Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6YK1Z

Calculation Name: 1NA5-A-Xray372

Preferred Name: Integrin alpha M

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NA5

Chain ID: A

ChEMBL ID: CHEMBL3826

UniProt ID: P11215

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2348437.940137
FMO2-HF: Nuclear repulsion 2271604.376377
FMO2-HF: Total energy -76833.56376
FMO2-MP2: Total energy -77062.205049


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:130:GLN)


Summations of interaction energy for fragment #1(A:130:GLN)
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.
-3.372-0.627000000000010.084-1.087-1.7410.003
Interaction energy analysis for fragmet #1(A:130:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.005
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].
3A132ASP-1-0.863-0.9383.8031.2052.571-0.022-0.567-0.7760.001
4A133SER0-0.053-0.0286.5900.5060.5060.0000.0000.0000.000
5A134ASP-1-0.770-0.8338.5490.9040.9040.0000.0000.0000.000
6A135ILE0-0.006-0.02310.106-0.011-0.0110.0000.0000.0000.000
7A136ALA00.0130.00113.709-0.133-0.1330.0000.0000.0000.000
8A137PHE0-0.004-0.00916.0420.0390.0390.0000.0000.0000.000
9A138LEU00.0030.00920.146-0.044-0.0440.0000.0000.0000.000
10A139ILE0-0.042-0.03823.7310.0050.0050.0000.0000.0000.000
11A140ASP-1-0.738-0.87026.1760.2950.2950.0000.0000.0000.000
12A141GLY00.004-0.01729.844-0.001-0.0010.0000.0000.0000.000
13A142SER00.0020.00432.134-0.024-0.0240.0000.0000.0000.000
14A143GLY0-0.046-0.03435.3850.0000.0000.0000.0000.0000.000
15A144SER0-0.078-0.03035.861-0.009-0.0090.0000.0000.0000.000
16A145ILE0-0.0030.02731.5070.0000.0000.0000.0000.0000.000
17A146ILE00.0300.02635.761-0.009-0.0090.0000.0000.0000.000
18A147PRO00.1020.02335.6040.0120.0120.0000.0000.0000.000
19A148HIS0-0.064-0.05734.308-0.001-0.0010.0000.0000.0000.000
20A149ASP-1-0.761-0.89333.0350.2440.2440.0000.0000.0000.000
21A150PHE00.0640.04930.0160.0210.0210.0000.0000.0000.000
22A151ARG10.8690.93229.760-0.174-0.1740.0000.0000.0000.000
23A152ARG10.8410.92728.969-0.207-0.2070.0000.0000.0000.000
24A153MET00.0330.03426.1490.0320.0320.0000.0000.0000.000
25A154LYS10.8080.90225.107-0.232-0.2320.0000.0000.0000.000
26A155GLU-1-0.817-0.86524.1790.3430.3430.0000.0000.0000.000
27A156PHE00.0210.00921.3130.0290.0290.0000.0000.0000.000
28A157VAL00.0230.00820.0880.0550.0550.0000.0000.0000.000
29A158SER0-0.034-0.02919.2600.0580.0580.0000.0000.0000.000
30A159THR00.0070.00518.8880.0250.0250.0000.0000.0000.000
31A160VAL0-0.007-0.00516.0470.0550.0550.0000.0000.0000.000
32A161MET0-0.044-0.01214.8170.1140.1140.0000.0000.0000.000
33A162GLU-1-0.924-0.97413.8000.5120.5120.0000.0000.0000.000
34A163GLN0-0.066-0.03613.8120.0950.0950.0000.0000.0000.000
35A164LEU0-0.024-0.00310.9770.1310.1310.0000.0000.0000.000
36A165LYS10.8970.9729.338-0.130-0.1300.0000.0000.0000.000
37A166LYS10.9560.9834.351-6.844-6.690-0.001-0.022-0.1310.000
38A167SER0-0.005-0.0075.4480.1760.1760.0000.0000.0000.000
39A168LYS10.8700.9432.9251.0222.2470.107-0.498-0.8340.002
40A169THR00.0130.0176.1990.5520.5520.0000.0000.0000.000
41A170LEU0-0.0310.0018.203-0.350-0.3500.0000.0000.0000.000
42A171PHE00.015-0.01111.9170.1550.1550.0000.0000.0000.000
43A172SER0-0.039-0.03614.879-0.113-0.1130.0000.0000.0000.000
44A173LEU0-0.034-0.01718.3760.0510.0510.0000.0000.0000.000
45A174MET00.0070.01021.488-0.044-0.0440.0000.0000.0000.000
46A175GLN0-0.027-0.03524.7570.0070.0070.0000.0000.0000.000
47A176TYR0-0.027-0.01427.785-0.003-0.0030.0000.0000.0000.000
48A177SER00.1310.07930.3410.0030.0030.0000.0000.0000.000
49A178GLU-1-0.834-0.92633.9470.2040.2040.0000.0000.0000.000
50A179GLU-1-0.986-0.97234.9240.2100.2100.0000.0000.0000.000
51A180PHE00.020-0.03429.8670.0200.0200.0000.0000.0000.000
52A181ARG10.9470.98628.960-0.266-0.2660.0000.0000.0000.000
53A182ILE00.0180.01623.8350.0300.0300.0000.0000.0000.000
54A183HIS0-0.045-0.02524.607-0.025-0.0250.0000.0000.0000.000
55A184PHE00.0620.02818.026-0.014-0.0140.0000.0000.0000.000
56A185THR0-0.0030.02220.7050.0570.0570.0000.0000.0000.000
57A186PHE00.0490.01614.7040.0050.0050.0000.0000.0000.000
58A187LYS10.9030.95516.564-0.340-0.3400.0000.0000.0000.000
59A188GLU-1-0.852-0.92718.7230.2930.2930.0000.0000.0000.000
60A189PHE0-0.0060.00812.827-0.009-0.0090.0000.0000.0000.000
61A190GLN0-0.010-0.01814.3070.0400.0400.0000.0000.0000.000
62A191ASN0-0.034-0.01915.866-0.070-0.0700.0000.0000.0000.000
63A192ASN00.0090.02018.762-0.061-0.0610.0000.0000.0000.000
64A193PRO00.0430.05314.5200.0390.0390.0000.0000.0000.000
65A194ASN0-0.079-0.06216.2540.0140.0140.0000.0000.0000.000
66A195PRO00.0490.02016.072-0.032-0.0320.0000.0000.0000.000
67A196ARG10.8350.88418.881-0.356-0.3560.0000.0000.0000.000
68A197SER0-0.076-0.03921.850-0.027-0.0270.0000.0000.0000.000
69A198LEU00.0200.01219.275-0.021-0.0210.0000.0000.0000.000
70A199VAL00.0050.00821.255-0.012-0.0120.0000.0000.0000.000
71A200LYS10.9590.98024.059-0.238-0.2380.0000.0000.0000.000
72A201PRO0-0.001-0.01026.349-0.015-0.0150.0000.0000.0000.000
73A202ILE0-0.0230.02626.111-0.016-0.0160.0000.0000.0000.000
74A203THR00.005-0.01329.4600.0000.0000.0000.0000.0000.000
75A204GLN0-0.064-0.04132.1690.0060.0060.0000.0000.0000.000
76A205LEU0-0.069-0.03231.602-0.014-0.0140.0000.0000.0000.000
77A206LEU00.0100.02234.992-0.016-0.0160.0000.0000.0000.000
78A207GLY00.0500.03036.9170.0060.0060.0000.0000.0000.000
79A208ARG10.8750.93138.301-0.187-0.1870.0000.0000.0000.000
80A209THR00.0830.03933.2490.0030.0030.0000.0000.0000.000
81A210HIS0-0.072-0.02634.075-0.007-0.0070.0000.0000.0000.000
82A211THR00.0860.02029.0370.0100.0100.0000.0000.0000.000
83A212ALA0-0.0060.01629.4740.0310.0310.0000.0000.0000.000
84A213THR0-0.031-0.05130.0200.0160.0160.0000.0000.0000.000
85A214GLY00.0120.00728.7100.0090.0090.0000.0000.0000.000
86A215ILE00.0120.00024.9000.0310.0310.0000.0000.0000.000
87A216ARG10.8980.95625.492-0.300-0.3000.0000.0000.0000.000
88A217LYS10.9250.96326.780-0.298-0.2980.0000.0000.0000.000
89A218VAL00.0100.01421.1320.0110.0110.0000.0000.0000.000
90A219VAL0-0.026-0.01722.1010.0330.0330.0000.0000.0000.000
91A220ARG10.8280.89722.844-0.347-0.3470.0000.0000.0000.000
92A221GLU-1-0.893-0.95824.7700.3310.3310.0000.0000.0000.000
93A222LEU0-0.0060.01120.069-0.008-0.0080.0000.0000.0000.000
94A223PHE0-0.058-0.02715.1980.0290.0290.0000.0000.0000.000
95A224ASN00.0430.03619.520-0.029-0.0290.0000.0000.0000.000
96A225ILE00.0520.01819.6490.0110.0110.0000.0000.0000.000
97A226THR0-0.024-0.01520.731-0.007-0.0070.0000.0000.0000.000
98A227ASN0-0.009-0.03821.383-0.058-0.0580.0000.0000.0000.000
99A228GLY0-0.090-0.05418.0630.0200.0200.0000.0000.0000.000
100A229ALA00.0040.03615.6780.0430.0430.0000.0000.0000.000
101A230ARG10.8160.8598.691-1.220-1.2200.0000.0000.0000.000
102A231LYS10.9420.96614.264-0.341-0.3410.0000.0000.0000.000
103A232ASN0-0.027-0.03212.309-0.037-0.0370.0000.0000.0000.000
104A233ALA00.0170.04310.0270.1610.1610.0000.0000.0000.000
105A234PHE00.0080.0035.908-0.581-0.5810.0000.0000.0000.000
106A235LYS10.9120.97010.877-0.916-0.9160.0000.0000.0000.000
107A236ILE0-0.0110.00010.587-0.030-0.0300.0000.0000.0000.000
108A237LEU00.0220.01314.921-0.082-0.0820.0000.0000.0000.000
109A238VAL0-0.019-0.00316.9660.0040.0040.0000.0000.0000.000
110A239VAL00.006-0.00519.650-0.049-0.0490.0000.0000.0000.000
111A240ILE0-0.032-0.01822.6060.0050.0050.0000.0000.0000.000
112A241THR0-0.007-0.01925.700-0.027-0.0270.0000.0000.0000.000
113A242ASP-1-0.831-0.93329.3480.2820.2820.0000.0000.0000.000
114A243GLY00.0120.01332.557-0.020-0.0200.0000.0000.0000.000
115A244GLU-1-0.972-0.97333.6690.2510.2510.0000.0000.0000.000
116A245LYS10.7930.90133.453-0.292-0.2920.0000.0000.0000.000
117A246PHE0-0.007-0.02335.527-0.015-0.0150.0000.0000.0000.000
118A247GLY0-0.019-0.01938.4950.0020.0020.0000.0000.0000.000
119A248ASP-1-0.760-0.85134.0620.2980.2980.0000.0000.0000.000
120A249PRO0-0.023-0.00437.222-0.004-0.0040.0000.0000.0000.000
121A250LEU0-0.022-0.00533.058-0.001-0.0010.0000.0000.0000.000
122A251GLY00.0600.01235.4160.0030.0030.0000.0000.0000.000
123A252TYR0-0.034-0.07630.0630.0200.0200.0000.0000.0000.000
124A253GLU-1-0.879-0.92830.8660.3160.3160.0000.0000.0000.000
125A254ASP-1-0.821-0.89932.6680.2790.2790.0000.0000.0000.000
126A255VAL0-0.102-0.06128.4840.0060.0060.0000.0000.0000.000
127A256ILE0-0.0020.00925.7610.0330.0330.0000.0000.0000.000
128A257PRO00.0140.00425.7460.0370.0370.0000.0000.0000.000
129A258GLU-1-0.837-0.90125.9100.4160.4160.0000.0000.0000.000
130A259ALA00.0370.01522.7230.0320.0320.0000.0000.0000.000
131A260ASP-1-0.855-0.91721.4360.6950.6950.0000.0000.0000.000
132A261ARG10.8820.94421.286-0.365-0.3650.0000.0000.0000.000
133A262GLU-1-0.942-0.96320.8260.5690.5690.0000.0000.0000.000
134A263GLY0-0.006-0.00517.4530.0660.0660.0000.0000.0000.000
135A264VAL0-0.040-0.01816.3600.1430.1430.0000.0000.0000.000
136A265ILE0-0.017-0.00512.888-0.093-0.0930.0000.0000.0000.000
137A266ARG10.7960.86616.922-0.651-0.6510.0000.0000.0000.000
138A267TYR00.008-0.00713.877-0.072-0.0720.0000.0000.0000.000
139A268VAL0-0.0230.00220.051-0.023-0.0230.0000.0000.0000.000
140A269ILE0-0.013-0.01821.310-0.002-0.0020.0000.0000.0000.000
141A270GLY00.0190.01525.135-0.016-0.0160.0000.0000.0000.000
142A271VAL0-0.057-0.04728.462-0.004-0.0040.0000.0000.0000.000
143A272GLY00.0780.04230.781-0.012-0.0120.0000.0000.0000.000
144A273ASP-1-0.918-1.00634.3970.2200.2200.0000.0000.0000.000
145A274ALA00.0140.03035.139-0.006-0.0060.0000.0000.0000.000
146A275PHE0-0.011-0.01632.0310.0060.0060.0000.0000.0000.000
147A276ARG10.8900.97033.690-0.215-0.2150.0000.0000.0000.000
148A277SER0-0.010-0.00435.968-0.001-0.0010.0000.0000.0000.000
149A278GLU-1-0.919-0.97133.9050.3050.3050.0000.0000.0000.000
150A279LYS10.9970.99434.975-0.187-0.1870.0000.0000.0000.000
151A280SER00.0610.02635.0850.0020.0020.0000.0000.0000.000
152A281ARG10.9120.97030.192-0.306-0.3060.0000.0000.0000.000
153A282GLN00.0380.02431.0750.0430.0430.0000.0000.0000.000
154A283GLU-1-0.763-0.84431.5810.3380.3380.0000.0000.0000.000
155A284LEU0-0.004-0.00527.7360.0240.0240.0000.0000.0000.000
156A285ASN0-0.010-0.02827.0260.0690.0690.0000.0000.0000.000
157A286THR0-0.071-0.01927.2090.0170.0170.0000.0000.0000.000
158A287ILE0-0.0070.01024.8330.0170.0170.0000.0000.0000.000
159A288ALA0-0.030-0.00922.5710.0470.0470.0000.0000.0000.000
160A289SER00.0320.03019.490-0.008-0.0080.0000.0000.0000.000
161A290LYS10.9530.99221.538-0.484-0.4840.0000.0000.0000.000
162A291PRO00.009-0.00920.0120.0510.0510.0000.0000.0000.000
163A292PRO00.1100.04422.0900.0530.0530.0000.0000.0000.000
164A293ARG10.9530.97323.308-0.465-0.4650.0000.0000.0000.000
165A294ASP-1-0.898-0.94518.4760.7070.7070.0000.0000.0000.000
166A295HIS10.8380.90816.682-0.863-0.8630.0000.0000.0000.000
167A296VAL00.0160.02020.6590.0110.0110.0000.0000.0000.000
168A297PHE0-0.034-0.01218.8520.0010.0010.0000.0000.0000.000
169A298GLN0-0.002-0.00324.722-0.004-0.0040.0000.0000.0000.000
170A299VAL00.0120.01926.803-0.007-0.0070.0000.0000.0000.000
171A300ASN00.025-0.01729.580-0.005-0.0050.0000.0000.0000.000
172A301ASN00.0590.02931.944-0.005-0.0050.0000.0000.0000.000
173A302PHE00.1010.03129.4170.0200.0200.0000.0000.0000.000
174A303GLU-1-0.964-0.96929.4840.2190.2190.0000.0000.0000.000
175A304ALA00.0200.00529.7140.0030.0030.0000.0000.0000.000
176A305LEU00.0270.06425.0520.0190.0190.0000.0000.0000.000
177A306LYS10.9310.95524.068-0.245-0.2450.0000.0000.0000.000
178A307THR0-0.086-0.07123.7640.0190.0190.0000.0000.0000.000
179A308ILE00.0210.01322.3350.0020.0020.0000.0000.0000.000
180A309GLN0-0.018-0.00619.5510.0520.0520.0000.0000.0000.000
181A310ASN00.0510.03117.2780.1130.1130.0000.0000.0000.000
182A311GLN00.0110.00416.6770.0890.0890.0000.0000.0000.000
183A312LEU00.0110.00716.4860.0780.0780.0000.0000.0000.000
184A313ARG10.9180.95612.432-0.667-0.6670.0000.0000.0000.000
185A314GLU-1-0.892-0.95212.2631.2081.2080.0000.0000.0000.000
186A315LYS10.8610.94212.585-0.631-0.6310.0000.0000.0000.000
187A316ILE0-0.0030.00010.3110.1540.1540.0000.0000.0000.000
188A317PHE0-0.017-0.0318.3160.7820.7820.0000.0000.0000.000
189A318ALA00.0240.0318.1530.4680.4680.0000.0000.0000.000
190A319ILE0-0.063-0.0199.161-0.309-0.3090.0000.0000.0000.000
191A320GLY0-0.0080.0057.5560.7670.7670.0000.0000.0000.000
192A321SER0-0.016-0.0126.5920.1210.1210.0000.0000.0000.000
193A322PRO00.0200.0118.685-0.329-0.3290.0000.0000.0000.000
194A323GLY0-0.029-0.00912.367-0.147-0.1470.0000.0000.0000.000
195A324ILE0-0.046-0.0148.027-0.324-0.3240.0000.0000.0000.000