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: NNN9Q

Calculation Name: 4D1E-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-methyl-lysine

ligand 3-letter code: MLZ

PDB ID: 4D1E

Chain ID: A

ChEMBL ID:

UniProt ID: P35609

Base Structure: X-ray

Registration Date: 2023-09-21

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 859
LigandResidueName
LigandFragmentNumber 0
LigandCharge MLZ=1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -14266414.616209
FMO2-HF: Nuclear repulsion 13914472.81927
FMO2-HF: Total energy -351941.796939
FMO2-MP2: Total energy -352960.386093


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:34:PRO)


Summations of interaction energy for fragment #1(A:34: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.
-11.48-5.4483.598-4.267-5.36-0.018
Interaction energy analysis for fragmet #1(A:34:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.020
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].
3A36TRP00.0370.0113.791-1.7140.420-0.018-0.822-1.2930.001
4A37GLU-1-0.822-0.9052.060-4.107-1.4433.562-3.124-3.102-0.018
5A38LYS10.8300.9123.2581.2922.3240.055-0.291-0.796-0.001
6A39GLN00.0640.0304.6220.0200.072-0.001-0.008-0.0420.000
7A40GLN0-0.112-0.0676.6890.0030.0030.0000.0000.0000.000
8A41ARG10.8050.8653.7860.1750.3250.000-0.022-0.1270.000
9A42MLZ10.8981.0028.9640.3970.3970.0000.0000.0000.000
10A43THR00.006-0.00611.2040.0380.0380.0000.0000.0000.000
11A44PHE00.0360.01311.9190.0230.0230.0000.0000.0000.000
12A45THR00.025-0.00112.0940.0050.0050.0000.0000.0000.000
13A46ALA00.015-0.00714.593-0.002-0.0020.0000.0000.0000.000
14A47TRP00.0790.02416.4640.0030.0030.0000.0000.0000.000
15A48CYS0-0.072-0.01916.5990.0060.0060.0000.0000.0000.000
16A49ASN00.0490.02018.3960.0090.0090.0000.0000.0000.000
17A50SER0-0.047-0.02820.778-0.008-0.0080.0000.0000.0000.000
18A51HIS00.0730.02222.183-0.016-0.0160.0000.0000.0000.000
19A52LEU0-0.026-0.00421.3630.0000.0000.0000.0000.0000.000
20A53ARG10.8020.86924.7930.0010.0010.0000.0000.0000.000
21A54LYS10.8160.90226.476-0.057-0.0570.0000.0000.0000.000
22A55ALA0-0.0030.00827.2580.0000.0000.0000.0000.0000.000
23A56GLY0-0.0110.01228.504-0.002-0.0020.0000.0000.0000.000
24A57THR0-0.056-0.03724.519-0.007-0.0070.0000.0000.0000.000
25A58GLN00.0460.01821.8230.0150.0150.0000.0000.0000.000
26A59ILE0-0.069-0.03016.0760.0040.0040.0000.0000.0000.000
27A60GLU-1-0.884-0.93117.517-0.130-0.1300.0000.0000.0000.000
28A61ASN0-0.031-0.03312.111-0.025-0.0250.0000.0000.0000.000
29A62ILE00.000-0.00110.5480.0500.0500.0000.0000.0000.000
30A63GLU-1-0.874-0.9328.354-0.105-0.1050.0000.0000.0000.000
31A64GLU-1-0.923-0.97012.222-0.038-0.0380.0000.0000.0000.000
32A65ASP-1-0.771-0.88015.559-0.002-0.0020.0000.0000.0000.000
33A66PHE0-0.011-0.02516.360-0.003-0.0030.0000.0000.0000.000
34A67ARG10.8310.95015.373-0.090-0.0900.0000.0000.0000.000
35A68ASN0-0.102-0.04619.2010.0020.0020.0000.0000.0000.000
36A69GLY00.1500.06822.047-0.006-0.0060.0000.0000.0000.000
37A70LEU0-0.025-0.03323.0020.0050.0050.0000.0000.0000.000
38A71MLZ10.8290.91321.191-0.005-0.0050.0000.0000.0000.000
39A72LEU00.0460.02119.807-0.001-0.0010.0000.0000.0000.000
40A73MET0-0.058-0.01622.3120.0000.0000.0000.0000.0000.000
41A74LEU00.0300.00025.9230.0000.0000.0000.0000.0000.000
42A75LEU00.0190.01620.288-0.004-0.0040.0000.0000.0000.000
43A76LEU0-0.010-0.00123.4810.0020.0020.0000.0000.0000.000
44A77GLU-1-0.831-0.90925.9110.0740.0740.0000.0000.0000.000
45A78VAL0-0.044-0.00426.799-0.007-0.0070.0000.0000.0000.000
46A79ILE0-0.055-0.02823.341-0.003-0.0030.0000.0000.0000.000
47A80SER0-0.102-0.05527.2810.0030.0030.0000.0000.0000.000
48A81GLY0-0.0160.00929.850-0.004-0.0040.0000.0000.0000.000
49A82GLU-1-0.828-0.89932.6260.0960.0960.0000.0000.0000.000
50A83ARG10.9380.96432.609-0.057-0.0570.0000.0000.0000.000
51A84LEU00.0010.00628.1480.0030.0030.0000.0000.0000.000
52A85PRO0-0.059-0.03132.335-0.008-0.0080.0000.0000.0000.000
53A86LYS10.9870.98032.635-0.054-0.0540.0000.0000.0000.000
54A87PRO0-0.0020.00029.7050.0000.0000.0000.0000.0000.000
55A88ASP-1-0.899-0.94831.5510.0570.0570.0000.0000.0000.000
56A89ARG10.9210.96429.871-0.042-0.0420.0000.0000.0000.000
57A90GLY00.0750.02829.570-0.006-0.0060.0000.0000.0000.000
58A91LYS10.9450.96727.7520.0040.0040.0000.0000.0000.000
59A92MET00.0240.02526.7390.0050.0050.0000.0000.0000.000
60A93ARG10.8780.88220.827-0.158-0.1580.0000.0000.0000.000
61A94PHE00.0590.01226.2450.0090.0090.0000.0000.0000.000
62A95HIS00.0420.03728.5110.0050.0050.0000.0000.0000.000
63A96MLZ10.9400.99422.341-0.064-0.0640.0000.0000.0000.000
64A97ILE00.0180.00123.8220.0080.0080.0000.0000.0000.000
65A98ALA00.0120.01525.6480.0110.0110.0000.0000.0000.000
66A99ASN0-0.049-0.05126.4170.0000.0000.0000.0000.0000.000
67A100VAL00.0550.02921.6400.0020.0020.0000.0000.0000.000
68A101ASN00.0190.00424.7100.0160.0160.0000.0000.0000.000
69A102MLZ10.9600.99326.927-0.096-0.0960.0000.0000.0000.000
70A103ALA0-0.017-0.01924.366-0.003-0.0030.0000.0000.0000.000
71A104LEU0-0.058-0.03621.2900.0130.0130.0000.0000.0000.000
72A105ASP-1-0.912-0.96325.0430.1770.1770.0000.0000.0000.000
73A106TYR0-0.076-0.03727.532-0.003-0.0030.0000.0000.0000.000
74A107ILE00.0130.02822.455-0.002-0.0020.0000.0000.0000.000
75A108ALA0-0.003-0.00426.4560.0020.0020.0000.0000.0000.000
76A109SER0-0.106-0.05827.486-0.009-0.0090.0000.0000.0000.000
77A110LYS10.8380.90628.820-0.123-0.1230.0000.0000.0000.000
78A111GLY0-0.048-0.02927.749-0.005-0.0050.0000.0000.0000.000
79A112VAL00.0120.02022.9120.0060.0060.0000.0000.0000.000
80A113LYS10.9230.97525.419-0.283-0.2830.0000.0000.0000.000
81A114LEU00.0330.01521.0400.0240.0240.0000.0000.0000.000
82A115VAL0-0.015-0.02420.224-0.033-0.0330.0000.0000.0000.000
83A116SER00.0060.00018.2670.0210.0210.0000.0000.0000.000
84A117ILE0-0.008-0.00715.8130.0550.0550.0000.0000.0000.000
85A118GLY00.0660.05118.545-0.034-0.0340.0000.0000.0000.000
86A119ALA00.013-0.00719.7480.0200.0200.0000.0000.0000.000
87A120GLU-1-0.883-0.95120.3130.2870.2870.0000.0000.0000.000
88A121GLU-1-0.839-0.91515.1470.4190.4190.0000.0000.0000.000
89A122ILE00.007-0.00216.1980.0100.0100.0000.0000.0000.000
90A123VAL0-0.011-0.00717.049-0.028-0.0280.0000.0000.0000.000
91A124ASP-1-0.812-0.85316.6260.1510.1510.0000.0000.0000.000
92A125GLY0-0.030-0.02414.239-0.022-0.0220.0000.0000.0000.000
93A126ASN0-0.071-0.03211.0390.1790.1790.0000.0000.0000.000
94A127VAL00.1030.0426.9340.1040.1040.0000.0000.0000.000
95A128LYS10.9490.9664.976-2.675-2.6750.0000.0000.0000.000
96A129MET00.0320.0189.0430.0020.0020.0000.0000.0000.000
97A130THR00.0110.00812.179-0.109-0.1090.0000.0000.0000.000
98A131LEU0-0.045-0.0347.800-0.086-0.0860.0000.0000.0000.000
99A132GLY00.0010.00111.108-0.093-0.0930.0000.0000.0000.000
100A133MET00.0340.01913.290-0.057-0.0570.0000.0000.0000.000
101A134ILE00.0160.03514.422-0.055-0.0550.0000.0000.0000.000
102A135TRP00.0550.02913.868-0.026-0.0260.0000.0000.0000.000
103A136THR0-0.059-0.03515.770-0.064-0.0640.0000.0000.0000.000
104A137ILE00.0730.03619.023-0.041-0.0410.0000.0000.0000.000
105A138ILE00.0260.02816.061-0.031-0.0310.0000.0000.0000.000
106A139LEU0-0.047-0.02619.435-0.025-0.0250.0000.0000.0000.000
107A140ARG10.8740.93020.979-0.202-0.2020.0000.0000.0000.000
108A141PHE0-0.032-0.05823.575-0.016-0.0160.0000.0000.0000.000
109A142ALA0-0.0070.01722.013-0.018-0.0180.0000.0000.0000.000
110A143ILE00.003-0.00119.326-0.010-0.0100.0000.0000.0000.000
111A144GLN0-0.013-0.02523.789-0.002-0.0020.0000.0000.0000.000
112A145ASP-1-0.937-0.96026.1780.1200.1200.0000.0000.0000.000
113A146ILE0-0.0190.02526.942-0.014-0.0140.0000.0000.0000.000
114A147SER00.015-0.01529.9510.0110.0110.0000.0000.0000.000
115A148VAL0-0.056-0.01731.582-0.009-0.0090.0000.0000.0000.000
116A149GLU-1-0.806-0.89334.1600.0750.0750.0000.0000.0000.000
117A150GLU-1-0.922-0.95236.4870.0960.0960.0000.0000.0000.000
118A151THR0-0.0330.01130.7130.0120.0120.0000.0000.0000.000
119A152SER00.059-0.00130.195-0.008-0.0080.0000.0000.0000.000
120A153ALA0-0.024-0.00625.7730.0140.0140.0000.0000.0000.000
121A154LYS10.9040.94719.101-0.379-0.3790.0000.0000.0000.000
122A155GLU-1-0.881-0.95624.1360.2040.2040.0000.0000.0000.000
123A156GLY00.0420.03126.662-0.016-0.0160.0000.0000.0000.000
124A157LEU0-0.017-0.01222.426-0.013-0.0130.0000.0000.0000.000
125A158LEU0-0.024-0.00523.221-0.015-0.0150.0000.0000.0000.000
126A159LEU0-0.0030.00225.979-0.015-0.0150.0000.0000.0000.000
127A160TRP00.017-0.00727.275-0.013-0.0130.0000.0000.0000.000
128A161CYS0-0.048-0.01925.563-0.011-0.0110.0000.0000.0000.000
129A162GLN00.0020.01527.978-0.011-0.0110.0000.0000.0000.000
130A163ARG10.7860.87829.650-0.080-0.0800.0000.0000.0000.000
131A164MLZ10.8450.91930.818-0.060-0.0600.0000.0000.0000.000
132A165THR0-0.026-0.04528.031-0.008-0.0080.0000.0000.0000.000
133A166ALA00.0350.05431.276-0.005-0.0050.0000.0000.0000.000
134A167PRO0-0.063-0.04533.690-0.004-0.0040.0000.0000.0000.000
135A168TYR0-0.050-0.04531.445-0.002-0.0020.0000.0000.0000.000
136A169ARG10.9460.97532.270-0.011-0.0110.0000.0000.0000.000
137A170ASN0-0.013-0.00829.4000.0070.0070.0000.0000.0000.000
138A171VAL0-0.0090.01826.727-0.002-0.0020.0000.0000.0000.000
139A172ASN00.0220.03027.3500.0130.0130.0000.0000.0000.000
140A173ILE0-0.034-0.02924.4140.0010.0010.0000.0000.0000.000
141A174GLN0-0.024-0.02923.9460.0110.0110.0000.0000.0000.000
142A175ASN0-0.025-0.02018.943-0.004-0.0040.0000.0000.0000.000
143A176PHE00.0660.01718.194-0.015-0.0150.0000.0000.0000.000
144A177HIS0-0.002-0.01215.123-0.008-0.0080.0000.0000.0000.000
145A178THR00.0490.00516.211-0.027-0.0270.0000.0000.0000.000
146A179SER0-0.0250.02218.196-0.023-0.0230.0000.0000.0000.000
147A180TRP00.0510.01518.616-0.024-0.0240.0000.0000.0000.000
148A181MLZ10.7960.91814.2590.1630.1630.0000.0000.0000.000
149A182ASP-1-0.799-0.91018.381-0.063-0.0630.0000.0000.0000.000
150A183GLY00.0590.02821.192-0.020-0.0200.0000.0000.0000.000
151A184LEU0-0.037-0.01321.9760.0080.0080.0000.0000.0000.000
152A185GLY00.016-0.00924.2690.0070.0070.0000.0000.0000.000
153A186LEU0-0.028-0.02420.0800.0080.0080.0000.0000.0000.000
154A187CYS0-0.0120.00024.1020.0010.0010.0000.0000.0000.000
155A188ALA00.0130.02626.7290.0000.0000.0000.0000.0000.000
156A189LEU00.0090.01125.6230.0000.0000.0000.0000.0000.000
157A190ILE00.0450.02825.5410.0020.0020.0000.0000.0000.000
158A191HIS00.0570.05229.8080.0010.0010.0000.0000.0000.000
159A192ARG10.8570.91832.179-0.021-0.0210.0000.0000.0000.000
160A193HIS0-0.103-0.05831.0480.0090.0090.0000.0000.0000.000
161A194ARG10.8400.89833.0950.0060.0060.0000.0000.0000.000
162A195PRO00.0170.00534.222-0.005-0.0050.0000.0000.0000.000
163A196ASP-1-0.847-0.89236.071-0.016-0.0160.0000.0000.0000.000
164A197LEU0-0.0140.00431.180-0.004-0.0040.0000.0000.0000.000
165A198ILE0-0.037-0.01028.910-0.007-0.0070.0000.0000.0000.000
166A199ASP-1-0.788-0.86632.885-0.041-0.0410.0000.0000.0000.000
167A200TYR00.000-0.01928.624-0.004-0.0040.0000.0000.0000.000
168A201SER0-0.036-0.04432.675-0.001-0.0010.0000.0000.0000.000
169A202LYS10.8290.90432.4820.0570.0570.0000.0000.0000.000
170A203LEU0-0.0170.02127.959-0.008-0.0080.0000.0000.0000.000
171A204ASN00.0090.00629.0030.0180.0180.0000.0000.0000.000
172A205LYS10.9330.95524.4560.0590.0590.0000.0000.0000.000
173A206ASP-1-0.906-0.96024.613-0.112-0.1120.0000.0000.0000.000
174A207ASP-1-0.821-0.90522.967-0.206-0.2060.0000.0000.0000.000
175A208PRO00.0210.01719.4100.0020.0020.0000.0000.0000.000
176A209ILE0-0.036-0.02416.9550.0050.0050.0000.0000.0000.000
177A210GLY00.0320.01319.554-0.001-0.0010.0000.0000.0000.000
178A211ASN0-0.043-0.02022.8750.0180.0180.0000.0000.0000.000
179A212ILE0-0.012-0.01217.0330.0140.0140.0000.0000.0000.000
180A213ASN0-0.061-0.05319.7480.0210.0210.0000.0000.0000.000
181A214LEU00.0400.05121.0240.0050.0050.0000.0000.0000.000
182A215ALA00.007-0.00522.7290.0140.0140.0000.0000.0000.000
183A216MET0-0.087-0.03816.9110.0010.0010.0000.0000.0000.000
184A217GLU-1-0.856-0.93922.058-0.090-0.0900.0000.0000.0000.000
185A218ILE00.0200.04024.6660.0070.0070.0000.0000.0000.000
186A219ALA0-0.023-0.01824.2200.0090.0090.0000.0000.0000.000
187A220GLU-1-0.866-0.94823.268-0.065-0.0650.0000.0000.0000.000
188A221LYS10.7640.88425.8070.0800.0800.0000.0000.0000.000
189A222HIS0-0.044-0.03628.941-0.002-0.0020.0000.0000.0000.000
190A223LEU0-0.0210.00827.6290.0050.0050.0000.0000.0000.000
191A224ASP-1-0.797-0.85427.391-0.013-0.0130.0000.0000.0000.000
192A225ILE0-0.012-0.01123.7720.0130.0130.0000.0000.0000.000
193A226PRO00.0560.03019.936-0.010-0.0100.0000.0000.0000.000
194A227LYS10.9320.97419.7910.1530.1530.0000.0000.0000.000
195A228MET0-0.088-0.02715.984-0.028-0.0280.0000.0000.0000.000
196A229LEU00.0740.00213.4230.0530.0530.0000.0000.0000.000
197A230ASP-1-0.875-0.9489.404-0.840-0.8400.0000.0000.0000.000
198A231ALA0-0.017-0.00712.047-0.010-0.0100.0000.0000.0000.000
199A232GLU-1-0.825-0.8998.309-1.411-1.4110.0000.0000.0000.000
200A233ASP-1-0.757-0.8796.638-1.990-1.9900.0000.0000.0000.000
201A234ILE0-0.045-0.00710.1820.1120.1120.0000.0000.0000.000
202A235VAL00.0340.01112.9880.0630.0630.0000.0000.0000.000
203A236ASN0-0.028-0.01611.2440.0870.0870.0000.0000.0000.000
204A237THR0-0.036-0.0198.138-0.049-0.0490.0000.0000.0000.000
205A238PRO0-0.013-0.0109.8220.0990.0990.0000.0000.0000.000
206A239MLZ10.9110.95911.298-0.550-0.5500.0000.0000.0000.000
207A240PRO00.0120.01310.6150.0980.0980.0000.0000.0000.000
208A241ASP-1-0.812-0.9088.7851.3041.3040.0000.0000.0000.000
209A242GLU-1-0.852-0.92810.8670.3560.3560.0000.0000.0000.000
210A243ARG10.9540.98910.968-1.153-1.1530.0000.0000.0000.000
211A244ALA0-0.0010.01010.742-0.089-0.0890.0000.0000.0000.000
212A245ILE00.0290.01712.894-0.083-0.0830.0000.0000.0000.000
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