FMO DATABASE

FMODB ID: J3ZR9

Calculation Name: 4Y66-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: E

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	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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1056176.709573
FMO2-HF: Nuclear repulsion	993889.16742
FMO2-HF: Total energy	-62287.542154
FMO2-MP2: Total energy	-62470.855583

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(E:9:ASP)

Summations of interaction energy for fragment #1(E:9: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.
-213.718	-213.45	25.632	-13.354	-12.547	0.133

Interaction energy analysis for fragmet #1(E:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.800 / q_NPA : -0.917

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	E	11	LYS	1	0.838	0.895	1.742	-151.376	-152.983	22.557	-11.723	-9.227	0.126
4	E	12	LYS	1	0.840	0.901	2.143	-54.987	-53.566	3.076	-1.551	-2.947	0.007
5	E	13	GLU	-1	-0.880	-0.935	4.112	23.359	23.676	0.000	-0.066	-0.251	0.000
6	E	14	ARG	1	0.856	0.928	6.373	-29.128	-29.128	0.000	0.000	0.000	0.000
7	E	15	LEU	0	-0.009	-0.013	7.347	-3.295	-3.295	0.000	0.000	0.000	0.000
8	E	16	LEU	0	0.018	-0.005	8.190	-2.650	-2.650	0.000	0.000	0.000	0.000
9	E	17	GLU	-1	-0.877	-0.936	10.041	19.952	19.952	0.000	0.000	0.000	0.000
10	E	18	GLU	-1	-0.886	-0.946	11.718	16.824	16.824	0.000	0.000	0.000	0.000
11	E	19	MET	0	-0.104	-0.065	12.371	-1.133	-1.133	0.000	0.000	0.000	0.000
12	E	20	LEU	0	-0.006	0.017	14.224	-1.146	-1.146	0.000	0.000	0.000	0.000
13	E	21	LYS	1	0.882	0.958	15.970	-17.409	-17.409	0.000	0.000	0.000	0.000
14	E	22	ARG	1	0.834	0.925	16.672	-17.005	-17.005	0.000	0.000	0.000	0.000
15	E	23	GLY	0	0.015	-0.002	18.761	0.311	0.311	0.000	0.000	0.000	0.000
16	E	24	GLU	-1	-0.955	-0.977	20.625	12.856	12.856	0.000	0.000	0.000	0.000
17	E	25	ILE	0	0.021	0.012	19.395	0.650	0.650	0.000	0.000	0.000	0.000
18	E	26	TYR	0	0.047	0.018	16.666	-0.160	-0.160	0.000	0.000	0.000	0.000
19	E	27	SER	0	0.016	-0.020	18.768	-0.139	-0.139	0.000	0.000	0.000	0.000
20	E	28	ASN	0	0.000	0.020	17.901	1.101	1.101	0.000	0.000	0.000	0.000
21	E	29	LYS	1	1.005	0.991	17.426	-12.118	-12.118	0.000	0.000	0.000	0.000
22	E	30	THR	0	0.016	0.017	19.182	0.015	0.015	0.000	0.000	0.000	0.000
23	E	31	ILE	0	0.019	0.027	12.908	-0.113	-0.113	0.000	0.000	0.000	0.000
24	E	32	GLU	-1	-0.828	-0.935	14.717	21.030	21.030	0.000	0.000	0.000	0.000
25	E	33	THR	0	-0.094	-0.041	16.686	-0.039	-0.039	0.000	0.000	0.000	0.000
26	E	34	LEU	0	-0.012	-0.004	13.553	-0.032	-0.032	0.000	0.000	0.000	0.000
27	E	35	SER	0	-0.029	-0.007	12.568	1.210	1.210	0.000	0.000	0.000	0.000
28	E	36	LYS	1	1.021	1.007	13.279	-15.336	-15.336	0.000	0.000	0.000	0.000
29	E	37	PRO	0	0.025	0.027	14.972	0.324	0.324	0.000	0.000	0.000	0.000
30	E	38	THR	0	-0.040	0.002	12.410	0.715	0.715	0.000	0.000	0.000	0.000
31	E	39	GLY	0	0.080	0.008	9.470	0.290	0.290	0.000	0.000	0.000	0.000
32	E	40	ILE	0	-0.085	-0.030	6.958	1.599	1.599	0.000	0.000	0.000	0.000
33	E	41	SER	0	0.006	-0.001	9.971	-3.065	-3.065	0.000	0.000	0.000	0.000
34	E	42	SER	0	0.049	0.000	11.848	0.932	0.932	0.000	0.000	0.000	0.000
35	E	43	MET	0	-0.020	0.016	11.900	-0.894	-0.894	0.000	0.000	0.000	0.000
36	E	44	VAL	0	0.001	-0.009	8.262	-0.145	-0.145	0.000	0.000	0.000	0.000
37	E	45	ILE	0	0.019	0.037	8.740	2.989	2.989	0.000	0.000	0.000	0.000
38	E	46	LYS	1	0.940	0.984	9.614	-18.559	-18.559	0.000	0.000	0.000	0.000
39	E	47	ASN	0	0.004	-0.006	8.653	-2.093	-2.093	0.000	0.000	0.000	0.000
40	E	48	VAL	0	0.005	0.008	4.323	1.402	1.539	-0.001	-0.014	-0.122	0.000
41	E	49	LEU	0	0.002	0.008	6.381	-0.373	-0.373	0.000	0.000	0.000	0.000
42	E	50	GLN	0	0.010	-0.016	9.388	-0.359	-0.359	0.000	0.000	0.000	0.000
43	E	51	ALA	0	-0.005	0.006	5.885	-0.738	-0.738	0.000	0.000	0.000	0.000
44	E	52	LEU	0	0.010	-0.007	6.469	-1.290	-1.290	0.000	0.000	0.000	0.000
45	E	53	VAL	0	-0.059	-0.017	8.647	-1.865	-1.865	0.000	0.000	0.000	0.000
46	E	54	ASN	0	-0.030	-0.013	10.499	-2.660	-2.660	0.000	0.000	0.000	0.000
47	E	55	GLU	-1	-0.890	-0.914	7.437	31.192	31.192	0.000	0.000	0.000	0.000
48	E	56	ASP	-1	-0.823	-0.908	11.394	15.567	15.567	0.000	0.000	0.000	0.000
49	E	57	LEU	0	-0.032	-0.022	8.685	-0.998	-0.998	0.000	0.000	0.000	0.000
50	E	58	VAL	0	-0.043	-0.031	11.617	-0.287	-0.287	0.000	0.000	0.000	0.000
51	E	59	ASP	-1	-0.872	-0.915	14.002	14.487	14.487	0.000	0.000	0.000	0.000
52	E	60	THR	0	-0.065	-0.053	16.531	0.492	0.492	0.000	0.000	0.000	0.000
53	E	61	ASP	-1	-0.818	-0.919	18.538	11.602	11.602	0.000	0.000	0.000	0.000
54	E	62	LYS	1	0.837	0.916	21.726	-11.396	-11.396	0.000	0.000	0.000	0.000
55	E	63	ILE	0	0.033	0.036	24.256	-0.433	-0.433	0.000	0.000	0.000	0.000
56	E	64	GLY	0	0.044	0.042	27.666	0.077	0.077	0.000	0.000	0.000	0.000
57	E	65	ALA	0	-0.036	-0.042	27.347	0.161	0.161	0.000	0.000	0.000	0.000
58	E	66	SER	0	-0.043	-0.030	23.622	0.165	0.165	0.000	0.000	0.000	0.000
59	E	67	THR	0	0.016	-0.019	19.209	-0.201	-0.201	0.000	0.000	0.000	0.000
60	E	68	TYR	0	-0.062	-0.037	19.767	0.240	0.240	0.000	0.000	0.000	0.000
61	E	69	TYR	0	0.056	0.008	15.250	0.360	0.360	0.000	0.000	0.000	0.000
62	E	70	TRP	0	-0.019	-0.005	16.971	-0.136	-0.136	0.000	0.000	0.000	0.000
63	E	71	CYS	0	0.032	0.020	13.803	-0.082	-0.082	0.000	0.000	0.000	0.000
64	E	72	PHE	0	0.077	0.059	16.845	-0.172	-0.172	0.000	0.000	0.000	0.000
65	E	73	ALA	0	0.058	0.021	18.618	0.220	0.220	0.000	0.000	0.000	0.000
66	E	74	SER	0	-0.025	-0.006	19.589	-0.014	-0.014	0.000	0.000	0.000	0.000
67	E	75	LYS	1	0.860	0.944	15.760	-16.851	-16.851	0.000	0.000	0.000	0.000
68	E	76	ARG	1	0.906	0.941	14.715	-17.086	-17.086	0.000	0.000	0.000	0.000
69	E	77	SER	0	0.032	0.010	19.841	-0.355	-0.355	0.000	0.000	0.000	0.000
70	E	78	GLN	0	0.039	0.017	23.115	-0.582	-0.582	0.000	0.000	0.000	0.000
71	E	79	ALA	0	0.014	0.025	21.230	-0.305	-0.305	0.000	0.000	0.000	0.000
72	E	80	ALA	0	0.000	-0.001	23.233	-0.367	-0.367	0.000	0.000	0.000	0.000
73	E	81	ARG	1	0.927	0.950	24.885	-10.969	-10.969	0.000	0.000	0.000	0.000
74	E	82	THR	0	-0.029	-0.024	25.965	-0.316	-0.316	0.000	0.000	0.000	0.000
75	E	83	GLU	-1	-0.825	-0.909	25.708	10.582	10.582	0.000	0.000	0.000	0.000
76	E	84	LEU	0	-0.030	-0.002	27.789	-0.282	-0.282	0.000	0.000	0.000	0.000
77	E	85	ALA	0	0.017	0.004	30.392	-0.302	-0.302	0.000	0.000	0.000	0.000
78	E	86	ARG	1	0.839	0.913	25.380	-11.190	-11.190	0.000	0.000	0.000	0.000
79	E	87	LEU	0	0.029	0.017	30.256	-0.265	-0.265	0.000	0.000	0.000	0.000
80	E	88	GLN	0	-0.002	-0.001	33.306	-0.176	-0.176	0.000	0.000	0.000	0.000
81	E	89	LYS	1	0.845	0.940	35.821	-7.825	-7.825	0.000	0.000	0.000	0.000
82	E	90	ALA	0	0.081	0.026	35.377	-0.210	-0.210	0.000	0.000	0.000	0.000
83	E	91	LEU	0	-0.032	-0.004	37.225	-0.183	-0.183	0.000	0.000	0.000	0.000
84	E	92	GLU	-1	-0.900	-0.938	39.034	6.957	6.957	0.000	0.000	0.000	0.000
85	E	93	GLU	-1	-0.946	-0.960	39.379	7.670	7.670	0.000	0.000	0.000	0.000
86	E	94	GLN	0	0.017	-0.009	38.977	-0.195	-0.195	0.000	0.000	0.000	0.000
87	E	95	THR	0	-0.018	-0.030	42.447	-0.169	-0.169	0.000	0.000	0.000	0.000
88	E	96	ASN	0	0.081	0.036	44.961	-0.098	-0.098	0.000	0.000	0.000	0.000
89	E	97	PHE	0	-0.075	-0.031	44.985	-0.168	-0.168	0.000	0.000	0.000	0.000
90	E	98	ILE	0	0.014	-0.006	44.047	-0.137	-0.137	0.000	0.000	0.000	0.000
91	E	99	ASP	-1	-0.820	-0.858	47.867	5.856	5.856	0.000	0.000	0.000	0.000
92	E	100	LYS	1	0.889	0.907	50.339	-6.038	-6.038	0.000	0.000	0.000	0.000
93	E	101	ALA	0	-0.078	-0.028	50.080	-0.125	-0.125	0.000	0.000	0.000	0.000
94	E	102	THR	0	-0.007	-0.022	51.155	-0.088	-0.088	0.000	0.000	0.000	0.000
95	E	103	ALA	0	0.027	0.031	53.587	-0.104	-0.104	0.000	0.000	0.000	0.000
96	E	104	ARG	1	0.923	0.936	50.315	-6.075	-6.075	0.000	0.000	0.000	0.000
97	E	105	ILE	0	-0.011	0.003	54.443	-0.077	-0.077	0.000	0.000	0.000	0.000
98	E	106	GLU	-1	-0.928	-0.957	57.208	5.166	5.166	0.000	0.000	0.000	0.000
99	E	107	GLU	-1	-0.947	-0.982	59.312	5.157	5.157	0.000	0.000	0.000	0.000
100	E	108	LEU	0	-0.093	-0.052	58.146	-0.090	-0.090	0.000	0.000	0.000	0.000
101	E	109	LYS	1	0.810	0.905	60.801	-4.930	-4.930	0.000	0.000	0.000	0.000
102	E	110	VAL	0	0.007	0.014	62.723	-0.082	-0.082	0.000	0.000	0.000	0.000
103	E	111	GLY	0	-0.015	0.006	65.572	-0.073	-0.073	0.000	0.000	0.000	0.000
104	E	112	ARG	1	0.817	0.911	62.946	-5.057	-5.057	0.000	0.000	0.000	0.000
105	E	113	GLU	-1	-0.783	-0.901	65.426	4.762	4.762	0.000	0.000	0.000	0.000
106	E	114	GLU	-1	-0.953	-0.964	64.931	4.859	4.859	0.000	0.000	0.000	0.000
107	E	115	THR	0	-0.082	-0.042	67.130	-0.057	-0.057	0.000	0.000	0.000	0.000
108	E	116	GLU	-1	-0.882	-0.942	70.254	4.394	4.394	0.000	0.000	0.000	0.000
109	E	117	GLU	-1	-0.905	-0.965	72.763	4.193	4.193	0.000	0.000	0.000	0.000
110	E	118	ARG	1	0.975	0.969	65.832	-4.695	-4.695	0.000	0.000	0.000	0.000
111	E	119	SER	0	0.079	0.046	68.468	0.055	0.055	0.000	0.000	0.000	0.000
112	E	120	SER	0	-0.048	-0.032	69.771	0.016	0.016	0.000	0.000	0.000	0.000
113	E	121	LEU	0	0.078	0.041	71.125	-0.003	-0.003	0.000	0.000	0.000	0.000
114	E	122	LEU	0	-0.047	-0.022	65.981	0.014	0.014	0.000	0.000	0.000	0.000
115	E	123	LYS	1	0.945	0.975	70.058	-4.362	-4.362	0.000	0.000	0.000	0.000
116	E	124	GLU	-1	-0.914	-0.964	71.257	4.137	4.137	0.000	0.000	0.000	0.000
117	E	125	LYS	1	0.967	1.000	68.011	-4.655	-4.655	0.000	0.000	0.000	0.000
118	E	126	LEU	0	-0.004	-0.007	67.447	-0.002	-0.002	0.000	0.000	0.000	0.000
119	E	127	ALA	0	-0.002	-0.009	70.450	-0.010	-0.010	0.000	0.000	0.000	0.000
120	E	128	LEU	0	0.009	0.009	73.577	-0.039	-0.039	0.000	0.000	0.000	0.000
121	E	129	GLN	0	-0.050	-0.027	68.981	0.016	0.016	0.000	0.000	0.000	0.000
122	E	130	VAL	0	0.002	0.014	70.755	0.029	0.029	0.000	0.000	0.000	0.000
123	E	131	LYS	1	0.812	0.889	72.851	-4.020	-4.020	0.000	0.000	0.000	0.000
124	E	132	LEU	0	-0.017	-0.021	74.654	-0.042	-0.042	0.000	0.000	0.000	0.000
125	E	133	GLU	-1	-0.884	-0.943	70.911	4.415	4.415	0.000	0.000	0.000	0.000
126	E	134	GLU	-1	-0.861	-0.898	74.384	4.018	4.018	0.000	0.000	0.000	0.000
127	E	135	GLN	0	0.056	0.026	76.741	-0.073	-0.073	0.000	0.000	0.000	0.000
128	E	136	ARG	1	0.913	0.978	75.024	-4.223	-4.223	0.000	0.000	0.000	0.000
129	E	137	GLY	0	0.034	0.005	76.869	-0.017	-0.017	0.000	0.000	0.000	0.000
130	E	138	THR	0	0.019	-0.009	77.442	-0.033	-0.033	0.000	0.000	0.000	0.000
131	E	139	PHE	0	-0.024	-0.016	80.153	-0.043	-0.043	0.000	0.000	0.000	0.000
132	E	140	ARG	1	0.816	0.900	76.667	-4.106	-4.106	0.000	0.000	0.000	0.000
133	E	141	ASP	-1	-0.820	-0.904	79.720	3.922	3.922	0.000	0.000	0.000	0.000
134	E	142	LEU	0	0.031	0.024	81.917	-0.035	-0.035	0.000	0.000	0.000	0.000
135	E	143	LEU	0	-0.026	-0.023	81.620	-0.026	-0.026	0.000	0.000	0.000	0.000
136	E	144	LYS	1	0.760	0.898	80.497	-3.915	-3.915	0.000	0.000	0.000	0.000
137	E	145	ASN	0	-0.044	-0.017	83.345	-0.017	-0.017	0.000	0.000	0.000	0.000
138	E	146	ASP	-1	-0.892	-0.944	86.894	3.691	3.691	0.000	0.000	0.000	0.000
139	E	147	PRO	0	0.015	0.008	87.547	-0.034	-0.034	0.000	0.000	0.000	0.000
140	E	148	ASP	-1	-0.898	-0.971	90.530	3.454	3.454	0.000	0.000	0.000	0.000
141	E	149	VAL	0	0.061	0.029	90.205	-0.048	-0.048	0.000	0.000	0.000	0.000
142	E	150	ALA	0	0.055	0.039	92.269	-0.031	-0.031	0.000	0.000	0.000	0.000
143	E	151	GLN	0	0.002	-0.008	93.900	-0.024	-0.024	0.000	0.000	0.000	0.000
144	E	152	LYS	1	0.884	0.937	96.063	-3.410	-3.410	0.000	0.000	0.000	0.000
145	E	153	LEU	0	0.025	0.020	93.667	-0.028	-0.028	0.000	0.000	0.000	0.000
146	E	154	ARG	1	0.920	0.951	95.151	-3.384	-3.384	0.000	0.000	0.000	0.000
147	E	155	ASN	0	0.006	0.007	99.742	-0.037	-0.037	0.000	0.000	0.000	0.000
148	E	156	TYR	0	0.042	0.031	99.215	-0.025	-0.025	0.000	0.000	0.000	0.000
149	E	157	THR	0	-0.019	-0.015	100.072	-0.015	-0.015	0.000	0.000	0.000	0.000
150	E	158	ASP	-1	-0.899	-0.936	102.028	3.020	3.020	0.000	0.000	0.000	0.000
151	E	159	ILE	0	0.023	-0.006	104.895	-0.033	-0.033	0.000	0.000	0.000	0.000
152	E	160	ALA	0	-0.022	-0.005	103.387	-0.021	-0.021	0.000	0.000	0.000	0.000
153	E	161	LYS	1	0.781	0.888	105.446	-3.037	-3.037	0.000	0.000	0.000	0.000
154	E	162	GLN	0	-0.121	-0.059	107.122	-0.027	-0.027	0.000	0.000	0.000	0.000
155	E	163	GLU	-1	-0.929	-0.934	109.299	2.900	2.900	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:9:ASP)