FMO DATABASE

FMODB ID: 175JZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-558297.19907
FMO2-HF: Nuclear repulsion	524329.620905
FMO2-HF: Total energy	-33967.578166
FMO2-MP2: Total energy	-34063.330856

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.
-24.746	-22.246	0.146	-1.262	-1.384	-0.007

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 : 0.973 / q_NPA : 0.967

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	C	22	LYS	1	0.939	0.976	2.992	23.815	26.199	0.147	-1.258	-1.273	-0.007
4	C	23	LEU	0	0.009	0.016	5.296	5.763	5.879	-0.001	-0.004	-0.111	0.000
5	C	24	TYR	0	0.018	-0.014	8.081	-1.003	-1.003	0.000	0.000	0.000	0.000
6	C	25	LYS	1	0.886	0.954	11.529	22.862	22.862	0.000	0.000	0.000	0.000
7	C	26	VAL	0	0.039	0.023	13.613	0.662	0.662	0.000	0.000	0.000	0.000
8	C	27	MET	0	-0.045	-0.025	17.003	-0.413	-0.413	0.000	0.000	0.000	0.000
9	C	28	LEU	0	0.019	0.020	19.333	0.450	0.450	0.000	0.000	0.000	0.000
10	C	29	LEU	0	-0.015	-0.019	22.610	-0.321	-0.321	0.000	0.000	0.000	0.000
11	C	30	ASN	0	-0.025	-0.016	25.149	0.293	0.293	0.000	0.000	0.000	0.000
12	C	31	ASP	-1	-0.796	-0.873	28.171	-9.850	-9.850	0.000	0.000	0.000	0.000
13	C	32	ASP	-1	-0.933	-0.965	31.690	-9.171	-9.171	0.000	0.000	0.000	0.000
14	C	33	TYR	0	-0.064	-0.047	34.752	0.396	0.396	0.000	0.000	0.000	0.000
15	C	34	THR	0	-0.054	-0.043	32.235	0.256	0.256	0.000	0.000	0.000	0.000
16	C	35	PRO	0	-0.015	0.007	34.517	-0.076	-0.076	0.000	0.000	0.000	0.000
17	C	36	ARG	1	1.006	0.981	32.516	8.820	8.820	0.000	0.000	0.000	0.000
18	C	37	GLU	-1	-0.887	-0.958	32.699	-9.075	-9.075	0.000	0.000	0.000	0.000
19	C	38	PHE	0	0.015	0.009	32.521	-0.070	-0.070	0.000	0.000	0.000	0.000
20	C	39	VAL	0	0.049	0.014	28.196	-0.250	-0.250	0.000	0.000	0.000	0.000
21	C	40	THR	0	-0.030	-0.015	29.041	-0.532	-0.532	0.000	0.000	0.000	0.000
22	C	41	VAL	0	0.002	-0.001	29.533	-0.291	-0.291	0.000	0.000	0.000	0.000
23	C	42	VAL	0	0.037	0.034	27.140	-0.152	-0.152	0.000	0.000	0.000	0.000
24	C	43	LEU	0	-0.009	-0.006	23.758	-0.460	-0.460	0.000	0.000	0.000	0.000
25	C	44	LYS	1	0.916	0.967	25.395	10.266	10.266	0.000	0.000	0.000	0.000
26	C	45	ALA	0	-0.034	-0.020	27.216	-0.216	-0.216	0.000	0.000	0.000	0.000
27	C	46	VAL	0	0.045	0.036	23.319	-0.143	-0.143	0.000	0.000	0.000	0.000
28	C	47	PHE	0	-0.004	-0.016	19.822	-0.644	-0.644	0.000	0.000	0.000	0.000
29	C	48	ARG	1	0.910	0.966	22.193	12.554	12.554	0.000	0.000	0.000	0.000
30	C	49	MET	0	-0.026	0.015	20.721	0.127	0.127	0.000	0.000	0.000	0.000
31	C	50	SER	0	-0.041	-0.030	24.611	0.440	0.440	0.000	0.000	0.000	0.000
32	C	51	GLU	-1	-0.817	-0.921	27.176	-9.532	-9.532	0.000	0.000	0.000	0.000
33	C	52	ASP	-1	-0.891	-0.956	28.605	-10.106	-10.106	0.000	0.000	0.000	0.000
34	C	53	THR	0	-0.075	-0.049	22.246	-0.074	-0.074	0.000	0.000	0.000	0.000
35	C	54	GLY	0	0.066	0.023	24.770	-0.335	-0.335	0.000	0.000	0.000	0.000
36	C	55	ARG	1	0.982	0.993	26.162	9.252	9.252	0.000	0.000	0.000	0.000
37	C	56	ARG	1	0.953	0.982	23.621	12.237	12.237	0.000	0.000	0.000	0.000
38	C	57	VAL	0	0.002	0.005	21.576	-0.157	-0.157	0.000	0.000	0.000	0.000
39	C	58	MET	0	0.027	0.022	24.006	0.001	0.001	0.000	0.000	0.000	0.000
40	C	59	MET	0	-0.037	-0.010	27.188	0.193	0.193	0.000	0.000	0.000	0.000
41	C	60	THR	0	-0.048	-0.015	21.436	0.065	0.065	0.000	0.000	0.000	0.000
42	C	61	ALA	0	0.009	0.002	24.412	-0.025	-0.025	0.000	0.000	0.000	0.000
43	C	62	HIS	0	-0.012	0.002	25.334	0.052	0.052	0.000	0.000	0.000	0.000
44	C	63	ARG	1	0.876	0.953	26.624	10.852	10.852	0.000	0.000	0.000	0.000
45	C	64	PHE	0	-0.036	-0.041	23.448	0.145	0.145	0.000	0.000	0.000	0.000
46	C	65	GLY	0	0.038	0.034	24.670	-0.298	-0.298	0.000	0.000	0.000	0.000
47	C	66	SER	0	-0.025	-0.008	20.899	-0.315	-0.315	0.000	0.000	0.000	0.000
48	C	67	ALA	0	0.013	-0.007	20.194	0.029	0.029	0.000	0.000	0.000	0.000
49	C	68	VAL	0	-0.019	-0.003	14.163	-0.058	-0.058	0.000	0.000	0.000	0.000
50	C	69	VAL	0	-0.036	-0.009	17.530	0.333	0.333	0.000	0.000	0.000	0.000
51	C	70	VAL	0	-0.012	-0.014	14.983	0.166	0.166	0.000	0.000	0.000	0.000
52	C	71	VAL	0	0.007	-0.002	9.293	0.036	0.036	0.000	0.000	0.000	0.000
53	C	72	CYS	0	-0.057	-0.021	11.680	0.002	0.002	0.000	0.000	0.000	0.000
54	C	73	GLU	-1	-0.860	-0.937	10.289	-22.520	-22.520	0.000	0.000	0.000	0.000
55	C	74	ARG	1	0.885	0.927	10.941	21.168	21.168	0.000	0.000	0.000	0.000
56	C	75	ASP	-1	-0.799	-0.897	12.606	-17.293	-17.293	0.000	0.000	0.000	0.000
57	C	76	ILE	0	-0.004	-0.001	14.585	1.228	1.228	0.000	0.000	0.000	0.000
58	C	77	ALA	0	-0.023	-0.019	14.328	0.935	0.935	0.000	0.000	0.000	0.000
59	C	78	GLU	-1	-0.879	-0.932	16.243	-16.697	-16.697	0.000	0.000	0.000	0.000
60	C	79	THR	0	-0.001	0.000	18.540	1.004	1.004	0.000	0.000	0.000	0.000
61	C	80	LYS	1	0.894	0.936	19.206	14.886	14.886	0.000	0.000	0.000	0.000
62	C	81	ALA	0	0.005	0.008	20.209	0.578	0.578	0.000	0.000	0.000	0.000
63	C	82	LYS	1	0.877	0.942	22.009	11.720	11.720	0.000	0.000	0.000	0.000
64	C	83	GLU	-1	-0.914	-0.952	24.306	-11.602	-11.602	0.000	0.000	0.000	0.000
65	C	84	ALA	0	-0.036	-0.020	25.074	0.498	0.498	0.000	0.000	0.000	0.000
66	C	85	THR	0	-0.026	-0.033	25.344	0.375	0.375	0.000	0.000	0.000	0.000
67	C	86	ASP	-1	-0.854	-0.923	27.895	-10.317	-10.317	0.000	0.000	0.000	0.000
68	C	87	LEU	0	-0.032	-0.010	29.279	0.412	0.412	0.000	0.000	0.000	0.000
69	C	88	GLY	0	0.013	0.002	31.076	0.329	0.329	0.000	0.000	0.000	0.000
70	C	89	LYS	1	0.969	0.990	32.050	9.848	9.848	0.000	0.000	0.000	0.000
71	C	90	GLU	-1	-0.966	-0.986	33.827	-8.539	-8.539	0.000	0.000	0.000	0.000
72	C	91	ALA	0	-0.079	-0.024	35.722	0.277	0.277	0.000	0.000	0.000	0.000
73	C	92	GLY	0	-0.030	-0.004	37.259	0.212	0.212	0.000	0.000	0.000	0.000
74	C	93	PHE	0	-0.038	-0.037	34.521	0.130	0.130	0.000	0.000	0.000	0.000
75	C	94	PRO	0	-0.030	-0.016	33.382	-0.123	-0.123	0.000	0.000	0.000	0.000
76	C	95	LEU	0	-0.014	0.006	28.312	-0.308	-0.308	0.000	0.000	0.000	0.000
77	C	96	MET	0	0.024	0.017	25.775	-0.174	-0.174	0.000	0.000	0.000	0.000
78	C	97	PHE	0	0.004	-0.006	22.139	-0.335	-0.335	0.000	0.000	0.000	0.000
79	C	98	THR	0	-0.017	-0.006	20.816	-0.053	-0.053	0.000	0.000	0.000	0.000
80	C	99	THR	0	-0.007	-0.020	15.997	-0.269	-0.269	0.000	0.000	0.000	0.000
81	C	100	GLU	-1	-0.864	-0.930	13.973	-19.546	-19.546	0.000	0.000	0.000	0.000
82	C	101	PRO	0	-0.056	-0.024	9.842	-1.095	-1.095	0.000	0.000	0.000	0.000
83	C	102	GLU	-1	-0.946	-0.974	5.340	-45.975	-45.975	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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