FMO DATABASE

FMODB ID: V5K51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-439043.540621
FMO2-HF: Nuclear repulsion	409117.343263
FMO2-HF: Total energy	-29926.197357
FMO2-MP2: Total energy	-30011.626134

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.
31.092	33.279	0.056	-1.326	-0.916	0.002

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 : -0.941 / q_NPA : -0.963

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	-0.025	-0.046	3.205	-5.521	-3.334	0.056	-1.326	-0.916	0.002
4	B	391	PRO	0	0.039	0.000	5.727	-0.086	-0.086	0.000	0.000	0.000	0.000
5	B	392	LEU	0	0.002	0.014	7.722	-0.735	-0.735	0.000	0.000	0.000	0.000
6	B	393	GLU	-1	-0.738	-0.819	7.610	28.103	28.103	0.000	0.000	0.000	0.000
7	B	394	THR	0	0.002	-0.001	6.273	0.425	0.425	0.000	0.000	0.000	0.000
8	B	395	PHE	0	-0.012	-0.008	8.641	-1.350	-1.350	0.000	0.000	0.000	0.000
9	B	396	LEU	0	0.003	0.007	12.052	-0.936	-0.936	0.000	0.000	0.000	0.000
10	B	397	ALA	0	0.047	0.029	10.873	-0.853	-0.853	0.000	0.000	0.000	0.000
11	B	398	SER	0	-0.118	-0.069	12.596	-1.084	-1.084	0.000	0.000	0.000	0.000
12	B	399	LEU	0	-0.039	-0.024	14.259	-1.276	-1.276	0.000	0.000	0.000	0.000
13	B	400	HIS	0	-0.033	-0.011	16.405	-1.538	-1.538	0.000	0.000	0.000	0.000
14	B	401	MET	0	-0.042	-0.012	16.499	-1.243	-1.243	0.000	0.000	0.000	0.000
15	B	402	GLU	-1	-0.808	-0.916	12.798	18.771	18.771	0.000	0.000	0.000	0.000
16	B	403	ASP	-1	-0.881	-0.937	14.714	15.342	15.342	0.000	0.000	0.000	0.000
17	B	404	PHE	0	0.012	-0.017	17.402	-0.472	-0.472	0.000	0.000	0.000	0.000
18	B	405	ALA	0	0.000	0.002	12.617	-0.163	-0.163	0.000	0.000	0.000	0.000
19	B	406	ALA	0	-0.045	-0.014	14.499	0.460	0.460	0.000	0.000	0.000	0.000
20	B	407	LEU	0	0.012	0.012	15.999	-0.188	-0.188	0.000	0.000	0.000	0.000
21	B	408	LEU	0	0.025	-0.005	16.519	-0.404	-0.404	0.000	0.000	0.000	0.000
22	B	409	ARG	1	0.865	0.925	9.029	-23.663	-23.663	0.000	0.000	0.000	0.000
23	B	410	GLN	0	-0.072	-0.034	16.042	0.002	0.002	0.000	0.000	0.000	0.000
24	B	411	GLU	-1	-0.860	-0.922	19.099	11.768	11.768	0.000	0.000	0.000	0.000
25	B	412	LYS	1	0.789	0.885	17.520	-13.230	-13.230	0.000	0.000	0.000	0.000
26	B	413	ILE	0	0.000	0.012	17.390	-0.107	-0.107	0.000	0.000	0.000	0.000
27	B	414	ASP	-1	-0.821	-0.915	12.361	16.999	16.999	0.000	0.000	0.000	0.000
28	B	415	LEU	0	-0.026	-0.035	11.392	-0.718	-0.718	0.000	0.000	0.000	0.000
29	B	416	GLU	-1	-0.957	-0.973	13.701	13.899	13.899	0.000	0.000	0.000	0.000
30	B	417	ALA	0	0.046	0.021	15.806	-0.749	-0.749	0.000	0.000	0.000	0.000
31	B	418	LEU	0	0.009	-0.004	16.212	-0.632	-0.632	0.000	0.000	0.000	0.000
32	B	419	MET	0	-0.071	-0.027	16.601	-0.428	-0.428	0.000	0.000	0.000	0.000
33	B	420	LEU	0	-0.022	-0.008	19.178	-0.581	-0.581	0.000	0.000	0.000	0.000
34	B	421	CYS	0	-0.065	0.002	21.075	-0.357	-0.357	0.000	0.000	0.000	0.000
35	B	422	SER	0	-0.039	-0.057	23.339	-0.169	-0.169	0.000	0.000	0.000	0.000
36	B	423	ASP	-1	-0.807	-0.913	26.221	9.784	9.784	0.000	0.000	0.000	0.000
37	B	424	LEU	0	0.008	-0.003	28.412	0.011	0.011	0.000	0.000	0.000	0.000
38	B	425	ASP	-1	-0.771	-0.830	25.233	10.210	10.210	0.000	0.000	0.000	0.000
39	B	426	LEU	0	0.042	0.006	21.444	0.121	0.121	0.000	0.000	0.000	0.000
40	B	427	ARG	1	0.889	0.953	25.336	-8.829	-8.829	0.000	0.000	0.000	0.000
41	B	428	SER	0	-0.050	-0.026	28.242	-0.208	-0.208	0.000	0.000	0.000	0.000
42	B	429	ILE	0	-0.026	0.000	21.963	-0.035	-0.035	0.000	0.000	0.000	0.000
43	B	430	SER	0	-0.030	-0.016	25.457	0.205	0.205	0.000	0.000	0.000	0.000
44	B	431	VAL	0	0.004	0.013	22.838	0.112	0.112	0.000	0.000	0.000	0.000
45	B	432	PRO	0	0.012	-0.001	25.700	-0.422	-0.422	0.000	0.000	0.000	0.000
46	B	433	LEU	0	-0.016	-0.015	27.164	0.252	0.252	0.000	0.000	0.000	0.000
47	B	434	GLY	0	0.093	0.061	27.973	0.158	0.158	0.000	0.000	0.000	0.000
48	B	435	PRO	0	0.007	-0.010	23.317	0.200	0.200	0.000	0.000	0.000	0.000
49	B	436	ARG	1	0.823	0.903	23.181	-9.602	-9.602	0.000	0.000	0.000	0.000
50	B	437	GLU	-1	-0.899	-0.959	24.561	9.733	9.733	0.000	0.000	0.000	0.000
51	B	438	LYS	1	0.841	0.925	20.718	-13.413	-13.413	0.000	0.000	0.000	0.000
52	B	439	ILE	0	0.040	0.020	19.212	0.269	0.269	0.000	0.000	0.000	0.000
53	B	440	LEU	0	0.013	-0.002	21.139	0.084	0.084	0.000	0.000	0.000	0.000
54	B	441	GLY	0	-0.029	-0.017	23.707	-0.167	-0.167	0.000	0.000	0.000	0.000
55	B	442	ALA	0	-0.019	-0.010	18.578	-0.054	-0.054	0.000	0.000	0.000	0.000
56	B	443	VAL	0	0.019	0.002	18.810	0.217	0.217	0.000	0.000	0.000	0.000
57	B	444	ARG	1	0.934	0.968	20.373	-10.205	-10.205	0.000	0.000	0.000	0.000
58	B	445	ARG	1	0.962	0.989	20.249	-12.581	-12.581	0.000	0.000	0.000	0.000
59	B	446	ARG	1	0.970	0.988	12.654	-16.431	-16.431	0.000	0.000	0.000	0.000
60	B	447	ARG	1	0.842	0.930	19.120	-11.289	-11.289	0.000	0.000	0.000	0.000
61	B	448	GLN	0	-0.009	-0.009	21.395	-0.134	-0.134	0.000	0.000	0.000	0.000
62	B	449	ALA	0	0.007	0.001	19.755	-0.204	-0.204	0.000	0.000	0.000	0.000
63	B	450	MET	0	-0.033	-0.012	16.897	0.319	0.319	0.000	0.000	0.000	0.000
64	B	451	GLU	-1	-0.905	-0.966	20.379	10.545	10.545	0.000	0.000	0.000	0.000
65	B	452	ARG	1	0.855	0.921	23.935	-9.698	-9.698	0.000	0.000	0.000	0.000
66	B	453	PRO	0	0.021	0.031	21.986	-0.101	-0.101	0.000	0.000	0.000	0.000
67	B	454	PRO	0	-0.021	-0.004	23.038	-0.382	-0.382	0.000	0.000	0.000	0.000
68	B	455	ALA	0	0.000	-0.003	25.097	0.159	0.159	0.000	0.000	0.000	0.000
69	B	456	LEU	0	-0.047	-0.028	20.947	0.327	0.327	0.000	0.000	0.000	0.000
70	B	457	GLU	-1	-0.934	-0.969	23.605	9.763	9.763	0.000	0.000	0.000	0.000
71	B	458	ASP	-1	-0.926	-0.955	23.172	12.236	12.236	0.000	0.000	0.000	0.000
72	B	459	THR	0	-0.066	-0.046	21.080	-0.214	-0.214	0.000	0.000	0.000	0.000
73	B	460	GLU	-1	-0.952	-0.963	22.406	10.914	10.914	0.000	0.000	0.000	0.000
74	B	461	LEU	0	-0.048	-0.022	19.257	0.156	0.156	0.000	0.000	0.000	0.000

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