FMO DATABASE

FMODB ID: 85M6Y

Calculation Name: 5HT6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HT6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IZD2

Base Structure: X-ray

Registration Date: 2023-09-19

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107157.145777
FMO2-HF: Nuclear repulsion	1056946.542506
FMO2-HF: Total energy	-50210.603271
FMO2-MP2: Total energy	-50358.272121

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:24:LEU)

Summations of interaction energy for fragment #1(A:24:LEU)

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.
-2.181	2.884	5.689	-4.193	-6.563	-0.007

Interaction energy analysis for fragmet #1(A:24:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.020

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	A	26	LYS	1	0.971	0.955	3.288	-1.881	0.896	0.038	-1.427	-1.388	0.000
4	A	27	PRO	0	-0.013	0.022	6.015	0.067	0.067	0.000	0.000	0.000	0.000
5	A	28	PRO	0	-0.009	0.006	9.786	0.005	0.005	0.000	0.000	0.000	0.000
6	A	37	LYS	1	1.003	1.001	17.487	-0.071	-0.071	0.000	0.000	0.000	0.000
7	A	38	LYS	1	0.943	0.960	13.896	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	39	ILE	0	0.017	0.017	12.933	0.023	0.023	0.000	0.000	0.000	0.000
9	A	40	LEU	0	0.003	0.009	7.375	-0.084	-0.084	0.000	0.000	0.000	0.000
10	A	41	LYS	1	0.921	0.967	8.495	0.187	0.187	0.000	0.000	0.000	0.000
11	A	42	SER	0	0.049	0.017	4.762	-0.269	-0.194	-0.001	-0.025	-0.049	0.000
12	A	43	ALA	0	-0.032	-0.019	2.376	-1.002	0.134	1.336	-0.855	-1.618	0.001
13	A	44	LYS	1	0.885	0.924	2.861	0.293	1.261	0.094	-0.202	-0.861	0.000
14	A	45	ASP	-1	-0.767	-0.898	4.760	-0.653	-0.597	-0.001	-0.007	-0.048	0.000
15	A	46	LEU	0	-0.053	-0.009	1.891	-0.380	-1.317	4.213	-1.424	-1.852	-0.009
16	A	47	PRO	0	0.047	0.033	5.554	0.075	0.075	0.000	0.000	0.000	0.000
17	A	48	PRO	0	0.019	0.009	8.179	0.176	0.176	0.000	0.000	0.000	0.000
18	A	49	ASP	-1	-0.842	-0.888	10.644	0.352	0.352	0.000	0.000	0.000	0.000
19	A	50	ALA	0	-0.023	-0.016	5.611	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	51	LEU	0	-0.001	-0.002	7.001	0.403	0.403	0.000	0.000	0.000	0.000
21	A	52	ILE	0	-0.056	-0.024	3.979	0.366	1.034	0.010	-0.196	-0.482	0.001
22	A	53	ILE	0	-0.045	-0.038	4.109	-0.132	0.190	0.000	-0.057	-0.265	0.000
23	A	54	GLU	-1	-0.786	-0.873	6.754	0.217	0.217	0.000	0.000	0.000	0.000
24	A	55	TYR	0	-0.052	-0.036	10.369	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	56	ARG	1	0.921	0.970	12.141	-0.317	-0.317	0.000	0.000	0.000	0.000
26	A	57	GLY	0	0.036	-0.003	14.767	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	58	LYS	1	0.915	0.962	18.193	-0.105	-0.105	0.000	0.000	0.000	0.000
28	A	59	PHE	0	0.028	0.013	17.979	0.003	0.003	0.000	0.000	0.000	0.000
29	A	60	MET	0	-0.076	-0.014	23.005	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	61	LEU	0	0.073	0.027	26.002	0.012	0.012	0.000	0.000	0.000	0.000
31	A	62	ARG	1	0.909	0.946	28.510	-0.099	-0.099	0.000	0.000	0.000	0.000
32	A	63	GLU	-1	-0.886	-0.944	30.082	0.072	0.072	0.000	0.000	0.000	0.000
33	A	64	GLN	0	0.087	0.048	29.235	0.004	0.004	0.000	0.000	0.000	0.000
34	A	65	PHE	0	-0.060	-0.045	26.507	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	66	GLU	-1	-0.862	-0.960	30.086	0.080	0.080	0.000	0.000	0.000	0.000
36	A	67	ALA	0	-0.009	0.016	33.486	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	68	ASN	0	-0.090	-0.056	29.466	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	69	GLY	0	0.008	0.014	33.118	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	70	TYR	0	-0.115	-0.045	29.452	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	71	PHE	0	0.063	0.007	31.644	0.000	0.000	0.000	0.000	0.000	0.000
41	A	72	PHE	0	0.060	0.003	26.429	0.007	0.007	0.000	0.000	0.000	0.000
42	A	73	LYS	1	0.928	0.979	25.760	-0.146	-0.146	0.000	0.000	0.000	0.000
43	A	74	ARG	1	1.001	1.021	27.808	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	75	PRO	0	0.012	0.003	25.137	0.007	0.007	0.000	0.000	0.000	0.000
45	A	76	TYR	0	-0.013	0.010	25.249	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	77	PRO	0	0.017	-0.012	22.067	0.014	0.014	0.000	0.000	0.000	0.000
47	A	78	PHE	0	-0.042	-0.030	17.930	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	79	VAL	0	0.019	0.034	19.417	0.011	0.011	0.000	0.000	0.000	0.000
49	A	80	LEU	0	-0.048	-0.006	15.954	0.005	0.005	0.000	0.000	0.000	0.000
50	A	81	PHE	0	-0.018	-0.003	19.741	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	82	TYR	0	-0.027	-0.071	18.801	0.025	0.025	0.000	0.000	0.000	0.000
52	A	83	SER	0	0.041	-0.004	22.099	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	84	LYS	1	0.967	0.985	19.624	-0.267	-0.267	0.000	0.000	0.000	0.000
54	A	85	PHE	0	0.042	0.029	22.993	0.004	0.004	0.000	0.000	0.000	0.000
55	A	86	HIS	0	0.016	-0.001	24.521	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	87	GLY	0	0.010	0.016	27.353	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	88	LEU	0	-0.017	0.002	27.277	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	89	GLU	-1	-0.952	-0.972	26.672	0.126	0.126	0.000	0.000	0.000	0.000
59	A	90	MET	0	0.002	0.010	22.992	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	91	CYS	0	-0.060	-0.029	22.633	0.006	0.006	0.000	0.000	0.000	0.000
61	A	92	VAL	0	0.007	0.020	17.747	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	93	ASP	-1	-0.791	-0.900	20.342	0.128	0.128	0.000	0.000	0.000	0.000
63	A	94	ALA	0	0.002	-0.005	16.531	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	95	ARG	1	0.828	0.896	18.308	-0.112	-0.112	0.000	0.000	0.000	0.000
65	A	96	THR	0	-0.019	-0.005	20.608	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	97	PHE	0	-0.006	-0.005	17.723	0.014	0.014	0.000	0.000	0.000	0.000
67	A	98	GLY	0	0.042	0.035	15.433	0.020	0.020	0.000	0.000	0.000	0.000
68	A	99	ASN	0	-0.014	-0.019	9.604	-0.050	-0.050	0.000	0.000	0.000	0.000
69	A	100	GLU	-1	-0.876	-0.966	7.562	0.163	0.163	0.000	0.000	0.000	0.000
70	A	101	ALA	0	0.054	0.032	10.104	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	102	ARG	1	0.909	0.973	11.022	-0.164	-0.164	0.000	0.000	0.000	0.000
72	A	103	PHE	0	-0.102	-0.069	11.765	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	104	ILE	0	-0.020	0.013	9.960	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	105	ARG	1	0.826	0.887	13.612	-0.112	-0.112	0.000	0.000	0.000	0.000
75	A	106	ARG	1	0.809	0.885	15.938	-0.196	-0.196	0.000	0.000	0.000	0.000
76	A	107	SER	0	0.020	0.010	17.266	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	108	CYS	0	-0.024	0.006	19.256	0.015	0.015	0.000	0.000	0.000	0.000
78	A	109	THR	0	-0.024	-0.021	18.406	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	110	PRO	0	-0.050	0.014	15.204	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	111	ASN	0	0.058	0.016	10.849	0.061	0.061	0.000	0.000	0.000	0.000
81	A	112	ALA	0	0.004	-0.011	9.839	0.089	0.089	0.000	0.000	0.000	0.000
82	A	113	GLU	-1	-0.848	-0.921	11.679	0.264	0.264	0.000	0.000	0.000	0.000
83	A	114	VAL	0	-0.028	-0.009	12.842	0.113	0.113	0.000	0.000	0.000	0.000
84	A	115	ARG	1	0.771	0.863	13.351	-0.540	-0.540	0.000	0.000	0.000	0.000
85	A	116	HIS	0	0.030	0.051	15.435	0.048	0.048	0.000	0.000	0.000	0.000
86	A	117	GLU	-1	-0.905	-0.950	15.068	0.383	0.383	0.000	0.000	0.000	0.000
87	A	118	ILE	0	-0.028	-0.018	18.497	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	119	GLN	0	0.003	-0.011	17.019	0.027	0.027	0.000	0.000	0.000	0.000
89	A	120	ASP	-1	-0.911	-0.957	20.822	0.099	0.099	0.000	0.000	0.000	0.000
90	A	121	GLY	0	0.012	0.014	23.834	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	122	THR	0	-0.024	-0.005	21.092	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	123	ILE	0	-0.031	-0.011	19.958	0.017	0.017	0.000	0.000	0.000	0.000
93	A	124	HIS	1	0.849	0.920	15.410	-0.277	-0.277	0.000	0.000	0.000	0.000
94	A	125	LEU	0	0.015	0.004	15.447	0.004	0.004	0.000	0.000	0.000	0.000
95	A	126	TYR	0	0.027	0.011	9.878	0.063	0.063	0.000	0.000	0.000	0.000
96	A	127	ILE	0	-0.045	-0.023	8.846	-0.136	-0.136	0.000	0.000	0.000	0.000
97	A	128	TYR	0	0.062	0.021	8.365	0.539	0.539	0.000	0.000	0.000	0.000
98	A	129	SER	0	-0.033	-0.013	7.408	-0.103	-0.103	0.000	0.000	0.000	0.000
99	A	130	ILE	0	-0.002	0.010	9.331	-0.060	-0.060	0.000	0.000	0.000	0.000
100	A	131	HIS	0	0.003	-0.017	11.691	-0.047	-0.047	0.000	0.000	0.000	0.000
101	A	132	SER	0	-0.012	-0.006	9.729	0.083	0.083	0.000	0.000	0.000	0.000
102	A	133	ILE	0	-0.041	-0.017	7.059	0.034	0.034	0.000	0.000	0.000	0.000
103	A	134	PRO	0	0.079	0.043	7.600	-0.164	-0.164	0.000	0.000	0.000	0.000
104	A	135	LYS	1	0.927	0.982	6.320	0.499	0.499	0.000	0.000	0.000	0.000
105	A	136	GLY	0	-0.062	-0.028	7.954	0.119	0.119	0.000	0.000	0.000	0.000
106	A	137	THR	0	0.028	-0.001	8.901	0.105	0.105	0.000	0.000	0.000	0.000
107	A	138	GLU	-1	-0.854	-0.905	9.168	0.084	0.084	0.000	0.000	0.000	0.000
108	A	139	ILE	0	-0.011	0.008	6.353	0.016	0.016	0.000	0.000	0.000	0.000
109	A	140	THR	0	-0.010	-0.006	10.196	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	141	ILE	0	0.033	0.017	13.147	0.055	0.055	0.000	0.000	0.000	0.000
111	A	142	ALA	0	0.052	0.016	15.282	-0.046	-0.046	0.000	0.000	0.000	0.000
112	A	143	PHE	0	-0.028	-0.032	18.897	0.012	0.012	0.000	0.000	0.000	0.000
113	A	144	ASP	-1	-0.716	-0.818	20.540	0.209	0.209	0.000	0.000	0.000	0.000
114	A	145	PHE	0	-0.061	-0.037	21.773	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	146	ASP	-1	-0.914	-0.967	25.506	0.105	0.105	0.000	0.000	0.000	0.000
116	A	147	TYR	0	-0.048	-0.042	25.635	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	148	GLY	0	0.003	-0.010	28.673	0.000	0.000	0.000	0.000	0.000	0.000
118	A	149	ASN	0	-0.054	-0.019	30.901	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	150	ALA	0	0.039	0.031	32.655	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	151	LYS	1	0.983	0.981	34.526	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	152	TYR	0	-0.004	0.003	34.092	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	153	LYS	1	0.976	0.979	29.706	-0.102	-0.102	0.000	0.000	0.000	0.000
123	A	154	VAL	0	0.027	0.026	27.507	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:24:LEU)