FMO DATABASE

FMODB ID: 85N3Y

Calculation Name: 4P6Z-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P6Z

Chain ID: S

ChEMBL ID:

UniProt ID: Q10567

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	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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1534184.133817
FMO2-HF: Nuclear repulsion	1471262.044564
FMO2-HF: Total energy	-62922.089253
FMO2-MP2: Total energy	-63100.551173

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(S:1:MET)

Summations of interaction energy for fragment #1(S:1:MET)

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.
-35.49	-24.504	19.495	-11.243	-19.236	-0.069

Interaction energy analysis for fragmet #1(S:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.043

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	S	3	ARG	1	0.879	0.912	2.716	-12.417	-8.494	5.045	-3.264	-5.704	0.016
4	S	4	PHE	0	-0.042	-0.031	3.794	-1.921	-2.622	0.001	1.038	-0.337	0.001
5	S	5	MET	0	0.033	0.024	6.580	-0.237	-0.237	0.000	0.000	0.000	0.000
6	S	6	LEU	0	-0.052	-0.021	9.656	-0.016	-0.016	0.000	0.000	0.000	0.000
7	S	7	LEU	0	0.050	0.034	13.175	-0.067	-0.067	0.000	0.000	0.000	0.000
8	S	8	PHE	0	0.059	0.015	15.823	0.022	0.022	0.000	0.000	0.000	0.000
9	S	9	SER	0	0.041	0.020	19.504	-0.016	-0.016	0.000	0.000	0.000	0.000
10	S	10	ARG	1	0.904	0.933	23.026	-0.005	-0.005	0.000	0.000	0.000	0.000
11	S	11	ARG	1	0.920	0.956	25.350	0.003	0.003	0.000	0.000	0.000	0.000
12	S	12	GLY	0	0.056	0.026	22.463	0.009	0.009	0.000	0.000	0.000	0.000
13	S	13	LYS	1	0.815	0.904	22.912	-0.059	-0.059	0.000	0.000	0.000	0.000
14	S	14	LEU	0	0.016	0.007	15.547	-0.015	-0.015	0.000	0.000	0.000	0.000
15	S	15	ARG	1	0.794	0.880	18.777	-0.008	-0.008	0.000	0.000	0.000	0.000
16	S	16	LEU	0	0.070	0.045	13.963	-0.011	-0.011	0.000	0.000	0.000	0.000
17	S	17	GLN	0	-0.016	0.007	12.316	0.103	0.103	0.000	0.000	0.000	0.000
18	S	18	LYS	1	0.882	0.941	8.003	0.310	0.310	0.000	0.000	0.000	0.000
19	S	19	TRP	0	-0.028	-0.047	6.727	0.234	0.234	0.000	0.000	0.000	0.000
20	S	20	TYR	0	0.027	0.021	2.432	-0.800	-0.277	0.742	-0.311	-0.953	0.001
21	S	21	LEU	0	0.051	0.033	2.506	-2.243	-0.948	0.996	-0.632	-1.658	-0.005
22	S	22	ALA	0	0.012	0.012	4.171	-0.197	-0.128	0.001	-0.022	-0.048	0.000
23	S	23	THR	0	-0.036	-0.033	7.832	0.265	0.265	0.000	0.000	0.000	0.000
24	S	24	SER	0	0.045	0.026	10.030	-0.111	-0.111	0.000	0.000	0.000	0.000
25	S	25	ASP	-1	-0.734	-0.861	13.555	0.295	0.295	0.000	0.000	0.000	0.000
26	S	26	LYS	1	1.002	0.997	15.266	-0.286	-0.286	0.000	0.000	0.000	0.000
27	S	27	GLU	-1	-0.788	-0.887	13.005	0.594	0.594	0.000	0.000	0.000	0.000
28	S	28	ARG	1	0.942	0.987	8.128	-0.476	-0.476	0.000	0.000	0.000	0.000
29	S	29	LYS	1	0.871	0.916	12.882	-0.237	-0.237	0.000	0.000	0.000	0.000
30	S	30	LYS	1	0.788	0.888	16.288	-0.551	-0.551	0.000	0.000	0.000	0.000
31	S	31	MET	0	0.006	0.001	10.154	0.011	0.011	0.000	0.000	0.000	0.000
32	S	32	VAL	0	0.053	0.034	13.417	-0.037	-0.037	0.000	0.000	0.000	0.000
33	S	33	ARG	1	0.913	0.948	15.383	-0.284	-0.284	0.000	0.000	0.000	0.000
34	S	34	GLU	-1	-0.838	-0.892	16.526	0.493	0.493	0.000	0.000	0.000	0.000
35	S	35	LEU	0	0.042	0.020	12.824	-0.059	-0.059	0.000	0.000	0.000	0.000
36	S	36	MET	0	-0.017	0.017	16.609	-0.070	-0.070	0.000	0.000	0.000	0.000
37	S	37	GLN	0	-0.018	-0.009	18.951	-0.045	-0.045	0.000	0.000	0.000	0.000
38	S	38	VAL	0	-0.011	-0.011	18.918	-0.035	-0.035	0.000	0.000	0.000	0.000
39	S	39	VAL	0	0.005	-0.002	16.941	-0.038	-0.038	0.000	0.000	0.000	0.000
40	S	40	LEU	0	-0.051	-0.012	20.190	-0.038	-0.038	0.000	0.000	0.000	0.000
41	S	41	ALA	0	-0.010	0.008	23.296	-0.021	-0.021	0.000	0.000	0.000	0.000
42	S	42	ARG	1	0.843	0.926	18.984	-0.020	-0.020	0.000	0.000	0.000	0.000
43	S	43	LYS	1	0.993	0.986	24.245	0.002	0.002	0.000	0.000	0.000	0.000
44	S	44	PRO	0	0.013	-0.018	24.990	-0.009	-0.009	0.000	0.000	0.000	0.000
45	S	45	LYS	1	0.910	0.963	24.720	0.089	0.089	0.000	0.000	0.000	0.000
46	S	46	MET	0	-0.024	0.007	21.980	-0.006	-0.006	0.000	0.000	0.000	0.000
47	S	47	CYS	0	0.030	0.032	17.995	-0.027	-0.027	0.000	0.000	0.000	0.000
48	S	48	SER	0	0.024	0.024	16.466	0.030	0.030	0.000	0.000	0.000	0.000
49	S	49	PHE	0	0.066	0.008	13.052	-0.042	-0.042	0.000	0.000	0.000	0.000
50	S	50	LEU	0	-0.093	-0.042	13.865	0.031	0.031	0.000	0.000	0.000	0.000
51	S	51	GLU	-1	-0.879	-0.932	13.377	0.106	0.106	0.000	0.000	0.000	0.000
52	S	52	TRP	0	-0.061	-0.055	10.419	0.017	0.017	0.000	0.000	0.000	0.000
53	S	53	ARG	1	0.794	0.886	12.838	-0.659	-0.659	0.000	0.000	0.000	0.000
54	S	54	ASP	-1	-0.884	-0.942	12.186	0.885	0.885	0.000	0.000	0.000	0.000
55	S	55	LEU	0	-0.025	-0.003	6.929	0.432	0.432	0.000	0.000	0.000	0.000
56	S	56	LYS	1	0.812	0.912	7.389	0.698	0.698	0.000	0.000	0.000	0.000
57	S	57	VAL	0	-0.020	-0.016	8.915	0.033	0.033	0.000	0.000	0.000	0.000
58	S	58	VAL	0	0.015	0.019	9.615	-0.031	-0.031	0.000	0.000	0.000	0.000
59	S	59	TYR	0	-0.014	-0.008	12.225	0.077	0.077	0.000	0.000	0.000	0.000
60	S	60	LYS	1	0.940	0.977	15.405	0.258	0.258	0.000	0.000	0.000	0.000
61	S	61	ARG	1	0.852	0.918	17.843	0.075	0.075	0.000	0.000	0.000	0.000
62	S	62	TYR	0	0.017	-0.001	17.712	-0.008	-0.008	0.000	0.000	0.000	0.000
63	S	63	ALA	0	0.064	0.027	22.679	0.015	0.015	0.000	0.000	0.000	0.000
64	S	64	SER	0	-0.056	-0.047	26.244	0.006	0.006	0.000	0.000	0.000	0.000
65	S	65	LEU	0	0.020	0.015	20.084	0.024	0.024	0.000	0.000	0.000	0.000
66	S	66	TYR	0	-0.024	-0.018	19.128	-0.024	-0.024	0.000	0.000	0.000	0.000
67	S	67	PHE	0	0.048	0.030	15.178	0.035	0.035	0.000	0.000	0.000	0.000
68	S	68	CYS	0	-0.020	-0.024	13.074	-0.036	-0.036	0.000	0.000	0.000	0.000
69	S	69	CYS	0	0.000	0.006	8.507	0.090	0.090	0.000	0.000	0.000	0.000
70	S	70	ALA	0	-0.006	-0.004	7.749	-0.162	-0.162	0.000	0.000	0.000	0.000
71	S	71	ILE	0	-0.021	-0.002	3.494	1.332	1.756	0.004	-0.114	-0.314	0.000
72	S	72	GLU	-1	-0.720	-0.841	2.821	6.546	8.839	0.312	-0.697	-1.908	-0.002
73	S	73	GLY	0	-0.002	-0.020	4.528	-0.835	-0.787	-0.001	-0.002	-0.045	0.000
74	S	74	GLN	0	-0.052	-0.020	4.385	-0.308	-0.151	-0.001	-0.008	-0.149	0.000
75	S	75	ASP	-1	-0.788	-0.893	1.998	-16.200	-17.371	9.175	-4.276	-3.729	-0.050
76	S	76	ASN	0	-0.007	-0.003	5.191	0.884	0.911	-0.001	-0.001	-0.024	0.000
77	S	77	GLU	-1	-0.759	-0.888	7.929	-0.944	-0.944	0.000	0.000	0.000	0.000
78	S	78	LEU	0	0.006	0.008	10.065	0.012	0.012	0.000	0.000	0.000	0.000
79	S	79	ILE	0	0.051	0.023	7.724	0.080	0.080	0.000	0.000	0.000	0.000
80	S	80	THR	0	0.004	-0.012	6.094	0.036	0.036	0.000	0.000	0.000	0.000
81	S	81	LEU	0	-0.048	-0.035	8.917	0.199	0.199	0.000	0.000	0.000	0.000
82	S	82	GLU	-1	-0.933	-0.974	12.345	-0.416	-0.416	0.000	0.000	0.000	0.000
83	S	83	LEU	0	-0.003	0.019	7.174	0.084	0.084	0.000	0.000	0.000	0.000
84	S	84	ILE	0	-0.008	-0.015	11.451	0.127	0.127	0.000	0.000	0.000	0.000
85	S	85	HIS	0	-0.003	0.015	13.394	0.085	0.085	0.000	0.000	0.000	0.000
86	S	86	ARG	1	0.935	0.967	14.049	0.544	0.544	0.000	0.000	0.000	0.000
87	S	87	TYR	0	0.010	-0.011	13.553	0.064	0.064	0.000	0.000	0.000	0.000
88	S	88	VAL	0	-0.008	-0.018	15.587	0.053	0.053	0.000	0.000	0.000	0.000
89	S	89	GLU	-1	-0.826	-0.889	18.591	-0.306	-0.306	0.000	0.000	0.000	0.000
90	S	90	LEU	0	-0.045	-0.009	15.617	0.030	0.030	0.000	0.000	0.000	0.000
91	S	91	LEU	0	0.000	0.000	18.130	0.032	0.032	0.000	0.000	0.000	0.000
92	S	92	ASP	-1	-0.905	-0.959	21.181	-0.156	-0.156	0.000	0.000	0.000	0.000
93	S	93	LYS	1	0.855	0.925	23.213	0.195	0.195	0.000	0.000	0.000	0.000
94	S	94	TYR	0	-0.097	-0.072	22.868	0.014	0.014	0.000	0.000	0.000	0.000
95	S	95	PHE	0	0.013	-0.008	21.763	0.011	0.011	0.000	0.000	0.000	0.000
96	S	96	GLY	0	-0.016	0.010	26.663	0.012	0.012	0.000	0.000	0.000	0.000
97	S	97	SER	0	-0.053	-0.025	28.123	0.012	0.012	0.000	0.000	0.000	0.000
98	S	98	VAL	0	-0.034	0.015	22.931	0.010	0.010	0.000	0.000	0.000	0.000
99	S	99	CYS	0	-0.070	-0.044	26.331	0.007	0.007	0.000	0.000	0.000	0.000
100	S	100	GLU	-1	-0.770	-0.884	23.589	-0.027	-0.027	0.000	0.000	0.000	0.000
101	S	101	LEU	0	0.012	-0.007	24.825	0.005	0.005	0.000	0.000	0.000	0.000
102	S	102	ASP	-1	-0.723	-0.844	25.408	-0.094	-0.094	0.000	0.000	0.000	0.000
103	S	103	ILE	0	-0.004	-0.009	19.915	0.002	0.002	0.000	0.000	0.000	0.000
104	S	104	ILE	0	-0.147	-0.081	22.324	0.012	0.012	0.000	0.000	0.000	0.000
105	S	105	PHE	0	-0.019	-0.015	24.469	0.011	0.011	0.000	0.000	0.000	0.000
106	S	106	ASN	0	-0.011	0.018	23.948	0.002	0.002	0.000	0.000	0.000	0.000
107	S	107	PHE	0	0.043	0.021	19.016	-0.014	-0.014	0.000	0.000	0.000	0.000
108	S	108	GLU	-1	-0.815	-0.896	18.747	-0.110	-0.110	0.000	0.000	0.000	0.000
109	S	109	LYS	1	0.954	0.964	18.984	0.078	0.078	0.000	0.000	0.000	0.000
110	S	110	ALA	0	-0.027	-0.010	17.948	-0.030	-0.030	0.000	0.000	0.000	0.000
111	S	111	TYR	0	-0.057	-0.060	12.648	-0.025	-0.025	0.000	0.000	0.000	0.000
112	S	112	PHE	0	0.061	0.035	14.567	-0.047	-0.047	0.000	0.000	0.000	0.000
113	S	113	ILE	0	0.042	0.015	16.078	-0.048	-0.048	0.000	0.000	0.000	0.000
114	S	114	LEU	0	-0.094	-0.052	10.757	-0.043	-0.043	0.000	0.000	0.000	0.000
115	S	115	ASP	-1	-0.829	-0.891	11.152	-0.496	-0.496	0.000	0.000	0.000	0.000
116	S	116	GLU	-1	-0.900	-0.932	12.638	-0.429	-0.429	0.000	0.000	0.000	0.000
117	S	117	PHE	0	-0.086	-0.043	11.903	-0.035	-0.035	0.000	0.000	0.000	0.000
118	S	118	LEU	0	-0.048	-0.035	7.433	-0.126	-0.126	0.000	0.000	0.000	0.000
119	S	119	MET	0	0.077	0.020	7.647	0.224	0.224	0.000	0.000	0.000	0.000
120	S	120	GLY	0	-0.027	0.001	4.854	-0.186	-0.186	0.000	0.000	0.000	0.000
121	S	121	GLY	0	-0.051	-0.024	2.117	-3.539	-2.095	2.330	-1.797	-1.977	-0.011
122	S	122	ASP	-1	-0.897	-0.949	2.684	-5.971	-3.348	0.893	-1.150	-2.366	-0.019
123	S	123	VAL	0	-0.028	-0.030	4.681	0.380	0.412	-0.001	-0.007	-0.024	0.000
124	S	124	GLN	0	0.009	0.012	8.236	-0.075	-0.075	0.000	0.000	0.000	0.000
125	S	125	ASP	-1	-0.787	-0.876	11.081	-0.350	-0.350	0.000	0.000	0.000	0.000
126	S	126	THR	0	-0.007	-0.001	12.067	-0.029	-0.029	0.000	0.000	0.000	0.000
127	S	127	SER	0	-0.085	-0.039	14.548	0.055	0.055	0.000	0.000	0.000	0.000
128	S	128	LYS	1	0.891	0.922	17.749	0.293	0.293	0.000	0.000	0.000	0.000
129	S	129	LYS	1	0.959	0.971	19.378	0.229	0.229	0.000	0.000	0.000	0.000
130	S	130	SER	0	-0.048	-0.045	18.762	0.037	0.037	0.000	0.000	0.000	0.000
131	S	131	VAL	0	0.079	0.045	15.573	0.021	0.021	0.000	0.000	0.000	0.000
132	S	132	LEU	0	-0.047	-0.028	18.736	0.022	0.022	0.000	0.000	0.000	0.000
133	S	133	LYS	1	0.765	0.864	21.828	0.201	0.201	0.000	0.000	0.000	0.000
134	S	134	ALA	0	0.014	0.024	19.974	0.020	0.020	0.000	0.000	0.000	0.000
135	S	135	ILE	0	0.006	-0.002	18.255	0.014	0.014	0.000	0.000	0.000	0.000
136	S	136	GLU	-1	-0.828	-0.894	22.053	-0.156	-0.156	0.000	0.000	0.000	0.000
137	S	137	GLN	0	0.013	0.004	25.349	0.011	0.011	0.000	0.000	0.000	0.000
138	S	138	ALA	0	-0.015	0.003	22.362	0.013	0.013	0.000	0.000	0.000	0.000
139	S	139	ASP	-1	-0.802	-0.888	24.387	-0.149	-0.149	0.000	0.000	0.000	0.000
140	S	140	LEU	0	-0.029	-0.010	26.356	0.011	0.011	0.000	0.000	0.000	0.000
141	S	141	LEU	0	-0.036	-0.020	25.556	0.008	0.008	0.000	0.000	0.000	0.000
142	S	142	GLN	0	-0.032	-0.018	24.446	0.002	0.002	0.000	0.000	0.000	0.000
143	S	143	GLU	-1	-0.987	-0.992	27.982	-0.085	-0.085	0.000	0.000	0.000	0.000
144	S	144	GLU	-1	-0.978	-0.994	31.126	-0.077	-0.077	0.000	0.000	0.000	0.000
145	S	145	ASP	-1	-0.986	-0.993	28.964	-0.083	-0.083	0.000	0.000	0.000	0.000
146	S	146	GLU	-1	-1.056	-1.009	32.438	-0.048	-0.048	0.000	0.000	0.000	0.000
147	S	147	SER	0	-0.084	-0.032	34.357	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:1:MET)