FMO DATABASE

FMODB ID: 2JZVR

Calculation Name: 1BYW-A-Xray372

Preferred Name: HERG

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1BYW

Chain ID: A

ChEMBL ID: CHEMBL240

UniProt ID: Q12809

Base Structure: X-ray

Registration Date: 2023-09-20

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	110
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-881409.063817
FMO2-HF: Nuclear repulsion	835843.784548
FMO2-HF: Total energy	-45565.279269
FMO2-MP2: Total energy	-45689.807547

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:26:DSN)

Summations of interaction energy for fragment #1(A:26:DSN)

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.
-2.929	-1.071	0.043	-0.865	-1.036	0.002

Interaction energy analysis for fragmet #1(A:26:DSN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.002

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	28	LYS	1	0.953	0.999	2.863	-1.930	-0.072	0.043	-0.865	-1.036	0.002
4	A	29	PHE	0	0.006	0.012	6.648	0.255	0.255	0.000	0.000	0.000	0.000
5	A	30	ILE	0	-0.014	-0.010	9.988	-0.056	-0.056	0.000	0.000	0.000	0.000
6	A	31	ILE	0	0.021	0.014	13.377	0.037	0.037	0.000	0.000	0.000	0.000
7	A	32	ALA	0	-0.021	-0.006	16.380	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	33	ASN	0	0.016	0.001	19.848	0.023	0.023	0.000	0.000	0.000	0.000
9	A	34	ALA	0	0.046	0.011	23.284	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	35	ARG	1	0.907	0.978	25.217	-0.078	-0.078	0.000	0.000	0.000	0.000
11	A	36	VAL	0	-0.050	-0.026	26.771	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	37	GLU	-1	-0.869	-0.925	28.309	0.017	0.017	0.000	0.000	0.000	0.000
13	A	38	ASN	0	-0.004	-0.016	26.620	0.003	0.003	0.000	0.000	0.000	0.000
14	A	39	CYS	0	0.003	0.002	22.913	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	40	ALA	0	0.003	0.007	22.388	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	41	VAL	0	0.002	0.002	16.830	0.016	0.016	0.000	0.000	0.000	0.000
17	A	42	ILE	0	-0.007	-0.009	18.859	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	43	TYR	0	-0.004	-0.018	11.268	0.028	0.028	0.000	0.000	0.000	0.000
19	A	44	CYS	0	0.033	0.040	12.750	0.002	0.002	0.000	0.000	0.000	0.000
20	A	45	ASN	0	0.019	0.022	5.669	-0.203	-0.203	0.000	0.000	0.000	0.000
21	A	46	ASP	-1	-0.785	-0.903	7.764	-0.277	-0.277	0.000	0.000	0.000	0.000
22	A	47	GLY	0	0.010	0.008	5.130	-0.237	-0.237	0.000	0.000	0.000	0.000
23	A	48	PHE	0	0.037	-0.002	5.693	0.004	0.004	0.000	0.000	0.000	0.000
24	A	49	CYS	0	-0.033	-0.015	8.710	0.070	0.070	0.000	0.000	0.000	0.000
25	A	50	GLU	-1	-0.910	-0.949	6.307	-1.310	-1.310	0.000	0.000	0.000	0.000
26	A	51	LEU	0	-0.069	-0.012	7.153	0.078	0.078	0.000	0.000	0.000	0.000
27	A	52	CYS	0	-0.071	-0.018	8.704	0.145	0.145	0.000	0.000	0.000	0.000
28	A	53	GLY	0	0.059	0.025	11.684	0.064	0.064	0.000	0.000	0.000	0.000
29	A	54	TYR	0	-0.042	-0.033	13.442	0.057	0.057	0.000	0.000	0.000	0.000
30	A	55	SER	0	0.011	-0.018	13.794	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	56	ARG	1	0.885	0.889	11.467	0.099	0.099	0.000	0.000	0.000	0.000
32	A	57	ALA	0	-0.027	-0.014	15.948	0.024	0.024	0.000	0.000	0.000	0.000
33	A	58	GLU	-1	-0.838	-0.896	18.371	-0.138	-0.138	0.000	0.000	0.000	0.000
34	A	59	VAL	0	-0.008	-0.007	14.710	0.011	0.011	0.000	0.000	0.000	0.000
35	A	60	MET	0	-0.036	-0.020	18.051	0.019	0.019	0.000	0.000	0.000	0.000
36	A	61	GLN	0	-0.009	-0.014	19.890	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	62	ARG	1	0.924	0.990	20.520	0.074	0.074	0.000	0.000	0.000	0.000
38	A	63	PRO	0	0.053	0.022	21.424	0.007	0.007	0.000	0.000	0.000	0.000
39	A	64	CYS	0	0.001	0.018	18.982	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	65	THR	0	-0.021	-0.006	18.841	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	66	CYS	0	-0.105	-0.053	16.875	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	67	ASP	-1	-0.806	-0.917	19.269	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	68	PHE	0	-0.060	-0.036	16.258	0.004	0.004	0.000	0.000	0.000	0.000
44	A	69	LEU	0	-0.004	0.010	14.807	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	70	HIS	0	0.009	0.011	18.646	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	71	GLY	0	0.030	-0.007	21.641	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	72	PRO	0	-0.047	-0.030	23.570	0.006	0.006	0.000	0.000	0.000	0.000
48	A	73	CYS	0	0.000	-0.018	22.731	0.006	0.006	0.000	0.000	0.000	0.000
49	A	74	THR	0	-0.039	0.013	21.253	0.003	0.003	0.000	0.000	0.000	0.000
50	A	75	GLN	0	0.066	0.029	22.499	0.004	0.004	0.000	0.000	0.000	0.000
51	A	76	ARG	1	0.964	0.977	25.171	0.043	0.043	0.000	0.000	0.000	0.000
52	A	77	ARG	1	0.914	0.952	26.876	0.013	0.013	0.000	0.000	0.000	0.000
53	A	78	ALA	0	0.080	0.047	21.944	0.005	0.005	0.000	0.000	0.000	0.000
54	A	79	ALA	0	0.041	0.015	22.831	0.003	0.003	0.000	0.000	0.000	0.000
55	A	80	ALA	0	0.003	-0.004	24.063	0.005	0.005	0.000	0.000	0.000	0.000
56	A	81	GLN	0	-0.041	-0.021	23.592	0.002	0.002	0.000	0.000	0.000	0.000
57	A	82	ILE	0	0.060	0.035	18.956	0.008	0.008	0.000	0.000	0.000	0.000
58	A	83	ALA	0	0.007	0.003	22.414	0.007	0.007	0.000	0.000	0.000	0.000
59	A	84	GLN	0	-0.031	-0.026	25.348	0.007	0.007	0.000	0.000	0.000	0.000
60	A	85	ALA	0	-0.015	-0.002	22.331	0.004	0.004	0.000	0.000	0.000	0.000
61	A	86	LEU	0	0.027	0.007	20.505	0.008	0.008	0.000	0.000	0.000	0.000
62	A	87	LEU	0	0.002	0.010	24.290	0.005	0.005	0.000	0.000	0.000	0.000
63	A	88	GLY	0	-0.021	-0.002	27.957	0.003	0.003	0.000	0.000	0.000	0.000
64	A	89	ALA	0	-0.055	-0.029	24.708	0.005	0.005	0.000	0.000	0.000	0.000
65	A	90	GLU	-1	-0.873	-0.912	24.420	0.040	0.040	0.000	0.000	0.000	0.000
66	A	91	GLU	-1	-0.918	-0.959	18.824	0.125	0.125	0.000	0.000	0.000	0.000
67	A	92	ARG	1	0.780	0.856	19.739	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	93	LYS	1	0.979	0.996	13.502	-0.053	-0.053	0.000	0.000	0.000	0.000
69	A	94	VAL	0	-0.059	-0.033	17.299	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	95	GLU	-1	-0.878	-0.932	16.731	-0.068	-0.068	0.000	0.000	0.000	0.000
71	A	96	ILE	0	-0.056	-0.037	17.278	0.009	0.009	0.000	0.000	0.000	0.000
72	A	97	ALA	0	-0.033	-0.008	17.282	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	98	PHE	0	0.022	-0.004	14.302	0.010	0.010	0.000	0.000	0.000	0.000
74	A	99	TYR	0	0.020	0.013	17.058	0.003	0.003	0.000	0.000	0.000	0.000
75	A	100	ARG	1	0.819	0.905	10.030	0.279	0.279	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.848	0.924	15.931	0.174	0.174	0.000	0.000	0.000	0.000
77	A	102	ASP	-1	-0.878	-0.939	16.575	-0.186	-0.186	0.000	0.000	0.000	0.000
78	A	103	GLY	0	-0.021	-0.006	18.808	0.013	0.013	0.000	0.000	0.000	0.000
79	A	104	SER	0	-0.034	0.005	15.979	0.008	0.008	0.000	0.000	0.000	0.000
80	A	105	CYS	0	-0.039	-0.015	17.432	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	106	PHE	0	0.007	-0.010	11.991	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	107	LEU	0	-0.051	-0.008	15.469	0.003	0.003	0.000	0.000	0.000	0.000
83	A	108	CYS	0	-0.002	0.023	12.768	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	109	LEU	0	0.004	0.009	11.999	0.023	0.023	0.000	0.000	0.000	0.000
85	A	110	VAL	0	-0.038	-0.033	12.516	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	111	ASP	-1	-0.918	-0.962	12.859	0.135	0.135	0.000	0.000	0.000	0.000
87	A	112	VAL	0	0.001	-0.013	14.740	0.023	0.023	0.000	0.000	0.000	0.000
88	A	113	VAL	0	0.076	0.032	14.583	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	114	PRO	0	-0.028	-0.012	17.597	0.014	0.014	0.000	0.000	0.000	0.000
90	A	115	VAL	0	0.004	0.013	18.310	0.014	0.014	0.000	0.000	0.000	0.000
91	A	116	LYS	1	0.878	0.942	21.231	-0.087	-0.087	0.000	0.000	0.000	0.000
92	A	117	ASN	0	0.010	0.020	24.443	0.010	0.010	0.000	0.000	0.000	0.000
93	A	118	GLU	-1	-0.874	-0.939	26.985	0.094	0.094	0.000	0.000	0.000	0.000
94	A	119	DAS	-1	-0.959	-0.986	29.776	0.063	0.063	0.000	0.000	0.000	0.000
95	A	120	GLY	0	0.002	0.009	28.773	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	121	ALA	0	-0.073	-0.043	29.130	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	122	VAL	0	0.001	-0.017	24.010	0.009	0.009	0.000	0.000	0.000	0.000
98	A	123	ILE	0	-0.043	-0.011	23.867	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	124	MET	0	-0.029	-0.021	17.599	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	125	PHE	0	0.024	0.008	19.347	0.003	0.003	0.000	0.000	0.000	0.000
101	A	126	ILE	0	-0.003	0.004	13.208	0.009	0.009	0.000	0.000	0.000	0.000
102	A	127	LEU	0	0.006	0.017	14.634	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	128	ASN	0	0.010	-0.008	7.641	0.197	0.197	0.000	0.000	0.000	0.000
104	A	129	PHE	0	-0.018	-0.027	9.743	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	130	GLU	-1	-0.897	-0.942	5.431	-0.347	-0.347	0.000	0.000	0.000	0.000
106	A	131	VAL	0	-0.030	-0.020	8.315	0.017	0.017	0.000	0.000	0.000	0.000
107	A	132	VAL	0	-0.027	-0.006	10.250	0.024	0.024	0.000	0.000	0.000	0.000
108	A	133	MET	0	-0.007	-0.030	12.948	0.009	0.009	0.000	0.000	0.000	0.000
109	A	134	GLU	-1	-0.841	-0.908	12.003	-0.186	-0.186	0.000	0.000	0.000	0.000
110	A	135	LYS	1	0.962	0.987	15.526	0.085	0.085	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:26:DSN)