FMO DATABASE

FMODB ID: 495MN

Calculation Name: 5IMK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IMK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y279

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptHSide
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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-985171.53783
FMO2-HF: Nuclear repulsion	938205.009226
FMO2-HF: Total energy	-46966.528604
FMO2-MP2: Total energy	-47104.368374

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(A:1:ARG)

Summations of interaction energy for fragment #1(A:1:ARG)

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.
-175.925	-177.284	31.295	-16.714	-13.223	-0.172

Interaction energy analysis for fragmet #1(A:1:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.911

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

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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	A	3	ILE	0	-0.013	-0.024	2.450	-25.771	-19.628	1.093	-3.632	-3.603	-0.029
4	A	4	LEU	0	0.019	0.021	2.697	-11.321	-9.575	0.299	-0.957	-1.088	-0.012
5	A	5	GLU	-1	-0.841	-0.910	4.459	-41.120	-40.924	-0.001	-0.007	-0.188	0.000
6	A	6	VAL	0	-0.010	-0.022	5.785	3.134	3.134	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.003	0.016	9.541	-0.132	-0.132	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.862	-0.928	12.248	-17.600	-17.600	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.034	-0.016	13.857	1.374	1.374	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.008	0.010	16.218	-0.518	-0.518	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.029	-0.013	18.723	0.827	0.827	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.046	0.028	22.421	-0.269	-0.269	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.025	0.001	24.198	0.403	0.403	0.000	0.000	0.000	0.000
14	A	14	TRP	0	0.077	-0.009	27.898	0.255	0.255	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.872	0.931	30.364	8.896	8.896	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.010	0.020	28.756	0.186	0.186	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.839	-0.908	24.150	-11.858	-11.858	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.033	-0.028	19.978	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.042	0.022	14.799	0.070	0.070	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.001	0.003	15.512	-0.172	-0.172	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.010	-0.009	11.095	-0.328	-0.328	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.005	0.018	9.162	-0.326	-0.326	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.041	-0.003	6.511	0.065	0.065	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.010	-0.024	3.184	-4.265	-3.905	0.014	-0.095	-0.279	0.000
25	A	25	ASP	-1	-0.790	-0.870	1.682	-116.805	-126.763	29.891	-11.962	-7.971	-0.131
26	A	26	PRO	0	-0.021	-0.019	4.095	2.748	2.902	-0.001	-0.061	-0.094	0.000
27	A	27	LEU	0	-0.004	0.006	6.212	-0.164	-0.164	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.005	-0.014	9.264	2.072	2.072	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.020	0.015	12.680	-0.117	-0.117	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.026	-0.004	12.105	1.121	1.121	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.019	-0.004	13.939	-0.227	-0.227	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.023	0.022	11.891	-1.840	-1.840	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.024	-0.019	14.218	0.933	0.933	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.016	-0.007	16.029	1.162	1.162	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.023	-0.002	13.692	-1.594	-1.594	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.845	0.903	15.614	17.352	17.352	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.015	0.007	13.421	-0.924	-0.924	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.035	-0.022	17.453	1.158	1.158	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.008	0.003	19.437	-0.508	-0.508	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.029	0.018	20.629	-0.159	-0.159	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.877	0.952	23.745	11.430	11.430	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.012	0.001	27.524	0.227	0.227	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.043	-0.040	26.599	-0.232	-0.232	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.851	-0.913	25.312	-11.454	-11.454	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.018	-0.003	21.159	0.124	0.124	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.016	-0.008	23.511	0.331	0.331	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.027	-0.001	21.530	-0.619	-0.619	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.034	-0.026	20.642	0.695	0.695	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.007	-0.003	18.026	0.429	0.429	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.013	0.012	20.212	-0.544	-0.544	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.742	0.811	15.883	17.570	17.570	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.734	-0.856	19.117	-13.584	-13.584	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.018	0.007	21.486	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.107	-0.061	23.484	0.444	0.444	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.006	0.000	23.193	0.453	0.453	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.767	-0.842	20.970	-15.470	-15.470	0.000	0.000	0.000	0.000
57	A	57	HIS	1	0.780	0.880	23.194	12.951	12.951	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.005	0.020	24.225	-0.434	-0.434	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.018	-0.021	24.650	0.465	0.465	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.003	0.002	26.911	0.489	0.489	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.043	0.011	28.650	-0.115	-0.115	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.815	0.905	27.914	10.847	10.847	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.023	-0.005	24.898	0.048	0.048	0.000	0.000	0.000	0.000
64	A	64	GLN	0	0.007	0.006	27.604	-0.316	-0.316	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.008	-0.004	29.354	0.222	0.222	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.737	0.859	27.494	10.988	10.988	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.019	0.014	21.078	-0.299	-0.299	0.000	0.000	0.000	0.000
68	A	68	HIS	0	-0.040	-0.023	19.487	0.612	0.612	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.043	0.024	15.971	-0.481	-0.481	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.011	0.011	14.357	1.184	1.184	0.000	0.000	0.000	0.000
71	A	71	HIS	0	0.095	0.046	15.545	-0.196	-0.196	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.839	0.924	16.172	14.594	14.594	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.042	0.027	10.865	0.644	0.644	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.005	-0.006	11.106	-0.860	-0.860	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.064	0.033	7.632	-1.601	-1.601	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.840	-0.890	7.710	-26.976	-26.976	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.034	-0.029	10.259	2.383	2.383	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.000	-0.024	11.910	0.397	0.397	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.004	0.021	13.651	1.200	1.200	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.039	-0.023	16.532	0.505	0.505	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.020	-0.002	20.179	0.446	0.446	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.042	0.001	23.395	-0.052	-0.052	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.070	-0.031	26.827	0.276	0.276	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.002	0.014	24.258	0.170	0.170	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.822	-0.908	28.264	-9.700	-9.700	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.043	-0.039	28.906	-0.266	-0.266	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.877	-0.928	29.584	-9.807	-9.807	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.775	-0.849	25.248	-11.603	-11.603	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.869	0.936	24.658	9.842	9.842	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.006	0.001	23.391	0.236	0.236	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.013	-0.001	19.129	-0.268	-0.268	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.056	-0.054	17.696	0.616	0.616	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.019	0.011	14.715	-0.669	-0.669	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.774	-0.879	12.059	-18.808	-18.808	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.018	-0.007	9.985	0.999	0.999	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.007	0.000	12.157	-0.472	-0.472	0.000	0.000	0.000	0.000
97	A	98	TRP	0	-0.013	-0.025	7.731	-0.071	-0.071	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.009	-0.025	14.046	0.635	0.635	0.000	0.000	0.000	0.000
99	A	100	THR	0	-0.033	-0.038	16.826	-0.805	-0.805	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.005	-0.005	18.859	0.489	0.489	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.850	-0.898	21.711	-14.434	-14.434	0.000	0.000	0.000	0.000
102	A	103	GLY	0	0.017	0.015	22.132	0.396	0.396	0.000	0.000	0.000	0.000
103	A	104	ASN	0	-0.074	-0.020	18.250	0.048	0.048	0.000	0.000	0.000	0.000
104	A	105	GLN	0	0.035	0.008	16.807	0.287	0.287	0.000	0.000	0.000	0.000
105	A	106	VAL	0	-0.038	-0.002	10.804	-0.154	-0.154	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.020	0.002	12.714	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.863	0.930	7.709	29.251	29.251	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.856	-0.937	10.537	-20.987	-20.987	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.769	0.881	6.663	35.528	35.528	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.002	0.001	11.438	0.750	0.750	0.000	0.000	0.000	0.000
111	A	112	THR	0	-0.022	-0.011	14.016	-0.248	-0.248	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.838	-0.913	15.575	-12.992	-12.992	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.028	0.002	19.189	-0.237	-0.237	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.874	0.917	20.852	14.821	14.821	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.012	-0.002	24.076	-0.119	-0.119	0.000	0.000	0.000	0.000
116	A	117	GLN	0	-0.003	0.001	26.876	0.302	0.302	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.936	0.977	29.167	9.005	9.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ARG)