FMO DATABASE

FMODB ID: KG583

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

Total energy (hartree)

FMO2-HF: Electronic energy	-604298.064709
FMO2-HF: Nuclear repulsion	568709.245633
FMO2-HF: Total energy	-35588.819076
FMO2-MP2: Total energy	-35691.438101

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.
1.217	2.876	0.007	-0.617	-1.049	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 : 0.063 / q_NPA : 0.018

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	-0.878	-0.936	3.819	-1.758	-0.515	0.001	-0.498	-0.746
4	A	13	ALA	0	0.079	0.032	3.676	-0.100	0.137	0.007	-0.054	-0.190
5	A	14	PHE	0	-0.040	-0.016	4.427	0.742	0.921	-0.001	-0.065	-0.113
6	A	15	LEU	0	0.006	0.000	6.077	0.561	0.561	0.000	0.000	0.000
7	A	16	LEU	0	0.011	0.008	7.924	0.200	0.200	0.000	0.000	0.000
8	A	17	LYS	1	0.890	0.936	8.621	0.647	0.647	0.000	0.000	0.000
9	A	18	LEU	0	-0.022	-0.006	10.144	0.153	0.153	0.000	0.000	0.000
10	A	19	ARG	1	0.942	0.972	12.158	0.330	0.330	0.000	0.000	0.000
11	A	20	GLU	-1	-0.935	-0.955	12.355	-0.429	-0.429	0.000	0.000	0.000
12	A	21	SER	0	-0.057	-0.050	13.496	0.033	0.033	0.000	0.000	0.000
13	A	22	ALA	0	-0.036	-0.006	16.112	0.014	0.014	0.000	0.000	0.000
14	A	23	LEU	0	0.015	0.020	17.885	0.022	0.022	0.000	0.000	0.000
15	A	24	SER	0	0.028	0.010	20.920	0.013	0.013	0.000	0.000	0.000
16	A	25	SER	0	-0.035	-0.022	24.203	0.001	0.001	0.000	0.000	0.000
17	A	26	GLY	0	-0.006	0.000	27.498	-0.002	-0.002	0.000	0.000	0.000
18	A	27	SER	0	-0.063	-0.042	25.374	-0.003	-0.003	0.000	0.000	0.000
19	A	28	MET	0	-0.036	0.006	23.045	-0.007	-0.007	0.000	0.000	0.000
20	A	29	SER	0	0.071	0.037	28.185	0.007	0.007	0.000	0.000	0.000
21	A	30	GLU	-1	-0.806	-0.916	29.734	-0.072	-0.072	0.000	0.000	0.000
22	A	31	GLU	-1	-0.927	-0.955	30.845	-0.088	-0.088	0.000	0.000	0.000
23	A	32	GLN	0	0.045	0.015	24.556	0.004	0.004	0.000	0.000	0.000
24	A	33	PHE	0	0.007	-0.008	25.374	-0.012	-0.012	0.000	0.000	0.000
25	A	34	PHE	0	-0.001	-0.017	26.138	-0.005	-0.005	0.000	0.000	0.000
26	A	35	LEU	0	0.007	0.018	26.494	0.000	0.000	0.000	0.000	0.000
27	A	36	LEU	0	-0.018	-0.013	20.548	-0.010	-0.010	0.000	0.000	0.000
28	A	37	ILE	0	-0.040	-0.027	22.261	-0.008	-0.008	0.000	0.000	0.000
29	A	38	GLY	0	0.020	0.033	24.091	0.003	0.003	0.000	0.000	0.000
30	A	39	ILE	0	-0.017	0.002	19.736	0.000	0.000	0.000	0.000	0.000
31	A	40	SER	0	-0.091	-0.058	19.651	-0.011	-0.011	0.000	0.000	0.000
32	A	41	SER	0	-0.014	-0.023	19.296	0.009	0.009	0.000	0.000	0.000
33	A	42	ILE	0	-0.051	-0.017	20.146	0.012	0.012	0.000	0.000	0.000
34	A	43	HIS	0	0.057	0.030	22.720	-0.002	-0.002	0.000	0.000	0.000
35	A	44	SER	0	-0.005	-0.004	25.622	0.009	0.009	0.000	0.000	0.000
36	A	45	ASP	-1	-0.808	-0.896	27.527	-0.043	-0.043	0.000	0.000	0.000
37	A	46	ARG	1	0.881	0.919	28.353	0.015	0.015	0.000	0.000	0.000
38	A	47	VAL	0	-0.010	-0.012	23.863	-0.002	-0.002	0.000	0.000	0.000
39	A	48	ILE	0	0.008	0.010	26.434	-0.009	-0.009	0.000	0.000	0.000
40	A	49	LEU	0	0.024	0.008	27.644	-0.006	-0.006	0.000	0.000	0.000
41	A	50	ALA	0	0.008	0.001	27.501	-0.002	-0.002	0.000	0.000	0.000
42	A	51	MET	0	-0.056	-0.033	23.194	-0.011	-0.011	0.000	0.000	0.000
43	A	52	LYS	1	0.888	0.960	26.392	0.058	0.058	0.000	0.000	0.000
44	A	53	ASP	-1	-0.761	-0.865	29.396	-0.055	-0.055	0.000	0.000	0.000
45	A	54	TYR	0	-0.097	-0.047	23.118	0.006	0.006	0.000	0.000	0.000
46	A	55	LEU	0	-0.007	-0.017	22.974	-0.003	-0.003	0.000	0.000	0.000
47	A	56	VAL	0	-0.040	-0.009	27.149	-0.004	-0.004	0.000	0.000	0.000
48	A	57	SER	0	-0.069	-0.064	30.667	0.002	0.002	0.000	0.000	0.000
49	A	58	GLY	0	0.042	0.044	31.485	0.004	0.004	0.000	0.000	0.000
50	A	59	HIS	0	0.001	0.007	31.830	0.001	0.001	0.000	0.000	0.000
51	A	60	SER	0	-0.016	-0.038	29.467	-0.008	-0.008	0.000	0.000	0.000
52	A	61	ARG	1	0.942	0.949	23.538	0.067	0.067	0.000	0.000	0.000
53	A	62	LYS	1	0.828	0.910	27.403	0.038	0.038	0.000	0.000	0.000
54	A	63	ASP	-1	-0.733	-0.832	30.026	-0.042	-0.042	0.000	0.000	0.000
55	A	64	VAL	0	0.010	0.005	27.998	0.004	0.004	0.000	0.000	0.000
56	A	65	CYS	0	-0.103	-0.046	27.065	0.002	0.002	0.000	0.000	0.000
57	A	66	GLU	-1	-0.833	-0.911	29.597	-0.022	-0.022	0.000	0.000	0.000
58	A	67	LYS	1	0.892	0.965	33.307	0.043	0.043	0.000	0.000	0.000
59	A	68	TYR	0	-0.027	-0.034	30.532	0.003	0.003	0.000	0.000	0.000
60	A	69	GLN	0	-0.021	0.004	30.798	0.001	0.001	0.000	0.000	0.000
61	A	70	MET	0	-0.046	0.003	24.051	0.001	0.001	0.000	0.000	0.000
62	A	71	ASN	0	0.059	0.033	23.617	-0.002	-0.002	0.000	0.000	0.000
63	A	72	ASN	0	0.099	0.024	22.982	-0.015	-0.015	0.000	0.000	0.000
64	A	73	GLY	0	0.056	0.057	19.797	-0.015	-0.015	0.000	0.000	0.000
65	A	74	TYR	0	0.008	0.010	19.522	-0.016	-0.016	0.000	0.000	0.000
66	A	75	PHE	0	0.065	0.030	21.216	-0.014	-0.014	0.000	0.000	0.000
67	A	76	SER	0	0.013	-0.017	17.927	-0.019	-0.019	0.000	0.000	0.000
68	A	77	THR	0	-0.038	-0.025	15.504	-0.031	-0.031	0.000	0.000	0.000
69	A	78	THR	0	-0.043	-0.032	16.770	-0.028	-0.028	0.000	0.000	0.000
70	A	79	LEU	0	0.065	0.031	19.009	-0.018	-0.018	0.000	0.000	0.000
71	A	80	GLY	0	0.004	0.021	15.024	-0.027	-0.027	0.000	0.000	0.000
72	A	81	ARG	1	0.861	0.916	14.783	0.057	0.057	0.000	0.000	0.000
73	A	82	LEU	0	0.063	0.024	15.800	-0.024	-0.024	0.000	0.000	0.000
74	A	83	THR	0	-0.005	-0.001	14.618	-0.005	-0.005	0.000	0.000	0.000
75	A	84	ARG	1	0.940	0.965	10.525	0.428	0.428	0.000	0.000	0.000
76	A	85	LEU	0	-0.035	-0.008	13.848	-0.022	-0.022	0.000	0.000	0.000
77	A	86	ASN	0	0.058	0.029	16.950	0.024	0.024	0.000	0.000	0.000
78	A	87	VAL	0	-0.005	-0.004	12.471	0.005	0.005	0.000	0.000	0.000
79	A	88	LEU	0	-0.064	-0.038	12.126	-0.017	-0.017	0.000	0.000	0.000
80	A	89	VAL	0	0.054	0.022	15.658	0.018	0.018	0.000	0.000	0.000
81	A	90	ALA	0	-0.007	-0.003	17.862	0.018	0.018	0.000	0.000	0.000
82	A	91	ARG	1	0.897	0.942	9.898	0.645	0.645	0.000	0.000	0.000
83	A	92	LEU	0	0.010	0.008	17.650	0.011	0.011	0.000	0.000	0.000
84	A	93	ALA	0	0.021	0.015	20.247	0.018	0.018	0.000	0.000	0.000
85	A	94	PRO	0	0.023	0.005	21.225	0.015	0.015	0.000	0.000	0.000
86	A	95	TYR	0	-0.058	-0.011	19.093	0.015	0.015	0.000	0.000	0.000
87	A	96	TYR	0	-0.066	-0.022	23.546	0.006	0.006	0.000	0.000	0.000
88	A	97	THR	0	-0.004	-0.001	27.215	0.006	0.006	0.000	0.000	0.000
89	A	98	ASP	-1	-0.891	-0.940	29.696	-0.091	-0.091	0.000	0.000	0.000
90	A	99	SER	0	-0.126	-0.063	28.895	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)