FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: PK293

Calculation Name: 3MC3-A-Xray28

Preferred Name:
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Target Type:
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Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 3MC3

Chain ID: A

ChEMBL ID:
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UniProt ID: Q97Z18

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge CL-=-1,MLY=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1300664.546293
FMO2-HF: Nuclear repulsion 1244139.62597
FMO2-HF: Total energy -56524.920323
FMO2-MP2: Total energy -56682.562312


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:12:ACE)


Summations of interaction energy for fragment #1(A:12:ACE)
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.
0.6411.53-0.011-0.423-0.455-0.001
Interaction energy analysis for fragmet #1(A:12:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / 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].
3A14MLY10.9401.0083.8581.4022.291-0.011-0.423-0.455-0.001
4A15MLY10.8600.9386.6990.2780.2780.0000.0000.0000.000
5A16MLY10.8660.9269.5810.7490.7490.0000.0000.0000.000
6A17ILE0-0.0050.00313.0250.0420.0420.0000.0000.0000.000
7A18LEU00.0130.01316.447-0.003-0.0030.0000.0000.0000.000
8A19ILE0-0.020-0.01019.7110.0170.0170.0000.0000.0000.000
9A20VAL0-0.005-0.00523.108-0.003-0.0030.0000.0000.0000.000
10A21VAL00.0130.00526.3070.0080.0080.0000.0000.0000.000
11A22THR0-0.039-0.05629.6000.0000.0000.0000.0000.0000.000
12A23HIS10.8320.91132.7430.0560.0560.0000.0000.0000.000
13A24GLY00.0530.01134.636-0.004-0.0040.0000.0000.0000.000
14A25PRO00.010-0.01737.2840.0020.0020.0000.0000.0000.000
15A26GLU-1-0.784-0.82739.033-0.046-0.0460.0000.0000.0000.000
16A27ASP-1-0.872-0.94538.228-0.035-0.0350.0000.0000.0000.000
17A28LEU00.0330.02736.870-0.003-0.0030.0000.0000.0000.000
18A29ASP-1-0.834-0.89135.922-0.034-0.0340.0000.0000.0000.000
19A30ARG10.8920.98534.0580.0400.0400.0000.0000.0000.000
20A31THR0-0.079-0.05932.136-0.006-0.0060.0000.0000.0000.000
21A32TYR00.0230.00631.084-0.005-0.0050.0000.0000.0000.000
22A33ALA00.0320.01229.260-0.003-0.0030.0000.0000.0000.000
23A34PRO00.0060.01826.626-0.003-0.0030.0000.0000.0000.000
24A35LEU00.0400.01325.435-0.009-0.0090.0000.0000.0000.000
25A36PHE0-0.0020.02425.543-0.004-0.0040.0000.0000.0000.000
26A37MET0-0.002-0.01522.2220.0020.0020.0000.0000.0000.000
27A38ALA0-0.001-0.00221.267-0.008-0.0080.0000.0000.0000.000
28A39SER00.0490.00220.466-0.015-0.0150.0000.0000.0000.000
29A40ILE0-0.034-0.00220.337-0.001-0.0010.0000.0000.0000.000
30A41SER0-0.003-0.00816.8950.0050.0050.0000.0000.0000.000
31A42ALA0-0.019-0.00316.075-0.012-0.0120.0000.0000.0000.000
32A43SER0-0.020-0.02216.116-0.002-0.0020.0000.0000.0000.000
33A44MET0-0.078-0.03315.1170.0190.0190.0000.0000.0000.000
34A45GLU-1-0.948-0.96611.148-0.053-0.0530.0000.0000.0000.000
35A46TYR0-0.034-0.00910.900-0.080-0.0800.0000.0000.0000.000
36A47GLU-1-0.862-0.94110.764-0.682-0.6820.0000.0000.0000.000
37A48THR00.0160.01413.7080.0120.0120.0000.0000.0000.000
38A49SER00.0220.01117.2430.0030.0030.0000.0000.0000.000
39A50VAL00.0100.00420.1640.0090.0090.0000.0000.0000.000
40A51PHE00.004-0.00823.792-0.001-0.0010.0000.0000.0000.000
41A52PHE00.0310.01526.0690.0090.0090.0000.0000.0000.000
42A53MET0-0.019-0.02029.821-0.004-0.0040.0000.0000.0000.000
43A54ILE0-0.008-0.00732.2720.0040.0040.0000.0000.0000.000
44A55MLY10.9700.97535.6680.0490.0490.0000.0000.0000.000
45A56GLY00.0250.01933.0460.0020.0020.0000.0000.0000.000
46A57PRO00.005-0.01333.6720.0000.0000.0000.0000.0000.000
47A58MLY10.9260.96034.9530.0500.0500.0000.0000.0000.000
48A59LEU0-0.044-0.00632.7840.0030.0030.0000.0000.0000.000
49A60LEU0-0.0010.00330.8880.0000.0000.0000.0000.0000.000
50A61ASP-1-0.740-0.84934.787-0.052-0.0520.0000.0000.0000.000
51A62MLY10.8640.92636.9630.0650.0650.0000.0000.0000.000
52A63MLY10.8750.92839.2550.0470.0470.0000.0000.0000.000
53A64TRP00.0130.01136.3540.0000.0000.0000.0000.0000.000
54A65GLN00.0440.00633.0880.0020.0020.0000.0000.0000.000
55A66GLU-1-0.906-0.95038.758-0.041-0.0410.0000.0000.0000.000
56A67GLU-1-0.876-0.93341.240-0.035-0.0350.0000.0000.0000.000
57A68GLU-1-0.714-0.82539.604-0.034-0.0340.0000.0000.0000.000
58A69ARG10.7600.86533.3050.0580.0580.0000.0000.0000.000
59A70MLY10.8730.94340.2770.0370.0370.0000.0000.0000.000
60A71MLY10.7830.88743.9180.0340.0340.0000.0000.0000.000
61A72GLY00.0000.01541.1310.0020.0020.0000.0000.0000.000
62A73GLY00.004-0.00740.3210.0000.0000.0000.0000.0000.000
63A74ASN00.0060.00037.307-0.001-0.0010.0000.0000.0000.000
64A75PRO00.026-0.00435.084-0.003-0.0030.0000.0000.0000.000
65A76PHE00.0360.02631.066-0.003-0.0030.0000.0000.0000.000
66A77ILE0-0.022-0.01032.368-0.005-0.0050.0000.0000.0000.000
67A78HIS00.0260.03731.205-0.004-0.0040.0000.0000.0000.000
68A79PHE0-0.010-0.01828.548-0.002-0.0020.0000.0000.0000.000
69A80PHE0-0.0010.01627.845-0.008-0.0080.0000.0000.0000.000
70A81ASP-1-0.692-0.80627.952-0.069-0.0690.0000.0000.0000.000
71A82MET00.0130.02025.535-0.004-0.0040.0000.0000.0000.000
72A83ALA0-0.009-0.00323.748-0.006-0.0060.0000.0000.0000.000
73A84MLY10.9130.96123.1210.0760.0760.0000.0000.0000.000
74A85GLU-1-0.938-0.96523.954-0.068-0.0680.0000.0000.0000.000
75A86ASN0-0.038-0.01320.3090.0000.0000.0000.0000.0000.000
76A87GLY0-0.018-0.00219.293-0.016-0.0160.0000.0000.0000.000
77A88VAL0-0.0260.00019.334-0.026-0.0260.0000.0000.0000.000
78A89MLY10.8780.98219.7200.2010.2010.0000.0000.0000.000
79A90MET0-0.037-0.02021.5050.0070.0070.0000.0000.0000.000
80A91TYR00.0020.01220.825-0.005-0.0050.0000.0000.0000.000
81A92VAL00.0120.00326.5040.0070.0070.0000.0000.0000.000
82A93CSO0-0.0280.01430.0290.0010.0010.0000.0000.0000.000
83A94VAL00.0520.00231.4680.0080.0080.0000.0000.0000.000
84A95GLN00.0930.03033.3030.0020.0020.0000.0000.0000.000
85A96SER0-0.017-0.01234.3480.0050.0050.0000.0000.0000.000
86A97LEU00.0160.00835.3500.0040.0040.0000.0000.0000.000
87A98MLY10.8960.95537.1330.0680.0680.0000.0000.0000.000
88A99ASP-1-0.894-0.94239.663-0.055-0.0550.0000.0000.0000.000
89A100MET0-0.079-0.02738.6090.0040.0040.0000.0000.0000.000
90A101CYS0-0.083-0.03338.3140.0020.0020.0000.0000.0000.000
91A102HIS00.0190.03141.0060.0010.0010.0000.0000.0000.000
92A103MET0-0.0350.03637.5740.0020.0020.0000.0000.0000.000
93A104MLY10.9160.94941.0050.0480.0480.0000.0000.0000.000
94A105GLU-1-0.852-0.95636.737-0.077-0.0770.0000.0000.0000.000
95A106ASP-1-0.926-0.96437.158-0.060-0.0600.0000.0000.0000.000
96A107ASP-1-0.799-0.87939.458-0.051-0.0510.0000.0000.0000.000
97A108VAL0-0.022-0.00232.8930.0010.0010.0000.0000.0000.000
98A109VAL0-0.043-0.01332.2760.0000.0000.0000.0000.0000.000
99A110GLU-1-0.926-0.98232.411-0.077-0.0770.0000.0000.0000.000
100A111GLY0-0.007-0.00628.6110.0000.0000.0000.0000.0000.000
101A112ILE0-0.0530.00327.134-0.011-0.0110.0000.0000.0000.000
102A113GLU-1-0.813-0.91024.095-0.174-0.1740.0000.0000.0000.000
103A114LEU0-0.008-0.01127.7710.0010.0010.0000.0000.0000.000
104A115VAL00.0100.00926.082-0.004-0.0040.0000.0000.0000.000
105A116GLY00.0470.02529.4100.0100.0100.0000.0000.0000.000
106A117GLY0-0.002-0.03328.941-0.007-0.0070.0000.0000.0000.000
107A118SER0-0.034-0.02727.9310.0000.0000.0000.0000.0000.000
108A119THR00.0600.02923.649-0.003-0.0030.0000.0000.0000.000
109A120LEU0-0.0030.01823.714-0.014-0.0140.0000.0000.0000.000
110A121ILE0-0.010-0.00523.508-0.007-0.0070.0000.0000.0000.000
111A122ASP-1-0.765-0.87621.164-0.190-0.1900.0000.0000.0000.000
112A123LEU00.0090.01019.428-0.022-0.0220.0000.0000.0000.000
113A124THR0-0.068-0.05718.673-0.019-0.0190.0000.0000.0000.000
114A125LEU0-0.048-0.02018.564-0.004-0.0040.0000.0000.0000.000
115A126GLU-1-0.849-0.89115.434-0.337-0.3370.0000.0000.0000.000
116A127ALA0-0.0010.01413.918-0.078-0.0780.0000.0000.0000.000
117A128ASP-1-0.732-0.83010.835-0.516-0.5160.0000.0000.0000.000
118A129ARG10.8230.91813.7940.1860.1860.0000.0000.0000.000
119A130THR00.0570.03217.133-0.019-0.0190.0000.0000.0000.000
120A131LEU0-0.047-0.00320.4630.0170.0170.0000.0000.0000.000
121A132PHE00.025-0.00323.285-0.007-0.0070.0000.0000.0000.000
122A133PHE-1-0.767-0.85625.275-0.057-0.0570.0000.0000.0000.000
123A134CL--1-0.915-0.94738.638-0.041-0.0410.0000.0000.0000.000
124A136HOH0-0.017-0.01620.6150.0020.0020.0000.0000.0000.000
125A137HOH0-0.019-0.00117.2310.0120.0120.0000.0000.0000.000
126A139HOH0-0.054-0.03916.9010.0040.0040.0000.0000.0000.000
127A140HOH0-0.018-0.02918.482-0.015-0.0150.0000.0000.0000.000
128A141HOH0-0.046-0.03811.6270.0320.0320.0000.0000.0000.000
129A142HOH0-0.004-0.01519.4410.0040.0040.0000.0000.0000.000
130A144HOH0-0.025-0.02029.9540.0020.0020.0000.0000.0000.000
131A145HOH0-0.035-0.02442.1670.0010.0010.0000.0000.0000.000
132A146HOH00.006-0.00438.6850.0000.0000.0000.0000.0000.000
133A147HOH00.0270.02541.6700.0010.0010.0000.0000.0000.000
134A149HOH0-0.005-0.0138.1390.0230.0230.0000.0000.0000.000
135A150HOH0-0.055-0.03943.9240.0010.0010.0000.0000.0000.000
136A151HOH0-0.043-0.02322.9220.0070.0070.0000.0000.0000.000
137A152HOH0-0.038-0.03039.553-0.001-0.0010.0000.0000.0000.000
138A153HOH00.006-0.00117.1310.0130.0130.0000.0000.0000.000
139A154HOH00.0140.01716.663-0.019-0.0190.0000.0000.0000.000
140A156HOH00.000-0.00524.633-0.006-0.0060.0000.0000.0000.000
141A157HOH0-0.029-0.03925.9330.0020.0020.0000.0000.0000.000
142A158HOH0-0.016-0.01744.619-0.001-0.0010.0000.0000.0000.000
143A160HOH00.0250.01736.832-0.001-0.0010.0000.0000.0000.000
144A161HOH00.0160.02814.556-0.032-0.0320.0000.0000.0000.000
145A162HOH00.0290.01735.735-0.001-0.0010.0000.0000.0000.000
146A163HOH0-0.010-0.00938.572-0.002-0.0020.0000.0000.0000.000
147A165HOH0-0.0030.00241.6270.0000.0000.0000.0000.0000.000
148A167HOH0-0.052-0.04242.0240.0010.0010.0000.0000.0000.000
149A169HOH0-0.063-0.04424.6570.0050.0050.0000.0000.0000.000
150A170HOH0-0.026-0.01831.990-0.001-0.0010.0000.0000.0000.000
151A172HOH00.0010.00635.9080.0000.0000.0000.0000.0000.000
152A173HOH00.0350.02129.959-0.001-0.0010.0000.0000.0000.000
153A174HOH00.007-0.00227.8090.0050.0050.0000.0000.0000.000
154A175HOH00.0090.00042.5950.0000.0000.0000.0000.0000.000
155A176HOH0-0.017-0.01844.9480.0000.0000.0000.0000.0000.000
156A177HOH0-0.038-0.0258.387-0.135-0.1350.0000.0000.0000.000
157A178HOH0-0.054-0.03443.3270.0000.0000.0000.0000.0000.000
158A179HOH0-0.012-0.01036.5720.0010.0010.0000.0000.0000.000
159A180HOH00.0010.02225.5780.0050.0050.0000.0000.0000.000
160A181HOH0-0.022-0.04632.954-0.002-0.0020.0000.0000.0000.000
161A182HOH0-0.027-0.01714.952-0.012-0.0120.0000.0000.0000.000
162A184HOH0-0.042-0.02727.0430.0030.0030.0000.0000.0000.000
163A186HOH0-0.036-0.0309.085-0.022-0.0220.0000.0000.0000.000
164A187HOH0-0.030-0.03340.8090.0000.0000.0000.0000.0000.000
165A188HOH0-0.0100.00021.345-0.008-0.0080.0000.0000.0000.000
166A190HOH0-0.043-0.02620.9530.0040.0040.0000.0000.0000.000
167A194HOH0-0.004-0.01233.639-0.002-0.0020.0000.0000.0000.000
168A195HOH0-0.023-0.01931.4430.0000.0000.0000.0000.0000.000
169A198HOH0-0.039-0.04730.5410.0000.0000.0000.0000.0000.000
170A199HOH0-0.047-0.02844.1210.0000.0000.0000.0000.0000.000
171A200HOH0-0.031-0.0285.2100.2500.2500.0000.0000.0000.000
172A201HOH0-0.041-0.03045.0330.0010.0010.0000.0000.0000.000
173A204HOH0-0.008-0.0095.4720.1740.1740.0000.0000.0000.000
174A206HOH00.0110.00941.6210.0000.0000.0000.0000.0000.000
175A208HOH0-0.030-0.02113.0610.0050.0050.0000.0000.0000.000
176A209HOH0-0.027-0.01734.1810.0010.0010.0000.0000.0000.000
177A211HOH0-0.018-0.01221.4660.0010.0010.0000.0000.0000.000
178A212HOH0-0.028-0.02231.334-0.001-0.0010.0000.0000.0000.000
179A213HOH0-0.017-0.02034.2180.0000.0000.0000.0000.0000.000
180A214HOH0-0.073-0.06219.160-0.001-0.0010.0000.0000.0000.000
181A228HOH0-0.021-0.02040.2840.0000.0000.0000.0000.0000.000
182A231HOH00.0310.01831.550-0.002-0.0020.0000.0000.0000.000
183A232HOH0-0.021-0.03423.8240.0030.0030.0000.0000.0000.000
184A233HOH0-0.073-0.04844.1550.0010.0010.0000.0000.0000.000
185A235HOH00.0170.0158.858-0.088-0.0880.0000.0000.0000.000
186A236HOH0-0.056-0.03529.7510.0010.0010.0000.0000.0000.000
187A237HOH0-0.033-0.05739.2330.0000.0000.0000.0000.0000.000
188A244HOH00.0040.00141.7750.0000.0000.0000.0000.0000.000