FMO DATABASE

FMODB ID: 85GJY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-560178.253103
FMO2-HF: Nuclear repulsion	526210.030321
FMO2-HF: Total energy	-33968.222781
FMO2-MP2: Total energy	-34064.031866

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.
-97.534	-93.304	15.728	-9.772	-10.187	-0.12

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 : 0.906 / q_NPA : 0.955

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	0.887	0.946	2.313	17.919	21.738	4.472	-3.751	-4.541	-0.035
4	C	23	LEU	0	0.012	0.008	3.567	10.655	11.059	0.000	-0.101	-0.303	0.000
5	C	24	TYR	0	0.027	-0.009	5.646	-0.412	-0.412	0.000	0.000	0.000	0.000
6	C	25	LYS	1	0.814	0.897	8.852	26.492	26.492	0.000	0.000	0.000	0.000
7	C	26	VAL	0	0.030	0.021	10.924	0.851	0.851	0.000	0.000	0.000	0.000
8	C	27	MET	0	-0.035	-0.019	14.467	-1.011	-1.011	0.000	0.000	0.000	0.000
9	C	28	LEU	0	0.019	0.033	16.937	0.508	0.508	0.000	0.000	0.000	0.000
10	C	29	LEU	0	-0.003	-0.016	20.273	-0.365	-0.365	0.000	0.000	0.000	0.000
11	C	30	ASN	0	-0.034	-0.026	22.920	0.201	0.201	0.000	0.000	0.000	0.000
12	C	31	ASP	-1	-0.767	-0.856	26.187	-10.374	-10.374	0.000	0.000	0.000	0.000
13	C	32	ASP	-1	-0.957	-0.977	29.694	-9.756	-9.756	0.000	0.000	0.000	0.000
14	C	33	TYR	0	-0.056	-0.028	32.871	0.451	0.451	0.000	0.000	0.000	0.000
15	C	34	THR	0	-0.041	-0.060	29.892	0.285	0.285	0.000	0.000	0.000	0.000
16	C	35	PRO	0	-0.028	-0.002	32.674	-0.070	-0.070	0.000	0.000	0.000	0.000
17	C	36	ARG	1	0.987	0.988	30.447	9.517	9.517	0.000	0.000	0.000	0.000
18	C	37	GLU	-1	-0.766	-0.865	30.691	-9.962	-9.962	0.000	0.000	0.000	0.000
19	C	38	PHE	0	0.025	0.016	30.215	-0.026	-0.026	0.000	0.000	0.000	0.000
20	C	39	VAL	0	0.052	0.019	26.091	-0.285	-0.285	0.000	0.000	0.000	0.000
21	C	40	THR	0	-0.045	-0.033	27.010	-0.565	-0.565	0.000	0.000	0.000	0.000
22	C	41	VAL	0	-0.002	0.000	27.800	-0.309	-0.309	0.000	0.000	0.000	0.000
23	C	42	VAL	0	0.030	0.032	24.904	-0.230	-0.230	0.000	0.000	0.000	0.000
24	C	43	LEU	0	-0.018	-0.010	21.727	-0.537	-0.537	0.000	0.000	0.000	0.000
25	C	44	LYS	1	0.822	0.918	23.517	11.334	11.334	0.000	0.000	0.000	0.000
26	C	45	ALA	0	-0.033	-0.020	25.532	-0.179	-0.179	0.000	0.000	0.000	0.000
27	C	46	VAL	0	-0.014	0.006	20.997	-0.197	-0.197	0.000	0.000	0.000	0.000
28	C	47	PHE	0	0.064	0.013	17.470	-0.682	-0.682	0.000	0.000	0.000	0.000
29	C	48	ARG	1	0.931	0.975	20.487	13.480	13.480	0.000	0.000	0.000	0.000
30	C	49	MET	0	0.015	0.030	19.235	0.648	0.648	0.000	0.000	0.000	0.000
31	C	50	SER	0	-0.029	-0.030	22.834	0.353	0.353	0.000	0.000	0.000	0.000
32	C	51	GLU	-1	-0.737	-0.859	25.519	-10.023	-10.023	0.000	0.000	0.000	0.000
33	C	52	ASP	-1	-0.769	-0.852	26.961	-11.765	-11.765	0.000	0.000	0.000	0.000
34	C	53	THR	0	-0.037	-0.034	20.892	-0.256	-0.256	0.000	0.000	0.000	0.000
35	C	54	GLY	0	0.061	0.027	23.156	-0.404	-0.404	0.000	0.000	0.000	0.000
36	C	55	ARG	1	0.729	0.816	24.669	9.861	9.861	0.000	0.000	0.000	0.000
37	C	56	ARG	1	0.857	0.915	22.898	12.632	12.632	0.000	0.000	0.000	0.000
38	C	57	VAL	0	0.007	0.014	19.553	-0.139	-0.139	0.000	0.000	0.000	0.000
39	C	58	MET	0	0.028	0.013	22.075	0.011	0.011	0.000	0.000	0.000	0.000
40	C	59	MET	0	-0.063	-0.030	25.240	0.238	0.238	0.000	0.000	0.000	0.000
41	C	60	THR	0	-0.058	-0.030	19.521	0.068	0.068	0.000	0.000	0.000	0.000
42	C	61	ALA	0	0.016	0.006	22.664	-0.030	-0.030	0.000	0.000	0.000	0.000
43	C	62	HIS	0	0.005	0.001	23.457	0.084	0.084	0.000	0.000	0.000	0.000
44	C	63	ARG	1	0.868	0.947	24.766	11.485	11.485	0.000	0.000	0.000	0.000
45	C	64	PHE	0	-0.016	-0.019	21.370	0.172	0.172	0.000	0.000	0.000	0.000
46	C	65	GLY	0	0.036	0.038	22.341	-0.419	-0.419	0.000	0.000	0.000	0.000
47	C	66	SER	0	-0.022	-0.011	19.296	-0.302	-0.302	0.000	0.000	0.000	0.000
48	C	67	ALA	0	-0.008	-0.008	18.348	0.022	0.022	0.000	0.000	0.000	0.000
49	C	68	VAL	0	-0.013	-0.010	12.329	-0.070	-0.070	0.000	0.000	0.000	0.000
50	C	69	VAL	0	-0.040	-0.010	15.645	0.689	0.689	0.000	0.000	0.000	0.000
51	C	70	VAL	0	-0.012	-0.012	13.222	0.314	0.314	0.000	0.000	0.000	0.000
52	C	71	VAL	0	-0.003	-0.008	7.421	-0.566	-0.566	0.000	0.000	0.000	0.000
53	C	72	CYS	0	-0.055	-0.014	9.575	0.465	0.465	0.000	0.000	0.000	0.000
54	C	73	GLU	-1	-0.863	-0.931	8.906	-29.767	-29.767	0.000	0.000	0.000	0.000
55	C	74	ARG	1	0.833	0.883	10.244	23.465	23.465	0.000	0.000	0.000	0.000
56	C	75	ASP	-1	-0.809	-0.902	11.727	-19.400	-19.400	0.000	0.000	0.000	0.000
57	C	76	ILE	0	-0.003	0.010	13.610	1.398	1.398	0.000	0.000	0.000	0.000
58	C	77	ALA	0	0.000	-0.014	12.134	1.158	1.158	0.000	0.000	0.000	0.000
59	C	78	GLU	-1	-0.814	-0.888	14.285	-18.978	-18.978	0.000	0.000	0.000	0.000
60	C	79	THR	0	-0.023	-0.014	16.826	1.336	1.336	0.000	0.000	0.000	0.000
61	C	80	LYS	1	0.789	0.877	17.424	15.737	15.737	0.000	0.000	0.000	0.000
62	C	81	ALA	0	-0.008	-0.004	17.568	0.677	0.677	0.000	0.000	0.000	0.000
63	C	82	LYS	1	0.860	0.919	19.480	12.888	12.888	0.000	0.000	0.000	0.000
64	C	83	GLU	-1	-0.795	-0.891	21.816	-13.431	-13.431	0.000	0.000	0.000	0.000
65	C	84	ALA	0	-0.022	-0.013	22.314	0.622	0.622	0.000	0.000	0.000	0.000
66	C	85	THR	0	0.003	-0.007	22.756	0.434	0.434	0.000	0.000	0.000	0.000
67	C	86	ASP	-1	-0.847	-0.901	25.386	-11.237	-11.237	0.000	0.000	0.000	0.000
68	C	87	LEU	0	-0.022	-0.017	26.619	0.482	0.482	0.000	0.000	0.000	0.000
69	C	88	GLY	0	0.007	0.005	28.301	0.370	0.370	0.000	0.000	0.000	0.000
70	C	89	LYS	1	0.829	0.893	29.572	10.186	10.186	0.000	0.000	0.000	0.000
71	C	90	GLU	-1	-0.829	-0.899	31.439	-9.333	-9.333	0.000	0.000	0.000	0.000
72	C	91	ALA	0	-0.063	-0.017	33.217	0.313	0.313	0.000	0.000	0.000	0.000
73	C	92	GLY	0	-0.027	0.000	34.613	0.255	0.255	0.000	0.000	0.000	0.000
74	C	93	PHE	0	-0.036	-0.036	31.921	0.166	0.166	0.000	0.000	0.000	0.000
75	C	94	PRO	0	-0.028	-0.013	30.772	-0.183	-0.183	0.000	0.000	0.000	0.000
76	C	95	LEU	0	-0.013	0.007	26.096	-0.356	-0.356	0.000	0.000	0.000	0.000
77	C	96	MET	0	0.012	0.012	23.086	-0.269	-0.269	0.000	0.000	0.000	0.000
78	C	97	PHE	0	-0.006	-0.011	19.752	-0.385	-0.385	0.000	0.000	0.000	0.000
79	C	98	THR	0	0.015	0.007	18.243	0.082	0.082	0.000	0.000	0.000	0.000
80	C	99	THR	0	0.004	-0.011	13.735	-0.308	-0.308	0.000	0.000	0.000	0.000
81	C	100	GLU	-1	-0.833	-0.896	12.302	-21.400	-21.400	0.000	0.000	0.000	0.000
82	C	101	PRO	0	-0.019	-0.012	7.636	-1.538	-1.538	0.000	0.000	0.000	0.000
83	C	102	GLU	-1	-0.847	-0.920	1.901	-110.319	-110.312	11.256	-5.920	-5.343	-0.085

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