FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: JV6G9

Calculation Name: 1ITV-A-Xray547

Preferred Name: Matrix metalloproteinase 9

Target Type: SINGLE PROTEIN

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ITV

Chain ID: A

ChEMBL ID: CHEMBL321

UniProt ID: P14780

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2301692.583812
FMO2-HF: Nuclear repulsion 2223422.204307
FMO2-HF: Total energy -78270.379505
FMO2-MP2: Total energy -78499.866487


3D Structure Molmil
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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-7.899-2.751.045-2.579-3.616-0.013
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.113 / q_NPA : -0.064
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].
3A3ALA0-0.022-0.0112.872-15.865-13.1470.143-1.532-1.329-0.012
4A4CYS0-0.081-0.0545.3990.7830.935-0.002-0.005-0.1450.000
5A5ASN0-0.031-0.0083.5921.0751.4000.001-0.083-0.2440.000
6A6VAL0-0.064-0.0244.191-1.032-0.933-0.001-0.017-0.0810.000
26A26LYS10.8590.9454.7923.9864.037-0.001-0.002-0.0480.000
28A28TRP00.0020.0042.156-0.1550.6680.576-0.507-0.893-0.003
41A41PRO0-0.0380.0012.5500.4651.4460.329-0.433-0.8760.002
7A7ASN00.0170.0146.3262.3812.3810.0000.0000.0000.000
8A8ILE00.0240.0119.6480.9380.9380.0000.0000.0000.000
9A9PHE00.0110.0016.705-1.155-1.1550.0000.0000.0000.000
10A10ASP-1-0.826-0.92410.194-5.369-5.3690.0000.0000.0000.000
11A11ALA0-0.0100.00512.0940.6760.6760.0000.0000.0000.000
12A12ILE0-0.029-0.01012.620-0.654-0.6540.0000.0000.0000.000
13A13ALA00.0040.00914.8230.3500.3500.0000.0000.0000.000
14A14GLU-1-0.885-0.93616.881-1.326-1.3260.0000.0000.0000.000
15A15ILE0-0.045-0.02617.2130.0600.0600.0000.0000.0000.000
16A16GLY00.005-0.00620.3870.0570.0570.0000.0000.0000.000
17A17ASN0-0.069-0.03321.9880.0460.0460.0000.0000.0000.000
18A18GLN0-0.0020.01116.624-0.052-0.0520.0000.0000.0000.000
19A19LEU00.0270.02914.026-0.019-0.0190.0000.0000.0000.000
20A20TYR0-0.016-0.01513.061-0.108-0.1080.0000.0000.0000.000
21A21LEU00.0120.0199.0800.0170.0170.0000.0000.0000.000
22A22PHE00.018-0.0099.505-0.283-0.2830.0000.0000.0000.000
23A23LYS10.8190.9005.9117.7687.7680.0000.0000.0000.000
24A24ASP-1-0.861-0.9187.264-8.901-8.9010.0000.0000.0000.000
25A25GLY00.005-0.0078.8660.2270.2270.0000.0000.0000.000
27A27TYR00.009-0.0047.6910.0180.0180.0000.0000.0000.000
29A29ARG10.8190.9088.8750.6650.6650.0000.0000.0000.000
30A30PHE00.0530.03612.3940.2920.2920.0000.0000.0000.000
31A31SER0-0.018-0.02213.7380.2480.2480.0000.0000.0000.000
32A32GLU-1-0.811-0.87017.290-0.921-0.9210.0000.0000.0000.000
33A33GLY00.0670.02619.5010.1480.1480.0000.0000.0000.000
34A34ARG10.9690.98620.0720.0220.0220.0000.0000.0000.000
35A35GLY00.0150.00118.4300.1450.1450.0000.0000.0000.000
36A36SER0-0.099-0.04316.8470.2620.2620.0000.0000.0000.000
37A37ARG11.0221.00611.025-0.046-0.0460.0000.0000.0000.000
38A38PRO0-0.026-0.0098.7780.3310.3310.0000.0000.0000.000
39A39GLN00.0420.0269.2670.5060.5060.0000.0000.0000.000
40A40GLY00.0220.0107.578-1.594-1.5940.0000.0000.0000.000
42A42PHE00.027-0.0045.6682.5652.5650.0000.0000.0000.000
43A43LEU00.0170.0038.662-1.625-1.6250.0000.0000.0000.000
44A44ILE0-0.014-0.01210.6400.2980.2980.0000.0000.0000.000
45A45ALA00.003-0.00613.0050.2840.2840.0000.0000.0000.000
46A46ASP-1-0.845-0.92213.2140.4100.4100.0000.0000.0000.000
47A47LYS10.8550.94215.7900.8430.8430.0000.0000.0000.000
48A48TRP0-0.020-0.02614.1170.0270.0270.0000.0000.0000.000
49A49PRO00.0350.01618.249-0.181-0.1810.0000.0000.0000.000
50A50ALA0-0.028-0.00319.6250.0220.0220.0000.0000.0000.000
51A51LEU0-0.038-0.00716.777-0.028-0.0280.0000.0000.0000.000
52A52PRO0-0.0020.00717.6610.0230.0230.0000.0000.0000.000
53A53ARG10.8730.9248.8724.2074.2070.0000.0000.0000.000
54A54LYS10.9490.97912.3823.6773.6770.0000.0000.0000.000
55A55LEU0-0.018-0.00214.0840.4820.4820.0000.0000.0000.000
56A56ASP-1-0.808-0.91115.508-2.564-2.5640.0000.0000.0000.000
57A57SER00.023-0.01017.7610.0580.0580.0000.0000.0000.000
58A58VAL0-0.033-0.02515.9150.0730.0730.0000.0000.0000.000
59A59PHE00.0050.00219.0900.0030.0030.0000.0000.0000.000
60A60GLU-1-0.818-0.90521.608-0.855-0.8550.0000.0000.0000.000
61A61GLU-1-0.785-0.85723.455-0.669-0.6690.0000.0000.0000.000
62A62PRO00.0250.00327.2280.0650.0650.0000.0000.0000.000
63A63LEU0-0.071-0.02229.0130.0560.0560.0000.0000.0000.000
64A64SER0-0.098-0.10630.5590.0280.0280.0000.0000.0000.000
65A65LYS10.8700.93326.1960.6600.6600.0000.0000.0000.000
66A66LYS10.9250.97925.6310.5640.5640.0000.0000.0000.000
67A67LEU00.0130.01619.723-0.042-0.0420.0000.0000.0000.000
68A68PHE0-0.023-0.00422.9850.0680.0680.0000.0000.0000.000
69A69PHE00.0430.01316.428-0.115-0.1150.0000.0000.0000.000
70A70PHE00.024-0.00319.8320.2380.2380.0000.0000.0000.000
71A71SER0-0.003-0.01318.173-0.190-0.1900.0000.0000.0000.000
72A72GLY00.0140.01820.4420.1810.1810.0000.0000.0000.000
73A73ARG10.9480.96223.1171.1841.1840.0000.0000.0000.000
74A74GLN0-0.051-0.03224.0050.2120.2120.0000.0000.0000.000
75A75VAL00.0270.01723.839-0.111-0.1110.0000.0000.0000.000
76A76TRP0-0.032-0.01521.9450.0780.0780.0000.0000.0000.000
77A77VAL00.0020.00023.846-0.065-0.0650.0000.0000.0000.000
78A78TYR00.0540.03121.0820.0350.0350.0000.0000.0000.000
79A79THR0-0.042-0.05124.5490.0020.0020.0000.0000.0000.000
80A80GLY00.0330.02724.8770.0760.0760.0000.0000.0000.000
81A81ALA00.0380.01123.763-0.074-0.0740.0000.0000.0000.000
82A82SER0-0.0170.00824.9230.0030.0030.0000.0000.0000.000
83A83VAL00.008-0.00223.971-0.067-0.0670.0000.0000.0000.000
84A84LEU0-0.0190.00126.5250.0590.0590.0000.0000.0000.000
85A85GLY0-0.006-0.01126.709-0.072-0.0720.0000.0000.0000.000
86A86PRO00.0110.03225.0380.0460.0460.0000.0000.0000.000
87A87ARG10.9000.94626.6930.8430.8430.0000.0000.0000.000
88A88ARG10.9920.99827.8340.6490.6490.0000.0000.0000.000
89A89LEU00.0220.01425.9150.0370.0370.0000.0000.0000.000
90A90ASP-1-0.837-0.92529.958-0.703-0.7030.0000.0000.0000.000
91A91LYS10.8580.92832.0660.6450.6450.0000.0000.0000.000
92A92LEU00.0000.00828.6310.0190.0190.0000.0000.0000.000
93A93GLY00.0300.00532.805-0.001-0.0010.0000.0000.0000.000
94A94LEU0-0.041-0.00428.9340.0050.0050.0000.0000.0000.000
95A95GLY00.0410.01733.1230.0320.0320.0000.0000.0000.000
96A96ALA0-0.003-0.01932.888-0.048-0.0480.0000.0000.0000.000
97A97ASP-1-0.825-0.87433.348-0.871-0.8710.0000.0000.0000.000
98A98VAL0-0.033-0.01227.904-0.053-0.0530.0000.0000.0000.000
99A99ALA0-0.024-0.01426.6020.0010.0010.0000.0000.0000.000
100A100GLN00.012-0.00121.7790.0650.0650.0000.0000.0000.000
101A101VAL0-0.0080.01423.5800.0840.0840.0000.0000.0000.000
102A102THR00.0200.02420.869-0.063-0.0630.0000.0000.0000.000
103A103GLY00.0800.02821.293-0.112-0.1120.0000.0000.0000.000
104A104ALA0-0.091-0.04222.2300.1600.1600.0000.0000.0000.000
105A105LEU00.0130.02724.066-0.048-0.0480.0000.0000.0000.000
106A106ARG10.9560.96826.7790.8490.8490.0000.0000.0000.000
107A107SER00.0150.01329.6120.0150.0150.0000.0000.0000.000
108A108GLY00.0380.02333.2080.0240.0240.0000.0000.0000.000
109A109ARG10.9560.96535.3770.4710.4710.0000.0000.0000.000
110A110GLY00.0030.00035.4300.0190.0190.0000.0000.0000.000
111A111LYS10.8210.89934.6130.5620.5620.0000.0000.0000.000
112A112MET0-0.0140.01526.3880.0230.0230.0000.0000.0000.000
113A113LEU00.0090.00429.5870.0570.0570.0000.0000.0000.000
114A114LEU0-0.012-0.00726.693-0.068-0.0680.0000.0000.0000.000
115A115PHE00.0600.01124.8160.0860.0860.0000.0000.0000.000
116A116SER0-0.024-0.02825.407-0.048-0.0480.0000.0000.0000.000
117A117GLY00.0410.03024.7670.0870.0870.0000.0000.0000.000
118A118ARG10.8960.93225.7871.2861.2860.0000.0000.0000.000
119A119ARG10.7970.88729.0701.0441.0440.0000.0000.0000.000
120A120LEU00.0160.01228.965-0.083-0.0830.0000.0000.0000.000
121A121TRP0-0.006-0.00129.3320.0600.0600.0000.0000.0000.000
122A122ARG10.9610.97532.0780.6120.6120.0000.0000.0000.000
123A123PHE00.0070.00630.9380.0140.0140.0000.0000.0000.000
124A124ASP-1-0.830-0.90133.623-0.543-0.5430.0000.0000.0000.000
125A125VAL00.0330.01131.587-0.003-0.0030.0000.0000.0000.000
126A126LYS10.9210.96834.0970.4120.4120.0000.0000.0000.000
127A127ALA0-0.011-0.01537.3360.0200.0200.0000.0000.0000.000
128A128GLN0-0.082-0.03931.388-0.031-0.0310.0000.0000.0000.000
129A129MET00.0100.01334.148-0.030-0.0300.0000.0000.0000.000
130A130VAL0-0.0100.00732.405-0.001-0.0010.0000.0000.0000.000
131A131ASP-1-0.791-0.88135.628-0.531-0.5310.0000.0000.0000.000
132A132PRO00.0350.01636.905-0.027-0.0270.0000.0000.0000.000
133A133ARG10.8880.92837.9640.4740.4740.0000.0000.0000.000
134A134SER0-0.126-0.07136.777-0.002-0.0020.0000.0000.0000.000
135A135ALA00.0040.01035.432-0.025-0.0250.0000.0000.0000.000
136A136SER0-0.029-0.02434.6610.0650.0650.0000.0000.0000.000
137A137GLU-1-0.860-0.92433.027-0.839-0.8390.0000.0000.0000.000
138A138VAL0-0.006-0.01827.5060.0400.0400.0000.0000.0000.000
139A139ASP-1-0.916-0.95330.876-0.890-0.8900.0000.0000.0000.000
140A140ARG10.9050.94532.4550.7520.7520.0000.0000.0000.000
141A141MET0-0.073-0.01733.0420.0330.0330.0000.0000.0000.000
142A142PHE0-0.009-0.01929.5170.0160.0160.0000.0000.0000.000
143A143PRO00.0720.04730.688-0.061-0.0610.0000.0000.0000.000
144A144GLY00.006-0.00830.7070.0080.0080.0000.0000.0000.000
145A145VAL0-0.034-0.01025.416-0.078-0.0780.0000.0000.0000.000
146A146PRO0-0.0100.00823.5400.0750.0750.0000.0000.0000.000
147A147LEU00.008-0.00826.403-0.040-0.0400.0000.0000.0000.000
148A148ASP-1-0.871-0.92224.165-1.384-1.3840.0000.0000.0000.000
149A149THR0-0.0120.00721.704-0.104-0.1040.0000.0000.0000.000
150A150HIS0-0.081-0.05815.4700.1920.1920.0000.0000.0000.000
151A151ASP-1-0.776-0.89616.136-2.904-2.9040.0000.0000.0000.000
152A152VAL0-0.056-0.01618.7310.1010.1010.0000.0000.0000.000
153A153PHE00.0500.02416.9790.0880.0880.0000.0000.0000.000
154A154GLN00.029-0.00220.9910.0990.0990.0000.0000.0000.000
155A155PHE00.006-0.00919.256-0.105-0.1050.0000.0000.0000.000
156A156ARG10.8480.92021.2511.0441.0440.0000.0000.0000.000
157A157GLU-1-0.968-0.99524.832-0.762-0.7620.0000.0000.0000.000
158A158LYS10.8760.96624.9930.9540.9540.0000.0000.0000.000
159A159ALA00.0110.00824.482-0.083-0.0830.0000.0000.0000.000
160A160TYR0-0.002-0.00520.0090.0460.0460.0000.0000.0000.000
161A161PHE00.0200.01021.305-0.085-0.0850.0000.0000.0000.000
162A162CYS0-0.015-0.00517.085-0.024-0.0240.0000.0000.0000.000
163A163GLN0-0.002-0.02518.8870.1490.1490.0000.0000.0000.000
164A164ASP-1-0.833-0.89416.294-3.168-3.1680.0000.0000.0000.000
165A165ARG10.8940.93912.4683.3833.3830.0000.0000.0000.000
166A166PHE0-0.028-0.00614.436-0.046-0.0460.0000.0000.0000.000
167A167TYR0-0.066-0.06917.666-0.001-0.0010.0000.0000.0000.000
168A168TRP00.0290.00819.7750.1150.1150.0000.0000.0000.000
169A169ARG10.8030.87923.3341.1241.1240.0000.0000.0000.000
170A170VAL0-0.005-0.00224.6640.0950.0950.0000.0000.0000.000
171A171SER0-0.036-0.04027.862-0.018-0.0180.0000.0000.0000.000
172A172SER00.0120.00630.5020.0170.0170.0000.0000.0000.000
173A173ARG10.9180.93733.6140.6530.6530.0000.0000.0000.000
174A174SER0-0.006-0.00937.170-0.006-0.0060.0000.0000.0000.000
175A175GLU-1-0.928-0.95738.671-0.565-0.5650.0000.0000.0000.000
176A176LEU0-0.042-0.00937.655-0.014-0.0140.0000.0000.0000.000
177A177ASN0-0.068-0.03631.990-0.009-0.0090.0000.0000.0000.000
178A178GLN00.0390.02032.6680.0610.0610.0000.0000.0000.000
179A179VAL00.0150.01026.878-0.024-0.0240.0000.0000.0000.000
180A180ASP-1-0.846-0.89127.776-0.939-0.9390.0000.0000.0000.000
181A181GLN00.000-0.00222.3900.1600.1600.0000.0000.0000.000
182A182VAL00.001-0.00222.800-0.062-0.0620.0000.0000.0000.000
183A183GLY00.0410.03620.4350.1310.1310.0000.0000.0000.000
184A184TYR00.0370.02114.692-0.223-0.2230.0000.0000.0000.000
185A185VAL0-0.028-0.03012.5960.1090.1090.0000.0000.0000.000
186A186THR00.0160.0019.4910.0160.0160.0000.0000.0000.000
187A187TYR00.0160.01812.1660.0870.0870.0000.0000.0000.000
188A188ASP-1-0.795-0.85815.178-1.502-1.5020.0000.0000.0000.000
189A189ILE0-0.048-0.01815.2210.2380.2380.0000.0000.0000.000
190A190LEU0-0.022-0.0219.566-0.321-0.3210.0000.0000.0000.000
191A191GLN0-0.096-0.05013.4680.3830.3830.0000.0000.0000.000
192A193PRO0-0.064-0.03211.7330.1900.1900.0000.0000.0000.000
193A194GLU-1-0.930-0.97513.838-1.323-1.3230.0000.0000.0000.000
194A195ASP-2-1.899-1.94013.377-1.962-1.9620.0000.0000.0000.000