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: 7MGLK

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 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 299
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4527807.718547
FMO2-HF: Nuclear repulsion 4404512.757883
FMO2-HF: Total energy -123294.960665
FMO2-MP2: Total energy -123656.89783


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.
0.1923.111-0.023-1.729-1.1660.007
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 : 0.062 / 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].
3A1MET00.0040.0143.791-0.7772.142-0.023-1.729-1.1660.007
4A2PRO00.0050.0087.294-0.053-0.0530.0000.0000.0000.000
5A3LYS10.9740.97010.0190.6780.6780.0000.0000.0000.000
6A4PRO00.0150.02313.2750.0760.0760.0000.0000.0000.000
7A5ILE0-0.024-0.01215.1780.0510.0510.0000.0000.0000.000
8A6ASN00.0120.00418.664-0.043-0.0430.0000.0000.0000.000
9A7VAL0-0.055-0.02921.2610.0360.0360.0000.0000.0000.000
10A8ARG10.8130.88323.5980.1870.1870.0000.0000.0000.000
11A9VAL0-0.054-0.03925.8720.0170.0170.0000.0000.0000.000
12A10THR00.0330.02928.581-0.001-0.0010.0000.0000.0000.000
13A11THR0-0.018-0.01232.0120.0070.0070.0000.0000.0000.000
14A12MET0-0.063-0.02734.230-0.002-0.0020.0000.0000.0000.000
15A13ASP-1-0.810-0.88136.643-0.111-0.1110.0000.0000.0000.000
16A14ALA00.0150.02432.401-0.005-0.0050.0000.0000.0000.000
17A15GLU-1-0.830-0.91330.395-0.169-0.1690.0000.0000.0000.000
18A16LEU0-0.024-0.01026.138-0.011-0.0110.0000.0000.0000.000
19A17GLU-1-0.810-0.89323.684-0.259-0.2590.0000.0000.0000.000
20A18PHE0-0.022-0.01320.060-0.021-0.0210.0000.0000.0000.000
21A19ALA00.0320.02115.6730.0040.0040.0000.0000.0000.000
22A20ILE0-0.034-0.02416.8170.0030.0030.0000.0000.0000.000
23A21GLN00.0460.01611.7260.0360.0360.0000.0000.0000.000
24A22PRO00.0530.02514.2630.0660.0660.0000.0000.0000.000
25A23ASN0-0.008-0.01413.371-0.004-0.0040.0000.0000.0000.000
26A24THR00.0100.00816.5290.0060.0060.0000.0000.0000.000
27A25THR0-0.027-0.02917.9960.0150.0150.0000.0000.0000.000
28A26GLY00.0500.00021.307-0.021-0.0210.0000.0000.0000.000
29A27LYS10.8170.88523.6440.0770.0770.0000.0000.0000.000
30A28GLN00.0730.05716.4220.0120.0120.0000.0000.0000.000
31A29LEU00.0070.01421.337-0.017-0.0170.0000.0000.0000.000
32A30PHE0-0.014-0.01622.581-0.008-0.0080.0000.0000.0000.000
33A31ASP-1-0.755-0.86423.012-0.107-0.1070.0000.0000.0000.000
34A32GLN00.0180.02419.956-0.017-0.0170.0000.0000.0000.000
35A33VAL0-0.0010.01823.369-0.005-0.0050.0000.0000.0000.000
36A34VAL00.0130.01126.5480.0040.0040.0000.0000.0000.000
37A35LYS10.8690.92921.1280.2570.2570.0000.0000.0000.000
38A36THR0-0.070-0.05625.025-0.005-0.0050.0000.0000.0000.000
39A37VAL0-0.018-0.00227.1330.0020.0020.0000.0000.0000.000
40A38GLY00.0400.03129.9440.0090.0090.0000.0000.0000.000
41A39LEU0-0.041-0.00231.6010.0090.0090.0000.0000.0000.000
42A40ARG10.9320.94231.6350.0720.0720.0000.0000.0000.000
43A41GLU-1-0.710-0.80233.680-0.067-0.0670.0000.0000.0000.000
44A42VAL0-0.008-0.03330.427-0.001-0.0010.0000.0000.0000.000
45A43TRP0-0.025-0.01333.440-0.003-0.0030.0000.0000.0000.000
46A44PHE00.0710.04335.6660.0030.0030.0000.0000.0000.000
47A45PHE00.0100.02733.683-0.001-0.0010.0000.0000.0000.000
48A46GLY0-0.039-0.02232.0930.0030.0030.0000.0000.0000.000
49A47LEU0-0.011-0.00626.876-0.005-0.0050.0000.0000.0000.000
50A48GLN0-0.026-0.02231.1770.0050.0050.0000.0000.0000.000
51A49TYR0-0.007-0.01830.427-0.007-0.0070.0000.0000.0000.000
52A50VAL00.0440.03432.5210.0100.0100.0000.0000.0000.000
53A51ASP-1-0.788-0.88932.490-0.073-0.0730.0000.0000.0000.000
54A52SER0-0.030-0.06232.050-0.004-0.0040.0000.0000.0000.000
55A53LYS10.8260.91134.2700.0570.0570.0000.0000.0000.000
56A54GLY00.0540.04036.7430.0030.0030.0000.0000.0000.000
57A55TYR00.001-0.01937.7120.0030.0030.0000.0000.0000.000
58A56SER00.0540.02236.719-0.003-0.0030.0000.0000.0000.000
59A57THR0-0.107-0.05533.6670.0100.0100.0000.0000.0000.000
60A58TRP00.0540.03633.877-0.006-0.0060.0000.0000.0000.000
61A59LEU0-0.046-0.01426.0960.0060.0060.0000.0000.0000.000
62A60LYS10.8800.93829.1390.0680.0680.0000.0000.0000.000
63A61LEU00.0680.03426.771-0.006-0.0060.0000.0000.0000.000
64A62ASN00.0260.01225.290-0.012-0.0120.0000.0000.0000.000
65A63LYS10.9090.96224.8150.0510.0510.0000.0000.0000.000
66A64LYS10.9370.96719.0520.0130.0130.0000.0000.0000.000
67A65VAL00.0500.02221.0400.0140.0140.0000.0000.0000.000
68A66THR0-0.012-0.00119.8490.0150.0150.0000.0000.0000.000
69A67GLN0-0.0080.00722.2870.0180.0180.0000.0000.0000.000
70A68GLN0-0.019-0.03124.9950.0220.0220.0000.0000.0000.000
71A69ASP-1-0.799-0.85827.969-0.074-0.0740.0000.0000.0000.000
72A70VAL00.0470.02526.8170.0050.0050.0000.0000.0000.000
73A71LYS10.8410.91228.7540.1190.1190.0000.0000.0000.000
74A72LYS10.8440.92126.5130.0930.0930.0000.0000.0000.000
75A73GLU-1-0.804-0.88827.095-0.128-0.1280.0000.0000.0000.000
76A74ASN0-0.0250.01923.836-0.026-0.0260.0000.0000.0000.000
77A75PRO00.0560.02924.7280.0030.0030.0000.0000.0000.000
78A76LEU00.023-0.02023.5320.0220.0220.0000.0000.0000.000
79A77GLN00.0210.02426.348-0.008-0.0080.0000.0000.0000.000
80A78PHE0-0.046-0.04225.0720.0160.0160.0000.0000.0000.000
81A79LYS10.9741.00430.1380.1040.1040.0000.0000.0000.000
82A80PHE00.0120.00530.4940.0040.0040.0000.0000.0000.000
83A81ARG10.8940.94332.6890.1040.1040.0000.0000.0000.000
84A82ALA00.0440.02735.8180.0000.0000.0000.0000.0000.000
85A83LYS10.8240.90935.5520.0570.0570.0000.0000.0000.000
86A84PHE0-0.056-0.03536.9830.0050.0050.0000.0000.0000.000
87A85PHE00.0700.02441.198-0.004-0.0040.0000.0000.0000.000
88A86PRO0-0.063-0.02043.4130.0030.0030.0000.0000.0000.000
89A87GLU-1-0.791-0.89345.337-0.027-0.0270.0000.0000.0000.000
90A88ASP-1-0.744-0.86147.951-0.038-0.0380.0000.0000.0000.000
91A89VAL0-0.028-0.03046.392-0.002-0.0020.0000.0000.0000.000
92A90SER0-0.028-0.00946.735-0.003-0.0030.0000.0000.0000.000
93A91GLU-1-0.965-0.97847.797-0.033-0.0330.0000.0000.0000.000
94A92GLU-1-0.772-0.87143.644-0.041-0.0410.0000.0000.0000.000
95A93LEU0-0.105-0.05041.572-0.004-0.0040.0000.0000.0000.000
96A94ILE00.0170.02941.0120.0000.0000.0000.0000.0000.000
97A95GLN0-0.046-0.04136.283-0.004-0.0040.0000.0000.0000.000
98A96GLU-1-0.809-0.90539.719-0.081-0.0810.0000.0000.0000.000
99A97ILE0-0.078-0.03134.4770.0000.0000.0000.0000.0000.000
100A98THR0-0.060-0.07537.907-0.003-0.0030.0000.0000.0000.000
101A99GLN00.0420.00738.801-0.001-0.0010.0000.0000.0000.000
102A100ARG10.9140.93836.8500.1050.1050.0000.0000.0000.000
103A101LEU0-0.076-0.04235.051-0.001-0.0010.0000.0000.0000.000
104A102PHE00.0200.00139.6930.0010.0010.0000.0000.0000.000
105A103PHE00.0950.05542.3640.0010.0010.0000.0000.0000.000
106A104LEU0-0.076-0.04540.3340.0020.0020.0000.0000.0000.000
107A105GLN00.0280.01039.546-0.004-0.0040.0000.0000.0000.000
108A106VAL00.0130.00442.9130.0020.0020.0000.0000.0000.000
109A107LYS10.9070.96946.2420.0720.0720.0000.0000.0000.000
110A108GLU-1-0.968-0.97742.295-0.082-0.0820.0000.0000.0000.000
111A109ALA00.0460.01646.2600.0020.0020.0000.0000.0000.000
112A110ILE00.0090.00647.8300.0030.0030.0000.0000.0000.000
113A111LEU0-0.030-0.01748.9500.0020.0020.0000.0000.0000.000
114A112ASN0-0.068-0.03645.8560.0000.0000.0000.0000.0000.000
115A113ASP-1-0.821-0.91050.364-0.046-0.0460.0000.0000.0000.000
116A114GLU-1-0.970-0.97446.533-0.059-0.0590.0000.0000.0000.000
117A115ILE0-0.067-0.02948.3420.0020.0020.0000.0000.0000.000
118A116TYR00.025-0.00852.359-0.001-0.0010.0000.0000.0000.000
119A117CYS00.0150.00555.6030.0000.0000.0000.0000.0000.000
120A118PRO0-0.0100.02257.5950.0000.0000.0000.0000.0000.000
121A119PRO00.0670.00960.423-0.001-0.0010.0000.0000.0000.000
122A120GLU-1-0.781-0.85061.535-0.036-0.0360.0000.0000.0000.000
123A121THR00.0390.01657.8170.0000.0000.0000.0000.0000.000
124A122ALA00.0130.00257.223-0.002-0.0020.0000.0000.0000.000
125A123VAL0-0.017-0.00857.388-0.002-0.0020.0000.0000.0000.000
126A124LEU00.0240.03158.453-0.002-0.0020.0000.0000.0000.000
127A125LEU00.0240.02653.190-0.002-0.0020.0000.0000.0000.000
128A126ALA00.0310.00854.240-0.003-0.0030.0000.0000.0000.000
129A127SER0-0.031-0.02554.740-0.002-0.0020.0000.0000.0000.000
130A128TYR00.0800.02553.092-0.001-0.0010.0000.0000.0000.000
131A129ALA0-0.067-0.03450.592-0.003-0.0030.0000.0000.0000.000
132A130VAL0-0.038-0.02450.965-0.003-0.0030.0000.0000.0000.000
133A131GLN00.0120.00153.268-0.001-0.0010.0000.0000.0000.000
134A132ALA0-0.0070.00048.132-0.002-0.0020.0000.0000.0000.000
135A133LYS10.7360.86748.1520.0690.0690.0000.0000.0000.000
136A134TYR0-0.042-0.05449.262-0.004-0.0040.0000.0000.0000.000
137A135GLY0-0.047-0.00152.086-0.001-0.0010.0000.0000.0000.000
138A136ASP-1-0.796-0.88752.914-0.050-0.0500.0000.0000.0000.000
139A137TYR0-0.0200.00356.5640.0000.0000.0000.0000.0000.000
140A138ASN00.030-0.00458.5150.0020.0020.0000.0000.0000.000
141A139LYS10.8960.92360.4370.0410.0410.0000.0000.0000.000
142A140GLU-1-0.873-0.90661.671-0.044-0.0440.0000.0000.0000.000
143A141ILE0-0.091-0.04155.611-0.001-0.0010.0000.0000.0000.000
144A142HIS0-0.0020.00254.7990.0000.0000.0000.0000.0000.000
145A143LYS10.9470.98259.3790.0540.0540.0000.0000.0000.000
146A144PRO00.0760.02361.352-0.001-0.0010.0000.0000.0000.000
147A145GLY00.0520.02261.4590.0000.0000.0000.0000.0000.000
148A146TYR0-0.090-0.06356.442-0.002-0.0020.0000.0000.0000.000
149A147LEU00.0040.00655.935-0.003-0.0030.0000.0000.0000.000
150A148ALA00.0200.02656.690-0.001-0.0010.0000.0000.0000.000
151A149ASN0-0.079-0.03952.9660.0010.0010.0000.0000.0000.000
152A150ASP-1-0.775-0.86051.138-0.072-0.0720.0000.0000.0000.000
153A151ARG10.8280.91448.0470.0660.0660.0000.0000.0000.000
154A152LEU0-0.003-0.00951.729-0.001-0.0010.0000.0000.0000.000
155A153LEU00.0130.00154.2940.0010.0010.0000.0000.0000.000
156A154PRO00.0030.01154.541-0.001-0.0010.0000.0000.0000.000
157A155GLN0-0.033-0.02654.6160.0000.0000.0000.0000.0000.000
158A156ARG10.9670.98057.0460.0400.0400.0000.0000.0000.000
159A157VAL0-0.039-0.01859.2330.0020.0020.0000.0000.0000.000
160A158LEU0-0.048-0.01757.4350.0010.0010.0000.0000.0000.000
161A159GLU-1-0.909-0.94958.938-0.043-0.0430.0000.0000.0000.000
162A160GLN0-0.058-0.01562.9850.0010.0010.0000.0000.0000.000
163A161HIS00.0310.04165.9400.0000.0000.0000.0000.0000.000
164A162LYS10.8790.90867.7060.0300.0300.0000.0000.0000.000
165A163LEU0-0.025-0.00466.4200.0010.0010.0000.0000.0000.000
166A164THR0-0.028-0.04166.364-0.001-0.0010.0000.0000.0000.000
167A165LYS10.8290.89057.9190.0520.0520.0000.0000.0000.000
168A166GLU-1-0.796-0.88662.465-0.042-0.0420.0000.0000.0000.000
169A167GLN00.0700.04364.3640.0000.0000.0000.0000.0000.000
170A168TRP00.002-0.01661.6590.0000.0000.0000.0000.0000.000
171A169GLU-1-0.825-0.91259.379-0.051-0.0510.0000.0000.0000.000
172A170GLU-1-0.924-0.95361.826-0.039-0.0390.0000.0000.0000.000
173A171ARG10.7480.83264.0210.0360.0360.0000.0000.0000.000
174A172ILE0-0.003-0.00857.7360.0000.0000.0000.0000.0000.000
175A173GLN0-0.019-0.00560.634-0.001-0.0010.0000.0000.0000.000
176A174ASN0-0.033-0.02661.8680.0000.0000.0000.0000.0000.000
177A175TRP00.0310.01660.7390.0010.0010.0000.0000.0000.000
178A176HIS00.0020.01055.9960.0000.0000.0000.0000.0000.000
179A177GLU-1-0.879-0.92559.663-0.042-0.0420.0000.0000.0000.000
180A178GLU-1-0.980-0.98862.313-0.036-0.0360.0000.0000.0000.000
181A179HIS0-0.054-0.01857.1470.0010.0010.0000.0000.0000.000
182A180ARG10.8070.88357.7480.0410.0410.0000.0000.0000.000
183A181GLY0-0.007-0.00657.3210.0020.0020.0000.0000.0000.000
184A182MET0-0.058-0.00253.533-0.001-0.0010.0000.0000.0000.000
185A183LEU00.0320.02249.500-0.002-0.0020.0000.0000.0000.000
186A184ARG10.8770.93847.3740.0730.0730.0000.0000.0000.000
187A185GLU-1-0.864-0.94644.579-0.073-0.0730.0000.0000.0000.000
188A186ASP-1-0.839-0.92547.151-0.053-0.0530.0000.0000.0000.000
189A187SER0-0.021-0.02850.3880.0020.0020.0000.0000.0000.000
190A188MET0-0.068-0.03444.362-0.001-0.0010.0000.0000.0000.000
191A189MET00.0290.01246.8930.0000.0000.0000.0000.0000.000
192A190GLU-1-0.793-0.86549.427-0.041-0.0410.0000.0000.0000.000
193A191TYR0-0.002-0.00549.9550.0010.0010.0000.0000.0000.000
194A192LEU0-0.057-0.04045.4240.0010.0010.0000.0000.0000.000
195A193LYS10.8250.89950.0320.0430.0430.0000.0000.0000.000
196A194ILE00.0190.02152.8130.0020.0020.0000.0000.0000.000
197A195ALA0-0.039-0.03750.7650.0010.0010.0000.0000.0000.000
198A196GLN0-0.038-0.04950.351-0.001-0.0010.0000.0000.0000.000
199A197ASP-1-0.876-0.92851.959-0.033-0.0330.0000.0000.0000.000
200A198LEU0-0.102-0.04753.4720.0020.0020.0000.0000.0000.000
201A199GLU-1-0.851-0.93654.692-0.031-0.0310.0000.0000.0000.000
202A200MET0-0.098-0.03253.0900.0000.0000.0000.0000.0000.000
203A201TYR00.0380.03847.309-0.004-0.0040.0000.0000.0000.000
204A202GLY0-0.017-0.00547.0300.0020.0020.0000.0000.0000.000
205A203VAL0-0.0250.00647.8880.0020.0020.0000.0000.0000.000
206A204ASN0-0.120-0.06743.986-0.005-0.0050.0000.0000.0000.000
207A205TYR00.0510.00547.2700.0020.0020.0000.0000.0000.000
208A206PHE0-0.088-0.06444.364-0.002-0.0020.0000.0000.0000.000
209A207GLU-1-0.780-0.87149.897-0.031-0.0310.0000.0000.0000.000
210A208ILE0-0.117-0.05751.5660.0010.0010.0000.0000.0000.000
211A209LYS10.8740.93453.9600.0200.0200.0000.0000.0000.000
212A210ASN00.0510.02256.5470.0010.0010.0000.0000.0000.000
213A211LYS10.9340.94059.1450.0100.0100.0000.0000.0000.000
214A212LYS10.9510.97960.9170.0110.0110.0000.0000.0000.000
215A213GLY00.0390.03860.6500.0000.0000.0000.0000.0000.000
216A214THR0-0.0020.00061.514-0.001-0.0010.0000.0000.0000.000
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