FMO DATABASE

FMODB ID: KR6V3

Calculation Name: 1IM3-D-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IM3

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-702654.008679
FMO2-HF: Nuclear repulsion	664377.065945
FMO2-HF: Total energy	-38276.942734
FMO2-MP2: Total energy	-38388.164244

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(D:43:PRO )

Summations of interaction energy for fragment #1(D:43:PRO )

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.
-96.082	-90.413	0.477	-2.681	-3.465	-0.017

Interaction energy analysis for fragmet #1(D:43:PRO )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.894

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	D	45	PHE	0	0.056	-0.002	3.806	1.350	3.182	-0.021	-0.809	-1.002	-0.001
4	D	46	GLN	0	-0.046	-0.008	6.873	1.500	1.500	0.000	0.000	0.000	0.000
5	D	47	ILE	0	0.009	-0.005	10.585	0.458	0.458	0.000	0.000	0.000	0.000
6	D	48	GLU	-1	-0.934	-0.942	13.625	-18.380	-18.380	0.000	0.000	0.000	0.000
7	D	49	ASP	-1	-0.883	-0.961	16.237	-13.075	-13.075	0.000	0.000	0.000	0.000
8	D	50	ASN	0	-0.047	-0.051	18.015	-0.680	-0.680	0.000	0.000	0.000	0.000
9	D	51	ARG	1	0.931	1.002	20.313	12.558	12.558	0.000	0.000	0.000	0.000
10	D	133	CYS	0	-0.041	-0.024	21.047	-0.301	-0.301	0.000	0.000	0.000	0.000
11	D	53	TYR	0	0.063	0.037	26.362	0.065	0.065	0.000	0.000	0.000	0.000
12	D	54	ILE	0	-0.003	-0.009	30.121	-0.119	-0.119	0.000	0.000	0.000	0.000
13	D	55	ASP	-1	-0.929	-0.958	32.652	-8.234	-8.234	0.000	0.000	0.000	0.000
14	D	56	ASN	0	-0.051	-0.041	35.683	0.098	0.098	0.000	0.000	0.000	0.000
15	D	57	GLY	0	0.002	0.005	36.206	0.049	0.049	0.000	0.000	0.000	0.000
16	D	58	LYS	1	0.927	1.001	33.068	8.485	8.485	0.000	0.000	0.000	0.000
17	D	59	LEU	0	-0.004	0.003	25.775	-0.052	-0.052	0.000	0.000	0.000	0.000
18	D	60	PHE	0	-0.018	-0.010	28.139	-0.065	-0.065	0.000	0.000	0.000	0.000
19	D	61	ALA	0	0.012	-0.005	23.252	-0.058	-0.058	0.000	0.000	0.000	0.000
20	D	62	ARG	1	0.884	0.954	22.103	11.930	11.930	0.000	0.000	0.000	0.000
21	D	63	GLY	0	0.050	0.004	18.877	0.057	0.057	0.000	0.000	0.000	0.000
22	D	64	SER	0	-0.100	-0.051	15.966	-0.123	-0.123	0.000	0.000	0.000	0.000
23	D	65	ILE	0	0.035	0.022	9.818	-0.363	-0.363	0.000	0.000	0.000	0.000
24	D	66	VAL	0	0.040	0.041	10.582	-0.152	-0.152	0.000	0.000	0.000	0.000
25	D	67	GLY	0	0.030	-0.031	6.586	-2.244	-2.244	0.000	0.000	0.000	0.000
26	D	68	ASN	0	-0.027	0.009	2.668	-5.687	-3.106	0.466	-1.476	-1.571	-0.014
27	D	69	MET	0	0.003	-0.014	5.018	-3.891	-3.891	0.000	0.000	0.000	0.000
28	D	70	SER	0	0.029	0.016	5.841	3.292	3.292	0.000	0.000	0.000	0.000
29	D	71	ARG	1	0.944	0.968	7.371	33.393	33.393	0.000	0.000	0.000	0.000
30	D	72	PHE	0	-0.002	-0.010	8.632	-2.950	-2.950	0.000	0.000	0.000	0.000
31	D	73	VAL	0	0.008	0.017	10.941	1.550	1.550	0.000	0.000	0.000	0.000
32	D	74	PHE	0	0.027	0.010	13.391	-0.859	-0.859	0.000	0.000	0.000	0.000
33	D	75	ASP	-1	-0.826	-0.915	15.953	-14.455	-14.455	0.000	0.000	0.000	0.000
34	D	76	PRO	0	0.009	0.010	17.975	-0.086	-0.086	0.000	0.000	0.000	0.000
35	D	77	LYS	1	0.824	0.889	19.267	14.605	14.605	0.000	0.000	0.000	0.000
36	D	78	ALA	0	0.033	0.017	23.293	-0.131	-0.131	0.000	0.000	0.000	0.000
37	D	79	ASP	-1	-0.887	-0.942	25.750	-11.161	-11.161	0.000	0.000	0.000	0.000
38	D	80	TYR	0	-0.082	-0.090	27.593	0.148	0.148	0.000	0.000	0.000	0.000
39	D	81	GLY	0	0.078	0.058	29.913	0.305	0.305	0.000	0.000	0.000	0.000
40	D	82	GLY	0	-0.114	-0.053	29.356	0.306	0.306	0.000	0.000	0.000	0.000
41	D	83	VAL	0	-0.043	-0.026	29.136	-0.237	-0.237	0.000	0.000	0.000	0.000
42	D	84	GLY	0	0.053	0.014	27.796	0.048	0.048	0.000	0.000	0.000	0.000
43	D	85	GLU	-1	-0.920	-0.923	27.438	-9.598	-9.598	0.000	0.000	0.000	0.000
44	D	86	ASN	0	-0.004	0.004	23.174	-0.545	-0.545	0.000	0.000	0.000	0.000
45	D	87	LEU	0	0.023	0.025	24.000	0.439	0.439	0.000	0.000	0.000	0.000
46	D	88	TYR	0	-0.019	-0.022	23.813	-0.617	-0.617	0.000	0.000	0.000	0.000
47	D	89	VAL	0	0.008	0.004	21.707	0.351	0.351	0.000	0.000	0.000	0.000
48	D	90	HIS	0	0.032	0.028	24.169	-0.456	-0.456	0.000	0.000	0.000	0.000
49	D	91	ALA	0	0.019	-0.006	22.576	-0.383	-0.383	0.000	0.000	0.000	0.000
50	D	92	ASP	-1	-0.864	-0.938	22.618	-11.721	-11.721	0.000	0.000	0.000	0.000
51	D	93	ASP	-1	-0.893	-0.922	23.692	-11.651	-11.651	0.000	0.000	0.000	0.000
52	D	94	VAL	0	-0.047	-0.033	17.516	-0.584	-0.584	0.000	0.000	0.000	0.000
53	D	95	GLU	-1	-0.938	-0.960	18.354	-13.890	-13.890	0.000	0.000	0.000	0.000
54	D	96	PHE	0	-0.023	-0.024	9.952	-1.088	-1.088	0.000	0.000	0.000	0.000
55	D	97	VAL	0	0.006	0.018	13.430	0.997	0.997	0.000	0.000	0.000	0.000
56	D	98	PRO	0	-0.014	-0.016	10.917	-2.010	-2.010	0.000	0.000	0.000	0.000
57	D	99	GLY	0	-0.046	-0.030	7.826	0.568	0.568	0.000	0.000	0.000	0.000
58	D	100	GLU	-1	-0.945	-0.971	8.786	-21.723	-21.723	0.000	0.000	0.000	0.000
59	D	101	SER	0	-0.018	-0.022	10.371	-0.191	-0.191	0.000	0.000	0.000	0.000
60	D	102	LEU	0	-0.014	0.013	11.702	0.449	0.449	0.000	0.000	0.000	0.000
61	D	103	LYS	1	0.958	0.975	13.352	16.852	16.852	0.000	0.000	0.000	0.000
62	D	104	TRP	0	0.023	0.040	14.842	-0.044	-0.044	0.000	0.000	0.000	0.000
63	D	105	ASN	0	0.002	-0.026	19.823	0.330	0.330	0.000	0.000	0.000	0.000
64	D	106	VAL	0	0.000	0.004	22.549	0.384	0.384	0.000	0.000	0.000	0.000
65	D	107	ARG	1	0.852	0.912	25.118	11.535	11.535	0.000	0.000	0.000	0.000
66	D	108	ASN	0	-0.049	-0.038	28.867	0.330	0.330	0.000	0.000	0.000	0.000
67	D	109	LEU	0	0.047	0.032	26.395	0.143	0.143	0.000	0.000	0.000	0.000
68	D	110	ASP	-1	-0.856	-0.925	30.246	-8.756	-8.756	0.000	0.000	0.000	0.000
69	D	111	VAL	0	-0.051	-0.007	29.356	-0.245	-0.245	0.000	0.000	0.000	0.000
70	D	112	MET	0	0.003	-0.009	32.288	0.299	0.299	0.000	0.000	0.000	0.000
71	D	113	PRO	0	0.011	-0.016	34.327	-0.152	-0.152	0.000	0.000	0.000	0.000
72	D	114	ILE	0	-0.028	-0.009	34.584	0.013	0.013	0.000	0.000	0.000	0.000
73	D	115	PHE	0	-0.040	-0.005	26.570	-0.280	-0.280	0.000	0.000	0.000	0.000
74	D	116	GLU	-1	-0.880	-0.936	30.385	-9.494	-9.494	0.000	0.000	0.000	0.000
75	D	117	THR	0	-0.099	-0.054	25.799	-0.308	-0.308	0.000	0.000	0.000	0.000
76	D	118	LEU	0	0.016	0.014	21.739	0.021	0.021	0.000	0.000	0.000	0.000
77	D	119	ALA	0	-0.005	-0.002	21.292	-0.497	-0.497	0.000	0.000	0.000	0.000
78	D	120	LEU	0	0.012	0.000	16.441	0.072	0.072	0.000	0.000	0.000	0.000
79	D	121	ARG	1	0.873	0.961	14.454	17.242	17.242	0.000	0.000	0.000	0.000
80	D	122	LEU	0	0.017	0.004	11.653	0.154	0.154	0.000	0.000	0.000	0.000
81	D	123	VAL	0	-0.015	-0.009	8.974	-0.826	-0.826	0.000	0.000	0.000	0.000
82	D	124	LEU	0	0.023	-0.003	6.289	0.978	0.978	0.000	0.000	0.000	0.000
83	D	125	GLN	0	-0.053	-0.009	3.431	-1.202	-0.768	0.010	-0.085	-0.359	0.000
84	D	126	GLY	0	-0.076	-0.040	5.008	-2.373	-2.273	0.000	-0.003	-0.096	0.000
85	D	127	ASP	-1	-0.887	-0.921	3.601	-50.703	-49.981	0.022	-0.308	-0.437	-0.002
86	D	128	VAL	0	-0.053	-0.031	6.668	1.809	1.809	0.000	0.000	0.000	0.000
87	D	129	ILE	0	-0.011	0.000	8.954	-0.377	-0.377	0.000	0.000	0.000	0.000
88	D	130	TRP	0	0.013	-0.003	11.751	0.857	0.857	0.000	0.000	0.000	0.000
89	D	131	LEU	0	-0.012	0.000	13.661	-0.318	-0.318	0.000	0.000	0.000	0.000
90	D	132	ARG	1	0.970	0.977	17.259	12.712	12.712	0.000	0.000	0.000	0.000
91	D	134	VAL	0	-0.012	-0.006	23.431	0.260	0.260	0.000	0.000	0.000	0.000
92	D	135	PRO	0	-0.017	-0.017	27.184	-0.068	-0.068	0.000	0.000	0.000	0.000
93	D	136	GLU	-1	-0.992	-0.996	28.734	-10.667	-10.667	0.000	0.000	0.000	0.000
94	D	137	LEU	-1	-0.942	-0.960	31.472	-9.004	-9.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:43:PRO )