FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 179MZ

Calculation Name: 5LZ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LZ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H3P7

Base Structure: X-ray

Registration Date: 2023-06-22

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

DOI:


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 124
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1139453.61948
FMO2-HF: Nuclear repulsion 1088667.108648
FMO2-HF: Total energy -50786.510832
FMO2-MP2: Total energy -50937.351727


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(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.
-2.1180.560.068-1.302-1.445-0.004
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 : -0.023 / q_NPA : -0.032
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].
3A370ALA00.0140.0213.169-0.9361.7420.068-1.302-1.445-0.004
4A371ALA00.0290.0095.467-0.292-0.2920.0000.0000.0000.000
5A372PRO0-0.0180.0057.8930.0030.0030.0000.0000.0000.000
6A373SER0-0.026-0.00611.4020.0600.0600.0000.0000.0000.000
7A374MET0-0.045-0.03014.618-0.037-0.0370.0000.0000.0000.000
8A375TRP0-0.042-0.01117.6180.0170.0170.0000.0000.0000.000
9A376THR00.0270.00821.350-0.009-0.0090.0000.0000.0000.000
10A377ARG10.8530.92325.0290.0080.0080.0000.0000.0000.000
11A378PRO00.0950.05328.396-0.005-0.0050.0000.0000.0000.000
12A379GLN0-0.0050.01031.747-0.003-0.0030.0000.0000.0000.000
13A380ILE00.039-0.00832.260-0.004-0.0040.0000.0000.0000.000
14A381LYS10.9340.95233.490-0.002-0.0020.0000.0000.0000.000
15A382ASP-1-0.870-0.92535.086-0.007-0.0070.0000.0000.0000.000
16A383PHE0-0.042-0.02528.371-0.002-0.0020.0000.0000.0000.000
17A384LYS10.8700.94733.0860.0100.0100.0000.0000.0000.000
18A385GLU-1-0.888-0.92834.805-0.013-0.0130.0000.0000.0000.000
19A386LYS10.8990.94931.1210.0140.0140.0000.0000.0000.000
20A387ILE0-0.080-0.03629.929-0.003-0.0030.0000.0000.0000.000
21A388GLN00.002-0.01033.816-0.002-0.0020.0000.0000.0000.000
22A389GLN0-0.081-0.02137.001-0.002-0.0020.0000.0000.0000.000
23A390ASP-1-0.833-0.86032.666-0.059-0.0590.0000.0000.0000.000
24A391ALA0-0.0130.00135.9300.0010.0010.0000.0000.0000.000
25A392ASP-1-0.899-0.94632.062-0.065-0.0650.0000.0000.0000.000
26A393SER0-0.105-0.11430.422-0.007-0.0070.0000.0000.0000.000
27A394VAL0-0.017-0.02331.0990.0030.0030.0000.0000.0000.000
28A395ILE0-0.0130.01727.535-0.001-0.0010.0000.0000.0000.000
29A396THR0-0.024-0.02531.9550.0060.0060.0000.0000.0000.000
30A397VAL0-0.0060.01628.751-0.002-0.0020.0000.0000.0000.000
31A398GLY00.0480.00931.9490.0060.0060.0000.0000.0000.000
32A399ARG10.8790.93233.0520.0260.0260.0000.0000.0000.000
33A400GLY00.0230.02431.879-0.002-0.0020.0000.0000.0000.000
34A401GLU-1-0.877-0.90630.136-0.062-0.0620.0000.0000.0000.000
35A402VAL0-0.011-0.02524.0820.0010.0010.0000.0000.0000.000
36A403VAL00.0200.02626.706-0.006-0.0060.0000.0000.0000.000
37A404THR0-0.029-0.01820.923-0.005-0.0050.0000.0000.0000.000
38A405VAL00.0330.02022.4460.0010.0010.0000.0000.0000.000
39A406ARG10.8350.92019.6710.2100.2100.0000.0000.0000.000
40A407VAL00.0180.00619.2560.0150.0150.0000.0000.0000.000
41A408PRO0-0.003-0.00918.230-0.034-0.0340.0000.0000.0000.000
42A409THR0-0.0290.00313.1100.0020.0020.0000.0000.0000.000
43A410HIS00.0640.03116.444-0.001-0.0010.0000.0000.0000.000
44A411GLU-1-0.966-0.98917.072-0.241-0.2410.0000.0000.0000.000
45A412GLU-1-0.944-0.96618.009-0.107-0.1070.0000.0000.0000.000
46A413GLY0-0.054-0.03017.0070.0320.0320.0000.0000.0000.000
47A414SER0-0.030-0.04712.418-0.029-0.0290.0000.0000.0000.000
48A415TYR0-0.0200.00111.878-0.017-0.0170.0000.0000.0000.000
49A416LEU0-0.0030.00414.3200.0040.0040.0000.0000.0000.000
50A417PHE0-0.001-0.01016.3020.0300.0300.0000.0000.0000.000
51A418TRP0-0.008-0.00714.621-0.022-0.0220.0000.0000.0000.000
52A419GLU-1-0.813-0.90321.142-0.009-0.0090.0000.0000.0000.000
53A420PHE0-0.022-0.03321.637-0.010-0.0100.0000.0000.0000.000
54A421ALA00.0280.01126.3440.0080.0080.0000.0000.0000.000
55A422THR0-0.003-0.00929.239-0.005-0.0050.0000.0000.0000.000
56A423ASP-1-0.799-0.89932.022-0.017-0.0170.0000.0000.0000.000
57A424ASN0-0.033-0.01735.6840.0040.0040.0000.0000.0000.000
58A425TYR0-0.026-0.01734.0080.0010.0010.0000.0000.0000.000
59A426ASP-1-0.696-0.80728.872-0.014-0.0140.0000.0000.0000.000
60A427ILE0-0.018-0.01826.173-0.003-0.0030.0000.0000.0000.000
61A428GLY0-0.0020.01024.2910.0040.0040.0000.0000.0000.000
62A429PHE00.0230.00018.812-0.006-0.0060.0000.0000.0000.000
63A430GLY00.0460.00717.6380.0160.0160.0000.0000.0000.000
64A431VAL0-0.067-0.02314.127-0.008-0.0080.0000.0000.0000.000
65A432TYR00.0270.02112.8480.0020.0020.0000.0000.0000.000
66A433PHE0-0.005-0.0089.9000.0160.0160.0000.0000.0000.000
67A434GLU-1-0.810-0.91211.842-0.311-0.3110.0000.0000.0000.000
68A435TRP0-0.053-0.0336.2310.0180.0180.0000.0000.0000.000
69A436THR0-0.026-0.01312.6190.0800.0800.0000.0000.0000.000
70A474PRO00.0220.00916.5590.0020.0020.0000.0000.0000.000
71A475LEU0-0.029-0.0139.0270.0340.0340.0000.0000.0000.000
72A476LEU0-0.005-0.01412.248-0.040-0.0400.0000.0000.0000.000
73A477ASP-1-0.822-0.8927.050-0.909-0.9090.0000.0000.0000.000
74A478GLU-1-0.940-0.9949.349-0.066-0.0660.0000.0000.0000.000
75A479ILE0-0.058-0.0098.6340.0210.0210.0000.0000.0000.000
76A480VAL0-0.042-0.03310.6360.0800.0800.0000.0000.0000.000
77A481PRO00.0600.06013.296-0.020-0.0200.0000.0000.0000.000
78A482VAL0-0.017-0.03015.5500.0100.0100.0000.0000.0000.000
79A483TYR00.0010.01317.1960.0100.0100.0000.0000.0000.000
80A484ARG10.8420.91021.6030.0040.0040.0000.0000.0000.000
81A485ARG10.9030.96618.0520.0140.0140.0000.0000.0000.000
82A486ASP-1-0.832-0.90625.5170.0040.0040.0000.0000.0000.000
83A487CYS0-0.054-0.02526.7230.0000.0000.0000.0000.0000.000
84A488HIS0-0.018-0.00728.595-0.005-0.0050.0000.0000.0000.000
85A489GLU-1-0.951-0.97931.3370.0100.0100.0000.0000.0000.000
86A490GLU-1-0.955-0.98228.6250.0280.0280.0000.0000.0000.000
87A491VAL0-0.051-0.02126.548-0.005-0.0050.0000.0000.0000.000
88A492TYR00.0290.01322.4220.0070.0070.0000.0000.0000.000
89A493ALA0-0.015-0.01721.973-0.011-0.0110.0000.0000.0000.000
90A494GLY00.0180.01117.7730.0170.0170.0000.0000.0000.000
91A495SER0-0.051-0.01015.406-0.012-0.0120.0000.0000.0000.000
92A496HIS00.051-0.0067.9020.0610.0610.0000.0000.0000.000
93A497GLN0-0.0040.0127.2150.0320.0320.0000.0000.0000.000
94A498TYR0-0.009-0.0118.956-0.130-0.1300.0000.0000.0000.000
95A499PRO00.0070.0205.984-0.039-0.0390.0000.0000.0000.000
96A500GLY00.020-0.0056.399-0.313-0.3130.0000.0000.0000.000
97A501ARG10.9250.9729.1690.5280.5280.0000.0000.0000.000
98A502GLY00.0470.01112.846-0.039-0.0390.0000.0000.0000.000
99A503VAL0-0.053-0.02214.0650.0590.0590.0000.0000.0000.000
100A504TYR00.0200.01211.455-0.030-0.0300.0000.0000.0000.000
101A505LEU0-0.032-0.01815.7410.0460.0460.0000.0000.0000.000
102A506LEU00.0310.00617.4850.0060.0060.0000.0000.0000.000
103A507LYS10.8780.94718.6000.1450.1450.0000.0000.0000.000
104A508PHE00.0470.02021.1570.0100.0100.0000.0000.0000.000
105A509ASP-1-0.850-0.92023.430-0.056-0.0560.0000.0000.0000.000
106A510ASN00.017-0.03425.3710.0110.0110.0000.0000.0000.000
107A511SER0-0.041-0.00926.7070.0060.0060.0000.0000.0000.000
108A512TYR0-0.067-0.03127.7700.0020.0020.0000.0000.0000.000
109A513SER0-0.086-0.04130.6800.0060.0060.0000.0000.0000.000
110A514LEU00.0610.01433.596-0.003-0.0030.0000.0000.0000.000
111A515TRP0-0.012-0.02236.770-0.001-0.0010.0000.0000.0000.000
112A516ARG10.8890.95935.9470.0150.0150.0000.0000.0000.000
113A517SER00.0760.03635.075-0.001-0.0010.0000.0000.0000.000
114A518LYS10.7860.89131.1810.0300.0300.0000.0000.0000.000
115A519SER00.0280.01632.962-0.004-0.0040.0000.0000.0000.000
116A520VAL0-0.024-0.01027.4770.0040.0040.0000.0000.0000.000
117A521TYR0-0.041-0.04930.526-0.003-0.0030.0000.0000.0000.000
118A522TYR0-0.023-0.02325.058-0.001-0.0010.0000.0000.0000.000
119A523ARG10.9220.96425.9570.0520.0520.0000.0000.0000.000
120A524VAL0-0.0030.00821.6830.0020.0020.0000.0000.0000.000
121A525TYR0-0.040-0.01921.4250.0050.0050.0000.0000.0000.000
122A526TYR00.020-0.00518.330-0.022-0.0220.0000.0000.0000.000
123A527THR00.0120.01817.0660.0260.0260.0000.0000.0000.000
124A528ARG10.9591.01016.6170.0670.0670.0000.0000.0000.000