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: G6561

Calculation Name: 1AM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AM2

Chain ID: A

ChEMBL ID:

UniProt ID: P72065

Base Structure: X-ray

Registration Date: 2023-06-22

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793317.603838
FMO2-HF: Nuclear repulsion 1726389.243164
FMO2-HF: Total energy -66928.360674
FMO2-MP2: Total energy -67128.638096


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-23.141-46.73342.746-8.218-10.936-0.005
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.072
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].
3A2ILE00.0050.0062.6128.0210.1270.3178.087-0.5100.000
4A3THR00.013-0.0046.0050.3090.3090.0000.0000.0000.000
5A4GLY00.000-0.0089.4650.1490.1490.0000.0000.0000.000
6A5ASP-1-0.966-0.99911.313-0.336-0.3360.0000.0000.0000.000
7A6ALA0-0.0120.0019.7700.0680.0680.0000.0000.0000.000
8A7LEU00.0150.00811.9000.1150.1150.0000.0000.0000.000
9A8VAL0-0.0010.00210.0280.0050.0050.0000.0000.0000.000
10A9ALA00.0020.00112.710-0.046-0.0460.0000.0000.0000.000
11A10LEU0-0.019-0.01715.1640.1130.1130.0000.0000.0000.000
12A11PRO00.015-0.00717.900-0.030-0.0300.0000.0000.0000.000
13A12GLU-1-0.937-0.97921.1140.2250.2250.0000.0000.0000.000
14A13GLY0-0.040-0.00321.881-0.024-0.0240.0000.0000.0000.000
15A14GLU-1-0.895-0.92720.8100.1350.1350.0000.0000.0000.000
16A15SER0-0.088-0.05817.1310.0140.0140.0000.0000.0000.000
17A16VAL00.0260.01514.387-0.022-0.0220.0000.0000.0000.000
18A17ARG10.8280.88813.8380.0390.0390.0000.0000.0000.000
19A18ILE00.0150.0146.5860.0700.0700.0000.0000.0000.000
20A19ALA0-0.020-0.00610.9030.0750.0750.0000.0000.0000.000
21A20ASP-1-0.858-0.89712.6740.0700.0700.0000.0000.0000.000
22A21ILE0-0.0040.00611.0490.0190.0190.0000.0000.0000.000
23A22VAL0-0.012-0.01013.8920.0190.0190.0000.0000.0000.000
24A23PRO00.0090.00915.363-0.039-0.0390.0000.0000.0000.000
25A24GLY0-0.025-0.00216.945-0.004-0.0040.0000.0000.0000.000
26A25ALA00.0010.00813.170-0.011-0.0110.0000.0000.0000.000
27A26ARG10.9440.96814.746-0.182-0.1820.0000.0000.0000.000
28A27PRO00.0400.02412.1800.0470.0470.0000.0000.0000.000
29A28ASN0-0.046-0.0169.923-0.040-0.0400.0000.0000.0000.000
30A29SER0-0.037-0.02510.3660.0560.0560.0000.0000.0000.000
31A30ASP-1-0.816-0.9029.7651.0801.0800.0000.0000.0000.000
32A31ASN0-0.076-0.04311.179-0.208-0.2080.0000.0000.0000.000
33A32ALA00.0200.00912.8070.1060.1060.0000.0000.0000.000
34A33ILE0-0.052-0.02012.392-0.094-0.0940.0000.0000.0000.000
35A34ASP-1-0.806-0.89015.9770.5150.5150.0000.0000.0000.000
36A35LEU00.0020.00813.892-0.056-0.0560.0000.0000.0000.000
37A36LYS10.7880.87516.542-0.423-0.4230.0000.0000.0000.000
38A37VAL00.0180.00911.968-0.045-0.0450.0000.0000.0000.000
39A38LEU0-0.0050.01114.924-0.017-0.0170.0000.0000.0000.000
40A39ASP-1-0.732-0.87113.3060.5640.5640.0000.0000.0000.000
41A40ARG10.8030.85713.407-0.454-0.4540.0000.0000.0000.000
42A41HIS10.7770.84914.227-0.330-0.3300.0000.0000.0000.000
43A42GLY00.0260.02416.808-0.052-0.0520.0000.0000.0000.000
44A43ASN0-0.074-0.03318.134-0.073-0.0730.0000.0000.0000.000
45A44PRO00.0180.01317.7260.0580.0580.0000.0000.0000.000
46A45VAL0-0.024-0.01114.241-0.014-0.0140.0000.0000.0000.000
47A46LEU00.0030.00715.7730.0000.0000.0000.0000.0000.000
48A47ALA00.0230.00311.4200.1510.1510.0000.0000.0000.000
49A48ASP-1-0.769-0.88111.6581.0111.0110.0000.0000.0000.000
50A49ARG10.7930.8859.518-1.083-1.0830.0000.0000.0000.000
51A50LEU00.0090.0148.6390.2630.2630.0000.0000.0000.000
52A51PHE0-0.035-0.0184.734-0.400-0.313-0.001-0.009-0.0760.000
53A52HIS00.0370.0297.191-0.079-0.0790.0000.0000.0000.000
54A53SER00.003-0.0094.171-0.219-0.0790.000-0.033-0.1070.000
55A54GLY00.0300.0356.485-0.144-0.1440.0000.0000.0000.000
56A55GLU-1-0.970-1.0069.744-0.438-0.4380.0000.0000.0000.000
57A56HIS0-0.025-0.0217.828-0.161-0.1610.0000.0000.0000.000
58A57PRO0-0.012-0.00710.5000.0420.0420.0000.0000.0000.000
59A58VAL0-0.0330.0108.728-0.371-0.3710.0000.0000.0000.000
60A59TYR0-0.019-0.02410.5800.2540.2540.0000.0000.0000.000
61A60ALA0-0.015-0.00311.125-0.119-0.1190.0000.0000.0000.000
62A61VAL00.0280.01410.7450.1120.1120.0000.0000.0000.000
63A62ARG10.8790.92813.5740.5350.5350.0000.0000.0000.000
64A63THR0-0.007-0.00716.899-0.013-0.0130.0000.0000.0000.000
65A64VAL0-0.028-0.01518.9320.0120.0120.0000.0000.0000.000
66A65GLU-1-0.756-0.85221.159-0.159-0.1590.0000.0000.0000.000
67A66GLY0-0.024-0.00721.5540.0180.0180.0000.0000.0000.000
68A67LEU0-0.015-0.00616.966-0.019-0.0190.0000.0000.0000.000
69A68ARG10.9610.96414.5560.3280.3280.0000.0000.0000.000
70A69VAL00.0240.0308.7530.0790.0790.0000.0000.0000.000
71A70THR00.000-0.00610.487-0.034-0.0340.0000.0000.0000.000
72A71GLY00.0580.0276.7130.0600.0600.0000.0000.0000.000
73A72THR00.021-0.0025.164-0.060-0.008-0.001-0.023-0.0280.000
74A73ALA00.0210.0206.886-0.478-0.4780.0000.0000.0000.000
75A74ASN00.0380.0263.3940.5850.9490.004-0.153-0.2150.000
76A75HIS00.0020.0162.018-9.956-12.6539.557-3.414-3.446-0.035
77A76PRO0-0.017-0.0172.7211.2491.9690.381-0.300-0.8010.000
78A77LEU00.0130.0035.1420.4460.500-0.001-0.002-0.0500.000
79A78LEU0-0.0070.0067.8950.0380.0380.0000.0000.0000.000
80A79CYS0-0.047-0.02311.072-0.066-0.0660.0000.0000.0000.000
81A80LEU0-0.020-0.00314.1680.0580.0580.0000.0000.0000.000
82A81VAL0-0.024-0.01616.541-0.043-0.0430.0000.0000.0000.000
83A82ASP-1-0.834-0.90419.365-0.058-0.0580.0000.0000.0000.000
84A83VAL00.0090.00220.330-0.018-0.0180.0000.0000.0000.000
85A84ALA0-0.026-0.01823.1370.0170.0170.0000.0000.0000.000
86A85GLY00.0210.01326.6200.0100.0100.0000.0000.0000.000
87A86VAL0-0.008-0.00124.3510.0080.0080.0000.0000.0000.000
88A87PRO0-0.027-0.00922.813-0.010-0.0100.0000.0000.0000.000
89A88THR00.000-0.00418.6690.0300.0300.0000.0000.0000.000
90A89LEU0-0.031-0.01015.889-0.040-0.0400.0000.0000.0000.000
91A90LEU0-0.006-0.01014.2110.0520.0520.0000.0000.0000.000
92A91TRP00.0040.0067.784-0.041-0.0410.0000.0000.0000.000
93A92LYS10.8030.8979.8650.5450.5450.0000.0000.0000.000
94A93LEU00.0260.0246.489-0.118-0.1180.0000.0000.0000.000
95A94ILE00.0060.0047.2430.4900.4900.0000.0000.0000.000
96A95ASP-1-0.906-0.9659.627-1.214-1.2140.0000.0000.0000.000
97A96GLU-1-0.945-0.96911.842-0.411-0.4110.0000.0000.0000.000
98A97ILE0-0.101-0.03110.3370.1790.1790.0000.0000.0000.000
99A98LYS10.8780.92514.1760.4210.4210.0000.0000.0000.000
100A99PRO0-0.004-0.01717.8080.0210.0210.0000.0000.0000.000
101A100GLY0-0.038-0.01320.5810.0160.0160.0000.0000.0000.000
102A101ASP-1-0.771-0.86216.700-0.402-0.4020.0000.0000.0000.000
103A102TYR00.009-0.01417.8090.0160.0160.0000.0000.0000.000
104A103ALA00.0600.03813.642-0.003-0.0030.0000.0000.0000.000
105A104VAL0-0.028-0.01313.7750.0440.0440.0000.0000.0000.000
106A105ILE0-0.040-0.01813.758-0.006-0.0060.0000.0000.0000.000
107A106GLN00.0450.03115.148-0.009-0.0090.0000.0000.0000.000
108A107ARG10.8720.91416.868-0.029-0.0290.0000.0000.0000.000
109A108SER0-0.005-0.01919.086-0.013-0.0130.0000.0000.0000.000
110A109ALA0-0.050-0.01016.2530.0200.0200.0000.0000.0000.000
111A110PHE0-0.047-0.01617.610-0.023-0.0230.0000.0000.0000.000
112A111SER00.0070.01521.5940.0010.0010.0000.0000.0000.000
113A130THR00.013-0.00924.823-0.002-0.0020.0000.0000.0000.000
114A131VAL0-0.037-0.02425.9530.0150.0150.0000.0000.0000.000
115A132GLY00.0080.01227.2050.0000.0000.0000.0000.0000.000
116A133VAL00.0220.01623.253-0.012-0.0120.0000.0000.0000.000
117A134PRO0-0.006-0.00822.1920.0010.0010.0000.0000.0000.000
118A135GLY0-0.0030.00024.9580.0010.0010.0000.0000.0000.000
119A136LEU00.0460.02326.6340.0030.0030.0000.0000.0000.000
120A137VAL00.0060.00328.1970.0060.0060.0000.0000.0000.000
121A138ARG10.8880.93727.2450.0790.0790.0000.0000.0000.000
122A139PHE00.0120.01928.5490.0030.0030.0000.0000.0000.000
123A140LEU0-0.007-0.00930.6930.0070.0070.0000.0000.0000.000
124A141GLU-1-0.902-0.97432.951-0.025-0.0250.0000.0000.0000.000
125A142ALA0-0.034-0.01333.9180.0020.0020.0000.0000.0000.000
126A143HIS0-0.0060.00530.8540.0090.0090.0000.0000.0000.000
127A144HIS10.8990.96333.9450.0000.0000.0000.0000.0000.000
128A145ARG10.7660.85834.601-0.034-0.0340.0000.0000.0000.000
129A146ASP-1-0.744-0.86030.8250.0360.0360.0000.0000.0000.000
130A147PRO0-0.072-0.03532.5510.0030.0030.0000.0000.0000.000
131A148ASP-1-0.846-0.92826.6890.0990.0990.0000.0000.0000.000
132A149ALA0-0.010-0.00128.6810.0050.0050.0000.0000.0000.000
133A150LYS10.7770.86429.443-0.082-0.0820.0000.0000.0000.000
134A151ALA00.0210.01226.8220.0030.0030.0000.0000.0000.000
135A152ILE00.0240.00924.1980.0080.0080.0000.0000.0000.000
136A153ALA0-0.009-0.00724.785-0.003-0.0030.0000.0000.0000.000
137A154ASP-1-0.800-0.86426.4390.0870.0870.0000.0000.0000.000
138A155GLU-1-0.800-0.87918.6040.2240.2240.0000.0000.0000.000
139A156LEU0-0.029-0.02221.0240.0000.0000.0000.0000.0000.000
140A157THR0-0.049-0.04022.935-0.021-0.0210.0000.0000.0000.000
141A158ASP-1-0.796-0.86721.4880.1580.1580.0000.0000.0000.000
142A159GLY00.0120.01123.431-0.011-0.0110.0000.0000.0000.000
143A160ARG10.8460.90921.064-0.231-0.2310.0000.0000.0000.000
144A161PHE0-0.020-0.00316.1060.0030.0030.0000.0000.0000.000
145A162TYR0-0.101-0.07619.227-0.004-0.0040.0000.0000.0000.000
146A163TYR0-0.002-0.02118.648-0.007-0.0070.0000.0000.0000.000
147A164ALA00.0040.01517.4640.0000.0000.0000.0000.0000.000
148A165LYS10.8490.93118.3000.1620.1620.0000.0000.0000.000
149A166VAL00.0350.02115.6040.0040.0040.0000.0000.0000.000
150A167ALA0-0.003-0.00218.4470.0230.0230.0000.0000.0000.000
151A168SER0-0.047-0.04718.7160.0090.0090.0000.0000.0000.000
152A169VAL00.0440.03313.392-0.012-0.0120.0000.0000.0000.000
153A170THR0-0.046-0.01215.8200.0750.0750.0000.0000.0000.000
154A171ASP-1-0.795-0.89015.294-0.834-0.8340.0000.0000.0000.000
155A172ALA0-0.028-0.01514.2950.0900.0900.0000.0000.0000.000
156A173GLY00.0180.02416.2280.0520.0520.0000.0000.0000.000
157A174VAL0-0.023-0.01713.416-0.119-0.1190.0000.0000.0000.000
158A175GLN00.001-0.00811.8700.0890.0890.0000.0000.0000.000
159A176PRO00.0130.01311.203-0.142-0.1420.0000.0000.0000.000
160A177VAL0-0.049-0.0175.848-0.063-0.0630.0000.0000.0000.000
161A178TYR00.0340.0016.0410.0910.0910.0000.0000.0000.000
162A179SER00.006-0.0192.241-4.854-3.0431.305-1.802-1.3140.002
163A180LEU00.0120.0134.357-1.053-1.005-0.001-0.042-0.0060.000
164A181ARG10.7800.8705.6190.0210.0210.0000.0000.0000.000
165A182VAL0-0.015-0.0068.092-0.544-0.5440.0000.0000.0000.000
166A183ASP-1-0.824-0.89510.8671.2271.2270.0000.0000.0000.000
167A184THR0-0.036-0.04612.775-0.243-0.2430.0000.0000.0000.000
168A185ALA0-0.022-0.00512.6740.1640.1640.0000.0000.0000.000
169A186ASP-1-0.792-0.87012.7270.6320.6320.0000.0000.0000.000
170A187HIS0-0.0100.0027.7890.3950.3950.0000.0000.0000.000
171A188ALA00.0240.0227.8150.6810.6810.0000.0000.0000.000
172A189PHE0-0.014-0.0135.095-0.455-0.4550.0000.0000.0000.000
173A190ILE0-0.043-0.0039.120-0.136-0.1360.0000.0000.0000.000
174A191THR00.0100.0177.490-0.007-0.0070.0000.0000.0000.000
175A192ASN0-0.019-0.02810.754-0.082-0.0820.0000.0000.0000.000
176A193GLY00.0560.02313.847-0.045-0.0450.0000.0000.0000.000
177A194PHE0-0.028-0.01710.6350.0170.0170.0000.0000.0000.000
178A195VAL00.0080.01110.0560.1060.1060.0000.0000.0000.000
179A196SER00.0300.0105.118-0.643-0.6430.0000.0000.0000.000
180A197HIS00.008-0.0044.091-1.306-1.126-0.001-0.062-0.1180.000
181A198ASN0-0.033-0.0611.637-17.007-33.46431.187-10.465-4.2650.028