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: 7Y77K

Calculation Name: 1V7P-C-Xray547

Preferred Name: Integrin alpha-2

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | phosphate ion | manganese (ii) ion

Ligand 3-letter code: NAG | PO4 | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V7P

Chain ID: C

ChEMBL ID: CHEMBL4998

UniProt ID: P17301

Base Structure: X-ray

Registration Date: 2025-10-03

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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2176695.368298
FMO2-HF: Nuclear repulsion 2102388.39984
FMO2-HF: Total energy -74306.968458
FMO2-MP2: Total energy -74524.93113


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:143:LEU)


Summations of interaction energy for fragment #1(A:143:LEU)
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.
-73.359-61.2468.991-6.765-14.337-0.071
Interaction energy analysis for fragmet #1(A:143:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.906
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].
3A145ASP-1-0.725-0.8423.869-40.718-38.953-0.015-0.752-0.998-0.002
36A178THR0-0.026-0.0103.485-4.565-3.9020.018-0.166-0.5140.000
37A179LYS10.8340.9082.61229.83632.3831.051-1.408-2.190-0.018
38A180THR0-0.0250.0002.763-18.272-15.5940.526-1.656-1.548-0.017
39A181GLN0-0.059-0.0375.2366.3276.454-0.001-0.003-0.1230.000
100A242ARG10.7170.8142.25150.75053.0923.231-1.357-4.216-0.013
101A243ARG10.9500.9554.84823.37223.438-0.001-0.002-0.0620.000
102A244SER0-0.0020.0012.666-0.3271.2710.660-0.831-1.427-0.010
103A245ALA0-0.049-0.0152.155-16.204-14.8133.377-2.129-2.639-0.009
104A246THR00.0430.0232.9518.8947.8300.1451.539-0.620-0.002
4A146VAL00.0270.0135.9282.2772.2770.0000.0000.0000.000
5A147VAL0-0.009-0.0059.4601.1651.1650.0000.0000.0000.000
6A148VAL00.0050.00312.6440.4190.4190.0000.0000.0000.000
7A149VAL0-0.024-0.02015.8480.3680.3680.0000.0000.0000.000
8A150CYS0-0.028-0.02218.9740.2720.2720.0000.0000.0000.000
9A151ASP-1-0.758-0.83121.814-10.895-10.8950.0000.0000.0000.000
10A152GLU-1-0.733-0.84625.480-11.679-11.6790.0000.0000.0000.000
11A153SER0-0.006-0.02527.8140.4530.4530.0000.0000.0000.000
12A154ASN0-0.008-0.02731.110-0.156-0.1560.0000.0000.0000.000
13A155SER0-0.065-0.02832.3160.2590.2590.0000.0000.0000.000
14A156ILE0-0.0010.01027.7650.0810.0810.0000.0000.0000.000
15A157TYR0-0.009-0.00231.9160.1140.1140.0000.0000.0000.000
16A158PRO0-0.016-0.00532.1960.0380.0380.0000.0000.0000.000
17A159TRP00.035-0.01824.748-0.215-0.2150.0000.0000.0000.000
18A160ASP-1-0.858-0.94427.948-10.559-10.5590.0000.0000.0000.000
19A161ALA0-0.040-0.00727.509-0.341-0.3410.0000.0000.0000.000
20A162VAL00.0360.01723.897-0.473-0.4730.0000.0000.0000.000
21A163LYS10.8560.95123.39210.36110.3610.0000.0000.0000.000
22A164ASN00.0350.01422.790-0.636-0.6360.0000.0000.0000.000
23A165PHE0-0.031-0.01619.211-0.564-0.5640.0000.0000.0000.000
24A166LEU0-0.012-0.01118.623-0.906-0.9060.0000.0000.0000.000
25A167GLU-1-0.903-0.94017.984-14.211-14.2110.0000.0000.0000.000
26A168LYS10.9340.95818.53813.84313.8430.0000.0000.0000.000
27A169PHE00.0040.00812.900-0.785-0.7850.0000.0000.0000.000
28A170VAL0-0.007-0.01213.786-1.537-1.5370.0000.0000.0000.000
29A171GLN0-0.027-0.01514.050-0.728-0.7280.0000.0000.0000.000
30A172GLY0-0.001-0.00214.975-0.061-0.0610.0000.0000.0000.000
31A173LEU0-0.0100.0149.523-1.517-1.5170.0000.0000.0000.000
32A174ASP-1-0.832-0.9007.730-31.721-31.7210.0000.0000.0000.000
33A175ILE0-0.004-0.0067.147-4.975-4.9750.0000.0000.0000.000
34A176GLY00.0560.0197.5812.3172.3170.0000.0000.0000.000
35A177PRO00.0420.0335.681-5.023-5.0230.0000.0000.0000.000
40A182VAL00.0660.0067.402-1.030-1.0300.0000.0000.0000.000
41A183GLY0-0.0190.01110.6680.9740.9740.0000.0000.0000.000
42A184LEU0-0.029-0.01213.017-0.295-0.2950.0000.0000.0000.000
43A185ILE0-0.002-0.00616.6030.5610.5610.0000.0000.0000.000
44A186GLN00.0050.01819.134-0.536-0.5360.0000.0000.0000.000
45A187TYR0-0.015-0.02522.640-0.137-0.1370.0000.0000.0000.000
46A188ALA00.0730.05325.2550.1020.1020.0000.0000.0000.000
47A189ASN00.0080.00328.837-0.269-0.2690.0000.0000.0000.000
48A190ASN0-0.022-0.00927.8710.0270.0270.0000.0000.0000.000
49A191PRO00.0090.00722.444-0.041-0.0410.0000.0000.0000.000
50A192ARG10.8060.88423.39112.15012.1500.0000.0000.0000.000
51A193VAL0-0.016-0.01617.908-0.459-0.4590.0000.0000.0000.000
52A194VAL0-0.041-0.00519.3940.6190.6190.0000.0000.0000.000
53A195PHE0-0.003-0.01414.3150.3120.3120.0000.0000.0000.000
54A196ASN00.0200.00613.366-0.446-0.4460.0000.0000.0000.000
55A197LEU0-0.035-0.0057.667-0.117-0.1170.0000.0000.0000.000
56A198ASN00.0130.0039.758-0.844-0.8440.0000.0000.0000.000
57A199THR0-0.0260.00311.1400.8190.8190.0000.0000.0000.000
58A200TYR0-0.009-0.01214.0131.0461.0460.0000.0000.0000.000
59A201LYS10.9060.95912.91414.63714.6370.0000.0000.0000.000
60A202THR0-0.011-0.00612.858-0.964-0.9640.0000.0000.0000.000
61A203LYS10.8800.91612.91221.39921.3990.0000.0000.0000.000
62A204GLU-1-0.922-0.94115.012-13.359-13.3590.0000.0000.0000.000
63A205GLU-1-0.786-0.90917.403-15.718-15.7180.0000.0000.0000.000
64A206MET0-0.036-0.00311.6070.0580.0580.0000.0000.0000.000
65A207ILE00.0190.02117.2270.2150.2150.0000.0000.0000.000
66A208VAL00.0440.02719.4490.6310.6310.0000.0000.0000.000
67A209ALA0-0.0020.00319.1390.6120.6120.0000.0000.0000.000
68A210THR0-0.080-0.05618.4270.1980.1980.0000.0000.0000.000
69A211SER0-0.009-0.01321.3060.6150.6150.0000.0000.0000.000
70A212GLN0-0.045-0.02924.0750.5860.5860.0000.0000.0000.000
71A213THR0-0.055-0.02322.4920.4640.4640.0000.0000.0000.000
72A214SER00.0340.01025.0620.0670.0670.0000.0000.0000.000
73A215GLN0-0.025-0.01227.079-0.346-0.3460.0000.0000.0000.000
74A216TYR0-0.074-0.06128.3310.2640.2640.0000.0000.0000.000
75A217GLY00.0280.03830.7020.3450.3450.0000.0000.0000.000
76A218GLY0-0.039-0.04231.442-0.249-0.2490.0000.0000.0000.000
77A219ASP-1-0.876-0.93433.463-8.523-8.5230.0000.0000.0000.000
78A220LEU0-0.040-0.00733.4130.0870.0870.0000.0000.0000.000
79A221THR00.0560.02628.567-0.102-0.1020.0000.0000.0000.000
80A222ASN0-0.044-0.02628.7320.1020.1020.0000.0000.0000.000
81A223THR00.0810.03024.083-0.388-0.3880.0000.0000.0000.000
82A224PHE0-0.023-0.01723.743-0.835-0.8350.0000.0000.0000.000
83A225GLY00.0270.00423.788-0.431-0.4310.0000.0000.0000.000
84A226ALA00.0030.00922.277-0.413-0.4130.0000.0000.0000.000
85A227ILE00.0270.00918.899-0.833-0.8330.0000.0000.0000.000
86A228GLN0-0.016-0.00418.900-1.465-1.4650.0000.0000.0000.000
87A229TYR0-0.004-0.00419.318-0.276-0.2760.0000.0000.0000.000
88A230ALA00.0310.00315.961-0.571-0.5710.0000.0000.0000.000
89A231ARG10.7830.86315.16814.99314.9930.0000.0000.0000.000
90A232LYS10.8690.95015.29413.15213.1520.0000.0000.0000.000
91A233TYR00.006-0.00716.5970.1500.1500.0000.0000.0000.000
92A234ALA00.0500.05113.879-0.462-0.4620.0000.0000.0000.000
93A235TYR0-0.009-0.0319.036-0.590-0.5900.0000.0000.0000.000
94A236SER0-0.046-0.03710.609-0.837-0.8370.0000.0000.0000.000
95A237ALA00.0130.0029.792-0.494-0.4940.0000.0000.0000.000
96A238ALA0-0.014-0.00610.869-0.291-0.2910.0000.0000.0000.000
97A239SER0-0.023-0.00312.7720.9270.9270.0000.0000.0000.000
98A240GLY00.0340.0089.192-0.528-0.5280.0000.0000.0000.000
99A241GLY00.0000.0117.001-3.050-3.0500.0000.0000.0000.000
105A247LYS10.9300.9845.68124.62024.6200.0000.0000.0000.000
106A248VAL00.0480.0208.3431.6941.6940.0000.0000.0000.000
107A249MET0-0.0390.01510.5091.0511.0510.0000.0000.0000.000
108A250VAL00.0100.00413.8410.0660.0660.0000.0000.0000.000
109A251VAL00.0200.01716.3710.4760.4760.0000.0000.0000.000
110A252VAL0-0.008-0.00419.8490.1240.1240.0000.0000.0000.000
111A253THR0-0.011-0.04322.6390.2890.2890.0000.0000.0000.000
112A254ASP-1-0.806-0.89126.317-10.221-10.2210.0000.0000.0000.000
113A255GLY00.0150.01429.8320.4340.4340.0000.0000.0000.000
114A256GLU-1-0.944-0.97730.198-9.369-9.3690.0000.0000.0000.000
115A257SER0-0.081-0.07028.6780.1520.1520.0000.0000.0000.000
116A258HIS0-0.023-0.01630.6650.5080.5080.0000.0000.0000.000
117A259ASP-1-0.777-0.89228.026-11.085-11.0850.0000.0000.0000.000
118A260GLY00.0630.03329.525-0.245-0.2450.0000.0000.0000.000
119A261SER0-0.056-0.02830.422-0.213-0.2130.0000.0000.0000.000
120A262MET0-0.022-0.01927.311-0.074-0.0740.0000.0000.0000.000
121A263LEU00.0000.02726.083-0.436-0.4360.0000.0000.0000.000
122A264LYS10.9090.94225.52711.41911.4190.0000.0000.0000.000
123A265ALA0-0.003-0.00326.079-0.239-0.2390.0000.0000.0000.000
124A266VAL00.0180.00421.668-0.525-0.5250.0000.0000.0000.000
125A267ILE00.0270.01721.054-0.917-0.9170.0000.0000.0000.000
126A268ASP-1-0.938-0.94820.587-13.823-13.8230.0000.0000.0000.000
127A269GLN00.0610.02220.211-0.593-0.5930.0000.0000.0000.000
128A270CYS0-0.040-0.01716.902-0.999-0.9990.0000.0000.0000.000
129A271ASN00.0280.02715.898-2.013-2.0130.0000.0000.0000.000
130A272HIS0-0.034-0.01016.366-0.446-0.4460.0000.0000.0000.000
131A273ASP-1-0.883-0.92414.014-19.190-19.1900.0000.0000.0000.000
132A274ASN0-0.078-0.05311.292-2.321-2.3210.0000.0000.0000.000
133A275ILE0-0.032-0.00711.138-2.334-2.3340.0000.0000.0000.000
134A276LEU0-0.0010.0139.7832.0912.0910.0000.0000.0000.000
135A277ARG10.8220.88613.02916.91316.9130.0000.0000.0000.000
136A278PHE00.0260.00712.2930.8550.8550.0000.0000.0000.000
137A279GLY00.0000.00417.4140.1600.1600.0000.0000.0000.000
138A280ILE0-0.022-0.02419.1260.3110.3110.0000.0000.0000.000
139A281ALA00.006-0.00122.9850.2470.2470.0000.0000.0000.000
140A282VAL00.007-0.00525.9890.1140.1140.0000.0000.0000.000
141A283LEU0-0.023-0.02028.4570.3180.3180.0000.0000.0000.000
142A284GLY00.0480.04131.6040.3420.3420.0000.0000.0000.000
143A285TYR00.0110.01533.4760.3670.3670.0000.0000.0000.000
144A286LEU00.0030.00233.7700.3040.3040.0000.0000.0000.000
145A287ASN0-0.045-0.03734.5270.4200.4200.0000.0000.0000.000
146A288ARG10.7770.85333.7939.4039.4030.0000.0000.0000.000
147A289ASN0-0.079-0.03639.1110.4050.4050.0000.0000.0000.000
148A290ALA0-0.031-0.00441.1460.1400.1400.0000.0000.0000.000
149A291LEU0-0.0030.01038.6590.1000.1000.0000.0000.0000.000
150A292ASP-1-0.809-0.89238.673-8.458-8.4580.0000.0000.0000.000
151A293THR00.0690.03433.991-0.161-0.1610.0000.0000.0000.000
152A294LYS10.7980.87433.6187.9247.9240.0000.0000.0000.000
153A295ASN0-0.051-0.02633.551-0.304-0.3040.0000.0000.0000.000
154A296LEU00.0880.05828.928-0.283-0.2830.0000.0000.0000.000
155A297ILE0-0.020-0.01329.285-0.499-0.4990.0000.0000.0000.000
156A298LYS10.9010.95128.7079.0699.0690.0000.0000.0000.000
157A299GLU-1-0.798-0.87327.603-11.196-11.1960.0000.0000.0000.000
158A300ILE00.0290.01123.837-0.542-0.5420.0000.0000.0000.000
159A301LYS10.8880.95123.84510.62710.6270.0000.0000.0000.000
160A302ALA0-0.033-0.00324.167-0.345-0.3450.0000.0000.0000.000
161A303ILE0-0.013-0.00220.760-0.321-0.3210.0000.0000.0000.000
162A304ALA0-0.0120.00619.759-0.885-0.8850.0000.0000.0000.000
163A305SER0-0.0050.01216.2870.0410.0410.0000.0000.0000.000
164A306ILE0-0.017-0.00318.3660.7080.7080.0000.0000.0000.000
165A307PRO00.0430.00817.873-0.811-0.8110.0000.0000.0000.000
166A308THR00.040-0.00520.051-0.277-0.2770.0000.0000.0000.000
167A309GLU-1-0.984-0.99121.018-14.770-14.7700.0000.0000.0000.000
168A310ARG10.9100.98412.82321.33721.3370.0000.0000.0000.000
169A311TYR0-0.005-0.01912.737-0.601-0.6010.0000.0000.0000.000
170A312PHE0-0.009-0.01518.4870.1880.1880.0000.0000.0000.000
171A313PHE00.0040.00317.9640.2600.2600.0000.0000.0000.000
172A314ASN0-0.023-0.01323.3310.2890.2890.0000.0000.0000.000
173A315VAL00.0030.00525.385-0.087-0.0870.0000.0000.0000.000
174A316SER00.011-0.00928.2970.0650.0650.0000.0000.0000.000
175A317ASP-1-0.794-0.89630.588-9.620-9.6200.0000.0000.0000.000
176A318GLU-1-0.680-0.81728.439-10.297-10.2970.0000.0000.0000.000
177A319ALA0-0.025-0.00427.972-0.341-0.3410.0000.0000.0000.000
178A320ALA0-0.005-0.00328.150-0.363-0.3630.0000.0000.0000.000
179A321LEU0-0.0020.00023.169-0.418-0.4180.0000.0000.0000.000
180A322LEU0-0.020-0.00923.310-0.686-0.6860.0000.0000.0000.000
181A323GLU-1-0.884-0.93423.252-11.869-11.8690.0000.0000.0000.000
182A324LYS10.8830.92621.40511.85411.8540.0000.0000.0000.000
183A325ALA0-0.0250.00318.946-0.885-0.8850.0000.0000.0000.000
184A326GLY0-0.034-0.01217.401-0.961-0.9610.0000.0000.0000.000
185A327THR00.0620.02516.839-0.872-0.8720.0000.0000.0000.000
186A328LEU0-0.0130.00015.006-0.804-0.8040.0000.0000.0000.000
187A329GLY00.0120.00112.780-1.612-1.6120.0000.0000.0000.000
188A330GLU-1-0.927-0.96812.152-19.140-19.1400.0000.0000.0000.000
189A331GLN0-0.001-0.00213.017-1.546-1.5460.0000.0000.0000.000
190A332ILE0-0.025-0.0148.770-1.404-1.4040.0000.0000.0000.000
191A333PHE0-0.068-0.0368.365-4.372-4.3720.0000.0000.0000.000
192A334SER0-0.070-0.0358.779-0.998-0.9980.0000.0000.0000.000
193A335ILE-1-0.940-0.9507.446-33.564-33.5640.0000.0000.0000.000