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: 17GQZ

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 OptAll
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 -1870446.519395
FMO2-HF: Nuclear repulsion 1801076.850208
FMO2-HF: Total energy -69369.669187
FMO2-MP2: Total energy -69573.491187


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.
-6.964-1.9040.846-2.173-3.7320.013
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 : -0.020 / q_NPA : -0.029
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].
3A402LYS10.8560.9213.479-6.074-3.3840.087-1.189-1.5880.004
4A403LEU0-0.055-0.0202.717-3.146-1.0210.761-0.974-1.9120.009
5A404THR0-0.041-0.0295.345-0.0950.025-0.001-0.004-0.1140.000
6A405LEU0-0.0110.0217.761-0.290-0.2900.0000.0000.0000.000
7A406TRP00.017-0.01011.0520.0590.0590.0000.0000.0000.000
8A407THR00.0320.01713.694-0.057-0.0570.0000.0000.0000.000
9A408THR0-0.051-0.01214.101-0.105-0.1050.0000.0000.0000.000
10A409PRO00.023-0.00813.776-0.003-0.0030.0000.0000.0000.000
11A410ALA0-0.023-0.00916.449-0.028-0.0280.0000.0000.0000.000
12A411PRO00.0040.04119.121-0.041-0.0410.0000.0000.0000.000
13A412SER00.0190.00820.976-0.030-0.0300.0000.0000.0000.000
14A413PRO0-0.050-0.04524.2940.0200.0200.0000.0000.0000.000
15A414ASN00.0090.01621.239-0.034-0.0340.0000.0000.0000.000
16A415CYS0-0.0280.00124.9360.0150.0150.0000.0000.0000.000
17A416ARG10.8230.89326.855-0.194-0.1940.0000.0000.0000.000
18A417LEU0-0.017-0.00428.6590.0070.0070.0000.0000.0000.000
19A418ASN0-0.042-0.02532.058-0.013-0.0130.0000.0000.0000.000
20A419ALA0-0.048-0.02934.950-0.007-0.0070.0000.0000.0000.000
21A420GLU-1-0.825-0.90730.9400.2080.2080.0000.0000.0000.000
22A421LYS10.8850.94126.629-0.233-0.2330.0000.0000.0000.000
23A422ASP-1-0.757-0.86330.5090.1890.1890.0000.0000.0000.000
24A423ALA00.0600.02328.427-0.007-0.0070.0000.0000.0000.000
25A424LYS10.8690.93624.451-0.249-0.2490.0000.0000.0000.000
26A425LEU00.0450.01221.208-0.005-0.0050.0000.0000.0000.000
27A426THR0-0.0220.00017.9530.0000.0000.0000.0000.0000.000
28A427LEU00.009-0.01016.828-0.011-0.0110.0000.0000.0000.000
29A428VAL0-0.006-0.00511.2430.0300.0300.0000.0000.0000.000
30A429LEU00.0130.01612.343-0.077-0.0770.0000.0000.0000.000
31A430THR00.019-0.0076.388-0.019-0.0190.0000.0000.0000.000
32A431LYS10.8230.9007.917-1.327-1.3270.0000.0000.0000.000
33A432CYS0-0.041-0.0047.7280.3310.3310.0000.0000.0000.000
34A433GLY00.0150.0009.280-0.336-0.3360.0000.0000.0000.000
35A434SER00.0070.00310.8960.0660.0660.0000.0000.0000.000
36A435GLN00.0140.01213.600-0.047-0.0470.0000.0000.0000.000
37A436ILE0-0.0450.00011.9910.1850.1850.0000.0000.0000.000
38A437LEU00.0000.00310.957-0.184-0.1840.0000.0000.0000.000
39A438ALA00.0100.00312.3780.1790.1790.0000.0000.0000.000
40A439THR0-0.033-0.02414.295-0.095-0.0950.0000.0000.0000.000
41A440VAL0-0.006-0.00616.7030.0320.0320.0000.0000.0000.000
42A441SER00.0070.00019.600-0.017-0.0170.0000.0000.0000.000
43A442VAL00.0060.00922.7270.0150.0150.0000.0000.0000.000
44A443LEU00.0230.01325.567-0.015-0.0150.0000.0000.0000.000
45A444ALA00.0050.01128.0500.0020.0020.0000.0000.0000.000
46A445VAL0-0.049-0.03829.548-0.005-0.0050.0000.0000.0000.000
47A446LYS10.8330.91032.497-0.178-0.1780.0000.0000.0000.000
48A447GLY00.0270.01435.6340.0070.0070.0000.0000.0000.000
49A448SER00.0090.00338.3320.0020.0020.0000.0000.0000.000
50A449LEU00.0360.02433.385-0.002-0.0020.0000.0000.0000.000
51A450ALA0-0.0070.01334.2840.0080.0080.0000.0000.0000.000
52A451PRO00.007-0.00736.396-0.004-0.0040.0000.0000.0000.000
53A452ILE0-0.0120.00335.3610.0000.0000.0000.0000.0000.000
54A453SER0-0.045-0.02538.969-0.009-0.0090.0000.0000.0000.000
55A454GLY00.016-0.00842.4320.0020.0020.0000.0000.0000.000
56A455THR00.0220.00744.522-0.002-0.0020.0000.0000.0000.000
57A456VAL0-0.027-0.00438.1310.0020.0020.0000.0000.0000.000
58A457GLN00.0370.00239.094-0.001-0.0010.0000.0000.0000.000
59A458SER00.0090.01335.5150.0040.0040.0000.0000.0000.000
60A459ALA0-0.0130.00032.187-0.005-0.0050.0000.0000.0000.000
61A460HIS0-0.013-0.01030.4910.0170.0170.0000.0000.0000.000
62A461LEU00.0430.02424.758-0.004-0.0040.0000.0000.0000.000
63A462ILE0-0.038-0.02627.3010.0130.0130.0000.0000.0000.000
64A463ILE00.0200.03021.106-0.013-0.0130.0000.0000.0000.000
65A464ARG10.8690.91024.578-0.243-0.2430.0000.0000.0000.000
66A465PHE00.007-0.00119.1680.0120.0120.0000.0000.0000.000
67A466ASP-1-0.725-0.85521.1340.3350.3350.0000.0000.0000.000
68A467GLU-1-0.869-0.95721.9120.2930.2930.0000.0000.0000.000
69A468ASN0-0.075-0.05818.9080.0150.0150.0000.0000.0000.000
70A469GLY0-0.013-0.02117.2770.0650.0650.0000.0000.0000.000
71A470VAL0-0.009-0.00917.8240.0540.0540.0000.0000.0000.000
72A471LEU0-0.041-0.02119.333-0.019-0.0190.0000.0000.0000.000
73A472LEU0-0.025-0.01421.804-0.019-0.0190.0000.0000.0000.000
74A473ASN0-0.013-0.02425.269-0.027-0.0270.0000.0000.0000.000
75A474ASN00.0030.00625.2830.0140.0140.0000.0000.0000.000
76A475SER00.0120.02026.302-0.006-0.0060.0000.0000.0000.000
77A476PHE0-0.011-0.01427.1980.0150.0150.0000.0000.0000.000
78A477LEU0-0.023-0.02220.3450.0090.0090.0000.0000.0000.000
79A478ASP-1-0.776-0.87623.2990.2590.2590.0000.0000.0000.000
80A479PRO00.0140.00220.1950.0300.0300.0000.0000.0000.000
81A480GLU-1-0.955-0.97119.0730.2400.2400.0000.0000.0000.000
82A481TYR0-0.049-0.03018.829-0.007-0.0070.0000.0000.0000.000
83A482TRP00.017-0.00516.1910.0470.0470.0000.0000.0000.000
84A483ASN00.0260.01213.4180.0020.0020.0000.0000.0000.000
85A484PHE00.0250.0228.4800.1260.1260.0000.0000.0000.000
86A485ARG10.7840.8814.562-0.663-0.538-0.001-0.006-0.1180.000
87A486ASN0-0.090-0.0687.1230.1240.1240.0000.0000.0000.000
88A487GLY00.0280.0329.116-0.093-0.0930.0000.0000.0000.000
89A488ASP-1-0.820-0.8839.7660.4320.4320.0000.0000.0000.000
90A489LEU00.009-0.01511.8800.1240.1240.0000.0000.0000.000
91A490THR0-0.038-0.04413.1350.0040.0040.0000.0000.0000.000
92A491GLU-1-0.838-0.8915.2492.9512.9510.0000.0000.0000.000
93A492GLY00.0270.0007.6890.6080.6080.0000.0000.0000.000
94A493ASN0-0.012-0.0089.299-0.248-0.2480.0000.0000.0000.000
95A494ALA00.0690.03711.7880.0780.0780.0000.0000.0000.000
96A495VAL00.0760.04613.8780.0080.0080.0000.0000.0000.000
97A496GLY0-0.0190.00111.903-0.032-0.0320.0000.0000.0000.000
98A497PHE00.002-0.0208.1260.0650.0650.0000.0000.0000.000
99A498MET0-0.0220.04813.843-0.055-0.0550.0000.0000.0000.000
100A499PRO00.007-0.00217.6480.0110.0110.0000.0000.0000.000
101A500ASN00.0000.02219.722-0.073-0.0730.0000.0000.0000.000
102A501LEU00.0500.01921.301-0.022-0.0220.0000.0000.0000.000
103A502SER0-0.073-0.03624.066-0.027-0.0270.0000.0000.0000.000
104A503ALA0-0.074-0.04423.207-0.019-0.0190.0000.0000.0000.000
105A504TYR0-0.010-0.01420.899-0.002-0.0020.0000.0000.0000.000
106A505PRO00.0450.02026.2740.0110.0110.0000.0000.0000.000
107A506LYS10.8430.94826.748-0.258-0.2580.0000.0000.0000.000
108A507SER0-0.069-0.02929.669-0.018-0.0180.0000.0000.0000.000
109A508HIS00.0600.02933.4790.0110.0110.0000.0000.0000.000
110A509GLY0-0.0120.00335.799-0.005-0.0050.0000.0000.0000.000
111A510LYS10.9700.96834.203-0.154-0.1540.0000.0000.0000.000
112A511THR00.0190.02530.389-0.010-0.0100.0000.0000.0000.000
113A512ALA00.009-0.00331.1040.0140.0140.0000.0000.0000.000
114A513LYS10.9300.96726.353-0.229-0.2290.0000.0000.0000.000
115A514SER00.0000.00826.5880.0180.0180.0000.0000.0000.000
116A515ASN0-0.032-0.00826.8730.0150.0150.0000.0000.0000.000
117A516ILE0-0.0030.00821.813-0.002-0.0020.0000.0000.0000.000
118A517VAL0-0.0010.00025.9780.0060.0060.0000.0000.0000.000
119A518SER0-0.0060.00326.452-0.012-0.0120.0000.0000.0000.000
120A519GLN00.0020.00728.616-0.014-0.0140.0000.0000.0000.000
121A520VAL0-0.0250.00125.6590.0210.0210.0000.0000.0000.000
122A521TYR0-0.002-0.01928.432-0.016-0.0160.0000.0000.0000.000
123A522LEU00.0480.03429.8280.0140.0140.0000.0000.0000.000
124A523ASN0-0.053-0.03930.786-0.005-0.0050.0000.0000.0000.000
125A524GLY0-0.022-0.00929.1650.0000.0000.0000.0000.0000.000
126A525ASP-1-0.821-0.87829.8360.1400.1400.0000.0000.0000.000
127A526LYS10.9670.96732.916-0.143-0.1430.0000.0000.0000.000
128A527THR0-0.116-0.08234.020-0.005-0.0050.0000.0000.0000.000
129A528LYS10.8190.91235.305-0.144-0.1440.0000.0000.0000.000
130A529PRO00.0010.01333.3510.0130.0130.0000.0000.0000.000
131A530VAL00.0000.00931.218-0.010-0.0100.0000.0000.0000.000
132A531THR0-0.011-0.00431.0820.0130.0130.0000.0000.0000.000
133A532LEU0-0.029-0.01824.4530.0020.0020.0000.0000.0000.000
134A533THR00.0070.00428.2390.0030.0030.0000.0000.0000.000
135A534ILE0-0.0040.00322.0390.0010.0010.0000.0000.0000.000
136A535THR0-0.030-0.03325.758-0.015-0.0150.0000.0000.0000.000
137A536LEU0-0.016-0.00721.2000.0230.0230.0000.0000.0000.000
138A537ASN00.009-0.03422.978-0.011-0.0110.0000.0000.0000.000
139A538GLY00.0030.01926.111-0.022-0.0220.0000.0000.0000.000
140A539THR0-0.082-0.06129.146-0.005-0.0050.0000.0000.0000.000
141A540GLN00.0390.01630.6110.0020.0020.0000.0000.0000.000
142A541GLU-1-0.741-0.80530.2780.2260.2260.0000.0000.0000.000
143A542THR00.0090.00234.105-0.007-0.0070.0000.0000.0000.000
144A543GLY00.0200.01837.7480.0010.0010.0000.0000.0000.000
145A544ASP-1-0.915-0.96038.8070.1190.1190.0000.0000.0000.000
146A545THR0-0.100-0.04633.9150.0050.0050.0000.0000.0000.000
147A546THR00.0290.00030.885-0.002-0.0020.0000.0000.0000.000
148A547PRO00.0060.00230.8710.0110.0110.0000.0000.0000.000
149A548SER0-0.056-0.04226.0930.0130.0130.0000.0000.0000.000
150A549ALA0-0.0060.00823.828-0.014-0.0140.0000.0000.0000.000
151A550TYR0-0.016-0.01320.908-0.001-0.0010.0000.0000.0000.000
152A551SER0-0.017-0.03123.806-0.005-0.0050.0000.0000.0000.000
153A552MET0-0.0130.00717.8740.0170.0170.0000.0000.0000.000
154A553SER0-0.0020.00423.435-0.008-0.0080.0000.0000.0000.000
155A554PHE0-0.013-0.00320.4590.0130.0130.0000.0000.0000.000
156A555SER00.0150.00126.670-0.021-0.0210.0000.0000.0000.000
157A556TRP00.000-0.00125.1610.0010.0010.0000.0000.0000.000
158A557ASP-1-0.822-0.90531.2630.1560.1560.0000.0000.0000.000
159A558TRP0-0.0140.00133.5200.0100.0100.0000.0000.0000.000
160A559SER0-0.015-0.03137.191-0.011-0.0110.0000.0000.0000.000
161A560GLY0-0.052-0.02240.5290.0000.0000.0000.0000.0000.000
162A561HIS0-0.051-0.01539.452-0.008-0.0080.0000.0000.0000.000
163A562ASN0-0.003-0.01441.1310.0070.0070.0000.0000.0000.000
164A563TYR00.016-0.02036.210-0.004-0.0040.0000.0000.0000.000
165A564ILE0-0.0020.00539.8500.0040.0040.0000.0000.0000.000
166A565ASN0-0.056-0.03941.742-0.007-0.0070.0000.0000.0000.000
167A566GLU-1-0.802-0.87636.7010.1430.1430.0000.0000.0000.000
168A567ILE0-0.005-0.00632.666-0.001-0.0010.0000.0000.0000.000
169A568PHE00.0190.00829.8790.0060.0060.0000.0000.0000.000
170A569ALA00.0120.00529.1670.0120.0120.0000.0000.0000.000
171A570THR0-0.018-0.01025.425-0.008-0.0080.0000.0000.0000.000
172A571SER00.0180.01125.7860.0010.0010.0000.0000.0000.000
173A572SER0-0.017-0.00520.239-0.003-0.0030.0000.0000.0000.000
174A573TYR00.0000.00521.154-0.039-0.0390.0000.0000.0000.000
175A574THR0-0.004-0.00816.2900.0530.0530.0000.0000.0000.000
176A575PHE0-0.020-0.00517.754-0.060-0.0600.0000.0000.0000.000
177A576SER00.007-0.00916.1660.0810.0810.0000.0000.0000.000
178A577TYR0-0.033-0.02816.210-0.075-0.0750.0000.0000.0000.000
179A578ILE00.003-0.00216.7570.0730.0730.0000.0000.0000.000
180A579ALA00.0390.01414.581-0.010-0.0100.0000.0000.0000.000
181A580GLN0-0.017-0.01816.572-0.074-0.0740.0000.0000.0000.000
182A581GLU-1-0.872-0.91513.9720.4160.4160.0000.0000.0000.000