Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: V5141

Calculation Name: 4ATZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ATZ

Chain ID: A

ChEMBL ID:

UniProt ID: P11818

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1869380.704569
FMO2-HF: Nuclear repulsion 1800012.015196
FMO2-HF: Total energy -69368.689373
FMO2-MP2: Total energy -69572.797644


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:400:ASN)


Summations of interaction energy for fragment #1(A:400:ASN)
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.
-2.9661.4850.72-1.841-3.330.012
Interaction energy analysis for fragmet #1(A:400:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.030
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].
3A402LYS10.8760.9253.474-4.494-2.2200.051-0.965-1.3600.004
4A403LEU0-0.077-0.0262.774-2.261-0.2110.671-0.872-1.8490.008
5A404THR0-0.009-0.0125.0860.5410.658-0.001-0.004-0.1120.000
6A405LEU00.0020.0317.712-0.296-0.2960.0000.0000.0000.000
7A406TRP00.0360.00710.6540.0740.0740.0000.0000.0000.000
8A407THR00.0220.01913.396-0.049-0.0490.0000.0000.0000.000
9A408THR0-0.043-0.02013.553-0.061-0.0610.0000.0000.0000.000
10A409PRO0-0.001-0.02013.0230.0410.0410.0000.0000.0000.000
11A410ALA0-0.010-0.00415.6620.0110.0110.0000.0000.0000.000
12A411PRO0-0.0120.03818.536-0.034-0.0340.0000.0000.0000.000
13A412SER00.0060.00320.397-0.003-0.0030.0000.0000.0000.000
14A413PRO0-0.030-0.03223.6580.0130.0130.0000.0000.0000.000
15A414ASN00.0190.02620.654-0.013-0.0130.0000.0000.0000.000
16A415CYS0-0.0210.00324.6530.0120.0120.0000.0000.0000.000
17A416ARG10.8390.92326.556-0.111-0.1110.0000.0000.0000.000
18A417LEU0-0.019-0.01628.5430.0080.0080.0000.0000.0000.000
19A418ASN0-0.058-0.03131.729-0.004-0.0040.0000.0000.0000.000
20A419ALA0-0.048-0.03534.323-0.006-0.0060.0000.0000.0000.000
21A420GLU-1-0.839-0.92330.6510.1070.1070.0000.0000.0000.000
22A421LYS10.8640.92326.543-0.095-0.0950.0000.0000.0000.000
23A422ASP-1-0.709-0.83729.9570.1120.1120.0000.0000.0000.000
24A423ALA00.0550.03528.072-0.001-0.0010.0000.0000.0000.000
25A424LYS10.8400.91523.765-0.117-0.1170.0000.0000.0000.000
26A425LEU00.0550.01321.2100.0060.0060.0000.0000.0000.000
27A426THR0-0.0070.00017.510-0.017-0.0170.0000.0000.0000.000
28A427LEU00.0210.00216.9700.0230.0230.0000.0000.0000.000
29A428VAL0-0.013-0.01711.323-0.037-0.0370.0000.0000.0000.000
30A429LEU00.0050.01112.5890.0350.0350.0000.0000.0000.000
31A430THR00.0250.0026.464-0.106-0.1060.0000.0000.0000.000
32A431LYS10.7930.8827.746-1.130-1.1300.0000.0000.0000.000
33A432CYS0-0.047-0.0147.2020.8980.8980.0000.0000.0000.000
34A433GLY00.0320.0079.138-0.377-0.3770.0000.0000.0000.000
35A434SER00.0080.00511.1640.0130.0130.0000.0000.0000.000
36A435GLN00.0210.01713.293-0.116-0.1160.0000.0000.0000.000
37A436ILE0-0.0300.01011.7870.2170.2170.0000.0000.0000.000
38A437LEU0-0.0090.00111.027-0.162-0.1620.0000.0000.0000.000
39A438ALA00.0320.00512.4570.1080.1080.0000.0000.0000.000
40A439THR0-0.046-0.02614.726-0.055-0.0550.0000.0000.0000.000
41A440VAL00.0210.01216.841-0.010-0.0100.0000.0000.0000.000
42A441SER0-0.018-0.01119.881-0.003-0.0030.0000.0000.0000.000
43A442VAL00.0130.00922.6790.0020.0020.0000.0000.0000.000
44A443LEU00.0060.01225.313-0.005-0.0050.0000.0000.0000.000
45A444ALA0-0.0020.00227.735-0.003-0.0030.0000.0000.0000.000
46A445VAL0-0.061-0.04328.846-0.004-0.0040.0000.0000.0000.000
47A446LYS10.8540.92531.719-0.091-0.0910.0000.0000.0000.000
48A447GLY00.010-0.00534.8040.0060.0060.0000.0000.0000.000
49A448SER00.0130.01537.5870.0010.0010.0000.0000.0000.000
50A449LEU00.0270.00933.2710.0010.0010.0000.0000.0000.000
51A450ALA0-0.0240.00534.0700.0060.0060.0000.0000.0000.000
52A451PRO00.0290.00736.168-0.005-0.0050.0000.0000.0000.000
53A452ILE0-0.019-0.00835.594-0.001-0.0010.0000.0000.0000.000
54A453SER0-0.024-0.00939.011-0.006-0.0060.0000.0000.0000.000
55A454GLY00.004-0.00842.4400.0030.0030.0000.0000.0000.000
56A455THR00.018-0.00644.5530.0000.0000.0000.0000.0000.000
57A456VAL0-0.0050.01238.1750.0030.0030.0000.0000.0000.000
58A457GLN00.006-0.01639.1170.0000.0000.0000.0000.0000.000
59A458SER00.0390.02835.6900.0040.0040.0000.0000.0000.000
60A459ALA0-0.032-0.00732.379-0.007-0.0070.0000.0000.0000.000
61A460HIS00.005-0.00230.6870.0160.0160.0000.0000.0000.000
62A461LEU00.0320.02624.914-0.009-0.0090.0000.0000.0000.000
63A462ILE0-0.039-0.02427.0260.0180.0180.0000.0000.0000.000
64A463ILE00.0020.01321.104-0.014-0.0140.0000.0000.0000.000
65A464ARG10.8840.91824.029-0.150-0.1500.0000.0000.0000.000
66A465PHE0-0.006-0.01518.5070.0000.0000.0000.0000.0000.000
67A466ASP-1-0.714-0.85021.1860.2050.2050.0000.0000.0000.000
68A467GLU-1-0.887-0.96221.5650.1960.1960.0000.0000.0000.000
69A468ASN0-0.089-0.04918.8500.0140.0140.0000.0000.0000.000
70A469GLY0-0.022-0.02817.1790.0370.0370.0000.0000.0000.000
71A470VAL0-0.010-0.01317.4280.0270.0270.0000.0000.0000.000
72A471LEU0-0.044-0.01319.101-0.011-0.0110.0000.0000.0000.000
73A472LEU00.003-0.01121.341-0.014-0.0140.0000.0000.0000.000
74A473ASN0-0.017-0.01724.882-0.018-0.0180.0000.0000.0000.000
75A474ASN0-0.023-0.00725.2130.0120.0120.0000.0000.0000.000
76A475SER00.0110.01926.302-0.004-0.0040.0000.0000.0000.000
77A476PHE0-0.015-0.02327.1780.0100.0100.0000.0000.0000.000
78A477LEU00.0040.00519.9340.0070.0070.0000.0000.0000.000
79A478ASP-1-0.818-0.89723.4630.0950.0950.0000.0000.0000.000
80A479PRO00.0240.00620.4470.0110.0110.0000.0000.0000.000
81A480GLU-1-0.948-0.97519.3020.0520.0520.0000.0000.0000.000
82A481TYR0-0.045-0.01718.212-0.019-0.0190.0000.0000.0000.000
83A482TRP00.0280.00016.1880.0420.0420.0000.0000.0000.000
84A483ASN00.0210.00513.4330.0090.0090.0000.0000.0000.000
85A484PHE0-0.045-0.0058.1970.0770.0770.0000.0000.0000.000
86A485ARG10.8330.8964.9691.1631.1630.0000.0000.0000.000
87A486ASN0-0.093-0.0727.0460.1350.1350.0000.0000.0000.000
88A487GLY00.0360.0389.047-0.009-0.0090.0000.0000.0000.000
89A488ASP-1-0.834-0.89410.1600.0960.0960.0000.0000.0000.000
90A489LEU00.020-0.02512.1620.0700.0700.0000.0000.0000.000
91A490THR0-0.061-0.04113.4990.0330.0330.0000.0000.0000.000
92A491GLU-1-0.829-0.8935.6831.8601.870-0.0010.000-0.0090.000
93A492GLY00.017-0.0027.9030.4830.4830.0000.0000.0000.000
94A493ASN0-0.002-0.0029.346-0.164-0.1640.0000.0000.0000.000
95A494ALA00.0500.02011.6230.0830.0830.0000.0000.0000.000
96A495VAL00.0870.05213.6070.0280.0280.0000.0000.0000.000
97A496GLY0-0.0250.00112.008-0.001-0.0010.0000.0000.0000.000
98A497PHE00.009-0.0117.7830.1060.1060.0000.0000.0000.000
99A498MET0-0.0380.03213.564-0.039-0.0390.0000.0000.0000.000
100A499PRO00.002-0.00417.2970.0310.0310.0000.0000.0000.000
101A500ASN00.0020.01019.748-0.073-0.0730.0000.0000.0000.000
102A501LEU00.0470.02521.067-0.018-0.0180.0000.0000.0000.000
103A502SER0-0.029-0.02024.179-0.023-0.0230.0000.0000.0000.000
104A503ALA0-0.113-0.05923.443-0.006-0.0060.0000.0000.0000.000
105A504TYR0-0.014-0.01321.0210.0070.0070.0000.0000.0000.000
106A505PRO00.0320.01526.0420.0060.0060.0000.0000.0000.000
107A506LYS10.8650.95526.748-0.190-0.1900.0000.0000.0000.000
108A507SER0-0.076-0.04729.647-0.013-0.0130.0000.0000.0000.000
109A508HIS00.0440.03233.3490.0060.0060.0000.0000.0000.000
110A509GLY0-0.0180.00036.088-0.002-0.0020.0000.0000.0000.000
111A510LYS10.9850.99334.403-0.136-0.1360.0000.0000.0000.000
112A511THR00.0520.01930.368-0.005-0.0050.0000.0000.0000.000
113A512ALA0-0.016-0.01531.2780.0100.0100.0000.0000.0000.000
114A513LYS10.9530.97426.150-0.249-0.2490.0000.0000.0000.000
115A514SER00.0260.01826.4810.0210.0210.0000.0000.0000.000
116A515ASN0-0.037-0.00526.6300.0060.0060.0000.0000.0000.000
117A516ILE0-0.0090.00921.8960.0040.0040.0000.0000.0000.000
118A517VAL0-0.007-0.01226.052-0.004-0.0040.0000.0000.0000.000
119A518SER0-0.033-0.00326.558-0.006-0.0060.0000.0000.0000.000
120A519GLN00.0330.02628.557-0.009-0.0090.0000.0000.0000.000
121A520VAL0-0.022-0.00125.8340.0180.0180.0000.0000.0000.000
122A521TYR00.003-0.01928.613-0.012-0.0120.0000.0000.0000.000
123A522LEU00.0310.02729.9680.0080.0080.0000.0000.0000.000
124A523ASN0-0.061-0.04331.004-0.003-0.0030.0000.0000.0000.000
125A524GLY0-0.022-0.00729.1250.0000.0000.0000.0000.0000.000
126A525ASP-1-0.820-0.88529.7890.1250.1250.0000.0000.0000.000
127A526LYS10.9720.97033.104-0.138-0.1380.0000.0000.0000.000
128A527THR0-0.112-0.07633.998-0.002-0.0020.0000.0000.0000.000
129A528LYS10.8290.92035.316-0.117-0.1170.0000.0000.0000.000
130A529PRO00.0010.01233.3300.0090.0090.0000.0000.0000.000
131A530VAL00.0130.01631.643-0.012-0.0120.0000.0000.0000.000
132A531THR0-0.040-0.02331.3650.0150.0150.0000.0000.0000.000
133A532LEU0-0.0080.00724.521-0.005-0.0050.0000.0000.0000.000
134A533THR00.002-0.00528.4390.0090.0090.0000.0000.0000.000
135A534ILE0-0.006-0.00222.103-0.007-0.0070.0000.0000.0000.000
136A535THR0-0.028-0.02825.833-0.004-0.0040.0000.0000.0000.000
137A536LEU0-0.037-0.00921.3260.0070.0070.0000.0000.0000.000
138A537ASN0-0.012-0.04522.784-0.011-0.0110.0000.0000.0000.000
139A538GLY00.0000.01225.954-0.015-0.0150.0000.0000.0000.000
140A539THR0-0.070-0.04028.780-0.008-0.0080.0000.0000.0000.000
141A540GLN00.0470.00830.4020.0030.0030.0000.0000.0000.000
142A541GLU-1-0.762-0.82430.3070.1620.1620.0000.0000.0000.000
143A542THR00.008-0.00134.008-0.004-0.0040.0000.0000.0000.000
144A543GLY00.0000.00237.6640.0010.0010.0000.0000.0000.000
145A544ASP-1-0.885-0.95239.1190.0770.0770.0000.0000.0000.000
146A545THR0-0.111-0.04033.4880.0010.0010.0000.0000.0000.000
147A546THR00.0250.00330.537-0.002-0.0020.0000.0000.0000.000
148A547PRO00.0230.01230.6100.0080.0080.0000.0000.0000.000
149A548SER0-0.046-0.02725.9100.0070.0070.0000.0000.0000.000
150A549ALA0-0.016-0.00523.535-0.008-0.0080.0000.0000.0000.000
151A550TYR00.001-0.00420.8280.0140.0140.0000.0000.0000.000
152A551SER0-0.017-0.03123.442-0.012-0.0120.0000.0000.0000.000
153A552MET0-0.0110.01618.0570.0190.0190.0000.0000.0000.000
154A553SER00.0090.01223.269-0.015-0.0150.0000.0000.0000.000
155A554PHE00.0080.00820.6740.0190.0190.0000.0000.0000.000
156A555SER00.007-0.00626.873-0.023-0.0230.0000.0000.0000.000
157A556TRP00.005-0.00625.5450.0060.0060.0000.0000.0000.000
158A557ASP-1-0.795-0.88631.5710.1250.1250.0000.0000.0000.000
159A558TRP0-0.039-0.01433.9280.0110.0110.0000.0000.0000.000
160A559SER0-0.042-0.04837.141-0.010-0.0100.0000.0000.0000.000
161A560GLY0-0.044-0.01740.4640.0020.0020.0000.0000.0000.000
162A561HIS0-0.047-0.00739.293-0.006-0.0060.0000.0000.0000.000
163A562ASN00.011-0.00541.5400.0020.0020.0000.0000.0000.000
164A563TYR00.000-0.03636.465-0.004-0.0040.0000.0000.0000.000
165A564ILE0-0.0010.01139.9380.0000.0000.0000.0000.0000.000
166A565ASN0-0.052-0.04041.605-0.005-0.0050.0000.0000.0000.000
167A566GLU-1-0.796-0.86736.5910.1060.1060.0000.0000.0000.000
168A567ILE00.010-0.00232.568-0.003-0.0030.0000.0000.0000.000
169A568PHE00.0140.00229.8690.0070.0070.0000.0000.0000.000
170A569ALA00.0280.01229.0630.0040.0040.0000.0000.0000.000
171A570THR0-0.028-0.02025.769-0.004-0.0040.0000.0000.0000.000
172A571SER00.0470.02525.975-0.001-0.0010.0000.0000.0000.000
173A572SER0-0.045-0.02120.406-0.008-0.0080.0000.0000.0000.000
174A573TYR0-0.0120.00421.291-0.010-0.0100.0000.0000.0000.000
175A574THR00.002-0.01416.2800.0190.0190.0000.0000.0000.000
176A575PHE0-0.0040.00717.823-0.047-0.0470.0000.0000.0000.000
177A576SER00.000-0.01316.0410.0770.0770.0000.0000.0000.000
178A577TYR0-0.052-0.03516.081-0.079-0.0790.0000.0000.0000.000
179A578ILE00.001-0.00416.7910.0800.0800.0000.0000.0000.000
180A579ALA00.0310.00714.502-0.035-0.0350.0000.0000.0000.000
181A580GLN00.018-0.01016.511-0.048-0.0480.0000.0000.0000.000
182A581GLU-1-0.884-0.91014.1190.3960.3960.0000.0000.0000.000