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: RY9J8

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 OptHSide
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 -2367193.709181
FMO2-HF: Nuclear repulsion 2286973.131285
FMO2-HF: Total energy -80220.577896
FMO2-MP2: Total energy -80452.376196


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.
37.02839.8541.507-1.841-2.4940.008
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 : -0.989 / q_NPA : -1.004
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].
3A7ALA0-0.014-0.0063.8272.6084.147-0.019-0.727-0.7940.002
4A8THR00.005-0.0225.684-4.041-4.0410.0000.0000.0000.000
5A9ILE0-0.008-0.0097.987-1.593-1.5930.0000.0000.0000.000
6A10LEU0-0.0240.02211.6980.0150.0150.0000.0000.0000.000
7A11LEU0-0.026-0.00914.582-0.620-0.6200.0000.0000.0000.000
8A12ILE00.0220.01117.815-0.233-0.2330.0000.0000.0000.000
9A13ASP-1-0.802-0.90721.10212.83412.8340.0000.0000.0000.000
10A14ASP-1-0.867-0.94124.05110.57610.5760.0000.0000.0000.000
11A15HIS00.0080.01426.048-0.346-0.3460.0000.0000.0000.000
12A16PRO00.0610.01925.8430.2990.2990.0000.0000.0000.000
13A17MET00.0000.00925.3670.3670.3670.0000.0000.0000.000
14A18LEU00.0120.01923.4460.1160.1160.0000.0000.0000.000
15A19ARG10.8050.87620.315-13.085-13.0850.0000.0000.0000.000
16A20THR0-0.045-0.03520.4950.6000.6000.0000.0000.0000.000
17A21GLY00.0290.01621.0370.3260.3260.0000.0000.0000.000
18A22VAL00.0280.01817.7200.4280.4280.0000.0000.0000.000
19A23LYS10.8500.89316.392-14.641-14.6410.0000.0000.0000.000
20A24GLN0-0.027-0.00616.3120.6730.6730.0000.0000.0000.000
21A25LEU0-0.0140.00317.3780.3310.3310.0000.0000.0000.000
22A26ILE00.0070.00011.6790.5650.5650.0000.0000.0000.000
23A27SER0-0.097-0.04012.2141.0141.0140.0000.0000.0000.000
24A28MET0-0.045-0.02613.772-0.367-0.3670.0000.0000.0000.000
25A29ALA0-0.0030.00911.918-0.414-0.4140.0000.0000.0000.000
26A30PRO0-0.026-0.0258.9021.2031.2030.0000.0000.0000.000
27A31ASP-1-0.858-0.9116.09528.65128.6510.0000.0000.0000.000
28A32ILE0-0.0200.0036.7441.9871.9870.0000.0000.0000.000
29A33THR00.021-0.0016.495-1.526-1.5260.0000.0000.0000.000
30A34VAL0-0.0050.0048.9510.5760.5760.0000.0000.0000.000
31A35VAL0-0.026-0.0237.8830.5820.5820.0000.0000.0000.000
32A36GLY00.000-0.00210.997-0.477-0.4770.0000.0000.0000.000
33A37GLU-1-0.801-0.88514.69915.20915.2090.0000.0000.0000.000
34A38ALA0-0.035-0.01118.232-0.256-0.2560.0000.0000.0000.000
35A39SER00.009-0.01121.4230.1150.1150.0000.0000.0000.000
36A40ASN00.0250.01824.749-0.355-0.3550.0000.0000.0000.000
37A41GLY00.0820.02724.7110.5040.5040.0000.0000.0000.000
38A42GLU-1-0.853-0.92324.76811.21411.2140.0000.0000.0000.000
39A43GLN00.0010.00821.5370.0030.0030.0000.0000.0000.000
40A44GLY00.011-0.02320.4760.6070.6070.0000.0000.0000.000
41A45ILE00.0020.00219.8920.9330.9330.0000.0000.0000.000
42A46GLU-1-0.803-0.88820.56613.78313.7830.0000.0000.0000.000
43A47LEU0-0.042-0.01816.5140.7270.7270.0000.0000.0000.000
44A48ALA00.006-0.00115.9701.3861.3860.0000.0000.0000.000
45A49GLU-1-0.844-0.91115.31116.15016.1500.0000.0000.0000.000
46A50SER0-0.081-0.04315.6930.8640.8640.0000.0000.0000.000
47A51LEU0-0.034-0.02311.5901.3031.3030.0000.0000.0000.000
48A52ASP-1-0.743-0.82210.57026.22626.2260.0000.0000.0000.000
49A53PRO00.0180.0189.7922.6642.6640.0000.0000.0000.000
50A54ASP-1-0.807-0.8906.88037.10037.1000.0000.0000.0000.000
51A55LEU0-0.017-0.00110.214-1.828-1.8280.0000.0000.0000.000
52A56ILE00.0000.01213.2200.3330.3330.0000.0000.0000.000
53A57LEU0-0.006-0.00816.370-0.644-0.6440.0000.0000.0000.000
54A58LEU00.002-0.00318.857-0.117-0.1170.0000.0000.0000.000
55A59ASP-1-0.760-0.85922.29710.80710.8070.0000.0000.0000.000
56A60LEU0-0.016-0.01325.344-0.174-0.1740.0000.0000.0000.000
57A61ASN0-0.065-0.05328.377-0.307-0.3070.0000.0000.0000.000
58A62MET0-0.0030.03525.744-0.077-0.0770.0000.0000.0000.000
59A63PRO0-0.005-0.01530.112-0.268-0.2680.0000.0000.0000.000
60A64GLY00.0480.02432.6040.1540.1540.0000.0000.0000.000
61A65MET0-0.089-0.03534.447-0.232-0.2320.0000.0000.0000.000
62A66ASN00.0240.00531.900-0.169-0.1690.0000.0000.0000.000
63A67GLY00.0640.03829.5720.2810.2810.0000.0000.0000.000
64A68LEU0-0.001-0.02028.8580.3470.3470.0000.0000.0000.000
65A69GLU-1-0.825-0.88729.8739.7999.7990.0000.0000.0000.000
66A70THR00.0000.00225.6340.2200.2200.0000.0000.0000.000
67A71LEU0-0.031-0.01723.9350.5180.5180.0000.0000.0000.000
68A72ASP-1-0.787-0.85625.36210.72710.7270.0000.0000.0000.000
69A73LYS10.8720.93426.773-10.154-10.1540.0000.0000.0000.000
70A74LEU0-0.035-0.01019.6080.4340.4340.0000.0000.0000.000
71A75ARG10.8320.91818.502-14.672-14.6720.0000.0000.0000.000
72A76GLU-1-0.942-0.96423.33811.11711.1170.0000.0000.0000.000
73A77LYS10.7190.85920.135-13.650-13.6500.0000.0000.0000.000
74A78SER0-0.076-0.03818.8270.1750.1750.0000.0000.0000.000
75A79LEU00.001-0.01215.8210.9970.9970.0000.0000.0000.000
76A80SER0-0.082-0.07412.079-0.056-0.0560.0000.0000.0000.000
77A81GLY00.0020.01412.9740.4480.4480.0000.0000.0000.000
78A82ARG10.7610.86313.392-21.566-21.5660.0000.0000.0000.000
79A83ILE00.0010.00315.8230.4670.4670.0000.0000.0000.000
80A84VAL0-0.0050.00817.994-0.542-0.5420.0000.0000.0000.000
81A85VAL0-0.0020.00820.1660.1380.1380.0000.0000.0000.000
82A86PHE00.0360.01120.578-0.019-0.0190.0000.0000.0000.000
83A87SER0-0.011-0.01325.172-0.306-0.3060.0000.0000.0000.000
84A88VAL00.0200.00028.9520.0610.0610.0000.0000.0000.000
85A89SER0-0.087-0.05932.013-0.376-0.3760.0000.0000.0000.000
86A90ASN00.0270.00032.5830.2640.2640.0000.0000.0000.000
87A91HIS0-0.0370.00334.874-0.181-0.1810.0000.0000.0000.000
88A92GLU-1-0.882-0.94434.2508.7158.7150.0000.0000.0000.000
89A93GLU-1-0.847-0.94133.7368.9958.9950.0000.0000.0000.000
90A94ASP-1-0.811-0.88932.2119.1429.1420.0000.0000.0000.000
91A95VAL0-0.033-0.00628.0790.3590.3590.0000.0000.0000.000
92A96VAL00.015-0.00229.1180.3930.3930.0000.0000.0000.000
93A97THR0-0.023-0.01630.9250.0900.0900.0000.0000.0000.000
94A98ALA00.0160.00926.7800.1680.1680.0000.0000.0000.000
95A99LEU0-0.044-0.01624.7410.3270.3270.0000.0000.0000.000
96A100LYS10.8730.94326.935-8.807-8.8070.0000.0000.0000.000
97A101ARG10.7590.82628.567-9.883-9.8830.0000.0000.0000.000
98A102GLY00.0020.00724.7070.1610.1610.0000.0000.0000.000
99A103ALA00.0040.01622.2650.7220.7220.0000.0000.0000.000
100A104ASP-1-0.806-0.94518.98615.53615.5360.0000.0000.0000.000
101A105GLY00.009-0.00221.111-0.102-0.1020.0000.0000.0000.000
102A106TYR0-0.009-0.02222.2400.0850.0850.0000.0000.0000.000
103A107LEU0-0.020-0.00820.418-0.040-0.0400.0000.0000.0000.000
104A108LEU00.0450.03024.966-0.082-0.0820.0000.0000.0000.000
105A109LYS10.7730.84826.416-10.505-10.5050.0000.0000.0000.000
106A110ASP-1-0.945-0.96827.8129.8859.8850.0000.0000.0000.000
107A111MET0-0.040-0.00423.632-0.016-0.0160.0000.0000.0000.000
108A112GLU-1-0.855-0.92226.68010.28510.2850.0000.0000.0000.000
109A113PRO00.017-0.00823.3680.5260.5260.0000.0000.0000.000
110A114GLU-1-0.885-0.95321.87312.28312.2830.0000.0000.0000.000
111A115ASP-1-0.882-0.92721.73012.04012.0400.0000.0000.0000.000
112A116LEU0-0.006-0.00620.5990.4810.4810.0000.0000.0000.000
113A117LEU00.0130.00815.6120.7420.7420.0000.0000.0000.000
114A118LYS10.8390.90717.023-11.614-11.6140.0000.0000.0000.000
115A119ALA00.0070.01317.7920.6330.6330.0000.0000.0000.000
116A120LEU0-0.004-0.01115.4930.6560.6560.0000.0000.0000.000
117A121HIS0-0.049-0.03510.5690.0740.0740.0000.0000.0000.000
118A122GLN0-0.015-0.00612.8071.0041.0040.0000.0000.0000.000
119A123ALA0-0.010-0.01214.2760.7080.7080.0000.0000.0000.000
120A124ALA0-0.031-0.00910.2950.6480.6480.0000.0000.0000.000
121A125ALA0-0.018-0.0208.8472.5282.5280.0000.0000.0000.000
122A126GLY0-0.0020.02210.0790.3760.3760.0000.0000.0000.000
123A127GLU-1-0.939-0.97513.25317.82617.8260.0000.0000.0000.000
124A128MET0-0.049-0.02915.844-0.375-0.3750.0000.0000.0000.000
125A129VAL00.0160.01618.3070.1200.1200.0000.0000.0000.000
126A130LEU0-0.0070.00421.761-0.102-0.1020.0000.0000.0000.000
127A131SER00.0230.01624.674-0.361-0.3610.0000.0000.0000.000
128A132GLU-1-0.842-0.93927.58410.18010.1800.0000.0000.0000.000
129A133ALA0-0.035-0.01530.659-0.240-0.2400.0000.0000.0000.000
130A134LEU00.0370.00428.830-0.204-0.2040.0000.0000.0000.000
131A135THR00.0060.00428.7620.1030.1030.0000.0000.0000.000
132A136PRO0-0.028-0.01730.420-0.019-0.0190.0000.0000.0000.000
133A137VAL0-0.0010.00132.571-0.167-0.1670.0000.0000.0000.000
134A138LEU00.010-0.00127.035-0.071-0.0710.0000.0000.0000.000
135A139ALA0-0.035-0.01631.0520.0180.0180.0000.0000.0000.000
136A140ALA0-0.023-0.00832.574-0.083-0.0830.0000.0000.0000.000
137A141SER0-0.053-0.01532.075-0.121-0.1210.0000.0000.0000.000
138A142LEU0-0.062-0.00928.603-0.083-0.0830.0000.0000.0000.000
139A150GLU-1-0.867-0.93632.7679.7489.7480.0000.0000.0000.000
140A151ARG10.7920.88028.498-10.504-10.5040.0000.0000.0000.000
141A152ASP-1-0.824-0.90831.2639.7849.7840.0000.0000.0000.000
142A153VAL00.034-0.01128.0070.3660.3660.0000.0000.0000.000
143A154ASN0-0.085-0.04028.4330.4120.4120.0000.0000.0000.000
144A155GLN00.0010.01927.5630.0220.0220.0000.0000.0000.000
145A156LEU0-0.063-0.02223.4030.4780.4780.0000.0000.0000.000
146A157THR0-0.003-0.03222.230-0.164-0.1640.0000.0000.0000.000
147A158PRO00.031-0.01223.0750.2920.2920.0000.0000.0000.000
148A159ARG10.8610.93115.882-18.191-18.1910.0000.0000.0000.000
149A160GLU-1-0.718-0.81818.87115.04915.0490.0000.0000.0000.000
150A161ARG10.9390.97720.482-11.724-11.7240.0000.0000.0000.000
151A162ASP-1-0.839-0.90618.78315.48215.4820.0000.0000.0000.000
152A163ILE0-0.029-0.01714.2430.5150.5150.0000.0000.0000.000
153A164LEU00.0190.00317.8060.2030.2030.0000.0000.0000.000
154A165LYS10.9310.96820.601-13.402-13.4020.0000.0000.0000.000
155A166LEU0-0.042-0.02515.791-0.310-0.3100.0000.0000.0000.000
156A167ILE00.0120.00714.6440.3360.3360.0000.0000.0000.000
157A168ALA00.0040.00017.654-0.187-0.1870.0000.0000.0000.000
158A169GLN0-0.061-0.03119.068-0.222-0.2220.0000.0000.0000.000
159A170GLY00.0610.04418.080-0.146-0.1460.0000.0000.0000.000
160A171LEU0-0.037-0.01614.0930.6460.6460.0000.0000.0000.000
161A172PRO00.0410.0319.7310.2320.2320.0000.0000.0000.000
162A173ASN00.0540.0087.821-2.956-2.9560.0000.0000.0000.000
163A174LYS10.9040.9542.069-59.122-58.3111.508-0.900-1.4190.007
164A175MET0-0.053-0.0137.286-0.926-0.9260.0000.0000.0000.000
165A176ILE0-0.022-0.01310.902-1.341-1.3410.0000.0000.0000.000
166A177ALA00.006-0.0017.670-1.421-1.4210.0000.0000.0000.000
167A178ARG10.9890.9999.667-24.254-24.2540.0000.0000.0000.000
168A179ARG10.8700.94610.806-19.544-19.5440.0000.0000.0000.000
169A180LEU0-0.062-0.03213.293-1.622-1.6220.0000.0000.0000.000
170A181ASP-1-0.930-0.95011.71122.87322.8730.0000.0000.0000.000
171A182ILE0-0.025-0.00710.673-1.081-1.0810.0000.0000.0000.000
172A183THR00.0740.0346.1021.1081.1080.0000.0000.0000.000
173A184GLU-1-0.714-0.8773.58851.69352.1690.018-0.214-0.281-0.001
174A185SER0-0.0070.0026.256-2.777-2.7770.0000.0000.0000.000
175A186THR0-0.018-0.0157.803-5.021-5.0210.0000.0000.0000.000
176A187VAL0-0.009-0.0029.695-3.116-3.1160.0000.0000.0000.000
177A188LYS10.8430.9007.016-36.605-36.6050.0000.0000.0000.000
178A189VAL0-0.024-0.01311.376-2.343-2.3430.0000.0000.0000.000
179A190HIS00.0240.00213.918-2.381-2.3810.0000.0000.0000.000
180A191VAL0-0.0020.00913.947-1.497-1.4970.0000.0000.0000.000
181A192LYS10.8360.93213.245-23.235-23.2350.0000.0000.0000.000
182A193HIS0-0.025-0.01117.479-1.394-1.3940.0000.0000.0000.000
183A194MET0-0.0080.00119.150-1.229-1.2290.0000.0000.0000.000
184A195LEU00.0250.01218.532-0.778-0.7780.0000.0000.0000.000
185A196LYS10.9810.99821.688-13.983-13.9830.0000.0000.0000.000
186A197LYS10.7540.85623.196-14.021-14.0210.0000.0000.0000.000
187A198MET0-0.021-0.00124.773-0.640-0.6400.0000.0000.0000.000
188A199LYS10.8920.95626.073-11.069-11.0690.0000.0000.0000.000
189A200LEU0-0.0570.00523.921-0.357-0.3570.0000.0000.0000.000
190A201LYS10.8580.89323.729-10.698-10.6980.0000.0000.0000.000
191A202SER00.0040.00020.8840.3950.3950.0000.0000.0000.000
192A203ARG10.8380.89412.299-22.272-22.2720.0000.0000.0000.000
193A204VAL00.0250.01819.509-0.237-0.2370.0000.0000.0000.000
194A205GLU-1-0.779-0.85722.11211.17111.1710.0000.0000.0000.000
195A206ALA00.012-0.00921.352-0.446-0.4460.0000.0000.0000.000
196A207ALA0-0.012-0.00421.658-0.279-0.2790.0000.0000.0000.000
197A208VAL0-0.0020.01023.525-0.418-0.4180.0000.0000.0000.000
198A209TRP00.0580.01826.647-0.180-0.1800.0000.0000.0000.000
199A210VAL0-0.016-0.02124.222-0.325-0.3250.0000.0000.0000.000
200A211HIS0-0.060-0.02027.257-0.314-0.3140.0000.0000.0000.000
201A212GLN0-0.013-0.00228.929-0.187-0.1870.0000.0000.0000.000
202A213GLU-1-0.907-0.97130.8219.1009.1000.0000.0000.0000.000
203A214ARG10.8760.95430.443-9.307-9.3070.0000.0000.0000.000
204A215ILE0-0.0120.00426.245-0.037-0.0370.0000.0000.0000.000
205A216PHE0-0.048-0.01624.218-0.082-0.0820.0000.0000.0000.000