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: Z7V3N

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 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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1139428.29527
FMO2-HF: Nuclear repulsion 1088667.108648
FMO2-HF: Total energy -50761.186622
FMO2-MP2: Total energy -50911.449364


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.
-1.979-0.104-0.023-1.011-0.840.003
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 : 0.191 / q_NPA : 0.079
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].
4A369ILE0-0.0320.1263.919-0.2300.104-0.001-0.131-0.2020.000
5A370ALA00.094-0.1153.811-0.8870.654-0.022-0.880-0.6380.003
6A370ALA0-0.0590.1406.6980.0550.0550.0000.0000.0000.000
7A371ALA00.086-0.1246.818-0.283-0.2830.0000.0000.0000.000
8A371ALA0-0.0590.1349.6280.0120.0120.0000.0000.0000.000
9A372PRO0-0.069-0.1089.8600.1250.1250.0000.0000.0000.000
10A373SER00.0280.00713.012-0.005-0.0050.0000.0000.0000.000
11A373SER0-0.0230.08515.1250.0200.0200.0000.0000.0000.000
12A374MET00.118-0.09016.446-0.002-0.0020.0000.0000.0000.000
13A374MET0-0.1460.08318.354-0.014-0.0140.0000.0000.0000.000
14A375TRP00.013-0.09219.5740.0010.0010.0000.0000.0000.000
15A375TRP0-0.1080.07219.0750.0040.0040.0000.0000.0000.000
16A376THR00.028-0.10423.218-0.008-0.0080.0000.0000.0000.000
17A376THR00.0050.10625.7010.0000.0000.0000.0000.0000.000
18A377ARG00.098-0.09326.8100.0080.0080.0000.0000.0000.000
19A377ARG10.7581.01827.4800.0130.0130.0000.0000.0000.000
20A378PRO00.078-0.05730.088-0.004-0.0040.0000.0000.0000.000
21A379GLN00.009-0.00233.441-0.003-0.0030.0000.0000.0000.000
22A379GLN0-0.0240.11033.254-0.001-0.0010.0000.0000.0000.000
23A380ILE00.155-0.13033.8360.0010.0010.0000.0000.0000.000
24A380ILE0-0.0530.13333.5390.0000.0000.0000.0000.0000.000
25A381LYS00.035-0.09834.810-0.002-0.0020.0000.0000.0000.000
26A381LYS10.9011.05839.1750.0190.0190.0000.0000.0000.000
27A382ASP00.148-0.05837.121-0.001-0.0010.0000.0000.0000.000
28A382ASP-1-1.020-0.86936.071-0.004-0.0040.0000.0000.0000.000
29A383PHE00.078-0.09532.8570.0020.0020.0000.0000.0000.000
30A383PHE0-0.1270.07029.0810.0010.0010.0000.0000.0000.000
31A384LYS00.088-0.10734.024-0.001-0.0010.0000.0000.0000.000
32A384LYS10.7741.04934.5610.0360.0360.0000.0000.0000.000
33A385GLU00.096-0.10735.631-0.003-0.0030.0000.0000.0000.000
34A385GLU-1-1.016-0.82738.973-0.012-0.0120.0000.0000.0000.000
35A386LYS00.074-0.09335.1610.0010.0010.0000.0000.0000.000
36A386LYS10.8501.04131.6670.0050.0050.0000.0000.0000.000
37A387ILE00.001-0.15133.2590.0020.0020.0000.0000.0000.000
38A387ILE0-0.1060.11330.3970.0000.0000.0000.0000.0000.000
39A388GLN00.106-0.07834.214-0.002-0.0020.0000.0000.0000.000
40A388GLN0-0.1160.07637.6420.0010.0010.0000.0000.0000.000
41A389GLN00.024-0.09237.390-0.002-0.0020.0000.0000.0000.000
42A389GLN0-0.1000.08237.6300.0020.0020.0000.0000.0000.000
43A390ASP00.060-0.08434.5730.0020.0020.0000.0000.0000.000
44A390ASP-1-0.877-0.76732.666-0.030-0.0300.0000.0000.0000.000
45A391ALA00.097-0.09136.038-0.002-0.0020.0000.0000.0000.000
46A391ALA0-0.0840.10537.0200.0000.0000.0000.0000.0000.000
47A392ASP00.082-0.12532.958-0.002-0.0020.0000.0000.0000.000
48A392ASP-1-1.025-0.84032.149-0.040-0.0400.0000.0000.0000.000
49A393SER0-0.041-0.11630.636-0.007-0.0070.0000.0000.0000.000
50A393SER0-0.117-0.02431.1090.0010.0010.0000.0000.0000.000
51A394VAL00.086-0.13031.497-0.003-0.0030.0000.0000.0000.000
52A394VAL0-0.0820.12034.1030.0000.0000.0000.0000.0000.000
53A395ILE00.080-0.07431.3310.0020.0020.0000.0000.0000.000
54A395ILE0-0.0740.08828.180-0.002-0.0020.0000.0000.0000.000
55A396THR0-0.007-0.09932.7210.0010.0010.0000.0000.0000.000
56A396THR0-0.0230.07536.3700.0020.0020.0000.0000.0000.000
57A397VAL00.080-0.10031.9650.0010.0010.0000.0000.0000.000
58A397VAL0-0.1110.12530.0140.0000.0000.0000.0000.0000.000
59A398GLY00.038-0.09533.2010.0040.0040.0000.0000.0000.000
60A399ARG00.023-0.01634.573-0.005-0.0050.0000.0000.0000.000
61A399ARG10.8601.05838.2720.0530.0530.0000.0000.0000.000
62A400GLY00.023-0.07833.6690.0010.0010.0000.0000.0000.000
63A401GLU00.099-0.02132.199-0.006-0.0060.0000.0000.0000.000
64A401GLU-1-0.925-0.79231.355-0.076-0.0760.0000.0000.0000.000
65A402VAL00.054-0.12127.5900.0010.0010.0000.0000.0000.000
66A402VAL0-0.0970.09725.543-0.003-0.0030.0000.0000.0000.000
67A403VAL00.050-0.11027.743-0.004-0.0040.0000.0000.0000.000
68A403VAL0-0.0320.13927.5480.0010.0010.0000.0000.0000.000
69A404THR00.005-0.07723.724-0.003-0.0030.0000.0000.0000.000
70A404THR0-0.0180.05921.714-0.009-0.0090.0000.0000.0000.000
71A405VAL00.064-0.10823.1800.0080.0080.0000.0000.0000.000
72A405VAL0-0.0450.13123.3210.0010.0010.0000.0000.0000.000
73A406ARG00.098-0.08620.735-0.016-0.0160.0000.0000.0000.000
74A406ARG10.7621.01419.6710.1600.1600.0000.0000.0000.000
75A407VAL00.067-0.11919.7370.0180.0180.0000.0000.0000.000
76A407VAL0-0.0870.10919.2560.0010.0010.0000.0000.0000.000
77A408PRO0-0.002-0.11318.230-0.021-0.0210.0000.0000.0000.000
78A409THR00.0440.02715.0480.0160.0160.0000.0000.0000.000
79A409THR0-0.0410.07013.110-0.008-0.0080.0000.0000.0000.000
80A410HIS00.113-0.06216.4440.0010.0010.0000.0000.0000.000
81A410HIS0-0.0450.11718.8350.0070.0070.0000.0000.0000.000
82A411GLU00.040-0.13417.0720.0070.0070.0000.0000.0000.000
83A411GLU-1-1.006-0.84918.537-0.006-0.0060.0000.0000.0000.000
84A412GLU00.017-0.12218.0090.0180.0180.0000.0000.0000.000
85A412GLU-1-1.002-0.85420.9250.0520.0520.0000.0000.0000.000
86A413GLY0-0.055-0.14517.0070.0120.0120.0000.0000.0000.000
87A414SER00.0330.00213.094-0.020-0.0200.0000.0000.0000.000
88A414SER0-0.0450.06012.4180.0230.0230.0000.0000.0000.000
89A415TYR00.043-0.09712.1900.0040.0040.0000.0000.0000.000
90A415TYR0-0.0870.08411.8780.0420.0420.0000.0000.0000.000
91A416LEU00.144-0.09914.3200.0100.0100.0000.0000.0000.000
92A416LEU0-0.1060.10915.043-0.007-0.0070.0000.0000.0000.000
93A417PHE00.041-0.10516.3020.0030.0030.0000.0000.0000.000
94A417PHE0-0.0790.09617.8680.0030.0030.0000.0000.0000.000
95A418TRP00.062-0.09519.236-0.003-0.0030.0000.0000.0000.000
96A418TRP0-0.0530.09615.664-0.009-0.0090.0000.0000.0000.000
97A419GLU00.091-0.12221.7020.0030.0030.0000.0000.0000.000
98A419GLU-1-0.885-0.78324.828-0.012-0.0120.0000.0000.0000.000
99A420PHE00.063-0.08325.117-0.001-0.0010.0000.0000.0000.000
100A420PHE0-0.0870.07222.765-0.003-0.0030.0000.0000.0000.000
101A421ALA00.126-0.09127.2170.0000.0000.0000.0000.0000.000
102A421ALA0-0.0590.11230.5690.0020.0020.0000.0000.0000.000
103A422THR00.010-0.06230.305-0.001-0.0010.0000.0000.0000.000
104A422THR0-0.0670.02430.7260.0000.0000.0000.0000.0000.000
105A423ASP00.089-0.10333.1280.0030.0030.0000.0000.0000.000
106A423ASP-1-0.885-0.78037.712-0.037-0.0370.0000.0000.0000.000
107A424ASN00.110-0.06636.8250.0020.0020.0000.0000.0000.000
108A424ASN0-0.1310.04339.0970.0020.0020.0000.0000.0000.000
109A425TYR00.104-0.04935.6520.0020.0020.0000.0000.0000.000
110A425TYR0-0.1070.04035.7050.0010.0010.0000.0000.0000.000
111A426ASP00.159-0.03731.6660.0020.0020.0000.0000.0000.000
112A426ASP-1-0.817-0.77330.589-0.080-0.0800.0000.0000.0000.000
113A427ILE00.002-0.12629.5300.0030.0030.0000.0000.0000.000
114A427ILE0-0.0540.11327.6310.0020.0020.0000.0000.0000.000
115A428GLY00.007-0.09226.148-0.002-0.0020.0000.0000.0000.000
116A429PHE00.081-0.01623.2890.0030.0030.0000.0000.0000.000
117A429PHE0-0.0650.10819.9790.0000.0000.0000.0000.0000.000
118A430GLY00.038-0.09619.237-0.004-0.0040.0000.0000.0000.000
119A431VAL00.031-0.01616.4560.0270.0270.0000.0000.0000.000
120A431VAL0-0.0850.10014.9880.0010.0010.0000.0000.0000.000
121A432TYR00.110-0.06914.107-0.053-0.0530.0000.0000.0000.000
122A432TYR0-0.0670.08414.7040.0310.0310.0000.0000.0000.000
123A433PHE00.111-0.10011.5000.0790.0790.0000.0000.0000.000
124A433PHE0-0.0800.1099.900-0.011-0.0110.0000.0000.0000.000
125A434GLU00.140-0.09612.116-0.078-0.0780.0000.0000.0000.000
126A434GLU-1-0.951-0.82115.642-0.199-0.1990.0000.0000.0000.000
127A435TRP00.042-0.12411.5550.0330.0330.0000.0000.0000.000
128A435TRP0-0.1360.0756.2310.1250.1250.0000.0000.0000.000
129A436THR0-0.112-0.16412.6190.0320.0320.0000.0000.0000.000
130A436THR00.0900.06316.2510.0050.0050.0000.0000.0000.000
131A474PRO00.014-0.00216.7060.0110.0110.0000.0000.0000.000
132A475LEU00.129-0.01112.4610.0050.0050.0000.0000.0000.000
133A475LEU0-0.1030.1119.3840.0150.0150.0000.0000.0000.000
134A476LEU00.022-0.13312.8300.0000.0000.0000.0000.0000.000
135A476LEU0-0.0710.10514.1160.0090.0090.0000.0000.0000.000
136A477ASP00.095-0.0919.1780.0110.0110.0000.0000.0000.000
137A477ASP-1-0.934-0.7967.561-1.204-1.2040.0000.0000.0000.000
138A478GLU00.120-0.14810.5590.0730.0730.0000.0000.0000.000
139A478GLU-1-1.002-0.83412.776-0.412-0.4120.0000.0000.0000.000
140A479ILE00.032-0.10111.115-0.102-0.1020.0000.0000.0000.000
141A479ILE0-0.1390.0789.7840.0100.0100.0000.0000.0000.000
142A480VAL00.091-0.12712.1150.0060.0060.0000.0000.0000.000
143A480VAL0-0.1340.09515.0460.0090.0090.0000.0000.0000.000
144A481PRO00.059-0.04015.1350.0200.0200.0000.0000.0000.000
145A482VAL00.082-0.04617.4980.0260.0260.0000.0000.0000.000
146A482VAL0-0.0800.12119.8870.0020.0020.0000.0000.0000.000
147A483TYR00.069-0.10121.0930.0020.0020.0000.0000.0000.000
148A483TYR0-0.0900.10219.101-0.003-0.0030.0000.0000.0000.000
149A484ARG00.066-0.09423.4950.0000.0000.0000.0000.0000.000
150A484ARG10.8191.03427.7020.0910.0910.0000.0000.0000.000
151A485ARG00.059-0.10526.190-0.002-0.0020.0000.0000.0000.000
152A485ARG10.8191.05519.7360.1560.1560.0000.0000.0000.000
153A486ASP00.087-0.10027.144-0.001-0.0010.0000.0000.0000.000
154A486ASP-1-0.939-0.80330.062-0.068-0.0680.0000.0000.0000.000
155A487CYS00.148-0.07929.1270.0070.0070.0000.0000.0000.000
156A487CYS0-0.1820.05728.102-0.004-0.0040.0000.0000.0000.000
157A488HIS00.056-0.09230.0600.0030.0030.0000.0000.0000.000
158A488HIS0-0.0740.08333.339-0.002-0.0020.0000.0000.0000.000
159A489GLU00.040-0.16132.9780.0040.0040.0000.0000.0000.000
160A489GLU-1-1.007-0.82433.571-0.044-0.0440.0000.0000.0000.000
161A490GLU0-0.003-0.16231.2740.0050.0050.0000.0000.0000.000
162A490GLU-1-0.950-0.81930.578-0.027-0.0270.0000.0000.0000.000
163A491VAL00.143-0.08929.577-0.008-0.0080.0000.0000.0000.000
164A491VAL0-0.1460.07827.7900.0010.0010.0000.0000.0000.000
165A492TYR00.099-0.09425.6880.0080.0080.0000.0000.0000.000
166A492TYR0-0.1130.09924.069-0.003-0.0030.0000.0000.0000.000
167A493ALA00.083-0.12523.133-0.006-0.0060.0000.0000.0000.000
168A493ALA0-0.0820.11323.3620.0030.0030.0000.0000.0000.000
169A494GLY0-0.004-0.10619.068-0.004-0.0040.0000.0000.0000.000
170A495SER0-0.0230.01216.800-0.002-0.0020.0000.0000.0000.000
171A495SER0-0.0190.06316.3830.0040.0040.0000.0000.0000.000
172A496HIS00.138-0.09912.7630.0040.0040.0000.0000.0000.000
173A496HIS0-0.0540.1018.6770.1100.1100.0000.0000.0000.000
174A497GLN00.110-0.0719.654-0.005-0.0050.0000.0000.0000.000
175A497GLN0-0.0960.0877.2150.1950.1950.0000.0000.0000.000
176A498TYR00.037-0.1328.956-0.155-0.1550.0000.0000.0000.000
177A498TYR0-0.0750.12110.6700.0070.0070.0000.0000.0000.000
178A499PRO0-0.036-0.0815.9840.1070.1070.0000.0000.0000.000
179A500GLY00.024-0.0116.3990.0340.0340.0000.0000.0000.000
180A501ARG00.1070.0119.1690.0240.0240.0000.0000.0000.000
181A501ARG10.8401.07113.5340.0450.0450.0000.0000.0000.000
182A502GLY00.024-0.10312.846-0.030-0.0300.0000.0000.0000.000
183A503VAL00.045-0.01314.0650.0380.0380.0000.0000.0000.000
184A503VAL0-0.1040.09517.3500.0060.0060.0000.0000.0000.000
185A504TYR00.120-0.07415.322-0.042-0.0420.0000.0000.0000.000
186A504TYR0-0.0830.08911.4550.0180.0180.0000.0000.0000.000
187A505LEU00.078-0.09816.2270.0410.0410.0000.0000.0000.000
188A505LEU0-0.1130.09016.2500.0040.0040.0000.0000.0000.000
189A506LEU00.078-0.11818.440-0.029-0.0290.0000.0000.0000.000
190A506LEU0-0.0890.12418.5060.0030.0030.0000.0000.0000.000
191A507LYS00.126-0.10920.5790.0210.0210.0000.0000.0000.000
192A507LYS10.8131.05419.8920.1900.1900.0000.0000.0000.000
193A508PHE00.080-0.07622.444-0.004-0.0040.0000.0000.0000.000
194A508PHE0-0.1080.09224.8720.0020.0020.0000.0000.0000.000
195A509ASP00.174-0.11325.8280.0090.0090.0000.0000.0000.000
196A509ASP-1-0.915-0.78925.197-0.139-0.1390.0000.0000.0000.000
197A510ASN00.082-0.14827.0700.0030.0030.0000.0000.0000.000
198A510ASN0-0.1290.08731.2570.0010.0010.0000.0000.0000.000
199A511SER00.044-0.09929.6570.0100.0100.0000.0000.0000.000
200A511SER0-0.0350.09328.670-0.001-0.0010.0000.0000.0000.000
201A512TYR00.054-0.09131.2120.0040.0040.0000.0000.0000.000
202A512TYR0-0.1570.05429.679-0.001-0.0010.0000.0000.0000.000
203A513SER00.019-0.10532.7310.0040.0040.0000.0000.0000.000
204A513SER0-0.1000.06034.6640.0020.0020.0000.0000.0000.000
205A514LEU00.106-0.11635.576-0.001-0.0010.0000.0000.0000.000
206A514LEU0-0.0520.13737.9320.0010.0010.0000.0000.0000.000
207A515TRP00.046-0.12038.7400.0010.0010.0000.0000.0000.000
208A515TRP0-0.0870.09741.4550.0010.0010.0000.0000.0000.000
209A516ARG00.019-0.13938.6630.0030.0030.0000.0000.0000.000
210A516ARG10.9011.09837.7060.0470.0470.0000.0000.0000.000
211A517SER00.073-0.03736.596-0.005-0.0050.0000.0000.0000.000
212A517SER00.0160.07937.4700.0000.0000.0000.0000.0000.000
213A518LYS00.010-0.13133.5660.0050.0050.0000.0000.0000.000
214A518LYS10.7601.02332.7450.0730.0730.0000.0000.0000.000
215A519SER00.030-0.07334.171-0.004-0.0040.0000.0000.0000.000
216A519SER0-0.0380.08236.4600.0000.0000.0000.0000.0000.000
217A520VAL00.116-0.09530.5400.0040.0040.0000.0000.0000.000
218A520VAL0-0.0860.08928.413-0.001-0.0010.0000.0000.0000.000
219A521TYR00.111-0.07631.3700.0000.0000.0000.0000.0000.000
220A521TYR0-0.1750.02232.1090.0020.0020.0000.0000.0000.000
221A522TYR00.067-0.08527.3230.0000.0000.0000.0000.0000.000
222A522TYR0-0.0810.07525.416-0.006-0.0060.0000.0000.0000.000
223A523ARG00.121-0.09126.3790.0020.0020.0000.0000.0000.000
224A523ARG10.8251.04926.9090.0260.0260.0000.0000.0000.000
225A524VAL00.003-0.12222.7590.0000.0000.0000.0000.0000.000
226A524VAL0-0.0270.12021.783-0.003-0.0030.0000.0000.0000.000
227A525TYR00.047-0.09821.4250.0040.0040.0000.0000.0000.000
228A525TYR0-0.1310.05821.6880.0040.0040.0000.0000.0000.000
229A526TYR00.084-0.09318.662-0.016-0.0160.0000.0000.0000.000
230A526TYR0-0.0180.12218.330-0.003-0.0030.0000.0000.0000.000
231A527THR0-0.001-0.09817.8420.0000.0000.0000.0000.0000.000
232A527THR0-0.0090.08917.0660.0030.0030.0000.0000.0000.000
233A528ARG0-0.005-0.07216.6170.0220.0220.0000.0000.0000.000
234A528ARG10.9781.00719.152-0.097-0.0970.0000.0000.0000.000