FMO DATABASE

FMODB ID: K9223

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

Total energy (hartree)

FMO2-HF: Electronic energy	-745161.012986
FMO2-HF: Nuclear repulsion	698226.958707
FMO2-HF: Total energy	-46934.054278
FMO2-MP2: Total energy	-47059.740259

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.
-6.181	-1.081	1.004	-2.052	-4.051	-0.014

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 : -0.013 / q_NPA : -0.016

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	-0.001	-0.015	2.830	-3.703	-1.347	0.320	-1.242	-1.434	-0.007
4	D	36	TYR	0	0.027	0.013	5.325	0.585	0.631	-0.001	-0.001	-0.043	0.000
5	D	37	PRO	0	-0.018	0.001	8.820	-0.045	-0.045	0.000	0.000	0.000	0.000
6	D	38	TRP	0	0.040	0.010	11.971	0.078	0.078	0.000	0.000	0.000	0.000
7	D	39	ARG	1	0.898	0.923	13.823	0.283	0.283	0.000	0.000	0.000	0.000
8	D	40	ASP	-1	-0.781	-0.859	15.896	-0.333	-0.333	0.000	0.000	0.000	0.000
9	D	41	ALA	0	0.002	-0.012	17.969	0.022	0.022	0.000	0.000	0.000	0.000
10	D	42	GLU	-1	-0.790	-0.846	20.162	-0.155	-0.155	0.000	0.000	0.000	0.000
11	D	43	THR	0	-0.026	-0.037	21.617	0.016	0.016	0.000	0.000	0.000	0.000
12	D	44	GLY	0	0.032	0.047	20.857	-0.022	-0.022	0.000	0.000	0.000	0.000
13	D	45	GLU	-1	-0.843	-0.905	18.201	-0.351	-0.351	0.000	0.000	0.000	0.000
14	D	46	ARG	1	0.826	0.899	14.318	0.626	0.626	0.000	0.000	0.000	0.000
15	D	47	LEU	0	0.022	0.022	11.630	-0.035	-0.035	0.000	0.000	0.000	0.000
16	D	48	VAL	0	-0.020	-0.031	8.731	0.063	0.063	0.000	0.000	0.000	0.000
17	D	49	CYS	0	-0.074	-0.002	7.701	0.006	0.006	0.000	0.000	0.000	0.000
18	D	50	ALA	0	0.046	0.039	3.079	-0.819	-0.495	0.091	-0.099	-0.317	0.000
19	D	51	GLN	0	0.012	-0.002	3.434	0.357	0.639	0.004	-0.051	-0.235	0.000
20	D	52	CYS	0	-0.040	-0.012	4.152	0.045	0.274	-0.001	-0.030	-0.198	0.000
21	D	53	PRO	0	0.034	0.019	5.164	0.014	0.014	0.000	0.000	0.000	0.000
22	D	54	PRO	0	0.000	0.001	6.973	-0.258	-0.258	0.000	0.000	0.000	0.000
23	D	55	GLY	0	-0.001	0.013	10.676	0.050	0.050	0.000	0.000	0.000	0.000
24	D	56	THR	0	-0.041	-0.034	9.291	-0.073	-0.073	0.000	0.000	0.000	0.000
25	D	57	PHE	0	-0.011	-0.003	11.273	0.007	0.007	0.000	0.000	0.000	0.000
26	D	58	VAL	0	0.053	0.023	10.142	0.011	0.011	0.000	0.000	0.000	0.000
27	D	59	GLN	0	-0.015	0.010	12.480	0.011	0.011	0.000	0.000	0.000	0.000
28	D	60	ARG	1	0.928	0.944	13.741	0.042	0.042	0.000	0.000	0.000	0.000
29	D	61	PRO	0	0.034	0.026	11.618	0.008	0.008	0.000	0.000	0.000	0.000
30	D	63	ARG	1	0.814	0.898	11.471	0.202	0.202	0.000	0.000	0.000	0.000
31	D	64	ARG	1	0.780	0.847	13.428	0.177	0.177	0.000	0.000	0.000	0.000
32	D	65	ASP	-1	-0.913	-0.959	14.717	-0.163	-0.163	0.000	0.000	0.000	0.000
33	D	66	SER	0	0.057	0.037	12.988	0.008	0.008	0.000	0.000	0.000	0.000
34	D	67	PRO	0	0.013	-0.002	7.688	-0.088	-0.088	0.000	0.000	0.000	0.000
35	D	68	THR	0	-0.022	-0.041	6.893	0.037	0.037	0.000	0.000	0.000	0.000
36	D	69	THR	0	-0.010	0.009	8.966	0.145	0.145	0.000	0.000	0.000	0.000
37	D	71	GLY	0	0.054	0.046	10.351	0.072	0.072	0.000	0.000	0.000	0.000
38	D	72	PRO	0	0.011	-0.006	13.247	0.036	0.036	0.000	0.000	0.000	0.000
39	D	73	CYS	0	-0.085	-0.011	14.890	-0.041	-0.041	0.000	0.000	0.000	0.000
40	D	74	PRO	0	0.023	0.022	16.869	0.001	0.001	0.000	0.000	0.000	0.000
41	D	75	PRO	0	0.046	0.000	20.627	0.014	0.014	0.000	0.000	0.000	0.000
42	D	76	ARG	1	0.947	0.962	23.376	-0.162	-0.162	0.000	0.000	0.000	0.000
43	D	77	HIS	0	0.002	0.005	19.820	-0.034	-0.034	0.000	0.000	0.000	0.000
44	D	78	TYR	0	0.013	0.009	16.948	0.019	0.019	0.000	0.000	0.000	0.000
45	D	79	THR	0	-0.037	-0.048	12.184	-0.027	-0.027	0.000	0.000	0.000	0.000
46	D	80	GLN	0	0.014	0.010	13.430	0.020	0.020	0.000	0.000	0.000	0.000
47	D	81	PHE	0	-0.015	-0.015	10.046	0.074	0.074	0.000	0.000	0.000	0.000
48	D	82	TRP	0	0.042	0.015	2.825	-1.918	-0.055	0.591	-0.629	-1.824	-0.007
49	D	83	ASN	0	-0.066	-0.035	7.076	-0.324	-0.324	0.000	0.000	0.000	0.000
50	D	84	TYR	0	0.044	0.011	8.397	-0.090	-0.090	0.000	0.000	0.000	0.000
51	D	85	LEU	0	-0.003	0.004	10.405	-0.015	-0.015	0.000	0.000	0.000	0.000
52	D	86	GLU	-1	-0.887	-0.939	13.735	-0.083	-0.083	0.000	0.000	0.000	0.000
53	D	87	ARG	1	0.871	0.932	16.057	-0.076	-0.076	0.000	0.000	0.000	0.000
54	D	89	ARG	1	0.943	0.972	16.946	-0.243	-0.243	0.000	0.000	0.000	0.000
55	D	90	TYR	0	0.055	0.024	19.652	0.023	0.023	0.000	0.000	0.000	0.000
56	D	91	CYS	0	-0.136	-0.060	22.877	0.034	0.034	0.000	0.000	0.000	0.000
57	D	92	ASN	0	0.005	-0.007	24.251	0.006	0.006	0.000	0.000	0.000	0.000
58	D	93	VAL	0	0.017	0.037	26.048	-0.012	-0.012	0.000	0.000	0.000	0.000
59	D	94	LEU	0	-0.017	-0.008	28.225	0.006	0.006	0.000	0.000	0.000	0.000
60	D	95	CYS	0	-0.069	-0.011	26.697	0.002	0.002	0.000	0.000	0.000	0.000
61	D	96	GLY	0	0.057	0.031	33.455	-0.005	-0.005	0.000	0.000	0.000	0.000
62	D	97	GLU	-1	-0.843	-0.925	36.988	0.091	0.091	0.000	0.000	0.000	0.000
63	D	98	ARG	1	0.788	0.896	39.950	-0.077	-0.077	0.000	0.000	0.000	0.000
64	D	99	GLU	-1	-0.853	-0.919	34.069	0.130	0.130	0.000	0.000	0.000	0.000
65	D	100	GLU	-1	-0.822	-0.900	34.372	0.126	0.126	0.000	0.000	0.000	0.000
66	D	101	GLU	-1	-0.802	-0.913	29.315	0.192	0.192	0.000	0.000	0.000	0.000
67	D	102	ALA	0	-0.051	-0.014	28.367	0.002	0.002	0.000	0.000	0.000	0.000
68	D	103	ARG	1	0.875	0.930	20.875	-0.335	-0.335	0.000	0.000	0.000	0.000
69	D	104	ALA	0	0.107	0.067	25.623	-0.008	-0.008	0.000	0.000	0.000	0.000
70	D	106	HIS	0	0.060	0.049	17.277	0.010	0.010	0.000	0.000	0.000	0.000
71	D	107	ALA	0	0.057	0.029	16.286	0.001	0.001	0.000	0.000	0.000	0.000
72	D	108	THR	0	0.014	-0.017	13.807	0.013	0.013	0.000	0.000	0.000	0.000
73	D	109	HIS	0	-0.029	-0.016	15.760	0.040	0.040	0.000	0.000	0.000	0.000
74	D	110	ASN	0	0.047	0.013	18.444	-0.034	-0.034	0.000	0.000	0.000	0.000
75	D	111	ARG	1	0.797	0.882	21.676	-0.156	-0.156	0.000	0.000	0.000	0.000
76	D	112	ALA	0	-0.013	-0.012	24.891	-0.001	-0.001	0.000	0.000	0.000	0.000
77	D	114	ARG	1	0.859	0.921	30.407	-0.155	-0.155	0.000	0.000	0.000	0.000
78	D	115	CYS	0	0.024	0.035	32.942	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	116	ARG	1	0.811	0.882	36.493	-0.097	-0.097	0.000	0.000	0.000	0.000
80	D	117	THR	0	0.033	-0.003	38.703	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	118	GLY	0	-0.005	0.017	40.393	-0.002	-0.002	0.000	0.000	0.000	0.000
82	D	119	PHE	0	-0.022	-0.030	40.617	-0.005	-0.005	0.000	0.000	0.000	0.000
83	D	120	PHE	0	-0.011	-0.013	38.762	0.006	0.006	0.000	0.000	0.000	0.000
84	D	121	ALA	0	0.042	0.011	35.673	-0.005	-0.005	0.000	0.000	0.000	0.000
85	D	122	HIS	0	-0.001	-0.003	37.592	0.004	0.004	0.000	0.000	0.000	0.000
86	D	123	ALA	0	0.001	-0.013	38.163	-0.002	-0.002	0.000	0.000	0.000	0.000
87	D	124	GLY	0	-0.011	0.006	36.133	-0.001	-0.001	0.000	0.000	0.000	0.000
88	D	125	PHE	0	-0.038	-0.013	37.215	0.000	0.000	0.000	0.000	0.000	0.000
89	D	127	LEU	0	-0.002	-0.001	39.699	-0.004	-0.004	0.000	0.000	0.000	0.000
90	D	128	GLU	-1	-0.805	-0.903	43.093	0.075	0.075	0.000	0.000	0.000	0.000
91	D	129	HIS	0	0.000	0.023	42.173	-0.005	-0.005	0.000	0.000	0.000	0.000
92	D	130	ALA	0	-0.004	0.001	46.165	-0.001	-0.001	0.000	0.000	0.000	0.000
93	D	131	SER	0	0.004	0.005	48.968	0.000	0.000	0.000	0.000	0.000	0.000
94	D	132	CYS	0	-0.023	0.005	48.297	-0.001	-0.001	0.000	0.000	0.000	0.000
95	D	142	GLY	0	0.027	0.018	42.279	-0.001	-0.001	0.000	0.000	0.000	0.000
96	D	143	THR	0	-0.013	0.013	35.999	0.004	0.004	0.000	0.000	0.000	0.000
97	D	144	PRO	0	0.026	-0.003	34.918	-0.002	-0.002	0.000	0.000	0.000	0.000
98	D	145	SER	0	-0.028	-0.017	33.689	0.003	0.003	0.000	0.000	0.000	0.000
99	D	146	GLN	0	-0.014	-0.009	35.687	-0.005	-0.005	0.000	0.000	0.000	0.000
100	D	147	ASN	0	0.034	0.024	39.042	0.001	0.001	0.000	0.000	0.000	0.000
101	D	148	THR	0	-0.014	-0.040	42.851	0.000	0.000	0.000	0.000	0.000	0.000
102	D	149	GLN	0	-0.019	-0.002	44.655	-0.005	-0.005	0.000	0.000	0.000	0.000

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