FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2L26R

Calculation Name: 3X23-A-Xray372

Preferred Name: Matrix metalloproteinase 14

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3X23

Chain ID: A

ChEMBL ID: CHEMBL3869

UniProt ID: P50281

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 299
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4534433.929911
FMO2-HF: Nuclear repulsion 4411138.173559
FMO2-HF: Total energy -123295.756352
FMO2-MP2: Total energy -123657.684743


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:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
1.063.074-0.011-1.18-0.8220.005
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.034
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].
3A1MET00.0100.0093.8690.1592.173-0.011-1.180-0.8220.005
4A2PRO00.0040.0097.280-0.014-0.0140.0000.0000.0000.000
5A3LYS10.9810.98310.2710.7020.7020.0000.0000.0000.000
6A4PRO0-0.0100.01213.4530.0730.0730.0000.0000.0000.000
7A5ILE0-0.010-0.00915.3860.0350.0350.0000.0000.0000.000
8A6ASN00.0090.00418.922-0.035-0.0350.0000.0000.0000.000
9A7VAL0-0.055-0.03121.1350.0340.0340.0000.0000.0000.000
10A8ARG10.8060.87823.6140.1690.1690.0000.0000.0000.000
11A9VAL0-0.046-0.03425.9620.0150.0150.0000.0000.0000.000
12A10THR00.0250.02428.651-0.001-0.0010.0000.0000.0000.000
13A11THR00.010-0.01431.9980.0060.0060.0000.0000.0000.000
14A12MET0-0.0300.01234.3160.0010.0010.0000.0000.0000.000
15A13ASP-1-0.807-0.87736.305-0.095-0.0950.0000.0000.0000.000
16A14ALA00.0180.02332.484-0.004-0.0040.0000.0000.0000.000
17A15GLU-1-0.847-0.92230.540-0.148-0.1480.0000.0000.0000.000
18A16LEU0-0.0070.00126.180-0.008-0.0080.0000.0000.0000.000
19A17GLU-1-0.807-0.89023.783-0.232-0.2320.0000.0000.0000.000
20A18PHE0-0.014-0.01419.971-0.014-0.0140.0000.0000.0000.000
21A19ALA00.0330.02315.5230.0050.0050.0000.0000.0000.000
22A20ILE0-0.017-0.01316.7990.0110.0110.0000.0000.0000.000
23A21GLN00.0470.02411.6330.0380.0380.0000.0000.0000.000
24A22PRO00.0570.02014.0900.0670.0670.0000.0000.0000.000
25A23ASN0-0.020-0.01613.410-0.009-0.0090.0000.0000.0000.000
26A24THR00.001-0.00116.5310.0190.0190.0000.0000.0000.000
27A25THR0-0.023-0.03117.8820.0040.0040.0000.0000.0000.000
28A26GLY00.051-0.00921.281-0.020-0.0200.0000.0000.0000.000
29A27LYS10.8070.88923.5920.0360.0360.0000.0000.0000.000
30A28GLN00.0790.06016.4420.0020.0020.0000.0000.0000.000
31A29LEU00.0100.01621.294-0.015-0.0150.0000.0000.0000.000
32A30PHE0-0.002-0.00422.606-0.008-0.0080.0000.0000.0000.000
33A31ASP-1-0.767-0.86422.888-0.064-0.0640.0000.0000.0000.000
34A32GLN0-0.0080.00319.650-0.019-0.0190.0000.0000.0000.000
35A33VAL00.0060.01923.097-0.008-0.0080.0000.0000.0000.000
36A34VAL00.0200.00826.3820.0010.0010.0000.0000.0000.000
37A35LYS10.8760.92820.8850.2040.2040.0000.0000.0000.000
38A36THR0-0.074-0.05224.682-0.007-0.0070.0000.0000.0000.000
39A37VAL0-0.0110.00126.9220.0000.0000.0000.0000.0000.000
40A38GLY00.0340.03029.8670.0070.0070.0000.0000.0000.000
41A39LEU0-0.0240.00331.5770.0080.0080.0000.0000.0000.000
42A40ARG10.8800.91531.6180.0490.0490.0000.0000.0000.000
43A41GLU-1-0.681-0.78033.578-0.046-0.0460.0000.0000.0000.000
44A42VAL0-0.029-0.04530.309-0.001-0.0010.0000.0000.0000.000
45A43TRP0-0.017-0.01333.516-0.002-0.0020.0000.0000.0000.000
46A44PHE00.0680.04535.5570.0020.0020.0000.0000.0000.000
47A45PHE00.0090.01733.730-0.002-0.0020.0000.0000.0000.000
48A46GLY0-0.041-0.02632.1610.0050.0050.0000.0000.0000.000
49A47LEU0-0.0030.00626.740-0.005-0.0050.0000.0000.0000.000
50A48GLN00.001-0.00731.1270.0050.0050.0000.0000.0000.000
51A49TYR00.000-0.01430.380-0.006-0.0060.0000.0000.0000.000
52A50VAL00.0410.02932.4110.0080.0080.0000.0000.0000.000
53A51ASP-1-0.750-0.87532.696-0.059-0.0590.0000.0000.0000.000
54A52SER0-0.011-0.04032.080-0.005-0.0050.0000.0000.0000.000
55A53LYS10.7720.88534.3130.0490.0490.0000.0000.0000.000
56A54GLY00.0410.03137.0800.0030.0030.0000.0000.0000.000
57A55TYR00.003-0.01037.8140.0030.0030.0000.0000.0000.000
58A56SER00.0760.04536.773-0.001-0.0010.0000.0000.0000.000
59A57THR0-0.098-0.04933.9690.0100.0100.0000.0000.0000.000
60A58TRP00.0770.04233.893-0.006-0.0060.0000.0000.0000.000
61A59LEU0-0.0110.00426.0560.0060.0060.0000.0000.0000.000
62A60LYS10.7830.88629.2990.0520.0520.0000.0000.0000.000
63A61LEU00.0710.02926.737-0.001-0.0010.0000.0000.0000.000
64A62ASN00.0310.01325.325-0.009-0.0090.0000.0000.0000.000
65A63LYS10.8970.95024.5830.0280.0280.0000.0000.0000.000
66A64LYS10.9230.96619.048-0.017-0.0170.0000.0000.0000.000
67A65VAL00.0430.02521.0360.0100.0100.0000.0000.0000.000
68A66THR00.0160.01319.9670.0120.0120.0000.0000.0000.000
69A67GLN00.0090.01422.5880.0150.0150.0000.0000.0000.000
70A68GLN0-0.005-0.01925.2890.0170.0170.0000.0000.0000.000
71A69ASP-1-0.784-0.85228.268-0.063-0.0630.0000.0000.0000.000
72A70VAL00.0450.03027.0680.0040.0040.0000.0000.0000.000
73A71LYS10.8240.89929.1610.1080.1080.0000.0000.0000.000
74A72LYS10.8440.90526.8780.0820.0820.0000.0000.0000.000
75A73GLU-1-0.802-0.87927.434-0.120-0.1200.0000.0000.0000.000
76A74ASN0-0.0080.01223.598-0.028-0.0280.0000.0000.0000.000
77A75PRO00.0460.03324.8020.0020.0020.0000.0000.0000.000
78A76LEU00.005-0.01324.0340.0210.0210.0000.0000.0000.000
79A77GLN00.0040.00426.4200.0000.0000.0000.0000.0000.000
80A78PHE0-0.055-0.03725.2040.0150.0150.0000.0000.0000.000
81A79LYS10.9210.96630.1870.0970.0970.0000.0000.0000.000
82A80PHE0-0.0150.00230.4600.0050.0050.0000.0000.0000.000
83A81ARG10.7940.88332.8160.0820.0820.0000.0000.0000.000
84A82ALA00.0490.02935.8540.0010.0010.0000.0000.0000.000
85A83LYS10.8300.91735.3590.0350.0350.0000.0000.0000.000
86A84PHE0-0.052-0.03136.6650.0040.0040.0000.0000.0000.000
87A85PHE00.0710.03541.178-0.004-0.0040.0000.0000.0000.000
88A86PRO0-0.036-0.00843.5390.0030.0030.0000.0000.0000.000
89A87GLU-1-0.780-0.87145.472-0.014-0.0140.0000.0000.0000.000
90A88ASP-1-0.722-0.82748.255-0.026-0.0260.0000.0000.0000.000
91A89VAL0-0.038-0.04246.548-0.001-0.0010.0000.0000.0000.000
92A90SER0-0.058-0.05146.533-0.003-0.0030.0000.0000.0000.000
93A91GLU-1-0.963-0.97247.212-0.020-0.0200.0000.0000.0000.000
94A92GLU-1-0.779-0.87643.508-0.024-0.0240.0000.0000.0000.000
95A93LEU0-0.081-0.03541.409-0.003-0.0030.0000.0000.0000.000
96A94ILE00.0050.01340.4680.0000.0000.0000.0000.0000.000
97A95GLN0-0.027-0.02735.834-0.003-0.0030.0000.0000.0000.000
98A96GLU-1-0.825-0.91339.207-0.067-0.0670.0000.0000.0000.000
99A97ILE0-0.071-0.02834.1470.0000.0000.0000.0000.0000.000
100A98THR0-0.052-0.06737.575-0.003-0.0030.0000.0000.0000.000
101A99GLN00.0420.00738.682-0.001-0.0010.0000.0000.0000.000
102A100ARG10.9180.94836.6170.0870.0870.0000.0000.0000.000
103A101LEU0-0.059-0.03535.018-0.001-0.0010.0000.0000.0000.000
104A102PHE00.0220.00339.6830.0010.0010.0000.0000.0000.000
105A103PHE00.0900.05142.5160.0010.0010.0000.0000.0000.000
106A104LEU0-0.057-0.01740.5460.0010.0010.0000.0000.0000.000
107A105GLN00.0260.00239.518-0.003-0.0030.0000.0000.0000.000
108A106VAL00.014-0.00342.8990.0010.0010.0000.0000.0000.000
109A107LYS10.8620.95446.3600.0590.0590.0000.0000.0000.000
110A108GLU-1-0.886-0.94441.576-0.072-0.0720.0000.0000.0000.000
111A109ALA00.0260.01046.0530.0010.0010.0000.0000.0000.000
112A110ILE00.0150.00447.5940.0020.0020.0000.0000.0000.000
113A111LEU0-0.026-0.01448.7360.0010.0010.0000.0000.0000.000
114A112ASN0-0.060-0.02545.954-0.001-0.0010.0000.0000.0000.000
115A113ASP-1-0.817-0.90550.446-0.039-0.0390.0000.0000.0000.000
116A114GLU-1-0.960-0.97046.540-0.048-0.0480.0000.0000.0000.000
117A115ILE0-0.061-0.03048.0670.0020.0020.0000.0000.0000.000
118A116TYR00.007-0.01752.290-0.001-0.0010.0000.0000.0000.000
119A117CYS00.0290.01955.6230.0000.0000.0000.0000.0000.000
120A118PRO0-0.0080.02257.603-0.001-0.0010.0000.0000.0000.000
121A119PRO00.0520.00260.497-0.001-0.0010.0000.0000.0000.000
122A120GLU-1-0.779-0.84261.374-0.030-0.0300.0000.0000.0000.000
123A121THR00.0440.02157.594-0.001-0.0010.0000.0000.0000.000
124A122ALA00.0160.00756.884-0.001-0.0010.0000.0000.0000.000
125A123VAL0-0.004-0.00757.093-0.002-0.0020.0000.0000.0000.000
126A124LEU00.0140.02658.410-0.001-0.0010.0000.0000.0000.000
127A125LEU00.0230.02152.834-0.002-0.0020.0000.0000.0000.000
128A126ALA00.007-0.00654.049-0.002-0.0020.0000.0000.0000.000
129A127SER0-0.025-0.02854.785-0.002-0.0020.0000.0000.0000.000
130A128TYR00.0520.01652.998-0.001-0.0010.0000.0000.0000.000
131A129ALA0-0.044-0.02650.619-0.002-0.0020.0000.0000.0000.000
132A130VAL0-0.035-0.01150.790-0.003-0.0030.0000.0000.0000.000
133A131GLN00.014-0.00252.920-0.002-0.0020.0000.0000.0000.000
134A132ALA00.0070.00247.891-0.002-0.0020.0000.0000.0000.000
135A133LYS10.7430.86948.1070.0610.0610.0000.0000.0000.000
136A134TYR0-0.047-0.05249.087-0.004-0.0040.0000.0000.0000.000
137A135GLY0-0.0140.01351.803-0.001-0.0010.0000.0000.0000.000
138A136ASP-1-0.793-0.88252.920-0.043-0.0430.0000.0000.0000.000
139A137TYR0-0.058-0.01656.682-0.001-0.0010.0000.0000.0000.000
140A138ASN00.035-0.00458.6530.0030.0030.0000.0000.0000.000
141A139LYS10.9150.93260.4530.0360.0360.0000.0000.0000.000
142A140GLU-1-0.833-0.89061.898-0.040-0.0400.0000.0000.0000.000
143A141ILE0-0.086-0.03655.638-0.001-0.0010.0000.0000.0000.000
144A142HIS00.0330.02854.5850.0000.0000.0000.0000.0000.000
145A143LYS10.9190.96559.1250.0490.0490.0000.0000.0000.000
146A144PRO00.0500.02161.141-0.001-0.0010.0000.0000.0000.000
147A145GLY00.0630.02761.1540.0000.0000.0000.0000.0000.000
148A146TYR0-0.097-0.06656.131-0.002-0.0020.0000.0000.0000.000
149A147LEU00.0120.01755.793-0.002-0.0020.0000.0000.0000.000
150A148ALA00.0000.01056.452-0.001-0.0010.0000.0000.0000.000
151A149ASN0-0.067-0.03452.7960.0000.0000.0000.0000.0000.000
152A150ASP-1-0.767-0.85450.878-0.063-0.0630.0000.0000.0000.000
153A151ARG10.8150.90148.0260.0570.0570.0000.0000.0000.000
154A152LEU00.014-0.00651.7450.0000.0000.0000.0000.0000.000
155A153LEU0-0.0010.00054.2840.0010.0010.0000.0000.0000.000
156A154PRO0-0.0050.00454.353-0.002-0.0020.0000.0000.0000.000
157A155GLN0-0.047-0.03554.544-0.001-0.0010.0000.0000.0000.000
158A156ARG10.9480.97456.9070.0340.0340.0000.0000.0000.000
159A157VAL0-0.017-0.01458.8200.0010.0010.0000.0000.0000.000
160A158LEU0-0.0300.00057.2050.0010.0010.0000.0000.0000.000
161A159GLU-1-0.906-0.94758.846-0.037-0.0370.0000.0000.0000.000
162A160GLN0-0.057-0.02362.7800.0010.0010.0000.0000.0000.000
163A161HIS00.0190.02265.4720.0000.0000.0000.0000.0000.000
164A162LYS10.8780.92167.3330.0250.0250.0000.0000.0000.000
165A163LEU0-0.0220.00166.4180.0010.0010.0000.0000.0000.000
166A164THR0-0.022-0.03766.3770.0000.0000.0000.0000.0000.000
167A165LYS10.8250.89757.8890.0470.0470.0000.0000.0000.000
168A166GLU-1-0.789-0.88162.414-0.037-0.0370.0000.0000.0000.000
169A167GLN00.0500.03564.1610.0000.0000.0000.0000.0000.000
170A168TRP00.023-0.00361.4500.0010.0010.0000.0000.0000.000
171A169GLU-1-0.834-0.91659.245-0.045-0.0450.0000.0000.0000.000
172A170GLU-1-0.896-0.94961.580-0.034-0.0340.0000.0000.0000.000
173A171ARG10.7520.84264.0160.0310.0310.0000.0000.0000.000
174A172ILE0-0.0080.00257.5910.0000.0000.0000.0000.0000.000
175A173GLN0-0.031-0.02160.568-0.001-0.0010.0000.0000.0000.000
176A174ASN0-0.083-0.06561.8270.0010.0010.0000.0000.0000.000
177A175TRP00.0520.03260.6970.0010.0010.0000.0000.0000.000
178A176HIS0-0.008-0.00255.7620.0000.0000.0000.0000.0000.000
179A177GLU-1-0.841-0.92159.591-0.037-0.0370.0000.0000.0000.000
180A178GLU-1-0.944-0.96462.299-0.029-0.0290.0000.0000.0000.000
181A179HIS0-0.069-0.03656.9850.0010.0010.0000.0000.0000.000
182A180ARG10.7620.87057.4420.0360.0360.0000.0000.0000.000
183A181GLY0-0.027-0.01856.9360.0020.0020.0000.0000.0000.000
184A182MET0-0.0620.00053.3800.0000.0000.0000.0000.0000.000
185A183LEU00.0090.01148.845-0.002-0.0020.0000.0000.0000.000
186A184ARG10.8380.91647.2540.0630.0630.0000.0000.0000.000
187A185GLU-1-0.851-0.93044.531-0.060-0.0600.0000.0000.0000.000
188A186ASP-1-0.817-0.90947.109-0.042-0.0420.0000.0000.0000.000
189A187SER0-0.011-0.03150.3470.0010.0010.0000.0000.0000.000
190A188MET0-0.047-0.03444.089-0.001-0.0010.0000.0000.0000.000
191A189MET00.0140.01146.5740.0000.0000.0000.0000.0000.000
192A190GLU-1-0.772-0.86949.149-0.031-0.0310.0000.0000.0000.000
193A191TYR0-0.027-0.01349.5210.0010.0010.0000.0000.0000.000
194A192LEU0-0.053-0.04345.0960.0010.0010.0000.0000.0000.000
195A193LYS10.8180.89149.7340.0330.0330.0000.0000.0000.000
196A194ILE00.0160.01652.5770.0020.0020.0000.0000.0000.000
197A195ALA0-0.036-0.02450.6040.0010.0010.0000.0000.0000.000
198A196GLN0-0.035-0.04550.223-0.001-0.0010.0000.0000.0000.000
199A197ASP-1-0.880-0.93151.804-0.024-0.0240.0000.0000.0000.000
200A198LEU0-0.073-0.02653.3210.0010.0010.0000.0000.0000.000
201A199GLU-1-0.864-0.95454.546-0.024-0.0240.0000.0000.0000.000
202A200MET0-0.055-0.00352.8410.0010.0010.0000.0000.0000.000
203A201TYR00.0210.02947.149-0.003-0.0030.0000.0000.0000.000
204A202GLY0-0.010-0.00946.7790.0020.0020.0000.0000.0000.000
205A203VAL0-0.043-0.00447.2790.0010.0010.0000.0000.0000.000
206A204ASN0-0.086-0.06143.875-0.004-0.0040.0000.0000.0000.000
207A205TYR00.023-0.01147.1450.0020.0020.0000.0000.0000.000
208A206PHE0-0.085-0.06144.288-0.002-0.0020.0000.0000.0000.000
209A207GLU-1-0.791-0.87650.044-0.023-0.0230.0000.0000.0000.000
210A208ILE0-0.110-0.05651.7510.0010.0010.0000.0000.0000.000
211A209LYS10.8350.91954.1090.0140.0140.0000.0000.0000.000
212A210ASN00.0540.02156.6660.0020.0020.0000.0000.0000.000
213A211LYS10.9150.93959.0610.0020.0020.0000.0000.0000.000
214A212LYS10.9440.97860.8790.0060.0060.0000.0000.0000.000
215A213GLY00.0200.02160.5550.0000.0000.0000.0000.0000.000
216A214THR0-0.009-0.00761.165-0.001-0.0010.0000.0000.0000.000
217A215GLU-1-0.808-0.90257.835-0.015-0.0150.0000.0000.0000.000
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