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: QY4VY

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287007.017028
FMO2-HF: Nuclear repulsion 2202201.230938
FMO2-HF: Total energy -84805.78609
FMO2-MP2: Total energy -85053.069431


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.
-32.199-22.0116.303-7.015-9.474-0.049
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 : -0.001 / 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].
3H5VAL00.0080.0022.748-0.9631.7010.441-1.489-1.616-0.009
4H6GLU-1-0.771-0.8815.357-2.466-2.431-0.001-0.002-0.0310.000
5H7SER0-0.065-0.0398.5490.5490.5490.0000.0000.0000.000
6H8GLY00.0570.02211.851-0.197-0.1970.0000.0000.0000.000
7H9GLY00.0020.00314.422-0.071-0.0710.0000.0000.0000.000
8H10GLY0-0.006-0.00315.9640.0630.0630.0000.0000.0000.000
9H11LEU0-0.026-0.00718.612-0.040-0.0400.0000.0000.0000.000
10H12VAL00.0050.01022.170-0.009-0.0090.0000.0000.0000.000
11H13GLN00.0250.01724.740-0.014-0.0140.0000.0000.0000.000
12H14PRO00.018-0.01427.854-0.017-0.0170.0000.0000.0000.000
13H15GLY0-0.020-0.00428.5020.0070.0070.0000.0000.0000.000
14H16GLY0-0.0200.00227.392-0.004-0.0040.0000.0000.0000.000
15H17SER0-0.029-0.04425.022-0.022-0.0220.0000.0000.0000.000
16H18LEU00.002-0.00519.2560.0350.0350.0000.0000.0000.000
17H19ARG10.9300.97518.5130.2250.2250.0000.0000.0000.000
18H20LEU00.0020.02113.8070.0650.0650.0000.0000.0000.000
19H21SER0-0.008-0.01513.159-0.068-0.0680.0000.0000.0000.000
20H22CYS0-0.079-0.0328.1390.2430.2430.0000.0000.0000.000
21H23ALA00.0440.0318.2440.0430.0430.0000.0000.0000.000
22H24ALA00.0260.0105.093-0.703-0.7030.0000.0000.0000.000
23H25SER0-0.038-0.0282.5360.8251.9660.115-0.482-0.7740.000
24H26GLY0-0.014-0.0015.2520.5230.643-0.001-0.003-0.1150.000
25H27PHE0-0.032-0.0183.048-0.0770.3280.019-0.107-0.3170.000
26H28ASN00.0130.0088.088-0.331-0.3310.0000.0000.0000.000
27H29PHE00.0170.0005.1650.0490.0490.0000.0000.0000.000
28H30SER00.0250.0159.9710.0110.0110.0000.0000.0000.000
29H31SER00.0130.00310.168-0.259-0.2590.0000.0000.0000.000
30H32SER00.0140.02412.2900.1800.1800.0000.0000.0000.000
31H33SER00.0270.00913.6330.0810.0810.0000.0000.0000.000
32H34ILE00.0030.01211.206-0.228-0.2280.0000.0000.0000.000
33H35HIS10.8640.90612.1241.5881.5880.0000.0000.0000.000
34H36TRP00.0130.01711.843-0.268-0.2680.0000.0000.0000.000
35H37VAL0-0.003-0.01112.1720.1540.1540.0000.0000.0000.000
36H38ARG10.8000.87413.0260.3690.3690.0000.0000.0000.000
37H39GLN00.007-0.00812.732-0.095-0.0950.0000.0000.0000.000
38H40ALA00.0200.01815.3520.0920.0920.0000.0000.0000.000
39H41PRO00.037-0.00417.407-0.029-0.0290.0000.0000.0000.000
40H42GLY0-0.0040.00617.8790.0100.0100.0000.0000.0000.000
41H43LYS10.9240.97318.7490.2310.2310.0000.0000.0000.000
42H44GLY00.0390.02717.406-0.031-0.0310.0000.0000.0000.000
43H45LEU0-0.013-0.00912.3330.0260.0260.0000.0000.0000.000
44H46GLU-1-0.809-0.89116.225-0.430-0.4300.0000.0000.0000.000
45H47TRP0-0.007-0.01816.276-0.019-0.0190.0000.0000.0000.000
46H48VAL0-0.0090.00816.5710.0990.0990.0000.0000.0000.000
47H49ALA00.0340.00317.5070.0920.0920.0000.0000.0000.000
48H50SER0-0.0050.02116.762-0.187-0.1870.0000.0000.0000.000
49H51ILE0-0.0080.01115.9630.1200.1200.0000.0000.0000.000
50H52TYR0-0.075-0.08216.566-0.112-0.1120.0000.0000.0000.000
51H53SER0-0.068-0.05214.9860.0610.0610.0000.0000.0000.000
52H54TYR0-0.021-0.00317.9020.0510.0510.0000.0000.0000.000
53H55SER00.0240.00521.1550.0220.0220.0000.0000.0000.000
54H56GLY00.0320.02821.2320.0390.0390.0000.0000.0000.000
55H57TYR0-0.058-0.02722.2650.0200.0200.0000.0000.0000.000
56H58THR00.0150.00320.741-0.052-0.0520.0000.0000.0000.000
57H59TYR0-0.026-0.01121.4340.0670.0670.0000.0000.0000.000
58H60TYR0-0.0100.00621.435-0.050-0.0500.0000.0000.0000.000
59H61ALA00.0590.04322.1200.0220.0220.0000.0000.0000.000
60H62ASP-1-0.854-0.93823.870-0.323-0.3230.0000.0000.0000.000
61H63SER0-0.0180.00223.7080.0190.0190.0000.0000.0000.000
62H64VAL0-0.007-0.00121.5800.0300.0300.0000.0000.0000.000
63H65LYS10.9941.00524.8750.3740.3740.0000.0000.0000.000
64H66GLY0-0.039-0.00527.2290.0250.0250.0000.0000.0000.000
65H67ARG10.7230.83724.9510.2770.2770.0000.0000.0000.000
66H68PHE0-0.009-0.02120.1810.0130.0130.0000.0000.0000.000
67H69THR0-0.011-0.01722.205-0.016-0.0160.0000.0000.0000.000
68H70ILE00.017-0.00315.6680.0010.0010.0000.0000.0000.000
69H71SER0-0.036-0.01818.3930.0290.0290.0000.0000.0000.000
70H72ALA00.0200.00016.226-0.092-0.0920.0000.0000.0000.000
71H73ASP-1-0.787-0.89316.189-0.631-0.6310.0000.0000.0000.000
72H74THR00.006-0.02018.406-0.043-0.0430.0000.0000.0000.000
73H75SER0-0.056-0.01716.523-0.011-0.0110.0000.0000.0000.000
74H76LYS10.9220.96815.2660.6110.6110.0000.0000.0000.000
75H77ASN00.0030.00211.760-0.309-0.3090.0000.0000.0000.000
76H78THR0-0.027-0.00311.142-0.200-0.2000.0000.0000.0000.000
77H79ALA0-0.027-0.00412.3450.1150.1150.0000.0000.0000.000
78H80TYR0-0.030-0.03113.9030.0370.0370.0000.0000.0000.000
79H81LEU00.0040.00416.156-0.038-0.0380.0000.0000.0000.000
80H82GLN0-0.047-0.01617.8120.0640.0640.0000.0000.0000.000
81H83MET0-0.0050.00019.056-0.014-0.0140.0000.0000.0000.000
82H84ASN00.0570.03222.4260.0630.0630.0000.0000.0000.000
83H85SER00.0130.00526.175-0.010-0.0100.0000.0000.0000.000
84H86LEU00.0000.01422.284-0.016-0.0160.0000.0000.0000.000
85H87ARG10.9831.00225.6850.2050.2050.0000.0000.0000.000
86H88ALA00.0820.02325.059-0.012-0.0120.0000.0000.0000.000
87H89GLU-1-0.970-0.99024.229-0.210-0.2100.0000.0000.0000.000
88H90ASP-1-0.772-0.84621.592-0.299-0.2990.0000.0000.0000.000
89H91THR0-0.0380.00319.962-0.004-0.0040.0000.0000.0000.000
90H92ALA0-0.017-0.01616.465-0.024-0.0240.0000.0000.0000.000
91H93VAL0-0.0140.00710.3560.1130.1130.0000.0000.0000.000
92H94TYR0-0.061-0.05212.715-0.201-0.2010.0000.0000.0000.000
93H95TYR00.0230.0197.2410.1490.1490.0000.0000.0000.000
94H97ALA00.0410.0087.332-0.873-0.8730.0000.0000.0000.000
95H98ARG10.8650.9316.9852.9472.9470.0000.0000.0000.000
96H99GLN00.0940.0669.271-0.215-0.2150.0000.0000.0000.000
97H100SER0-0.065-0.0678.5540.2870.2870.0000.0000.0000.000
98H101SER0-0.048-0.04910.4450.1110.1110.0000.0000.0000.000
99H102ALA0-0.007-0.00512.5490.0960.0960.0000.0000.0000.000
100H103GLU-1-0.858-0.8999.157-1.620-1.6200.0000.0000.0000.000
101H104ILE0-0.054-0.01412.3630.0560.0560.0000.0000.0000.000
102H105GLU-1-0.950-0.96514.660-0.567-0.5670.0000.0000.0000.000
103H106SER0-0.058-0.05618.3220.0400.0400.0000.0000.0000.000
104H107TRP00.0060.01019.832-0.030-0.0300.0000.0000.0000.000
105H108TYR0-0.001-0.00222.5340.0170.0170.0000.0000.0000.000
106H109TYR00.0690.01024.193-0.025-0.0250.0000.0000.0000.000
107H110TYR0-0.015-0.00925.317-0.020-0.0200.0000.0000.0000.000
108H111SER0-0.071-0.01022.728-0.006-0.0060.0000.0000.0000.000
109H112GLY0-0.0180.00221.442-0.038-0.0380.0000.0000.0000.000
110H113GLU-1-0.831-0.87616.861-0.938-0.9380.0000.0000.0000.000
111H114ALA0-0.011-0.01314.0630.0390.0390.0000.0000.0000.000
112H115MET0-0.075-0.03710.4400.0020.0020.0000.0000.0000.000
113H116ASP-1-0.691-0.8238.803-2.511-2.5110.0000.0000.0000.000
114H117TYR0-0.100-0.0512.919-1.493-0.9940.085-0.152-0.4310.000
115H118TRP0-0.002-0.0154.0720.9691.270-0.001-0.036-0.2640.000
116H119GLY00.0060.0152.587-8.634-6.4330.946-1.383-1.764-0.018
117H120GLN00.016-0.0112.091-17.078-14.3314.701-3.347-4.102-0.022
118H121GLY0-0.010-0.0014.4920.2700.345-0.001-0.014-0.0600.000
119H122THR0-0.046-0.0178.1930.8110.8110.0000.0000.0000.000
120H123LEU0-0.025-0.02311.368-0.205-0.2050.0000.0000.0000.000
121H124VAL00.0020.01314.2620.0780.0780.0000.0000.0000.000
122H125THR0-0.022-0.01917.587-0.023-0.0230.0000.0000.0000.000
123H126VAL00.0180.00120.6240.0210.0210.0000.0000.0000.000
124H127SER0-0.027-0.03823.923-0.007-0.0070.0000.0000.0000.000
125H128SER00.0130.00426.8060.0130.0130.0000.0000.0000.000
126H129ALA0-0.0190.01627.8980.0080.0080.0000.0000.0000.000
127H130SER00.0340.01028.1980.0040.0040.0000.0000.0000.000
128H131THR0-0.034-0.01423.8800.0060.0060.0000.0000.0000.000
129H132LYS10.8910.95226.127-0.277-0.2770.0000.0000.0000.000
130H133GLY00.0670.03524.9010.0240.0240.0000.0000.0000.000
131H134PRO0-0.078-0.02123.220-0.034-0.0340.0000.0000.0000.000
132H135SER00.0060.00826.3640.0000.0000.0000.0000.0000.000
133H136VAL00.0180.00025.7020.0160.0160.0000.0000.0000.000
134H137PHE0-0.026-0.03028.319-0.018-0.0180.0000.0000.0000.000
135H138PRO00.0100.01129.5790.0230.0230.0000.0000.0000.000
136H139LEU0-0.019-0.01028.906-0.030-0.0300.0000.0000.0000.000
137H140ALA00.0240.01231.8010.0160.0160.0000.0000.0000.000
138H141PRO00.0610.02633.038-0.016-0.0160.0000.0000.0000.000
139H142SER00.012-0.02535.412-0.015-0.0150.0000.0000.0000.000
140H143SER00.0340.01239.0370.0050.0050.0000.0000.0000.000
141H144LYS10.9400.96739.764-0.164-0.1640.0000.0000.0000.000
142H145SER0-0.0350.01834.606-0.002-0.0020.0000.0000.0000.000
143H146THR0-0.025-0.01334.8310.0180.0180.0000.0000.0000.000
144H147SER00.003-0.00135.524-0.015-0.0150.0000.0000.0000.000
145H148GLY00.0000.00937.328-0.011-0.0110.0000.0000.0000.000
146H149GLY00.0380.01336.6570.0020.0020.0000.0000.0000.000
147H150THR0-0.025-0.01231.6710.0130.0130.0000.0000.0000.000
148H151ALA00.0300.01032.429-0.024-0.0240.0000.0000.0000.000
149H152ALA0-0.0160.00630.0500.0260.0260.0000.0000.0000.000
150H153LEU00.0010.01028.284-0.026-0.0260.0000.0000.0000.000
151H154GLY00.033-0.01726.9810.0300.0300.0000.0000.0000.000
152H155CYS0-0.053-0.00123.6530.0410.0410.0000.0000.0000.000
153H156LEU00.0190.02026.0740.0050.0050.0000.0000.0000.000
154H157VAL00.000-0.00722.7350.0020.0020.0000.0000.0000.000
155H158LYS10.9540.96825.716-0.255-0.2550.0000.0000.0000.000
156H159ASP-1-0.863-0.93428.1280.2480.2480.0000.0000.0000.000
157H160TYR0-0.052-0.02020.2210.0070.0070.0000.0000.0000.000
158H161PHE00.0250.03723.747-0.022-0.0220.0000.0000.0000.000
159H162PRO00.0320.00420.3780.0070.0070.0000.0000.0000.000
160H163GLU-1-0.790-0.91817.3240.5200.5200.0000.0000.0000.000
161H164PRO0-0.007-0.00313.767-0.029-0.0290.0000.0000.0000.000
162H165VAL00.003-0.01016.6700.0040.0040.0000.0000.0000.000
163H166THR0-0.066-0.02513.1610.1360.1360.0000.0000.0000.000
164H167VAL00.035-0.01416.139-0.125-0.1250.0000.0000.0000.000
165H168SER0-0.0090.01116.5670.0960.0960.0000.0000.0000.000
166H169TRP00.0140.01018.387-0.120-0.1200.0000.0000.0000.000
167H170ASN00.0290.00821.1110.0350.0350.0000.0000.0000.000
168H171SER0-0.012-0.01219.944-0.030-0.0300.0000.0000.0000.000
169H172GLY00.0030.00817.6280.1170.1170.0000.0000.0000.000
170H173ALA0-0.056-0.01018.2580.0140.0140.0000.0000.0000.000
171H174LEU0-0.024-0.01121.359-0.031-0.0310.0000.0000.0000.000
172H175THR00.0180.00616.3190.0270.0270.0000.0000.0000.000
173H176SER00.020-0.00519.098-0.050-0.0500.0000.0000.0000.000
174H177GLY00.0240.01421.285-0.040-0.0400.0000.0000.0000.000
175H178VAL0-0.067-0.02819.472-0.049-0.0490.0000.0000.0000.000
176H179HIS00.0290.02420.0860.0520.0520.0000.0000.0000.000
177H180THR0-0.026-0.04317.8630.0070.0070.0000.0000.0000.000
178H181PHE0-0.035-0.01418.958-0.008-0.0080.0000.0000.0000.000
179H182PRO00.013-0.00518.4040.0490.0490.0000.0000.0000.000
180H183ALA0-0.0010.01719.296-0.021-0.0210.0000.0000.0000.000
181H184VAL00.002-0.00121.293-0.047-0.0470.0000.0000.0000.000
182H185LEU0-0.048-0.02424.4140.0200.0200.0000.0000.0000.000
183H186GLN0-0.069-0.04226.134-0.026-0.0260.0000.0000.0000.000
184H187SER00.012-0.00129.697-0.004-0.0040.0000.0000.0000.000
185H188SER00.0100.00231.987-0.010-0.0100.0000.0000.0000.000
186H189GLY00.0160.01729.298-0.005-0.0050.0000.0000.0000.000
187H190LEU0-0.044-0.01027.3800.0170.0170.0000.0000.0000.000
188H191TYR00.0260.00922.439-0.019-0.0190.0000.0000.0000.000
189H192SER0-0.021-0.02324.8620.0110.0110.0000.0000.0000.000
190H193LEU00.0130.02819.760-0.016-0.0160.0000.0000.0000.000
191H194SER00.010-0.00923.507-0.017-0.0170.0000.0000.0000.000
192H195SER00.0260.03720.5070.0170.0170.0000.0000.0000.000
193H196VAL00.0180.00823.184-0.034-0.0340.0000.0000.0000.000
194H197VAL00.0190.01323.8240.0450.0450.0000.0000.0000.000
195H198THR0-0.042-0.01025.594-0.044-0.0440.0000.0000.0000.000
196H199VAL00.0290.01027.2070.0260.0260.0000.0000.0000.000
197H200PRO00.0390.00629.433-0.031-0.0310.0000.0000.0000.000
198H201SER0-0.025-0.02132.5530.0070.0070.0000.0000.0000.000
199H202SER00.0230.01135.6000.0000.0000.0000.0000.0000.000
200H203SER0-0.024-0.00532.802-0.007-0.0070.0000.0000.0000.000
201H204LEU0-0.031-0.01633.5400.0250.0250.0000.0000.0000.000
202H205GLY00.0410.02135.399-0.019-0.0190.0000.0000.0000.000
203H206THR0-0.045-0.01635.2380.0070.0070.0000.0000.0000.000
204H207GLN00.0230.01330.4550.0140.0140.0000.0000.0000.000
205H208THR0-0.0020.00430.813-0.001-0.0010.0000.0000.0000.000
206H209TYR00.0180.00627.3040.0450.0450.0000.0000.0000.000
207H210ILE0-0.025-0.02724.782-0.033-0.0330.0000.0000.0000.000
208H212ASN00.016-0.01419.8890.0030.0030.0000.0000.0000.000
209H213VAL00.0200.01419.7670.0950.0950.0000.0000.0000.000
210H214ASN0-0.006-0.00616.193-0.147-0.1470.0000.0000.0000.000
211H215HIS00.0300.00618.0170.0840.0840.0000.0000.0000.000
212H216LYS11.0060.97511.993-1.978-1.9780.0000.0000.0000.000
213H217PRO00.0070.01517.715-0.037-0.0370.0000.0000.0000.000
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