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: 49KJN

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2291932.458657
FMO2-HF: Nuclear repulsion 2207125.123969
FMO2-HF: Total energy -84807.334688
FMO2-MP2: Total energy -85054.724965


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.
-30.951-23.53716.991-10.21-14.194-0.07
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 : 0.015 / q_NPA : 0.008
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].
3H5VAL0-0.014-0.0152.476-4.880-1.3311.344-2.380-2.512-0.013
4H6GLU-1-0.774-0.8815.174-4.053-3.975-0.001-0.003-0.0750.000
5H7SER0-0.046-0.0308.3090.5110.5110.0000.0000.0000.000
6H8GLY00.0420.01111.622-0.086-0.0860.0000.0000.0000.000
7H9GLY00.0220.01414.2680.0250.0250.0000.0000.0000.000
8H10GLY00.002-0.00815.8160.0720.0720.0000.0000.0000.000
9H11LEU0-0.047-0.01418.284-0.018-0.0180.0000.0000.0000.000
10H12VAL0-0.0010.00621.672-0.011-0.0110.0000.0000.0000.000
11H13GLN00.0280.01624.1260.0100.0100.0000.0000.0000.000
12H14PRO0-0.024-0.02727.350-0.023-0.0230.0000.0000.0000.000
13H15GLY0-0.0040.00628.3820.0170.0170.0000.0000.0000.000
14H16GLY0-0.0030.00727.059-0.005-0.0050.0000.0000.0000.000
15H17SER0-0.026-0.04524.526-0.007-0.0070.0000.0000.0000.000
16H18LEU0-0.034-0.00818.3290.0240.0240.0000.0000.0000.000
17H19ARG10.8940.95417.7540.7750.7750.0000.0000.0000.000
18H20LEU00.0220.03413.301-0.009-0.0090.0000.0000.0000.000
19H21SER0-0.030-0.02913.1820.0830.0830.0000.0000.0000.000
20H22CYS0-0.098-0.0427.1720.3160.3160.0000.0000.0000.000
21H23ALA00.0280.0238.1810.3770.3770.0000.0000.0000.000
22H24ALA00.0590.0325.106-1.142-1.1420.0000.0000.0000.000
23H25SER0-0.039-0.0392.3410.0411.6311.412-1.264-1.738-0.001
24H26GLY0-0.022-0.0124.9130.6490.779-0.001-0.006-0.1230.000
25H27PHE0-0.048-0.0172.6830.0560.7330.102-0.195-0.5840.000
26H28ASN0-0.015-0.0128.052-0.400-0.4000.0000.0000.0000.000
27H29PHE00.017-0.0025.2530.1840.1840.0000.0000.0000.000
28H30SER00.0230.02410.090-0.138-0.1380.0000.0000.0000.000
29H31SER00.0290.0139.924-0.147-0.1470.0000.0000.0000.000
30H32SER00.0230.03112.2020.0500.0500.0000.0000.0000.000
31H33SER0-0.071-0.06013.8650.0450.0450.0000.0000.0000.000
32H34ILE0-0.0010.00311.245-0.205-0.2050.0000.0000.0000.000
33H35HIS10.8120.89511.9311.5261.5260.0000.0000.0000.000
34H36TRP0-0.0060.00810.623-0.417-0.4170.0000.0000.0000.000
35H37VAL0-0.004-0.00611.1990.2640.2640.0000.0000.0000.000
36H38ARG10.7940.87411.8880.4310.4310.0000.0000.0000.000
37H39GLN00.0270.02111.947-0.070-0.0700.0000.0000.0000.000
38H40ALA00.0410.03114.6550.0380.0380.0000.0000.0000.000
39H41PRO00.002-0.02117.2850.0130.0130.0000.0000.0000.000
40H42GLY00.0090.01317.8170.0140.0140.0000.0000.0000.000
41H43LYS10.8980.96017.9600.2510.2510.0000.0000.0000.000
42H44GLY00.0540.02816.421-0.007-0.0070.0000.0000.0000.000
43H45LEU0-0.005-0.00411.472-0.014-0.0140.0000.0000.0000.000
44H46GLU-1-0.781-0.85015.314-0.487-0.4870.0000.0000.0000.000
45H47TRP0-0.008-0.01415.394-0.060-0.0600.0000.0000.0000.000
46H48VAL00.000-0.00515.7320.0990.0990.0000.0000.0000.000
47H49ALA00.0270.00516.5420.0940.0940.0000.0000.0000.000
48H50SER00.0070.02315.963-0.190-0.1900.0000.0000.0000.000
49H51ILE0-0.0130.00216.1760.1060.1060.0000.0000.0000.000
50H52TYR0-0.030-0.04016.830-0.113-0.1130.0000.0000.0000.000
51H53SER0-0.044-0.04414.8800.0410.0410.0000.0000.0000.000
52H54TYR0-0.0140.00117.9080.0330.0330.0000.0000.0000.000
53H55SER00.0280.01021.0510.0200.0200.0000.0000.0000.000
54H56GLY0-0.0040.00621.3490.0320.0320.0000.0000.0000.000
55H57TYR0-0.0080.00022.350-0.002-0.0020.0000.0000.0000.000
56H58THR0-0.021-0.01620.904-0.058-0.0580.0000.0000.0000.000
57H59TYR00.0120.00421.1270.0560.0560.0000.0000.0000.000
58H60TYR00.0330.01420.645-0.087-0.0870.0000.0000.0000.000
59H61ALA00.0630.04720.9670.0590.0590.0000.0000.0000.000
60H62ASP-1-0.843-0.92922.780-0.384-0.3840.0000.0000.0000.000
61H63SER0-0.016-0.01022.0030.0170.0170.0000.0000.0000.000
62H64VAL0-0.012-0.00620.4000.0100.0100.0000.0000.0000.000
63H65LYS10.8520.91423.7040.4290.4290.0000.0000.0000.000
64H66GLY0-0.0080.00326.1190.0260.0260.0000.0000.0000.000
65H67ARG10.7050.83123.5810.4550.4550.0000.0000.0000.000
66H68PHE0-0.004-0.02219.201-0.007-0.0070.0000.0000.0000.000
67H69THR0-0.044-0.01821.3900.0250.0250.0000.0000.0000.000
68H70ILE00.0040.00815.115-0.040-0.0400.0000.0000.0000.000
69H71SER0-0.016-0.00817.9060.0770.0770.0000.0000.0000.000
70H72ALA00.0530.01115.684-0.131-0.1310.0000.0000.0000.000
71H73ASP-1-0.770-0.84315.564-0.917-0.9170.0000.0000.0000.000
72H74THR00.004-0.00618.369-0.021-0.0210.0000.0000.0000.000
73H75SER0-0.044-0.03615.9470.0030.0030.0000.0000.0000.000
74H76LYS10.8340.91215.0600.7610.7610.0000.0000.0000.000
75H77ASN00.0550.02711.427-0.265-0.2650.0000.0000.0000.000
76H78THR0-0.026-0.00210.728-0.430-0.4300.0000.0000.0000.000
77H79ALA0-0.009-0.00912.4250.2220.2220.0000.0000.0000.000
78H80TYR00.011-0.01913.378-0.096-0.0960.0000.0000.0000.000
79H81LEU00.0080.00215.5060.0110.0110.0000.0000.0000.000
80H82GLN0-0.018-0.00217.1530.0090.0090.0000.0000.0000.000
81H83MET0-0.0170.00017.745-0.013-0.0130.0000.0000.0000.000
82H84ASN00.0800.04421.7470.0360.0360.0000.0000.0000.000
83H85SER00.0180.01525.4610.0040.0040.0000.0000.0000.000
84H86LEU00.0070.01921.3010.0030.0030.0000.0000.0000.000
85H87ARG10.9030.94424.8410.3650.3650.0000.0000.0000.000
86H88ALA00.0700.02524.308-0.025-0.0250.0000.0000.0000.000
87H89GLU-1-0.930-0.97123.428-0.306-0.3060.0000.0000.0000.000
88H90ASP-1-0.767-0.83120.795-0.496-0.4960.0000.0000.0000.000
89H91THR0-0.027-0.00519.208-0.055-0.0550.0000.0000.0000.000
90H92ALA0-0.006-0.00715.6230.0310.0310.0000.0000.0000.000
91H93VAL00.0100.0229.6180.0190.0190.0000.0000.0000.000
92H94TYR0-0.027-0.04211.931-0.037-0.0370.0000.0000.0000.000
93H95TYR00.012-0.0036.499-0.022-0.0220.0000.0000.0000.000
94H97ALA00.0290.0096.467-1.174-1.1740.0000.0000.0000.000
95H98ARG10.8460.9027.4603.1683.1680.0000.0000.0000.000
96H99GLN00.0960.0679.740-0.043-0.0430.0000.0000.0000.000
97H100SER00.003-0.0398.6930.0910.0910.0000.0000.0000.000
98H101SER0-0.078-0.06410.5290.0700.0700.0000.0000.0000.000
99H102ALA0-0.016-0.00712.3380.0680.0680.0000.0000.0000.000
100H103GLU-1-0.850-0.8988.7420.3620.3620.0000.0000.0000.000
101H104ILE0-0.072-0.02612.0770.0340.0340.0000.0000.0000.000
102H105GLU-1-0.895-0.93614.588-0.224-0.2240.0000.0000.0000.000
103H106SER0-0.042-0.03318.2050.0430.0430.0000.0000.0000.000
104H107TRP0-0.035-0.01419.780-0.059-0.0590.0000.0000.0000.000
105H108TYR0-0.008-0.00422.6100.0030.0030.0000.0000.0000.000
106H109TYR00.0420.00524.033-0.015-0.0150.0000.0000.0000.000
107H110TYR0-0.037-0.01825.355-0.013-0.0130.0000.0000.0000.000
108H111SER0-0.033-0.03022.1100.0290.0290.0000.0000.0000.000
109H112GLY0-0.0090.01821.334-0.015-0.0150.0000.0000.0000.000
110H113GLU-1-0.773-0.83616.416-0.897-0.8970.0000.0000.0000.000
111H114ALA00.001-0.00414.3500.0430.0430.0000.0000.0000.000
112H115MET0-0.056-0.02610.009-0.084-0.0840.0000.0000.0000.000
113H116ASP-1-0.718-0.8158.795-1.303-1.3030.0000.0000.0000.000
114H117TYR0-0.079-0.0572.762-0.857-0.2940.151-0.177-0.536-0.001
115H118TRP0-0.016-0.0373.7640.1210.6240.000-0.138-0.3650.000
116H119GLY00.0140.0152.213-13.694-11.3564.215-3.077-3.476-0.036
117H120GLN00.0030.0001.869-10.196-12.3329.766-2.921-4.709-0.019
118H121GLY00.0040.0054.0300.8861.0080.003-0.049-0.0760.000
119H122THR0-0.049-0.0217.6080.6320.6320.0000.0000.0000.000
120H123LEU0-0.037-0.01810.856-0.031-0.0310.0000.0000.0000.000
121H124VAL0-0.017-0.00213.6770.0110.0110.0000.0000.0000.000
122H125THR0-0.020-0.01717.0790.0360.0360.0000.0000.0000.000
123H126VAL00.0170.01320.3600.0110.0110.0000.0000.0000.000
124H127SER0-0.002-0.01023.6730.0240.0240.0000.0000.0000.000
125H128SER00.0290.00426.583-0.006-0.0060.0000.0000.0000.000
126H129ALA0-0.034-0.00227.7920.0110.0110.0000.0000.0000.000
127H130SER00.0320.00927.701-0.015-0.0150.0000.0000.0000.000
128H131THR0-0.0040.00623.9910.0040.0040.0000.0000.0000.000
129H132LYS10.7960.88726.099-0.042-0.0420.0000.0000.0000.000
130H133GLY00.0960.05225.2400.0060.0060.0000.0000.0000.000
131H134PRO0-0.085-0.02423.826-0.013-0.0130.0000.0000.0000.000
132H135SER00.0240.01626.9120.0020.0020.0000.0000.0000.000
133H136VAL00.0210.00526.3030.0130.0130.0000.0000.0000.000
134H137PHE0-0.004-0.00628.962-0.013-0.0130.0000.0000.0000.000
135H138PRO00.0110.02130.1010.0160.0160.0000.0000.0000.000
136H139LEU0-0.037-0.02029.028-0.018-0.0180.0000.0000.0000.000
137H140ALA00.0400.01632.2270.0160.0160.0000.0000.0000.000
138H141PRO00.0560.02633.474-0.007-0.0070.0000.0000.0000.000
139H142SER00.014-0.02035.620-0.016-0.0160.0000.0000.0000.000
140H143SER00.0360.01838.8860.0090.0090.0000.0000.0000.000
141H144LYS10.9340.95839.641-0.145-0.1450.0000.0000.0000.000
142H145SER0-0.0250.03434.495-0.004-0.0040.0000.0000.0000.000
143H146THR0-0.024-0.02634.8920.0140.0140.0000.0000.0000.000
144H147SER00.0150.00935.661-0.012-0.0120.0000.0000.0000.000
145H148GLY0-0.0160.00737.5650.0000.0000.0000.0000.0000.000
146H149GLY00.0330.01736.7520.0010.0010.0000.0000.0000.000
147H150THR0-0.021-0.01531.7020.0080.0080.0000.0000.0000.000
148H151ALA00.004-0.00332.667-0.023-0.0230.0000.0000.0000.000
149H152ALA0-0.0100.00430.2240.0250.0250.0000.0000.0000.000
150H153LEU0-0.0080.00628.463-0.027-0.0270.0000.0000.0000.000
151H154GLY00.0490.00227.2810.0300.0300.0000.0000.0000.000
152H155CYS0-0.0490.00324.2970.0210.0210.0000.0000.0000.000
153H156LEU00.0190.01826.0350.0160.0160.0000.0000.0000.000
154H157VAL00.0280.01522.994-0.011-0.0110.0000.0000.0000.000
155H158LYS10.8710.90226.104-0.085-0.0850.0000.0000.0000.000
156H159ASP-1-0.804-0.86428.1840.0620.0620.0000.0000.0000.000
157H160TYR0-0.044-0.04320.1080.0040.0040.0000.0000.0000.000
158H161PHE00.0530.03023.757-0.010-0.0100.0000.0000.0000.000
159H162PRO00.0290.02820.2880.0080.0080.0000.0000.0000.000
160H163GLU-1-0.776-0.87917.1100.1930.1930.0000.0000.0000.000
161H164PRO0-0.010-0.00413.987-0.059-0.0590.0000.0000.0000.000
162H165VAL0-0.019-0.02116.696-0.014-0.0140.0000.0000.0000.000
163H166THR0-0.062-0.02613.7690.0920.0920.0000.0000.0000.000
164H167VAL00.027-0.01116.738-0.080-0.0800.0000.0000.0000.000
165H168SER0-0.022-0.00217.4040.1070.1070.0000.0000.0000.000
166H169TRP00.0090.00219.158-0.104-0.1040.0000.0000.0000.000
167H170ASN00.008-0.01421.6860.0320.0320.0000.0000.0000.000
168H171SER0-0.024-0.01920.879-0.002-0.0020.0000.0000.0000.000
169H172GLY00.0170.01418.2730.0510.0510.0000.0000.0000.000
170H173ALA0-0.034-0.00818.9470.0510.0510.0000.0000.0000.000
171H174LEU0-0.036-0.01121.545-0.019-0.0190.0000.0000.0000.000
172H175THR00.0360.00316.6710.0250.0250.0000.0000.0000.000
173H176SER00.0190.00719.293-0.012-0.0120.0000.0000.0000.000
174H177GLY00.0370.02321.238-0.050-0.0500.0000.0000.0000.000
175H178VAL0-0.059-0.02519.640-0.058-0.0580.0000.0000.0000.000
176H179HIS0-0.0020.00620.4270.0430.0430.0000.0000.0000.000
177H180THR00.0060.00318.072-0.070-0.0700.0000.0000.0000.000
178H181PHE0-0.0190.00519.1770.0280.0280.0000.0000.0000.000
179H182PRO00.031-0.00318.4110.0120.0120.0000.0000.0000.000
180H183ALA0-0.0120.01519.121-0.015-0.0150.0000.0000.0000.000
181H184VAL0-0.008-0.00821.047-0.028-0.0280.0000.0000.0000.000
182H185LEU0-0.033-0.01124.3610.0030.0030.0000.0000.0000.000
183H186GLN0-0.022-0.02025.8760.0070.0070.0000.0000.0000.000
184H187SER00.0260.00129.555-0.011-0.0110.0000.0000.0000.000
185H188SER0-0.006-0.00231.654-0.009-0.0090.0000.0000.0000.000
186H189GLY00.0190.01629.241-0.007-0.0070.0000.0000.0000.000
187H190LEU0-0.049-0.01527.191-0.007-0.0070.0000.0000.0000.000
188H191TYR00.0210.01121.377-0.002-0.0020.0000.0000.0000.000
189H192SER0-0.072-0.05525.0700.0060.0060.0000.0000.0000.000
190H193LEU00.0410.03019.960-0.006-0.0060.0000.0000.0000.000
191H194SER00.005-0.00723.921-0.007-0.0070.0000.0000.0000.000
192H195SER00.0150.00220.9190.0260.0260.0000.0000.0000.000
193H196VAL00.017-0.00123.430-0.040-0.0400.0000.0000.0000.000
194H197VAL00.0130.00823.8040.0470.0470.0000.0000.0000.000
195H198THR0-0.032-0.01125.619-0.035-0.0350.0000.0000.0000.000
196H199VAL00.0260.01127.2090.0320.0320.0000.0000.0000.000
197H200PRO00.0500.01929.675-0.022-0.0220.0000.0000.0000.000
198H201SER0-0.005-0.02232.833-0.005-0.0050.0000.0000.0000.000
199H202SER0-0.0010.00135.893-0.008-0.0080.0000.0000.0000.000
200H203SER0-0.0070.00533.181-0.007-0.0070.0000.0000.0000.000
201H204LEU0-0.028-0.00833.5890.0120.0120.0000.0000.0000.000
202H205GLY00.0280.00435.678-0.016-0.0160.0000.0000.0000.000
203H206THR0-0.0100.00436.339-0.001-0.0010.0000.0000.0000.000
204H207GLN0-0.0090.00530.9110.0150.0150.0000.0000.0000.000
205H208THR0-0.0020.01030.119-0.011-0.0110.0000.0000.0000.000
206H209TYR00.003-0.01128.0140.0320.0320.0000.0000.0000.000
207H210ILE0-0.023-0.01926.091-0.032-0.0320.0000.0000.0000.000
208H212ASN00.027-0.00120.8570.0050.0050.0000.0000.0000.000
209H213VAL00.0120.00320.9580.0500.0500.0000.0000.0000.000
210H214ASN0-0.006-0.01218.102-0.072-0.0720.0000.0000.0000.000
211H215HIS00.0260.02918.5630.0530.0530.0000.0000.0000.000
212H216LYS11.0280.99912.839-0.606-0.6060.0000.0000.0000.000
213H217PRO00.0050.01118.215-0.036-0.0360.0000.0000.0000.000
214H218SER0-0.021-0.02220.777-0.021-0.0210.0000.0000.0000.000
215H219ASN0-0.037-0.01822.0500.0090.0090.0000.0000.0000.000
216H220THR00.0190.01423.0840.0150.0150.0000.0000.0000.000
217H221LYS10.8960.95821.927-0.218-0.2180.0000.0000.0000.000
218H222VAL0-0.032-0.02323.658-0.023-0.0230.0000.0000.0000.000
219H223ASP-1-0.823-0.90324.3050.3720.3720.0000.0000.0000.000
220H224LYS10.8490.90926.613-0.203-0.2030.0000.0000.0000.000
221H225LYS10.9020.94628.651-0.168-0.1680.0000.0000.0000.000
222H226VAL0-0.033-0.01929.037-0.016-0.0160.0000.0000.0000.000
223H227GLU-1-0.854-0.91031.9970.1880.1880.0000.0000.0000.000
224H228PRO00.004-0.01135.566-0.004-0.0040.0000.0000.0000.000
225H229LYS10.9611.00237.653-0.140-0.1400.0000.0000.0000.000