FMO DATABASE

FMODB ID: 941V2

Calculation Name: 3H6X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3H6X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DVY3

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1068006.877238
FMO2-HF: Nuclear repulsion	1018022.598447
FMO2-HF: Total energy	-49984.278791
FMO2-MP2: Total energy	-50130.034446

3D Structure Molmil

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:4:THR)

Summations of interaction energy for fragment #1(A:4:THR)

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.
-7.119	-3.381	3.243	-2.456	-4.525	-0.008

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.034

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	6	GLY	0	-0.041	-0.005	3.870	-1.318	0.345	-0.014	-0.877	-0.772	0.001
4	A	7	PHE	0	0.013	-0.011	6.161	0.123	0.123	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.814	-0.881	8.921	0.355	0.355	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.005	0.004	11.265	-0.039	-0.039	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.054	-0.010	14.686	0.028	0.028	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.032	-0.061	17.037	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.936	-0.951	19.632	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.102	-0.084	19.809	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.007	-0.011	19.486	0.002	0.002	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.816	-0.890	20.476	-0.096	-0.096	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.884	-0.950	15.550	-0.096	-0.096	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.085	-0.051	16.848	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.020	-0.012	18.342	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.001	0.017	11.996	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	20	PRO	0	-0.022	-0.002	12.855	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.948	0.973	12.898	0.147	0.147	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.843	0.918	11.838	0.383	0.383	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.837	-0.891	15.585	-0.134	-0.134	0.000	0.000	0.000	0.000
21	A	24	THR	0	-0.005	-0.020	18.260	0.017	0.017	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.041	0.012	16.251	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	26	HIS	0	0.012	0.012	15.610	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.021	0.014	17.200	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	ALA	0	0.054	0.018	14.923	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	29	GLY	0	0.013	0.021	13.827	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	30	TYR	0	-0.043	-0.034	8.751	0.011	0.011	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.785	-0.872	14.662	-0.203	-0.203	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.025	0.015	14.992	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.835	0.904	18.129	0.186	0.186	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.005	0.019	20.856	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.023	0.012	22.045	0.004	0.004	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.853	-0.913	23.286	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.783	0.858	27.087	0.053	0.053	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.000	-0.004	28.308	0.002	0.002	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.935	-0.971	30.743	-0.054	-0.054	0.000	0.000	0.000	0.000
37	A	40	ILE	0	-0.008	-0.015	30.135	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.041	0.016	34.616	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.026	0.022	37.854	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.027	-0.002	39.078	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.025	-0.003	36.692	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.015	-0.030	31.283	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.017	0.010	29.340	0.004	0.004	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.027	-0.011	25.329	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	48	VAL	0	0.005	0.002	24.953	0.006	0.006	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.056	0.041	23.165	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.047	-0.054	17.645	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.022	0.016	18.812	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.057	-0.019	13.723	0.008	0.008	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.829	0.922	11.994	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.024	-0.032	9.855	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	55	TYR	0	0.024	0.028	2.799	-2.369	-1.282	0.700	-0.568	-1.219	0.004
53	A	56	MET	0	-0.050	-0.020	4.981	-0.552	-0.552	0.000	0.000	0.000	0.000
54	A	57	GLN	0	0.021	0.010	2.489	-0.658	0.214	2.559	-0.995	-2.436	-0.013
55	A	58	VAL	0	0.023	0.000	5.290	0.274	0.319	-0.001	-0.002	-0.042	0.000
56	A	59	GLY	0	0.015	0.014	8.402	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.836	-0.888	4.523	-2.762	-2.691	-0.001	-0.014	-0.056	0.000
58	A	61	VAL	0	0.042	0.011	8.823	0.062	0.062	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.027	-0.003	10.767	-0.074	-0.074	0.000	0.000	0.000	0.000
60	A	63	TYR	0	0.028	0.015	12.078	0.095	0.095	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.012	-0.004	15.268	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	65	PHE	0	0.022	0.006	16.703	0.031	0.031	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.681	-0.834	20.825	-0.139	-0.139	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.799	0.892	21.329	0.166	0.166	0.000	0.000	0.000	0.000
65	A	68	SER	0	0.013	0.003	24.941	0.015	0.015	0.000	0.000	0.000	0.000
66	A	69	SER	0	-0.008	-0.012	27.795	0.007	0.007	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.004	-0.015	26.003	0.014	0.014	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.069	0.030	29.544	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.870	0.929	30.548	0.098	0.098	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.862	0.925	32.451	0.076	0.076	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.814	0.895	29.260	0.094	0.094	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.062	0.056	33.826	0.002	0.002	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.016	-0.006	30.129	0.002	0.002	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.009	-0.012	29.507	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.020	0.009	22.505	0.004	0.004	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.026	-0.007	27.055	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	80	ASN	0	-0.010	-0.012	23.091	0.012	0.012	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.049	-0.016	25.643	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.036	-0.031	19.837	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.036	-0.006	20.086	0.015	0.015	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.005	-0.012	16.598	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.009	0.003	13.577	0.036	0.036	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.837	-0.923	13.077	-0.379	-0.379	0.000	0.000	0.000	0.000
84	A	87	GLY	0	-0.008	-0.021	10.649	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.940	-0.971	11.039	-0.151	-0.151	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.025	-0.011	13.744	0.055	0.055	0.000	0.000	0.000	0.000
87	A	90	TYR	0	-0.057	-0.055	9.529	0.074	0.074	0.000	0.000	0.000	0.000
88	A	91	ASN	0	0.008	0.008	11.763	0.001	0.001	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.041	-0.016	15.010	0.024	0.024	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.005	-0.028	17.955	0.002	0.002	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.034	-0.004	21.394	0.010	0.010	0.000	0.000	0.000	0.000
92	A	95	ASN	0	0.006	-0.006	19.957	0.000	0.000	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.722	-0.819	16.017	0.007	0.007	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.055	0.027	15.468	0.006	0.006	0.000	0.000	0.000	0.000
95	A	98	HIS	0	-0.020	-0.007	16.013	-0.042	-0.042	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.020	-0.001	13.868	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	100	PHE	0	0.007	-0.001	18.298	0.015	0.015	0.000	0.000	0.000	0.000
98	A	101	ALA	0	-0.022	-0.002	21.835	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	102	GLN	0	0.007	0.000	23.600	0.019	0.019	0.000	0.000	0.000	0.000
100	A	103	MET	0	-0.015	0.010	26.557	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.935	0.970	29.006	0.076	0.076	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.018	-0.007	32.600	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	106	MET	0	-0.090	-0.042	34.183	0.002	0.002	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.051	-0.035	37.515	0.004	0.004	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.852	-0.929	40.388	-0.048	-0.048	0.000	0.000	0.000	0.000
106	A	109	GLN	0	-0.040	-0.030	41.277	0.003	0.003	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.013	-0.012	37.754	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	111	VAL	0	-0.014	0.020	33.389	0.001	0.001	0.000	0.000	0.000	0.000
109	A	112	VAL	0	0.000	-0.010	33.359	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.044	-0.015	27.553	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.777	-0.858	29.860	-0.061	-0.061	0.000	0.000	0.000	0.000
112	A	115	ALA	0	0.022	0.012	26.456	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.018	0.011	23.314	0.003	0.003	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.838	-0.902	23.747	-0.102	-0.102	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.737	0.848	21.499	0.151	0.151	0.000	0.000	0.000	0.000
116	A	119	VAL	0	0.013	0.007	22.427	0.009	0.009	0.000	0.000	0.000	0.000
117	A	120	VAL	0	0.009	0.002	19.544	0.008	0.008	0.000	0.000	0.000	0.000
118	A	121	GLN	0	-0.070	-0.037	17.970	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	122	GLY	0	0.028	0.020	14.650	0.015	0.015	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.011	-0.029	12.751	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	124	PHE	0	0.021	0.017	7.623	-0.065	-0.065	0.000	0.000	0.000	0.000
122	A	125	MET	0	-0.059	-0.025	9.746	0.088	0.088	0.000	0.000	0.000	0.000
123	A	126	PRO	0	0.033	0.022	9.515	-0.069	-0.069	0.000	0.000	0.000	0.000
124	A	127	PHE	0	-0.048	-0.020	10.498	0.072	0.072	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.017	-0.010	13.410	0.009	0.009	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.002	-0.003	15.913	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	130	ILE	0	0.019	0.008	18.586	0.009	0.009	0.000	0.000	0.000	0.000
128	A	131	ASP	-1	-0.914	-0.952	22.062	-0.056	-0.056	0.000	0.000	0.000	0.000
129	A	132	GLY	0	-0.073	-0.031	22.356	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)