FMO DATABASE

FMODB ID: 228JR

Calculation Name: 1IM3-D-Xray372

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: 2023-06-19

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702672.065398
FMO2-HF: Nuclear repulsion	664394.872156
FMO2-HF: Total energy	-38277.193242
FMO2-MP2: Total energy	-38388.419286

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.
-8.089	-2.738	0.579	-2.558	-3.372	-0.004

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 : 0 / q_Mulliken : -0.054 / q_NPA : -0.028

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	0.029	-0.022	3.806	-1.987	0.266	-0.031	-1.127	-1.095	0.006
4	D	46	GLN	0	-0.053	-0.012	6.869	0.076	0.076	0.000	0.000	0.000	0.000
5	D	47	ILE	0	-0.002	-0.011	10.581	0.005	0.005	0.000	0.000	0.000	0.000
6	D	48	GLU	-1	-0.927	-0.940	13.619	0.007	0.007	0.000	0.000	0.000	0.000
7	D	49	ASP	-1	-0.886	-0.964	16.233	-0.067	-0.067	0.000	0.000	0.000	0.000
8	D	50	ASN	0	-0.040	-0.047	18.007	-0.032	-0.032	0.000	0.000	0.000	0.000
9	D	51	ARG	1	0.923	0.997	20.312	0.071	0.071	0.000	0.000	0.000	0.000
10	D	52	CYS	0	-0.027	-0.015	21.046	0.002	0.002	0.000	0.000	0.000	0.000
11	D	53	TYR	0	0.019	0.013	26.361	0.005	0.005	0.000	0.000	0.000	0.000
12	D	54	ILE	0	0.007	-0.001	30.121	-0.003	-0.003	0.000	0.000	0.000	0.000
13	D	55	ASP	-1	-0.946	-0.968	32.652	-0.044	-0.044	0.000	0.000	0.000	0.000
14	D	56	ASN	0	-0.045	-0.036	35.683	-0.001	-0.001	0.000	0.000	0.000	0.000
15	D	57	GLY	0	0.010	0.008	36.206	0.000	0.000	0.000	0.000	0.000	0.000
16	D	58	LYS	1	0.930	1.004	33.068	0.055	0.055	0.000	0.000	0.000	0.000
17	D	59	LEU	0	-0.003	0.003	25.776	0.001	0.001	0.000	0.000	0.000	0.000
18	D	60	PHE	0	-0.026	-0.014	28.138	0.001	0.001	0.000	0.000	0.000	0.000
19	D	61	ALA	0	0.012	-0.007	23.251	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	62	ARG	1	0.881	0.953	22.096	0.066	0.066	0.000	0.000	0.000	0.000
21	D	63	GLY	0	0.047	0.003	18.875	-0.001	-0.001	0.000	0.000	0.000	0.000
22	D	64	SER	0	-0.101	-0.051	15.962	0.002	0.002	0.000	0.000	0.000	0.000
23	D	65	ILE	0	0.037	0.023	9.811	-0.017	-0.017	0.000	0.000	0.000	0.000
24	D	66	VAL	0	0.036	0.038	10.582	0.004	0.004	0.000	0.000	0.000	0.000
25	D	67	GLY	0	0.037	-0.025	6.583	-0.110	-0.110	0.000	0.000	0.000	0.000
26	D	68	ASN	0	-0.017	0.014	2.656	-2.521	-0.563	0.573	-1.117	-1.413	-0.009
27	D	69	MET	0	0.011	-0.009	5.010	-0.055	-0.055	0.000	0.000	0.000	0.000
28	D	70	SER	0	0.026	0.014	5.836	0.132	0.132	0.000	0.000	0.000	0.000
29	D	71	ARG	1	0.940	0.965	7.384	0.704	0.704	0.000	0.000	0.000	0.000
30	D	72	PHE	0	-0.002	-0.010	8.635	-0.140	-0.140	0.000	0.000	0.000	0.000
31	D	73	VAL	0	0.002	0.016	10.944	0.062	0.062	0.000	0.000	0.000	0.000
32	D	74	PHE	0	0.030	0.010	13.393	-0.040	-0.040	0.000	0.000	0.000	0.000
33	D	75	ASP	-1	-0.826	-0.915	15.955	-0.235	-0.235	0.000	0.000	0.000	0.000
34	D	76	PRO	0	0.008	0.009	17.976	-0.007	-0.007	0.000	0.000	0.000	0.000
35	D	77	LYS	1	0.820	0.889	19.268	0.237	0.237	0.000	0.000	0.000	0.000
36	D	78	ALA	0	0.035	0.016	23.294	0.000	0.000	0.000	0.000	0.000	0.000
37	D	79	ASP	-1	-0.888	-0.942	25.750	-0.134	-0.134	0.000	0.000	0.000	0.000
38	D	80	TYR	0	-0.084	-0.092	27.593	0.006	0.006	0.000	0.000	0.000	0.000
39	D	81	GLY	0	0.075	0.057	29.914	0.006	0.006	0.000	0.000	0.000	0.000
40	D	82	GLY	0	-0.112	-0.053	29.356	0.006	0.006	0.000	0.000	0.000	0.000
41	D	83	VAL	0	-0.040	-0.024	29.137	-0.007	-0.007	0.000	0.000	0.000	0.000
42	D	84	GLY	0	0.052	0.012	27.797	0.003	0.003	0.000	0.000	0.000	0.000
43	D	85	GLU	-1	-0.918	-0.921	27.440	-0.102	-0.102	0.000	0.000	0.000	0.000
44	D	86	ASN	0	-0.003	0.004	23.176	-0.013	-0.013	0.000	0.000	0.000	0.000
45	D	87	LEU	0	0.020	0.023	24.001	0.012	0.012	0.000	0.000	0.000	0.000
46	D	88	TYR	0	-0.016	-0.021	23.814	-0.016	-0.016	0.000	0.000	0.000	0.000
47	D	89	VAL	0	0.004	0.003	21.708	0.009	0.009	0.000	0.000	0.000	0.000
48	D	90	HIS	0	0.032	0.028	24.171	-0.009	-0.009	0.000	0.000	0.000	0.000
49	D	91	ALA	0	0.021	-0.005	22.577	-0.006	-0.006	0.000	0.000	0.000	0.000
50	D	92	ASP	-1	-0.863	-0.938	22.619	-0.078	-0.078	0.000	0.000	0.000	0.000
51	D	93	ASP	-1	-0.894	-0.924	23.692	-0.088	-0.088	0.000	0.000	0.000	0.000
52	D	94	VAL	0	-0.042	-0.031	17.517	-0.014	-0.014	0.000	0.000	0.000	0.000
53	D	95	GLU	-1	-0.946	-0.962	18.348	-0.064	-0.064	0.000	0.000	0.000	0.000
54	D	96	PHE	0	-0.023	-0.023	9.947	-0.018	-0.018	0.000	0.000	0.000	0.000
55	D	97	VAL	0	0.003	0.017	13.427	0.019	0.019	0.000	0.000	0.000	0.000
56	D	98	PRO	0	-0.013	-0.017	10.914	-0.012	-0.012	0.000	0.000	0.000	0.000
57	D	99	GLY	0	-0.042	-0.027	7.829	0.050	0.050	0.000	0.000	0.000	0.000
58	D	100	GLU	-1	-0.942	-0.968	8.791	0.157	0.157	0.000	0.000	0.000	0.000
59	D	101	SER	0	-0.014	-0.020	10.372	-0.010	-0.010	0.000	0.000	0.000	0.000
60	D	102	LEU	0	-0.016	0.013	11.700	-0.010	-0.010	0.000	0.000	0.000	0.000
61	D	103	LYS	1	0.957	0.974	13.345	0.054	0.054	0.000	0.000	0.000	0.000
62	D	104	TRP	0	0.020	0.039	14.841	-0.008	-0.008	0.000	0.000	0.000	0.000
63	D	105	ASN	0	0.000	-0.028	19.814	0.012	0.012	0.000	0.000	0.000	0.000
64	D	106	VAL	0	0.002	0.006	22.549	0.006	0.006	0.000	0.000	0.000	0.000
65	D	107	ARG	1	0.849	0.909	25.118	0.081	0.081	0.000	0.000	0.000	0.000
66	D	108	ASN	0	-0.046	-0.039	28.867	0.002	0.002	0.000	0.000	0.000	0.000
67	D	109	LEU	0	0.050	0.035	26.396	0.001	0.001	0.000	0.000	0.000	0.000
68	D	110	ASP	-1	-0.854	-0.925	30.247	-0.068	-0.068	0.000	0.000	0.000	0.000
69	D	111	VAL	0	-0.050	-0.006	29.356	-0.006	-0.006	0.000	0.000	0.000	0.000
70	D	112	MET	0	0.004	-0.008	32.289	0.006	0.006	0.000	0.000	0.000	0.000
71	D	113	PRO	0	0.009	-0.018	34.328	-0.002	-0.002	0.000	0.000	0.000	0.000
72	D	114	ILE	0	-0.026	-0.008	34.584	0.001	0.001	0.000	0.000	0.000	0.000
73	D	115	PHE	0	-0.037	-0.004	26.569	-0.006	-0.006	0.000	0.000	0.000	0.000
74	D	116	GLU	-1	-0.885	-0.938	30.386	-0.086	-0.086	0.000	0.000	0.000	0.000
75	D	117	THR	0	-0.105	-0.057	25.799	-0.002	-0.002	0.000	0.000	0.000	0.000
76	D	118	LEU	0	0.016	0.014	21.739	-0.002	-0.002	0.000	0.000	0.000	0.000
77	D	119	ALA	0	-0.004	-0.002	21.292	-0.009	-0.009	0.000	0.000	0.000	0.000
78	D	120	LEU	0	0.014	0.001	16.441	0.000	0.000	0.000	0.000	0.000	0.000
79	D	121	ARG	1	0.870	0.960	14.456	0.350	0.350	0.000	0.000	0.000	0.000
80	D	122	LEU	0	0.015	0.003	11.654	0.020	0.020	0.000	0.000	0.000	0.000
81	D	123	VAL	0	-0.015	-0.010	8.977	-0.053	-0.053	0.000	0.000	0.000	0.000
82	D	124	LEU	0	0.024	-0.004	6.289	0.144	0.144	0.000	0.000	0.000	0.000
83	D	125	GLN	0	-0.029	0.003	3.434	-0.764	-0.315	0.012	-0.075	-0.386	0.000
84	D	126	GLY	0	-0.080	-0.041	5.012	-0.219	-0.128	-0.001	-0.002	-0.088	0.000
85	D	127	ASP	-1	-0.874	-0.913	3.601	-3.685	-3.085	0.026	-0.237	-0.390	-0.001
86	D	128	VAL	0	-0.064	-0.038	6.670	0.164	0.164	0.000	0.000	0.000	0.000
87	D	129	ILE	0	-0.006	0.003	8.954	-0.009	-0.009	0.000	0.000	0.000	0.000
88	D	130	TRP	0	0.011	-0.005	11.751	0.040	0.040	0.000	0.000	0.000	0.000
89	D	131	LEU	0	-0.009	0.002	13.660	0.003	0.003	0.000	0.000	0.000	0.000
90	D	132	ARG	1	0.971	0.977	17.258	0.142	0.142	0.000	0.000	0.000	0.000
91	D	134	VAL	0	-0.003	0.000	23.430	0.000	0.000	0.000	0.000	0.000	0.000
92	D	135	PRO	0	-0.005	-0.007	27.183	0.004	0.004	0.000	0.000	0.000	0.000
93	D	136	GLU	-1	-0.956	-0.978	28.733	-0.059	-0.059	0.000	0.000	0.000	0.000
94	D	137	LEU	0	-0.020	-0.003	31.471	0.003	0.003	0.000	0.000	0.000	0.000

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