FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 1NLMZ

Calculation Name: 2P4H-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P4H

Chain ID: X

ChEMBL ID:

UniProt ID: Q40316

Base Structure: X-ray

Registration Date: 2023-09-23

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 314
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4666428.704572
FMO2-HF: Nuclear repulsion 4545108.127601
FMO2-HF: Total energy -121320.57697
FMO2-MP2: Total energy -121675.637775


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(X:5:LYS)


Summations of interaction energy for fragment #1(X:5:LYS)
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.
-213.37-208.26736.932-19.075-22.96-0.22
Interaction energy analysis for fragmet #1(X:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.896
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].
3X7ARG10.8480.9273.88020.07521.740-0.018-0.917-0.7290.003
4X8VAL00.0270.0235.7390.2000.2000.0000.0000.0000.000
5X9CYS00.0140.0188.3591.7091.7090.0000.0000.0000.000
6X10VAL00.0020.01310.988-0.195-0.1950.0000.0000.0000.000
7X11THR00.012-0.00713.5591.0431.0430.0000.0000.0000.000
8X12GLY00.0180.01017.391-0.361-0.3610.0000.0000.0000.000
9X13GLY00.0280.00717.037-0.030-0.0300.0000.0000.0000.000
10X14THR0-0.008-0.01717.844-0.302-0.3020.0000.0000.0000.000
11X15GLY0-0.0020.00820.5680.6650.6650.0000.0000.0000.000
12X16PHE00.0180.00119.382-0.860-0.8600.0000.0000.0000.000
13X17LEU00.0470.02515.008-0.629-0.6290.0000.0000.0000.000
14X18GLY00.0500.02915.294-1.395-1.3950.0000.0000.0000.000
15X19SER0-0.018-0.02114.832-1.350-1.3500.0000.0000.0000.000
16X20TRP00.008-0.01912.403-0.202-0.2020.0000.0000.0000.000
17X21ILE00.0050.00210.323-2.182-2.1820.0000.0000.0000.000
18X22ILE0-0.028-0.00310.153-2.805-2.8050.0000.0000.0000.000
19X23LYS10.8210.90910.45623.19923.1990.0000.0000.0000.000
20X24SER00.0320.0238.239-3.277-3.2770.0000.0000.0000.000
21X25LEU0-0.012-0.0055.459-6.463-6.4630.0000.0000.0000.000
22X26LEU0-0.033-0.0105.866-5.273-5.2730.0000.0000.0000.000
23X27GLU-1-0.853-0.9117.283-28.898-28.8980.0000.0000.0000.000
24X28ASN0-0.069-0.0432.676-19.502-16.7930.472-1.319-1.861-0.016
25X29GLY00.0030.0002.260-20.439-17.8743.147-2.399-3.314-0.037
26X30TYR0-0.113-0.0782.4451.7386.5607.034-3.866-7.991-0.029
27X31SER0-0.043-0.0243.3096.0246.1270.0120.158-0.2720.000
28X32VAL00.005-0.0176.148-1.828-1.8280.0000.0000.0000.000
29X33ASN00.0530.0309.2381.7091.7090.0000.0000.0000.000
30X34THR0-0.024-0.01812.554-0.467-0.4670.0000.0000.0000.000
31X35THR00.0370.01715.3921.0611.0610.0000.0000.0000.000
32X36ILE0-0.021-0.01218.989-0.290-0.2900.0000.0000.0000.000
33X37ARG10.8810.92121.37411.96811.9680.0000.0000.0000.000
34X38ALA00.0240.01524.927-0.103-0.1030.0000.0000.0000.000
35X39ASP-1-0.761-0.88527.778-10.533-10.5330.0000.0000.0000.000
36X40PRO00.0220.01730.1440.1230.1230.0000.0000.0000.000
37X41GLU-1-0.779-0.86333.397-8.251-8.2510.0000.0000.0000.000
38X42ARG10.8270.90030.5578.6818.6810.0000.0000.0000.000
39X43LYS10.8560.92522.64312.28512.2850.0000.0000.0000.000
40X44ARG10.8380.91626.9009.7599.7590.0000.0000.0000.000
41X45ASP-1-0.748-0.86525.322-11.935-11.9350.0000.0000.0000.000
42X46VAL0-0.037-0.01820.250-0.225-0.2250.0000.0000.0000.000
43X47SER00.0350.01420.396-0.708-0.7080.0000.0000.0000.000
44X48PHE0-0.028-0.01920.527-0.470-0.4700.0000.0000.0000.000
45X49LEU0-0.050-0.02816.768-0.888-0.8880.0000.0000.0000.000
46X50THR00.025-0.01516.045-0.947-0.9470.0000.0000.0000.000
47X51ASN0-0.034-0.01017.7230.6050.6050.0000.0000.0000.000
48X52LEU0-0.0060.01713.980-0.162-0.1620.0000.0000.0000.000
49X53PRO00.033-0.00312.4090.1760.1760.0000.0000.0000.000
50X54GLY00.0320.02810.337-2.047-2.0470.0000.0000.0000.000
51X55ALA0-0.005-0.01310.910-0.195-0.1950.0000.0000.0000.000
52X56SER0-0.025-0.03712.7930.5490.5490.0000.0000.0000.000
53X57GLU-1-0.842-0.90510.800-19.439-19.4390.0000.0000.0000.000
54X58LYS10.8880.9606.29028.61028.6100.0000.0000.0000.000
55X59LEU0-0.0220.0079.390-1.363-1.3630.0000.0000.0000.000
56X60HIS0-0.039-0.01111.2481.9591.9590.0000.0000.0000.000
57X61PHE00.033-0.00214.261-0.439-0.4390.0000.0000.0000.000
58X62PHE00.0120.01714.6140.6080.6080.0000.0000.0000.000
59X63ASN0-0.063-0.04419.681-0.011-0.0110.0000.0000.0000.000
60X64ALA00.0570.02722.115-0.016-0.0160.0000.0000.0000.000
61X65ASP-1-0.846-0.90324.070-10.470-10.4700.0000.0000.0000.000
62X66LEU0-0.026-0.01922.785-0.163-0.1630.0000.0000.0000.000
63X67SER0-0.040-0.03025.365-0.161-0.1610.0000.0000.0000.000
64X68ASN0-0.027-0.01726.9040.1920.1920.0000.0000.0000.000
65X69PRO0-0.0020.00023.976-0.305-0.3050.0000.0000.0000.000
66X70ASP-1-0.883-0.93423.337-11.216-11.2160.0000.0000.0000.000
67X71SER0-0.038-0.02523.866-0.293-0.2930.0000.0000.0000.000
68X72PHE0-0.011-0.01619.198-0.460-0.4600.0000.0000.0000.000
69X73ALA00.0410.03218.971-0.778-0.7780.0000.0000.0000.000
70X74ALA00.007-0.01118.659-0.563-0.5630.0000.0000.0000.000
71X75ALA0-0.022-0.00616.451-0.468-0.4680.0000.0000.0000.000
72X76ILE00.016-0.01414.248-1.345-1.3450.0000.0000.0000.000
73X77GLU-1-0.776-0.86614.285-15.757-15.7570.0000.0000.0000.000
74X78GLY0-0.020-0.01012.268-0.586-0.5860.0000.0000.0000.000
75X79CYS0-0.127-0.0269.685-1.671-1.6710.0000.0000.0000.000
76X80VAL00.0370.0194.8900.9560.9560.0000.0000.0000.000
77X81GLY00.0110.0028.403-0.433-0.4330.0000.0000.0000.000
78X82ILE0-0.013-0.0029.8120.7450.7450.0000.0000.0000.000
79X83PHE00.0240.0017.5460.2430.2430.0000.0000.0000.000
80X84HIS00.0410.04513.4610.1980.1980.0000.0000.0000.000
81X85THR0-0.020-0.03815.7170.3180.3180.0000.0000.0000.000
82X86ALA0-0.0060.00818.5670.7760.7760.0000.0000.0000.000
83X87SER0-0.022-0.03021.6980.0770.0770.0000.0000.0000.000
84X88PRO0-0.0080.00325.2460.0630.0630.0000.0000.0000.000
85X89ILE0-0.0070.01228.3350.2460.2460.0000.0000.0000.000
86X98GLU-1-0.878-0.94339.772-7.485-7.4850.0000.0000.0000.000
87X99ILE00.0300.00838.079-0.316-0.3160.0000.0000.0000.000
88X100VAL00.0250.00735.416-0.255-0.2550.0000.0000.0000.000
89X101THR00.0210.01534.518-0.376-0.3760.0000.0000.0000.000
90X102LYS10.9240.95033.5898.7368.7360.0000.0000.0000.000
91X103ARG10.9860.99031.5599.2069.2060.0000.0000.0000.000
92X104THR0-0.054-0.01829.727-0.427-0.4270.0000.0000.0000.000
93X105VAL00.0300.01728.781-0.454-0.4540.0000.0000.0000.000
94X106ASP-1-0.800-0.88728.190-10.247-10.2470.0000.0000.0000.000
95X107GLY0-0.017-0.01126.759-0.311-0.3110.0000.0000.0000.000
96X108ALA0-0.035-0.02324.424-0.574-0.5740.0000.0000.0000.000
97X109LEU00.0330.01223.289-0.593-0.5930.0000.0000.0000.000
98X110GLY0-0.0230.01124.088-0.138-0.1380.0000.0000.0000.000
99X111ILE00.001-0.01316.5340.0140.0140.0000.0000.0000.000
100X112LEU00.0080.00819.690-0.468-0.4680.0000.0000.0000.000
101X113LYS10.8610.90921.15811.03111.0310.0000.0000.0000.000
102X114ALA0-0.034-0.00720.5380.2070.2070.0000.0000.0000.000
103X115CYS0-0.032-0.01416.926-0.587-0.5870.0000.0000.0000.000
104X116VAL00.0280.02618.975-0.417-0.4170.0000.0000.0000.000
105X117ASN0-0.028-0.01020.8640.1040.1040.0000.0000.0000.000
106X118SER00.0040.01015.268-0.045-0.0450.0000.0000.0000.000
107X119LYS10.8520.89816.40114.09214.0920.0000.0000.0000.000
108X120THR0-0.042-0.03111.0750.2970.2970.0000.0000.0000.000
109X121VAL0-0.066-0.01711.042-1.778-1.7780.0000.0000.0000.000
110X122LYS10.9120.9585.78739.20939.2090.0000.0000.0000.000
111X123ARG10.7360.85111.13623.57323.5730.0000.0000.0000.000
112X124PHE00.0140.01012.321-0.613-0.6130.0000.0000.0000.000
113X125ILE0-0.008-0.00310.7380.4890.4890.0000.0000.0000.000
114X126TYR0-0.006-0.00614.8130.1440.1440.0000.0000.0000.000
115X127THR0-0.015-0.00817.504-0.525-0.5250.0000.0000.0000.000
116X128SER0-0.017-0.03119.0241.0571.0570.0000.0000.0000.000
117X129SER0-0.003-0.01221.831-0.173-0.1730.0000.0000.0000.000
118X130GLY00.1140.06224.2230.2750.2750.0000.0000.0000.000
119X131SER0-0.046-0.02226.3860.5310.5310.0000.0000.0000.000
120X132ALA00.0240.01626.4430.4740.4740.0000.0000.0000.000
121X133VAL00.0060.00826.8290.1640.1640.0000.0000.0000.000
122X134SER00.016-0.00829.5340.3180.3180.0000.0000.0000.000
123X135PHE0-0.038-0.02231.8040.2710.2710.0000.0000.0000.000
124X136ASN0-0.022-0.02132.8970.4410.4410.0000.0000.0000.000
125X137GLY00.009-0.00935.4140.1280.1280.0000.0000.0000.000
126X138LYS10.8560.94334.3469.4859.4850.0000.0000.0000.000
127X139ASP-1-0.896-0.93637.457-8.086-8.0860.0000.0000.0000.000
128X140LYS10.7630.87931.69610.13610.1360.0000.0000.0000.000
129X141ASP-1-0.836-0.91334.364-9.610-9.6100.0000.0000.0000.000
130X142VAL00.0220.02329.578-0.297-0.2970.0000.0000.0000.000
131X143LEU0-0.052-0.02428.8670.2630.2630.0000.0000.0000.000
132X144ASP-1-0.798-0.89226.591-11.294-11.2940.0000.0000.0000.000
133X145GLU-1-0.817-0.92021.919-14.125-14.1250.0000.0000.0000.000
134X146SER0-0.087-0.04825.6760.1490.1490.0000.0000.0000.000
135X147ASP-1-0.782-0.87429.204-9.797-9.7970.0000.0000.0000.000
136X148TRP00.027-0.00826.230-0.422-0.4220.0000.0000.0000.000
137X149SER0-0.050-0.04431.0960.3900.3900.0000.0000.0000.000
138X150ASP-1-0.809-0.89933.134-8.365-8.3650.0000.0000.0000.000
139X151VAL00.004-0.02434.2180.0120.0120.0000.0000.0000.000
140X152ASP-1-0.817-0.90636.782-7.987-7.9870.0000.0000.0000.000
141X153LEU00.0150.03939.1500.2190.2190.0000.0000.0000.000
142X154LEU0-0.045-0.01934.3390.1060.1060.0000.0000.0000.000
143X155ARG10.8520.90937.8768.4428.4420.0000.0000.0000.000
144X156SER0-0.076-0.04441.2640.1920.1920.0000.0000.0000.000
145X157VAL00.008-0.01142.0850.1530.1530.0000.0000.0000.000
146X158LYS10.8630.95240.7537.2127.2120.0000.0000.0000.000
147X159PRO00.0460.03437.8760.0580.0580.0000.0000.0000.000
148X160PHE00.030-0.00435.273-0.107-0.1070.0000.0000.0000.000
149X161GLY00.0520.02634.640-0.218-0.2180.0000.0000.0000.000
150X162TRP00.0130.00834.298-0.325-0.3250.0000.0000.0000.000
151X163ASN00.000-0.00735.241-0.172-0.1720.0000.0000.0000.000
152X164TYR00.0210.02525.770-0.212-0.2120.0000.0000.0000.000
153X165ALA00.0700.03630.520-0.341-0.3410.0000.0000.0000.000
154X166VAL0-0.0200.01031.373-0.205-0.2050.0000.0000.0000.000
155X167SER0-0.025-0.01630.483-0.274-0.2740.0000.0000.0000.000
156X168LYS10.8940.92923.21413.10713.1070.0000.0000.0000.000
157X169THR00.006-0.02227.363-0.352-0.3520.0000.0000.0000.000
158X170LEU0-0.058-0.02929.516-0.037-0.0370.0000.0000.0000.000
159X171ALA0-0.006-0.00126.002-0.078-0.0780.0000.0000.0000.000
160X172GLU-1-0.726-0.79622.991-13.857-13.8570.0000.0000.0000.000
161X173LYS10.8890.96725.3229.9269.9260.0000.0000.0000.000
162X174ALA00.0150.01127.9750.0120.0120.0000.0000.0000.000
163X175VAL0-0.002-0.01121.331-0.076-0.0760.0000.0000.0000.000
164X176LEU0-0.036-0.01822.224-0.346-0.3460.0000.0000.0000.000
165X177GLU-1-0.859-0.89624.597-10.524-10.5240.0000.0000.0000.000
166X178PHE00.003-0.00923.8690.1470.1470.0000.0000.0000.000
167X179GLY00.031-0.00122.499-0.079-0.0790.0000.0000.0000.000
168X180GLU-1-0.944-0.95923.157-12.004-12.0040.0000.0000.0000.000
169X181GLN0-0.093-0.07025.2370.1910.1910.0000.0000.0000.000
170X182ASN0-0.101-0.05624.0550.4480.4480.0000.0000.0000.000
171X183GLY0-0.0070.01122.929-0.232-0.2320.0000.0000.0000.000
172X184ILE0-0.042-0.02117.746-0.656-0.6560.0000.0000.0000.000
173X185ASP-1-0.836-0.89915.447-19.571-19.5710.0000.0000.0000.000
174X186VAL0-0.027-0.01716.076-1.363-1.3630.0000.0000.0000.000
175X187VAL00.0040.01414.3840.3040.3040.0000.0000.0000.000
176X188THR0-0.077-0.06617.111-0.175-0.1750.0000.0000.0000.000
177X189LEU00.0240.00713.463-0.007-0.0070.0000.0000.0000.000
178X190ILE0-0.015-0.01218.1620.3980.3980.0000.0000.0000.000
179X191LEU0-0.021-0.00616.916-0.282-0.2820.0000.0000.0000.000
180X192PRO00.0080.02320.5240.7770.7770.0000.0000.0000.000
181X193PHE0-0.043-0.03123.153-0.141-0.1410.0000.0000.0000.000
182X194ILE0-0.0120.00618.487-0.365-0.3650.0000.0000.0000.000
183X195VAL00.0320.01320.5530.6360.6360.0000.0000.0000.000
184X196GLY00.0740.03519.043-0.981-0.9810.0000.0000.0000.000
185X197ARG10.8030.87418.03915.67015.6700.0000.0000.0000.000
186X198PHE00.003-0.03218.821-0.754-0.7540.0000.0000.0000.000
187X199VAL00.0410.00717.6150.5670.5670.0000.0000.0000.000
188X200CYS0-0.071-0.01220.4350.4120.4120.0000.0000.0000.000
189X201PRO00.0180.00522.8430.2490.2490.0000.0000.0000.000
190X202LYS10.8570.92026.44511.13811.1380.0000.0000.0000.000
191X203LEU00.0850.04926.206-0.576-0.5760.0000.0000.0000.000
192X204PRO0-0.037-0.01823.0620.2030.2030.0000.0000.0000.000
193X205ASP-1-0.858-0.92025.823-10.516-10.5160.0000.0000.0000.000
194X206SER0-0.016-0.02823.5610.2830.2830.0000.0000.0000.000
195X207ILE00.0110.00422.2570.0680.0680.0000.0000.0000.000
196X208GLU-1-0.889-0.94426.385-9.603-9.6030.0000.0000.0000.000
197X209LYS10.8200.88529.98910.38810.3880.0000.0000.0000.000
198X210ALA0-0.0110.00427.0950.2180.2180.0000.0000.0000.000
199X211LEU00.0230.01127.1960.0300.0300.0000.0000.0000.000
200X212VAL00.0240.01130.7410.3120.3120.0000.0000.0000.000
201X213LEU0-0.046-0.02734.0290.2660.2660.0000.0000.0000.000
202X214VAL00.005-0.00131.7900.1390.1390.0000.0000.0000.000
203X215LEU0-0.040-0.00530.4470.0750.0750.0000.0000.0000.000
204X216GLY0-0.048-0.01334.9080.1370.1370.0000.0000.0000.000
205X217LYS10.8870.94237.9127.4807.4800.0000.0000.0000.000
206X218LYS10.9590.96540.3017.0517.0510.0000.0000.0000.000
207X219GLU-1-0.873-0.94242.159-7.381-7.3810.0000.0000.0000.000
208X220GLN0-0.033-0.01437.9240.1300.1300.0000.0000.0000.000
209X221ILE0-0.0130.01437.615-0.272-0.2720.0000.0000.0000.000
210X222GLY00.0240.00837.2000.2110.2110.0000.0000.0000.000
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