FMO DATABASE

FMODB ID: K3Y83

Calculation Name: 4R8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R8O

Chain ID: A

ChEMBL ID:

UniProt ID: A6KZN2

Base Structure: X-ray

Registration Date: 2023-06-20

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-746726.996049
FMO2-HF: Nuclear repulsion	704000.961141
FMO2-HF: Total energy	-42726.034908
FMO2-MP2: Total energy	-42846.425939

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:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-33.134	-29.252	0.336	-1.87	-2.348	0.008

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.927 / q_NPA : -0.976

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	A	32	LEU	0	-0.087	-0.061	2.560	-12.149	-8.699	0.333	-1.748	-2.035	0.008
4	A	33	ILE	0	0.021	0.021	4.014	-0.238	-0.080	-0.001	-0.064	-0.094	0.000
5	A	34	TYR	0	0.012	-0.001	3.400	-2.812	-2.538	0.004	-0.058	-0.219	0.000
6	A	35	ASN	0	-0.030	-0.018	8.843	-1.126	-1.126	0.000	0.000	0.000	0.000
7	A	36	ALA	0	0.018	0.005	12.649	0.035	0.035	0.000	0.000	0.000	0.000
8	A	37	GLU	-1	-0.859	-0.878	15.071	12.549	12.549	0.000	0.000	0.000	0.000
9	A	38	GLU	-1	-0.922	-0.972	18.797	12.590	12.590	0.000	0.000	0.000	0.000
10	A	39	VAL	0	-0.009	-0.013	20.855	-0.400	-0.400	0.000	0.000	0.000	0.000
11	A	40	ASN	0	-0.043	-0.030	24.545	0.023	0.023	0.000	0.000	0.000	0.000
12	A	41	GLY	0	0.053	0.042	23.740	-0.243	-0.243	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.027	-0.004	21.218	0.387	0.387	0.000	0.000	0.000	0.000
14	A	43	VAL	0	0.008	0.006	15.962	-0.125	-0.125	0.000	0.000	0.000	0.000
15	A	44	VAL	0	0.042	0.034	18.985	0.028	0.028	0.000	0.000	0.000	0.000
16	A	45	SER	0	-0.091	-0.086	17.806	0.287	0.287	0.000	0.000	0.000	0.000
17	A	46	GLU	-1	-0.784	-0.876	10.621	21.030	21.030	0.000	0.000	0.000	0.000
18	A	47	THR	0	-0.064	-0.021	12.994	-0.562	-0.562	0.000	0.000	0.000	0.000
19	A	48	ILE	0	0.011	0.004	6.878	0.667	0.667	0.000	0.000	0.000	0.000
20	A	49	PHE	0	-0.026	-0.024	8.373	-1.662	-1.662	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.936	0.980	7.388	-26.620	-26.620	0.000	0.000	0.000	0.000
22	A	51	MET	0	0.014	-0.004	9.045	-2.496	-2.496	0.000	0.000	0.000	0.000
23	A	52	GLU	-1	-0.916	-0.929	10.957	24.861	24.861	0.000	0.000	0.000	0.000
24	A	53	GLY	0	0.081	0.038	12.380	-1.930	-1.930	0.000	0.000	0.000	0.000
25	A	54	THR	0	-0.050	-0.058	13.827	0.181	0.181	0.000	0.000	0.000	0.000
26	A	55	MET	0	-0.057	-0.015	15.567	-0.754	-0.754	0.000	0.000	0.000	0.000
27	A	56	LEU	0	0.011	0.013	11.225	1.216	1.216	0.000	0.000	0.000	0.000
28	A	57	THR	0	-0.028	-0.014	12.545	-1.756	-1.756	0.000	0.000	0.000	0.000
29	A	58	ASN	0	0.021	0.009	12.134	1.922	1.922	0.000	0.000	0.000	0.000
30	A	59	TYR	0	-0.009	-0.015	8.059	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	60	MET	0	-0.036	-0.028	10.444	-0.357	-0.357	0.000	0.000	0.000	0.000
32	A	61	LYS	1	0.886	0.945	12.359	-14.064	-14.064	0.000	0.000	0.000	0.000
33	A	62	HIS	1	0.881	0.941	10.837	-19.283	-19.283	0.000	0.000	0.000	0.000
34	A	63	ASN	0	-0.065	-0.046	15.605	0.164	0.164	0.000	0.000	0.000	0.000
35	A	64	TYR	0	-0.059	-0.050	12.830	-0.701	-0.701	0.000	0.000	0.000	0.000
36	A	65	LYS	1	0.825	0.911	19.857	-12.254	-12.254	0.000	0.000	0.000	0.000
37	A	66	TYR	0	0.017	-0.006	19.500	0.450	0.450	0.000	0.000	0.000	0.000
38	A	67	ASP	-1	-0.758	-0.853	25.648	9.461	9.461	0.000	0.000	0.000	0.000
39	A	68	ALA	0	-0.002	-0.012	29.179	0.069	0.069	0.000	0.000	0.000	0.000
40	A	69	ASN	0	-0.093	-0.044	30.265	-0.302	-0.302	0.000	0.000	0.000	0.000
41	A	70	ASN	0	-0.001	-0.002	25.966	0.236	0.236	0.000	0.000	0.000	0.000
42	A	71	GLN	0	-0.027	-0.012	25.021	0.521	0.521	0.000	0.000	0.000	0.000
43	A	72	ARG	1	0.865	0.936	15.562	-15.208	-15.208	0.000	0.000	0.000	0.000
44	A	73	THR	0	0.034	0.021	23.047	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.817	-0.908	22.271	11.175	11.175	0.000	0.000	0.000	0.000
46	A	75	ASP	-1	-0.812	-0.896	16.197	16.353	16.353	0.000	0.000	0.000	0.000
47	A	76	GLU	-1	-0.777	-0.862	18.687	12.427	12.427	0.000	0.000	0.000	0.000
48	A	77	ALA	0	0.022	0.007	15.427	0.605	0.605	0.000	0.000	0.000	0.000
49	A	78	GLN	0	-0.015	-0.019	16.626	-0.178	-0.178	0.000	0.000	0.000	0.000
50	A	79	LYS	1	0.890	0.949	14.991	-13.642	-13.642	0.000	0.000	0.000	0.000
51	A	80	TRP	0	0.050	0.024	14.988	-1.172	-1.172	0.000	0.000	0.000	0.000
52	A	81	ASN	0	-0.116	-0.084	16.684	0.356	0.356	0.000	0.000	0.000	0.000
53	A	82	SER	0	0.096	0.037	18.519	-0.302	-0.302	0.000	0.000	0.000	0.000
54	A	83	ASN	0	-0.014	0.000	20.143	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	84	LYS	1	0.912	0.965	22.919	-11.418	-11.418	0.000	0.000	0.000	0.000
56	A	85	ASN	0	0.001	0.000	22.002	0.025	0.025	0.000	0.000	0.000	0.000
57	A	86	ARG	1	0.847	0.930	21.710	-12.213	-12.213	0.000	0.000	0.000	0.000
58	A	87	TRP	0	0.099	0.055	14.027	0.546	0.546	0.000	0.000	0.000	0.000
59	A	88	GLU	-1	-0.853	-0.921	19.433	11.841	11.841	0.000	0.000	0.000	0.000
60	A	89	ASN	0	0.039	0.044	19.648	0.874	0.874	0.000	0.000	0.000	0.000
61	A	90	ASN	0	-0.003	-0.009	16.882	-0.789	-0.789	0.000	0.000	0.000	0.000
62	A	91	LEU	0	0.022	0.001	16.872	-0.361	-0.361	0.000	0.000	0.000	0.000
63	A	92	CYS	0	-0.039	-0.008	19.787	0.075	0.075	0.000	0.000	0.000	0.000
64	A	93	ILE	0	0.024	0.041	16.538	-0.325	-0.325	0.000	0.000	0.000	0.000
65	A	94	ARG	1	0.824	0.889	20.940	-10.865	-10.865	0.000	0.000	0.000	0.000
66	A	95	TYR	0	-0.004	-0.005	18.091	0.221	0.221	0.000	0.000	0.000	0.000
67	A	96	THR	0	-0.006	-0.004	24.963	-0.359	-0.359	0.000	0.000	0.000	0.000
68	A	97	TYR	0	-0.021	-0.027	23.982	0.155	0.155	0.000	0.000	0.000	0.000
69	A	98	GLY	0	0.053	0.022	29.669	-0.303	-0.303	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.027	-0.033	32.184	0.265	0.265	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.929	0.968	33.007	-8.108	-8.108	0.000	0.000	0.000	0.000
72	A	101	SER	0	0.024	0.040	29.548	0.261	0.261	0.000	0.000	0.000	0.000
73	A	102	MET	0	0.007	0.019	21.856	-0.098	-0.098	0.000	0.000	0.000	0.000
74	A	103	THR	0	-0.005	-0.006	26.562	0.107	0.107	0.000	0.000	0.000	0.000
75	A	104	THR	0	-0.019	-0.017	21.676	0.084	0.084	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.762	-0.860	24.171	9.877	9.877	0.000	0.000	0.000	0.000
77	A	106	TYR	0	0.001	-0.005	18.713	0.751	0.751	0.000	0.000	0.000	0.000
78	A	107	TYR	0	-0.014	-0.024	23.134	-0.427	-0.427	0.000	0.000	0.000	0.000
79	A	108	LYS	1	0.885	0.936	21.237	-12.477	-12.477	0.000	0.000	0.000	0.000
80	A	109	TRP	0	-0.053	-0.007	23.157	-0.513	-0.513	0.000	0.000	0.000	0.000
81	A	110	ASN	0	0.012	0.006	24.958	0.080	0.080	0.000	0.000	0.000	0.000
82	A	111	SER	0	0.021	-0.014	26.657	-0.216	-0.216	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.927	0.963	28.880	-9.103	-9.103	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.833	0.899	31.824	-8.804	-8.804	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.900	0.963	30.187	-8.806	-8.806	0.000	0.000	0.000	0.000
86	A	115	GLU	-1	-0.736	-0.844	29.939	8.669	8.669	0.000	0.000	0.000	0.000
87	A	116	TYR	0	-0.051	-0.066	21.990	0.366	0.366	0.000	0.000	0.000	0.000
88	A	117	ILE	0	-0.022	-0.006	27.075	-0.257	-0.257	0.000	0.000	0.000	0.000
89	A	118	LEU	0	0.013	0.011	26.980	0.410	0.410	0.000	0.000	0.000	0.000
90	A	119	VAL	0	-0.024	-0.010	24.915	-0.192	-0.192	0.000	0.000	0.000	0.000
91	A	120	PRO	0	0.022	0.020	26.566	0.258	0.258	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.907	-0.967	27.377	10.256	10.256	0.000	0.000	0.000	0.000
93	A	122	MET	0	-0.050	-0.028	20.794	0.208	0.208	0.000	0.000	0.000	0.000
94	A	123	THR	0	-0.066	-0.037	24.018	0.495	0.495	0.000	0.000	0.000	0.000
95	A	124	VAL	0	-0.001	0.013	22.766	-0.182	-0.182	0.000	0.000	0.000	0.000
96	A	125	THR	0	-0.034	-0.026	25.663	-0.280	-0.280	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.030	-0.003	23.130	0.159	0.159	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.941	-0.976	27.045	9.864	9.864	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)