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

tag_button

FMODB ID: 72ZZK

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167383.033276
FMO2-HF: Nuclear repulsion 2084369.908072
FMO2-HF: Total energy -83013.125204
FMO2-MP2: Total energy -83251.035567


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.
-7.79-0.5047.863-6.324-8.826-0.04
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 : -0.027 / q_NPA : -0.012
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].
3H3LEU0-0.004-0.0173.798-1.0161.257-0.031-1.166-1.0770.004
4H4GLU-1-0.927-0.9616.8900.2020.2020.0000.0000.0000.000
5H5GLU-1-0.776-0.86510.295-0.699-0.6990.0000.0000.0000.000
6H6SER0-0.013-0.01213.6320.0800.0800.0000.0000.0000.000
7H7GLY00.0290.00416.704-0.019-0.0190.0000.0000.0000.000
8H8GLY00.0130.01419.959-0.007-0.0070.0000.0000.0000.000
9H9GLY00.0310.00621.5610.0290.0290.0000.0000.0000.000
10H10PRO0-0.044-0.02225.049-0.016-0.0160.0000.0000.0000.000
11H11VAL00.0390.01627.3420.0130.0130.0000.0000.0000.000
12H12LYS10.8500.93530.1620.0600.0600.0000.0000.0000.000
13H13PRO00.017-0.01232.637-0.003-0.0030.0000.0000.0000.000
14H14GLY0-0.029-0.00633.3220.0100.0100.0000.0000.0000.000
15H15GLY0-0.026-0.00531.5330.0060.0060.0000.0000.0000.000
16H16THR0-0.016-0.02927.273-0.012-0.0120.0000.0000.0000.000
17H17LEU0-0.0020.00923.4510.0120.0120.0000.0000.0000.000
18H18THR0-0.035-0.02020.343-0.009-0.0090.0000.0000.0000.000
19H19LEU0-0.0130.01917.4260.0190.0190.0000.0000.0000.000
20H20THR00.003-0.00215.222-0.004-0.0040.0000.0000.0000.000
21H21CYS0-0.033-0.0119.821-0.012-0.0120.0000.0000.0000.000
22H22LYS10.8970.9528.657-0.648-0.6480.0000.0000.0000.000
23H23ALA00.0320.0055.395-0.174-0.1740.0000.0000.0000.000
24H24SER0-0.014-0.0194.3970.0910.284-0.001-0.081-0.1110.000
25H25GLY00.0170.0052.194-1.933-1.7235.237-2.940-2.508-0.023
26H26ILE0-0.018-0.0112.535-1.9630.8581.658-1.552-2.926-0.017
27H27ASP-1-0.768-0.8413.8361.6441.7280.0020.002-0.0870.000
28H28PHE0-0.043-0.0436.364-0.556-0.5560.0000.0000.0000.000
29H29SER0-0.102-0.0629.634-0.280-0.2800.0000.0000.0000.000
30H30SER00.0200.0058.571-0.227-0.2270.0000.0000.0000.000
31H31PHE0-0.044-0.02910.3290.0300.0300.0000.0000.0000.000
32H32TYR0-0.003-0.0225.940-0.228-0.2280.0000.0000.0000.000
33H33TYR00.0290.01810.0440.1670.1670.0000.0000.0000.000
34H34MET0-0.033-0.0198.179-0.321-0.3210.0000.0000.0000.000
35H34CYS0-0.062-0.00311.0610.0620.0620.0000.0000.0000.000
36H35TRP00.0300.01412.825-0.096-0.0960.0000.0000.0000.000
37H36VAL0-0.008-0.01415.1860.0440.0440.0000.0000.0000.000
38H37ARG10.7880.88217.2200.3150.3150.0000.0000.0000.000
39H38GLN00.009-0.00219.826-0.056-0.0560.0000.0000.0000.000
40H39ALA00.0310.02521.8310.0250.0250.0000.0000.0000.000
41H40PRO00.015-0.00725.286-0.018-0.0180.0000.0000.0000.000
42H41GLY00.0010.00126.0390.0180.0180.0000.0000.0000.000
43H42LYS10.8860.95325.9020.2780.2780.0000.0000.0000.000
44H43GLY00.0470.02523.427-0.027-0.0270.0000.0000.0000.000
45H44LEU00.001-0.00116.7890.0240.0240.0000.0000.0000.000
46H45GLU-1-0.843-0.90120.678-0.329-0.3290.0000.0000.0000.000
47H46TRP0-0.017-0.02817.1660.0070.0070.0000.0000.0000.000
48H47ILE0-0.032-0.01118.9450.0570.0570.0000.0000.0000.000
49H48ALA00.027-0.00218.3960.0550.0550.0000.0000.0000.000
50H50ILE0-0.012-0.01314.0890.0750.0750.0000.0000.0000.000
51H51VAL00.0500.04513.677-0.093-0.0930.0000.0000.0000.000
52H51THR0-0.034-0.0199.7810.0280.0280.0000.0000.0000.000
53H51ASP-1-0.781-0.85413.0870.0080.0080.0000.0000.0000.000
54H52ILE0-0.041-0.03415.809-0.003-0.0030.0000.0000.0000.000
55H53THR0-0.042-0.05118.954-0.009-0.0090.0000.0000.0000.000
56H54GLY0-0.0150.00817.6460.0000.0000.0000.0000.0000.000
57H55GLU-1-0.858-0.89518.724-0.215-0.2150.0000.0000.0000.000
58H56SER0-0.007-0.01718.397-0.039-0.0390.0000.0000.0000.000
59H57TYR0-0.074-0.05617.615-0.007-0.0070.0000.0000.0000.000
60H58TYR00.0080.00820.209-0.040-0.0400.0000.0000.0000.000
61H59ALA00.0390.02322.7100.0090.0090.0000.0000.0000.000
62H60THR0-0.015-0.03724.3420.0190.0190.0000.0000.0000.000
63H61TRP00.0050.00023.3390.0330.0330.0000.0000.0000.000
64H62ALA00.0210.01824.1110.0130.0130.0000.0000.0000.000
65H63LYS10.9200.96626.1660.2400.2400.0000.0000.0000.000
66H64GLY00.0130.01427.6920.0080.0080.0000.0000.0000.000
67H65ARG10.7850.86728.0680.1950.1950.0000.0000.0000.000
68H66PHE00.007-0.01022.3870.0020.0020.0000.0000.0000.000
69H67ALA00.0090.01422.8210.0010.0010.0000.0000.0000.000
70H68ILE0-0.0140.00615.0290.0000.0000.0000.0000.0000.000
71H69SER00.0130.00217.7420.0350.0350.0000.0000.0000.000
72H70LYS10.9070.94512.733-0.127-0.1270.0000.0000.0000.000
73H71THR0-0.0040.00015.6620.0320.0320.0000.0000.0000.000
74H72SER00.0330.00413.7740.0700.0700.0000.0000.0000.000
75H73SER0-0.006-0.00112.148-0.065-0.0650.0000.0000.0000.000
76H74THR00.0020.0038.5290.0580.0580.0000.0000.0000.000
77H75THR0-0.0180.0129.898-0.029-0.0290.0000.0000.0000.000
78H76VAL00.0130.01811.4660.0070.0070.0000.0000.0000.000
79H77THR0-0.023-0.01313.604-0.020-0.0200.0000.0000.0000.000
80H78LEU00.0090.00416.766-0.019-0.0190.0000.0000.0000.000
81H79GLN0-0.017-0.00918.9490.0110.0110.0000.0000.0000.000
82H80MET0-0.015-0.00322.224-0.024-0.0240.0000.0000.0000.000
83H81THR00.0420.02024.9680.0200.0200.0000.0000.0000.000
84H81SER00.018-0.00328.756-0.009-0.0090.0000.0000.0000.000
85H81LEU0-0.0260.00926.282-0.011-0.0110.0000.0000.0000.000
86H82THR00.0440.01330.3110.0180.0180.0000.0000.0000.000
87H83ALA00.0350.01630.397-0.012-0.0120.0000.0000.0000.000
88H84ALA0-0.006-0.01230.501-0.012-0.0120.0000.0000.0000.000
89H85ASP-1-0.750-0.82926.464-0.228-0.2280.0000.0000.0000.000
90H86THR0-0.041-0.00525.713-0.008-0.0080.0000.0000.0000.000
91H87ALA0-0.020-0.01722.871-0.010-0.0100.0000.0000.0000.000
92H88THR00.0090.01718.0390.0530.0530.0000.0000.0000.000
93H89TYR0-0.038-0.05217.964-0.032-0.0320.0000.0000.0000.000
94H90PHE00.0160.00013.4650.0340.0340.0000.0000.0000.000
95H92ALA00.007-0.0059.350-0.199-0.1990.0000.0000.0000.000
96H93ARG10.9290.9733.4821.6352.3610.037-0.219-0.545-0.002
97H94GLY00.0340.0177.803-0.477-0.4770.0000.0000.0000.000
98H95ASP-1-0.802-0.8947.222-1.680-1.6800.0000.0000.0000.000
99H96THR0-0.013-0.0029.6750.0780.0780.0000.0000.0000.000
100H97TYR00.0220.01513.130-0.058-0.0580.0000.0000.0000.000
101H98GLY00.0160.02315.448-0.014-0.0140.0000.0000.0000.000
102H99TYR0-0.060-0.04816.2020.0420.0420.0000.0000.0000.000
103H99GLY0-0.037-0.01217.5710.0160.0160.0000.0000.0000.000
104H99ASP-1-0.900-0.94315.842-0.368-0.3680.0000.0000.0000.000
105H99THR0-0.037-0.02811.248-0.067-0.0670.0000.0000.0000.000
106H99VAL0-0.021-0.0218.179-0.060-0.0600.0000.0000.0000.000
107H99TYR0-0.041-0.00510.366-0.124-0.1240.0000.0000.0000.000
108H99ALA00.000-0.01911.4130.1330.1330.0000.0000.0000.000
109H99LEU0-0.024-0.0129.931-0.159-0.1590.0000.0000.0000.000
110H100ASN0-0.029-0.0065.758-0.501-0.5010.0000.0000.0000.000
111H101LEU0-0.0160.0062.694-1.799-0.8200.961-0.368-1.572-0.002
112H102TRP0-0.002-0.0285.8531.1001.1000.0000.0000.0000.000
113H103GLY00.0220.0298.178-0.201-0.2010.0000.0000.0000.000
114H104PRO0-0.034-0.02010.113-0.015-0.0150.0000.0000.0000.000
115H105GLY00.0130.00313.1410.0480.0480.0000.0000.0000.000
116H106THR0-0.043-0.02215.5000.1020.1020.0000.0000.0000.000
117H107LEU0-0.025-0.01118.146-0.020-0.0200.0000.0000.0000.000
118H108VAL00.0010.01021.6780.0380.0380.0000.0000.0000.000
119H109THR0-0.037-0.02624.167-0.013-0.0130.0000.0000.0000.000
120H110VAL00.0000.01327.8510.0190.0190.0000.0000.0000.000
121H111SER0-0.006-0.01730.382-0.002-0.0020.0000.0000.0000.000
122H112SER00.0600.01633.7710.0050.0050.0000.0000.0000.000
123H113GLY0-0.019-0.00136.4780.0090.0090.0000.0000.0000.000
124H114GLN00.0370.01735.433-0.009-0.0090.0000.0000.0000.000
125H115PRO00.0090.00332.251-0.004-0.0040.0000.0000.0000.000
126H116LYS10.8580.92234.2740.0670.0670.0000.0000.0000.000
127H117ALA00.0580.03334.536-0.008-0.0080.0000.0000.0000.000
128H118PRO0-0.0350.00133.376-0.002-0.0020.0000.0000.0000.000
129H119SER0-0.028-0.01036.4200.0080.0080.0000.0000.0000.000
130H120VAL00.0220.00636.184-0.007-0.0070.0000.0000.0000.000
131H121PHE0-0.025-0.02239.0680.0070.0070.0000.0000.0000.000
132H122PRO00.0590.03440.537-0.005-0.0050.0000.0000.0000.000
133H123LEU0-0.070-0.03039.034-0.003-0.0030.0000.0000.0000.000
134H124ALA00.0390.01642.0450.0000.0000.0000.0000.0000.000
135H125PRO00.0060.01144.337-0.002-0.0020.0000.0000.0000.000
136H126CYM-1-0.834-0.90646.928-0.042-0.0420.0000.0000.0000.000
137H127CYS0-0.012-0.02350.5660.0020.0020.0000.0000.0000.000
138H128GLY0-0.061-0.03452.9530.0020.0020.0000.0000.0000.000
139H129ASP-1-0.946-0.96049.266-0.053-0.0530.0000.0000.0000.000
140H130THR0-0.037-0.01752.5700.0040.0040.0000.0000.0000.000
141H131PRO0-0.017-0.00849.982-0.002-0.0020.0000.0000.0000.000
142H132SER00.0450.02646.1010.0000.0000.0000.0000.0000.000
143H133SER0-0.008-0.01045.5450.0020.0020.0000.0000.0000.000
144H134THR0-0.054-0.02241.1520.0030.0030.0000.0000.0000.000
145H135VAL00.0620.03641.837-0.001-0.0010.0000.0000.0000.000
146H136THR0-0.032-0.01938.137-0.005-0.0050.0000.0000.0000.000
147H137LEU00.0110.02139.0420.0010.0010.0000.0000.0000.000
148H138GLY00.040-0.00637.292-0.008-0.0080.0000.0000.0000.000
149H139CYS0-0.104-0.01234.1870.0100.0100.0000.0000.0000.000
150H140LEU0-0.0100.00536.582-0.010-0.0100.0000.0000.0000.000
151H141VAL00.0170.00933.0200.0100.0100.0000.0000.0000.000
152H142LYS10.9980.98435.9870.0610.0610.0000.0000.0000.000
153H143GLY00.0280.01137.7520.0080.0080.0000.0000.0000.000
154H144TYR0-0.001-0.02029.9890.0130.0130.0000.0000.0000.000
155H145LEU0-0.0240.00532.720-0.014-0.0140.0000.0000.0000.000
156H146PRO00.003-0.00128.2700.0150.0150.0000.0000.0000.000
157H147GLU-1-0.727-0.80826.438-0.165-0.1650.0000.0000.0000.000
158H148PRO00.001-0.00123.1410.0010.0010.0000.0000.0000.000
159H149VAL00.001-0.01626.2520.0230.0230.0000.0000.0000.000
160H150THR0-0.0010.00023.949-0.014-0.0140.0000.0000.0000.000
161H151VAL0-0.018-0.02027.0280.0130.0130.0000.0000.0000.000
162H152THR0-0.024-0.01326.626-0.007-0.0070.0000.0000.0000.000
163H153TRP00.0320.01429.3260.0050.0050.0000.0000.0000.000
164H154ASN00.022-0.01431.5700.0040.0040.0000.0000.0000.000
165H155SER0-0.026-0.02030.4750.0050.0050.0000.0000.0000.000
166H156GLY00.0050.00927.5830.0130.0130.0000.0000.0000.000
167H157THR0-0.052-0.02128.1300.0040.0040.0000.0000.0000.000
168H158LEU0-0.038-0.01030.805-0.004-0.0040.0000.0000.0000.000
169H159THR00.0150.00225.741-0.009-0.0090.0000.0000.0000.000
170H160ASN00.0160.00428.212-0.032-0.0320.0000.0000.0000.000
171H161GLY00.0610.03029.7240.0070.0070.0000.0000.0000.000
172H162VAL00.0040.00928.9780.0060.0060.0000.0000.0000.000
173H163ARG10.8520.93529.6020.0970.0970.0000.0000.0000.000
174H164THR00.0330.01728.1790.0190.0190.0000.0000.0000.000
175H165PHE0-0.0240.00229.007-0.020-0.0200.0000.0000.0000.000
176H166PRO00.0280.00527.9630.0070.0070.0000.0000.0000.000
177H167SER0-0.037-0.04029.3790.0130.0130.0000.0000.0000.000
178H168VAL00.0120.00831.427-0.012-0.0120.0000.0000.0000.000
179H169ARG10.8590.93232.3520.1660.1660.0000.0000.0000.000
180H170GLN0-0.0010.00235.0010.0050.0050.0000.0000.0000.000
181H171SER00.0540.02138.145-0.003-0.0030.0000.0000.0000.000
182H172SER0-0.001-0.00340.497-0.002-0.0020.0000.0000.0000.000
183H173GLY00.0100.01136.5040.0030.0030.0000.0000.0000.000
184H174LEU0-0.063-0.01635.232-0.005-0.0050.0000.0000.0000.000
185H175TYR00.0300.01029.527-0.005-0.0050.0000.0000.0000.000
186H176SER0-0.023-0.02934.6910.0170.0170.0000.0000.0000.000
187H177LEU00.0130.02029.962-0.011-0.0110.0000.0000.0000.000
188H178SER00.0260.01334.1620.0100.0100.0000.0000.0000.000
189H179SER00.006-0.00531.202-0.008-0.0080.0000.0000.0000.000
190H180VAL00.0280.00433.6400.0100.0100.0000.0000.0000.000
191H181VAL00.010-0.00133.331-0.008-0.0080.0000.0000.0000.000
192H182SER0-0.019-0.00935.1000.0030.0030.0000.0000.0000.000
193H183VAL0-0.027-0.01236.1020.0010.0010.0000.0000.0000.000
194H184THR00.0300.00438.425-0.005-0.0050.0000.0000.0000.000
195H185SER0-0.021-0.01140.9870.0030.0030.0000.0000.0000.000
196H186SER0-0.007-0.02141.8420.0020.0020.0000.0000.0000.000
197H187SER00.0180.00344.530-0.001-0.0010.0000.0000.0000.000
198H188GLN0-0.0360.00738.7500.0000.0000.0000.0000.0000.000
199H189PRO00.0350.03040.523-0.005-0.0050.0000.0000.0000.000
200H190VAL00.0410.03036.9480.0020.0020.0000.0000.0000.000
201H191THR00.0340.01836.333-0.004-0.0040.0000.0000.0000.000
202H193ASN00.0570.01231.1290.0010.0010.0000.0000.0000.000
203H194VAL0-0.026-0.01331.151-0.009-0.0090.0000.0000.0000.000
204H195ALA00.0100.00427.8190.0110.0110.0000.0000.0000.000
205H196HIS00.0110.00929.057-0.005-0.0050.0000.0000.0000.000
206H197PRO00.0460.01724.6960.0100.0100.0000.0000.0000.000
207H198ALA0-0.0050.00927.2530.0110.0110.0000.0000.0000.000
208H199THR0-0.034-0.03628.8670.0060.0060.0000.0000.0000.000
209H200ASN0-0.0030.00129.7680.0110.0110.0000.0000.0000.000
210H201THR00.0010.00130.7510.0070.0070.0000.0000.0000.000
211H202LYS10.9050.93429.066-0.043-0.0430.0000.0000.0000.000
212H203VAL0-0.031-0.00132.9730.0040.0040.0000.0000.0000.000
213H204ASP-1-0.817-0.88834.9030.0090.0090.0000.0000.0000.000
214H205LYS10.8530.90336.9990.0260.0260.0000.0000.0000.000
215H206THR0-0.017-0.01338.937-0.002-0.0020.0000.0000.0000.000
216H207VAL0-0.056-0.03639.510-0.001-0.0010.0000.0000.0000.000
217H208ALA00.0000.00742.2220.0020.0020.0000.0000.0000.000
218H209PRO00.009-0.01845.405-0.004-0.0040.0000.0000.0000.000
219H210SER0-0.0360.00446.376-0.002-0.0020.0000.0000.0000.000
220H211THR00.0530.02749.2100.0010.0010.0000.0000.0000.000