FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N2YZQ

Calculation Name: 4AFL-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4AFL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UNL4

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -685281.548577
FMO2-HF: Nuclear repulsion 642260.313662
FMO2-HF: Total energy -43021.234915
FMO2-MP2: Total energy -43142.952786


3D Structure Molmil
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:3:ALA)


Summations of interaction energy for fragment #1(A:3: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.
-6.147-3.3390.044-1.531-1.3220.005
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.140 / q_NPA : -0.007
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].
4A5MET00.2150.0563.239-3.799-1.4310.026-1.371-1.0230.004
5A5MET0-0.1120.0953.5120.7101.0520.020-0.152-0.2100.001
6A6TYR00.042-0.1124.968-1.271-1.173-0.002-0.008-0.0890.000
7A6TYR0-0.1040.0766.5790.1030.1030.0000.0000.0000.000
8A7LEU00.136-0.0697.455-0.380-0.3800.0000.0000.0000.000
9A7LEU0-0.1110.0838.0640.0050.0050.0000.0000.0000.000
10A8GLU00.100-0.1137.753-0.266-0.2660.0000.0000.0000.000
11A8GLU-1-1.038-0.8496.331-0.458-0.4580.0000.0000.0000.000
12A9HIS00.066-0.0888.827-0.265-0.2650.0000.0000.0000.000
13A9HIS0-0.1340.0448.5080.3950.3950.0000.0000.0000.000
14A10TYR00.105-0.07210.818-0.117-0.1170.0000.0000.0000.000
15A10TYR0-0.1490.03812.4880.0230.0230.0000.0000.0000.000
16A11LEU00.040-0.12112.404-0.055-0.0550.0000.0000.0000.000
17A11LEU0-0.1010.09411.927-0.019-0.0190.0000.0000.0000.000
18A12ASP00.064-0.11613.102-0.139-0.1390.0000.0000.0000.000
19A12ASP-1-0.872-0.77711.4280.3370.3370.0000.0000.0000.000
20A13SER00.002-0.08014.391-0.061-0.0610.0000.0000.0000.000
21A13SER0-0.0460.07817.5160.0280.0280.0000.0000.0000.000
22A14ILE00.106-0.07517.746-0.016-0.0160.0000.0000.0000.000
23A14ILE0-0.0740.09221.141-0.005-0.0050.0000.0000.0000.000
24A15GLU00.024-0.14220.671-0.041-0.0410.0000.0000.0000.000
25A15GLU-1-0.913-0.83221.0510.2330.2330.0000.0000.0000.000
26A16ASN00.045-0.10718.386-0.020-0.0200.0000.0000.0000.000
27A16ASN0-0.0840.09817.260-0.022-0.0220.0000.0000.0000.000
28A17LEU00.116-0.08419.446-0.015-0.0150.0000.0000.0000.000
29A17LEU0-0.0880.11619.196-0.001-0.0010.0000.0000.0000.000
30A18PRO0-0.012-0.11920.356-0.033-0.0330.0000.0000.0000.000
31A19PHE00.0750.00521.876-0.032-0.0320.0000.0000.0000.000
32A19PHE0-0.0970.09620.9650.0040.0040.0000.0000.0000.000
33A20GLU00.166-0.09017.858-0.011-0.0110.0000.0000.0000.000
34A20GLU-1-0.886-0.78115.2700.0550.0550.0000.0000.0000.000
35A21LEU00.050-0.11619.160-0.046-0.0460.0000.0000.0000.000
36A21LEU0-0.0790.10220.808-0.001-0.0010.0000.0000.0000.000
37A22GLN00.108-0.08521.706-0.030-0.0300.0000.0000.0000.000
38A22GLN0-0.1260.08623.9870.0160.0160.0000.0000.0000.000
39A23ARG00.084-0.11219.977-0.011-0.0110.0000.0000.0000.000
40A23ARG10.7561.01314.063-0.034-0.0340.0000.0000.0000.000
41A24ASN00.087-0.10120.027-0.008-0.0080.0000.0000.0000.000
42A24ASN0-0.0910.07316.9600.0180.0180.0000.0000.0000.000
43A25PHE00.127-0.06120.668-0.029-0.0290.0000.0000.0000.000
44A25PHE0-0.0800.07925.0950.0060.0060.0000.0000.0000.000
45A26GLN00.049-0.11023.738-0.005-0.0050.0000.0000.0000.000
46A26GLN0-0.1010.07823.3520.0170.0170.0000.0000.0000.000
47A27LEU00.063-0.11320.9540.0080.0080.0000.0000.0000.000
48A27LEU0-0.0810.09118.032-0.005-0.0050.0000.0000.0000.000
49A28MET00.150-0.08122.462-0.019-0.0190.0000.0000.0000.000
50A28MET0-0.1310.10323.102-0.003-0.0030.0000.0000.0000.000
51A29ARG00.127-0.05824.661-0.010-0.0100.0000.0000.0000.000
52A29ARG10.7371.00827.3270.0600.0600.0000.0000.0000.000
53A30ASP00.060-0.10525.6050.0050.0050.0000.0000.0000.000
54A30ASP-1-0.948-0.82424.669-0.079-0.0790.0000.0000.0000.000
55A31LEU00.001-0.14425.3180.0030.0030.0000.0000.0000.000
56A31LEU0-0.0340.10921.869-0.003-0.0030.0000.0000.0000.000
57A32ASP00.034-0.12526.481-0.010-0.0100.0000.0000.0000.000
58A32ASP-1-0.898-0.80429.014-0.144-0.1440.0000.0000.0000.000
59A33GLN00.148-0.07529.764-0.001-0.0010.0000.0000.0000.000
60A33GLN0-0.1380.06430.7070.0060.0060.0000.0000.0000.000
61A34ARG00.091-0.09929.2940.0080.0080.0000.0000.0000.000
62A34ARG10.8141.05025.9890.1510.1510.0000.0000.0000.000
63A35THR00.025-0.06530.4090.0000.0000.0000.0000.0000.000
64A35THR0-0.0580.04828.987-0.006-0.0060.0000.0000.0000.000
65A36GLU00.004-0.10331.663-0.002-0.0020.0000.0000.0000.000
66A36GLU-1-0.817-0.74933.263-0.127-0.1270.0000.0000.0000.000
67A37ASP00.100-0.10334.2620.0070.0070.0000.0000.0000.000
68A37ASP-1-0.931-0.82633.466-0.097-0.0970.0000.0000.0000.000
69A38LEU00.082-0.10533.9180.0090.0090.0000.0000.0000.000
70A38LEU0-0.1260.10030.963-0.002-0.0020.0000.0000.0000.000
71A39LYS00.082-0.10335.2250.0010.0010.0000.0000.0000.000
72A39LYS10.7250.98133.6090.1350.1350.0000.0000.0000.000
73A40ALA00.152-0.07137.3860.0020.0020.0000.0000.0000.000
74A40ALA0-0.0760.11139.2500.0010.0010.0000.0000.0000.000
75A41GLU00.017-0.11938.7070.0080.0080.0000.0000.0000.000
76A41GLU-1-0.892-0.79438.467-0.087-0.0870.0000.0000.0000.000
77A42ILE00.085-0.09138.9510.0050.0050.0000.0000.0000.000
78A42ILE0-0.1140.07735.958-0.001-0.0010.0000.0000.0000.000
79A43ASP00.076-0.11440.3020.0000.0000.0000.0000.0000.000
80A43ASP-1-0.993-0.84142.297-0.080-0.0800.0000.0000.0000.000
81A44LYS00.111-0.08443.1570.0040.0040.0000.0000.0000.000
82A44LYS10.7130.98641.5720.0800.0800.0000.0000.0000.000
83A45LEU00.112-0.08643.4180.0060.0060.0000.0000.0000.000
84A45LEU0-0.1080.08740.794-0.002-0.0020.0000.0000.0000.000
85A46ALA00.087-0.10744.2670.0010.0010.0000.0000.0000.000
86A46ALA0-0.0770.10743.987-0.001-0.0010.0000.0000.0000.000
87A47THR0-0.004-0.11645.7340.0010.0010.0000.0000.0000.000
88A47THR0-0.0510.07247.0760.0020.0020.0000.0000.0000.000
89A48GLU00.113-0.11147.9540.0040.0040.0000.0000.0000.000
90A48GLU-1-1.017-0.83847.348-0.078-0.0780.0000.0000.0000.000
91A49TYR00.047-0.07348.1140.0040.0040.0000.0000.0000.000
92A49TYR0-0.0960.06146.757-0.001-0.0010.0000.0000.0000.000
93A50MET00.023-0.12549.4350.0010.0010.0000.0000.0000.000
94A50MET0-0.1150.09448.4500.0000.0000.0000.0000.0000.000
95A51SER00.061-0.09951.6810.0030.0030.0000.0000.0000.000
96A51SER0-0.0840.05752.7020.0010.0010.0000.0000.0000.000
97A52SER00.046-0.09253.9840.0040.0040.0000.0000.0000.000
98A52SER0-0.0590.06256.0740.0010.0010.0000.0000.0000.000
99A53ALA00.094-0.05855.653-0.003-0.0030.0000.0000.0000.000
100A53ALA0-0.0850.09458.7550.0000.0000.0000.0000.0000.000
101A54ARG00.021-0.11058.0210.0000.0000.0000.0000.0000.000
102A54ARG10.8781.04558.8900.0520.0520.0000.0000.0000.000
103A55SER00.025-0.07156.563-0.002-0.0020.0000.0000.0000.000
104A55SER0-0.0530.05756.6650.0000.0000.0000.0000.0000.000
105A56LEU00.053-0.09553.4320.0040.0040.0000.0000.0000.000
106A56LEU0-0.0540.11151.149-0.001-0.0010.0000.0000.0000.000
107A57SER00.025-0.09354.899-0.001-0.0010.0000.0000.0000.000
108A57SER0-0.0790.02254.4770.0000.0000.0000.0000.0000.000
109A58SER00.039-0.09451.583-0.002-0.0020.0000.0000.0000.000
110A58SER0-0.0730.04251.2000.0010.0010.0000.0000.0000.000
111A59GLU00.048-0.10449.644-0.005-0.0050.0000.0000.0000.000
112A59GLU-1-0.896-0.79549.882-0.085-0.0850.0000.0000.0000.000
113A60GLU00.076-0.10349.005-0.004-0.0040.0000.0000.0000.000
114A60GLU-1-0.872-0.76351.961-0.066-0.0660.0000.0000.0000.000
115A61LYS00.133-0.05648.850-0.002-0.0020.0000.0000.0000.000
116A61LYS10.8261.05648.3100.0890.0890.0000.0000.0000.000
117A62LEU00.072-0.12045.836-0.004-0.0040.0000.0000.0000.000
118A62LEU0-0.1030.10643.824-0.001-0.0010.0000.0000.0000.000
119A63ALA00.109-0.11044.454-0.008-0.0080.0000.0000.0000.000
120A63ALA0-0.0600.11946.4400.0010.0010.0000.0000.0000.000
121A64LEU00.087-0.09544.090-0.004-0.0040.0000.0000.0000.000
122A64LEU0-0.1020.13044.9980.0000.0000.0000.0000.0000.000
123A65LEU00.058-0.12543.177-0.003-0.0030.0000.0000.0000.000
124A65LEU0-0.0820.09243.1030.0000.0000.0000.0000.0000.000
125A66LYS00.111-0.08840.268-0.008-0.0080.0000.0000.0000.000
126A66LYS10.7761.03436.9250.1380.1380.0000.0000.0000.000
127A67GLN00.035-0.14138.933-0.011-0.0110.0000.0000.0000.000
128A67GLN0-0.0790.09840.9300.0020.0020.0000.0000.0000.000
129A68ILE00.112-0.07138.433-0.006-0.0060.0000.0000.0000.000
130A68ILE0-0.0850.10639.950-0.001-0.0010.0000.0000.0000.000
131A69GLN00.134-0.09037.342-0.006-0.0060.0000.0000.0000.000
132A69GLN0-0.1210.07936.1150.0030.0030.0000.0000.0000.000
133A70GLU00.062-0.10834.395-0.014-0.0140.0000.0000.0000.000
134A70GLU-1-0.932-0.80233.833-0.143-0.1430.0000.0000.0000.000
135A71ALA00.089-0.10633.439-0.014-0.0140.0000.0000.0000.000
136A71ALA0-0.0620.12336.3780.0020.0020.0000.0000.0000.000
137A72TYR00.069-0.11033.537-0.006-0.0060.0000.0000.0000.000
138A72TYR0-0.1120.08834.6930.0000.0000.0000.0000.0000.000
139A73GLY00.013-0.11131.246-0.012-0.0120.0000.0000.0000.000
140A74LYS00.1360.03928.999-0.022-0.0220.0000.0000.0000.000
141A74LYS10.8121.02529.7850.1610.1610.0000.0000.0000.000
142A75CYS00.125-0.10128.684-0.012-0.0120.0000.0000.0000.000
143A75CYS0-0.1400.09231.0110.0070.0070.0000.0000.0000.000
144A76LYS00.069-0.06728.626-0.003-0.0030.0000.0000.0000.000
145A76LYS10.6960.95125.0860.3400.3400.0000.0000.0000.000
146A77GLU00.075-0.13024.971-0.022-0.0220.0000.0000.0000.000
147A77GLU-1-1.000-0.84924.999-0.259-0.2590.0000.0000.0000.000
148A78PHE00.073-0.10124.010-0.035-0.0350.0000.0000.0000.000
149A78PHE0-0.0690.09424.6790.0110.0110.0000.0000.0000.000
150A79GLY00.014-0.09325.1440.0050.0050.0000.0000.0000.000
151A80ASP00.0820.00622.5740.0020.0020.0000.0000.0000.000
152A80ASP-1-0.923-0.80221.554-0.377-0.3770.0000.0000.0000.000
153A81ASP00.083-0.11820.081-0.055-0.0550.0000.0000.0000.000
154A81ASP-1-0.954-0.84120.334-0.365-0.3650.0000.0000.0000.000
155A82LYS00.096-0.09820.439-0.028-0.0280.0000.0000.0000.000
156A82LYS10.7321.00324.5960.1870.1870.0000.0000.0000.000
157A83VAL00.082-0.07322.3440.0130.0130.0000.0000.0000.000
158A83VAL0-0.0980.08721.3280.0000.0000.0000.0000.0000.000
159A84GLN00.073-0.11017.7930.0050.0050.0000.0000.0000.000
160A84GLN0-0.0700.11315.605-0.057-0.0570.0000.0000.0000.000
161A85LEU00.137-0.09517.762-0.053-0.0530.0000.0000.0000.000
162A85LEU0-0.0870.12618.2930.0050.0050.0000.0000.0000.000
163A86ALA00.093-0.08219.0900.0180.0180.0000.0000.0000.000
164A86ALA0-0.0800.10122.6180.0060.0060.0000.0000.0000.000
165A87MET00.072-0.09718.8530.0500.0500.0000.0000.0000.000
166A87MET0-0.1070.08017.971-0.011-0.0110.0000.0000.0000.000
167A88GLN00.102-0.10115.7240.0090.0090.0000.0000.0000.000
168A88GLN0-0.1190.08713.9200.0260.0260.0000.0000.0000.000
169A89THR00.038-0.08616.4390.0190.0190.0000.0000.0000.000
170A89THR0-0.0840.03919.6810.0200.0200.0000.0000.0000.000
171A90TYR00.082-0.05819.1680.0530.0530.0000.0000.0000.000
172A90TYR0-0.1710.02920.3400.0140.0140.0000.0000.0000.000
173A91GLU00.073-0.12016.1930.0760.0760.0000.0000.0000.000
174A91GLU-1-0.985-0.86115.418-0.499-0.4990.0000.0000.0000.000
175A92MET00.080-0.10216.0720.0210.0210.0000.0000.0000.000
176A92MET0-0.1300.09515.9960.0250.0250.0000.0000.0000.000
177A93VAL00.037-0.10817.0150.0600.0600.0000.0000.0000.000
178A93VAL0-0.0790.09321.0760.0050.0050.0000.0000.0000.000
179A94ASP00.115-0.07620.1740.0500.0500.0000.0000.0000.000
180A94ASP-1-0.906-0.80819.444-0.232-0.2320.0000.0000.0000.000
181A95LYS00.113-0.09516.4660.0240.0240.0000.0000.0000.000
182A95LYS10.7951.03012.6700.0520.0520.0000.0000.0000.000
183A96HIS00.033-0.10817.8900.0340.0340.0000.0000.0000.000
184A96HIS0-0.0800.08817.605-0.006-0.0060.0000.0000.0000.000
185A97ILE00.088-0.08620.4610.0310.0310.0000.0000.0000.000
186A97ILE0-0.0990.08723.212-0.001-0.0010.0000.0000.0000.000
187A98ARG00.132-0.06321.3010.0200.0200.0000.0000.0000.000
188A98ARG10.8541.03719.5930.1790.1790.0000.0000.0000.000
189A99ARG00.113-0.05120.886-0.001-0.0010.0000.0000.0000.000
190A99ARG10.7471.00719.880-0.081-0.0810.0000.0000.0000.000
191A100LEU00.062-0.10021.8970.0170.0170.0000.0000.0000.000
192A100LEU0-0.1240.06824.0920.0030.0030.0000.0000.0000.000
193A101ASP00.086-0.11325.2140.0130.0130.0000.0000.0000.000
194A101ASP-1-1.000-0.86725.410-0.079-0.0790.0000.0000.0000.000
195A102THR0-0.061-0.09424.5220.0020.0020.0000.0000.0000.000
196A102THR0-0.0680.03423.255-0.003-0.0030.0000.0000.0000.000
197A103ASP00.073-0.09325.8440.0060.0060.0000.0000.0000.000
198A103ASP-1-0.945-0.82424.7810.0770.0770.0000.0000.0000.000
199A104LEU0-0.168-0.15927.2740.0060.0060.0000.0000.0000.000
200A104LEU00.0360.02529.441-0.001-0.0010.0000.0000.0000.000