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: K9ZG3

Calculation Name: 4NNP-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NNP

Chain ID: H

ChEMBL ID:

UniProt ID: A0A0H3

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287923.376626
FMO2-HF: Nuclear repulsion 2203116.560196
FMO2-HF: Total energy -84806.81643
FMO2-MP2: Total energy -85054.099841


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:3:GLN)


Summations of interaction energy for fragment #1(H:3: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.
-29.914-23.2514.997-9.67-11.988-0.064
Interaction energy analysis for fragmet #1(H:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.006
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].
3H5VAL00.0090.0002.669-4.911-0.7530.598-2.389-2.367-0.006
4H6GLU-1-0.776-0.8855.359-3.778-3.732-0.001-0.002-0.0430.000
5H7SER0-0.058-0.0348.4630.4770.4770.0000.0000.0000.000
6H8GLY00.0490.01511.808-0.081-0.0810.0000.0000.0000.000
7H9GLY0-0.0050.00314.3410.0230.0230.0000.0000.0000.000
8H10GLY00.0010.00015.8500.0650.0650.0000.0000.0000.000
9H11LEU0-0.048-0.01718.389-0.011-0.0110.0000.0000.0000.000
10H12VAL00.0060.01221.839-0.006-0.0060.0000.0000.0000.000
11H13GLN00.0320.02224.3580.0050.0050.0000.0000.0000.000
12H14PRO00.012-0.01627.427-0.021-0.0210.0000.0000.0000.000
13H15GLY0-0.017-0.00427.9560.0170.0170.0000.0000.0000.000
14H16GLY0-0.0210.00227.0250.0010.0010.0000.0000.0000.000
15H17SER0-0.032-0.04524.778-0.010-0.0100.0000.0000.0000.000
16H18LEU0-0.0070.00018.5860.0190.0190.0000.0000.0000.000
17H19ARG10.8960.96918.3360.6430.6430.0000.0000.0000.000
18H20LEU00.0000.01913.4560.0000.0000.0000.0000.0000.000
19H21SER0-0.002-0.01312.9830.0630.0630.0000.0000.0000.000
20H22CYS0-0.077-0.0317.7470.2780.2780.0000.0000.0000.000
21H23ALA00.0240.0208.2350.3080.3080.0000.0000.0000.000
22H24ALA00.0370.0195.191-0.978-0.9780.0000.0000.0000.000
23H25SER0-0.031-0.0352.8630.9302.0970.094-0.516-0.7440.001
24H26GLY0-0.018-0.0055.4820.5180.5180.0000.0000.0000.000
25H27PHE0-0.033-0.0152.8730.0890.6310.045-0.145-0.4420.000
26H28ASN0-0.002-0.0028.094-0.424-0.4240.0000.0000.0000.000
27H29PHE00.0110.0034.8800.2420.2420.0000.0000.0000.000
28H30SER00.0290.0189.919-0.099-0.0990.0000.0000.0000.000
29H31SER00.014-0.00110.127-0.108-0.1080.0000.0000.0000.000
30H32SER00.0200.03312.2860.0320.0320.0000.0000.0000.000
31H33SER0-0.018-0.02113.6540.0230.0230.0000.0000.0000.000
32H34ILE0-0.0080.00510.904-0.170-0.1700.0000.0000.0000.000
33H35HIS10.8410.90912.1271.2901.2900.0000.0000.0000.000
34H36TRP00.0090.01310.866-0.347-0.3470.0000.0000.0000.000
35H37VAL0-0.012-0.01211.4590.2280.2280.0000.0000.0000.000
36H38ARG10.7850.86812.2460.4160.4160.0000.0000.0000.000
37H39GLN00.0310.01512.117-0.065-0.0650.0000.0000.0000.000
38H40ALA00.0230.02114.8240.0340.0340.0000.0000.0000.000
39H41PRO00.0450.00117.004-0.002-0.0020.0000.0000.0000.000
40H42GLY0-0.0090.00217.5000.0250.0250.0000.0000.0000.000
41H43LYS10.9140.96818.3120.2740.2740.0000.0000.0000.000
42H44GLY00.0400.02016.936-0.021-0.0210.0000.0000.0000.000
43H45LEU0-0.012-0.00511.958-0.018-0.0180.0000.0000.0000.000
44H46GLU-1-0.795-0.87415.685-0.466-0.4660.0000.0000.0000.000
45H47TRP0-0.016-0.01815.761-0.049-0.0490.0000.0000.0000.000
46H48VAL00.0060.00615.8510.0840.0840.0000.0000.0000.000
47H49ALA00.0310.00716.9090.0940.0940.0000.0000.0000.000
48H50SER00.0010.01816.434-0.165-0.1650.0000.0000.0000.000
49H51ILE0-0.0050.00616.0630.0990.0990.0000.0000.0000.000
50H52TYR0-0.063-0.07016.584-0.098-0.0980.0000.0000.0000.000
51H53SER0-0.067-0.05914.9900.0090.0090.0000.0000.0000.000
52H54TYR0-0.025-0.00517.9050.0280.0280.0000.0000.0000.000
53H55SER00.0270.01021.1540.0050.0050.0000.0000.0000.000
54H56GLY00.0350.02621.2410.0210.0210.0000.0000.0000.000
55H57TYR0-0.062-0.02822.2740.0010.0010.0000.0000.0000.000
56H58THR00.0200.00220.810-0.051-0.0510.0000.0000.0000.000
57H59TYR0-0.010-0.00121.4130.0480.0480.0000.0000.0000.000
58H60TYR00.0300.00821.187-0.068-0.0680.0000.0000.0000.000
59H61ALA00.0520.03521.2900.0440.0440.0000.0000.0000.000
60H62ASP-1-0.837-0.92923.139-0.348-0.3480.0000.0000.0000.000
61H63SER0-0.0020.01422.7500.0130.0130.0000.0000.0000.000
62H64VAL0-0.001-0.00420.7030.0110.0110.0000.0000.0000.000
63H65LYS10.8970.95424.0280.3860.3860.0000.0000.0000.000
64H66GLY0-0.025-0.00126.5720.0230.0230.0000.0000.0000.000
65H67ARG10.7030.82223.8800.4170.4170.0000.0000.0000.000
66H68PHE0-0.008-0.02619.228-0.013-0.0130.0000.0000.0000.000
67H69THR0-0.024-0.00821.7690.0200.0200.0000.0000.0000.000
68H70ILE00.0010.00515.600-0.040-0.0400.0000.0000.0000.000
69H71SER0-0.023-0.01518.4470.0690.0690.0000.0000.0000.000
70H72ALA00.0270.00316.204-0.115-0.1150.0000.0000.0000.000
71H73ASP-1-0.766-0.85615.622-0.791-0.7910.0000.0000.0000.000
72H74THR00.002-0.01618.404-0.019-0.0190.0000.0000.0000.000
73H75SER0-0.076-0.03816.2430.0030.0030.0000.0000.0000.000
74H76LYS10.9070.95815.3370.6330.6330.0000.0000.0000.000
75H77ASN00.0280.01011.779-0.199-0.1990.0000.0000.0000.000
76H78THR0-0.032-0.01311.134-0.311-0.3110.0000.0000.0000.000
77H79ALA0-0.018-0.00312.3330.1930.1930.0000.0000.0000.000
78H80TYR00.002-0.02913.819-0.054-0.0540.0000.0000.0000.000
79H81LEU00.0100.00615.6240.0300.0300.0000.0000.0000.000
80H82GLN0-0.038-0.02117.4710.0000.0000.0000.0000.0000.000
81H83MET0-0.0150.00117.7690.0020.0020.0000.0000.0000.000
82H84ASN00.0690.03821.7920.0300.0300.0000.0000.0000.000
83H85SER00.0180.01025.5560.0070.0070.0000.0000.0000.000
84H86LEU00.0170.01621.4490.0010.0010.0000.0000.0000.000
85H87ARG10.9420.97725.0910.3390.3390.0000.0000.0000.000
86H88ALA00.0860.02724.552-0.025-0.0250.0000.0000.0000.000
87H89GLU-1-0.966-0.98323.738-0.291-0.2910.0000.0000.0000.000
88H90ASP-1-0.774-0.84020.950-0.459-0.4590.0000.0000.0000.000
89H91THR0-0.0090.01219.459-0.054-0.0540.0000.0000.0000.000
90H92ALA0-0.027-0.01715.9560.0190.0190.0000.0000.0000.000
91H93VAL0-0.0140.0059.9820.0320.0320.0000.0000.0000.000
92H94TYR0-0.040-0.04112.047-0.079-0.0790.0000.0000.0000.000
93H95TYR00.0280.0126.818-0.041-0.0410.0000.0000.0000.000
94H97ALA00.0290.0046.890-0.995-0.9950.0000.0000.0000.000
95H98ARG10.8580.9166.8782.7012.7010.0000.0000.0000.000
96H99GLN00.0910.0669.296-0.029-0.0290.0000.0000.0000.000
97H100SER0-0.061-0.0688.5400.0700.0700.0000.0000.0000.000
98H101SER0-0.050-0.05010.4420.0520.0520.0000.0000.0000.000
99H102ALA0-0.004-0.00412.5200.0410.0410.0000.0000.0000.000
100H103GLU-1-0.862-0.9018.8250.5250.5250.0000.0000.0000.000
101H104ILE0-0.062-0.01412.2010.0200.0200.0000.0000.0000.000
102H105GLU-1-0.942-0.96114.662-0.136-0.1360.0000.0000.0000.000
103H106SER0-0.037-0.02618.3200.0310.0310.0000.0000.0000.000
104H107TRP0-0.0010.00619.838-0.050-0.0500.0000.0000.0000.000
105H108TYR00.0040.00022.538-0.016-0.0160.0000.0000.0000.000
106H109TYR00.0520.00924.208-0.007-0.0070.0000.0000.0000.000
107H110TYR0-0.031-0.01625.339-0.014-0.0140.0000.0000.0000.000
108H111SER0-0.032-0.02522.2450.0200.0200.0000.0000.0000.000
109H112GLY0-0.0370.00221.454-0.011-0.0110.0000.0000.0000.000
110H113GLU-1-0.789-0.86016.853-0.717-0.7170.0000.0000.0000.000
111H114ALA0-0.011-0.01014.2160.0310.0310.0000.0000.0000.000
112H115MET0-0.048-0.02710.157-0.063-0.0630.0000.0000.0000.000
113H116ASP-1-0.704-0.8178.898-1.006-1.0060.0000.0000.0000.000
114H117TYR0-0.071-0.0442.721-0.650-0.0700.171-0.192-0.560-0.001
115H118TRP0-0.015-0.0253.9270.0450.4580.000-0.095-0.3170.000
116H119GLY00.0180.0162.263-13.088-10.2942.296-2.293-2.796-0.034
117H120GLN00.0060.0021.827-11.166-14.33511.791-3.985-4.637-0.024
118H121GLY0-0.0100.0004.0940.8410.9740.003-0.053-0.0820.000
119H122THR0-0.046-0.0257.7330.6160.6160.0000.0000.0000.000
120H123LEU0-0.032-0.02310.979-0.039-0.0390.0000.0000.0000.000
121H124VAL00.0060.01513.8770.0620.0620.0000.0000.0000.000
122H125THR0-0.010-0.01017.1610.0250.0250.0000.0000.0000.000
123H126VAL00.007-0.00420.2240.0150.0150.0000.0000.0000.000
124H127SER0-0.014-0.03123.4920.0220.0220.0000.0000.0000.000
125H128SER00.0150.00426.413-0.003-0.0030.0000.0000.0000.000
126H129ALA0-0.0330.01027.5600.0140.0140.0000.0000.0000.000
127H130SER00.0490.01527.896-0.014-0.0140.0000.0000.0000.000
128H131THR0-0.031-0.01324.1410.0050.0050.0000.0000.0000.000
129H132LYS10.8120.90426.249-0.036-0.0360.0000.0000.0000.000
130H133GLY00.0840.04625.3050.0050.0050.0000.0000.0000.000
131H134PRO0-0.063-0.01523.540-0.011-0.0110.0000.0000.0000.000
132H135SER0-0.0030.00726.7180.0030.0030.0000.0000.0000.000
133H136VAL00.0200.00325.9860.0100.0100.0000.0000.0000.000
134H137PHE00.002-0.01328.629-0.008-0.0080.0000.0000.0000.000
135H138PRO00.0200.01929.7960.0150.0150.0000.0000.0000.000
136H139LEU0-0.025-0.01428.903-0.018-0.0180.0000.0000.0000.000
137H140ALA00.0260.01231.9130.0160.0160.0000.0000.0000.000
138H141PRO00.0530.02133.287-0.008-0.0080.0000.0000.0000.000
139H142SER0-0.020-0.03935.485-0.013-0.0130.0000.0000.0000.000
140H143SER00.0400.01539.0500.0070.0070.0000.0000.0000.000
141H144LYS10.9360.96439.720-0.120-0.1200.0000.0000.0000.000
142H145SER00.0060.03334.575-0.003-0.0030.0000.0000.0000.000
143H146THR0-0.006-0.00334.8010.0140.0140.0000.0000.0000.000
144H147SER0-0.012-0.00835.497-0.011-0.0110.0000.0000.0000.000
145H148GLY0-0.0050.00837.216-0.004-0.0040.0000.0000.0000.000
146H149GLY00.0440.01936.517-0.001-0.0010.0000.0000.0000.000
147H150THR0-0.034-0.02031.5320.0110.0110.0000.0000.0000.000
148H151ALA00.0300.01532.369-0.021-0.0210.0000.0000.0000.000
149H152ALA0-0.0140.00430.0210.0220.0220.0000.0000.0000.000
150H153LEU0-0.0010.01028.234-0.023-0.0230.0000.0000.0000.000
151H154GLY00.032-0.00927.1100.0260.0260.0000.0000.0000.000
152H155CYS0-0.072-0.01223.9230.0190.0190.0000.0000.0000.000
153H156LEU00.0170.01926.2090.0080.0080.0000.0000.0000.000
154H157VAL00.0030.00022.884-0.005-0.0050.0000.0000.0000.000
155H158LYS10.8800.90325.877-0.075-0.0750.0000.0000.0000.000
156H159ASP-1-0.815-0.88328.0670.0500.0500.0000.0000.0000.000
157H160TYR0-0.046-0.03919.9700.0100.0100.0000.0000.0000.000
158H161PHE00.0370.04623.575-0.012-0.0120.0000.0000.0000.000
159H162PRO00.0390.00820.1810.0110.0110.0000.0000.0000.000
160H163GLU-1-0.770-0.88217.0530.1360.1360.0000.0000.0000.000
161H164PRO0-0.015-0.00613.781-0.047-0.0470.0000.0000.0000.000
162H165VAL0-0.003-0.01716.594-0.005-0.0050.0000.0000.0000.000
163H166THR0-0.028-0.01013.4670.0750.0750.0000.0000.0000.000
164H167VAL00.013-0.01616.448-0.074-0.0740.0000.0000.0000.000
165H168SER0-0.0190.00616.8670.0830.0830.0000.0000.0000.000
166H169TRP00.0190.00018.640-0.094-0.0940.0000.0000.0000.000
167H170ASN00.012-0.01421.3350.0250.0250.0000.0000.0000.000
168H171SER0-0.016-0.01420.295-0.007-0.0070.0000.0000.0000.000
169H172GLY00.0090.01117.8680.0560.0560.0000.0000.0000.000
170H173ALA0-0.052-0.00818.5180.0400.0400.0000.0000.0000.000
171H174LEU0-0.025-0.01121.5080.0020.0020.0000.0000.0000.000
172H175THR00.0190.00516.4260.0200.0200.0000.0000.0000.000
173H176SER00.017-0.00319.111-0.015-0.0150.0000.0000.0000.000
174H177GLY00.0280.01521.183-0.045-0.0450.0000.0000.0000.000
175H178VAL0-0.068-0.03219.506-0.050-0.0500.0000.0000.0000.000
176H179HIS00.0190.02319.9790.0460.0460.0000.0000.0000.000
177H180THR00.0130.00217.871-0.058-0.0580.0000.0000.0000.000
178H181PHE0-0.040-0.00519.0450.0130.0130.0000.0000.0000.000
179H182PRO00.022-0.00218.3910.0130.0130.0000.0000.0000.000
180H183ALA00.0030.01719.182-0.008-0.0080.0000.0000.0000.000
181H184VAL0-0.018-0.01121.180-0.026-0.0260.0000.0000.0000.000
182H185LEU0-0.043-0.01924.2510.0040.0040.0000.0000.0000.000
183H186GLN0-0.032-0.03425.9100.0090.0090.0000.0000.0000.000
184H187SER00.0220.00329.495-0.010-0.0100.0000.0000.0000.000
185H188SER0-0.001-0.00131.696-0.008-0.0080.0000.0000.0000.000
186H189GLY00.0200.01629.019-0.007-0.0070.0000.0000.0000.000
187H190LEU0-0.058-0.01727.199-0.004-0.0040.0000.0000.0000.000
188H191TYR00.0340.02021.625-0.005-0.0050.0000.0000.0000.000
189H192SER0-0.012-0.01424.7210.0090.0090.0000.0000.0000.000
190H193LEU00.0070.02819.762-0.006-0.0060.0000.0000.0000.000
191H194SER00.013-0.00823.551-0.006-0.0060.0000.0000.0000.000
192H195SER00.0000.00120.7680.0200.0200.0000.0000.0000.000
193H196VAL00.0270.00523.252-0.030-0.0300.0000.0000.0000.000
194H197VAL00.0210.01423.8150.0410.0410.0000.0000.0000.000
195H198THR0-0.040-0.01225.590-0.034-0.0340.0000.0000.0000.000
196H199VAL00.0310.01427.2620.0290.0290.0000.0000.0000.000
197H200PRO00.0400.01029.406-0.022-0.0220.0000.0000.0000.000
198H201SER0-0.009-0.01532.506-0.004-0.0040.0000.0000.0000.000
199H202SER00.0040.00135.574-0.006-0.0060.0000.0000.0000.000
200H203SER0-0.0210.00332.943-0.010-0.0100.0000.0000.0000.000
201H204LEU0-0.015-0.00733.5780.0140.0140.0000.0000.0000.000
202H205GLY00.0460.02435.570-0.014-0.0140.0000.0000.0000.000
203H206THR0-0.032-0.00635.769-0.001-0.0010.0000.0000.0000.000
204H207GLN00.0120.00630.5540.0080.0080.0000.0000.0000.000
205H208THR00.0020.01230.084-0.008-0.0080.0000.0000.0000.000
206H209TYR00.003-0.01427.5190.0330.0330.0000.0000.0000.000
207H210ILE0-0.031-0.02325.464-0.028-0.0280.0000.0000.0000.000
208H212ASN00.019-0.00320.2790.0050.0050.0000.0000.0000.000
209H213VAL00.0340.01820.1180.0560.0560.0000.0000.0000.000
210H214ASN0-0.027-0.02217.653-0.081-0.0810.0000.0000.0000.000
211H215HIS00.0260.02618.4350.0430.0430.0000.0000.0000.000
212H216LYS11.0200.98412.606-0.583-0.5830.0000.0000.0000.000
213H217PRO00.0080.01618.297-0.031-0.0310.0000.0000.0000.000
214H218SER0-0.029-0.02020.841-0.020-0.0200.0000.0000.0000.000
215H219ASN0-0.049-0.02122.1960.0100.0100.0000.0000.0000.000
216H220THR00.0160.01823.1300.0050.0050.0000.0000.0000.000
217H221LYS10.9090.95321.939-0.215-0.2150.0000.0000.0000.000
218H222VAL0-0.022-0.02423.589-0.026-0.0260.0000.0000.0000.000
219H223ASP-1-0.821-0.89424.1180.3500.3500.0000.0000.0000.000
220H224LYS10.8490.92026.379-0.188-0.1880.0000.0000.0000.000
221H225LYS11.0000.99828.372-0.166-0.1660.0000.0000.0000.000
222H226VAL0-0.017-0.01429.018-0.018-0.0180.0000.0000.0000.000
223H227GLU-1-0.969-0.96731.9120.1620.1620.0000.0000.0000.000
224H228PRO0-0.004-0.01735.550-0.005-0.0050.0000.0000.0000.000
225H229LYS10.9801.01137.472-0.121-0.1210.0000.0000.0000.000