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: 9LYL2

Calculation Name: 1SFP-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1SFP

Chain ID: A

ChEMBL ID:

UniProt ID: P29392

Base Structure: X-ray

Registration Date: 2025-07-11

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 OptH
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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -892219.70831
FMO2-HF: Nuclear repulsion 847463.9641
FMO2-HF: Total energy -44755.74421
FMO2-MP2: Total energy -44882.379556


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:4:LEU)


Summations of interaction energy for fragment #1(A:4:LEU)
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.
0.2580.9470.0030.249-0.9380.005
Interaction energy analysis for fragmet #1(A:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.098 / q_NPA : -0.024
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].
4A6ARG00.1990.0363.790-2.941-2.000-0.004-0.500-0.4370.004
5A6ARG10.7561.0285.3402.1442.1440.0000.0000.0000.000
6A7ASN00.081-0.0886.1160.8280.8280.0000.0000.0000.000
7A7ASN0-0.0730.0809.2010.0910.0910.0000.0000.0000.000
8A8THR0-0.010-0.0889.483-0.178-0.1780.0000.0000.0000.000
9A8THR0-0.0070.09310.5370.0200.0200.0000.0000.0000.000
10A9ASN00.132-0.08012.5920.1250.1250.0000.0000.0000.000
11A9ASN0-0.1090.08414.3020.0330.0330.0000.0000.0000.000
12A10CYS00.147-0.09115.245-0.092-0.0920.0000.0000.0000.000
13A10CYS0-0.3060.18417.9460.0210.0210.0000.0000.0000.000
14A11GLY0-0.004-0.10716.0410.0640.0640.0000.0000.0000.000
15A12GLY0-0.021-0.01716.1560.0210.0210.0000.0000.0000.000
16A13ILE00.0990.01615.836-0.087-0.0870.0000.0000.0000.000
17A13ILE0-0.1170.08016.2000.0110.0110.0000.0000.0000.000
18A14LEU00.037-0.13911.7830.1230.1230.0000.0000.0000.000
19A14LEU0-0.0840.11110.043-0.041-0.0410.0000.0000.0000.000
20A15LYS00.052-0.09511.669-0.064-0.0640.0000.0000.0000.000
21A15LYS10.8321.04713.0130.1230.1230.0000.0000.0000.000
22A16GLU00.099-0.1127.4900.1810.1810.0000.0000.0000.000
23A16GLU-1-0.999-0.8456.5990.7350.7350.0000.0000.0000.000
24A17GLU00.168-0.1148.303-0.344-0.3440.0000.0000.0000.000
25A17GLU-1-0.929-0.7508.1980.2950.2950.0000.0000.0000.000
26A18SER0-0.020-0.1235.5790.0020.020-0.002-0.002-0.0140.000
27A18SER00.0030.0944.726-0.087-0.007-0.001-0.008-0.0710.000
28A19GLY0-0.001-0.0883.4210.7930.772-0.0020.199-0.1750.000
29A20VAL00.085-0.0194.324-0.224-0.117-0.001-0.015-0.0900.000
30A20VAL0-0.0660.1053.1590.4780.0050.0160.576-0.1180.001
31A21ILE00.049-0.0985.5660.4850.499-0.0020.000-0.0130.000
32A21ILE0-0.0980.1119.1600.0510.0510.0000.0000.0000.000
33A22ALA00.141-0.0799.288-0.052-0.0520.0000.0000.0000.000
34A22ALA0-0.1230.0869.458-0.011-0.0110.0000.0000.0000.000
35A23THR00.026-0.10811.0430.0950.0950.0000.0000.0000.000
36A23THR0-0.0570.08615.303-0.039-0.0390.0000.0000.0000.000
37A24TYR00.115-0.07214.7360.0080.0080.0000.0000.0000.000
38A24TYR0-0.1520.10516.0900.0370.0370.0000.0000.0000.000
39A25TYR00.006-0.12816.6120.0120.0120.0000.0000.0000.000
40A25TYR0-0.0750.11716.205-0.012-0.0120.0000.0000.0000.000
41A26GLY00.019-0.12319.5530.0480.0480.0000.0000.0000.000
42A27PRO00.022-0.00822.067-0.016-0.0160.0000.0000.0000.000
43A28LYS00.1020.01823.4280.0120.0120.0000.0000.0000.000
44A28LYS10.8721.04021.0160.2500.2500.0000.0000.0000.000
45A29THR00.010-0.10923.333-0.031-0.0310.0000.0000.0000.000
46A29THR00.0040.11526.2010.0080.0080.0000.0000.0000.000
47A30ASN00.120-0.08223.154-0.016-0.0160.0000.0000.0000.000
48A30ASN0-0.1400.07524.3170.0070.0070.0000.0000.0000.000
49A31CYS00.088-0.11818.7020.0440.0440.0000.0000.0000.000
50A32VAL00.094-0.06918.979-0.045-0.0450.0000.0000.0000.000
51A32VAL0-0.1000.08419.7360.0100.0100.0000.0000.0000.000
52A33TRP00.087-0.09914.4220.0840.0840.0000.0000.0000.000
53A33TRP0-0.0720.10413.272-0.033-0.0330.0000.0000.0000.000
54A34THR00.073-0.05215.818-0.043-0.0430.0000.0000.0000.000
55A34THR0-0.0850.04818.0140.0250.0250.0000.0000.0000.000
56A35ILE00.087-0.10413.2620.0700.0700.0000.0000.0000.000
57A35ILE0-0.0830.11811.456-0.025-0.0250.0000.0000.0000.000
58A36GLN00.155-0.07714.2610.0180.0180.0000.0000.0000.000
59A36GLN0-0.1360.05216.4820.0500.0500.0000.0000.0000.000
60A37MET00.069-0.10915.0090.0420.0420.0000.0000.0000.000
61A37MET0-0.0840.14510.7260.0480.0480.0000.0000.0000.000
62A38PRO0-0.034-0.11615.0640.0200.0200.0000.0000.0000.000
63A39PRO00.0630.00418.377-0.029-0.0290.0000.0000.0000.000
64A40GLU00.061-0.01221.413-0.021-0.0210.0000.0000.0000.000
65A40GLU-1-1.056-0.85522.450-0.059-0.0590.0000.0000.0000.000
66A41TYR00.068-0.05917.3990.0010.0010.0000.0000.0000.000
67A41TYR0-0.1180.04816.5510.0160.0160.0000.0000.0000.000
68A42HIS00.113-0.10817.3030.0080.0080.0000.0000.0000.000
69A42HIS0-0.1630.06817.6790.0230.0230.0000.0000.0000.000
70A43VAL00.108-0.09413.8210.0040.0040.0000.0000.0000.000
71A43VAL0-0.0440.10012.540-0.018-0.0180.0000.0000.0000.000
72A44ARG00.102-0.09212.6470.0790.0790.0000.0000.0000.000
73A44ARG10.6600.98212.3570.6260.6260.0000.0000.0000.000
74A45VAL00.044-0.13011.430-0.214-0.2140.0000.0000.0000.000
75A45VAL0-0.0860.08411.9880.0120.0120.0000.0000.0000.000
76A46SER00.039-0.08310.8650.2440.2440.0000.0000.0000.000
77A46SER0-0.0080.07710.414-0.065-0.0650.0000.0000.0000.000
78A47ILE00.015-0.09710.962-0.330-0.3300.0000.0000.0000.000
79A47ILE0-0.0760.10213.1650.0170.0170.0000.0000.0000.000
80A48GLN00.133-0.09212.4740.1580.1580.0000.0000.0000.000
81A48GLN0-0.0860.11512.1650.0490.0490.0000.0000.0000.000
82A49TYR00.104-0.12114.1160.1340.1340.0000.0000.0000.000
83A49TYR0-0.0410.11015.6430.0080.0080.0000.0000.0000.000
84A50LEU00.105-0.08015.744-0.104-0.1040.0000.0000.0000.000
85A50LEU0-0.1240.09816.349-0.015-0.0150.0000.0000.0000.000
86A51GLN00.006-0.11617.9920.0460.0460.0000.0000.0000.000
87A51GLN0-0.0770.09720.236-0.021-0.0210.0000.0000.0000.000
88A52LEU00.137-0.08020.870-0.003-0.0030.0000.0000.0000.000
89A52LEU0-0.0920.09318.660-0.002-0.0020.0000.0000.0000.000
90A53ASN00.162-0.04922.2270.0230.0230.0000.0000.0000.000
91A53ASN0-0.0810.07326.1290.0130.0130.0000.0000.0000.000
92A54CYS00.154-0.08025.8380.0010.0010.0000.0000.0000.000
93A54CYS0-0.2470.18823.9700.0140.0140.0000.0000.0000.000
94A55ASN00.152-0.03527.0500.0060.0060.0000.0000.0000.000
95A55ASN0-0.203-0.02130.5970.0100.0100.0000.0000.0000.000
96A56LYS00.050-0.07427.7420.0160.0160.0000.0000.0000.000
97A56LYS10.8391.05927.3550.2360.2360.0000.0000.0000.000
98A57GLU00.120-0.09823.8180.0140.0140.0000.0000.0000.000
99A57GLU-1-0.799-0.67322.042-0.438-0.4380.0000.0000.0000.000
100A58SER0-0.081-0.11222.6950.0040.0040.0000.0000.0000.000
101A58SER0-0.0090.07123.7720.0100.0100.0000.0000.0000.000
102A59LEU00.192-0.08118.7660.0120.0120.0000.0000.0000.000
103A59LEU0-0.1140.11515.705-0.012-0.0120.0000.0000.0000.000
104A60GLU00.093-0.12619.9660.0110.0110.0000.0000.0000.000
105A60GLU-1-1.040-0.85121.880-0.348-0.3480.0000.0000.0000.000
106A61ILE00.022-0.12818.649-0.043-0.0430.0000.0000.0000.000
107A61ILE0-0.0510.11816.146-0.012-0.0120.0000.0000.0000.000
108A62ILE00.111-0.09319.4080.0430.0430.0000.0000.0000.000
109A62ILE0-0.1390.08020.9250.0060.0060.0000.0000.0000.000
110A63ASP00.158-0.07119.906-0.052-0.0520.0000.0000.0000.000
111A63ASP-1-0.853-0.70921.701-0.350-0.3500.0000.0000.0000.000
112A64GLY00.072-0.07720.7720.0420.0420.0000.0000.0000.000
113A65LEU00.021-0.02320.957-0.050-0.0500.0000.0000.0000.000
114A65LEU0-0.0100.12921.4980.0030.0030.0000.0000.0000.000
115A66PRO0-0.026-0.11422.0330.0040.0040.0000.0000.0000.000
116A67GLY00.004-0.00424.5250.0220.0220.0000.0000.0000.000
117A68SER0-0.0060.00125.1860.0240.0240.0000.0000.0000.000
118A68SER0-0.0410.08124.3460.0010.0010.0000.0000.0000.000
119A69PRO0-0.001-0.09626.209-0.008-0.0080.0000.0000.0000.000
120A70VAL00.1460.00624.217-0.027-0.0270.0000.0000.0000.000
121A70VAL0-0.0990.11824.1310.0030.0030.0000.0000.0000.000
122A71LEU00.023-0.14022.1400.0330.0330.0000.0000.0000.000
123A71LEU0-0.0490.12520.055-0.009-0.0090.0000.0000.0000.000
124A72GLY0-0.005-0.09722.8740.0070.0070.0000.0000.0000.000
125A73LYS00.1460.01722.289-0.036-0.0360.0000.0000.0000.000
126A73LYS10.8461.08324.5960.3150.3150.0000.0000.0000.000
127A74ILE00.018-0.12621.5340.0460.0460.0000.0000.0000.000
128A74ILE0-0.0500.11518.326-0.007-0.0070.0000.0000.0000.000
129A75CYS00.038-0.09421.839-0.029-0.0290.0000.0000.0000.000
130A76GLU00.123-0.15922.181-0.034-0.0340.0000.0000.0000.000
131A76GLU-1-1.009-0.82523.342-0.360-0.3600.0000.0000.0000.000
132A77GLY0-0.008-0.11321.2840.0370.0370.0000.0000.0000.000
133A78SER0-0.024-0.00118.224-0.048-0.0480.0000.0000.0000.000
134A78SER00.0070.07818.8610.0140.0140.0000.0000.0000.000
135A79LEU00.002-0.11216.8570.0140.0140.0000.0000.0000.000
136A79LEU0-0.0700.09317.2110.0090.0090.0000.0000.0000.000
137A80MET00.129-0.07416.6590.0670.0670.0000.0000.0000.000
138A80MET0-0.1590.09016.7300.0140.0140.0000.0000.0000.000
139A81ASP00.117-0.10715.295-0.145-0.1450.0000.0000.0000.000
140A81ASP-1-0.901-0.78814.885-0.750-0.7500.0000.0000.0000.000
141A82TYR00.042-0.12215.5630.0970.0970.0000.0000.0000.000
142A82TYR0-0.0810.09116.2060.0250.0250.0000.0000.0000.000
143A83ARG00.128-0.08815.804-0.097-0.0970.0000.0000.0000.000
144A83ARG10.7911.03617.2830.3700.3700.0000.0000.0000.000
145A84SER00.044-0.07017.4690.0370.0370.0000.0000.0000.000
146A84SER0-0.0790.05617.657-0.024-0.0240.0000.0000.0000.000
147A85SER00.010-0.12619.2860.0130.0130.0000.0000.0000.000
148A85SER0-0.1170.00523.7400.0090.0090.0000.0000.0000.000
149A86GLY0-0.015-0.09221.6340.0350.0350.0000.0000.0000.000
150A87SER00.1090.02618.904-0.051-0.0510.0000.0000.0000.000
151A87SER0-0.0010.11019.4540.0170.0170.0000.0000.0000.000
152A88ILE00.007-0.09217.725-0.022-0.0220.0000.0000.0000.000
153A88ILE0-0.1170.06118.5400.0080.0080.0000.0000.0000.000
154A89MET00.089-0.09016.6210.0430.0430.0000.0000.0000.000
155A89MET0-0.0790.11915.5700.0080.0080.0000.0000.0000.000
156A90THR0-0.019-0.07916.450-0.055-0.0550.0000.0000.0000.000
157A90THR0-0.0810.02118.7660.0160.0160.0000.0000.0000.000
158A91VAL00.119-0.10715.2700.0430.0430.0000.0000.0000.000
159A91VAL0-0.0780.13113.656-0.020-0.0200.0000.0000.0000.000
160A92LYS00.129-0.09016.715-0.007-0.0070.0000.0000.0000.000
161A92LYS10.8011.05920.7350.3510.3510.0000.0000.0000.000
162A93TYR00.163-0.07918.719-0.002-0.0020.0000.0000.0000.000
163A93TYR0-0.1480.03517.820-0.002-0.0020.0000.0000.0000.000
164A94ILE00.004-0.12619.7430.0160.0160.0000.0000.0000.000
165A94ILE0-0.0800.10623.4840.0030.0030.0000.0000.0000.000
166A95ARG00.122-0.06723.252-0.018-0.0180.0000.0000.0000.000
167A95ARG10.7751.02222.8140.3000.3000.0000.0000.0000.000
168A96GLU00.098-0.11925.0690.0090.0090.0000.0000.0000.000
169A96GLU-1-0.976-0.83929.155-0.208-0.2080.0000.0000.0000.000
170A97PRO0-0.024-0.11627.650-0.012-0.0120.0000.0000.0000.000
171A98GLU00.047-0.05829.135-0.002-0.0020.0000.0000.0000.000
172A98GLU-1-0.974-0.81831.856-0.159-0.1590.0000.0000.0000.000
173A99HIS00.004-0.11227.7250.0110.0110.0000.0000.0000.000
174A99HIS0-0.1160.09224.4040.0270.0270.0000.0000.0000.000
175A100PRO0-0.010-0.09924.335-0.015-0.0150.0000.0000.0000.000
176A101ALA00.1680.00420.5210.0090.0090.0000.0000.0000.000
177A101ALA0-0.0890.11019.737-0.007-0.0070.0000.0000.0000.000
178A102SER0-0.055-0.11120.3440.0100.0100.0000.0000.0000.000
179A102SER0-0.0490.01320.2350.0130.0130.0000.0000.0000.000
180A103PHE00.144-0.07016.490-0.033-0.0330.0000.0000.0000.000
181A103PHE0-0.1050.08912.2020.0250.0250.0000.0000.0000.000
182A104TYR00.046-0.10014.5620.0600.0600.0000.0000.0000.000
183A104TYR0-0.0790.09913.4420.0070.0070.0000.0000.0000.000
184A105GLU00.087-0.12710.3500.0340.0340.0000.0000.0000.000
185A105GLU-1-0.968-0.8228.296-2.023-2.0230.0000.0000.0000.000
186A106VAL00.062-0.1019.8070.0870.0870.0000.0000.0000.000
187A106VAL0-0.0930.08610.6040.0540.0540.0000.0000.0000.000
188A107LEU00.091-0.0936.730-0.416-0.4160.0000.0000.0000.000
189A107LEU0-0.0520.1095.181-0.089-0.066-0.001-0.001-0.0200.000
190A108TYR00.063-0.0816.6750.5800.5800.0000.0000.0000.000
191A108TYR0-0.0820.0887.6020.1250.1250.0000.0000.0000.000
192A109PHE00.069-0.1276.983-0.588-0.5880.0000.0000.0000.000
193A109PHE0-0.0780.0956.180-0.119-0.1190.0000.0000.0000.000
194A110GLN00.136-0.0819.2310.0630.0630.0000.0000.0000.000
195A110GLN0-0.0620.09711.5710.0320.0320.0000.0000.0000.000
196A111ASP00.108-0.05912.029-0.002-0.0020.0000.0000.0000.000
197A111ASP-1-0.958-0.79514.059-0.456-0.4560.0000.0000.0000.000
198A112PRO00.006-0.12014.7720.0170.0170.0000.0000.0000.000
199A113GLN00.112-0.01812.296-0.021-0.0210.0000.0000.0000.000
200A113GLN0-0.1580.0659.2520.1210.1210.0000.0000.0000.000
201A114ALA0-0.094-0.15612.5920.0420.0420.0000.0000.0000.000
202A114ALA00.0280.02514.174-0.002-0.0020.0000.0000.0000.000