FMO DATABASE

FMODB ID: QV6MY

Calculation Name: 3M8J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M8J

Chain ID: A

ChEMBL ID:

UniProt ID: Q93K76

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601871.755493
FMO2-HF: Nuclear repulsion	566283.200503
FMO2-HF: Total energy	-35588.55499
FMO2-MP2: Total energy	-35691.177569

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:10:GLY)

Summations of interaction energy for fragment #1(A:10:GLY)

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.
1.258	3.108	0.008	-0.72	-1.137	0

Interaction energy analysis for fragmet #1(A:10:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.014

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].
3	A	12	ASP	-1	-0.883	-0.936	3.629	-1.661	-0.224	0.001	-0.605	-0.833
4	A	13	ALA	0	0.062	0.016	3.708	-0.126	0.124	0.008	-0.056	-0.202
5	A	14	PHE	0	-0.038	-0.016	4.424	0.735	0.898	-0.001	-0.059	-0.102
6	A	15	LEU	0	0.007	-0.001	6.070	0.541	0.541	0.000	0.000	0.000
7	A	16	LEU	0	0.026	0.019	8.140	0.177	0.177	0.000	0.000	0.000
8	A	17	LYS	1	0.891	0.949	8.775	0.620	0.620	0.000	0.000	0.000
9	A	18	LEU	0	-0.004	-0.008	10.292	0.150	0.150	0.000	0.000	0.000
10	A	19	ARG	1	0.939	0.971	12.304	0.292	0.292	0.000	0.000	0.000
11	A	20	GLU	-1	-0.929	-0.954	13.066	-0.389	-0.389	0.000	0.000	0.000
12	A	21	SER	0	-0.059	-0.054	13.536	0.034	0.034	0.000	0.000	0.000
13	A	22	ALA	0	-0.043	-0.001	16.101	0.014	0.014	0.000	0.000	0.000
14	A	23	LEU	0	0.012	0.012	17.928	0.019	0.019	0.000	0.000	0.000
15	A	24	SER	0	0.013	-0.002	21.038	0.013	0.013	0.000	0.000	0.000
16	A	25	SER	0	-0.039	-0.005	24.376	-0.001	-0.001	0.000	0.000	0.000
17	A	26	GLY	0	0.001	0.003	27.518	0.000	0.000	0.000	0.000	0.000
18	A	27	SER	0	-0.078	-0.049	25.617	-0.002	-0.002	0.000	0.000	0.000
19	A	28	MET	0	-0.029	0.009	23.323	-0.005	-0.005	0.000	0.000	0.000
20	A	29	SER	0	0.084	0.042	28.650	0.006	0.006	0.000	0.000	0.000
21	A	30	GLU	-1	-0.809	-0.923	30.065	-0.075	-0.075	0.000	0.000	0.000
22	A	31	GLU	-1	-0.923	-0.953	31.025	-0.092	-0.092	0.000	0.000	0.000
23	A	32	GLN	0	0.033	0.011	24.444	0.003	0.003	0.000	0.000	0.000
24	A	33	PHE	0	0.011	-0.003	25.940	-0.011	-0.011	0.000	0.000	0.000
25	A	34	PHE	0	0.001	-0.023	26.519	-0.006	-0.006	0.000	0.000	0.000
26	A	35	LEU	0	0.026	0.033	26.776	-0.001	-0.001	0.000	0.000	0.000
27	A	36	LEU	0	-0.024	-0.014	20.856	-0.011	-0.011	0.000	0.000	0.000
28	A	37	ILE	0	-0.056	-0.038	22.747	-0.009	-0.009	0.000	0.000	0.000
29	A	38	GLY	0	0.015	0.026	24.318	0.001	0.001	0.000	0.000	0.000
30	A	39	ILE	0	-0.010	0.006	19.971	-0.002	-0.002	0.000	0.000	0.000
31	A	40	SER	0	-0.098	-0.051	19.861	-0.008	-0.008	0.000	0.000	0.000
32	A	41	SER	0	0.000	-0.013	19.282	0.007	0.007	0.000	0.000	0.000
33	A	42	ILE	0	-0.092	-0.053	20.640	0.014	0.014	0.000	0.000	0.000
34	A	43	HIS	0	0.082	0.037	22.744	0.000	0.000	0.000	0.000	0.000
35	A	44	SER	0	-0.030	-0.008	25.595	0.005	0.005	0.000	0.000	0.000
36	A	45	ASP	-1	-0.780	-0.892	27.626	-0.051	-0.051	0.000	0.000	0.000
37	A	46	ARG	1	0.851	0.898	28.702	0.022	0.022	0.000	0.000	0.000
38	A	47	VAL	0	-0.023	-0.013	23.877	-0.002	-0.002	0.000	0.000	0.000
39	A	48	ILE	0	0.025	0.017	26.598	-0.008	-0.008	0.000	0.000	0.000
40	A	49	LEU	0	0.013	0.001	27.937	-0.005	-0.005	0.000	0.000	0.000
41	A	50	ALA	0	0.021	0.008	27.830	-0.001	-0.001	0.000	0.000	0.000
42	A	51	MET	0	-0.067	-0.039	23.638	-0.010	-0.010	0.000	0.000	0.000
43	A	52	LYS	1	0.893	0.964	26.849	0.062	0.062	0.000	0.000	0.000
44	A	53	ASP	-1	-0.792	-0.891	29.720	-0.058	-0.058	0.000	0.000	0.000
45	A	54	TYR	0	-0.066	-0.029	23.641	0.005	0.005	0.000	0.000	0.000
46	A	55	LEU	0	-0.002	-0.020	23.228	-0.003	-0.003	0.000	0.000	0.000
47	A	56	VAL	0	-0.046	-0.006	27.449	-0.003	-0.003	0.000	0.000	0.000
48	A	57	SER	0	-0.038	-0.026	30.828	0.001	0.001	0.000	0.000	0.000
49	A	58	GLY	0	0.043	0.033	31.122	0.005	0.005	0.000	0.000	0.000
50	A	59	HIS	0	-0.019	-0.001	32.038	0.001	0.001	0.000	0.000	0.000
51	A	60	SER	0	-0.032	-0.048	30.178	-0.007	-0.007	0.000	0.000	0.000
52	A	61	ARG	1	0.963	0.960	24.136	0.064	0.064	0.000	0.000	0.000
53	A	62	LYS	1	0.947	0.969	28.006	0.040	0.040	0.000	0.000	0.000
54	A	63	ASP	-1	-0.746	-0.836	30.675	-0.043	-0.043	0.000	0.000	0.000
55	A	64	VAL	0	-0.016	-0.007	27.997	0.004	0.004	0.000	0.000	0.000
56	A	65	CYS	0	-0.114	-0.059	27.344	0.001	0.001	0.000	0.000	0.000
57	A	66	GLU	-1	-0.911	-0.952	29.764	-0.022	-0.022	0.000	0.000	0.000
58	A	67	LYS	1	0.918	0.978	33.435	0.044	0.044	0.000	0.000	0.000
59	A	68	TYR	0	-0.043	-0.044	30.663	0.004	0.004	0.000	0.000	0.000
60	A	69	GLN	0	-0.003	0.013	31.035	0.000	0.000	0.000	0.000	0.000
61	A	70	MET	0	-0.059	0.000	24.640	0.002	0.002	0.000	0.000	0.000
62	A	71	ASN	0	0.070	0.035	24.117	-0.005	-0.005	0.000	0.000	0.000
63	A	72	ASN	0	0.096	0.025	23.244	-0.016	-0.016	0.000	0.000	0.000
64	A	73	GLY	0	0.051	0.048	20.226	-0.015	-0.015	0.000	0.000	0.000
65	A	74	TYR	0	0.005	0.006	19.972	-0.015	-0.015	0.000	0.000	0.000
66	A	75	PHE	0	0.086	0.051	21.583	-0.016	-0.016	0.000	0.000	0.000
67	A	76	SER	0	-0.010	-0.025	18.414	-0.018	-0.018	0.000	0.000	0.000
68	A	77	THR	0	-0.027	-0.022	15.739	-0.032	-0.032	0.000	0.000	0.000
69	A	78	THR	0	-0.040	-0.031	17.187	-0.032	-0.032	0.000	0.000	0.000
70	A	79	LEU	0	0.049	0.024	19.351	-0.020	-0.020	0.000	0.000	0.000
71	A	80	GLY	0	0.015	0.016	15.291	-0.027	-0.027	0.000	0.000	0.000
72	A	81	ARG	1	0.885	0.937	14.958	0.082	0.082	0.000	0.000	0.000
73	A	82	LEU	0	0.068	0.031	16.227	-0.027	-0.027	0.000	0.000	0.000
74	A	83	THR	0	-0.017	0.001	14.733	-0.004	-0.004	0.000	0.000	0.000
75	A	84	ARG	1	0.941	0.971	10.717	0.476	0.476	0.000	0.000	0.000
76	A	85	LEU	0	-0.036	-0.017	13.878	-0.025	-0.025	0.000	0.000	0.000
77	A	86	ASN	0	0.058	0.032	16.828	0.025	0.025	0.000	0.000	0.000
78	A	87	VAL	0	-0.005	-0.001	12.502	0.005	0.005	0.000	0.000	0.000
79	A	88	LEU	0	-0.068	-0.048	11.818	-0.009	-0.009	0.000	0.000	0.000
80	A	89	VAL	0	0.052	0.024	15.547	0.018	0.018	0.000	0.000	0.000
81	A	90	ALA	0	0.005	0.008	18.115	0.020	0.020	0.000	0.000	0.000
82	A	91	ARG	1	0.896	0.937	10.012	0.634	0.634	0.000	0.000	0.000
83	A	92	LEU	0	0.010	0.006	17.747	0.011	0.011	0.000	0.000	0.000
84	A	93	ALA	0	0.019	0.017	20.186	0.019	0.019	0.000	0.000	0.000
85	A	94	PRO	0	0.035	0.014	21.295	0.015	0.015	0.000	0.000	0.000
86	A	95	TYR	0	-0.061	-0.010	19.231	0.015	0.015	0.000	0.000	0.000
87	A	96	TYR	0	-0.066	-0.031	23.441	0.004	0.004	0.000	0.000	0.000
88	A	97	THR	0	-0.049	-0.024	27.060	0.009	0.009	0.000	0.000	0.000
89	A	98	ASP	-1	-0.900	-0.954	29.441	-0.092	-0.092	0.000	0.000	0.000
90	A	99	SER	0	-0.086	-0.026	29.022	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:GLY)