FMO DATABASE

FMODB ID: G68Q1

Calculation Name: 4YJM-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YJM

Chain ID: C

ChEMBL ID:

UniProt ID: Q8UD95

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	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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-559378.98079
FMO2-HF: Nuclear repulsion	525411.005922
FMO2-HF: Total energy	-33967.974868
FMO2-MP2: Total energy	-34063.771797

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(C:20:ARG)

Summations of interaction energy for fragment #1(C:20:ARG)

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.
-31.809	-28.212	0.208	-1.876	-1.93	-0.006

Interaction energy analysis for fragmet #1(C:20:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.007 / q_NPA : 1.000

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	C	22	LYS	1	0.904	0.965	2.932	23.864	27.238	0.210	-1.865	-1.719	-0.006
4	C	23	LEU	0	0.004	0.011	5.175	6.657	6.783	-0.001	-0.004	-0.121	0.000
5	C	24	TYR	0	0.017	-0.019	7.956	-0.911	-0.911	0.000	0.000	0.000	0.000
6	C	25	LYS	1	0.832	0.910	10.870	23.515	23.515	0.000	0.000	0.000	0.000
7	C	26	VAL	0	0.040	0.023	12.811	0.678	0.678	0.000	0.000	0.000	0.000
8	C	27	MET	0	-0.050	-0.024	16.233	-0.606	-0.606	0.000	0.000	0.000	0.000
9	C	28	LEU	0	0.021	0.019	18.572	0.471	0.471	0.000	0.000	0.000	0.000
10	C	29	LEU	0	-0.010	-0.013	21.734	-0.296	-0.296	0.000	0.000	0.000	0.000
11	C	30	ASN	0	-0.037	-0.023	24.391	0.250	0.250	0.000	0.000	0.000	0.000
12	C	31	ASP	-1	-0.768	-0.860	27.466	-9.987	-9.987	0.000	0.000	0.000	0.000
13	C	32	ASP	-1	-0.958	-0.979	30.953	-9.352	-9.352	0.000	0.000	0.000	0.000
14	C	33	TYR	0	-0.049	-0.033	34.033	0.408	0.408	0.000	0.000	0.000	0.000
15	C	34	THR	0	-0.054	-0.051	31.376	0.261	0.261	0.000	0.000	0.000	0.000
16	C	35	PRO	0	-0.021	0.001	33.840	-0.078	-0.078	0.000	0.000	0.000	0.000
17	C	36	ARG	1	0.999	0.984	31.916	9.006	9.006	0.000	0.000	0.000	0.000
18	C	37	GLU	-1	-0.774	-0.885	32.124	-9.368	-9.368	0.000	0.000	0.000	0.000
19	C	38	PHE	0	0.027	0.018	31.690	-0.067	-0.067	0.000	0.000	0.000	0.000
20	C	39	VAL	0	0.052	0.016	27.520	-0.256	-0.256	0.000	0.000	0.000	0.000
21	C	40	THR	0	-0.029	-0.013	28.438	-0.521	-0.521	0.000	0.000	0.000	0.000
22	C	41	VAL	0	-0.004	-0.004	29.005	-0.291	-0.291	0.000	0.000	0.000	0.000
23	C	42	VAL	0	0.028	0.032	26.506	-0.154	-0.154	0.000	0.000	0.000	0.000
24	C	43	LEU	0	0.005	-0.002	22.993	-0.464	-0.464	0.000	0.000	0.000	0.000
25	C	44	LYS	1	0.913	0.968	24.861	10.542	10.542	0.000	0.000	0.000	0.000
26	C	45	ALA	0	-0.037	-0.020	26.724	-0.220	-0.220	0.000	0.000	0.000	0.000
27	C	46	VAL	0	-0.006	0.012	22.716	-0.138	-0.138	0.000	0.000	0.000	0.000
28	C	47	PHE	0	0.040	-0.005	19.096	-0.598	-0.598	0.000	0.000	0.000	0.000
29	C	48	ARG	1	0.909	0.967	21.739	12.836	12.836	0.000	0.000	0.000	0.000
30	C	49	MET	0	-0.023	0.012	20.194	0.174	0.174	0.000	0.000	0.000	0.000
31	C	50	SER	0	-0.016	-0.012	24.205	0.388	0.388	0.000	0.000	0.000	0.000
32	C	51	GLU	-1	-0.753	-0.872	26.808	-9.592	-9.592	0.000	0.000	0.000	0.000
33	C	52	ASP	-1	-0.889	-0.953	28.136	-10.327	-10.327	0.000	0.000	0.000	0.000
34	C	53	THR	0	-0.070	-0.056	21.931	-0.187	-0.187	0.000	0.000	0.000	0.000
35	C	54	GLY	0	0.055	0.020	24.396	-0.345	-0.345	0.000	0.000	0.000	0.000
36	C	55	ARG	1	0.780	0.849	25.721	9.429	9.429	0.000	0.000	0.000	0.000
37	C	56	ARG	1	0.951	0.989	23.475	12.375	12.375	0.000	0.000	0.000	0.000
38	C	57	VAL	0	-0.002	0.011	20.985	-0.143	-0.143	0.000	0.000	0.000	0.000
39	C	58	MET	0	0.030	0.026	23.539	-0.005	-0.005	0.000	0.000	0.000	0.000
40	C	59	MET	0	-0.039	-0.010	26.659	0.194	0.194	0.000	0.000	0.000	0.000
41	C	60	THR	0	-0.051	-0.032	21.029	0.071	0.071	0.000	0.000	0.000	0.000
42	C	61	ALA	0	0.009	0.005	23.810	-0.026	-0.026	0.000	0.000	0.000	0.000
43	C	62	HIS	0	0.002	0.009	24.751	0.084	0.084	0.000	0.000	0.000	0.000
44	C	63	ARG	1	0.860	0.944	26.215	10.983	10.983	0.000	0.000	0.000	0.000
45	C	64	PHE	0	-0.034	-0.039	22.936	0.162	0.162	0.000	0.000	0.000	0.000
46	C	65	GLY	0	0.042	0.035	24.053	-0.304	-0.304	0.000	0.000	0.000	0.000
47	C	66	SER	0	-0.024	-0.014	20.408	-0.333	-0.333	0.000	0.000	0.000	0.000
48	C	67	ALA	0	-0.003	-0.005	19.626	0.031	0.031	0.000	0.000	0.000	0.000
49	C	68	VAL	0	-0.014	-0.004	13.483	-0.060	-0.060	0.000	0.000	0.000	0.000
50	C	69	VAL	0	-0.037	-0.011	16.924	0.395	0.395	0.000	0.000	0.000	0.000
51	C	70	VAL	0	-0.012	-0.014	14.503	0.166	0.166	0.000	0.000	0.000	0.000
52	C	71	VAL	0	0.003	-0.003	8.668	-0.048	-0.048	0.000	0.000	0.000	0.000
53	C	72	CYS	0	-0.053	-0.019	11.172	0.065	0.065	0.000	0.000	0.000	0.000
54	C	73	GLU	-1	-0.867	-0.934	10.242	-25.167	-25.167	0.000	0.000	0.000	0.000
55	C	74	ARG	1	0.848	0.899	10.853	21.761	21.761	0.000	0.000	0.000	0.000
56	C	75	ASP	-1	-0.822	-0.910	12.510	-17.739	-17.739	0.000	0.000	0.000	0.000
57	C	76	ILE	0	0.010	0.016	14.832	1.345	1.345	0.000	0.000	0.000	0.000
58	C	77	ALA	0	-0.006	-0.011	14.211	1.034	1.034	0.000	0.000	0.000	0.000
59	C	78	GLU	-1	-0.834	-0.907	16.255	-17.551	-17.551	0.000	0.000	0.000	0.000
60	C	79	THR	0	-0.007	-0.007	18.443	1.093	1.093	0.000	0.000	0.000	0.000
61	C	80	LYS	1	0.810	0.897	19.494	14.665	14.665	0.000	0.000	0.000	0.000
62	C	81	ALA	0	0.003	0.003	19.638	0.642	0.642	0.000	0.000	0.000	0.000
63	C	82	LYS	1	0.863	0.918	21.585	12.013	12.013	0.000	0.000	0.000	0.000
64	C	83	GLU	-1	-0.814	-0.900	24.137	-12.386	-12.386	0.000	0.000	0.000	0.000
65	C	84	ALA	0	-0.035	-0.021	24.277	0.541	0.541	0.000	0.000	0.000	0.000
66	C	85	THR	0	-0.015	-0.026	24.757	0.421	0.421	0.000	0.000	0.000	0.000
67	C	86	ASP	-1	-0.839	-0.895	27.303	-10.597	-10.597	0.000	0.000	0.000	0.000
68	C	87	LEU	0	-0.026	-0.008	28.653	0.437	0.437	0.000	0.000	0.000	0.000
69	C	88	GLY	0	0.017	0.003	30.342	0.350	0.350	0.000	0.000	0.000	0.000
70	C	89	LYS	1	0.833	0.905	31.489	9.729	9.729	0.000	0.000	0.000	0.000
71	C	90	GLU	-1	-0.848	-0.904	33.311	-8.887	-8.887	0.000	0.000	0.000	0.000
72	C	91	ALA	0	-0.075	-0.027	35.104	0.290	0.290	0.000	0.000	0.000	0.000
73	C	92	GLY	0	-0.029	-0.001	36.610	0.221	0.221	0.000	0.000	0.000	0.000
74	C	93	PHE	0	-0.040	-0.037	33.749	0.143	0.143	0.000	0.000	0.000	0.000
75	C	94	PRO	0	-0.027	-0.013	32.571	-0.121	-0.121	0.000	0.000	0.000	0.000
76	C	95	LEU	0	-0.019	0.002	27.563	-0.312	-0.312	0.000	0.000	0.000	0.000
77	C	96	MET	0	0.014	0.013	24.965	-0.201	-0.201	0.000	0.000	0.000	0.000
78	C	97	PHE	0	0.004	-0.006	21.494	-0.304	-0.304	0.000	0.000	0.000	0.000
79	C	98	THR	0	-0.003	-0.002	19.941	0.147	0.147	0.000	0.000	0.000	0.000
80	C	99	THR	0	-0.006	-0.013	15.640	-0.283	-0.283	0.000	0.000	0.000	0.000
81	C	100	GLU	-1	-0.838	-0.900	13.578	-19.821	-19.821	0.000	0.000	0.000	0.000
82	C	101	PRO	0	-0.030	-0.013	9.625	-1.179	-1.179	0.000	0.000	0.000	0.000
83	C	102	GLU	-1	-0.908	-0.954	4.689	-50.421	-50.324	-0.001	-0.007	-0.090	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:20:ARG)