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: ZN6QN

Calculation Name: 1A04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A04

Chain ID: A

ChEMBL ID:

UniProt ID: P0AF28

Base Structure: X-ray

Registration Date: 2023-09-27

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2367540.966586
FMO2-HF: Nuclear repulsion 2287321.346839
FMO2-HF: Total energy -80219.619746
FMO2-MP2: Total energy -80451.469047


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
46.71550.621.015-1.945-2.9750.004
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.988 / q_NPA : -1.003
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].
3A7ALA00.0150.0073.8273.2204.789-0.017-0.713-0.8390.002
4A8THR00.0080.0025.532-4.832-4.8320.0000.0000.0000.000
5A9ILE0-0.003-0.0057.861-1.586-1.5860.0000.0000.0000.000
6A10LEU0-0.0220.02211.5810.0000.0000.0000.0000.0000.000
7A11LEU0-0.024-0.01214.495-0.596-0.5960.0000.0000.0000.000
8A12ILE00.0160.01017.732-0.239-0.2390.0000.0000.0000.000
9A13ASP-1-0.822-0.94121.01813.10813.1080.0000.0000.0000.000
10A14ASP-1-0.884-0.93923.97010.65110.6510.0000.0000.0000.000
11A15HIS00.0160.02325.981-0.416-0.4160.0000.0000.0000.000
12A16PRO00.0540.01325.8350.3250.3250.0000.0000.0000.000
13A17MET00.0120.00625.3500.3730.3730.0000.0000.0000.000
14A18LEU00.0080.01923.3260.1050.1050.0000.0000.0000.000
15A19ARG10.8630.92920.317-13.286-13.2860.0000.0000.0000.000
16A20THR0-0.050-0.03220.4800.6090.6090.0000.0000.0000.000
17A21GLY00.0290.01621.0300.3240.3240.0000.0000.0000.000
18A22VAL00.0270.01917.6480.4250.4250.0000.0000.0000.000
19A23LYS10.8510.89616.381-14.815-14.8150.0000.0000.0000.000
20A24GLN0-0.0150.00016.3070.6540.6540.0000.0000.0000.000
21A25LEU0-0.0040.01017.3830.3480.3480.0000.0000.0000.000
22A26ILE00.0010.00211.6870.5660.5660.0000.0000.0000.000
23A27SER0-0.092-0.04712.2180.9600.9600.0000.0000.0000.000
24A28MET0-0.056-0.02813.778-0.438-0.4380.0000.0000.0000.000
25A29ALA0-0.0050.01111.770-0.448-0.4480.0000.0000.0000.000
26A30PRO0-0.028-0.0269.0151.2321.2320.0000.0000.0000.000
27A31ASP-1-0.864-0.9266.09628.95428.9540.0000.0000.0000.000
28A32ILE0-0.0210.0036.7442.2032.2030.0000.0000.0000.000
29A33THR00.007-0.0076.316-1.635-1.6350.0000.0000.0000.000
30A34VAL00.0030.0078.9340.7220.7220.0000.0000.0000.000
31A35VAL0-0.035-0.0287.8740.5880.5880.0000.0000.0000.000
32A36GLY0-0.002-0.00110.992-0.530-0.5300.0000.0000.0000.000
33A37GLU-1-0.844-0.92014.68915.68015.6800.0000.0000.0000.000
34A38ALA0-0.031-0.00718.208-0.282-0.2820.0000.0000.0000.000
35A39SER0-0.004-0.01921.3910.1180.1180.0000.0000.0000.000
36A40ASN00.0470.03724.701-0.323-0.3230.0000.0000.0000.000
37A41GLY00.0840.02724.6550.5310.5310.0000.0000.0000.000
38A42GLU-1-0.909-0.95424.44611.30111.3010.0000.0000.0000.000
39A43GLN00.0040.00022.0440.0470.0470.0000.0000.0000.000
40A44GLY00.005-0.02720.4180.6220.6220.0000.0000.0000.000
41A45ILE00.0090.00319.5750.9620.9620.0000.0000.0000.000
42A46GLU-1-0.880-0.95220.29213.70313.7030.0000.0000.0000.000
43A47LEU0-0.036-0.01516.0860.7500.7500.0000.0000.0000.000
44A48ALA00.010-0.00815.6751.4801.4800.0000.0000.0000.000
45A49GLU-1-0.914-0.96515.03216.56916.5690.0000.0000.0000.000
46A50SER0-0.061-0.02815.5130.4180.4180.0000.0000.0000.000
47A51LEU0-0.060-0.03211.5041.2091.2090.0000.0000.0000.000
48A52ASP-1-0.794-0.87210.34427.49027.4900.0000.0000.0000.000
49A53PRO0-0.005-0.0029.4112.9462.9460.0000.0000.0000.000
50A54ASP-1-0.827-0.9266.95039.87439.8740.0000.0000.0000.000
51A55LEU0-0.023-0.00910.108-2.060-2.0600.0000.0000.0000.000
52A56ILE00.0040.01413.3420.2960.2960.0000.0000.0000.000
53A57LEU0-0.006-0.00916.218-0.679-0.6790.0000.0000.0000.000
54A58LEU00.004-0.00418.717-0.129-0.1290.0000.0000.0000.000
55A59ASP-1-0.736-0.85222.16510.98010.9800.0000.0000.0000.000
56A60LEU0-0.025-0.02325.222-0.189-0.1890.0000.0000.0000.000
57A61ASN0-0.068-0.05228.243-0.304-0.3040.0000.0000.0000.000
58A62MET00.0020.03925.576-0.120-0.1200.0000.0000.0000.000
59A63PRO0-0.011-0.01630.019-0.284-0.2840.0000.0000.0000.000
60A64GLY00.0600.02832.5230.1560.1560.0000.0000.0000.000
61A65MET0-0.093-0.03734.335-0.219-0.2190.0000.0000.0000.000
62A66ASN00.0300.01431.647-0.128-0.1280.0000.0000.0000.000
63A67GLY00.0650.03529.3860.2870.2870.0000.0000.0000.000
64A68LEU00.006-0.01828.5320.3580.3580.0000.0000.0000.000
65A69GLU-1-0.854-0.91529.4529.8099.8090.0000.0000.0000.000
66A70THR00.0030.00625.1930.2100.2100.0000.0000.0000.000
67A71LEU0-0.042-0.01923.7420.5350.5350.0000.0000.0000.000
68A72ASP-1-0.793-0.87524.96010.98010.9800.0000.0000.0000.000
69A73LYS10.9390.97526.415-10.221-10.2210.0000.0000.0000.000
70A74LEU0-0.027-0.00219.4720.4170.4170.0000.0000.0000.000
71A75ARG10.8260.91718.445-14.817-14.8170.0000.0000.0000.000
72A76GLU-1-0.939-0.96423.00011.35411.3540.0000.0000.0000.000
73A77LYS10.8350.95119.822-13.601-13.6010.0000.0000.0000.000
74A78SER0-0.062-0.02818.4100.1540.1540.0000.0000.0000.000
75A79LEU0-0.006-0.01015.5331.0201.0200.0000.0000.0000.000
76A80SER0-0.087-0.07111.800-0.113-0.1130.0000.0000.0000.000
77A81GLY00.0100.03112.7140.4940.4940.0000.0000.0000.000
78A82ARG10.7620.87013.374-22.351-22.3510.0000.0000.0000.000
79A83ILE0-0.0010.00315.8360.4610.4610.0000.0000.0000.000
80A84VAL0-0.0090.00618.276-0.558-0.5580.0000.0000.0000.000
81A85VAL0-0.0100.00220.4990.1280.1280.0000.0000.0000.000
82A86PHE00.0410.01520.445-0.037-0.0370.0000.0000.0000.000
83A87SER0-0.009-0.01925.151-0.311-0.3110.0000.0000.0000.000
84A88VAL00.0110.00028.9380.0660.0660.0000.0000.0000.000
85A89SER0-0.115-0.08431.956-0.357-0.3570.0000.0000.0000.000
86A90ASN00.0590.01532.8410.4400.4400.0000.0000.0000.000
87A91HIS0-0.039-0.00335.105-0.193-0.1930.0000.0000.0000.000
88A92GLU-1-0.888-0.94934.5098.8228.8220.0000.0000.0000.000
89A93GLU-1-0.919-0.97433.9769.0129.0120.0000.0000.0000.000
90A94ASP-1-0.801-0.86932.5729.2899.2890.0000.0000.0000.000
91A95VAL0-0.034-0.00528.3250.3760.3760.0000.0000.0000.000
92A96VAL00.0280.00429.4050.4180.4180.0000.0000.0000.000
93A97THR0-0.022-0.01731.1760.0920.0920.0000.0000.0000.000
94A98ALA00.0130.00626.9430.1720.1720.0000.0000.0000.000
95A99LEU0-0.031-0.00925.2330.3450.3450.0000.0000.0000.000
96A100LYS10.9270.97027.009-8.976-8.9760.0000.0000.0000.000
97A101ARG10.7710.84528.373-10.116-10.1160.0000.0000.0000.000
98A102GLY0-0.008-0.00524.5110.1690.1690.0000.0000.0000.000
99A103ALA00.0100.02122.2890.7420.7420.0000.0000.0000.000
100A104ASP-1-0.826-0.94619.04816.13516.1350.0000.0000.0000.000
101A105GLY00.003-0.00921.405-0.115-0.1150.0000.0000.0000.000
102A106TYR0-0.015-0.02222.4910.0880.0880.0000.0000.0000.000
103A107LEU0-0.015-0.00820.524-0.040-0.0400.0000.0000.0000.000
104A108LEU00.0540.03725.181-0.075-0.0750.0000.0000.0000.000
105A109LYS10.7510.84026.482-10.593-10.5930.0000.0000.0000.000
106A110ASP-1-0.959-0.97227.72410.00010.0000.0000.0000.0000.000
107A111MET0-0.0220.00423.7200.0310.0310.0000.0000.0000.000
108A112GLU-1-0.879-0.92626.68010.26710.2670.0000.0000.0000.000
109A113PRO00.020-0.01023.4590.5450.5450.0000.0000.0000.000
110A114GLU-1-0.933-0.98021.87312.28912.2890.0000.0000.0000.000
111A115ASP-1-0.916-0.95321.73012.06312.0630.0000.0000.0000.000
112A116LEU0-0.009-0.01320.4660.5300.5300.0000.0000.0000.000
113A117LEU00.0030.00415.4050.7820.7820.0000.0000.0000.000
114A118LYS10.9440.96917.023-12.167-12.1670.0000.0000.0000.000
115A119ALA00.0110.01717.7530.6690.6690.0000.0000.0000.000
116A120LEU00.001-0.00815.4750.7030.7030.0000.0000.0000.000
117A121HIS0-0.038-0.02010.3390.2650.2650.0000.0000.0000.000
118A122GLN00.0010.00712.7931.1541.1540.0000.0000.0000.000
119A123ALA0-0.009-0.01214.3280.7840.7840.0000.0000.0000.000
120A124ALA0-0.027-0.00810.4990.6850.6850.0000.0000.0000.000
121A125ALA0-0.010-0.0138.8102.7472.7470.0000.0000.0000.000
122A126GLY0-0.0100.01310.0780.3540.3540.0000.0000.0000.000
123A127GLU-1-0.960-0.99213.16918.12818.1280.0000.0000.0000.000
124A128MET0-0.055-0.02915.782-0.347-0.3470.0000.0000.0000.000
125A129VAL00.0140.01318.3470.1370.1370.0000.0000.0000.000
126A130LEU0-0.0020.00021.811-0.109-0.1090.0000.0000.0000.000
127A131SER00.0360.02424.780-0.259-0.2590.0000.0000.0000.000
128A132GLU-1-0.844-0.92027.64410.22910.2290.0000.0000.0000.000
129A133ALA0-0.044-0.01930.704-0.244-0.2440.0000.0000.0000.000
130A134LEU00.0440.00428.479-0.242-0.2420.0000.0000.0000.000
131A135THR0-0.014-0.02229.2320.1080.1080.0000.0000.0000.000
132A136PRO0-0.021-0.01130.563-0.019-0.0190.0000.0000.0000.000
133A137VAL00.0060.00432.716-0.174-0.1740.0000.0000.0000.000
134A138LEU00.000-0.00827.113-0.083-0.0830.0000.0000.0000.000
135A139ALA0-0.017-0.00731.3030.0190.0190.0000.0000.0000.000
136A140ALA0-0.019-0.00832.799-0.087-0.0870.0000.0000.0000.000
137A141SER0-0.060-0.02132.235-0.095-0.0950.0000.0000.0000.000
138A142LEU0-0.076-0.01128.699-0.100-0.1000.0000.0000.0000.000
139A150GLU-1-0.909-0.96531.9429.9469.9460.0000.0000.0000.000
140A151ARG10.8410.90428.233-10.810-10.8100.0000.0000.0000.000
141A152ASP-1-0.871-0.92330.8739.8499.8490.0000.0000.0000.000
142A153VAL00.045-0.00327.2820.3640.3640.0000.0000.0000.000
143A154ASN0-0.038-0.02227.7750.5710.5710.0000.0000.0000.000
144A155GLN0-0.0060.02027.249-0.033-0.0330.0000.0000.0000.000
145A156LEU0-0.060-0.03222.8690.4450.4450.0000.0000.0000.000
146A157THR0-0.0020.00321.311-0.198-0.1980.0000.0000.0000.000
147A158PRO00.046-0.00322.4310.3030.3030.0000.0000.0000.000
148A159ARG10.9010.95415.388-18.401-18.4010.0000.0000.0000.000
149A160GLU-1-0.754-0.88818.13915.47715.4770.0000.0000.0000.000
150A161ARG10.9580.98519.737-11.981-11.9810.0000.0000.0000.000
151A162ASP-1-0.864-0.92218.14315.48315.4830.0000.0000.0000.000
152A163ILE0-0.035-0.01813.6690.5790.5790.0000.0000.0000.000
153A164LEU00.0230.00516.9810.2430.2430.0000.0000.0000.000
154A165LYS10.9410.96419.978-13.700-13.7000.0000.0000.0000.000
155A166LEU0-0.050-0.03115.243-0.314-0.3140.0000.0000.0000.000
156A167ILE00.0120.01114.6520.3680.3680.0000.0000.0000.000
157A168ALA0-0.002-0.00917.616-0.188-0.1880.0000.0000.0000.000
158A169GLN0-0.065-0.03318.903-0.198-0.1980.0000.0000.0000.000
159A170GLY00.0640.04818.168-0.160-0.1600.0000.0000.0000.000
160A171LEU0-0.035-0.01513.9550.7340.7340.0000.0000.0000.000
161A172PRO00.0280.0239.8030.3730.3730.0000.0000.0000.000
162A173ASN00.0880.0198.035-3.258-3.2580.0000.0000.0000.000
163A174LYS10.9480.9932.426-57.428-56.3700.697-0.550-1.2050.004
164A175MET0-0.042-0.0087.198-1.206-1.2060.0000.0000.0000.000
165A176ILE0-0.024-0.01410.727-1.533-1.5330.0000.0000.0000.000
166A177ALA00.0220.0047.076-1.631-1.6310.0000.0000.0000.000
167A178ARG10.9780.9959.053-24.776-24.7760.0000.0000.0000.000
168A179ARG10.8700.94410.330-20.486-20.4860.0000.0000.0000.000
169A180LEU0-0.053-0.03112.701-1.703-1.7030.0000.0000.0000.000
170A181ASP-1-0.946-0.95611.43722.75222.7520.0000.0000.0000.000
171A182ILE0-0.042-0.01010.064-1.234-1.2340.0000.0000.0000.000
172A183THR00.0730.0265.7361.4761.4760.0000.0000.0000.000
173A184GLU-1-0.763-0.9173.29562.39963.6770.335-0.682-0.931-0.002
174A185SER0-0.0100.0015.900-3.510-3.5100.0000.0000.0000.000
175A186THR0-0.020-0.0147.822-5.328-5.3280.0000.0000.0000.000
176A187VAL0-0.017-0.0029.017-3.302-3.3020.0000.0000.0000.000
177A188LYS10.8570.9186.511-40.313-40.3130.0000.0000.0000.000
178A189VAL0-0.018-0.01011.188-2.534-2.5340.0000.0000.0000.000
179A190HIS00.0220.00013.656-2.428-2.4280.0000.0000.0000.000
180A191VAL0-0.0010.01313.288-1.584-1.5840.0000.0000.0000.000
181A192LYS10.9040.97913.763-23.023-23.0230.0000.0000.0000.000
182A193HIS0-0.020-0.00717.268-1.453-1.4530.0000.0000.0000.000
183A194MET0-0.0080.00018.709-1.257-1.2570.0000.0000.0000.000
184A195LEU00.0260.01318.275-0.822-0.8220.0000.0000.0000.000
185A196LYS10.9710.99521.459-14.220-14.2200.0000.0000.0000.000
186A197LYS10.7740.89123.186-14.135-14.1350.0000.0000.0000.000
187A198MET0-0.017-0.00124.542-0.631-0.6310.0000.0000.0000.000
188A199LYS10.9130.97025.819-10.915-10.9150.0000.0000.0000.000
189A200LEU0-0.058-0.00323.546-0.366-0.3660.0000.0000.0000.000
190A201LYS10.9020.95223.397-10.902-10.9020.0000.0000.0000.000
191A202SER00.0140.00420.5520.4420.4420.0000.0000.0000.000
192A203ARG10.8440.89512.251-23.067-23.0670.0000.0000.0000.000
193A204VAL00.0360.02719.523-0.260-0.2600.0000.0000.0000.000
194A205GLU-1-0.822-0.90922.36311.33011.3300.0000.0000.0000.000
195A206ALA00.008-0.01121.362-0.471-0.4710.0000.0000.0000.000
196A207ALA0-0.008-0.00421.830-0.297-0.2970.0000.0000.0000.000
197A208VAL0-0.0040.01423.696-0.439-0.4390.0000.0000.0000.000
198A209TRP00.0540.01626.510-0.230-0.2300.0000.0000.0000.000
199A210VAL0-0.012-0.02223.936-0.341-0.3410.0000.0000.0000.000
200A211HIS0-0.061-0.01627.141-0.292-0.2920.0000.0000.0000.000
201A212GLN0-0.032-0.01629.038-0.132-0.1320.0000.0000.0000.000
202A213GLU-1-0.903-0.96630.5339.2159.2150.0000.0000.0000.000
203A214ARG10.8870.95930.299-9.381-9.3810.0000.0000.0000.000
204A215ILE0-0.0090.00225.534-0.059-0.0590.0000.0000.0000.000
205A216PHE0-0.081-0.01823.499-0.127-0.1270.0000.0000.0000.000