FMO DATABASE

FMODB ID: YYK72

Calculation Name: 4Y66-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: A

ChEMBL ID:

UniProt ID: E2RTU1

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-730410.547779
FMO2-HF: Nuclear repulsion	678480.738442
FMO2-HF: Total energy	-51929.809337
FMO2-MP2: Total energy	-52081.88012

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:76:ARG)

Summations of interaction energy for fragment #1(A:76: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.
41.061	44.319	0.278	-1.187	-2.348	0

Interaction energy analysis for fragmet #1(A:76:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.039 / q_NPA : 1.011

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	A	78	GLN	0	0.100	0.037	3.683	-0.811	0.942	-0.002	-0.742	-1.009	0.001
4	A	79	ALA	0	0.000	0.006	2.780	1.352	2.244	0.279	-0.311	-0.860	-0.001
5	A	80	ALA	0	0.036	0.006	3.747	2.726	3.221	0.002	-0.130	-0.366	0.000
6	A	81	ARG	1	0.889	0.949	5.384	33.231	33.349	-0.001	-0.004	-0.113	0.000
7	A	82	THR	0	0.004	-0.008	7.338	3.564	3.564	0.000	0.000	0.000	0.000
8	A	83	GLU	-1	-0.785	-0.846	7.694	-26.794	-26.794	0.000	0.000	0.000	0.000
9	A	84	LEU	0	0.009	0.006	10.295	2.166	2.166	0.000	0.000	0.000	0.000
10	A	85	ALA	0	-0.013	-0.003	12.303	1.779	1.779	0.000	0.000	0.000	0.000
11	A	86	ARG	1	0.825	0.880	11.328	25.250	25.250	0.000	0.000	0.000	0.000
12	A	87	LEU	0	0.017	-0.011	13.290	1.127	1.127	0.000	0.000	0.000	0.000
13	A	88	GLN	0	0.013	0.022	16.271	0.613	0.613	0.000	0.000	0.000	0.000
14	A	89	LYS	1	0.945	0.969	17.106	16.702	16.702	0.000	0.000	0.000	0.000
15	A	90	ALA	0	-0.022	-0.002	19.135	0.685	0.685	0.000	0.000	0.000	0.000
16	A	91	LEU	0	0.012	0.014	20.544	0.607	0.607	0.000	0.000	0.000	0.000
17	A	92	GLU	-1	-0.902	-0.945	21.790	-12.841	-12.841	0.000	0.000	0.000	0.000
18	A	93	GLU	-1	-0.789	-0.881	24.333	-10.191	-10.191	0.000	0.000	0.000	0.000
19	A	94	GLN	0	-0.002	-0.006	24.607	0.799	0.799	0.000	0.000	0.000	0.000
20	A	95	THR	0	-0.008	-0.022	25.952	0.429	0.429	0.000	0.000	0.000	0.000
21	A	96	ASN	0	-0.020	-0.025	28.239	0.720	0.720	0.000	0.000	0.000	0.000
22	A	97	PHE	0	-0.061	-0.023	29.166	0.436	0.436	0.000	0.000	0.000	0.000
23	A	98	ILE	0	0.026	0.006	28.424	0.339	0.339	0.000	0.000	0.000	0.000
24	A	99	ASP	-1	-0.927	-0.937	32.034	-8.493	-8.493	0.000	0.000	0.000	0.000
25	A	100	LYS	1	0.892	0.929	30.697	10.367	10.367	0.000	0.000	0.000	0.000
26	A	101	ALA	0	-0.078	-0.019	34.405	0.283	0.283	0.000	0.000	0.000	0.000
27	A	102	THR	0	-0.001	-0.015	35.531	0.243	0.243	0.000	0.000	0.000	0.000
28	A	103	ALA	0	0.023	0.014	37.993	0.242	0.242	0.000	0.000	0.000	0.000
29	A	104	ARG	1	0.887	0.923	34.972	8.757	8.757	0.000	0.000	0.000	0.000
30	A	105	ILE	0	-0.027	-0.015	38.171	0.189	0.189	0.000	0.000	0.000	0.000
31	A	106	GLU	-1	-0.916	-0.950	41.987	-6.979	-6.979	0.000	0.000	0.000	0.000
32	A	107	GLU	-1	-0.911	-0.962	43.846	-6.966	-6.966	0.000	0.000	0.000	0.000
33	A	108	LEU	0	-0.072	-0.040	43.376	0.202	0.202	0.000	0.000	0.000	0.000
34	A	109	LYS	1	0.824	0.886	45.413	6.741	6.741	0.000	0.000	0.000	0.000
35	A	110	VAL	0	0.002	0.024	47.788	0.136	0.136	0.000	0.000	0.000	0.000
36	A	111	GLY	0	-0.026	-0.008	50.717	0.133	0.133	0.000	0.000	0.000	0.000
37	A	112	ARG	1	0.791	0.889	49.238	6.519	6.519	0.000	0.000	0.000	0.000
38	A	113	GLU	-1	-0.734	-0.846	50.448	-6.490	-6.490	0.000	0.000	0.000	0.000
39	A	114	GLU	-1	-0.871	-0.905	49.362	-6.156	-6.156	0.000	0.000	0.000	0.000
40	A	115	THR	0	-0.024	-0.007	52.559	0.046	0.046	0.000	0.000	0.000	0.000
41	A	116	GLU	-1	-0.757	-0.889	56.104	-5.532	-5.532	0.000	0.000	0.000	0.000
42	A	117	GLU	-1	-0.878	-0.924	58.480	-5.132	-5.132	0.000	0.000	0.000	0.000
43	A	118	ARG	1	0.894	0.928	50.879	6.167	6.167	0.000	0.000	0.000	0.000
44	A	119	SER	0	-0.054	-0.038	55.900	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	120	SER	0	-0.032	-0.044	56.803	0.026	0.026	0.000	0.000	0.000	0.000
46	A	121	LEU	0	0.045	0.031	58.627	0.041	0.041	0.000	0.000	0.000	0.000
47	A	122	LEU	0	-0.010	-0.020	53.633	0.023	0.023	0.000	0.000	0.000	0.000
48	A	123	LYS	1	0.826	0.922	57.287	5.523	5.523	0.000	0.000	0.000	0.000
49	A	124	GLU	-1	-0.837	-0.908	59.398	-4.884	-4.884	0.000	0.000	0.000	0.000
50	A	125	LYS	1	0.818	0.892	58.876	5.153	5.153	0.000	0.000	0.000	0.000
51	A	126	LEU	0	0.010	0.030	56.457	0.002	0.002	0.000	0.000	0.000	0.000
52	A	127	ALA	0	0.016	0.003	59.675	0.048	0.048	0.000	0.000	0.000	0.000
53	A	128	LEU	0	0.002	-0.004	63.052	0.069	0.069	0.000	0.000	0.000	0.000
54	A	129	GLN	0	-0.049	-0.035	58.129	0.030	0.030	0.000	0.000	0.000	0.000
55	A	130	VAL	0	0.006	0.008	61.163	0.032	0.032	0.000	0.000	0.000	0.000
56	A	131	LYS	1	0.803	0.885	63.613	4.606	4.606	0.000	0.000	0.000	0.000
57	A	132	LEU	0	0.029	0.011	65.337	0.075	0.075	0.000	0.000	0.000	0.000
58	A	133	GLU	-1	-0.876	-0.922	63.508	-4.880	-4.880	0.000	0.000	0.000	0.000
59	A	134	GLU	-1	-0.804	-0.872	66.692	-4.498	-4.498	0.000	0.000	0.000	0.000
60	A	135	GLN	0	0.006	0.010	69.035	0.031	0.031	0.000	0.000	0.000	0.000
61	A	136	ARG	1	0.873	0.926	64.639	4.932	4.932	0.000	0.000	0.000	0.000
62	A	137	GLY	0	-0.005	-0.006	70.172	0.037	0.037	0.000	0.000	0.000	0.000
63	A	138	THR	0	0.000	-0.014	71.106	0.064	0.064	0.000	0.000	0.000	0.000
64	A	139	PHE	0	-0.020	-0.021	73.946	0.060	0.060	0.000	0.000	0.000	0.000
65	A	140	ARG	1	0.881	0.939	68.617	4.622	4.622	0.000	0.000	0.000	0.000
66	A	141	ASP	-1	-0.818	-0.887	73.320	-4.345	-4.345	0.000	0.000	0.000	0.000
67	A	142	LEU	0	-0.005	-0.010	76.373	0.057	0.057	0.000	0.000	0.000	0.000
68	A	143	LEU	0	-0.009	-0.008	77.339	0.061	0.061	0.000	0.000	0.000	0.000
69	A	144	LYS	1	0.813	0.912	76.148	4.233	4.233	0.000	0.000	0.000	0.000
70	A	145	ASN	0	-0.081	-0.037	80.192	0.027	0.027	0.000	0.000	0.000	0.000
71	A	146	ASP	-1	-0.806	-0.906	83.821	-3.660	-3.660	0.000	0.000	0.000	0.000
72	A	147	PRO	0	0.016	-0.006	86.245	0.042	0.042	0.000	0.000	0.000	0.000
73	A	148	ASP	-1	-0.863	-0.905	89.399	-3.426	-3.426	0.000	0.000	0.000	0.000
74	A	149	VAL	0	0.008	0.000	89.102	0.047	0.047	0.000	0.000	0.000	0.000
75	A	150	ALA	0	-0.002	0.000	89.679	0.036	0.036	0.000	0.000	0.000	0.000
76	A	151	GLN	0	-0.005	-0.004	91.703	0.001	0.001	0.000	0.000	0.000	0.000
77	A	152	LYS	1	0.875	0.929	94.212	3.480	3.480	0.000	0.000	0.000	0.000
78	A	153	LEU	0	-0.002	-0.004	91.750	0.040	0.040	0.000	0.000	0.000	0.000
79	A	154	ARG	1	0.923	0.966	91.248	3.513	3.513	0.000	0.000	0.000	0.000
80	A	155	ASN	0	0.067	0.040	97.698	0.023	0.023	0.000	0.000	0.000	0.000
81	A	156	TYR	0	-0.006	-0.007	98.958	0.033	0.033	0.000	0.000	0.000	0.000
82	A	157	THR	0	-0.047	-0.028	97.873	0.021	0.021	0.000	0.000	0.000	0.000
83	A	158	ASP	-1	-0.845	-0.930	100.924	-3.165	-3.165	0.000	0.000	0.000	0.000
84	A	159	ILE	0	-0.017	-0.006	103.608	0.035	0.035	0.000	0.000	0.000	0.000
85	A	160	ALA	0	-0.013	-0.014	103.125	0.030	0.030	0.000	0.000	0.000	0.000
86	A	161	LYS	1	0.870	0.945	102.010	3.187	3.187	0.000	0.000	0.000	0.000
87	A	162	GLN	0	-0.059	-0.023	106.140	0.021	0.021	0.000	0.000	0.000	0.000
88	A	163	GLU	-1	-0.856	-0.927	108.899	-2.881	-2.881	0.000	0.000	0.000	0.000
89	A	164	ALA	0	-0.013	-0.005	107.247	0.027	0.027	0.000	0.000	0.000	0.000
90	A	165	ASN	0	0.010	0.015	108.318	0.023	0.023	0.000	0.000	0.000	0.000
91	A	166	LEU	0	0.013	0.017	111.456	0.031	0.031	0.000	0.000	0.000	0.000
92	A	167	TRP	0	-0.021	-0.026	112.254	0.047	0.047	0.000	0.000	0.000	0.000
93	A	168	THR	0	0.001	-0.002	111.366	0.015	0.015	0.000	0.000	0.000	0.000
94	A	169	ASP	-1	-0.865	-0.906	113.960	-2.738	-2.738	0.000	0.000	0.000	0.000
95	A	170	ASN	0	-0.040	-0.026	117.120	0.048	0.048	0.000	0.000	0.000	0.000
96	A	171	ILE	0	0.011	0.014	113.990	0.032	0.032	0.000	0.000	0.000	0.000
97	A	172	PHE	0	0.027	0.008	114.575	0.034	0.034	0.000	0.000	0.000	0.000
98	A	173	CYS	0	-0.059	-0.026	119.553	0.041	0.041	0.000	0.000	0.000	0.000
99	A	174	LEU	0	0.033	0.005	119.814	0.033	0.033	0.000	0.000	0.000	0.000
100	A	175	GLN	0	0.049	0.035	118.974	0.035	0.035	0.000	0.000	0.000	0.000
101	A	176	LYS	1	0.961	0.985	122.709	2.597	2.597	0.000	0.000	0.000	0.000
102	A	177	TYR	0	0.012	0.016	125.495	0.035	0.035	0.000	0.000	0.000	0.000
103	A	178	MET	0	0.026	-0.002	121.897	0.026	0.026	0.000	0.000	0.000	0.000
104	A	179	LEU	0	-0.022	0.008	123.680	0.015	0.015	0.000	0.000	0.000	0.000
105	A	180	THR	0	-0.046	-0.039	127.713	0.029	0.029	0.000	0.000	0.000	0.000
106	A	181	LYS	1	0.834	0.908	130.535	2.491	2.491	0.000	0.000	0.000	0.000
107	A	182	LEU	0	0.008	0.007	128.378	0.018	0.018	0.000	0.000	0.000	0.000
108	A	183	GLN	0	-0.059	-0.010	131.225	0.001	0.001	0.000	0.000	0.000	0.000
109	A	184	MET	0	-0.008	0.001	125.386	0.003	0.003	0.000	0.000	0.000	0.000
110	A	185	ASP	-1	-0.753	-0.854	124.105	-2.639	-2.639	0.000	0.000	0.000	0.000
111	A	186	LYS	1	0.960	0.974	120.708	2.671	2.671	0.000	0.000	0.000	0.000
112	A	187	LYS	1	0.924	0.976	116.328	2.758	2.758	0.000	0.000	0.000	0.000
113	A	188	THR	0	-0.018	-0.047	119.769	-0.027	-0.027	0.000	0.000	0.000	0.000
114	A	189	VAL	0	-0.014	-0.013	120.358	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	190	SER	0	-0.002	-0.005	117.094	-0.016	-0.016	0.000	0.000	0.000	0.000
116	A	191	THR	0	-0.039	-0.033	115.079	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	192	ALA	0	-0.049	-0.021	115.921	-0.019	-0.019	0.000	0.000	0.000	0.000
118	A	193	LEU	0	-0.037	-0.019	117.121	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	194	GLY	0	-0.003	0.015	112.990	-0.018	-0.018	0.000	0.000	0.000	0.000
120	A	195	ILE	0	-0.059	-0.015	111.977	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	196	THR	0	-0.060	-0.045	108.746	0.007	0.007	0.000	0.000	0.000	0.000
122	A	197	GLY	0	-0.001	-0.005	109.574	0.020	0.020	0.000	0.000	0.000	0.000
123	A	198	GLU	-1	-0.930	-0.974	106.074	-3.029	-3.029	0.000	0.000	0.000	0.000
124	A	199	PHE	0	-0.046	-0.010	107.951	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	200	ASP	-1	-0.868	-0.931	108.491	-2.925	-2.925	0.000	0.000	0.000	0.000
126	A	201	TYR	0	-0.091	-0.082	108.914	-0.015	-0.015	0.000	0.000	0.000	0.000
127	A	202	LEU	0	-0.030	-0.013	104.182	-0.029	-0.029	0.000	0.000	0.000	0.000
128	A	203	GLU	-1	-0.953	-0.974	103.624	-3.094	-3.094	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:76:ARG)