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: 24N6R

Calculation Name: 5LZ3-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LZ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H3P7

Base Structure: X-ray

Registration Date: 2025-07-14

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 OptHSide
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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1139523.299631
FMO2-HF: Nuclear repulsion 1088760.269001
FMO2-HF: Total energy -50763.03063
FMO2-MP2: Total energy -50913.389738


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:368:VAL)


Summations of interaction energy for fragment #1(A:368:VAL)
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.
-3.728-0.723-0.02-1.721-1.2620.008
Interaction energy analysis for fragmet #1(A:368:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.205 / q_NPA : 0.087
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].
4A369ILE0-0.0390.1214.229-0.3460.1770.002-0.248-0.2760.001
5A370ALA00.088-0.1203.811-2.3560.126-0.022-1.473-0.9860.007
6A370ALA0-0.0570.1276.2990.1210.1210.0000.0000.0000.000
7A371ALA00.090-0.1136.6570.1130.1130.0000.0000.0000.000
8A371ALA0-0.0610.1219.5750.0310.0310.0000.0000.0000.000
9A372PRO0-0.056-0.1109.8400.0950.0950.0000.0000.0000.000
10A373SER00.0330.00213.0120.0020.0020.0000.0000.0000.000
11A373SER0-0.0220.09014.7420.0320.0320.0000.0000.0000.000
12A374MET00.098-0.07916.2770.0090.0090.0000.0000.0000.000
13A374MET0-0.1460.07418.321-0.011-0.0110.0000.0000.0000.000
14A375TRP00.029-0.07819.574-0.001-0.0010.0000.0000.0000.000
15A375TRP0-0.1310.06118.609-0.004-0.0040.0000.0000.0000.000
16A376THR00.005-0.11423.153-0.009-0.0090.0000.0000.0000.000
17A376THR0-0.0070.06825.775-0.003-0.0030.0000.0000.0000.000
18A377ARG00.108-0.06426.8060.0030.0030.0000.0000.0000.000
19A377ARG10.7330.98828.0370.1720.1720.0000.0000.0000.000
20A378PRO00.075-0.05929.9750.0000.0000.0000.0000.0000.000
21A379GLN0-0.0220.00733.2790.0060.0060.0000.0000.0000.000
22A379GLN0-0.0150.09532.648-0.007-0.0070.0000.0000.0000.000
23A380ILE00.171-0.11733.849-0.003-0.0030.0000.0000.0000.000
24A380ILE0-0.0690.13933.3200.0020.0020.0000.0000.0000.000
25A381LYS00.036-0.11834.810-0.002-0.0020.0000.0000.0000.000
26A381LYS10.9201.06239.2700.0930.0930.0000.0000.0000.000
27A382ASP00.154-0.01937.0870.0030.0030.0000.0000.0000.000
28A382ASP-1-0.937-0.84334.942-0.116-0.1160.0000.0000.0000.000
29A383PHE00.084-0.09032.8420.0060.0060.0000.0000.0000.000
30A383PHE0-0.1110.08028.785-0.001-0.0010.0000.0000.0000.000
31A384LYS00.127-0.11534.024-0.003-0.0030.0000.0000.0000.000
32A384LYS10.7361.02434.5280.1280.1280.0000.0000.0000.000
33A385GLU00.067-0.09435.631-0.001-0.0010.0000.0000.0000.000
34A385GLU-1-1.016-0.84239.000-0.087-0.0870.0000.0000.0000.000
35A386LYS00.089-0.07935.3530.0070.0070.0000.0000.0000.000
36A386LYS10.7260.96933.5090.1180.1180.0000.0000.0000.000
37A387ILE0-0.004-0.13233.2090.0050.0050.0000.0000.0000.000
38A387ILE0-0.1090.10330.409-0.001-0.0010.0000.0000.0000.000
39A388GLN00.144-0.08134.227-0.001-0.0010.0000.0000.0000.000
40A388GLN0-0.1160.07337.3980.0030.0030.0000.0000.0000.000
41A389GLN00.023-0.08837.3900.0030.0030.0000.0000.0000.000
42A389GLN0-0.1230.05937.7870.0030.0030.0000.0000.0000.000
43A390ASP00.086-0.07934.7270.0070.0070.0000.0000.0000.000
44A390ASP-1-0.935-0.78732.660-0.114-0.1140.0000.0000.0000.000
45A391ALA00.124-0.08136.093-0.004-0.0040.0000.0000.0000.000
46A391ALA0-0.0840.09737.0910.0010.0010.0000.0000.0000.000
47A392ASP00.056-0.11533.004-0.001-0.0010.0000.0000.0000.000
48A392ASP-1-1.008-0.84632.169-0.096-0.0960.0000.0000.0000.000
49A393SER00.013-0.10130.651-0.010-0.0100.0000.0000.0000.000
50A393SER0-0.0900.04330.966-0.004-0.0040.0000.0000.0000.000
51A394VAL00.090-0.13631.497-0.012-0.0120.0000.0000.0000.000
52A394VAL0-0.0860.11534.1740.0000.0000.0000.0000.0000.000
53A395ILE00.067-0.07431.3150.0090.0090.0000.0000.0000.000
54A395ILE0-0.0670.08527.995-0.002-0.0020.0000.0000.0000.000
55A396THR00.023-0.08632.721-0.004-0.0040.0000.0000.0000.000
56A396THR0-0.0430.07536.3180.0030.0030.0000.0000.0000.000
57A397VAL00.074-0.09931.9540.0070.0070.0000.0000.0000.000
58A397VAL0-0.1090.12029.966-0.001-0.0010.0000.0000.0000.000
59A398GLY00.063-0.07833.2200.0030.0030.0000.0000.0000.000
60A399ARG00.025-0.01634.607-0.010-0.0100.0000.0000.0000.000
61A399ARG10.8441.04038.3040.0890.0890.0000.0000.0000.000
62A400GLY00.014-0.07333.7050.0040.0040.0000.0000.0000.000
63A401GLU00.085-0.00632.233-0.002-0.0020.0000.0000.0000.000
64A401GLU-1-0.939-0.81931.589-0.123-0.1230.0000.0000.0000.000
65A402VAL00.058-0.12127.629-0.005-0.0050.0000.0000.0000.000
66A402VAL0-0.0940.09625.587-0.003-0.0030.0000.0000.0000.000
67A403VAL00.055-0.11027.7740.0040.0040.0000.0000.0000.000
68A403VAL0-0.0260.14427.5610.0000.0000.0000.0000.0000.000
69A404THR00.024-0.08123.760-0.015-0.0150.0000.0000.0000.000
70A404THR0-0.0220.06421.730-0.007-0.0070.0000.0000.0000.000
71A405VAL00.064-0.09523.1970.0220.0220.0000.0000.0000.000
72A405VAL0-0.0570.12523.532-0.001-0.0010.0000.0000.0000.000
73A406ARG00.096-0.09320.758-0.034-0.0340.0000.0000.0000.000
74A406ARG10.7180.93619.6840.1820.1820.0000.0000.0000.000
75A407VAL00.073-0.10519.7490.0340.0340.0000.0000.0000.000
76A407VAL0-0.0970.10719.366-0.002-0.0020.0000.0000.0000.000
77A408PRO0-0.010-0.12618.249-0.037-0.0370.0000.0000.0000.000
78A409THR00.0450.02115.135-0.001-0.0010.0000.0000.0000.000
79A409THR0-0.0340.07713.113-0.004-0.0040.0000.0000.0000.000
80A410HIS00.120-0.05516.5040.0350.0350.0000.0000.0000.000
81A410HIS0-0.0610.11518.9310.0010.0010.0000.0000.0000.000
82A411GLU00.096-0.10617.140-0.025-0.0250.0000.0000.0000.000
83A411GLU-1-0.904-0.79118.601-0.021-0.0210.0000.0000.0000.000
84A412GLU0-0.005-0.13418.0570.0200.0200.0000.0000.0000.000
85A412GLU-1-0.951-0.81421.011-0.064-0.0640.0000.0000.0000.000
86A413GLY0-0.046-0.14617.1080.0030.0030.0000.0000.0000.000
87A414SER00.0290.01013.2130.0090.0090.0000.0000.0000.000
88A414SER0-0.0480.06212.522-0.003-0.0030.0000.0000.0000.000
89A415TYR00.040-0.10012.329-0.098-0.0980.0000.0000.0000.000
90A415TYR0-0.0720.09111.873-0.029-0.0290.0000.0000.0000.000
91A416LEU00.143-0.09514.4710.0820.0820.0000.0000.0000.000
92A416LEU0-0.0830.10815.188-0.006-0.0060.0000.0000.0000.000
93A417PHE00.013-0.09516.445-0.053-0.0530.0000.0000.0000.000
94A417PHE0-0.0710.09417.8760.0000.0000.0000.0000.0000.000
95A418TRP00.070-0.09219.3940.0210.0210.0000.0000.0000.000
96A418TRP0-0.0540.09315.510-0.014-0.0140.0000.0000.0000.000
97A419GLU00.100-0.11021.702-0.017-0.0170.0000.0000.0000.000
98A419GLU-1-0.882-0.76024.894-0.182-0.1820.0000.0000.0000.000
99A420PHE00.057-0.08125.1170.0070.0070.0000.0000.0000.000
100A420PHE0-0.0790.06322.828-0.001-0.0010.0000.0000.0000.000
101A421ALA00.110-0.07827.217-0.009-0.0090.0000.0000.0000.000
102A421ALA0-0.0430.09530.6200.0030.0030.0000.0000.0000.000
103A422THR0-0.017-0.07430.3050.0030.0030.0000.0000.0000.000
104A422THR0-0.0170.05130.841-0.002-0.0020.0000.0000.0000.000
105A423ASP00.081-0.09033.128-0.002-0.0020.0000.0000.0000.000
106A423ASP-1-0.856-0.77037.782-0.112-0.1120.0000.0000.0000.000
107A424ASN00.090-0.06436.8250.0010.0010.0000.0000.0000.000
108A424ASN0-0.1310.04639.0970.0030.0030.0000.0000.0000.000
109A425TYR00.084-0.05635.6520.0030.0030.0000.0000.0000.000
110A425TYR0-0.0810.04235.6790.0040.0040.0000.0000.0000.000
111A426ASP00.174-0.01931.653-0.001-0.0010.0000.0000.0000.000
112A426ASP-1-0.806-0.74730.683-0.166-0.1660.0000.0000.0000.000
113A427ILE00.021-0.09529.5300.0120.0120.0000.0000.0000.000
114A427ILE0-0.0500.10327.6820.0030.0030.0000.0000.0000.000
115A428GLY00.017-0.09226.120-0.011-0.0110.0000.0000.0000.000
116A429PHE00.080-0.01223.2890.0130.0130.0000.0000.0000.000
117A429PHE0-0.0630.11019.903-0.002-0.0020.0000.0000.0000.000
118A430GLY00.036-0.08919.234-0.015-0.0150.0000.0000.0000.000
119A431VAL00.034-0.01116.4630.0550.0550.0000.0000.0000.000
120A431VAL0-0.0870.09715.007-0.004-0.0040.0000.0000.0000.000
121A432TYR00.124-0.05214.123-0.094-0.0940.0000.0000.0000.000
122A432TYR0-0.1380.03314.7360.0390.0390.0000.0000.0000.000
123A433PHE00.106-0.10511.5490.0670.0670.0000.0000.0000.000
124A433PHE0-0.0830.1049.889-0.055-0.0550.0000.0000.0000.000
125A434GLU00.154-0.09212.143-0.041-0.0410.0000.0000.0000.000
126A434GLU-1-0.917-0.75715.672-0.187-0.1870.0000.0000.0000.000
127A435TRP00.049-0.12411.590-0.011-0.0110.0000.0000.0000.000
128A435TRP0-0.1260.0826.0490.1760.1760.0000.0000.0000.000
129A436THR0-0.086-0.15912.6360.0480.0480.0000.0000.0000.000
130A436THR00.0570.05716.0710.0050.0050.0000.0000.0000.000
131A474PRO00.010-0.00516.7110.0100.0100.0000.0000.0000.000
132A475LEU00.117-0.00512.500-0.020-0.0200.0000.0000.0000.000
133A475LEU0-0.1000.1069.3280.0220.0220.0000.0000.0000.000
134A476LEU00.026-0.11712.883-0.008-0.0080.0000.0000.0000.000
135A476LEU0-0.0610.09114.2520.0010.0010.0000.0000.0000.000
136A477ASP00.073-0.1009.2470.0730.0730.0000.0000.0000.000
137A477ASP-1-0.917-0.8057.709-1.176-1.1760.0000.0000.0000.000
138A478GLU00.103-0.12010.5920.0300.0300.0000.0000.0000.000
139A478GLU-1-0.941-0.80312.865-0.520-0.5200.0000.0000.0000.000
140A479ILE00.033-0.10211.112-0.152-0.1520.0000.0000.0000.000
141A479ILE0-0.1380.0739.6940.0010.0010.0000.0000.0000.000
142A480VAL00.096-0.11912.115-0.059-0.0590.0000.0000.0000.000
143A480VAL0-0.1300.09215.0250.0090.0090.0000.0000.0000.000
144A481PRO00.069-0.04414.9860.0580.0580.0000.0000.0000.000
145A482VAL00.083-0.03517.4690.0110.0110.0000.0000.0000.000
146A482VAL0-0.0840.11619.9060.0040.0040.0000.0000.0000.000
147A483TYR00.074-0.09721.0640.0200.0200.0000.0000.0000.000
148A483TYR0-0.0790.10819.206-0.005-0.0050.0000.0000.0000.000
149A484ARG00.087-0.08023.467-0.007-0.0070.0000.0000.0000.000
150A484ARG10.7730.99227.6120.1760.1760.0000.0000.0000.000
151A485ARG00.060-0.11726.238-0.006-0.0060.0000.0000.0000.000
152A485ARG10.8021.03419.8210.3560.3560.0000.0000.0000.000
153A486ASP00.036-0.08227.1170.0080.0080.0000.0000.0000.000
154A486ASP-1-0.924-0.83029.533-0.191-0.1910.0000.0000.0000.000
155A487CYS00.172-0.07129.0130.0060.0060.0000.0000.0000.000
156A487CYS0-0.2010.06528.035-0.005-0.0050.0000.0000.0000.000
157A488HIS00.060-0.10530.0600.0020.0020.0000.0000.0000.000
158A488HIS0-0.1140.05433.265-0.005-0.0050.0000.0000.0000.000
159A489GLU00.054-0.14532.9650.0110.0110.0000.0000.0000.000
160A489GLU-1-0.974-0.81233.599-0.140-0.1400.0000.0000.0000.000
161A490GLU00.005-0.16031.1960.0110.0110.0000.0000.0000.000
162A490GLU-1-0.876-0.78730.409-0.177-0.1770.0000.0000.0000.000
163A491VAL00.121-0.08629.577-0.006-0.0060.0000.0000.0000.000
164A491VAL0-0.1460.08327.8700.0010.0010.0000.0000.0000.000
165A492TYR00.098-0.08225.6960.0000.0000.0000.0000.0000.000
166A492TYR0-0.1300.08723.998-0.012-0.0120.0000.0000.0000.000
167A493ALA00.083-0.11823.1430.0050.0050.0000.0000.0000.000
168A493ALA0-0.0730.11223.4640.0050.0050.0000.0000.0000.000
169A494GLY00.006-0.11119.068-0.012-0.0120.0000.0000.0000.000
170A495SER0-0.0060.02416.7120.0380.0380.0000.0000.0000.000
171A495SER0-0.0250.06216.420-0.012-0.0120.0000.0000.0000.000
172A496HIS00.117-0.10812.669-0.046-0.0460.0000.0000.0000.000
173A496HIS0-0.0300.1278.6400.2650.2650.0000.0000.0000.000
174A497GLN00.105-0.0689.7180.1760.1760.0000.0000.0000.000
175A497GLN0-0.1020.0787.463-0.228-0.2280.0000.0000.0000.000
176A498TYR00.035-0.1279.103-0.289-0.2890.0000.0000.0000.000
177A498TYR0-0.0690.11410.7340.0440.0440.0000.0000.0000.000
178A499PRO0-0.028-0.0805.987-0.068-0.0680.0000.0000.0000.000
179A500GLY00.028-0.0106.4070.2450.2450.0000.0000.0000.000
180A501ARG00.1020.0129.171-0.056-0.0560.0000.0000.0000.000
181A501ARG10.7150.99613.4360.0320.0320.0000.0000.0000.000
182A502GLY00.038-0.10212.8360.0260.0260.0000.0000.0000.000
183A503VAL00.050-0.01214.0790.0080.0080.0000.0000.0000.000
184A503VAL0-0.1140.09217.4280.0090.0090.0000.0000.0000.000
185A504TYR00.131-0.07615.349-0.026-0.0260.0000.0000.0000.000
186A504TYR0-0.1030.07311.5280.0390.0390.0000.0000.0000.000
187A505LEU00.051-0.09416.2520.0560.0560.0000.0000.0000.000
188A505LEU0-0.1160.07817.0490.0080.0080.0000.0000.0000.000
189A506LEU00.102-0.10118.470-0.042-0.0420.0000.0000.0000.000
190A506LEU0-0.0830.11518.5120.0020.0020.0000.0000.0000.000
191A507LYS00.113-0.11820.5790.0390.0390.0000.0000.0000.000
192A507LYS10.8251.04719.9650.2530.2530.0000.0000.0000.000
193A508PHE00.086-0.06022.477-0.019-0.0190.0000.0000.0000.000
194A508PHE0-0.1120.08624.7340.0010.0010.0000.0000.0000.000
195A509ASP00.159-0.10325.8130.0210.0210.0000.0000.0000.000
196A509ASP-1-0.906-0.77925.170-0.209-0.2090.0000.0000.0000.000
197A510ASN00.068-0.07927.081-0.004-0.0040.0000.0000.0000.000
198A510ASN0-0.1360.03431.189-0.003-0.0030.0000.0000.0000.000
199A511SER00.085-0.11129.6820.0140.0140.0000.0000.0000.000
200A511SER0-0.0510.06428.7030.0000.0000.0000.0000.0000.000
201A512TYR00.046-0.08731.1970.0110.0110.0000.0000.0000.000
202A512TYR0-0.1660.02329.854-0.002-0.0020.0000.0000.0000.000
203A513SER00.029-0.11232.7010.0060.0060.0000.0000.0000.000
204A513SER0-0.1020.05134.6250.0020.0020.0000.0000.0000.000
205A514LEU00.089-0.10235.5590.0000.0000.0000.0000.0000.000
206A514LEU0-0.0380.13137.8770.0010.0010.0000.0000.0000.000
207A515TRP00.033-0.12138.7700.0040.0040.0000.0000.0000.000
208A515TRP0-0.0740.09941.7520.0010.0010.0000.0000.0000.000
209A516ARG00.016-0.11938.6920.0060.0060.0000.0000.0000.000
210A516ARG10.9051.09437.7580.0940.0940.0000.0000.0000.000
211A517SER00.086-0.03136.600-0.007-0.0070.0000.0000.0000.000
212A517SER00.0190.07737.4650.0010.0010.0000.0000.0000.000
213A518LYS0-0.004-0.12033.5520.0060.0060.0000.0000.0000.000
214A518LYS10.7400.99032.6500.1490.1490.0000.0000.0000.000
215A519SER00.041-0.06434.171-0.004-0.0040.0000.0000.0000.000
216A519SER0-0.0380.06636.5060.0020.0020.0000.0000.0000.000
217A520VAL00.111-0.07830.5490.0010.0010.0000.0000.0000.000
218A520VAL0-0.1010.08328.411-0.002-0.0020.0000.0000.0000.000
219A521TYR00.135-0.07331.3920.0060.0060.0000.0000.0000.000
220A521TYR0-0.1610.03632.1110.0030.0030.0000.0000.0000.000
221A522TYR00.073-0.07327.339-0.008-0.0080.0000.0000.0000.000
222A522TYR0-0.1150.04125.495-0.011-0.0110.0000.0000.0000.000
223A523ARG00.108-0.08426.3800.0130.0130.0000.0000.0000.000
224A523ARG10.7860.99526.8680.1370.1370.0000.0000.0000.000
225A524VAL00.000-0.10522.778-0.014-0.0140.0000.0000.0000.000
226A524VAL0-0.0430.11321.774-0.004-0.0040.0000.0000.0000.000
227A525TYR00.054-0.09521.5560.0240.0240.0000.0000.0000.000
228A525TYR0-0.1440.02821.9630.0070.0070.0000.0000.0000.000
229A526TYR00.085-0.10418.796-0.033-0.0330.0000.0000.0000.000
230A526TYR0-0.0310.10718.4420.0000.0000.0000.0000.0000.000
231A527THR0-0.015-0.09317.9820.0290.0290.0000.0000.0000.000
232A527THR0-0.0060.09317.274-0.011-0.0110.0000.0000.0000.000
233A528ARG0-0.003-0.08216.746-0.036-0.0360.0000.0000.0000.000
234A528ARG10.9420.97319.1720.0440.0440.0000.0000.0000.000