FMO DATABASE

FMODB ID: 52NJZ

Calculation Name: 3K1R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1R

Chain ID: B

ChEMBL ID:

UniProt ID: Q9Y6N9

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-436408.428191
FMO2-HF: Nuclear repulsion	406482.611601
FMO2-HF: Total energy	-29925.81659
FMO2-MP2: Total energy	-30011.210335

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:388:GLU)

Summations of interaction energy for fragment #1(B:388:GLU)

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.
33.942	35.567	-0.012	-0.878	-0.734	0.003

Interaction energy analysis for fragmet #1(B:388:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.957 / q_NPA : -0.987

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 ES EX CT+mix DI(MP2)

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].
3	B	390	SER	0	-0.017	-0.003	3.733	-3.398	-1.773	-0.012	-0.878	-0.734	0.003
4	B	391	PRO	0	0.040	-0.011	6.074	-0.152	-0.152	0.000	0.000	0.000	0.000
5	B	392	LEU	0	-0.012	-0.006	8.379	-0.823	-0.823	0.000	0.000	0.000	0.000
6	B	393	GLU	-1	-0.840	-0.930	6.942	29.765	29.765	0.000	0.000	0.000	0.000
7	B	394	THR	0	0.025	0.016	7.195	0.184	0.184	0.000	0.000	0.000	0.000
8	B	395	PHE	0	-0.036	-0.019	9.894	-1.609	-1.609	0.000	0.000	0.000	0.000
9	B	396	LEU	0	0.004	-0.002	12.931	-1.028	-1.028	0.000	0.000	0.000	0.000
10	B	397	ALA	0	0.041	0.033	11.477	-0.901	-0.901	0.000	0.000	0.000	0.000
11	B	398	SER	0	-0.091	-0.033	13.424	-1.038	-1.038	0.000	0.000	0.000	0.000
12	B	399	LEU	0	-0.061	-0.042	15.381	-1.307	-1.307	0.000	0.000	0.000	0.000
13	B	400	HIS	0	-0.036	-0.014	17.102	-0.888	-0.888	0.000	0.000	0.000	0.000
14	B	401	MET	0	-0.057	-0.013	16.955	-0.930	-0.930	0.000	0.000	0.000	0.000
15	B	402	GLU	-1	-0.817	-0.924	13.427	18.125	18.125	0.000	0.000	0.000	0.000
16	B	403	ASP	-1	-0.908	-0.951	15.065	15.520	15.520	0.000	0.000	0.000	0.000
17	B	404	PHE	0	-0.001	-0.012	17.702	-0.816	-0.816	0.000	0.000	0.000	0.000
18	B	405	ALA	0	-0.003	-0.007	13.228	-0.202	-0.202	0.000	0.000	0.000	0.000
19	B	406	ALA	0	-0.049	-0.025	15.364	0.155	0.155	0.000	0.000	0.000	0.000
20	B	407	LEU	0	0.028	0.017	16.564	-0.171	-0.171	0.000	0.000	0.000	0.000
21	B	408	LEU	0	0.031	0.006	16.815	-0.415	-0.415	0.000	0.000	0.000	0.000
22	B	409	ARG	1	0.954	0.989	10.901	-21.931	-21.931	0.000	0.000	0.000	0.000
23	B	410	GLN	0	-0.098	-0.043	16.296	0.044	0.044	0.000	0.000	0.000	0.000
24	B	411	GLU	-1	-0.925	-0.963	19.495	11.497	11.497	0.000	0.000	0.000	0.000
25	B	412	LYS	1	0.865	0.932	17.886	-13.992	-13.992	0.000	0.000	0.000	0.000
26	B	413	ILE	0	-0.001	0.009	17.459	-0.234	-0.234	0.000	0.000	0.000	0.000
27	B	414	ASP	-1	-0.834	-0.915	12.611	17.163	17.163	0.000	0.000	0.000	0.000
28	B	415	LEU	0	-0.023	-0.039	11.872	-0.701	-0.701	0.000	0.000	0.000	0.000
29	B	416	GLU	-1	-0.952	-0.975	14.071	13.922	13.922	0.000	0.000	0.000	0.000
30	B	417	ALA	0	0.041	0.022	15.937	-0.777	-0.777	0.000	0.000	0.000	0.000
31	B	418	LEU	0	-0.003	-0.008	16.780	-0.626	-0.626	0.000	0.000	0.000	0.000
32	B	419	MET	0	-0.067	-0.028	17.210	-0.469	-0.469	0.000	0.000	0.000	0.000
33	B	420	LEU	0	-0.026	0.002	19.830	-0.583	-0.583	0.000	0.000	0.000	0.000
34	B	421	CYS	0	-0.021	0.026	21.808	-0.369	-0.369	0.000	0.000	0.000	0.000
35	B	422	SER	0	-0.041	-0.016	23.911	-0.156	-0.156	0.000	0.000	0.000	0.000
36	B	423	ASP	-1	-0.827	-0.934	26.863	9.698	9.698	0.000	0.000	0.000	0.000
37	B	424	LEU	0	0.012	-0.011	28.978	0.045	0.045	0.000	0.000	0.000	0.000
38	B	425	ASP	-1	-0.779	-0.884	25.709	10.230	10.230	0.000	0.000	0.000	0.000
39	B	426	LEU	0	0.022	0.001	22.325	0.151	0.151	0.000	0.000	0.000	0.000
40	B	427	ARG	1	0.888	0.943	26.078	-8.743	-8.743	0.000	0.000	0.000	0.000
41	B	428	SER	0	-0.060	-0.029	28.825	-0.207	-0.207	0.000	0.000	0.000	0.000
42	B	429	ILE	0	-0.006	0.021	22.804	-0.059	-0.059	0.000	0.000	0.000	0.000
43	B	430	SER	0	-0.029	-0.014	25.913	0.204	0.204	0.000	0.000	0.000	0.000
44	B	431	VAL	0	0.019	0.026	23.420	0.203	0.203	0.000	0.000	0.000	0.000
45	B	432	PRO	0	0.012	0.007	26.140	-0.457	-0.457	0.000	0.000	0.000	0.000
46	B	433	LEU	0	0.027	-0.003	27.844	0.240	0.240	0.000	0.000	0.000	0.000
47	B	434	GLY	0	0.043	0.029	28.764	0.098	0.098	0.000	0.000	0.000	0.000
48	B	435	PRO	0	0.031	-0.008	23.758	0.134	0.134	0.000	0.000	0.000	0.000
49	B	436	ARG	1	0.825	0.909	23.922	-9.499	-9.499	0.000	0.000	0.000	0.000
50	B	437	GLU	-1	-0.909	-0.965	25.483	9.657	9.657	0.000	0.000	0.000	0.000
51	B	438	LYS	1	0.900	0.966	21.747	-13.055	-13.055	0.000	0.000	0.000	0.000
52	B	439	ILE	0	0.046	0.018	19.722	0.252	0.252	0.000	0.000	0.000	0.000
53	B	440	LEU	0	0.015	0.005	21.622	0.133	0.133	0.000	0.000	0.000	0.000
54	B	441	GLY	0	-0.027	-0.012	24.237	-0.145	-0.145	0.000	0.000	0.000	0.000
55	B	442	ALA	0	-0.014	-0.017	19.422	-0.083	-0.083	0.000	0.000	0.000	0.000
56	B	443	VAL	0	0.019	0.014	19.494	0.277	0.277	0.000	0.000	0.000	0.000
57	B	444	ARG	1	0.930	0.963	20.925	-10.213	-10.213	0.000	0.000	0.000	0.000
58	B	445	ARG	1	0.959	0.986	21.120	-12.681	-12.681	0.000	0.000	0.000	0.000
59	B	446	ARG	1	0.969	0.998	12.733	-16.848	-16.848	0.000	0.000	0.000	0.000
60	B	447	ARG	1	0.901	0.928	19.859	-11.395	-11.395	0.000	0.000	0.000	0.000
61	B	448	GLN	0	-0.003	-0.007	22.013	-0.270	-0.270	0.000	0.000	0.000	0.000
62	B	449	ALA	0	0.010	0.011	20.479	-0.237	-0.237	0.000	0.000	0.000	0.000
63	B	450	MET	0	-0.044	-0.028	17.078	0.237	0.237	0.000	0.000	0.000	0.000
64	B	451	GLU	-1	-0.969	-0.978	20.897	10.372	10.372	0.000	0.000	0.000	0.000
65	B	452	ARG	1	0.871	0.930	24.440	-9.627	-9.627	0.000	0.000	0.000	0.000
66	B	453	PRO	0	0.009	0.029	22.495	-0.058	-0.058	0.000	0.000	0.000	0.000
67	B	454	PRO	0	-0.014	-0.005	23.800	-0.369	-0.369	0.000	0.000	0.000	0.000
68	B	455	ALA	0	0.002	-0.002	25.850	0.162	0.162	0.000	0.000	0.000	0.000
69	B	456	LEU	0	-0.033	-0.027	21.153	0.257	0.257	0.000	0.000	0.000	0.000
70	B	457	GLU	-1	-0.942	-0.972	24.466	9.758	9.758	0.000	0.000	0.000	0.000
71	B	458	ASP	-1	-0.939	-0.954	23.954	12.324	12.324	0.000	0.000	0.000	0.000
72	B	459	THR	0	-0.064	-0.041	22.333	-0.287	-0.287	0.000	0.000	0.000	0.000
73	B	460	GLU	-1	-0.948	-0.968	23.689	10.873	10.873	0.000	0.000	0.000	0.000
74	B	461	LEU	0	-0.052	-0.023	19.880	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:388:GLU)