Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 947M2

Calculation Name: 1ZP2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZP2

Chain ID: A

ChEMBL ID:

UniProt ID: O94503

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2790810.237441
FMO2-HF: Nuclear repulsion 2699184.678999
FMO2-HF: Total energy -91625.558442
FMO2-MP2: Total energy -91890.195394


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:6:TRP)


Summations of interaction energy for fragment #1(A:6:TRP)
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.
-3.689-0.9660.111-0.818-2.0150.003
Interaction energy analysis for fragmet #1(A:6:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.010
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].
3A8SER00.0600.0333.574-3.707-1.3560.113-0.777-1.6860.003
4A9SER00.0210.0144.025-0.457-0.139-0.001-0.037-0.2810.000
5A10GLN00.0130.0055.0580.3090.363-0.001-0.004-0.0480.000
6A11LEU00.0120.0147.3690.0430.0430.0000.0000.0000.000
7A12THR0-0.002-0.0208.2790.0010.0010.0000.0000.0000.000
8A13GLN0-0.029-0.01610.5440.0520.0520.0000.0000.0000.000
9A14LEU0-0.029-0.00611.9550.0360.0360.0000.0000.0000.000
10A15PHE0-0.037-0.01911.8990.0460.0460.0000.0000.0000.000
11A16LEU00.0130.00915.689-0.031-0.0310.0000.0000.0000.000
12A17SER0-0.012-0.02617.9730.0220.0220.0000.0000.0000.000
13A18THR0-0.036-0.00317.5410.0190.0190.0000.0000.0000.000
14A19ASP-1-0.918-0.96119.5680.0040.0040.0000.0000.0000.000
15A20LEU0-0.045-0.02922.416-0.006-0.0060.0000.0000.0000.000
16A21GLU-1-0.847-0.90324.095-0.078-0.0780.0000.0000.0000.000
17A22SER0-0.053-0.01926.9550.0020.0020.0000.0000.0000.000
18A23LEU0-0.053-0.03226.7070.0080.0080.0000.0000.0000.000
19A24GLU-1-0.958-0.97626.5980.0590.0590.0000.0000.0000.000
20A25PRO0-0.008-0.00727.783-0.009-0.0090.0000.0000.0000.000
21A26THR00.0080.00626.1050.0090.0090.0000.0000.0000.000
22A27CYS0-0.071-0.03124.1310.0020.0020.0000.0000.0000.000
23A28LEU0-0.020-0.01121.364-0.004-0.0040.0000.0000.0000.000
24A29SER00.0220.01623.595-0.010-0.0100.0000.0000.0000.000
25A30LYS10.8680.89421.1970.2020.2020.0000.0000.0000.000
26A31ASP-1-0.816-0.87926.103-0.085-0.0850.0000.0000.0000.000
27A32THR0-0.091-0.04027.4560.0110.0110.0000.0000.0000.000
28A33ILE00.0720.03223.4680.0110.0110.0000.0000.0000.000
29A34TYR0-0.019-0.00828.1600.0060.0060.0000.0000.0000.000
30A35GLN00.0340.00731.0790.0120.0120.0000.0000.0000.000
31A36TRP0-0.031-0.00929.9050.0040.0040.0000.0000.0000.000
32A37LYS10.9260.96327.1930.0570.0570.0000.0000.0000.000
33A38VAL0-0.0240.00933.0350.0010.0010.0000.0000.0000.000
34A39VAL0-0.032-0.02736.1990.0030.0030.0000.0000.0000.000
35A40GLN0-0.019-0.00232.408-0.002-0.0020.0000.0000.0000.000
36A41THR00.0210.00236.1130.0010.0010.0000.0000.0000.000
37A42PHE0-0.039-0.01838.4610.0010.0010.0000.0000.0000.000
38A43GLY00.008-0.01440.6810.0020.0020.0000.0000.0000.000
39A44ASP-1-0.866-0.94337.888-0.010-0.0100.0000.0000.0000.000
40A45ARG10.7550.88741.4640.0260.0260.0000.0000.0000.000
41A46LEU0-0.053-0.03144.2960.0010.0010.0000.0000.0000.000
42A47ARG10.8900.95044.1580.0120.0120.0000.0000.0000.000
43A48LEU0-0.0080.00843.4490.0030.0030.0000.0000.0000.000
44A49ARG10.9280.95742.292-0.015-0.0150.0000.0000.0000.000
45A50GLN00.1040.03334.718-0.005-0.0050.0000.0000.0000.000
46A51ARG10.8450.89938.702-0.022-0.0220.0000.0000.0000.000
47A52VAL00.0130.01140.6030.0000.0000.0000.0000.0000.000
48A53LEU00.0180.03837.961-0.002-0.0020.0000.0000.0000.000
49A54ALA00.0410.02136.476-0.002-0.0020.0000.0000.0000.000
50A55THR0-0.014-0.04137.4610.0010.0010.0000.0000.0000.000
51A56ALA00.0090.01440.374-0.001-0.0010.0000.0000.0000.000
52A57ILE0-0.0080.00033.835-0.003-0.0030.0000.0000.0000.000
53A58VAL00.010-0.00635.507-0.001-0.0010.0000.0000.0000.000
54A59LEU0-0.036-0.01037.435-0.001-0.0010.0000.0000.0000.000
55A60LEU00.0410.01036.968-0.001-0.0010.0000.0000.0000.000
56A61ARG10.7420.85930.9300.0130.0130.0000.0000.0000.000
57A62ARG10.8840.92836.277-0.017-0.0170.0000.0000.0000.000
58A63TYR0-0.057-0.06038.675-0.002-0.0020.0000.0000.0000.000
59A64MET0-0.021-0.01436.388-0.003-0.0030.0000.0000.0000.000
60A65LEU0-0.0160.01534.575-0.003-0.0030.0000.0000.0000.000
61A66LYS10.7820.86337.410-0.001-0.0010.0000.0000.0000.000
62A67LYS10.8000.89738.8570.0370.0370.0000.0000.0000.000
63A68ASN00.004-0.00740.660-0.002-0.0020.0000.0000.0000.000
64A69GLU-1-0.853-0.93542.472-0.025-0.0250.0000.0000.0000.000
65A70GLU-1-0.861-0.92639.863-0.047-0.0470.0000.0000.0000.000
66A71LYS10.7620.87643.6430.0210.0210.0000.0000.0000.000
67A72GLY0-0.0010.00645.0010.0010.0010.0000.0000.0000.000
68A73PHE0-0.018-0.01445.084-0.001-0.0010.0000.0000.0000.000
69A74SER0-0.019-0.03042.7230.0000.0000.0000.0000.0000.000
70A75LEU00.0630.03036.0090.0040.0040.0000.0000.0000.000
71A76GLU-1-0.819-0.88639.935-0.047-0.0470.0000.0000.0000.000
72A77ALA0-0.005-0.00342.3320.0040.0040.0000.0000.0000.000
73A78LEU00.0130.02140.5570.0040.0040.0000.0000.0000.000
74A79VAL00.0340.02438.8170.0040.0040.0000.0000.0000.000
75A80ALA00.003-0.00141.8770.0040.0040.0000.0000.0000.000
76A81THR0-0.031-0.02945.2590.0030.0030.0000.0000.0000.000
77A82CYS0-0.044-0.01442.0430.0030.0030.0000.0000.0000.000
78A83ILE00.0220.01141.2320.0040.0040.0000.0000.0000.000
79A84TYR0-0.035-0.02344.5230.0030.0030.0000.0000.0000.000
80A85LEU00.0030.00445.8930.0020.0020.0000.0000.0000.000
81A86SER00.004-0.01742.8800.0040.0040.0000.0000.0000.000
82A87CYS0-0.068-0.03845.6170.0020.0020.0000.0000.0000.000
83A88LYS10.7240.83748.1630.0040.0040.0000.0000.0000.000
84A89VAL00.0030.00946.5410.0010.0010.0000.0000.0000.000
85A90GLU-1-0.809-0.85544.0290.0210.0210.0000.0000.0000.000
86A91GLU-1-0.937-0.96347.5000.0180.0180.0000.0000.0000.000
87A92CYS0-0.087-0.03447.9410.0010.0010.0000.0000.0000.000
88A93PRO00.0290.02249.768-0.002-0.0020.0000.0000.0000.000
89A94VAL00.0380.00949.5200.0000.0000.0000.0000.0000.000
90A95HIS0-0.033-0.01652.426-0.002-0.0020.0000.0000.0000.000
91A96ILE00.0780.02953.806-0.001-0.0010.0000.0000.0000.000
92A97ARG10.9440.97654.0380.0090.0090.0000.0000.0000.000
93A98THR00.0190.00751.828-0.002-0.0020.0000.0000.0000.000
94A99ILE00.0640.04748.302-0.001-0.0010.0000.0000.0000.000
95A100CYS0-0.045-0.01449.873-0.002-0.0020.0000.0000.0000.000
96A101ASN0-0.098-0.06151.729-0.001-0.0010.0000.0000.0000.000
97A102GLU-1-0.798-0.89448.259-0.023-0.0230.0000.0000.0000.000
98A103ALA00.0300.02846.556-0.002-0.0020.0000.0000.0000.000
99A104ASN0-0.038-0.04047.088-0.005-0.0050.0000.0000.0000.000
100A105ASP-1-0.925-0.95549.441-0.028-0.0280.0000.0000.0000.000
101A106LEU0-0.056-0.01942.2320.0010.0010.0000.0000.0000.000
102A107TRP00.0180.00840.669-0.002-0.0020.0000.0000.0000.000
103A108SER00.0240.01445.5610.0020.0020.0000.0000.0000.000
104A109LEU0-0.019-0.01744.555-0.003-0.0030.0000.0000.0000.000
105A110LYS10.9310.95345.9590.0620.0620.0000.0000.0000.000
106A111VAL00.0170.01249.5540.0010.0010.0000.0000.0000.000
107A112LYS10.9330.98650.5250.0280.0280.0000.0000.0000.000
108A113LEU00.0300.02447.3040.0020.0020.0000.0000.0000.000
109A114SER0-0.004-0.02851.9280.0020.0020.0000.0000.0000.000
110A115ARG10.9770.95554.3110.0120.0120.0000.0000.0000.000
111A116SER0-0.036-0.01355.9000.0010.0010.0000.0000.0000.000
112A117ASN00.0330.03451.8840.0000.0000.0000.0000.0000.000
113A118ILE00.0580.01949.7480.0000.0000.0000.0000.0000.000
114A119SER0-0.018-0.00651.3280.0020.0020.0000.0000.0000.000
115A120GLU-1-0.853-0.91852.755-0.021-0.0210.0000.0000.0000.000
116A121ILE00.0120.01046.6020.0010.0010.0000.0000.0000.000
117A122GLU-1-0.784-0.85848.640-0.004-0.0040.0000.0000.0000.000
118A123PHE0-0.025-0.00950.2730.0020.0020.0000.0000.0000.000
119A124GLU-1-0.756-0.84146.704-0.018-0.0180.0000.0000.0000.000
120A125ILE0-0.005-0.00944.6500.0010.0010.0000.0000.0000.000
121A126ILE0-0.016-0.01746.9120.0020.0020.0000.0000.0000.000
122A127SER0-0.011-0.00649.3820.0020.0020.0000.0000.0000.000
123A128VAL0-0.0160.00344.1330.0010.0010.0000.0000.0000.000
124A129LEU0-0.037-0.01642.1050.0020.0020.0000.0000.0000.000
125A130ASP-1-0.836-0.89645.7890.0070.0070.0000.0000.0000.000
126A131ALA0-0.017-0.00849.0430.0020.0020.0000.0000.0000.000
127A132PHE0-0.0290.00444.9390.0030.0030.0000.0000.0000.000
128A133LEU0-0.027-0.02944.5860.0000.0000.0000.0000.0000.000
129A134ILE00.0150.01544.3740.0000.0000.0000.0000.0000.000
130A135VAL0-0.005-0.00238.8290.0010.0010.0000.0000.0000.000
131A136HIS00.0040.02339.8110.0010.0010.0000.0000.0000.000
132A137HIS00.0440.00736.8310.0030.0030.0000.0000.0000.000
133A138PRO00.0050.00632.6140.0020.0020.0000.0000.0000.000
134A139TYR00.003-0.02034.5590.0030.0030.0000.0000.0000.000
135A140THR00.0250.01236.9710.0010.0010.0000.0000.0000.000
136A141SER00.0200.00535.4450.0010.0010.0000.0000.0000.000
137A142LEU0-0.049-0.00531.8170.0050.0050.0000.0000.0000.000
138A143GLU-1-0.888-0.93335.6400.0590.0590.0000.0000.0000.000
139A144GLN0-0.024-0.01439.193-0.002-0.0020.0000.0000.0000.000
140A145ALA00.0440.02135.3800.0020.0020.0000.0000.0000.000
141A146PHE0-0.065-0.03637.4400.0040.0040.0000.0000.0000.000
142A147HIS0-0.064-0.05238.6060.0000.0000.0000.0000.0000.000
143A148ASP-1-0.887-0.92539.8290.0780.0780.0000.0000.0000.000
144A149GLY0-0.033-0.00839.8420.0040.0040.0000.0000.0000.000
145A150ILE0-0.036-0.01734.1810.0080.0080.0000.0000.0000.000
146A151ILE00.0060.00432.4140.0100.0100.0000.0000.0000.000
147A152ASN00.0230.00832.210-0.013-0.0130.0000.0000.0000.000
148A153GLN00.0520.00334.839-0.002-0.0020.0000.0000.0000.000
149A154LYS10.9830.99928.100-0.110-0.1100.0000.0000.0000.000
150A155GLN00.001-0.00729.524-0.009-0.0090.0000.0000.0000.000
151A156LEU00.0320.02530.9830.0000.0000.0000.0000.0000.000
152A157GLU-1-0.911-0.94231.3770.0550.0550.0000.0000.0000.000
153A158PHE00.0550.03623.195-0.004-0.0040.0000.0000.0000.000
154A159ALA00.0350.00928.413-0.002-0.0020.0000.0000.0000.000
155A160TRP0-0.002-0.01729.562-0.004-0.0040.0000.0000.0000.000
156A161SER0-0.067-0.05429.293-0.010-0.0100.0000.0000.0000.000
157A162ILE00.0370.02624.757-0.007-0.0070.0000.0000.0000.000
158A163VAL0-0.026-0.01427.371-0.006-0.0060.0000.0000.0000.000
159A164ASN00.0070.02030.134-0.005-0.0050.0000.0000.0000.000
160A165ASP-1-0.776-0.85526.1700.0070.0070.0000.0000.0000.000
161A166SER0-0.061-0.04426.719-0.007-0.0070.0000.0000.0000.000
162A167TYR0-0.026-0.01527.766-0.002-0.0020.0000.0000.0000.000
163A168ALA00.0520.02026.521-0.007-0.0070.0000.0000.0000.000
164A169SER00.027-0.00325.224-0.006-0.0060.0000.0000.0000.000
165A170SER0-0.042-0.03126.643-0.003-0.0030.0000.0000.0000.000
166A171LEU00.0960.02624.9330.0030.0030.0000.0000.0000.000
167A172CYS0-0.057-0.01328.8690.0040.0040.0000.0000.0000.000
168A173LEU0-0.043-0.01331.667-0.001-0.0010.0000.0000.0000.000
169A174MET0-0.0220.00425.344-0.001-0.0010.0000.0000.0000.000
170A175ALA0-0.0010.00029.1140.0100.0100.0000.0000.0000.000
171A176HIS00.0200.02031.244-0.010-0.0100.0000.0000.0000.000
172A177PRO00.0400.00432.7870.0060.0060.0000.0000.0000.000
173A178HIS0-0.003-0.00833.566-0.004-0.0040.0000.0000.0000.000
174A179GLN0-0.004-0.01229.9830.0030.0030.0000.0000.0000.000
175A180LEU00.0490.01728.0100.0100.0100.0000.0000.0000.000
176A181ALA0-0.004-0.00428.9240.0040.0040.0000.0000.0000.000
177A182TYR0-0.057-0.04529.5060.0020.0020.0000.0000.0000.000
178A183ALA00.0100.01224.8930.0130.0130.0000.0000.0000.000
179A184ALA00.0190.01225.1920.0110.0110.0000.0000.0000.000
180A185LEU0-0.007-0.00926.8320.0030.0030.0000.0000.0000.000
181A186LEU00.0060.00224.2270.0070.0070.0000.0000.0000.000
182A187ILE0-0.0080.00121.1210.0170.0170.0000.0000.0000.000
183A188SER0-0.060-0.03223.2630.0090.0090.0000.0000.0000.000
184A189CYS0-0.052-0.02925.974-0.002-0.0020.0000.0000.0000.000
185A190CYS0-0.042-0.01121.2760.0130.0130.0000.0000.0000.000
186A191ASN0-0.010-0.01521.0740.0430.0430.0000.0000.0000.000
187A192ASP-1-0.874-0.92524.1830.1580.1580.0000.0000.0000.000
188A193GLU-1-0.929-0.96627.4320.2340.2340.0000.0000.0000.000
189A194ASN0-0.025-0.02328.434-0.006-0.0060.0000.0000.0000.000
190A195THR0-0.034-0.02330.220-0.009-0.0090.0000.0000.0000.000
191A196ILE00.0120.01524.615-0.005-0.0050.0000.0000.0000.000
192A197PRO00.004-0.00628.698-0.003-0.0030.0000.0000.0000.000
193A198LYS10.8880.95631.165-0.127-0.1270.0000.0000.0000.000
194A199LEU0-0.026-0.01728.705-0.009-0.0090.0000.0000.0000.000
195A200LEU0-0.052-0.02726.434-0.002-0.0020.0000.0000.0000.000
196A201ASP-1-0.889-0.93530.5580.1420.1420.0000.0000.0000.000
197A202LEU0-0.045-0.01833.718-0.009-0.0090.0000.0000.0000.000
198A203ILE0-0.072-0.01328.085-0.009-0.0090.0000.0000.0000.000
199A204LYS10.9841.00432.087-0.090-0.0900.0000.0000.0000.000
200A205SER00.033-0.00130.9790.0020.0020.0000.0000.0000.000
201A206THR0-0.021-0.01830.9990.0040.0040.0000.0000.0000.000
202A207ASP-1-0.790-0.88131.3640.0990.0990.0000.0000.0000.000
203A208ALA00.0170.01327.2800.0010.0010.0000.0000.0000.000
204A209PHE00.0320.02023.4700.0090.0090.0000.0000.0000.000
205A210LYS10.9270.95925.357-0.077-0.0770.0000.0000.0000.000
206A211VAL00.0200.01725.516-0.007-0.0070.0000.0000.0000.000
207A212ILE00.0160.00520.5440.0020.0020.0000.0000.0000.000
208A213LEU0-0.0140.00221.5440.0030.0030.0000.0000.0000.000
209A214CYS0-0.027-0.02122.669-0.017-0.0170.0000.0000.0000.000
210A215VAL00.0150.00419.375-0.010-0.0100.0000.0000.0000.000
211A216GLN00.0340.02716.633-0.032-0.0320.0000.0000.0000.000
212A217ARG10.8760.91118.778-0.079-0.0790.0000.0000.0000.000
213A218ILE00.0370.01021.348-0.022-0.0220.0000.0000.0000.000
214A219ILE0-0.0100.00315.546-0.014-0.0140.0000.0000.0000.000
215A220SER0-0.005-0.01417.114-0.018-0.0180.0000.0000.0000.000
216A221ILE0-0.052-0.02018.096-0.031-0.0310.0000.0000.0000.000
217A222TYR0-0.011-0.02618.911-0.013-0.0130.0000.0000.0000.000
218A223TYR0-0.070-0.04414.317-0.010-0.0100.0000.0000.0000.000
219A224PHE0-0.050-0.03215.913-0.052-0.0520.0000.0000.0000.000
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