Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 5JMJZ

Calculation Name: 3PSS-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 3PSS

Chain ID: A

ChEMBL ID:

UniProt ID: A0KF03

Base Structure: X-ray

Registration Date: 2023-09-24

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 216
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2520878.631344
FMO2-HF: Nuclear repulsion 2431913.660206
FMO2-HF: Total energy -88964.971138
FMO2-MP2: Total energy -89212.242518


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-6.81.4767.394-5.321-10.347-0.034
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / 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].
3A3MLY10.9430.9522.406-0.9182.2500.516-1.140-2.544-0.003
4A4ASP-1-0.918-0.9524.2030.1770.3180.001-0.036-0.1060.000
5A5MLY10.8860.9507.481-0.520-0.5200.0000.0000.0000.000
6A6CYS0-0.031-0.0219.5310.1270.1270.0000.0000.0000.000
7A7PHE00.010-0.0049.113-0.053-0.0530.0000.0000.0000.000
8A8GLU-1-0.891-0.95914.7500.2130.2130.0000.0000.0000.000
9A9GLY0-0.014-0.00218.483-0.015-0.0150.0000.0000.0000.000
10A10VAL0-0.033-0.01515.348-0.017-0.0170.0000.0000.0000.000
11A11ARG10.8170.90118.112-0.265-0.2650.0000.0000.0000.000
12A12PHE00.010-0.00112.240-0.004-0.0040.0000.0000.0000.000
13A13GLU-1-0.924-0.96215.6700.2380.2380.0000.0000.0000.000
14A14GLN00.0320.00414.3580.0260.0260.0000.0000.0000.000
15A15GLN0-0.039-0.02513.2080.0620.0620.0000.0000.0000.000
16A16ASP-1-0.907-0.95111.0340.6700.6700.0000.0000.0000.000
17A17LEU0-0.056-0.0428.9750.2020.2020.0000.0000.0000.000
18A18GLU-1-0.919-0.9409.0680.6560.6560.0000.0000.0000.000
19A19GLY0-0.042-0.0144.9290.0430.126-0.001-0.009-0.0720.000
20A20GLU-1-0.889-0.9525.2110.9120.9120.0000.0000.0000.000
21A21GLN0-0.086-0.0422.279-6.641-4.8563.500-1.887-3.398-0.017
22A22PHE00.0490.0132.873-0.7341.7160.593-1.475-1.568-0.014
23A23GLN0-0.023-0.0263.179-1.809-1.2332.784-0.829-2.5310.000
24A24GLY00.0600.0364.608-0.508-0.5030.0020.057-0.0640.000
25A25CYS0-0.073-0.0176.579-0.334-0.3340.0000.0000.0000.000
26A26ARG10.8970.9469.276-0.407-0.4070.0000.0000.0000.000
27A27PHE00.004-0.0079.240-0.028-0.0280.0000.0000.0000.000
28A28ILE00.0310.01814.834-0.022-0.0220.0000.0000.0000.000
29A29GLY00.0460.01918.519-0.010-0.0100.0000.0000.0000.000
30A30CYS0-0.062-0.00916.5230.0030.0030.0000.0000.0000.000
31A31ASN00.0170.00518.489-0.006-0.0060.0000.0000.0000.000
32A32PHE00.0910.02712.141-0.001-0.0010.0000.0000.0000.000
33A33SER0-0.014-0.02717.310-0.008-0.0080.0000.0000.0000.000
34A34TRP0-0.097-0.05520.645-0.005-0.0050.0000.0000.0000.000
35A35LEU0-0.0400.00915.200-0.012-0.0120.0000.0000.0000.000
36A36ASP-1-0.892-0.95916.2720.2530.2530.0000.0000.0000.000
37A37LEU0-0.014-0.02812.6170.0680.0680.0000.0000.0000.000
38A38ALA00.0080.01913.0480.0000.0000.0000.0000.0000.000
39A39GLU-1-0.928-0.95811.8100.1020.1020.0000.0000.0000.000
40A40CYS0-0.0650.0008.9760.0360.0360.0000.0000.0000.000
41A41ARG10.9010.9554.5790.0740.142-0.001-0.002-0.0640.000
42A42PHE00.0260.0015.5700.3670.3670.0000.0000.0000.000
43A43VAL0-0.024-0.0184.950-0.331-0.3310.0000.0000.0000.000
44A44ASP-1-0.783-0.8747.0191.0481.0480.0000.0000.0000.000
45A45CYS0-0.050-0.0147.8760.1660.1660.0000.0000.0000.000
46A46SER0-0.037-0.01810.548-0.144-0.1440.0000.0000.0000.000
47A47PHE00.022-0.00311.5700.0330.0330.0000.0000.0000.000
48A48TYR00.0170.00316.117-0.042-0.0420.0000.0000.0000.000
49A49ASP-1-0.880-0.94719.1280.2280.2280.0000.0000.0000.000
50A50ARG10.8700.93020.859-0.208-0.2080.0000.0000.0000.000
51A51GLU-1-0.955-0.97423.7640.1240.1240.0000.0000.0000.000
52A52SER0-0.048-0.03423.871-0.014-0.0140.0000.0000.0000.000
53A53GLU-1-0.974-0.97824.9540.1150.1150.0000.0000.0000.000
54A54GLN0-0.0160.01522.6090.0000.0000.0000.0000.0000.000
55A55SER00.0280.01221.1220.0140.0140.0000.0000.0000.000
56A56CYS0-0.049-0.00517.6670.0160.0160.0000.0000.0000.000
57A57LEU0-0.056-0.02620.081-0.022-0.0220.0000.0000.0000.000
58A58LEU00.0480.00615.8170.0300.0300.0000.0000.0000.000
59A59GLN0-0.028-0.03019.850-0.013-0.0130.0000.0000.0000.000
60A60GLY0-0.031-0.03022.4970.0100.0100.0000.0000.0000.000
61A61CYS0-0.0700.00017.9130.0010.0010.0000.0000.0000.000
62A62ASP-1-0.824-0.90018.2410.1380.1380.0000.0000.0000.000
63A63LEU00.015-0.01615.4600.0390.0390.0000.0000.0000.000
64A64ARG10.8160.89516.533-0.141-0.1410.0000.0000.0000.000
65A65GLU-1-0.894-0.95214.8010.0040.0040.0000.0000.0000.000
66A66ALA0-0.0140.03012.044-0.026-0.0260.0000.0000.0000.000
67A67SER0-0.069-0.0709.248-0.049-0.0490.0000.0000.0000.000
68A68PHE0-0.001-0.0059.4420.0780.0780.0000.0000.0000.000
69A69LEU0-0.016-0.0168.790-0.077-0.0770.0000.0000.0000.000
70A70ARG10.8230.8909.676-0.171-0.1710.0000.0000.0000.000
71A71CYS0-0.041-0.01010.7090.1090.1090.0000.0000.0000.000
72A72ASP-1-0.841-0.92013.1730.1870.1870.0000.0000.0000.000
73A73LEU00.011-0.00714.7120.0250.0250.0000.0000.0000.000
74A74THR0-0.031-0.03017.783-0.033-0.0330.0000.0000.0000.000
75A75MET0-0.066-0.03821.3470.0100.0100.0000.0000.0000.000
76A76ALA0-0.0020.02519.2490.0000.0000.0000.0000.0000.000
77A77ASP-1-0.796-0.87621.2960.1400.1400.0000.0000.0000.000
78A78CYS00.0150.01419.4990.0240.0240.0000.0000.0000.000
79A79SER0-0.014-0.01722.207-0.014-0.0140.0000.0000.0000.000
80A80ARG10.8460.91125.198-0.112-0.1120.0000.0000.0000.000
81A81SER00.0030.02021.005-0.004-0.0040.0000.0000.0000.000
82A82GLN0-0.025-0.02121.853-0.034-0.0340.0000.0000.0000.000
83A83CYS00.0190.01619.6820.0210.0210.0000.0000.0000.000
84A84LEU0-0.0010.00420.428-0.010-0.0100.0000.0000.0000.000
85A85GLY00.0710.01718.9410.0050.0050.0000.0000.0000.000
86A86LEU0-0.062-0.00715.021-0.010-0.0100.0000.0000.0000.000
87A87GLU-1-0.827-0.88012.220-0.107-0.1070.0000.0000.0000.000
88A88LEU0-0.031-0.01813.8080.0330.0330.0000.0000.0000.000
89A89ARG10.8310.87813.534-0.007-0.0070.0000.0000.0000.000
90A90ASP-1-0.897-0.95114.3600.1130.1130.0000.0000.0000.000
91A91CYS0-0.054-0.00414.6940.0490.0490.0000.0000.0000.000
92A92GLN0-0.0060.01916.670-0.043-0.0430.0000.0000.0000.000
93A93ALA00.0370.01218.6780.0250.0250.0000.0000.0000.000
94A94LEU00.0170.01520.787-0.013-0.0130.0000.0000.0000.000
95A95GLY00.0260.00524.1450.0120.0120.0000.0000.0000.000
96A96ILE0-0.0360.01119.4140.0020.0020.0000.0000.0000.000
97A97ASN00.005-0.00423.527-0.024-0.0240.0000.0000.0000.000
98A98PHE00.0760.02519.6660.0120.0120.0000.0000.0000.000
99A99SER00.0370.01925.318-0.009-0.0090.0000.0000.0000.000
100A100ARG10.9120.92328.004-0.097-0.0970.0000.0000.0000.000
101A101ALA00.0040.02823.9830.0020.0020.0000.0000.0000.000
102A102SER0-0.033-0.01025.120-0.012-0.0120.0000.0000.0000.000
103A103PHE00.0660.02521.0950.0080.0080.0000.0000.0000.000
104A104ALA00.0230.00624.777-0.011-0.0110.0000.0000.0000.000
105A105ASN0-0.050-0.01126.9220.0080.0080.0000.0000.0000.000
106A106GLN00.019-0.01428.565-0.004-0.0040.0000.0000.0000.000
107A107ILE00.0030.02132.1100.0030.0030.0000.0000.0000.000
108A108THR0-0.025-0.02434.6490.0000.0000.0000.0000.0000.000
109A109VAL00.0540.01236.302-0.001-0.0010.0000.0000.0000.000
110A110MLY10.8950.94338.101-0.021-0.0210.0000.0000.0000.000
111A111SER0-0.043-0.02335.718-0.003-0.0030.0000.0000.0000.000
112A112TYR0-0.081-0.06831.6460.0020.0020.0000.0000.0000.000
113A113PHE00.0190.02024.925-0.003-0.0030.0000.0000.0000.000
114A114CYS0-0.0400.00826.8900.0080.0080.0000.0000.0000.000
115A115GLU-1-0.829-0.91420.384-0.013-0.0130.0000.0000.0000.000
116A116ALA00.0190.00720.3880.0120.0120.0000.0000.0000.000
117A117HIS10.7620.87117.251-0.002-0.0020.0000.0000.0000.000
118A118LEU00.0160.01417.6740.0110.0110.0000.0000.0000.000
119A119THR00.0260.03718.275-0.011-0.0110.0000.0000.0000.000
120A120GLY00.0490.03118.5980.0090.0090.0000.0000.0000.000
121A121ASN0-0.048-0.02117.7950.0320.0320.0000.0000.0000.000
122A122ASN0-0.044-0.04120.522-0.023-0.0230.0000.0000.0000.000
123A123PHE00.0440.01120.5370.0150.0150.0000.0000.0000.000
124A124SER0-0.011-0.01724.657-0.009-0.0090.0000.0000.0000.000
125A125TYR0-0.055-0.04727.0980.0070.0070.0000.0000.0000.000
126A126ALA00.0110.03725.4110.0040.0040.0000.0000.0000.000
127A127ASN0-0.032-0.03027.047-0.015-0.0150.0000.0000.0000.000
128A128PHE00.0460.00823.3500.0080.0080.0000.0000.0000.000
129A129GLU-1-0.909-0.94028.7570.0650.0650.0000.0000.0000.000
130A130GLY0-0.043-0.02331.6320.0040.0040.0000.0000.0000.000
131A131CYS0-0.094-0.02527.8760.0010.0010.0000.0000.0000.000
132A132LEU0-0.013-0.00429.677-0.005-0.0050.0000.0000.0000.000
133A133LEU00.009-0.01624.4580.0030.0030.0000.0000.0000.000
134A134GLU-1-0.741-0.80328.0530.0300.0300.0000.0000.0000.000
135A135GLN0-0.062-0.03528.6400.0000.0000.0000.0000.0000.000
136A136CYS0-0.059-0.01324.229-0.002-0.0020.0000.0000.0000.000
137A137GLU-1-0.792-0.87720.058-0.019-0.0190.0000.0000.0000.000
138A138LEU0-0.043-0.02922.2640.0080.0080.0000.0000.0000.000
139A139SER00.0560.04023.7720.0070.0070.0000.0000.0000.000
140A140GLY00.016-0.00623.1670.0050.0050.0000.0000.0000.000
141A141ASN0-0.048-0.02021.9800.0160.0160.0000.0000.0000.000
142A142ARG10.9050.97124.586-0.080-0.0800.0000.0000.0000.000
143A143TRP00.032-0.00725.8190.0110.0110.0000.0000.0000.000
144A144GLN00.0120.00928.885-0.004-0.0040.0000.0000.0000.000
145A145GLY00.014-0.00130.8120.0060.0060.0000.0000.0000.000
146A146ALA0-0.0340.00029.1140.0030.0030.0000.0000.0000.000
147A147ASN0-0.064-0.03030.901-0.010-0.0100.0000.0000.0000.000
148A148LEU00.045-0.00129.5720.0040.0040.0000.0000.0000.000
149A149PHE00.0110.01932.901-0.005-0.0050.0000.0000.0000.000
150A150GLY00.017-0.00735.2770.0030.0030.0000.0000.0000.000
151A151ALA0-0.0420.00431.4200.0000.0000.0000.0000.0000.000
152A152SER0-0.094-0.11632.333-0.005-0.0050.0000.0000.0000.000
153A153LEU00.0410.01528.6720.0020.0020.0000.0000.0000.000
154A154ALA00.0340.01731.380-0.003-0.0030.0000.0000.0000.000
155A155GLY00.017-0.00632.1950.0000.0000.0000.0000.0000.000
156A156SER0-0.036-0.00227.945-0.005-0.0050.0000.0000.0000.000
157A157ASP-1-0.837-0.89126.5560.0080.0080.0000.0000.0000.000
158A158LEU00.000-0.01626.8820.0040.0040.0000.0000.0000.000
159A159SER0-0.0340.00528.2420.0030.0030.0000.0000.0000.000
160A160GLY00.008-0.01727.6120.0020.0020.0000.0000.0000.000
161A161SER0-0.044-0.05128.0490.0060.0060.0000.0000.0000.000
162A162GLU-1-0.903-0.95528.6190.0600.0600.0000.0000.0000.000
163A163PHE0-0.022-0.03230.1260.0070.0070.0000.0000.0000.000
164A164GLY00.0120.00432.4900.0040.0040.0000.0000.0000.000
165A165GLN0-0.095-0.06935.296-0.001-0.0010.0000.0000.0000.000
166A166ILE00.0310.02832.4780.0020.0020.0000.0000.0000.000
167A167ASP-1-0.873-0.90836.6910.0410.0410.0000.0000.0000.000
168A168TRP00.017-0.01135.3500.0000.0000.0000.0000.0000.000
169A169ALA0-0.063-0.03539.196-0.001-0.0010.0000.0000.0000.000
170A170SER0-0.080-0.05538.910-0.001-0.0010.0000.0000.0000.000
171A171VAL00.0180.02533.3960.0030.0030.0000.0000.0000.000
172A172ASN0-0.047-0.02435.856-0.005-0.0050.0000.0000.0000.000
173A173LEU00.0710.01433.9480.0010.0010.0000.0000.0000.000
174A174GLN00.0220.00836.169-0.004-0.0040.0000.0000.0000.000
175A175GLY0-0.008-0.01136.0400.0010.0010.0000.0000.0000.000
176A176CYS0-0.0740.00332.045-0.001-0.0010.0000.0000.0000.000
177A177ASP-1-0.787-0.88130.8900.0070.0070.0000.0000.0000.000
178A178LEU00.013-0.01431.7670.0040.0040.0000.0000.0000.000
179A179ARG10.8600.92832.991-0.002-0.0020.0000.0000.0000.000
180A180GLN0-0.022-0.01231.5700.0020.0020.0000.0000.0000.000
181A181CYS0-0.0420.04332.2110.0040.0040.0000.0000.0000.000
182A182ASP-1-0.799-0.88433.6750.0410.0410.0000.0000.0000.000
183A183LEU00.006-0.01735.7260.0020.0020.0000.0000.0000.000
184A184PRO0-0.017-0.00337.471-0.002-0.0020.0000.0000.0000.000
185A185GLY00.019-0.00340.6690.0020.0020.0000.0000.0000.000
186A186LEU0-0.0170.01338.9780.0000.0000.0000.0000.0000.000
187A187ASP-1-0.782-0.87542.5670.0210.0210.0000.0000.0000.000
188A188LEU00.0840.01644.1830.0000.0000.0000.0000.0000.000
189A189ARG10.7770.87046.412-0.022-0.0220.0000.0000.0000.000
190A190ARG10.8730.94044.486-0.031-0.0310.0000.0000.0000.000
191A191VAL00.0050.01640.5930.0010.0010.0000.0000.0000.000
192A192ASN0-0.002-0.00242.579-0.002-0.0020.0000.0000.0000.000
193A193LEU00.0400.01139.0720.0010.0010.0000.0000.0000.000
194A194ASP-1-0.894-0.93941.3230.0110.0110.0000.0000.0000.000
195A195GLY00.0240.00239.7570.0010.0010.0000.0000.0000.000
196A196VAL0-0.041-0.00136.928-0.001-0.0010.0000.0000.0000.000
197A197GLN0-0.116-0.05034.089-0.003-0.0030.0000.0000.0000.000
198A198ILE00.0090.00136.4020.0020.0020.0000.0000.0000.000
199A199ASN0-0.014-0.03236.138-0.001-0.0010.0000.0000.0000.000
200A200GLU-1-0.927-0.98039.3520.0050.0050.0000.0000.0000.000
201A201ASP-1-0.935-0.96639.3740.0150.0150.0000.0000.0000.000
202A202GLN00.0260.01336.262-0.001-0.0010.0000.0000.0000.000
203A203GLN0-0.038-0.01841.5350.0010.0010.0000.0000.0000.000
204A204GLN0-0.039-0.02644.8730.0000.0000.0000.0000.0000.000
205A205ALA00.0750.03243.4900.0000.0000.0000.0000.0000.000
206A206LEU00.0150.01341.5990.0010.0010.0000.0000.0000.000
207A207LEU0-0.029-0.03145.5100.0000.0000.0000.0000.0000.000
208A208GLU-1-0.889-0.94348.7150.0180.0180.0000.0000.0000.000
209A209GLN0-0.0340.01046.2740.0010.0010.0000.0000.0000.000
210A210ILE0-0.104-0.05948.8890.0000.0000.0000.0000.0000.000
211A211GLY0-0.042-0.02251.496-0.001-0.0010.0000.0000.0000.000
212A212LEU0-0.055-0.01752.367-0.001-0.0010.0000.0000.0000.000
213A213ILE00.0060.00253.5800.0010.0010.0000.0000.0000.000
214A214VAL00.0130.00851.018-0.001-0.0010.0000.0000.0000.000
215A215PHE0-0.030-0.01053.8490.0000.0000.0000.0000.0000.000
216A216PRO00.0060.00653.655-0.001-0.0010.0000.0000.0000.000