FMO DATABASE

FMODB ID: R9YY8

Calculation Name: 3MI8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MI8

Chain ID: D

ChEMBL ID:

UniProt ID: O95150

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742323.180355
FMO2-HF: Nuclear repulsion	695389.830448
FMO2-HF: Total energy	-46933.349907
FMO2-MP2: Total energy	-47058.983164

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:33:THR)

Summations of interaction energy for fragment #1(D:33:THR)

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.
-5.805	-1.792	1.595	-2.028	-3.582	-0.016

Interaction energy analysis for fragmet #1(D:33:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.021

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	D	35	THR	0	-0.033	-0.028	2.497	-4.099	-2.084	1.343	-1.435	-1.923	-0.011
4	D	36	TYR	0	0.025	0.005	4.916	0.732	0.789	-0.001	-0.007	-0.049	0.000
5	D	37	PRO	0	-0.013	-0.001	8.480	-0.064	-0.064	0.000	0.000	0.000	0.000
6	D	38	TRP	0	0.034	0.015	11.698	0.094	0.094	0.000	0.000	0.000	0.000
7	D	39	ARG	1	0.898	0.944	13.749	0.442	0.442	0.000	0.000	0.000	0.000
8	D	40	ASP	-1	-0.833	-0.899	16.141	-0.678	-0.678	0.000	0.000	0.000	0.000
9	D	41	ALA	0	0.015	0.001	18.071	0.045	0.045	0.000	0.000	0.000	0.000
10	D	42	GLU	-1	-0.806	-0.852	20.066	-0.440	-0.440	0.000	0.000	0.000	0.000
11	D	43	THR	0	0.011	-0.014	21.599	0.035	0.035	0.000	0.000	0.000	0.000
12	D	44	GLY	0	0.035	0.026	20.426	-0.039	-0.039	0.000	0.000	0.000	0.000
13	D	45	GLU	-1	-0.885	-0.932	17.574	-0.548	-0.548	0.000	0.000	0.000	0.000
14	D	46	ARG	1	0.871	0.926	13.552	0.852	0.852	0.000	0.000	0.000	0.000
15	D	47	LEU	0	0.047	0.034	11.456	-0.018	-0.018	0.000	0.000	0.000	0.000
16	D	48	VAL	0	-0.045	-0.033	8.357	0.092	0.092	0.000	0.000	0.000	0.000
17	D	49	CYS	0	-0.054	-0.004	7.876	-0.092	-0.092	0.000	0.000	0.000	0.000
18	D	50	ALA	0	0.019	0.020	3.746	-0.690	-0.543	0.004	-0.038	-0.113	0.000
19	D	51	GLN	0	0.022	0.009	3.569	0.469	0.712	0.002	-0.047	-0.199	0.000
20	D	52	CYS	0	-0.013	-0.007	4.399	-0.206	-0.054	-0.002	-0.014	-0.137	0.000
21	D	53	PRO	0	0.053	0.027	5.524	0.204	0.204	0.000	0.000	0.000	0.000
22	D	54	PRO	0	-0.014	0.019	7.147	-0.274	-0.274	0.000	0.000	0.000	0.000
23	D	55	GLY	0	0.007	0.020	10.732	0.044	0.044	0.000	0.000	0.000	0.000
24	D	56	THR	0	-0.076	-0.070	9.663	-0.112	-0.112	0.000	0.000	0.000	0.000
25	D	57	PHE	0	-0.019	-0.014	11.719	0.036	0.036	0.000	0.000	0.000	0.000
26	D	58	VAL	0	0.057	0.021	9.984	-0.041	-0.041	0.000	0.000	0.000	0.000
27	D	59	GLN	0	-0.027	0.004	12.254	0.045	0.045	0.000	0.000	0.000	0.000
28	D	60	ARG	1	0.953	0.953	13.887	0.390	0.390	0.000	0.000	0.000	0.000
29	D	61	PRO	0	0.026	0.023	12.177	-0.076	-0.076	0.000	0.000	0.000	0.000
30	D	63	ARG	1	0.863	0.915	11.673	0.592	0.592	0.000	0.000	0.000	0.000
31	D	64	ARG	1	0.806	0.858	13.362	0.432	0.432	0.000	0.000	0.000	0.000
32	D	65	ASP	-1	-0.957	-0.956	15.425	-0.579	-0.579	0.000	0.000	0.000	0.000
33	D	66	SER	0	0.038	0.021	13.300	-0.026	-0.026	0.000	0.000	0.000	0.000
34	D	67	PRO	0	0.031	0.002	8.009	-0.072	-0.072	0.000	0.000	0.000	0.000
35	D	68	THR	0	-0.028	-0.025	7.415	0.149	0.149	0.000	0.000	0.000	0.000
36	D	69	THR	0	-0.030	-0.001	9.130	0.049	0.049	0.000	0.000	0.000	0.000
37	D	71	GLY	0	0.053	0.038	10.909	0.048	0.048	0.000	0.000	0.000	0.000
38	D	72	PRO	0	-0.001	-0.009	13.723	0.037	0.037	0.000	0.000	0.000	0.000
39	D	73	CYS	0	-0.057	-0.013	15.493	-0.034	-0.034	0.000	0.000	0.000	0.000
40	D	74	PRO	0	0.026	0.021	17.164	0.016	0.016	0.000	0.000	0.000	0.000
41	D	75	PRO	0	0.045	0.004	20.912	0.025	0.025	0.000	0.000	0.000	0.000
42	D	76	ARG	1	0.915	0.956	23.791	-0.114	-0.114	0.000	0.000	0.000	0.000
43	D	77	HIS	0	-0.026	-0.020	19.714	-0.023	-0.023	0.000	0.000	0.000	0.000
44	D	78	TYR	0	0.006	-0.001	17.298	0.030	0.030	0.000	0.000	0.000	0.000
45	D	79	THR	0	-0.017	-0.030	12.550	-0.014	-0.014	0.000	0.000	0.000	0.000
46	D	80	GLN	0	0.012	0.010	13.743	-0.006	-0.006	0.000	0.000	0.000	0.000
47	D	81	PHE	0	-0.011	-0.009	10.406	0.148	0.148	0.000	0.000	0.000	0.000
48	D	82	TRP	0	0.046	0.024	3.105	-1.451	-0.052	0.249	-0.487	-1.161	-0.005
49	D	83	ASN	0	-0.072	-0.042	7.682	-0.275	-0.275	0.000	0.000	0.000	0.000
50	D	84	TYR	0	0.053	0.012	8.512	-0.183	-0.183	0.000	0.000	0.000	0.000
51	D	85	LEU	0	-0.014	0.005	10.801	0.019	0.019	0.000	0.000	0.000	0.000
52	D	86	GLU	-1	-0.887	-0.938	13.626	-0.354	-0.354	0.000	0.000	0.000	0.000
53	D	87	ARG	1	0.929	0.956	16.164	0.068	0.068	0.000	0.000	0.000	0.000
54	D	89	ARG	1	0.953	0.985	17.054	-0.159	-0.159	0.000	0.000	0.000	0.000
55	D	90	TYR	0	0.047	0.021	19.582	0.022	0.022	0.000	0.000	0.000	0.000
56	D	91	CYS	0	-0.122	-0.057	23.017	0.040	0.040	0.000	0.000	0.000	0.000
57	D	92	ASN	0	-0.033	-0.020	24.452	0.004	0.004	0.000	0.000	0.000	0.000
58	D	93	VAL	0	0.032	0.033	26.386	-0.008	-0.008	0.000	0.000	0.000	0.000
59	D	94	LEU	0	-0.010	-0.016	28.835	0.007	0.007	0.000	0.000	0.000	0.000
60	D	95	CYS	0	-0.053	-0.006	27.023	0.004	0.004	0.000	0.000	0.000	0.000
61	D	96	GLY	0	0.053	0.029	33.952	-0.008	-0.008	0.000	0.000	0.000	0.000
62	D	97	GLU	-1	-0.931	-0.978	37.408	0.084	0.084	0.000	0.000	0.000	0.000
63	D	98	ARG	1	0.862	0.931	39.890	-0.084	-0.084	0.000	0.000	0.000	0.000
64	D	99	GLU	-1	-0.847	-0.925	34.701	0.142	0.142	0.000	0.000	0.000	0.000
65	D	100	GLU	-1	-0.979	-0.994	34.675	0.139	0.139	0.000	0.000	0.000	0.000
66	D	101	GLU	-1	-0.821	-0.944	29.425	0.193	0.193	0.000	0.000	0.000	0.000
67	D	102	ALA	0	-0.085	-0.033	28.533	0.005	0.005	0.000	0.000	0.000	0.000
68	D	103	ARG	1	0.901	0.945	20.082	-0.408	-0.408	0.000	0.000	0.000	0.000
69	D	104	ALA	0	0.097	0.066	25.740	-0.014	-0.014	0.000	0.000	0.000	0.000
70	D	106	HIS	0	0.056	0.054	17.871	0.007	0.007	0.000	0.000	0.000	0.000
71	D	107	ALA	0	0.057	0.020	16.822	-0.014	-0.014	0.000	0.000	0.000	0.000
72	D	108	THR	0	-0.016	-0.031	14.107	0.009	0.009	0.000	0.000	0.000	0.000
73	D	109	HIS	0	-0.031	-0.024	16.081	0.077	0.077	0.000	0.000	0.000	0.000
74	D	110	ASN	0	0.091	0.039	18.760	-0.046	-0.046	0.000	0.000	0.000	0.000
75	D	111	ARG	1	0.825	0.934	21.936	-0.130	-0.130	0.000	0.000	0.000	0.000
76	D	112	ALA	0	-0.014	-0.012	25.184	-0.001	-0.001	0.000	0.000	0.000	0.000
77	D	114	ARG	1	0.976	1.010	30.717	-0.194	-0.194	0.000	0.000	0.000	0.000
78	D	115	CYS	0	0.040	0.028	32.855	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	116	ARG	1	0.945	0.972	36.430	-0.105	-0.105	0.000	0.000	0.000	0.000
80	D	117	THR	0	0.032	0.002	38.890	0.002	0.002	0.000	0.000	0.000	0.000
81	D	118	GLY	0	-0.011	0.006	40.749	-0.001	-0.001	0.000	0.000	0.000	0.000
82	D	119	PHE	0	-0.022	-0.032	40.813	-0.005	-0.005	0.000	0.000	0.000	0.000
83	D	120	PHE	0	-0.002	0.000	38.938	0.008	0.008	0.000	0.000	0.000	0.000
84	D	121	ALA	0	0.057	0.016	35.865	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	122	HIS	0	0.023	0.002	37.788	0.006	0.006	0.000	0.000	0.000	0.000
86	D	123	ALA	0	-0.021	-0.013	38.069	-0.006	-0.006	0.000	0.000	0.000	0.000
87	D	124	GLY	0	0.011	0.016	36.122	-0.002	-0.002	0.000	0.000	0.000	0.000
88	D	125	PHE	0	-0.042	-0.011	37.154	-0.002	-0.002	0.000	0.000	0.000	0.000
89	D	127	LEU	0	-0.020	-0.010	39.913	-0.007	-0.007	0.000	0.000	0.000	0.000
90	D	128	GLU	-1	-0.927	-0.966	43.071	0.089	0.089	0.000	0.000	0.000	0.000
91	D	129	HIS	0	-0.007	0.014	41.872	-0.005	-0.005	0.000	0.000	0.000	0.000
92	D	130	ALA	0	-0.008	0.002	46.294	-0.001	-0.001	0.000	0.000	0.000	0.000
93	D	131	SER	0	0.019	0.015	49.273	0.001	0.001	0.000	0.000	0.000	0.000
94	D	132	CYS	0	-0.005	0.011	48.086	-0.002	-0.002	0.000	0.000	0.000	0.000
95	D	142	GLY	0	0.020	0.004	42.518	0.001	0.001	0.000	0.000	0.000	0.000
96	D	143	THR	0	-0.028	0.001	36.183	0.002	0.002	0.000	0.000	0.000	0.000
97	D	144	PRO	0	0.043	0.000	34.765	-0.001	-0.001	0.000	0.000	0.000	0.000
98	D	145	SER	0	-0.053	-0.020	33.322	-0.003	-0.003	0.000	0.000	0.000	0.000
99	D	146	GLN	0	-0.018	-0.018	35.548	-0.012	-0.012	0.000	0.000	0.000	0.000
100	D	147	ASN	0	0.055	0.038	38.873	-0.001	-0.001	0.000	0.000	0.000	0.000
101	D	148	THR	0	-0.034	-0.036	42.662	0.003	0.003	0.000	0.000	0.000	0.000
102	D	149	GLN	0	-0.003	0.004	44.496	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:33:THR)