FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 9M9L2

Calculation Name: 4LBI-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 4LBI

Chain ID: C

ChEMBL ID:

UniProt ID: Q45075

Base Structure: X-ray

Registration Date: 2025-07-09

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -652637.181686
FMO2-HF: Nuclear repulsion 616044.764065
FMO2-HF: Total energy -36592.417621
FMO2-MP2: Total energy -36698.905078


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(C:1:MET)


Summations of interaction energy for fragment #1(C:1:MET)
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.
-10.398-9.2129.218-5.233-5.171-0.027
Interaction energy analysis for fragmet #1(C:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.179 / q_NPA : 0.046
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].
4C2LEU0-0.0830.1043.892-0.1470.3930.004-0.216-0.3280.001
5C3PHE00.069-0.0983.855-2.4720.208-0.015-1.631-1.0340.009
6C3PHE0-0.0740.0983.3210.600-0.0010.0040.911-0.3150.000
7C4LEU00.079-0.1186.6150.2660.2660.0000.0000.0000.000
8C4LEU0-0.0770.10210.0350.0500.0500.0000.0000.0000.000
9C5ILE00.127-0.09010.309-0.111-0.1110.0000.0000.0000.000
10C5ILE0-0.1180.1049.8940.0210.0210.0000.0000.0000.000
11C6TYR00.159-0.08212.4420.0880.0880.0000.0000.0000.000
12C6TYR0-0.1380.08015.6610.0370.0370.0000.0000.0000.000
13C7ARG00.078-0.10615.942-0.007-0.0070.0000.0000.0000.000
14C7ARG10.7941.03116.0680.7260.7260.0000.0000.0000.000
15C8LYS00.079-0.08118.9030.0160.0160.0000.0000.0000.000
16C8LYS10.8401.05021.5260.3060.3060.0000.0000.0000.000
17C9ASP00.152-0.09922.618-0.014-0.0140.0000.0000.0000.000
18C9ASP-1-0.790-0.74024.629-0.328-0.3280.0000.0000.0000.000
19C10ARG00.056-0.10325.5480.0090.0090.0000.0000.0000.000
20C10ARG10.8531.07827.7750.2460.2460.0000.0000.0000.000
21C11PRO0-0.050-0.11228.1670.0060.0060.0000.0000.0000.000
22C12GLY00.021-0.00531.2540.0050.0050.0000.0000.0000.000
23C13SER0-0.0210.00430.0980.0130.0130.0000.0000.0000.000
24C13SER0-0.0090.08429.361-0.005-0.0050.0000.0000.0000.000
25C14LEU00.210-0.07930.356-0.017-0.0170.0000.0000.0000.000
26C14LEU0-0.0900.13030.5910.0020.0020.0000.0000.0000.000
27C15GLN00.108-0.11031.278-0.009-0.0090.0000.0000.0000.000
28C15GLN0-0.1090.09834.5330.0070.0070.0000.0000.0000.000
29C16VAL00.082-0.09730.1160.0050.0050.0000.0000.0000.000
30C16VAL0-0.0650.11328.244-0.001-0.0010.0000.0000.0000.000
31C17ARG00.132-0.05027.300-0.013-0.0130.0000.0000.0000.000
32C17ARG10.7000.94422.6750.3380.3380.0000.0000.0000.000
33C18ILE00.002-0.13428.223-0.017-0.0170.0000.0000.0000.000
34C18ILE0-0.0470.09530.6930.0020.0020.0000.0000.0000.000
35C19ASP00.110-0.10930.539-0.003-0.0030.0000.0000.0000.000
36C19ASP-1-0.974-0.82031.492-0.187-0.1870.0000.0000.0000.000
37C20ASN0-0.026-0.09427.1430.0080.0080.0000.0000.0000.000
38C20ASN0-0.1160.03426.231-0.006-0.0060.0000.0000.0000.000
39C21TYR00.108-0.13225.523-0.032-0.0320.0000.0000.0000.000
40C21TYR0-0.0560.13223.635-0.014-0.0140.0000.0000.0000.000
41C22ALA00.117-0.08925.023-0.026-0.0260.0000.0000.0000.000
42C22ALA0-0.0660.11828.4400.0050.0050.0000.0000.0000.000
43C23ALA00.103-0.09025.197-0.009-0.0090.0000.0000.0000.000
44C23ALA0-0.0560.11225.2760.0010.0010.0000.0000.0000.000
45C24HIS00.084-0.06621.674-0.022-0.0220.0000.0000.0000.000
46C24HIS10.7340.96718.5550.5020.5020.0000.0000.0000.000
47C25LEU00.045-0.14120.514-0.059-0.0590.0000.0000.0000.000
48C25LEU0-0.0670.11621.6140.0010.0010.0000.0000.0000.000
49C26ALA00.124-0.08021.153-0.019-0.0190.0000.0000.0000.000
50C26ALA0-0.1040.09723.6890.0060.0060.0000.0000.0000.000
51C27TYR00.068-0.10019.6420.0070.0070.0000.0000.0000.000
52C27TYR0-0.1470.04015.4270.0250.0250.0000.0000.0000.000
53C28LEU00.050-0.12416.335-0.048-0.0480.0000.0000.0000.000
54C28LEU0-0.0860.08615.347-0.011-0.0110.0000.0000.0000.000
55C29GLU00.052-0.09316.455-0.062-0.0620.0000.0000.0000.000
56C29GLU-1-1.006-0.84520.446-0.310-0.3100.0000.0000.0000.000
57C30PRO0-0.043-0.12716.6130.0100.0100.0000.0000.0000.000
58C31LEU0-0.017-0.05713.3050.0470.0470.0000.0000.0000.000
59C31LEU0-0.0210.14812.271-0.025-0.0250.0000.0000.0000.000
60C32LYS00.160-0.06312.738-0.146-0.1460.0000.0000.0000.000
61C32LYS10.8721.08116.2270.3480.3480.0000.0000.0000.000
62C33ALA00.079-0.12312.834-0.024-0.0240.0000.0000.0000.000
63C33ALA0-0.0790.10712.5910.0190.0190.0000.0000.0000.000
64C34LYS00.009-0.1318.8710.1430.1430.0000.0000.0000.000
65C34LYS10.8871.0915.9721.4211.4210.0000.0000.0000.000
66C35ILE00.068-0.0868.857-0.379-0.3790.0000.0000.0000.000
67C35ILE0-0.0850.09212.0880.0050.0050.0000.0000.0000.000
68C36GLN00.094-0.09610.4980.1610.1610.0000.0000.0000.000
69C36GLN0-0.0310.1367.5080.1370.1370.0000.0000.0000.000
70C37VAL00.045-0.11211.6770.1400.1400.0000.0000.0000.000
71C37VAL0-0.0720.10213.2110.0080.0080.0000.0000.0000.000
72C38GLY0-0.008-0.10013.877-0.131-0.1310.0000.0000.0000.000
73C39GLY0-0.027-0.00116.5340.0680.0680.0000.0000.0000.000
74C40PRO00.0060.00319.577-0.042-0.0420.0000.0000.0000.000
75C41THR00.0600.03222.2260.0160.0160.0000.0000.0000.000
76C41THR0-0.0260.06020.941-0.010-0.0100.0000.0000.0000.000
77C42LEU0-0.003-0.15323.271-0.005-0.0050.0000.0000.0000.000
78C42LEU0-0.0110.17525.7920.0030.0030.0000.0000.0000.000
79C43GLY0-0.040-0.12727.024-0.002-0.0020.0000.0000.0000.000
80C44ALA00.118-0.00730.0470.0020.0020.0000.0000.0000.000
81C44ALA0-0.1080.10034.3350.0020.0020.0000.0000.0000.000
82C45GLY0-0.055-0.10833.3360.0010.0010.0000.0000.0000.000
83C46THR00.0230.01832.879-0.007-0.0070.0000.0000.0000.000
84C46THR0-0.0440.04834.2670.0010.0010.0000.0000.0000.000
85C47GLY00.005-0.06932.9940.0020.0020.0000.0000.0000.000
86C48THR00.0310.01829.889-0.009-0.0090.0000.0000.0000.000
87C48THR0-0.0560.05629.0640.0040.0040.0000.0000.0000.000
88C49ASP00.146-0.05929.929-0.009-0.0090.0000.0000.0000.000
89C49ASP-1-1.032-0.88133.275-0.141-0.1410.0000.0000.0000.000
90C50ASP00.188-0.11329.562-0.009-0.0090.0000.0000.0000.000
91C50ASP-1-1.002-0.82529.680-0.205-0.2050.0000.0000.0000.000
92C51LYS00.000-0.08430.286-0.014-0.0140.0000.0000.0000.000
93C51LYS10.8881.04434.4270.1410.1410.0000.0000.0000.000
94C52ASP00.013-0.14430.9910.0030.0030.0000.0000.0000.000
95C52ASP-1-0.917-0.81230.383-0.159-0.1590.0000.0000.0000.000
96C53MET00.051-0.12526.967-0.003-0.0030.0000.0000.0000.000
97C53MET0-0.0930.10526.153-0.016-0.0160.0000.0000.0000.000
98C54THR0-0.009-0.09826.1180.0070.0070.0000.0000.0000.000
99C54THR0-0.0570.07726.407-0.007-0.0070.0000.0000.0000.000
100C55GLY00.028-0.09322.777-0.003-0.0030.0000.0000.0000.000
101C56SER0-0.0320.00119.5310.0330.0330.0000.0000.0000.000
102C56SER0-0.0290.06718.7750.0090.0090.0000.0000.0000.000
103C57PHE00.121-0.05816.312-0.041-0.0410.0000.0000.0000.000
104C57PHE0-0.0770.09513.495-0.001-0.0010.0000.0000.0000.000
105C58LEU00.035-0.14013.3400.1130.1130.0000.0000.0000.000
106C58LEU0-0.0500.11212.521-0.008-0.0080.0000.0000.0000.000
107C59ILE00.118-0.07410.047-0.079-0.0790.0000.0000.0000.000
108C59ILE0-0.1090.1048.7760.0380.0380.0000.0000.0000.000
109C60MET00.066-0.1088.4050.3080.3080.0000.0000.0000.000
110C60MET0-0.1030.0957.9980.1750.1750.0000.0000.0000.000
111C61GLU00.142-0.1434.534-0.931-0.942-0.002-0.0350.0480.000
112C61GLU-1-1.050-0.8422.984-1.415-0.7640.046-0.209-0.4880.000
113C62ALA00.107-0.0893.1551.3211.8590.006-0.247-0.2980.000
114C62ALA0-0.1100.0864.7500.2550.285-0.001-0.010-0.0180.000
115C63GLU00.088-0.0981.866-8.843-11.9499.176-3.719-2.350-0.038
116C63GLU-1-0.989-0.8374.505-0.226-0.098-0.001-0.032-0.0950.000
117C64SER0-0.045-0.1243.8191.3341.472-0.0020.018-0.1550.000
118C64SER0-0.0170.0806.8250.1950.1950.0000.0000.0000.000
119C65TRP00.121-0.0885.666-0.713-0.7130.0000.0000.0000.000
120C65TRP0-0.0520.0946.740-0.188-0.1880.0000.0000.0000.000
121C66ASP00.107-0.1037.428-0.004-0.0040.0000.0000.0000.000
122C66ASP-1-0.992-0.83810.416-0.721-0.7210.0000.0000.0000.000
123C67GLU00.115-0.1157.8720.2870.2870.0000.0000.0000.000
124C67GLU-1-1.007-0.8306.911-2.021-2.0210.0000.0000.0000.000
125C68VAL00.071-0.1547.9580.2470.2470.0000.0000.0000.000
126C68VAL0-0.0780.1076.465-0.017-0.0170.0000.0000.0000.000
127C69HIS00.086-0.0649.1170.2160.2160.0000.0000.0000.000
128C69HIS0-0.0980.09212.018-0.044-0.0440.0000.0000.0000.000
129C70SER00.025-0.07412.1070.1340.1340.0000.0000.0000.000
130C70SER0-0.0340.08212.6630.0740.0740.0000.0000.0000.000
131C71PHE00.103-0.08511.7920.1920.1920.0000.0000.0000.000
132C71PHE0-0.0790.08911.133-0.033-0.0330.0000.0000.0000.000
133C72VAL00.071-0.09013.0630.1160.1160.0000.0000.0000.000
134C72VAL0-0.0730.11112.688-0.003-0.0030.0000.0000.0000.000
135C73GLU00.069-0.09215.0620.0940.0940.0000.0000.0000.000
136C73GLU-1-0.973-0.84616.290-0.642-0.6420.0000.0000.0000.000
137C74ASN00.021-0.09516.7210.0840.0840.0000.0000.0000.000
138C74ASN0-0.1210.07516.3240.0470.0470.0000.0000.0000.000
139C75ASP00.156-0.09317.9250.0510.0510.0000.0000.0000.000
140C75ASP-1-0.866-0.74817.502-0.582-0.5820.0000.0000.0000.000
141C76PRO0-0.025-0.11619.1000.0340.0340.0000.0000.0000.000
142C77PHE00.085-0.02221.8010.0390.0390.0000.0000.0000.000
143C77PHE0-0.0610.10321.198-0.005-0.0050.0000.0000.0000.000
144C78THR0-0.078-0.11220.6510.0360.0360.0000.0000.0000.000
145C78THR0-0.0270.03718.7090.0000.0000.0000.0000.0000.000
146C79LYS00.121-0.05821.9280.0220.0220.0000.0000.0000.000
147C79LYS10.8321.06022.1730.3400.3400.0000.0000.0000.000
148C80ALA00.037-0.12424.4410.0250.0250.0000.0000.0000.000
149C80ALA0-0.0540.13026.4650.0010.0010.0000.0000.0000.000
150C81GLY0-0.074-0.12025.4060.0230.0230.0000.0000.0000.000
151C82LEU00.105-0.01425.2450.0240.0240.0000.0000.0000.000
152C82LEU0-0.1460.10723.9380.0020.0020.0000.0000.0000.000
153C83PHE00.014-0.12922.1400.0320.0320.0000.0000.0000.000
154C83PHE0-0.0680.10920.246-0.021-0.0210.0000.0000.0000.000
155C84ALA00.117-0.08023.664-0.002-0.0020.0000.0000.0000.000
156C84ALA0-0.0820.09325.8660.0070.0070.0000.0000.0000.000
157C85ALA00.047-0.09721.6840.0110.0110.0000.0000.0000.000
158C85ALA0-0.0910.08021.4000.0050.0050.0000.0000.0000.000
159C86THR00.019-0.11817.7670.0070.0070.0000.0000.0000.000
160C86THR00.0110.10915.683-0.009-0.0090.0000.0000.0000.000
161C87ILE00.042-0.09415.3180.0240.0240.0000.0000.0000.000
162C87ILE0-0.0750.09614.0600.0110.0110.0000.0000.0000.000
163C88VAL00.059-0.10111.0130.0400.0400.0000.0000.0000.000
164C88VAL0-0.0470.1078.989-0.016-0.0160.0000.0000.0000.000
165C89GLU00.041-0.1339.6020.0420.0420.0000.0000.0000.000
166C89GLU-1-0.980-0.83210.309-0.661-0.6610.0000.0000.0000.000
167C90ARG00.210-0.0405.563-0.398-0.3980.0000.0000.0000.000
168C90ARG10.8091.0493.8710.3290.4980.005-0.062-0.1110.001
169C91TRP00.007-0.1275.5280.5920.5920.0000.0000.0000.000
170C91TRP0-0.0390.1087.3760.0390.0390.0000.0000.0000.000
171C92LYS00.000-0.0975.1730.2670.297-0.002-0.001-0.0270.000
172C92LYS10.9011.0596.350-0.718-0.7180.0000.0000.0000.000
173C93HIS00.100-0.0887.221-0.208-0.2080.0000.0000.0000.000
174C93HIS0-0.0800.0728.2860.0450.0450.0000.0000.0000.000
175C94GLY0-0.049-0.10610.2440.1400.1400.0000.0000.0000.000