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: MV22Z

Calculation Name: 4ZTP-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZTP

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166885.218609
FMO2-HF: Nuclear repulsion 2083872.474438
FMO2-HF: Total energy -83012.744171
FMO2-MP2: Total energy -83250.666656


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
-4.7163.8927.742-7.26-9.093-0.033
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.023
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].
3H3LEU0-0.005-0.0223.798-2.0501.539-0.031-1.983-1.5760.010
4H4GLU-1-0.926-0.9586.8840.0370.0370.0000.0000.0000.000
5H5GLU-1-0.775-0.87110.277-0.594-0.5940.0000.0000.0000.000
6H6SER0-0.005-0.00113.6360.0650.0650.0000.0000.0000.000
7H7GLY00.0340.00416.685-0.015-0.0150.0000.0000.0000.000
8H8GLY0-0.013-0.00220.023-0.011-0.0110.0000.0000.0000.000
9H9GLY00.0390.00921.5620.0270.0270.0000.0000.0000.000
10H10PRO0-0.037-0.01825.035-0.016-0.0160.0000.0000.0000.000
11H11VAL00.0290.01627.6230.0140.0140.0000.0000.0000.000
12H12LYS10.8930.95530.1620.0390.0390.0000.0000.0000.000
13H13PRO00.026-0.00632.637-0.002-0.0020.0000.0000.0000.000
14H14GLY0-0.030-0.00533.3170.0090.0090.0000.0000.0000.000
15H15GLY0-0.033-0.00931.5440.0070.0070.0000.0000.0000.000
16H16THR00.000-0.02226.992-0.013-0.0130.0000.0000.0000.000
17H17LEU0-0.020-0.00123.5130.0120.0120.0000.0000.0000.000
18H18THR0-0.021-0.00920.399-0.010-0.0100.0000.0000.0000.000
19H19LEU0-0.0180.01317.4470.0190.0190.0000.0000.0000.000
20H20THR0-0.012-0.00514.8770.0040.0040.0000.0000.0000.000
21H21CYS0-0.026-0.0099.788-0.014-0.0140.0000.0000.0000.000
22H22LYS10.9130.9678.635-0.810-0.8100.0000.0000.0000.000
23H23ALA00.0360.0055.373-0.207-0.2070.0000.0000.0000.000
24H24SER0-0.020-0.0194.3680.1530.333-0.001-0.083-0.0970.000
25H25GLY00.0110.0002.183-2.211-1.8725.335-3.068-2.606-0.024
26H26ILE0-0.020-0.0102.5452.5185.0191.374-1.392-2.484-0.015
27H27ASP-1-0.777-0.8533.8111.4041.4720.0020.005-0.0750.000
28H28PHE0-0.035-0.0466.366-0.661-0.6610.0000.0000.0000.000
29H29SER0-0.105-0.0589.620-0.322-0.3220.0000.0000.0000.000
30H30SER00.0200.0098.618-0.282-0.2820.0000.0000.0000.000
31H31PHE0-0.036-0.01810.3080.1190.1190.0000.0000.0000.000
32H32TYR0-0.017-0.0236.0860.0270.0270.0000.0000.0000.000
33H33TYR00.0270.01810.2170.2070.2070.0000.0000.0000.000
34H34MET0-0.038-0.0248.080-0.290-0.2900.0000.0000.0000.000
35H34CYS0-0.064-0.00311.0570.0470.0470.0000.0000.0000.000
36H35TRP00.0210.01212.791-0.079-0.0790.0000.0000.0000.000
37H36VAL00.000-0.01215.1230.0320.0320.0000.0000.0000.000
38H37ARG10.8090.91117.1560.3010.3010.0000.0000.0000.000
39H38GLN00.013-0.00119.913-0.048-0.0480.0000.0000.0000.000
40H39ALA00.0240.02122.0370.0240.0240.0000.0000.0000.000
41H40PRO00.009-0.01125.475-0.019-0.0190.0000.0000.0000.000
42H41GLY00.0100.00626.2000.0170.0170.0000.0000.0000.000
43H42LYS10.8910.95626.0850.2720.2720.0000.0000.0000.000
44H43GLY00.0450.02123.606-0.026-0.0260.0000.0000.0000.000
45H44LEU0-0.002-0.00417.1030.0240.0240.0000.0000.0000.000
46H45GLU-1-0.870-0.92520.913-0.324-0.3240.0000.0000.0000.000
47H46TRP0-0.010-0.02117.2620.0080.0080.0000.0000.0000.000
48H47ILE0-0.030-0.01218.8950.0550.0550.0000.0000.0000.000
49H48ALA00.027-0.00618.3610.0500.0500.0000.0000.0000.000
50H50ILE0-0.016-0.01414.2180.0730.0730.0000.0000.0000.000
51H51VAL00.0550.04413.693-0.094-0.0940.0000.0000.0000.000
52H51THR0-0.045-0.0249.9000.0310.0310.0000.0000.0000.000
53H51ASP-1-0.718-0.78113.147-0.003-0.0030.0000.0000.0000.000
54H52ILE0-0.061-0.04715.8770.0110.0110.0000.0000.0000.000
55H53THR0-0.107-0.12918.942-0.003-0.0030.0000.0000.0000.000
56H54GLY00.0020.01417.7040.0050.0050.0000.0000.0000.000
57H55GLU-1-0.909-0.94918.783-0.221-0.2210.0000.0000.0000.000
58H56SER0-0.023-0.02418.419-0.040-0.0400.0000.0000.0000.000
59H57TYR00.0010.00618.060-0.006-0.0060.0000.0000.0000.000
60H58TYR00.0010.00720.191-0.034-0.0340.0000.0000.0000.000
61H59ALA00.0330.02322.6940.0040.0040.0000.0000.0000.000
62H60THR0-0.011-0.03224.3020.0200.0200.0000.0000.0000.000
63H61TRP00.004-0.00123.3840.0350.0350.0000.0000.0000.000
64H62ALA00.0140.01224.1130.0150.0150.0000.0000.0000.000
65H63LYS10.9530.97226.1420.2310.2310.0000.0000.0000.000
66H64GLY00.0060.01227.6830.0070.0070.0000.0000.0000.000
67H65ARG10.7960.88528.0060.1860.1860.0000.0000.0000.000
68H66PHE00.002-0.00922.5300.0040.0040.0000.0000.0000.000
69H67ALA00.0190.01722.844-0.002-0.0020.0000.0000.0000.000
70H68ILE0-0.0130.00415.0350.0060.0060.0000.0000.0000.000
71H69SER00.0140.00017.7970.0310.0310.0000.0000.0000.000
72H70LYS10.9040.95212.488-0.233-0.2330.0000.0000.0000.000
73H71THR0-0.0060.00015.7450.0340.0340.0000.0000.0000.000
74H72SER00.0480.01913.7510.0700.0700.0000.0000.0000.000
75H73SER00.0010.00512.261-0.068-0.0680.0000.0000.0000.000
76H74THR00.008-0.0078.0670.0570.0570.0000.0000.0000.000
77H75THR0-0.0310.00110.001-0.007-0.0070.0000.0000.0000.000
78H76VAL0-0.0020.01311.425-0.010-0.0100.0000.0000.0000.000
79H77THR0-0.026-0.01613.665-0.022-0.0220.0000.0000.0000.000
80H78LEU00.0040.00116.813-0.024-0.0240.0000.0000.0000.000
81H79GLN0-0.009-0.00418.9710.0070.0070.0000.0000.0000.000
82H80MET0-0.015-0.00622.399-0.026-0.0260.0000.0000.0000.000
83H81THR00.0330.02124.9770.0190.0190.0000.0000.0000.000
84H81SER00.018-0.00628.767-0.011-0.0110.0000.0000.0000.000
85H81LEU0-0.0230.00726.402-0.012-0.0120.0000.0000.0000.000
86H82THR00.0540.01230.3000.0170.0170.0000.0000.0000.000
87H83ALA00.0270.00930.366-0.011-0.0110.0000.0000.0000.000
88H84ALA0-0.020-0.01730.454-0.012-0.0120.0000.0000.0000.000
89H85ASP-1-0.755-0.84226.478-0.211-0.2110.0000.0000.0000.000
90H86THR0-0.0340.00525.675-0.005-0.0050.0000.0000.0000.000
91H87ALA0-0.022-0.01822.815-0.011-0.0110.0000.0000.0000.000
92H88THR00.0160.02418.0920.0420.0420.0000.0000.0000.000
93H89TYR0-0.052-0.05817.941-0.030-0.0300.0000.0000.0000.000
94H90PHE00.0160.00413.4840.0350.0350.0000.0000.0000.000
95H92ALA00.009-0.0029.273-0.179-0.1790.0000.0000.0000.000
96H93ARG10.9430.9742.9171.6852.6760.134-0.345-0.780-0.002
97H94GLY00.0360.0187.987-0.448-0.4480.0000.0000.0000.000
98H95ASP-1-0.821-0.8987.510-2.217-2.2170.0000.0000.0000.000
99H96THR0-0.030-0.0159.8040.1540.1540.0000.0000.0000.000
100H97TYR00.0210.01313.262-0.099-0.0990.0000.0000.0000.000
101H98GLY00.0240.02515.502-0.034-0.0340.0000.0000.0000.000
102H99TYR0-0.053-0.04416.2670.0880.0880.0000.0000.0000.000
103H99GLY0-0.037-0.01117.4930.0300.0300.0000.0000.0000.000
104H99ASP-1-0.910-0.94815.141-0.659-0.6590.0000.0000.0000.000
105H99THR0-0.040-0.02811.145-0.136-0.1360.0000.0000.0000.000
106H99VAL0-0.023-0.0197.7580.0200.0200.0000.0000.0000.000
107H99TYR0-0.042-0.00610.409-0.087-0.0870.0000.0000.0000.000
108H99ALA0-0.003-0.02411.5250.1780.1780.0000.0000.0000.000
109H99LEU0-0.021-0.01110.089-0.195-0.1950.0000.0000.0000.000
110H100ASN00.0250.0165.2990.4020.4020.0000.0000.0000.000
111H101LEU0-0.036-0.0062.629-1.576-0.6360.929-0.394-1.475-0.002
112H102TRP00.009-0.0196.0510.8870.8870.0000.0000.0000.000
113H103GLY00.0170.0268.343-0.192-0.1920.0000.0000.0000.000
114H104PRO0-0.032-0.01910.102-0.016-0.0160.0000.0000.0000.000
115H105GLY00.0160.00713.2880.0480.0480.0000.0000.0000.000
116H106THR0-0.043-0.01615.4480.0900.0900.0000.0000.0000.000
117H107LEU0-0.016-0.00718.117-0.019-0.0190.0000.0000.0000.000
118H108VAL0-0.0060.00621.7300.0380.0380.0000.0000.0000.000
119H109THR0-0.036-0.02824.141-0.016-0.0160.0000.0000.0000.000
120H110VAL00.0010.01327.8220.0190.0190.0000.0000.0000.000
121H111SER0-0.017-0.02430.359-0.003-0.0030.0000.0000.0000.000
122H112SER00.0410.00833.7480.0050.0050.0000.0000.0000.000
123H113GLY0-0.024-0.00336.4290.0090.0090.0000.0000.0000.000
124H114GLN00.0440.01035.421-0.006-0.0060.0000.0000.0000.000
125H115PRO0-0.005-0.00532.263-0.005-0.0050.0000.0000.0000.000
126H116LYS10.8680.93234.2600.0610.0610.0000.0000.0000.000
127H117ALA00.0590.02934.533-0.008-0.0080.0000.0000.0000.000
128H118PRO0-0.048-0.00533.140-0.002-0.0020.0000.0000.0000.000
129H119SER0-0.031-0.01536.2160.0090.0090.0000.0000.0000.000
130H120VAL00.010-0.00435.646-0.007-0.0070.0000.0000.0000.000
131H121PHE0-0.044-0.02938.5610.0060.0060.0000.0000.0000.000
132H122PRO00.0500.03039.938-0.006-0.0060.0000.0000.0000.000
133H123LEU0-0.065-0.02738.517-0.002-0.0020.0000.0000.0000.000
134H124ALA00.0410.01741.5020.0000.0000.0000.0000.0000.000
135H125PRO00.0030.00443.726-0.002-0.0020.0000.0000.0000.000
136H126CYM-1-0.853-0.90346.461-0.041-0.0410.0000.0000.0000.000
137H127CYS0-0.015-0.01650.0980.0020.0020.0000.0000.0000.000
138H128GLY0-0.043-0.04152.4310.0020.0020.0000.0000.0000.000
139H129ASP-1-0.958-0.96848.724-0.052-0.0520.0000.0000.0000.000
140H130THR0-0.040-0.01552.1380.0040.0040.0000.0000.0000.000
141H131PRO0-0.0020.00049.504-0.002-0.0020.0000.0000.0000.000
142H132SER00.0460.02245.8040.0000.0000.0000.0000.0000.000
143H133SER0-0.021-0.01644.7330.0020.0020.0000.0000.0000.000
144H134THR0-0.052-0.01740.8060.0010.0010.0000.0000.0000.000
145H135VAL00.0670.03641.348-0.001-0.0010.0000.0000.0000.000
146H136THR0-0.040-0.02337.600-0.005-0.0050.0000.0000.0000.000
147H137LEU00.0080.01838.5330.0020.0020.0000.0000.0000.000
148H138GLY00.039-0.00836.755-0.008-0.0080.0000.0000.0000.000
149H139CYS0-0.112-0.01933.4650.0100.0100.0000.0000.0000.000
150H140LEU0-0.0130.00436.059-0.011-0.0110.0000.0000.0000.000
151H141VAL00.0190.01132.7160.0100.0100.0000.0000.0000.000
152H142LYS11.0010.98635.6690.0570.0570.0000.0000.0000.000
153H143GLY00.0030.00237.6220.0090.0090.0000.0000.0000.000
154H144TYR00.018-0.00129.9210.0120.0120.0000.0000.0000.000
155H145LEU0-0.0100.01032.561-0.014-0.0140.0000.0000.0000.000
156H146PRO00.002-0.00228.2700.0160.0160.0000.0000.0000.000
157H147GLU-1-0.733-0.81226.426-0.164-0.1640.0000.0000.0000.000
158H148PRO00.0080.00223.0910.0030.0030.0000.0000.0000.000
159H149VAL00.006-0.01426.1970.0230.0230.0000.0000.0000.000
160H150THR0-0.045-0.01523.491-0.011-0.0110.0000.0000.0000.000
161H151VAL00.018-0.00726.4840.0130.0130.0000.0000.0000.000
162H152THR0-0.016-0.00525.919-0.009-0.0090.0000.0000.0000.000
163H153TRP00.0300.01128.6050.0070.0070.0000.0000.0000.000
164H154ASN00.027-0.00330.8220.0020.0020.0000.0000.0000.000
165H155SER0-0.026-0.02429.6210.0050.0050.0000.0000.0000.000
166H156GLY0-0.0030.00326.7630.0120.0120.0000.0000.0000.000
167H157THR0-0.041-0.00927.3660.0030.0030.0000.0000.0000.000
168H158LEU0-0.038-0.01230.032-0.004-0.0040.0000.0000.0000.000
169H159THR00.0170.00325.033-0.008-0.0080.0000.0000.0000.000
170H160ASN00.0210.00727.657-0.032-0.0320.0000.0000.0000.000
171H161GLY00.0510.02529.2670.0080.0080.0000.0000.0000.000
172H162VAL00.0100.01228.5010.0070.0070.0000.0000.0000.000
173H163ARG10.8640.93729.2350.1010.1010.0000.0000.0000.000
174H164THR00.0310.01827.7520.0200.0200.0000.0000.0000.000
175H165PHE0-0.032-0.00328.692-0.021-0.0210.0000.0000.0000.000
176H166PRO00.0280.00528.0780.0070.0070.0000.0000.0000.000
177H167SER0-0.041-0.04629.4970.0130.0130.0000.0000.0000.000
178H168VAL00.0170.00931.538-0.011-0.0110.0000.0000.0000.000
179H169ARG10.8630.93432.2780.1600.1600.0000.0000.0000.000
180H170GLN00.005-0.00335.1570.0040.0040.0000.0000.0000.000
181H171SER00.0430.01538.301-0.002-0.0020.0000.0000.0000.000
182H172SER00.0040.00040.368-0.002-0.0020.0000.0000.0000.000
183H173GLY00.0020.00736.4860.0040.0040.0000.0000.0000.000
184H174LEU0-0.068-0.02435.185-0.004-0.0040.0000.0000.0000.000
185H175TYR00.0410.01629.986-0.005-0.0050.0000.0000.0000.000
186H176SER0-0.025-0.02134.7300.0170.0170.0000.0000.0000.000
187H177LEU00.0140.02129.610-0.011-0.0110.0000.0000.0000.000
188H178SER00.0200.01233.7260.0120.0120.0000.0000.0000.000
189H179SER00.003-0.01030.687-0.009-0.0090.0000.0000.0000.000
190H180VAL00.0310.01133.1980.0100.0100.0000.0000.0000.000
191H181VAL00.010-0.00232.805-0.009-0.0090.0000.0000.0000.000
192H182SER0-0.057-0.01834.6120.0070.0070.0000.0000.0000.000
193H183VAL00.0250.00935.6180.0010.0010.0000.0000.0000.000
194H184THR00.007-0.00437.899-0.002-0.0020.0000.0000.0000.000
195H185SER0-0.006-0.01340.4540.0030.0030.0000.0000.0000.000
196H186SER00.0060.00541.0890.0020.0020.0000.0000.0000.000
197H187SER00.0200.00243.867-0.001-0.0010.0000.0000.0000.000
198H188GLN0-0.054-0.01938.1390.0010.0010.0000.0000.0000.000
199H189PRO00.0390.02939.869-0.005-0.0050.0000.0000.0000.000
200H190VAL00.0400.02636.2530.0020.0020.0000.0000.0000.000
201H191THR00.0230.01535.642-0.002-0.0020.0000.0000.0000.000
202H193ASN00.0410.00030.2940.0020.0020.0000.0000.0000.000
203H194VAL0-0.013-0.00630.390-0.010-0.0100.0000.0000.0000.000
204H195ALA00.0160.00527.3570.0120.0120.0000.0000.0000.000
205H196HIS0-0.0040.00328.729-0.006-0.0060.0000.0000.0000.000
206H197PRO00.0450.01824.7490.0110.0110.0000.0000.0000.000
207H198ALA0-0.0050.00827.2480.0130.0130.0000.0000.0000.000
208H199THR0-0.044-0.04428.8570.0070.0070.0000.0000.0000.000
209H200ASN0-0.040-0.01829.7470.0110.0110.0000.0000.0000.000
210H201THR0-0.009-0.00230.7470.0060.0060.0000.0000.0000.000
211H202LYS10.9640.96228.652-0.064-0.0640.0000.0000.0000.000
212H203VAL0-0.0230.00332.6690.0050.0050.0000.0000.0000.000
213H204ASP-1-0.816-0.88434.0730.0130.0130.0000.0000.0000.000
214H205LYS10.9020.93136.2810.0170.0170.0000.0000.0000.000
215H206THR0-0.016-0.01238.186-0.002-0.0020.0000.0000.0000.000
216H207VAL0-0.053-0.03338.860-0.001-0.0010.0000.0000.0000.000
217H208ALA0-0.0040.00441.5320.0010.0010.0000.0000.0000.000
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