FMO DATABASE

FMODB ID: 82Z6Y

Calculation Name: 4Y66-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: F

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:

Apendix: None

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1122766.688247
FMO2-HF: Nuclear repulsion	1055911.483833
FMO2-HF: Total energy	-66855.204414
FMO2-MP2: Total energy	-67047.823124

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(F:3:ALA)

Summations of interaction energy for fragment #1(F:3:ALA)

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.
-9.272	-5.49	1.302	-2.259	-2.825	0.008

Interaction energy analysis for fragmet #1(F:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.016

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	F	5	TYR	0	-0.077	-0.071	3.169	-3.646	-0.904	0.109	-1.384	-1.467	0.009
4	F	6	LYS	1	0.992	0.992	2.574	-3.237	-2.390	1.189	-0.830	-1.206	-0.001
5	F	7	GLU	-1	-0.905	-0.954	3.942	-1.929	-1.736	0.004	-0.045	-0.152	0.000
6	F	8	ALA	0	-0.020	-0.002	6.240	0.018	0.018	0.000	0.000	0.000	0.000
7	F	9	PHE	0	0.017	0.006	7.338	-0.148	-0.148	0.000	0.000	0.000	0.000
8	F	10	ALA	0	-0.012	-0.015	7.989	-0.155	-0.155	0.000	0.000	0.000	0.000
9	F	11	ALA	0	0.046	0.031	9.852	-0.100	-0.100	0.000	0.000	0.000	0.000
10	F	12	VAL	0	-0.014	-0.012	11.807	-0.046	-0.046	0.000	0.000	0.000	0.000
11	F	13	LYS	1	0.829	0.912	12.041	-0.217	-0.217	0.000	0.000	0.000	0.000
12	F	14	GLU	-1	-0.848	-0.898	14.052	0.051	0.051	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.034	-0.017	15.837	-0.022	-0.022	0.000	0.000	0.000	0.000
14	F	16	MET	0	-0.043	-0.035	17.644	-0.024	-0.024	0.000	0.000	0.000	0.000
15	F	17	GLN	0	-0.006	-0.007	17.045	0.009	0.009	0.000	0.000	0.000	0.000
16	F	18	THR	0	-0.012	0.003	19.948	-0.020	-0.020	0.000	0.000	0.000	0.000
17	F	19	SER	0	-0.075	-0.038	21.685	-0.015	-0.015	0.000	0.000	0.000	0.000
18	F	20	ASN	0	0.027	0.025	23.522	0.009	0.009	0.000	0.000	0.000	0.000
19	F	21	LYS	1	0.939	0.976	24.687	-0.098	-0.098	0.000	0.000	0.000	0.000
20	F	22	PRO	0	0.004	0.020	24.394	0.013	0.013	0.000	0.000	0.000	0.000
21	F	23	GLN	0	0.020	-0.011	20.856	-0.005	-0.005	0.000	0.000	0.000	0.000
22	F	24	ASN	0	0.000	-0.017	22.273	0.008	0.008	0.000	0.000	0.000	0.000
23	F	25	VAL	0	0.019	0.018	17.955	0.000	0.000	0.000	0.000	0.000	0.000
24	F	26	GLN	0	0.060	0.032	19.129	0.036	0.036	0.000	0.000	0.000	0.000
25	F	27	THR	0	0.017	0.010	21.150	-0.006	-0.006	0.000	0.000	0.000	0.000
26	F	28	ALA	0	0.056	0.026	17.027	-0.015	-0.015	0.000	0.000	0.000	0.000
27	F	29	ILE	0	0.008	0.025	15.742	-0.011	-0.011	0.000	0.000	0.000	0.000
28	F	30	ASN	0	0.008	0.002	17.724	-0.028	-0.028	0.000	0.000	0.000	0.000
29	F	31	ASN	0	-0.019	-0.015	20.240	-0.022	-0.022	0.000	0.000	0.000	0.000
30	F	32	THR	0	-0.003	-0.004	14.727	-0.009	-0.009	0.000	0.000	0.000	0.000
31	F	33	GLY	0	-0.014	-0.008	15.980	-0.027	-0.027	0.000	0.000	0.000	0.000
32	F	34	SER	0	-0.031	-0.019	17.967	-0.017	-0.017	0.000	0.000	0.000	0.000
33	F	35	LYS	1	0.926	0.973	13.213	0.016	0.016	0.000	0.000	0.000	0.000
34	F	36	TYR	0	0.005	0.005	9.536	0.061	0.061	0.000	0.000	0.000	0.000
35	F	37	GLY	0	0.065	0.036	12.626	-0.046	-0.046	0.000	0.000	0.000	0.000
36	F	38	LYS	1	0.939	0.948	14.412	-0.222	-0.222	0.000	0.000	0.000	0.000
37	F	39	THR	0	0.024	-0.002	14.201	0.031	0.031	0.000	0.000	0.000	0.000
38	F	40	THR	0	0.022	0.013	8.917	-0.014	-0.014	0.000	0.000	0.000	0.000
39	F	41	VAL	0	0.076	0.043	11.550	0.106	0.106	0.000	0.000	0.000	0.000
40	F	42	GLN	0	-0.016	-0.004	13.668	0.045	0.045	0.000	0.000	0.000	0.000
41	F	43	LYS	1	0.822	0.905	11.511	-0.659	-0.659	0.000	0.000	0.000	0.000
42	F	44	ALA	0	0.079	0.050	10.585	-0.004	-0.004	0.000	0.000	0.000	0.000
43	F	45	LEU	0	-0.039	-0.021	12.134	-0.092	-0.092	0.000	0.000	0.000	0.000
44	F	46	ASP	-1	-0.767	-0.888	15.817	0.387	0.387	0.000	0.000	0.000	0.000
45	F	47	GLU	-1	-0.845	-0.877	10.032	1.264	1.264	0.000	0.000	0.000	0.000
46	F	48	LEU	0	-0.001	-0.006	13.898	-0.061	-0.061	0.000	0.000	0.000	0.000
47	F	49	VAL	0	-0.045	-0.029	15.923	-0.050	-0.050	0.000	0.000	0.000	0.000
48	F	50	ALA	0	-0.049	-0.005	16.410	-0.037	-0.037	0.000	0.000	0.000	0.000
49	F	51	GLN	0	-0.057	-0.028	13.725	0.020	0.020	0.000	0.000	0.000	0.000
50	F	52	ASN	0	0.005	-0.005	17.875	-0.034	-0.034	0.000	0.000	0.000	0.000
51	F	53	LEU	0	0.036	0.023	16.466	-0.025	-0.025	0.000	0.000	0.000	0.000
52	F	54	CYS	0	-0.100	-0.037	19.232	-0.004	-0.004	0.000	0.000	0.000	0.000
53	F	55	ILE	0	0.044	0.043	21.083	0.009	0.009	0.000	0.000	0.000	0.000
54	F	56	TYR	0	-0.007	-0.033	22.876	0.020	0.020	0.000	0.000	0.000	0.000
55	F	57	THR	0	0.002	0.005	24.921	-0.014	-0.014	0.000	0.000	0.000	0.000
56	F	58	GLU	-1	-0.865	-0.933	27.406	0.199	0.199	0.000	0.000	0.000	0.000
57	F	59	ILE	0	0.029	0.021	29.191	-0.010	-0.010	0.000	0.000	0.000	0.000
58	F	60	GLY	0	0.051	0.012	32.133	0.002	0.002	0.000	0.000	0.000	0.000
59	F	61	LYS	1	0.835	0.914	29.617	-0.165	-0.165	0.000	0.000	0.000	0.000
60	F	62	THR	0	-0.018	0.007	30.402	0.003	0.003	0.000	0.000	0.000	0.000
61	F	63	GLY	0	0.018	0.004	27.334	0.007	0.007	0.000	0.000	0.000	0.000
62	F	64	LYS	1	0.868	0.959	20.967	-0.322	-0.322	0.000	0.000	0.000	0.000
63	F	65	LEU	0	-0.045	-0.028	24.663	0.009	0.009	0.000	0.000	0.000	0.000
64	F	66	TYR	0	-0.038	-0.048	19.556	-0.011	-0.011	0.000	0.000	0.000	0.000
65	F	67	LEU	0	0.007	-0.012	22.901	-0.012	-0.012	0.000	0.000	0.000	0.000
66	F	68	TRP	0	0.115	0.052	17.506	0.026	0.026	0.000	0.000	0.000	0.000
67	F	69	ASN	0	-0.001	0.002	22.425	-0.028	-0.028	0.000	0.000	0.000	0.000
68	F	70	GLN	0	0.062	0.010	24.491	0.001	0.001	0.000	0.000	0.000	0.000
69	F	71	ASN	0	-0.069	-0.039	27.630	-0.016	-0.016	0.000	0.000	0.000	0.000
70	F	72	LEU	0	-0.021	-0.005	22.712	-0.003	-0.003	0.000	0.000	0.000	0.000
71	F	73	LEU	0	-0.069	-0.021	25.924	-0.005	-0.005	0.000	0.000	0.000	0.000
72	F	74	GLU	-1	-0.890	-0.942	28.660	0.050	0.050	0.000	0.000	0.000	0.000
73	F	75	VAL	0	-0.018	-0.012	31.668	-0.001	-0.001	0.000	0.000	0.000	0.000
74	F	76	LEU	0	-0.021	-0.007	34.568	-0.003	-0.003	0.000	0.000	0.000	0.000
75	F	77	SER	0	0.009	0.001	37.256	-0.001	-0.001	0.000	0.000	0.000	0.000
76	F	78	ASP	-1	-0.839	-0.924	40.762	0.038	0.038	0.000	0.000	0.000	0.000
77	F	79	ALA	0	-0.017	-0.021	43.582	-0.002	-0.002	0.000	0.000	0.000	0.000
78	F	80	GLN	0	-0.006	-0.003	36.401	-0.004	-0.004	0.000	0.000	0.000	0.000
79	F	81	LEU	0	0.020	0.010	38.444	-0.002	-0.002	0.000	0.000	0.000	0.000
80	F	82	MET	0	-0.050	-0.017	40.817	-0.002	-0.002	0.000	0.000	0.000	0.000
81	F	83	GLU	-1	-0.870	-0.916	40.379	0.016	0.016	0.000	0.000	0.000	0.000
82	F	84	VAL	0	0.046	0.022	36.906	-0.002	-0.002	0.000	0.000	0.000	0.000
83	F	85	ASN	0	-0.076	-0.060	39.799	-0.002	-0.002	0.000	0.000	0.000	0.000
84	F	86	ALA	0	0.005	0.020	42.096	-0.002	-0.002	0.000	0.000	0.000	0.000
85	F	87	GLN	0	-0.013	-0.016	38.105	-0.002	-0.002	0.000	0.000	0.000	0.000
86	F	88	ILE	0	-0.039	-0.016	37.589	-0.002	-0.002	0.000	0.000	0.000	0.000
87	F	89	ASN	0	0.002	-0.023	40.623	0.000	0.000	0.000	0.000	0.000	0.000
88	F	90	ASP	-1	-0.835	-0.889	43.346	0.005	0.005	0.000	0.000	0.000	0.000
89	F	91	LEU	0	0.003	-0.013	37.645	-0.002	-0.002	0.000	0.000	0.000	0.000
90	F	92	LYS	1	0.887	0.948	41.489	-0.023	-0.023	0.000	0.000	0.000	0.000
91	F	93	ALA	0	0.021	0.018	42.734	-0.001	-0.001	0.000	0.000	0.000	0.000
92	F	94	GLN	0	-0.103	-0.077	43.025	-0.004	-0.004	0.000	0.000	0.000	0.000
93	F	95	VAL	0	0.054	0.030	39.492	-0.002	-0.002	0.000	0.000	0.000	0.000
94	F	96	GLU	-1	-0.878	-0.912	42.709	0.003	0.003	0.000	0.000	0.000	0.000
95	F	97	LYS	1	0.896	0.958	45.645	0.000	0.000	0.000	0.000	0.000	0.000
96	F	98	LEU	0	0.014	-0.007	41.520	-0.001	-0.001	0.000	0.000	0.000	0.000
97	F	99	THR	0	-0.017	-0.010	42.985	-0.002	-0.002	0.000	0.000	0.000	0.000
98	F	100	GLN	0	-0.021	-0.018	44.391	-0.002	-0.002	0.000	0.000	0.000	0.000
99	F	101	GLN	0	-0.022	0.000	47.029	-0.001	-0.001	0.000	0.000	0.000	0.000
100	F	102	GLY	0	0.023	0.006	44.787	-0.001	-0.001	0.000	0.000	0.000	0.000
101	F	103	GLU	-1	-0.848	-0.905	45.390	-0.004	-0.004	0.000	0.000	0.000	0.000
102	F	104	THR	0	-0.024	-0.019	47.554	0.000	0.000	0.000	0.000	0.000	0.000
103	F	105	LEU	0	-0.018	-0.006	46.040	-0.001	-0.001	0.000	0.000	0.000	0.000
104	F	106	ARG	1	0.868	0.914	43.938	0.005	0.005	0.000	0.000	0.000	0.000
105	F	107	ILE	0	-0.038	-0.017	47.771	-0.001	-0.001	0.000	0.000	0.000	0.000
106	F	108	THR	0	-0.039	-0.032	51.345	0.000	0.000	0.000	0.000	0.000	0.000
107	F	109	GLN	0	-0.065	-0.039	45.447	0.000	0.000	0.000	0.000	0.000	0.000
108	F	110	ARG	1	0.922	0.960	49.485	0.008	0.008	0.000	0.000	0.000	0.000
109	F	111	ASN	0	-0.032	-0.027	50.814	0.000	0.000	0.000	0.000	0.000	0.000
110	F	112	LEU	0	-0.027	-0.010	52.770	0.000	0.000	0.000	0.000	0.000	0.000
111	F	113	GLU	-1	-0.893	-0.918	48.059	-0.019	-0.019	0.000	0.000	0.000	0.000
112	F	114	ALA	0	-0.055	-0.017	52.221	0.000	0.000	0.000	0.000	0.000	0.000
113	F	115	ALA	0	-0.009	-0.010	55.038	0.000	0.000	0.000	0.000	0.000	0.000
114	F	116	PRO	0	0.051	0.041	55.471	-0.001	-0.001	0.000	0.000	0.000	0.000
115	F	117	ILE	0	-0.001	-0.014	53.264	0.001	0.001	0.000	0.000	0.000	0.000
116	F	118	THR	0	0.059	0.013	57.235	0.000	0.000	0.000	0.000	0.000	0.000
117	F	119	GLU	-1	-0.885	-0.936	59.166	-0.019	-0.019	0.000	0.000	0.000	0.000
118	F	120	VAL	0	0.045	0.014	56.407	0.000	0.000	0.000	0.000	0.000	0.000
119	F	121	LEU	0	0.028	0.031	59.841	0.001	0.001	0.000	0.000	0.000	0.000
120	F	122	LYS	1	0.838	0.900	62.038	0.018	0.018	0.000	0.000	0.000	0.000
121	F	123	GLN	0	0.019	0.009	60.504	0.000	0.000	0.000	0.000	0.000	0.000
122	F	124	GLU	-1	-0.905	-0.941	61.009	-0.014	-0.014	0.000	0.000	0.000	0.000
123	F	125	VAL	0	-0.011	-0.015	64.069	0.001	0.001	0.000	0.000	0.000	0.000
124	F	126	ASP	-1	-0.853	-0.913	67.245	-0.014	-0.014	0.000	0.000	0.000	0.000
125	F	127	GLU	-1	-0.952	-0.975	63.808	-0.017	-0.017	0.000	0.000	0.000	0.000
126	F	128	LEU	0	-0.042	-0.012	66.915	0.001	0.001	0.000	0.000	0.000	0.000
127	F	129	ARG	1	0.808	0.892	69.126	0.014	0.014	0.000	0.000	0.000	0.000
128	F	130	GLN	0	-0.017	-0.009	71.474	0.000	0.000	0.000	0.000	0.000	0.000
129	F	131	GLN	0	-0.028	-0.030	67.276	0.001	0.001	0.000	0.000	0.000	0.000
130	F	132	VAL	0	0.045	0.030	72.830	0.000	0.000	0.000	0.000	0.000	0.000
131	F	133	SER	0	-0.018	0.009	75.313	0.000	0.000	0.000	0.000	0.000	0.000
132	F	134	ALA	0	0.000	-0.008	75.152	0.000	0.000	0.000	0.000	0.000	0.000
133	F	135	ASN	0	-0.026	-0.027	74.043	0.000	0.000	0.000	0.000	0.000	0.000
134	F	136	ASP	-1	-0.764	-0.880	77.804	-0.009	-0.009	0.000	0.000	0.000	0.000
135	F	137	GLU	-1	-0.824	-0.903	80.453	-0.009	-0.009	0.000	0.000	0.000	0.000
136	F	138	LYS	1	0.831	0.911	79.690	0.010	0.010	0.000	0.000	0.000	0.000
137	F	139	LEU	0	-0.022	0.003	80.875	0.000	0.000	0.000	0.000	0.000	0.000
138	F	140	ARG	1	0.749	0.856	82.067	0.009	0.009	0.000	0.000	0.000	0.000
139	F	141	LEU	0	-0.082	-0.030	83.945	0.000	0.000	0.000	0.000	0.000	0.000
140	F	142	VAL	0	-0.035	-0.001	84.360	0.000	0.000	0.000	0.000	0.000	0.000
141	F	153	ASP	-1	-0.814	-0.895	95.936	-0.004	-0.004	0.000	0.000	0.000	0.000
142	F	154	MET	0	0.017	0.003	92.736	0.000	0.000	0.000	0.000	0.000	0.000
143	F	155	LEU	0	0.020	0.016	95.900	0.000	0.000	0.000	0.000	0.000	0.000
144	F	156	THR	0	0.010	-0.035	98.348	0.000	0.000	0.000	0.000	0.000	0.000
145	F	157	LEU	0	-0.037	-0.009	97.103	0.000	0.000	0.000	0.000	0.000	0.000
146	F	158	GLN	0	0.006	-0.007	97.938	0.000	0.000	0.000	0.000	0.000	0.000
147	F	159	LYS	1	0.776	0.865	100.121	0.002	0.002	0.000	0.000	0.000	0.000
148	F	160	ASN	0	-0.030	-0.009	103.396	0.000	0.000	0.000	0.000	0.000	0.000
149	F	161	TYR	0	0.020	-0.001	101.404	0.000	0.000	0.000	0.000	0.000	0.000
150	F	162	LYS	1	0.877	0.941	102.085	0.002	0.002	0.000	0.000	0.000	0.000
151	F	163	ASP	-1	-0.814	-0.891	104.865	-0.002	-0.002	0.000	0.000	0.000	0.000
152	F	164	ALA	0	-0.067	-0.008	106.941	0.000	0.000	0.000	0.000	0.000	0.000
153	F	165	MET	0	0.019	0.035	105.532	0.000	0.000	0.000	0.000	0.000	0.000
154	F	205	MET	0	0.077	0.023	110.619	0.000	0.000	0.000	0.000	0.000	0.000
155	F	206	THR	0	0.018	0.019	107.813	0.000	0.000	0.000	0.000	0.000	0.000
156	F	207	THR	0	0.075	0.040	105.677	0.000	0.000	0.000	0.000	0.000	0.000
157	F	208	TYR	0	0.008	-0.006	105.025	0.000	0.000	0.000	0.000	0.000	0.000
158	F	209	THR	0	-0.050	-0.036	104.314	0.000	0.000	0.000	0.000	0.000	0.000
159	F	210	GLU	-1	-0.919	-0.967	101.432	-0.002	-0.002	0.000	0.000	0.000	0.000
160	F	211	MET	0	0.033	0.017	99.913	0.000	0.000	0.000	0.000	0.000	0.000
161	F	212	LYS	1	0.876	0.928	100.335	0.002	0.002	0.000	0.000	0.000	0.000
162	F	213	LYS	1	0.891	0.952	98.475	0.002	0.002	0.000	0.000	0.000	0.000
163	F	214	ALA	0	-0.025	-0.008	96.126	0.000	0.000	0.000	0.000	0.000	0.000
164	F	215	LEU	0	-0.022	-0.005	96.201	0.000	0.000	0.000	0.000	0.000	0.000
165	F	216	PRO	0	0.060	0.017	95.124	0.000	0.000	0.000	0.000	0.000	0.000
166	F	217	PRO	0	-0.035	0.000	98.469	0.000	0.000	0.000	0.000	0.000	0.000
167	F	218	VAL	0	0.031	0.019	98.246	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:3:ALA)