GLY0-0.011-0.00721.1200.0120.0120.0000.0000.0000.000
136A144GLY0-0.014-0.01118.6900.0060.0060.0000.0000.0000.000
137A145LYS10.9210.96317.091-0.067-0.0670.0000.0000.0000.000
138A146PRO00.0430.03113.425-0.017-0.0170.0000.0000.0000.000
139A147LEU0-0.031-0.01915.5190.0490.0490.0000.0000.0000.000
140A148CYM-1-0.823-0.88315.9980.3870.3870.0000.0000.0000.000
141A149MET00.0000.01514.601-0.058-0.0580.0000.0000.0000.000
142A150ASN00.031-0.00716.9190.0300.0300.0000.0000.0000.000
143A151GLN00.0440.00118.005-0.021-0.0210.0000.0000.0000.000
144A152TYR00.015-0.02118.346-0.005-0.0050.0000.0000.0000.000
145A153TYR0-0.0200.01013.056-0.006-0.0060.0000.0000.0000.000
146A154GLN0-0.060-0.03319.0470.0120.0120.0000.0000.0000.000
147A155ILE0-0.0010.01422.562-0.015-0.0150.0000.0000.0000.000
148A156LEU00.0220.01322.061-0.011-0.0110.0000.0000.0000.000
149A157SER0-0.028-0.01723.9990.0210.0210.0000.0000.0000.000
150A158SER00.0000.01825.4480.0160.0160.0000.0000.0000.000
151A159CYS0-0.088-0.03027.314-0.026-0.0260.0000.0000.0000.000
152A160ARG10.8540.93130.841-0.130-0.1300.0000.0000.0000.000
153A161VAL0-0.014-0.01332.828-0.008-0.0080.0000.0000.0000.000
154A162PRO0-0.0070.00635.3680.0050.0050.0000.0000.0000.000
155A163GLY00.0520.02438.7470.0050.0050.0000.0000.0000.000
156A164PRO0-0.046-0.02839.838-0.006-0.0060.0000.0000.0000.000
157A165LYS10.9210.95841.174-0.150-0.1500.0000.0000.0000.000
158A166GLN00.0590.02735.144-0.013-0.0130.0000.0000.0000.000
159A167ASP-1-0.763-0.85735.7170.1430.1430.0000.0000.0000.000
160A168THR0-0.028-0.01532.1130.0120.0120.0000.0000.0000.000
161A169VAL00.0610.01827.658-0.014-0.0140.0000.0000.0000.000
162A170SER0-0.051-0.00828.0650.0200.0200.0000.0000.0000.000
163A171ASN00.0440.04421.721-0.019-0.0190.0000.0000.0000.000
164A172PHE0-0.045-0.04824.3970.0220.0220.0000.0000.0000.000
165A173SER00.044-0.01020.4030.0160.0160.0000.0000.0000.000
166A174LYS11.0251.02715.570-0.715-0.7150.0000.0000.0000.000
167A175THR0-0.074-0.02619.7480.0260.0260.0000.0000.0000.000
168A176LYS10.9610.96421.527-0.345-0.3450.0000.0000.0000.000
169A177LYS10.9350.95722.537-0.221-0.2210.0000.0000.0000.000
170A178PRO00.0310.04720.995-0.021-0.0210.0000.0000.0000.000
171A179PRO0-0.028-0.01524.092-0.017-0.0170.0000.0000.0000.000
172A180THR00.0510.03025.5500.0050.0050.0000.0000.0000.000
173A181HIS0-0.023-0.01227.560-0.013-0.0130.0000.0000.0000.000
174A182ILE00.006-0.00229.5220.0110.0110.0000.0000.0000.000
175A183THR00.0040.02031.846-0.003-0.0030.0000.0000.0000.000
176A184VAL0-0.0090.00535.147-0.003-0.0030.0000.0000.0000.000
177A185VAL0-0.013-0.00837.8100.0030.0030.0000.0000.0000.000
178A186HIS10.8800.95240.940-0.037-0.0370.0000.0000.0000.000
179A187ASN00.0140.00944.1430.0010.0010.0000.0000.0000.000
180A188TYR0-0.055-0.04445.3330.0020.0020.0000.0000.0000.000
181A189GLN0-0.085-0.03045.0720.0050.0050.0000.0000.0000.000
182A190PHE00.0620.02538.843-0.002-0.0020.0000.0000.0000.000
183A191PHE0-0.034-0.02539.712-0.001-0.0010.0000.0000.0000.000
184A192GLU-1-0.888-0.91334.7410.1140.1140.0000.0000.0000.000
185A193LEU0-0.022-0.03133.991-0.005-0.0050.0000.0000.0000.000
186A194ASP-1-0.877-0.93531.8290.1070.1070.0000.0000.0000.000
187A195VAL0-0.044-0.03727.895-0.010-0.0100.0000.0000.0000.000
188A196TYR00.0250.01923.1540.0040.0040.0000.0000.0000.000
189A197HIS10.8460.92628.404-0.030-0.0300.0000.0000.0000.000
190A198SER0-0.004-0.01128.4850.0080.0080.0000.0000.0000.000
191A199ASP-1-0.864-0.91526.8760.0620.0620.0000.0000.0000.000
192A200GLY0-0.005-0.00324.0870.0060.0060.0000.0000.0000.000
193A201THR0-0.016-0.02123.934-0.003-0.0030.0000.0000.0000.000
194A202PRO00.0230.01124.3660.0080.0080.0000.0000.0000.000
195A203LEU0-0.120-0.05027.055-0.006-0.0060.0000.0000.0000.000
196A204THR00.0610.03229.4770.0000.0000.0000.0000.0000.000
197A205ALA00.0610.01631.2400.0070.0070.0000.0000.0000.000
198A206ASP-1-0.869-0.91533.504-0.012-0.0120.0000.0000.0000.000
199A207GLN00.0440.01332.9100.0080.0080.0000.0000.0000.000
200A208ILE00.0240.01530.7720.0070.0070.0000.0000.0000.000
201A209PHE0-0.025-0.01535.3540.0040.0040.0000.0000.0000.000
202A210VAL00.0140.01238.5350.0030.0030.0000.0000.0000.000
203A211GLN00.022-0.00136.475-0.002-0.0020.0000.0000.0000.000
204A212LEU00.009-0.00436.8250.0050.0050.0000.0000.0000.000
205A213GLU-1-0.893-0.93740.1630.0080.0080.0000.0000.0000.000
206A214LYS10.8170.91440.981-0.029-0.0290.0000.0000.0000.000
207A215ILE00.0050.00938.5730.0020.0020.0000.0000.0000.000
208A216TRP00.0170.02043.0430.0030.0030.0000.0000.0000.000
209A217ASN00.031-0.00745.2940.0010.0010.0000.0000.0000.000
210A218SER0-0.084-0.03045.6560.0010.0010.0000.0000.0000.000
211A219SER0-0.088-0.07045.5900.0040.0040.0000.0000.0000.000
212A220LEU00.0430.03648.0130.0000.0000.0000.0000.0000.000
213A221GLN0-0.044-0.02050.891-0.001-0.0010.0000.0000.0000.000
214A222THR00.0680.02751.2260.0020.0020.0000.0000.0000.000
215A223ASN0-0.026-0.01053.1880.0010.0010.0000.0000.0000.000
216A224LYS10.9250.96650.256-0.046-0.0460.0000.0000.0000.000
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