FMO DATABASE

FMODB ID: 6Y34Z

Calculation Name: 3M8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M8F

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KNP2

Base Structure: X-ray

Registration Date: 2023-09-20

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-685479.232777
FMO2-HF: Nuclear repulsion	646155.113009
FMO2-HF: Total energy	-39324.119768
FMO2-MP2: Total energy	-39434.841835

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:5:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
1.563	4.018	0.086	-1.039	-1.502	0.002

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.034

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	A	7	TYR	0	0.013	-0.003	3.654	1.328	3.783	0.086	-1.039	-1.502	0.002
4	A	8	THR	0	-0.059	-0.027	5.460	-0.596	-0.596	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.065	0.034	9.067	-0.164	-0.164	0.000	0.000	0.000	0.000
6	A	10	ASN	0	0.027	0.008	10.967	0.048	0.048	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.071	0.029	14.077	-0.063	-0.063	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.031	0.012	16.010	-0.038	-0.038	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.888	-0.945	16.738	-0.181	-0.181	0.000	0.000	0.000	0.000
10	A	14	ILE	0	-0.021	-0.009	13.016	-0.035	-0.035	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.042	0.010	17.538	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.972	-0.975	20.583	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.875	0.940	16.170	0.238	0.238	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.010	0.000	18.658	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.012	0.008	22.354	0.002	0.002	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.114	-0.053	24.654	0.002	0.002	0.000	0.000	0.000	0.000
17	A	21	ASP	-1	-0.907	-0.955	24.412	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.895	-0.938	26.411	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	23	CYS	0	0.003	-0.010	26.686	0.011	0.011	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.025	-0.009	23.388	0.011	0.011	0.000	0.000	0.000	0.000
21	A	25	TYR	0	0.009	0.008	25.473	0.017	0.017	0.000	0.000	0.000	0.000
22	A	26	GLN	0	-0.005	-0.023	26.826	0.019	0.019	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.026	-0.014	25.162	0.008	0.008	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.035	-0.014	21.883	0.012	0.012	0.000	0.000	0.000	0.000
25	A	29	MET	0	0.015	0.001	25.373	0.017	0.017	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.027	0.029	28.582	0.005	0.005	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.098	-0.056	24.824	0.004	0.004	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.013	0.009	26.497	0.016	0.016	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.025	0.021	29.808	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.898	-0.968	33.200	0.049	0.049	0.000	0.000	0.000	0.000
31	A	35	ASN	0	-0.091	-0.036	34.749	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.028	-0.010	32.315	0.005	0.005	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.986	-0.981	29.518	0.123	0.123	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.023	0.004	25.688	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.058	-0.027	27.664	0.002	0.002	0.000	0.000	0.000	0.000
36	A	40	MET	0	-0.028	-0.022	26.644	0.004	0.004	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.009	0.012	26.969	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	42	ASN	0	0.032	0.028	27.019	0.007	0.007	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.932	0.962	24.920	-0.037	-0.037	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.076	-0.044	28.706	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.076	0.043	31.918	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.056	0.034	27.644	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.078	-0.071	31.008	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.986	-0.983	32.812	0.023	0.023	0.000	0.000	0.000	0.000
45	A	49	MET	0	-0.007	0.001	33.256	0.000	0.000	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.005	0.031	30.540	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	51	GLN	0	0.001	0.000	34.781	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.043	0.003	31.453	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.020	0.007	33.851	0.005	0.005	0.000	0.000	0.000	0.000
50	A	54	LYS	1	1.009	1.029	33.061	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.024	-0.015	31.607	0.002	0.002	0.000	0.000	0.000	0.000
52	A	56	THR	0	-0.009	-0.019	29.257	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	57	VAL	0	0.091	0.047	28.156	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.033	-0.029	27.454	0.011	0.011	0.000	0.000	0.000	0.000
55	A	59	ALA	0	-0.047	-0.027	25.389	0.004	0.004	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.033	0.004	23.708	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	61	VAL	0	0.018	0.020	22.656	0.006	0.006	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.046	-0.033	21.509	0.029	0.029	0.000	0.000	0.000	0.000
59	A	63	TRP	0	0.034	0.014	17.729	0.005	0.005	0.000	0.000	0.000	0.000
60	A	64	PHE	0	0.017	0.012	17.620	0.008	0.008	0.000	0.000	0.000	0.000
61	A	65	TYR	0	-0.027	0.003	16.642	0.047	0.047	0.000	0.000	0.000	0.000
62	A	66	CYS	0	-0.031	-0.026	14.627	0.031	0.031	0.000	0.000	0.000	0.000
63	A	67	ALA	0	-0.061	-0.024	13.133	0.031	0.031	0.000	0.000	0.000	0.000
64	A	68	GLY	0	0.029	0.035	12.965	0.060	0.060	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.040	-0.003	13.924	0.038	0.038	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.008	0.002	17.336	0.005	0.005	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.839	-0.910	16.281	0.374	0.374	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.887	-0.963	18.447	0.088	0.088	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.004	-0.002	20.039	0.033	0.033	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.873	0.925	22.573	-0.142	-0.142	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.046	0.030	25.209	0.006	0.006	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.007	-0.012	28.740	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	77	ARG	1	0.917	0.960	30.591	-0.060	-0.060	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.037	-0.009	29.704	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	79	LYN	0	0.015	0.005	24.252	0.005	0.005	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.038	-0.025	25.522	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.029	-0.010	21.381	0.000	0.000	0.000	0.000	0.000	0.000
78	A	82	THR	0	0.059	0.028	21.295	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.024	-0.001	20.858	0.007	0.007	0.000	0.000	0.000	0.000
80	A	84	SER	0	0.026	0.005	15.641	0.000	0.000	0.000	0.000	0.000	0.000
81	A	85	ASP	-1	-0.882	-0.964	15.221	0.414	0.414	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.030	-0.012	13.001	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.013	-0.012	16.506	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	88	VAL	0	-0.007	-0.009	19.542	-0.032	-0.032	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.909	-0.959	17.626	0.224	0.224	0.000	0.000	0.000	0.000
86	A	90	ILE	0	-0.052	-0.021	17.291	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	91	VAL	0	0.006	-0.009	20.759	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.908	-0.953	22.817	0.126	0.126	0.000	0.000	0.000	0.000
89	A	93	CYS	0	-0.057	-0.003	21.425	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	94	PHE	0	-0.015	-0.016	23.482	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	95	LYS	1	0.960	0.976	26.817	-0.112	-0.112	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.007	-0.014	25.701	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.943	0.968	23.065	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	98	ALA	0	-0.042	-0.009	29.248	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	99	MET	0	-0.114	-0.042	31.850	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.995	-0.983	29.864	0.052	0.052	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)