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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

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FMODB ID: YVLZ2

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 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 216
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2522479.290221
FMO2-HF: Nuclear repulsion 2433513.60894
FMO2-HF: Total energy -88965.681282
FMO2-MP2: Total energy -89212.966717


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.
-8.744-0.4236.926-5.198-10.047-0.03
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 : -0.010 / q_NPA : 0.007
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].
3A3MLY10.9230.9452.461-0.9322.6400.392-1.394-2.5700.001
4A4ASP-1-0.923-0.9584.242-0.0240.1100.001-0.031-0.1030.000
5A5MLY10.8910.9527.4890.6010.6010.0000.0000.0000.000
6A6CYS0-0.009-0.0109.5700.1710.1710.0000.0000.0000.000
7A7PHE0-0.012-0.0159.043-0.117-0.1170.0000.0000.0000.000
8A8GLU-1-0.900-0.96314.764-0.019-0.0190.0000.0000.0000.000
9A9GLY0-0.0080.00118.496-0.018-0.0180.0000.0000.0000.000
10A10VAL0-0.034-0.01515.050-0.005-0.0050.0000.0000.0000.000
11A11ARG10.8090.90018.1150.0810.0810.0000.0000.0000.000
12A12PHE0-0.010-0.00811.915-0.005-0.0050.0000.0000.0000.000
13A13GLU-1-0.893-0.94514.905-0.126-0.1260.0000.0000.0000.000
14A14GLN00.011-0.01113.394-0.034-0.0340.0000.0000.0000.000
15A15GLN0-0.046-0.03612.2150.0030.0030.0000.0000.0000.000
16A16ASP-1-0.892-0.93810.056-0.413-0.4130.0000.0000.0000.000
17A17LEU0-0.056-0.0438.448-0.140-0.1400.0000.0000.0000.000
18A18GLU-1-0.929-0.9448.3480.0480.0480.0000.0000.0000.000
19A19GLY0-0.034-0.0123.9480.1300.234-0.001-0.022-0.0810.000
20A20GLU-1-0.899-0.9514.5580.2880.376-0.001-0.004-0.0830.000
21A21GLN0-0.082-0.0412.407-4.367-3.1143.660-1.571-3.342-0.016
22A22PHE00.0500.0132.875-2.896-0.3950.694-1.511-1.683-0.015
23A23GLN00.000-0.0143.234-1.142-0.4922.179-0.687-2.1420.000
24A24GLY00.0700.0404.702-0.750-0.7310.0020.022-0.0430.000
25A25CYS0-0.080-0.0226.750-0.450-0.4500.0000.0000.0000.000
26A26ARG10.8430.9059.383-0.069-0.0690.0000.0000.0000.000
27A27PHE0-0.001-0.0069.155-0.084-0.0840.0000.0000.0000.000
28A28ILE00.0420.02014.8700.0250.0250.0000.0000.0000.000
29A29GLY00.0530.02718.569-0.023-0.0230.0000.0000.0000.000
30A30CYS0-0.073-0.01816.481-0.024-0.0240.0000.0000.0000.000
31A31ASN00.011-0.00118.4970.0270.0270.0000.0000.0000.000
32A32PHE00.1040.03212.167-0.020-0.0200.0000.0000.0000.000
33A33SER0-0.010-0.02317.3070.0090.0090.0000.0000.0000.000
34A34TRP0-0.088-0.04920.519-0.011-0.0110.0000.0000.0000.000
35A35LEU0-0.0480.01015.052-0.005-0.0050.0000.0000.0000.000
36A36ASP-1-0.889-0.96415.9310.0750.0750.0000.0000.0000.000
37A37LEU0-0.007-0.01812.684-0.008-0.0080.0000.0000.0000.000
38A38ALA00.0160.02113.0360.0260.0260.0000.0000.0000.000
39A39GLU-1-0.947-0.96711.6870.1940.1940.0000.0000.0000.000
40A40CYS0-0.0650.0018.8510.0180.0180.0000.0000.0000.000
41A41ARG10.9110.9594.879-0.123-0.1230.0000.0000.0000.000
42A42PHE00.029-0.0035.5590.2940.2940.0000.0000.0000.000
43A43VAL0-0.021-0.0165.295-0.264-0.2640.0000.0000.0000.000
44A44ASP-1-0.777-0.8537.2140.9930.9930.0000.0000.0000.000
45A45CYS0-0.043-0.0137.9240.0710.0710.0000.0000.0000.000
46A46SER0-0.031-0.02010.591-0.101-0.1010.0000.0000.0000.000
47A47PHE00.0270.00011.374-0.018-0.0180.0000.0000.0000.000
48A48TYR00.0270.01216.125-0.028-0.0280.0000.0000.0000.000
49A49ASP-1-0.858-0.92219.1890.0480.0480.0000.0000.0000.000
50A50ARG10.8350.90920.736-0.090-0.0900.0000.0000.0000.000
51A51GLU-1-0.946-0.96623.8480.0130.0130.0000.0000.0000.000
52A52SER0-0.044-0.03824.056-0.005-0.0050.0000.0000.0000.000
53A53GLU-1-0.964-0.97025.0430.0210.0210.0000.0000.0000.000
54A54GLN0-0.0370.00422.676-0.001-0.0010.0000.0000.0000.000
55A55SER00.0160.00421.1220.0080.0080.0000.0000.0000.000
56A56CYS0-0.046-0.00517.822-0.015-0.0150.0000.0000.0000.000
57A57LEU0-0.054-0.02820.0810.0060.0060.0000.0000.0000.000
58A58LEU00.0520.00415.871-0.007-0.0070.0000.0000.0000.000
59A59GLN0-0.029-0.02119.8500.0010.0010.0000.0000.0000.000
60A60GLY0-0.007-0.03122.491-0.006-0.0060.0000.0000.0000.000
61A61CYS0-0.081-0.00117.894-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.796-0.86718.2140.0610.0610.0000.0000.0000.000
63A63LEU00.016-0.01515.2930.0060.0060.0000.0000.0000.000
64A64ARG10.8130.87416.416-0.052-0.0520.0000.0000.0000.000
65A65GLU-1-0.903-0.95614.7470.1030.1030.0000.0000.0000.000
66A66ALA0-0.0200.02411.8980.0050.0050.0000.0000.0000.000
67A67SER0-0.062-0.0779.425-0.014-0.0140.0000.0000.0000.000
68A68PHE00.0030.0029.4250.0490.0490.0000.0000.0000.000
69A69LEU0-0.022-0.0148.762-0.047-0.0470.0000.0000.0000.000
70A70ARG10.8230.87410.011-0.276-0.2760.0000.0000.0000.000
71A71CYS0-0.054-0.01710.8460.0750.0750.0000.0000.0000.000
72A72ASP-1-0.818-0.89513.3640.0810.0810.0000.0000.0000.000
73A73LEU00.014-0.00514.791-0.006-0.0060.0000.0000.0000.000
74A74THR0-0.037-0.04217.937-0.020-0.0200.0000.0000.0000.000
75A75MET0-0.045-0.02821.480-0.005-0.0050.0000.0000.0000.000
76A76ALA00.0020.02619.388-0.009-0.0090.0000.0000.0000.000
77A77ASP-1-0.774-0.86921.4090.0240.0240.0000.0000.0000.000
78A78CYS00.0150.02519.8910.0000.0000.0000.0000.0000.000
79A79SER0-0.023-0.01622.228-0.002-0.0020.0000.0000.0000.000
80A80ARG10.8580.91525.195-0.014-0.0140.0000.0000.0000.000
81A81SER0-0.0020.00720.9420.0000.0000.0000.0000.0000.000
82A82GLN0-0.053-0.03121.5920.0010.0010.0000.0000.0000.000
83A83CYS00.0180.01419.5800.0070.0070.0000.0000.0000.000
84A84LEU0-0.0120.00320.3200.0020.0020.0000.0000.0000.000
85A85GLY00.0730.02118.7760.0040.0040.0000.0000.0000.000
86A86LEU0-0.068-0.01314.9580.0040.0040.0000.0000.0000.000
87A87GLU-1-0.840-0.88812.0020.0750.0750.0000.0000.0000.000
88A88LEU0-0.027-0.01313.7840.0150.0150.0000.0000.0000.000
89A89ARG10.8570.89713.465-0.107-0.1070.0000.0000.0000.000
90A90ASP-1-0.901-0.95414.4630.1780.1780.0000.0000.0000.000
91A91CYS0-0.0460.00914.6590.0350.0350.0000.0000.0000.000
92A92GLN0-0.0040.00816.816-0.034-0.0340.0000.0000.0000.000
93A93ALA00.0350.00818.8460.0090.0090.0000.0000.0000.000
94A94LEU00.0030.01220.927-0.010-0.0100.0000.0000.0000.000
95A95GLY00.0340.00724.3000.0000.0000.0000.0000.0000.000
96A96ILE0-0.0390.00919.425-0.005-0.0050.0000.0000.0000.000
97A97ASN0-0.015-0.02823.626-0.005-0.0050.0000.0000.0000.000
98A98PHE00.0660.02019.5490.0000.0000.0000.0000.0000.000
99A99SER00.0360.02425.331-0.003-0.0030.0000.0000.0000.000
100A100ARG10.9070.92727.994-0.021-0.0210.0000.0000.0000.000
101A101ALA00.0090.03123.932-0.002-0.0020.0000.0000.0000.000
102A102SER0-0.019-0.00325.046-0.001-0.0010.0000.0000.0000.000
103A103PHE00.0650.02121.0360.0030.0030.0000.0000.0000.000
104A104ALA00.0200.00524.6710.0010.0010.0000.0000.0000.000
105A105ASN0-0.038-0.00726.767-0.003-0.0030.0000.0000.0000.000
106A106GLN00.008-0.02128.389-0.002-0.0020.0000.0000.0000.000
107A107ILE00.0020.02131.742-0.002-0.0020.0000.0000.0000.000
108A108THR0-0.025-0.02934.469-0.002-0.0020.0000.0000.0000.000
109A109VAL00.0500.01236.1330.0010.0010.0000.0000.0000.000
110A110MLY10.8980.94937.947-0.020-0.0200.0000.0000.0000.000
111A111SER0-0.035-0.01935.5890.0010.0010.0000.0000.0000.000
112A112TYR0-0.069-0.04431.561-0.001-0.0010.0000.0000.0000.000
113A113PHE00.0180.02024.701-0.001-0.0010.0000.0000.0000.000
114A114CYS0-0.0310.00626.735-0.001-0.0010.0000.0000.0000.000
115A115GLU-1-0.839-0.91320.1170.0680.0680.0000.0000.0000.000
116A116ALA00.0200.01220.2930.0010.0010.0000.0000.0000.000
117A117HIS10.7850.86817.128-0.076-0.0760.0000.0000.0000.000
118A118LEU00.0100.01117.6390.0090.0090.0000.0000.0000.000
119A119THR00.0340.03818.415-0.007-0.0070.0000.0000.0000.000
120A120GLY00.0410.02818.6600.0120.0120.0000.0000.0000.000
121A121ASN0-0.049-0.01617.9210.0220.0220.0000.0000.0000.000
122A122ASN0-0.014-0.00220.629-0.017-0.0170.0000.0000.0000.000
123A123PHE00.0390.00820.3920.0040.0040.0000.0000.0000.000
124A124SER0-0.015-0.03524.765-0.008-0.0080.0000.0000.0000.000
125A125TYR0-0.049-0.04327.2340.0010.0010.0000.0000.0000.000
126A126ALA00.0090.03525.515-0.002-0.0020.0000.0000.0000.000
127A127ASN0-0.037-0.03027.131-0.004-0.0040.0000.0000.0000.000
128A128PHE00.0540.00823.2930.0010.0010.0000.0000.0000.000
129A129GLU-1-0.922-0.93528.7770.0230.0230.0000.0000.0000.000
130A130GLY0-0.032-0.01831.6240.0000.0000.0000.0000.0000.000
131A131CYS0-0.099-0.02227.8660.0010.0010.0000.0000.0000.000
132A132LEU0-0.032-0.01329.6070.0000.0000.0000.0000.0000.000
133A133LEU00.006-0.01624.1460.0020.0020.0000.0000.0000.000
134A134GLU-1-0.740-0.83627.9810.0340.0340.0000.0000.0000.000
135A135GLN0-0.057-0.02628.5270.0000.0000.0000.0000.0000.000
136A136CYS0-0.061-0.01324.2180.0020.0020.0000.0000.0000.000
137A137GLU-1-0.806-0.87819.9820.0700.0700.0000.0000.0000.000
138A138LEU0-0.037-0.02922.2220.0040.0040.0000.0000.0000.000
139A139SER00.0420.00623.8270.0010.0010.0000.0000.0000.000
140A140GLY0-0.011-0.01523.2010.0060.0060.0000.0000.0000.000
141A141ASN0-0.048-0.02322.1210.0130.0130.0000.0000.0000.000
142A142ARG10.8570.92724.667-0.061-0.0610.0000.0000.0000.000
143A143TRP00.008-0.01725.6700.0030.0030.0000.0000.0000.000
144A144GLN00.0070.00528.982-0.004-0.0040.0000.0000.0000.000
145A145GLY00.019-0.00330.9420.0010.0010.0000.0000.0000.000
146A146ALA0-0.040-0.00229.179-0.001-0.0010.0000.0000.0000.000
147A147ASN0-0.055-0.03530.990-0.002-0.0020.0000.0000.0000.000
148A148LEU00.0500.00529.8640.0020.0020.0000.0000.0000.000
149A149PHE00.0090.01532.931-0.001-0.0010.0000.0000.0000.000
150A150GLY00.013-0.00735.2810.0000.0000.0000.0000.0000.000
151A151ALA0-0.0460.00231.3730.0000.0000.0000.0000.0000.000
152A152SER0-0.073-0.09132.301-0.002-0.0020.0000.0000.0000.000
153A153LEU00.0350.01428.6960.0020.0020.0000.0000.0000.000
154A154ALA00.0270.01231.3350.0010.0010.0000.0000.0000.000
155A155GLY00.025-0.00432.1090.0010.0010.0000.0000.0000.000
156A156SER0-0.0310.00127.8720.0010.0010.0000.0000.0000.000
157A157ASP-1-0.796-0.85526.1120.0530.0530.0000.0000.0000.000
158A158LEU0-0.014-0.01726.8580.0030.0030.0000.0000.0000.000
159A159SER0-0.031-0.01628.2160.0010.0010.0000.0000.0000.000
160A160GLY00.013-0.01427.6430.0040.0040.0000.0000.0000.000
161A161SER0-0.036-0.03028.1270.0040.0040.0000.0000.0000.000
162A162GLU-1-0.863-0.91328.7520.0570.0570.0000.0000.0000.000
163A163PHE0-0.016-0.03030.2300.0020.0020.0000.0000.0000.000
164A164GLY00.0250.01332.5790.0000.0000.0000.0000.0000.000
165A165GLN0-0.088-0.06435.408-0.001-0.0010.0000.0000.0000.000
166A166ILE00.0210.02332.676-0.001-0.0010.0000.0000.0000.000
167A167ASP-1-0.867-0.90936.7640.0230.0230.0000.0000.0000.000
168A168TRP00.005-0.01935.3200.0000.0000.0000.0000.0000.000
169A169ALA0-0.053-0.02639.2270.0000.0000.0000.0000.0000.000
170A170SER0-0.073-0.05039.0350.0000.0000.0000.0000.0000.000
171A171VAL00.0100.02133.4400.0010.0010.0000.0000.0000.000
172A172ASN0-0.029-0.01035.992-0.001-0.0010.0000.0000.0000.000
173A173LEU00.0640.01333.9690.0020.0020.0000.0000.0000.000
174A174GLN0-0.018-0.01636.1400.0000.0000.0000.0000.0000.000
175A175GLY00.006-0.00635.9730.0010.0010.0000.0000.0000.000
176A176CYS0-0.0720.00732.0350.0010.0010.0000.0000.0000.000
177A177ASP-1-0.774-0.84830.8730.0410.0410.0000.0000.0000.000
178A178LEU00.018-0.01131.7570.0020.0020.0000.0000.0000.000
179A179ARG10.8560.89632.342-0.041-0.0410.0000.0000.0000.000
180A180GLN0-0.027-0.01431.6450.0020.0020.0000.0000.0000.000
181A181CYS0-0.0490.03832.1940.0030.0030.0000.0000.0000.000
182A182ASP-1-0.808-0.89533.7730.0390.0390.0000.0000.0000.000
183A183LEU00.014-0.01335.7990.0000.0000.0000.0000.0000.000
184A184PRO0-0.015-0.00237.528-0.002-0.0020.0000.0000.0000.000
185A185GLY00.017-0.00140.7580.0000.0000.0000.0000.0000.000
186A186LEU0-0.0250.01239.208-0.001-0.0010.0000.0000.0000.000
187A187ASP-1-0.788-0.87542.6160.0190.0190.0000.0000.0000.000
188A188LEU00.0730.00944.2130.0000.0000.0000.0000.0000.000
189A189ARG10.7870.87846.423-0.019-0.0190.0000.0000.0000.000
190A190ARG10.8770.94244.372-0.022-0.0220.0000.0000.0000.000
191A191VAL00.0030.01040.5750.0000.0000.0000.0000.0000.000
192A192ASN0-0.0040.00542.6150.0000.0000.0000.0000.0000.000
193A193LEU00.0310.00439.1720.0010.0010.0000.0000.0000.000
194A194ASP-1-0.877-0.93641.2840.0260.0260.0000.0000.0000.000
195A195GLY00.0240.00639.6830.0010.0010.0000.0000.0000.000
196A196VAL0-0.053-0.00536.8260.0010.0010.0000.0000.0000.000
197A197GLN0-0.118-0.05434.1240.0000.0000.0000.0000.0000.000
198A198ILE00.0160.00236.3900.0010.0010.0000.0000.0000.000
199A199ASN0-0.014-0.02136.1080.0010.0010.0000.0000.0000.000
200A200GLU-1-0.924-0.97939.3670.0260.0260.0000.0000.0000.000
201A201ASP-1-0.929-0.96839.4440.0330.0330.0000.0000.0000.000
202A202GLN00.003-0.00436.1890.0000.0000.0000.0000.0000.000
203A203GLN0-0.039-0.01441.582-0.001-0.0010.0000.0000.0000.000
204A204GLN0-0.049-0.03344.9060.0000.0000.0000.0000.0000.000
205A205ALA00.0730.03143.544-0.001-0.0010.0000.0000.0000.000
206A206LEU00.0140.01041.440-0.001-0.0010.0000.0000.0000.000
207A207LEU0-0.027-0.02645.554-0.001-0.0010.0000.0000.0000.000
208A208GLU-1-0.867-0.93248.7900.0210.0210.0000.0000.0000.000
209A209GLN0-0.057-0.00146.2290.0000.0000.0000.0000.0000.000
210A210ILE0-0.082-0.05348.951-0.001-0.0010.0000.0000.0000.000
211A211GLY0-0.048-0.02451.539-0.001-0.0010.0000.0000.0000.000
212A212LEU0-0.052-0.01452.260-0.001-0.0010.0000.0000.0000.000
213A213ILE00.0110.00053.6420.0000.0000.0000.0000.0000.000
214A214VAL00.0080.01050.9040.0000.0000.0000.0000.0000.000
215A215PHE0-0.028-0.01153.9080.0000.0000.0000.0000.0000.000
216A216PRO00.0070.00753.7170.0000.0000.0000.0000.0000.000