FMO DATABASE

FMODB ID: JLGR9

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	OptAll
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	-1106527.873337
FMO2-HF: Nuclear repulsion	1056316.332248
FMO2-HF: Total energy	-50211.541089
FMO2-MP2: Total energy	-50359.255231

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.
-3.588	2.694	4.951	-4.464	-6.766	0.001

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 : 0.087 / q_NPA : 0.053

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

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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	0.979	0.964	3.079	-2.238	1.691	0.136	-2.145	-1.920	0.001
4	A	27	PRO	0	0.016	0.037	5.782	-0.047	-0.047	0.000	0.000	0.000	0.000
5	A	28	PRO	0	-0.053	-0.024	9.508	0.148	0.148	0.000	0.000	0.000	0.000
6	A	37	LYS	1	0.999	1.000	18.366	0.229	0.229	0.000	0.000	0.000	0.000
7	A	38	LYS	1	0.955	0.973	13.997	0.235	0.235	0.000	0.000	0.000	0.000
8	A	39	ILE	0	-0.007	0.003	12.745	0.013	0.013	0.000	0.000	0.000	0.000
9	A	40	LEU	0	-0.005	0.001	7.116	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	41	LYS	1	0.872	0.944	8.442	0.647	0.647	0.000	0.000	0.000	0.000
11	A	42	SER	0	0.052	0.017	5.053	-0.310	-0.310	0.000	0.000	0.000	0.000
12	A	43	ALA	0	-0.030	-0.018	2.328	-0.674	0.532	1.418	-0.918	-1.705	0.002
13	A	44	LYS	1	0.797	0.876	2.736	-0.346	0.885	0.207	-0.336	-1.101	-0.001
14	A	45	ASP	-1	-0.770	-0.878	4.313	-1.245	-1.164	-0.001	-0.027	-0.052	0.000
15	A	46	LEU	0	-0.005	0.017	2.041	0.270	-0.460	3.189	-0.942	-1.517	-0.001
16	A	47	PRO	0	0.063	0.036	5.674	0.005	0.005	0.000	0.000	0.000	0.000
17	A	48	PRO	0	0.028	0.015	8.377	-0.183	-0.183	0.000	0.000	0.000	0.000
18	A	49	ASP	-1	-0.800	-0.883	10.256	0.101	0.101	0.000	0.000	0.000	0.000
19	A	50	ALA	0	-0.016	-0.001	5.094	0.158	0.158	0.000	0.000	0.000	0.000
20	A	51	LEU	0	0.002	0.005	6.782	-0.420	-0.420	0.000	0.000	0.000	0.000
21	A	52	ILE	0	-0.065	-0.031	3.584	-0.005	0.363	0.003	-0.066	-0.305	0.000
22	A	53	ILE	0	-0.059	-0.039	4.334	-0.107	0.090	-0.001	-0.030	-0.166	0.000
23	A	54	GLU	-1	-0.756	-0.841	7.015	0.049	0.049	0.000	0.000	0.000	0.000
24	A	55	TYR	0	-0.046	-0.049	10.624	-0.095	-0.095	0.000	0.000	0.000	0.000
25	A	56	ARG	1	0.892	0.933	12.131	0.073	0.073	0.000	0.000	0.000	0.000
26	A	57	GLY	0	0.046	-0.008	14.894	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	58	LYS	1	0.872	0.938	18.395	0.087	0.087	0.000	0.000	0.000	0.000
28	A	59	PHE	0	0.033	0.010	17.879	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	60	MET	0	-0.059	-0.009	22.819	0.007	0.007	0.000	0.000	0.000	0.000
30	A	61	LEU	0	0.048	0.017	26.024	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	62	ARG	1	0.812	0.867	28.600	0.053	0.053	0.000	0.000	0.000	0.000
32	A	63	GLU	-1	-0.867	-0.935	29.994	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	64	GLN	0	0.090	0.059	29.443	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	65	PHE	0	-0.029	-0.022	26.153	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	66	GLU	-1	-0.828	-0.919	30.113	-0.057	-0.057	0.000	0.000	0.000	0.000
36	A	67	ALA	0	0.010	0.012	33.532	0.000	0.000	0.000	0.000	0.000	0.000
37	A	68	ASN	0	-0.123	-0.072	30.705	0.000	0.000	0.000	0.000	0.000	0.000
38	A	69	GLY	0	0.013	0.018	32.929	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	70	TYR	0	-0.078	-0.034	29.112	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	71	PHE	0	0.033	-0.002	31.838	0.002	0.002	0.000	0.000	0.000	0.000
41	A	72	PHE	0	0.054	0.009	26.532	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	73	LYS	1	0.797	0.911	25.331	0.092	0.092	0.000	0.000	0.000	0.000
43	A	74	ARG	1	1.001	1.014	27.828	0.079	0.079	0.000	0.000	0.000	0.000
44	A	75	PRO	0	0.011	0.015	25.208	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	76	TYR	0	0.003	0.000	25.893	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	77	PRO	0	-0.001	-0.021	22.492	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	78	PHE	0	-0.026	-0.027	17.986	0.011	0.011	0.000	0.000	0.000	0.000
48	A	79	VAL	0	0.024	0.041	19.654	0.004	0.004	0.000	0.000	0.000	0.000
49	A	80	LEU	0	-0.032	0.008	15.923	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	81	PHE	0	-0.007	-0.005	20.025	0.020	0.020	0.000	0.000	0.000	0.000
51	A	82	TYR	0	-0.026	-0.060	17.977	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	83	SER	0	0.044	0.003	22.108	0.005	0.005	0.000	0.000	0.000	0.000
53	A	84	LYS	1	0.858	0.925	17.187	0.136	0.136	0.000	0.000	0.000	0.000
54	A	85	PHE	0	0.016	0.014	22.601	0.009	0.009	0.000	0.000	0.000	0.000
55	A	86	HIS	0	0.017	0.001	24.138	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	87	GLY	0	0.035	0.030	26.811	0.002	0.002	0.000	0.000	0.000	0.000
57	A	88	LEU	0	-0.039	-0.015	26.972	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	89	GLU	-1	-0.783	-0.869	26.356	-0.077	-0.077	0.000	0.000	0.000	0.000
59	A	90	MET	0	-0.010	0.009	23.147	0.005	0.005	0.000	0.000	0.000	0.000
60	A	91	CYS	0	-0.058	-0.030	22.709	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	92	VAL	0	0.013	0.030	17.799	0.010	0.010	0.000	0.000	0.000	0.000
62	A	93	ASP	-1	-0.781	-0.891	20.429	-0.121	-0.121	0.000	0.000	0.000	0.000
63	A	94	ALA	0	0.008	0.001	16.444	0.009	0.009	0.000	0.000	0.000	0.000
64	A	95	ARG	1	0.828	0.910	18.267	0.099	0.099	0.000	0.000	0.000	0.000
65	A	96	THR	0	-0.025	-0.006	21.013	0.009	0.009	0.000	0.000	0.000	0.000
66	A	97	PHE	0	0.005	-0.008	18.299	0.000	0.000	0.000	0.000	0.000	0.000
67	A	98	GLY	0	0.067	0.049	15.642	0.005	0.005	0.000	0.000	0.000	0.000
68	A	99	ASN	0	-0.035	-0.019	8.952	0.029	0.029	0.000	0.000	0.000	0.000
69	A	100	GLU	-1	-0.848	-0.946	7.953	-0.367	-0.367	0.000	0.000	0.000	0.000
70	A	101	ALA	0	0.039	0.027	10.350	-0.058	-0.058	0.000	0.000	0.000	0.000
71	A	102	ARG	1	0.873	0.955	11.253	0.226	0.226	0.000	0.000	0.000	0.000
72	A	103	PHE	0	-0.083	-0.051	11.675	0.048	0.048	0.000	0.000	0.000	0.000
73	A	104	ILE	0	-0.013	0.007	9.955	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	105	ARG	1	0.847	0.901	13.654	0.427	0.427	0.000	0.000	0.000	0.000
75	A	106	ARG	1	0.804	0.870	15.644	0.214	0.214	0.000	0.000	0.000	0.000
76	A	107	SER	0	0.004	-0.004	17.368	0.016	0.016	0.000	0.000	0.000	0.000
77	A	108	CYS	0	-0.022	-0.012	19.216	0.008	0.008	0.000	0.000	0.000	0.000
78	A	109	THR	0	0.002	0.010	19.277	0.025	0.025	0.000	0.000	0.000	0.000
79	A	110	PRO	0	-0.052	-0.003	15.172	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	111	ASN	0	0.042	0.009	11.305	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	112	ALA	0	-0.003	-0.001	9.642	-0.047	-0.047	0.000	0.000	0.000	0.000
82	A	113	GLU	-1	-0.822	-0.906	11.549	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	114	VAL	0	0.005	0.010	12.328	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	115	ARG	1	0.748	0.858	13.014	0.086	0.086	0.000	0.000	0.000	0.000
85	A	116	HIS	0	0.056	0.041	15.259	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	117	GLU	-1	-0.834	-0.882	15.525	0.157	0.157	0.000	0.000	0.000	0.000
87	A	118	ILE	0	-0.023	-0.018	18.448	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	119	GLN	0	-0.036	-0.032	15.981	0.002	0.002	0.000	0.000	0.000	0.000
89	A	120	ASP	-1	-0.867	-0.935	21.079	0.045	0.045	0.000	0.000	0.000	0.000
90	A	121	GLY	0	0.014	0.011	24.176	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	122	THR	0	-0.045	-0.010	21.557	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	123	ILE	0	-0.030	-0.018	20.266	0.009	0.009	0.000	0.000	0.000	0.000
93	A	124	HIS	1	0.860	0.935	15.506	-0.049	-0.049	0.000	0.000	0.000	0.000
94	A	125	LEU	0	0.005	-0.005	15.591	0.000	0.000	0.000	0.000	0.000	0.000
95	A	126	TYR	0	-0.037	-0.044	10.284	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	127	ILE	0	-0.040	-0.018	8.528	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	128	TYR	0	0.048	0.017	8.170	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	129	SER	0	-0.037	-0.032	7.442	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	130	ILE	0	-0.004	0.002	9.248	0.126	0.126	0.000	0.000	0.000	0.000
100	A	131	HIS	0	0.000	-0.013	11.832	0.068	0.068	0.000	0.000	0.000	0.000
101	A	132	SER	0	0.026	0.014	9.928	-0.065	-0.065	0.000	0.000	0.000	0.000
102	A	133	ILE	0	-0.051	-0.014	7.182	-0.018	-0.018	0.000	0.000	0.000	0.000
103	A	134	PRO	0	0.066	0.035	7.303	-0.244	-0.244	0.000	0.000	0.000	0.000
104	A	135	LYS	1	0.903	0.956	6.176	-0.095	-0.095	0.000	0.000	0.000	0.000
105	A	136	GLY	0	0.000	0.005	7.986	0.188	0.188	0.000	0.000	0.000	0.000
106	A	137	THR	0	-0.011	-0.014	9.230	0.177	0.177	0.000	0.000	0.000	0.000
107	A	138	GLU	-1	-0.811	-0.896	9.450	-0.677	-0.677	0.000	0.000	0.000	0.000
108	A	139	ILE	0	0.008	0.019	6.137	0.000	0.000	0.000	0.000	0.000	0.000
109	A	140	THR	0	-0.026	-0.016	9.945	0.137	0.137	0.000	0.000	0.000	0.000
110	A	141	ILE	0	0.023	0.014	12.761	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	142	ALA	0	0.057	0.019	15.013	0.021	0.021	0.000	0.000	0.000	0.000
112	A	143	PHE	0	-0.024	-0.025	18.576	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	144	ASP	-1	-0.730	-0.825	20.037	-0.177	-0.177	0.000	0.000	0.000	0.000
114	A	145	PHE	0	-0.048	-0.028	21.797	0.016	0.016	0.000	0.000	0.000	0.000
115	A	146	ASP	-1	-0.831	-0.904	25.183	-0.096	-0.096	0.000	0.000	0.000	0.000
116	A	147	TYR	0	-0.005	-0.015	25.354	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	148	GLY	0	0.009	-0.005	28.609	0.004	0.004	0.000	0.000	0.000	0.000
118	A	149	ASN	0	-0.052	-0.020	30.722	0.005	0.005	0.000	0.000	0.000	0.000
119	A	150	ALA	0	0.034	0.030	32.265	0.005	0.005	0.000	0.000	0.000	0.000
120	A	151	LYS	1	0.962	0.969	34.094	0.055	0.055	0.000	0.000	0.000	0.000
121	A	152	TYR	0	0.005	0.010	33.734	0.005	0.005	0.000	0.000	0.000	0.000
122	A	153	LYS	1	0.860	0.906	28.809	0.079	0.079	0.000	0.000	0.000	0.000
123	A	154	VAL	0	0.032	0.031	26.603	0.006	0.006	0.000	0.000	0.000	0.000

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