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: N142Q

Calculation Name: 4KRD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KRD

Chain ID: B

ChEMBL ID:

UniProt ID: P53124

Base Structure: X-ray

Registration Date: 2023-06-20

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2224229.724108
FMO2-HF: Nuclear repulsion 2147678.32594
FMO2-HF: Total energy -76551.398168
FMO2-MP2: Total energy -76772.958583


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(B:243:SER)


Summations of interaction energy for fragment #1(B:243:SER)
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.
-8.798-4.3850.122-2.205-2.329-0.001
Interaction energy analysis for fragmet #1(B:243:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.021
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].
3B245ASN00.006-0.0102.956-5.393-2.7200.064-1.550-1.187-0.005
4B246PRO00.0690.0324.6960.0370.168-0.001-0.006-0.1240.000
5B247LEU00.0160.0125.6180.4880.4880.0000.0000.0000.000
6B248LEU0-0.068-0.0386.9330.1360.1360.0000.0000.0000.000
7B249HIS10.8130.8902.983-1.315-0.6790.022-0.223-0.4350.001
8B250GLY00.0380.0227.733-0.048-0.0480.0000.0000.0000.000
9B251ILE0-0.0390.00010.234-0.019-0.0190.0000.0000.0000.000
10B252PRO00.0710.03911.0000.0020.0020.0000.0000.0000.000
11B253VAL0-0.022-0.0389.752-0.067-0.0670.0000.0000.0000.000
12B254ASP-1-0.897-0.95111.631-0.084-0.0840.0000.0000.0000.000
13B255VAL0-0.070-0.01514.7080.0050.0050.0000.0000.0000.000
14B256GLU-1-0.846-0.91316.643-0.123-0.1230.0000.0000.0000.000
15B257VAL0-0.082-0.05519.646-0.011-0.0110.0000.0000.0000.000
16B258PRO0-0.009-0.01419.5410.0160.0160.0000.0000.0000.000
17B259HIS00.0190.02222.4890.0010.0010.0000.0000.0000.000
18B260ILE0-0.044-0.02422.8330.0060.0060.0000.0000.0000.000
19B261SER00.0620.03326.643-0.003-0.0030.0000.0000.0000.000
20B262VAL00.0580.01628.658-0.005-0.0050.0000.0000.0000.000
21B263ASP-1-0.871-0.93429.832-0.054-0.0540.0000.0000.0000.000
22B264GLU-1-0.887-0.94126.392-0.064-0.0640.0000.0000.0000.000
23B265ALA0-0.017-0.01725.355-0.004-0.0040.0000.0000.0000.000
24B266LEU0-0.043-0.02425.843-0.006-0.0060.0000.0000.0000.000
25B267ALA0-0.016-0.00528.2460.0000.0000.0000.0000.0000.000
26B268ASN00.0550.00523.1640.0080.0080.0000.0000.0000.000
27B269PHE00.0000.02823.241-0.004-0.0040.0000.0000.0000.000
28B270LYS10.8390.90224.7460.0500.0500.0000.0000.0000.000
29B271GLU-1-0.873-0.95025.798-0.052-0.0520.0000.0000.0000.000
30B272THR00.0430.00920.0790.0010.0010.0000.0000.0000.000
31B273ILE0-0.028-0.01423.1070.0010.0010.0000.0000.0000.000
32B274GLU-1-0.876-0.93325.037-0.043-0.0430.0000.0000.0000.000
33B275LEU00.012-0.00223.3880.0060.0060.0000.0000.0000.000
34B276LEU00.0420.02519.2380.0050.0050.0000.0000.0000.000
35B277LEU0-0.057-0.00923.1930.0060.0060.0000.0000.0000.000
36B278LYS10.9440.97326.5310.0420.0420.0000.0000.0000.000
37B279LEU00.0300.01220.3710.0060.0060.0000.0000.0000.000
38B280SER0-0.081-0.05124.2310.0020.0020.0000.0000.0000.000
39B281GLY0-0.016-0.00525.3880.0030.0030.0000.0000.0000.000
40B282ASN00.0090.01225.7920.0050.0050.0000.0000.0000.000
41B283ARG10.9251.00318.4000.0390.0390.0000.0000.0000.000
42B284LYS10.9460.96925.3180.0200.0200.0000.0000.0000.000
43B285CYS0-0.071-0.01921.0000.0050.0050.0000.0000.0000.000
44B286THR00.0530.02718.4650.0030.0030.0000.0000.0000.000
45B287GLY0-0.045-0.00720.7570.0050.0050.0000.0000.0000.000
46B288PHE00.013-0.00518.934-0.002-0.0020.0000.0000.0000.000
47B289ASN00.011-0.01315.3560.0090.0090.0000.0000.0000.000
48B290THR0-0.001-0.01418.6130.0110.0110.0000.0000.0000.000
49B291ARG10.8480.90521.4810.0120.0120.0000.0000.0000.000
50B292VAL00.0910.04822.392-0.003-0.0030.0000.0000.0000.000
51B293GLU-1-0.733-0.83217.443-0.063-0.0630.0000.0000.0000.000
52B294LYS10.9700.99522.1960.0180.0180.0000.0000.0000.000
53B295LYS10.9110.95824.9040.0340.0340.0000.0000.0000.000
54B296GLU-1-0.869-0.93823.658-0.052-0.0520.0000.0000.0000.000
55B297TYR00.026-0.00622.878-0.004-0.0040.0000.0000.0000.000
56B298SER0-0.087-0.04825.4300.0020.0020.0000.0000.0000.000
57B299ASN0-0.041-0.03828.3360.0070.0070.0000.0000.0000.000
58B300PHE00.015-0.00823.8580.0010.0010.0000.0000.0000.000
59B301TYR0-0.0110.00429.1600.0020.0020.0000.0000.0000.000
60B302MET0-0.062-0.02331.8440.0010.0010.0000.0000.0000.000
61B303LYS10.9810.98134.8470.0260.0260.0000.0000.0000.000
62B304SER00.0340.03238.0680.0010.0010.0000.0000.0000.000
63B305LYS10.9970.99436.0980.0330.0330.0000.0000.0000.000
64B306PRO0-0.013-0.01335.5290.0010.0010.0000.0000.0000.000
65B307THR00.0240.01138.4330.0000.0000.0000.0000.0000.000
66B308LEU00.0160.02337.8900.0010.0010.0000.0000.0000.000
67B309SER00.0160.00936.412-0.002-0.0020.0000.0000.0000.000
68B310SER00.051-0.00131.098-0.001-0.0010.0000.0000.0000.000
69B311ALA00.0530.02832.911-0.003-0.0030.0000.0000.0000.000
70B312ASP-1-0.789-0.90134.071-0.038-0.0380.0000.0000.0000.000
71B313PHE0-0.080-0.03431.9860.0000.0000.0000.0000.0000.000
72B314LEU00.028-0.00128.773-0.001-0.0010.0000.0000.0000.000
73B315LYS10.9400.98532.8040.0380.0380.0000.0000.0000.000
74B316ARG10.9110.96235.8190.0420.0420.0000.0000.0000.000
75B317ILE0-0.046-0.04131.2200.0000.0000.0000.0000.0000.000
76B318GLN00.0960.06932.039-0.005-0.0050.0000.0000.0000.000
77B319ASP-1-0.899-0.93734.211-0.043-0.0430.0000.0000.0000.000
78B320LYS10.8450.92637.1940.0410.0410.0000.0000.0000.000
79B321CYS0-0.102-0.04333.2930.0010.0010.0000.0000.0000.000
80B322GLU-1-0.909-0.94334.523-0.051-0.0510.0000.0000.0000.000
81B323TYR0-0.046-0.03929.036-0.003-0.0030.0000.0000.0000.000
82B324GLN00.1050.04527.7250.0070.0070.0000.0000.0000.000
83B325PRO00.0510.00726.281-0.005-0.0050.0000.0000.0000.000
84B326THR00.0330.00721.807-0.004-0.0040.0000.0000.0000.000
85B327VAL00.0290.03622.513-0.015-0.0150.0000.0000.0000.000
86B328TYR00.008-0.02423.485-0.010-0.0100.0000.0000.0000.000
87B329LEU00.0110.02720.182-0.006-0.0060.0000.0000.0000.000
88B330VAL00.0330.01718.375-0.024-0.0240.0000.0000.0000.000
89B331ALA0-0.017-0.00718.924-0.015-0.0150.0000.0000.0000.000
90B332THR0-0.017-0.03319.1960.0040.0040.0000.0000.0000.000
91B333PHE00.0550.02310.555-0.029-0.0290.0000.0000.0000.000
92B334LEU0-0.069-0.02715.498-0.032-0.0320.0000.0000.0000.000
93B335ILE0-0.032-0.01817.2380.0010.0010.0000.0000.0000.000
94B336ASP-1-0.801-0.91014.636-0.208-0.2080.0000.0000.0000.000
95B337THR0-0.022-0.02611.887-0.055-0.0550.0000.0000.0000.000
96B338LEU0-0.035-0.00713.6880.0030.0030.0000.0000.0000.000
97B339PHE0-0.034-0.03616.5130.0180.0180.0000.0000.0000.000
98B340LEU00.0240.03014.2410.0340.0340.0000.0000.0000.000
99B341THR0-0.012-0.0129.901-0.129-0.1290.0000.0000.0000.000
100B342ARG10.7470.8488.6610.1750.1750.0000.0000.0000.000
101B343ASP-1-0.857-0.9219.5720.0530.0530.0000.0000.0000.000
102B344GLY0-0.006-0.0189.9950.0320.0320.0000.0000.0000.000
103B345ASN0-0.026-0.00710.6910.1490.1490.0000.0000.0000.000
104B346ASN00.013-0.0068.538-0.011-0.0110.0000.0000.0000.000
105B347ILE00.0440.04210.940-0.056-0.0560.0000.0000.0000.000
106B348LEU00.0160.01112.944-0.035-0.0350.0000.0000.0000.000
107B349GLN0-0.034-0.02314.0980.0250.0250.0000.0000.0000.000
108B350LEU0-0.021-0.02615.359-0.031-0.0310.0000.0000.0000.000
109B351LYS10.8640.93212.7660.2710.2710.0000.0000.0000.000
110B352LEU0-0.013-0.02017.2840.0190.0190.0000.0000.0000.000
111B353ASN0-0.039-0.02920.645-0.002-0.0020.0000.0000.0000.000
112B354LEU00.0250.02923.590-0.001-0.0010.0000.0000.0000.000
113B355GLN0-0.046-0.05025.2170.0110.0110.0000.0000.0000.000
114B356GLU-1-0.835-0.94029.050-0.050-0.0500.0000.0000.0000.000
115B357LYS10.7960.88231.3700.0280.0280.0000.0000.0000.000
116B358GLU-1-0.796-0.87827.097-0.054-0.0540.0000.0000.0000.000
117B359VAL00.0600.04527.675-0.006-0.0060.0000.0000.0000.000
118B360HIS10.8970.95528.8250.0460.0460.0000.0000.0000.000
119B361ARG10.8990.93130.0700.0440.0440.0000.0000.0000.000
120B362MET00.0400.04223.231-0.006-0.0060.0000.0000.0000.000
121B363ILE00.0140.01425.580-0.008-0.0080.0000.0000.0000.000
122B364ILE0-0.046-0.02527.344-0.003-0.0030.0000.0000.0000.000
123B365ALA0-0.008-0.00425.286-0.002-0.0020.0000.0000.0000.000
124B366ALA00.0360.01722.418-0.006-0.0060.0000.0000.0000.000
125B367VAL00.0240.01323.507-0.009-0.0090.0000.0000.0000.000
126B368ARG10.8250.93426.1020.0710.0710.0000.0000.0000.000
127B369LEU00.011-0.00820.8440.0010.0010.0000.0000.0000.000
128B370SER0-0.017-0.03221.618-0.010-0.0100.0000.0000.0000.000
129B371THR0-0.013-0.01622.700-0.001-0.0010.0000.0000.0000.000
130B372LYS10.8520.91523.9810.0810.0810.0000.0000.0000.000
131B373LEU0-0.062-0.02217.380-0.003-0.0030.0000.0000.0000.000
132B374LEU0-0.078-0.03320.134-0.013-0.0130.0000.0000.0000.000
133B375GLU-1-0.927-0.95922.358-0.096-0.0960.0000.0000.0000.000
134B376ASP-1-0.895-0.93125.601-0.098-0.0980.0000.0000.0000.000
135B377PHE0-0.064-0.03127.3440.0070.0070.0000.0000.0000.000
136B378VAL0-0.0030.00827.375-0.002-0.0020.0000.0000.0000.000
137B379HIS00.0610.04530.5620.0020.0020.0000.0000.0000.000
138B380SER00.0890.04132.751-0.002-0.0020.0000.0000.0000.000
139B381HIS00.025-0.01731.611-0.002-0.0020.0000.0000.0000.000
140B382GLU-1-0.966-0.98234.574-0.036-0.0360.0000.0000.0000.000
141B383TYR0-0.029-0.02636.2810.0020.0020.0000.0000.0000.000
142B384PHE00.1090.04130.1340.0020.0020.0000.0000.0000.000
143B385SER0-0.027-0.03635.0960.0000.0000.0000.0000.0000.000
144B386LYS10.9330.96836.5840.0370.0370.0000.0000.0000.000
145B387VAL00.0190.02935.5870.0020.0020.0000.0000.0000.000
146B388CYS0-0.041-0.01033.3540.0000.0000.0000.0000.0000.000
147B389GLY0-0.0150.00735.9390.0010.0010.0000.0000.0000.000
148B390ILE0-0.057-0.01533.4760.0020.0020.0000.0000.0000.000
149B391SER00.0180.00337.8440.0000.0000.0000.0000.0000.000
150B392LYS11.0411.00336.0920.0360.0360.0000.0000.0000.000
151B393ARG10.9710.99934.8060.0310.0310.0000.0000.0000.000
152B394LEU0-0.033-0.02133.201-0.001-0.0010.0000.0000.0000.000
153B395LEU00.0760.03530.560-0.002-0.0020.0000.0000.0000.000
154B396THR00.0260.01430.183-0.003-0.0030.0000.0000.0000.000
155B397LYS10.8980.95729.1090.0370.0370.0000.0000.0000.000
156B398LEU0-0.022-0.00828.176-0.001-0.0010.0000.0000.0000.000
157B399GLU-1-0.811-0.90125.861-0.080-0.0800.0000.0000.0000.000
158B400VAL00.0230.01124.224-0.008-0.0080.0000.0000.0000.000
159B401SER00.0190.01923.6210.0000.0000.0000.0000.0000.000
160B402LEU0-0.0130.00820.156-0.001-0.0010.0000.0000.0000.000
161B403LEU00.0350.01418.690-0.013-0.0130.0000.0000.0000.000
162B404ILE0-0.016-0.01818.737-0.007-0.0070.0000.0000.0000.000
163B405CYS0-0.088-0.04818.5350.0050.0050.0000.0000.0000.000
164B406VAL00.0300.03215.478-0.010-0.0100.0000.0000.0000.000
165B407CYS0-0.045-0.00614.163-0.035-0.0350.0000.0000.0000.000
166B408ASN00.0300.02012.677-0.005-0.0050.0000.0000.0000.000
167B409THR0-0.078-0.0259.776-0.035-0.0350.0000.0000.0000.000
168B410LYS10.9030.9403.283-3.539-2.5660.037-0.426-0.5830.003
169B411LEU00.0630.0189.245-0.108-0.1080.0000.0000.0000.000
170B412MET0-0.0390.0039.3570.0330.0330.0000.0000.0000.000
171B413VAL00.1070.04911.980-0.076-0.0760.0000.0000.0000.000
172B414SER00.000-0.00312.234-0.029-0.0290.0000.0000.0000.000
173B415ASN00.1550.05614.307-0.006-0.0060.0000.0000.0000.000
174B416ARG10.8320.9036.8950.2680.2680.0000.0000.0000.000
175B417LYS10.7830.9119.0880.7740.7740.0000.0000.0000.000
176B418LEU00.0170.01613.5730.0310.0310.0000.0000.0000.000
177B419ALA00.0300.02015.2350.0230.0230.0000.0000.0000.000
178B420ALA00.002-0.01412.4960.0260.0260.0000.0000.0000.000
179B421SER0-0.042-0.00414.5590.0300.0300.0000.0000.0000.000
180B422LYS10.9290.97517.4340.0870.0870.0000.0000.0000.000
181B423LEU0-0.035-0.02915.0280.0190.0190.0000.0000.0000.000
182B424LEU00.0220.00512.4940.0140.0140.0000.0000.0000.000
183B425LEU0-0.0090.02316.5740.0180.0180.0000.0000.0000.000
184B426ASN00.0130.00020.1030.0130.0130.0000.0000.0000.000
185B427GLU-1-0.769-0.85515.047-0.042-0.0420.0000.0000.0000.000
186B428LEU0-0.0170.00018.5660.0120.0120.0000.0000.0000.000
187B429ARG10.8320.90120.7130.0630.0630.0000.0000.0000.000
188B430SER0-0.098-0.05221.4270.0100.0100.0000.0000.0000.000
189B431PHE0-0.020-0.00718.3360.0060.0060.0000.0000.0000.000
190B432CYS0-0.064-0.00824.0010.0010.0010.0000.0000.0000.000