FMO DATABASE

FMODB ID: G6Y91

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1534749.478156
FMO2-HF: Nuclear repulsion	1471828.640499
FMO2-HF: Total energy	-62920.837657
FMO2-MP2: Total energy	-63099.348746

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.
-27.229	-21.72	28.091	-14.901	-18.697	-0.08

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 : 0.051 / q_NPA : 0.040

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	0.941	0.968	2.352	-9.134	-3.740	1.816	-2.745	-4.465	0.015
4	S	4	PHE	0	-0.019	-0.021	3.392	0.220	0.157	-0.004	0.366	-0.298	0.000
5	S	5	MET	0	0.021	0.016	6.571	-0.370	-0.370	0.000	0.000	0.000	0.000
6	S	6	LEU	0	-0.055	-0.022	9.907	0.183	0.183	0.000	0.000	0.000	0.000
7	S	7	LEU	0	0.047	0.031	13.251	-0.066	-0.066	0.000	0.000	0.000	0.000
8	S	8	PHE	0	0.056	0.018	15.803	0.067	0.067	0.000	0.000	0.000	0.000
9	S	9	SER	0	0.048	0.026	19.510	-0.017	-0.017	0.000	0.000	0.000	0.000
10	S	10	ARG	1	0.939	0.970	22.940	0.214	0.214	0.000	0.000	0.000	0.000
11	S	11	ARG	1	0.904	0.938	25.200	0.148	0.148	0.000	0.000	0.000	0.000
12	S	12	GLY	0	0.033	0.023	22.401	0.020	0.020	0.000	0.000	0.000	0.000
13	S	13	LYS	1	0.868	0.941	22.957	0.135	0.135	0.000	0.000	0.000	0.000
14	S	14	LEU	0	0.035	0.012	15.832	-0.022	-0.022	0.000	0.000	0.000	0.000
15	S	15	ARG	1	0.786	0.874	18.949	0.216	0.216	0.000	0.000	0.000	0.000
16	S	16	LEU	0	0.073	0.045	14.353	0.009	0.009	0.000	0.000	0.000	0.000
17	S	17	GLN	0	-0.025	-0.007	12.636	-0.010	-0.010	0.000	0.000	0.000	0.000
18	S	18	LYS	1	0.917	0.976	8.400	0.459	0.459	0.000	0.000	0.000	0.000
19	S	19	TRP	0	-0.029	-0.042	7.141	-0.082	-0.082	0.000	0.000	0.000	0.000
20	S	20	TYR	0	0.020	0.017	2.941	-0.309	0.248	0.079	-0.109	-0.527	0.000
21	S	21	LEU	0	0.039	0.025	2.703	-2.062	-0.579	0.736	-0.635	-1.583	-0.003
22	S	22	ALA	0	-0.006	0.008	4.358	-0.346	-0.282	0.000	-0.019	-0.045	0.000
23	S	23	THR	0	-0.013	-0.023	7.692	0.089	0.089	0.000	0.000	0.000	0.000
24	S	24	SER	0	0.036	0.020	10.145	-0.090	-0.090	0.000	0.000	0.000	0.000
25	S	25	ASP	-1	-0.819	-0.920	13.949	0.083	0.083	0.000	0.000	0.000	0.000
26	S	26	LYS	1	0.997	0.985	15.758	-0.193	-0.193	0.000	0.000	0.000	0.000
27	S	27	GLU	-1	-0.888	-0.961	13.168	0.261	0.261	0.000	0.000	0.000	0.000
28	S	28	ARG	1	0.972	1.004	9.771	-0.254	-0.254	0.000	0.000	0.000	0.000
29	S	29	LYS	1	0.958	0.984	13.141	-0.101	-0.101	0.000	0.000	0.000	0.000
30	S	30	LYS	1	0.855	0.940	16.333	-0.238	-0.238	0.000	0.000	0.000	0.000
31	S	31	MET	0	0.008	0.003	9.773	-0.047	-0.047	0.000	0.000	0.000	0.000
32	S	32	VAL	0	0.058	0.035	13.488	-0.058	-0.058	0.000	0.000	0.000	0.000
33	S	33	ARG	1	0.911	0.950	15.382	-0.028	-0.028	0.000	0.000	0.000	0.000
34	S	34	GLU	-1	-0.831	-0.894	16.583	0.017	0.017	0.000	0.000	0.000	0.000
35	S	35	LEU	0	0.035	0.019	12.393	-0.026	-0.026	0.000	0.000	0.000	0.000
36	S	36	MET	0	-0.004	0.000	16.319	-0.043	-0.043	0.000	0.000	0.000	0.000
37	S	37	GLN	0	-0.011	-0.002	18.749	-0.011	-0.011	0.000	0.000	0.000	0.000
38	S	38	VAL	0	-0.022	-0.016	18.523	-0.011	-0.011	0.000	0.000	0.000	0.000
39	S	39	VAL	0	0.002	-0.003	16.612	-0.012	-0.012	0.000	0.000	0.000	0.000
40	S	40	LEU	0	-0.065	-0.022	19.871	-0.004	-0.004	0.000	0.000	0.000	0.000
41	S	41	ALA	0	-0.014	0.001	22.964	0.009	0.009	0.000	0.000	0.000	0.000
42	S	42	ARG	1	0.836	0.930	19.668	0.379	0.379	0.000	0.000	0.000	0.000
43	S	43	LYS	1	0.985	0.988	24.171	0.204	0.204	0.000	0.000	0.000	0.000
44	S	44	PRO	0	0.008	-0.020	24.901	-0.022	-0.022	0.000	0.000	0.000	0.000
45	S	45	LYS	1	0.912	0.964	24.617	0.264	0.264	0.000	0.000	0.000	0.000
46	S	46	MET	0	-0.027	0.002	21.812	0.002	0.002	0.000	0.000	0.000	0.000
47	S	47	CYS	0	0.029	0.039	17.764	-0.030	-0.030	0.000	0.000	0.000	0.000
48	S	48	SER	0	0.020	0.010	16.372	0.029	0.029	0.000	0.000	0.000	0.000
49	S	49	PHE	0	0.067	0.012	12.739	-0.083	-0.083	0.000	0.000	0.000	0.000
50	S	50	LEU	0	-0.082	-0.040	13.798	0.123	0.123	0.000	0.000	0.000	0.000
51	S	51	GLU	-1	-0.882	-0.939	13.329	-0.424	-0.424	0.000	0.000	0.000	0.000
52	S	52	TRP	0	-0.080	-0.070	10.332	0.093	0.093	0.000	0.000	0.000	0.000
53	S	53	ARG	1	0.844	0.932	12.554	-0.212	-0.212	0.000	0.000	0.000	0.000
54	S	54	ASP	-1	-0.892	-0.948	11.997	0.325	0.325	0.000	0.000	0.000	0.000
55	S	55	LEU	0	-0.027	-0.011	7.042	0.210	0.210	0.000	0.000	0.000	0.000
56	S	56	LYS	1	0.856	0.961	7.785	1.666	1.666	0.000	0.000	0.000	0.000
57	S	57	VAL	0	-0.023	-0.011	8.863	-0.233	-0.233	0.000	0.000	0.000	0.000
58	S	58	VAL	0	0.024	0.025	9.318	0.168	0.168	0.000	0.000	0.000	0.000
59	S	59	TYR	0	-0.004	-0.005	12.127	0.053	0.053	0.000	0.000	0.000	0.000
60	S	60	LYS	1	0.967	0.985	15.303	0.574	0.574	0.000	0.000	0.000	0.000
61	S	61	ARG	1	0.864	0.930	17.925	0.287	0.287	0.000	0.000	0.000	0.000
62	S	62	TYR	0	-0.011	-0.012	17.780	0.004	0.004	0.000	0.000	0.000	0.000
63	S	63	ALA	0	0.058	0.026	22.719	0.019	0.019	0.000	0.000	0.000	0.000
64	S	64	SER	0	-0.078	-0.067	26.128	0.000	0.000	0.000	0.000	0.000	0.000
65	S	65	LEU	0	0.023	0.017	20.257	0.018	0.018	0.000	0.000	0.000	0.000
66	S	66	TYR	0	-0.039	-0.031	18.649	-0.005	-0.005	0.000	0.000	0.000	0.000
67	S	67	PHE	0	0.056	0.032	15.103	0.025	0.025	0.000	0.000	0.000	0.000
68	S	68	CYS	0	-0.041	-0.031	13.615	-0.034	-0.034	0.000	0.000	0.000	0.000
69	S	69	CYS	0	0.021	0.014	8.430	0.104	0.104	0.000	0.000	0.000	0.000
70	S	70	ALA	0	0.003	0.003	7.390	0.064	0.064	0.000	0.000	0.000	0.000
71	S	71	ILE	0	-0.014	0.001	3.617	-0.001	0.297	0.001	-0.106	-0.194	0.000
72	S	72	GLU	-1	-0.821	-0.921	2.771	6.285	9.794	1.078	-1.461	-3.125	-0.014
73	S	73	GLY	0	-0.012	-0.030	4.546	-0.524	-0.453	-0.001	-0.005	-0.066	0.000
74	S	74	GLN	0	-0.030	-0.007	4.218	-0.384	-0.173	-0.001	-0.021	-0.188	0.000
75	S	75	ASP	-1	-0.812	-0.894	1.728	-14.656	-25.324	21.947	-7.219	-4.060	-0.053
76	S	76	ASN	0	-0.024	-0.022	5.125	0.884	0.909	-0.001	-0.002	-0.021	0.000
77	S	77	GLU	-1	-0.739	-0.895	8.053	-1.650	-1.650	0.000	0.000	0.000	0.000
78	S	78	LEU	0	0.011	0.035	10.054	-0.003	-0.003	0.000	0.000	0.000	0.000
79	S	79	ILE	0	0.036	0.026	7.652	0.111	0.111	0.000	0.000	0.000	0.000
80	S	80	THR	0	-0.014	-0.050	6.295	0.040	0.040	0.000	0.000	0.000	0.000
81	S	81	LEU	0	-0.039	-0.036	9.038	0.203	0.203	0.000	0.000	0.000	0.000
82	S	82	GLU	-1	-0.923	-0.970	12.353	-0.637	-0.637	0.000	0.000	0.000	0.000
83	S	83	LEU	0	-0.019	0.020	7.428	0.105	0.105	0.000	0.000	0.000	0.000
84	S	84	ILE	0	-0.016	-0.019	11.576	0.161	0.161	0.000	0.000	0.000	0.000
85	S	85	HIS	0	0.037	0.035	13.427	0.103	0.103	0.000	0.000	0.000	0.000
86	S	86	ARG	1	0.941	0.987	13.999	0.706	0.706	0.000	0.000	0.000	0.000
87	S	87	TYR	0	-0.006	-0.021	13.558	0.071	0.071	0.000	0.000	0.000	0.000
88	S	88	VAL	0	0.004	-0.015	15.575	0.081	0.081	0.000	0.000	0.000	0.000
89	S	89	GLU	-1	-0.929	-0.968	18.602	-0.416	-0.416	0.000	0.000	0.000	0.000
90	S	90	LEU	0	-0.061	-0.022	15.565	0.049	0.049	0.000	0.000	0.000	0.000
91	S	91	LEU	0	-0.003	0.001	18.405	0.047	0.047	0.000	0.000	0.000	0.000
92	S	92	ASP	-1	-0.936	-0.977	21.167	-0.254	-0.254	0.000	0.000	0.000	0.000
93	S	93	LYS	1	0.871	0.937	23.202	0.266	0.266	0.000	0.000	0.000	0.000
94	S	94	TYR	0	-0.099	-0.071	22.859	0.014	0.014	0.000	0.000	0.000	0.000
95	S	95	PHE	0	-0.001	-0.010	22.452	0.016	0.016	0.000	0.000	0.000	0.000
96	S	96	GLY	0	0.000	0.018	26.652	0.018	0.018	0.000	0.000	0.000	0.000
97	S	97	SER	0	-0.045	-0.017	28.133	0.011	0.011	0.000	0.000	0.000	0.000
98	S	98	VAL	0	-0.027	0.019	23.026	0.008	0.008	0.000	0.000	0.000	0.000
99	S	99	CYS	0	-0.043	-0.005	26.315	-0.003	-0.003	0.000	0.000	0.000	0.000
100	S	100	GLU	-1	-0.780	-0.890	23.962	-0.228	-0.228	0.000	0.000	0.000	0.000
101	S	101	LEU	0	0.013	-0.004	25.487	0.001	0.001	0.000	0.000	0.000	0.000
102	S	102	ASP	-1	-0.744	-0.877	26.104	-0.193	-0.193	0.000	0.000	0.000	0.000
103	S	103	ILE	0	0.003	0.010	20.639	0.002	0.002	0.000	0.000	0.000	0.000
104	S	104	ILE	0	-0.158	-0.087	23.077	0.009	0.009	0.000	0.000	0.000	0.000
105	S	105	PHE	0	-0.028	-0.020	25.142	0.014	0.014	0.000	0.000	0.000	0.000
106	S	106	ASN	0	-0.013	-0.005	24.673	0.022	0.022	0.000	0.000	0.000	0.000
107	S	107	PHE	0	0.009	0.007	19.397	-0.017	-0.017	0.000	0.000	0.000	0.000
108	S	108	GLU	-1	-0.832	-0.928	19.432	-0.178	-0.178	0.000	0.000	0.000	0.000
109	S	109	LYS	1	0.993	1.005	19.626	0.136	0.136	0.000	0.000	0.000	0.000
110	S	110	ALA	0	-0.023	-0.005	18.683	-0.029	-0.029	0.000	0.000	0.000	0.000
111	S	111	TYR	0	-0.051	-0.059	13.236	-0.051	-0.051	0.000	0.000	0.000	0.000
112	S	112	PHE	0	0.067	0.045	15.269	-0.034	-0.034	0.000	0.000	0.000	0.000
113	S	113	ILE	0	0.039	0.012	16.799	-0.034	-0.034	0.000	0.000	0.000	0.000
114	S	114	LEU	0	-0.114	-0.067	11.536	-0.063	-0.063	0.000	0.000	0.000	0.000
115	S	115	ASP	-1	-0.855	-0.921	12.081	-0.500	-0.500	0.000	0.000	0.000	0.000
116	S	116	GLU	-1	-0.903	-0.923	13.339	-0.262	-0.262	0.000	0.000	0.000	0.000
117	S	117	PHE	0	-0.069	-0.037	11.487	-0.057	-0.057	0.000	0.000	0.000	0.000
118	S	118	LEU	0	-0.086	-0.061	7.253	-0.183	-0.183	0.000	0.000	0.000	0.000
119	S	119	MET	0	0.093	0.028	7.728	0.233	0.233	0.000	0.000	0.000	0.000
120	S	120	GLY	0	-0.033	0.004	5.007	-0.146	-0.146	0.000	0.000	0.000	0.000
121	S	121	GLY	0	-0.048	-0.020	2.173	-2.622	-0.909	1.493	-1.541	-1.666	-0.006
122	S	122	ASP	-1	-0.894	-0.951	2.670	-6.414	-3.526	0.949	-1.397	-2.441	-0.019
123	S	123	VAL	0	-0.022	-0.024	4.680	0.395	0.422	-0.001	-0.007	-0.018	0.000
124	S	124	GLN	0	0.016	0.017	8.236	0.090	0.090	0.000	0.000	0.000	0.000
125	S	125	ASP	-1	-0.759	-0.858	11.082	-0.285	-0.285	0.000	0.000	0.000	0.000
126	S	126	THR	0	-0.002	0.007	12.136	-0.057	-0.057	0.000	0.000	0.000	0.000
127	S	127	SER	0	-0.079	-0.036	14.552	0.030	0.030	0.000	0.000	0.000	0.000
128	S	128	LYS	1	0.982	0.980	17.748	0.348	0.348	0.000	0.000	0.000	0.000
129	S	129	LYS	1	0.947	0.962	19.375	0.228	0.228	0.000	0.000	0.000	0.000
130	S	130	SER	0	-0.081	-0.070	18.519	0.035	0.035	0.000	0.000	0.000	0.000
131	S	131	VAL	0	0.099	0.056	15.721	0.023	0.023	0.000	0.000	0.000	0.000
132	S	132	LEU	0	-0.048	-0.036	18.731	0.023	0.023	0.000	0.000	0.000	0.000
133	S	133	LYS	1	0.916	0.976	21.821	0.175	0.175	0.000	0.000	0.000	0.000
134	S	134	ALA	0	0.025	0.024	19.975	0.022	0.022	0.000	0.000	0.000	0.000
135	S	135	ILE	0	-0.006	-0.004	18.857	0.012	0.012	0.000	0.000	0.000	0.000
136	S	136	GLU	-1	-0.952	-0.963	22.380	-0.147	-0.147	0.000	0.000	0.000	0.000
137	S	137	GLN	0	-0.013	-0.029	25.550	0.006	0.006	0.000	0.000	0.000	0.000
138	S	138	ALA	0	-0.013	0.005	22.948	0.016	0.016	0.000	0.000	0.000	0.000
139	S	139	ASP	-1	-0.790	-0.893	24.888	-0.167	-0.167	0.000	0.000	0.000	0.000
140	S	140	LEU	0	-0.018	-0.009	26.987	0.011	0.011	0.000	0.000	0.000	0.000
141	S	141	LEU	0	-0.037	-0.016	26.059	0.010	0.010	0.000	0.000	0.000	0.000
142	S	142	GLN	0	-0.035	-0.014	25.161	-0.001	-0.001	0.000	0.000	0.000	0.000
143	S	143	GLU	-1	-1.004	-1.010	28.469	-0.083	-0.083	0.000	0.000	0.000	0.000
144	S	144	GLU	-1	-0.973	-0.986	31.653	-0.055	-0.055	0.000	0.000	0.000	0.000
145	S	145	ASP	-1	-0.990	-0.994	29.415	-0.041	-0.041	0.000	0.000	0.000	0.000
146	S	146	GLU	-1	-1.060	-1.009	32.823	-0.045	-0.045	0.000	0.000	0.000	0.000
147	S	147	SER	0	-0.080	-0.032	34.795	0.007	0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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