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: V5Q51

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793820.013764
FMO2-HF: Nuclear repulsion 1726893.95934
FMO2-HF: Total energy -66926.054424
FMO2-MP2: Total energy -67126.434552


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.
-8.659-27.30829.8621.475-12.686-0.025
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 : -0.023 / q_NPA : 0.020
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].
3A2ILE0-0.004-0.0082.59910.650-0.553-0.01911.704-0.482-0.002
4A3THR00.0320.0285.5960.3800.3800.0000.0000.0000.000
5A4GLY0-0.003-0.0109.0870.1460.1460.0000.0000.0000.000
6A5ASP-1-0.945-0.99011.099-0.307-0.3070.0000.0000.0000.000
7A6ALA0-0.031-0.0019.3590.0370.0370.0000.0000.0000.000
8A7LEU00.016-0.00511.3610.1080.1080.0000.0000.0000.000
9A8VAL0-0.004-0.0069.7260.0030.0030.0000.0000.0000.000
10A9ALA0-0.010-0.01112.336-0.042-0.0420.0000.0000.0000.000
11A10LEU0-0.023-0.00214.9720.1130.1130.0000.0000.0000.000
12A11PRO0-0.003-0.02117.400-0.035-0.0350.0000.0000.0000.000
13A12GLU-1-0.932-0.97120.7220.2080.2080.0000.0000.0000.000
14A13GLY0-0.055-0.01022.215-0.019-0.0190.0000.0000.0000.000
15A14GLU-1-0.901-0.93220.5430.1470.1470.0000.0000.0000.000
16A15SER0-0.055-0.04516.3650.0150.0150.0000.0000.0000.000
17A16VAL00.0230.01914.060-0.030-0.0300.0000.0000.0000.000
18A17ARG10.8560.91213.6180.0190.0190.0000.0000.0000.000
19A18ILE00.0320.0196.5960.0530.0530.0000.0000.0000.000
20A19ALA0-0.058-0.02710.9200.0620.0620.0000.0000.0000.000
21A20ASP-1-0.844-0.90412.8040.0950.0950.0000.0000.0000.000
22A21ILE0-0.0090.00711.0380.0160.0160.0000.0000.0000.000
23A22VAL0-0.0020.00713.6900.0090.0090.0000.0000.0000.000
24A23PRO0-0.007-0.00915.562-0.038-0.0380.0000.0000.0000.000
25A24GLY0-0.023-0.01417.5010.0020.0020.0000.0000.0000.000
26A25ALA00.0080.01913.215-0.012-0.0120.0000.0000.0000.000
27A26ARG10.9240.96515.264-0.196-0.1960.0000.0000.0000.000
28A27PRO00.0540.01812.5040.0590.0590.0000.0000.0000.000
29A28ASN0-0.039-0.02010.274-0.065-0.0650.0000.0000.0000.000
30A29SER0-0.080-0.05610.9470.0450.0450.0000.0000.0000.000
31A30ASP-1-0.847-0.93710.2290.9560.9560.0000.0000.0000.000
32A31ASN0-0.079-0.05310.951-0.189-0.1890.0000.0000.0000.000
33A32ALA00.0270.00812.1530.1200.1200.0000.0000.0000.000
34A33ILE0-0.051-0.01611.688-0.085-0.0850.0000.0000.0000.000
35A34ASP-1-0.913-0.96215.1270.5500.5500.0000.0000.0000.000
36A35LEU00.0000.00113.522-0.071-0.0710.0000.0000.0000.000
37A36LYS10.8690.95315.725-0.442-0.4420.0000.0000.0000.000
38A37VAL00.0130.00011.772-0.039-0.0390.0000.0000.0000.000
39A38LEU00.0110.01115.013-0.009-0.0090.0000.0000.0000.000
40A39ASP-1-0.787-0.91312.9950.6220.6220.0000.0000.0000.000
41A40ARG10.8670.92212.532-0.531-0.5310.0000.0000.0000.000
42A41HIS10.8260.90913.858-0.385-0.3850.0000.0000.0000.000
43A42GLY00.0260.02416.480-0.055-0.0550.0000.0000.0000.000
44A43ASN0-0.0180.00117.773-0.060-0.0600.0000.0000.0000.000
45A44PRO0-0.010-0.00317.3430.0620.0620.0000.0000.0000.000
46A45VAL00.0050.01013.614-0.019-0.0190.0000.0000.0000.000
47A46LEU00.0270.00215.356-0.040-0.0400.0000.0000.0000.000
48A47ALA00.0170.01010.9970.1480.1480.0000.0000.0000.000
49A48ASP-1-0.761-0.88611.6941.0701.0700.0000.0000.0000.000
50A49ARG10.8460.9199.177-1.025-1.0250.0000.0000.0000.000
51A50LEU00.0270.0358.4610.2810.2810.0000.0000.0000.000
52A51PHE0-0.038-0.0324.755-0.301-0.249-0.001-0.005-0.0460.000
53A52HIS00.0470.0826.8690.0040.0040.0000.0000.0000.000
54A53SER0-0.006-0.0304.850-0.098-0.037-0.001-0.002-0.0580.000
55A54GLY00.0460.0307.212-0.170-0.1700.0000.0000.0000.000
56A55GLU-1-0.957-0.9979.523-0.459-0.4590.0000.0000.0000.000
57A56HIS0-0.048-0.0257.484-0.131-0.1310.0000.0000.0000.000
58A57PRO00.0090.00410.3930.0610.0610.0000.0000.0000.000
59A58VAL0-0.0170.0029.052-0.396-0.3960.0000.0000.0000.000
60A59TYR00.0470.01910.5670.2200.2200.0000.0000.0000.000
61A60ALA0-0.043-0.02611.304-0.118-0.1180.0000.0000.0000.000
62A61VAL00.0230.01610.8490.0860.0860.0000.0000.0000.000
63A62ARG10.8900.94213.6020.5070.5070.0000.0000.0000.000
64A63THR00.0010.01216.841-0.023-0.0230.0000.0000.0000.000
65A64VAL0-0.037-0.01718.4820.0160.0160.0000.0000.0000.000
66A65GLU-1-0.759-0.87820.756-0.163-0.1630.0000.0000.0000.000
67A66GLY0-0.013-0.01021.1470.0200.0200.0000.0000.0000.000
68A67LEU0-0.025-0.00716.289-0.014-0.0140.0000.0000.0000.000
69A68ARG10.9790.97214.4360.3230.3230.0000.0000.0000.000
70A69VAL00.0070.0228.9100.0860.0860.0000.0000.0000.000
71A70THR0-0.003-0.00510.679-0.025-0.0250.0000.0000.0000.000
72A71GLY00.0680.0366.7240.1010.1010.0000.0000.0000.000
73A72THR00.0450.0195.1840.0830.128-0.001-0.016-0.0280.000
74A73ALA00.0660.0307.028-0.407-0.4070.0000.0000.0000.000
75A74ASN00.0350.0175.153-0.283-0.2830.0000.0000.0000.000
76A75HIS00.0120.0251.973-8.221-13.33312.398-3.652-3.633-0.026
77A76PRO00.000-0.0092.7031.4322.1570.447-0.319-0.8540.000
78A77LEU00.0100.0155.0590.3750.425-0.001-0.002-0.0470.000
79A78LEU0-0.0170.0007.7610.0420.0420.0000.0000.0000.000
80A79CYS0-0.043-0.01210.801-0.052-0.0520.0000.0000.0000.000
81A80LEU0-0.023-0.00913.8410.0650.0650.0000.0000.0000.000
82A81VAL0-0.031-0.02915.873-0.039-0.0390.0000.0000.0000.000
83A82ASP-1-0.926-0.95318.705-0.069-0.0690.0000.0000.0000.000
84A83VAL00.0170.00019.989-0.022-0.0220.0000.0000.0000.000
85A84ALA0-0.027-0.01722.8560.0180.0180.0000.0000.0000.000
86A85GLY00.0080.00426.2170.0140.0140.0000.0000.0000.000
87A86VAL0-0.015-0.00423.7180.0100.0100.0000.0000.0000.000
88A87PRO0-0.027-0.00422.398-0.015-0.0150.0000.0000.0000.000
89A88THR00.014-0.00318.0720.0340.0340.0000.0000.0000.000
90A89LEU0-0.029-0.00315.455-0.044-0.0440.0000.0000.0000.000
91A90LEU0-0.015-0.01913.8480.0520.0520.0000.0000.0000.000
92A91TRP00.0060.0117.673-0.053-0.0530.0000.0000.0000.000
93A92LYS10.7790.8779.7230.5780.5780.0000.0000.0000.000
94A93LEU00.0030.0046.043-0.107-0.1070.0000.0000.0000.000
95A94ILE0-0.032-0.0207.0220.5060.5060.0000.0000.0000.000
96A95ASP-1-0.919-0.9709.256-0.962-0.9620.0000.0000.0000.000
97A96GLU-1-0.951-0.97111.392-0.527-0.5270.0000.0000.0000.000
98A97ILE0-0.076-0.02710.1770.1860.1860.0000.0000.0000.000
99A98LYS10.8880.94713.9750.4740.4740.0000.0000.0000.000
100A99PRO00.003-0.00817.5520.0180.0180.0000.0000.0000.000
101A100GLY0-0.088-0.05619.8550.0210.0210.0000.0000.0000.000
102A101ASP-1-0.719-0.83715.879-0.439-0.4390.0000.0000.0000.000
103A102TYR0-0.011-0.01417.5840.0120.0120.0000.0000.0000.000
104A103ALA00.0720.04113.079-0.007-0.0070.0000.0000.0000.000
105A104VAL0-0.029-0.02613.5350.0430.0430.0000.0000.0000.000
106A105ILE0-0.044-0.01713.569-0.016-0.0160.0000.0000.0000.000
107A106GLN00.0640.02714.975-0.003-0.0030.0000.0000.0000.000
108A107ARG10.8860.90116.620-0.039-0.0390.0000.0000.0000.000
109A108SER0-0.019-0.00919.053-0.013-0.0130.0000.0000.0000.000
110A109ALA0-0.074-0.01816.1020.0190.0190.0000.0000.0000.000
111A110PHE0-0.041-0.01117.311-0.025-0.0250.0000.0000.0000.000
112A111SER00.0110.01421.1590.0110.0110.0000.0000.0000.000
113A130THR00.022-0.02924.172-0.002-0.0020.0000.0000.0000.000
114A131VAL0-0.047-0.03225.5610.0140.0140.0000.0000.0000.000
115A132GLY00.0060.00827.212-0.006-0.0060.0000.0000.0000.000
116A133VAL00.0270.03622.885-0.013-0.0130.0000.0000.0000.000
117A134PRO0-0.004-0.01522.3920.0020.0020.0000.0000.0000.000
118A135GLY0-0.001-0.00724.392-0.001-0.0010.0000.0000.0000.000
119A136LEU00.0420.03526.0420.0040.0040.0000.0000.0000.000
120A137VAL00.0470.01427.8400.0060.0060.0000.0000.0000.000
121A138ARG11.0010.99528.0900.0860.0860.0000.0000.0000.000
122A139PHE00.0330.03528.2160.0030.0030.0000.0000.0000.000
123A140LEU0-0.016-0.00830.3010.0070.0070.0000.0000.0000.000
124A141GLU-1-0.935-0.98932.451-0.026-0.0260.0000.0000.0000.000
125A142ALA0-0.044-0.01833.0070.0020.0020.0000.0000.0000.000
126A143HIS00.0250.01930.5300.0090.0090.0000.0000.0000.000
127A144HIS10.9160.98632.718-0.001-0.0010.0000.0000.0000.000
128A145ARG10.7540.83333.833-0.029-0.0290.0000.0000.0000.000
129A146ASP-1-0.791-0.87130.2150.0180.0180.0000.0000.0000.000
130A147PRO0-0.086-0.04832.6150.0030.0030.0000.0000.0000.000
131A148ASP-1-0.811-0.90627.0660.0970.0970.0000.0000.0000.000
132A149ALA0-0.030-0.01428.2010.0030.0030.0000.0000.0000.000
133A150LYS10.8950.94129.248-0.073-0.0730.0000.0000.0000.000
134A151ALA00.0250.01026.6250.0020.0020.0000.0000.0000.000
135A152ILE00.0370.02224.2650.0100.0100.0000.0000.0000.000
136A153ALA0-0.037-0.03124.6120.0000.0000.0000.0000.0000.000
137A154ASP-1-0.958-0.97226.2240.1070.1070.0000.0000.0000.000
138A155GLU-1-0.789-0.90918.3630.2080.2080.0000.0000.0000.000
139A156LEU0-0.067-0.04320.616-0.002-0.0020.0000.0000.0000.000
140A157THR0-0.016-0.01022.518-0.020-0.0200.0000.0000.0000.000
141A158ASP-1-0.836-0.88221.4010.1590.1590.0000.0000.0000.000
142A159GLY00.0240.00423.213-0.014-0.0140.0000.0000.0000.000
143A160ARG10.8310.90020.520-0.232-0.2320.0000.0000.0000.000
144A161PHE0-0.0410.00716.0440.0070.0070.0000.0000.0000.000
145A162TYR0-0.114-0.06218.811-0.001-0.0010.0000.0000.0000.000
146A163TYR00.002-0.01918.375-0.010-0.0100.0000.0000.0000.000
147A164ALA0-0.0020.01717.2580.0050.0050.0000.0000.0000.000
148A165LYS10.8560.94918.0770.1780.1780.0000.0000.0000.000
149A166VAL00.0190.01815.2610.0050.0050.0000.0000.0000.000
150A167ALA0-0.008-0.00218.1790.0280.0280.0000.0000.0000.000
151A168SER0-0.032-0.03418.4870.0070.0070.0000.0000.0000.000
152A169VAL00.0860.05413.295-0.005-0.0050.0000.0000.0000.000
153A170THR0-0.076-0.04515.8730.0670.0670.0000.0000.0000.000
154A171ASP-1-0.873-0.93915.659-0.800-0.8000.0000.0000.0000.000
155A172ALA0-0.041-0.02613.8960.0830.0830.0000.0000.0000.000
156A173GLY00.0300.03015.8010.0490.0490.0000.0000.0000.000
157A174VAL0-0.025-0.01613.264-0.126-0.1260.0000.0000.0000.000
158A175GLN0-0.019-0.01311.9010.1410.1410.0000.0000.0000.000
159A176PRO0-0.0130.01110.998-0.130-0.1300.0000.0000.0000.000
160A177VAL0-0.046-0.0175.524-0.111-0.1110.0000.0000.0000.000
161A178TYR00.030-0.0086.1890.1280.1280.0000.0000.0000.000
162A179SER00.018-0.0182.377-3.881-1.7232.007-1.943-2.223-0.001
163A180LEU00.0040.0224.205-1.057-1.0090.000-0.044-0.0030.000
164A181ARG10.8220.9235.335-0.052-0.0520.0000.0000.0000.000
165A182VAL0-0.0170.0007.611-0.539-0.5390.0000.0000.0000.000
166A183ASP-1-0.878-0.94510.4031.1121.1120.0000.0000.0000.000
167A184THR0-0.126-0.04312.427-0.232-0.2320.0000.0000.0000.000
168A185ALA0-0.015-0.01712.6230.1390.1390.0000.0000.0000.000
169A186ASP-1-0.790-0.91212.1120.7790.7790.0000.0000.0000.000
170A187HIS0-0.007-0.0107.7180.3770.3770.0000.0000.0000.000
171A188ALA00.0430.0237.4210.7110.7110.0000.0000.0000.000
172A189PHE00.006-0.0034.629-0.501-0.432-0.001-0.006-0.0620.000
173A190ILE0-0.0170.0098.945-0.182-0.1820.0000.0000.0000.000
174A191THR00.0210.0237.0910.0000.0000.0000.0000.0000.000
175A192ASN00.0230.01110.295-0.096-0.0960.0000.0000.0000.000
176A193GLY00.0260.01413.401-0.056-0.0560.0000.0000.0000.000
177A194PHE0-0.025-0.01310.0330.0140.0140.0000.0000.0000.000
178A195VAL00.0270.0209.6730.1100.1100.0000.0000.0000.000
179A196SER0-0.002-0.0274.684-0.670-0.657-0.001-0.001-0.0110.000
180A197HIS00.0240.0124.203-1.325-1.0440.000-0.116-0.1640.001
181A198ASN00.000-0.0061.946-7.604-13.44015.035-4.123-5.0750.003