FMO DATABASE

FMODB ID: G6YL1

Calculation Name: 3A7M-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A7M

Chain ID: B

ChEMBL ID:

UniProt ID: P0A1N2

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-787629.191313
FMO2-HF: Nuclear repulsion	741281.553036
FMO2-HF: Total energy	-46347.638277
FMO2-MP2: Total energy	-46483.450865

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(B:2:THR)

Summations of interaction energy for fragment #1(B:2: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.
-11.782	-8.927	12.717	-6.531	-9.04	0.036

Interaction energy analysis for fragmet #1(B:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.091 / q_NPA : 0.037

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	B	4	THR	0	-0.006	-0.006	2.636	-3.898	1.683	1.049	-3.096	-3.534	0.015
4	B	5	VAL	0	0.050	0.038	1.952	-3.781	-7.404	11.664	-3.210	-4.831	0.021
5	B	6	GLU	-1	-0.911	-0.954	3.601	-4.565	-3.668	0.004	-0.225	-0.675	0.000
6	B	7	PHE	0	-0.056	-0.027	5.616	0.367	0.367	0.000	0.000	0.000	0.000
7	B	8	ILE	0	0.031	-0.002	7.109	-0.148	-0.148	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.023	-0.025	7.523	-0.146	-0.146	0.000	0.000	0.000	0.000
9	B	10	ARG	1	0.925	0.986	8.332	0.679	0.679	0.000	0.000	0.000	0.000
10	B	11	TRP	0	0.071	0.016	11.467	0.037	0.037	0.000	0.000	0.000	0.000
11	B	12	GLN	0	-0.031	0.008	10.683	-0.114	-0.114	0.000	0.000	0.000	0.000
12	B	13	ARG	1	0.949	0.968	13.324	0.417	0.417	0.000	0.000	0.000	0.000
13	B	14	ILE	0	0.012	0.025	15.104	0.019	0.019	0.000	0.000	0.000	0.000
14	B	15	ALA	0	0.036	0.025	17.152	0.017	0.017	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.017	0.011	16.359	0.012	0.012	0.000	0.000	0.000	0.000
16	B	17	LEU	0	0.001	-0.008	19.136	0.014	0.014	0.000	0.000	0.000	0.000
17	B	18	SER	0	0.011	0.014	21.597	0.019	0.019	0.000	0.000	0.000	0.000
18	B	19	GLN	0	0.008	-0.002	22.848	0.019	0.019	0.000	0.000	0.000	0.000
19	B	20	SER	0	-0.090	-0.037	23.654	0.001	0.001	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.042	-0.004	25.282	0.006	0.006	0.000	0.000	0.000	0.000
21	B	22	LEU	0	-0.005	0.008	27.523	0.008	0.008	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.897	-0.956	27.805	-0.086	-0.086	0.000	0.000	0.000	0.000
23	B	24	LEU	0	-0.116	-0.037	28.212	0.004	0.004	0.000	0.000	0.000	0.000
24	B	25	ALA	0	0.008	0.018	31.687	0.003	0.003	0.000	0.000	0.000	0.000
25	B	26	GLN	0	-0.070	-0.036	31.548	0.000	0.000	0.000	0.000	0.000	0.000
26	B	27	ARG	1	0.845	0.931	29.946	0.093	0.093	0.000	0.000	0.000	0.000
27	B	28	GLY	0	0.036	0.018	35.651	0.004	0.004	0.000	0.000	0.000	0.000
28	B	29	GLU	-1	-0.917	-0.961	33.862	-0.076	-0.076	0.000	0.000	0.000	0.000
29	B	30	TRP	0	0.096	0.019	34.284	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	31	ASP	-1	-0.928	-0.959	35.372	-0.073	-0.073	0.000	0.000	0.000	0.000
31	B	32	LEU	0	-0.007	0.001	31.204	-0.005	-0.005	0.000	0.000	0.000	0.000
32	B	33	LEU	0	0.005	0.004	30.056	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	34	LEU	0	0.011	-0.006	30.845	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	35	GLN	0	-0.074	-0.034	31.084	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	36	GLN	0	-0.024	-0.025	25.673	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	37	GLU	-1	-0.891	-0.935	26.413	-0.101	-0.101	0.000	0.000	0.000	0.000
37	B	38	VAL	0	0.068	0.032	26.892	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	39	SER	0	-0.041	-0.017	23.819	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	40	TYR	0	0.036	0.020	21.816	-0.018	-0.018	0.000	0.000	0.000	0.000
40	B	41	LEU	0	0.048	0.024	22.575	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	42	GLN	0	0.065	0.027	23.185	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	43	SER	0	-0.178	-0.088	18.834	-0.039	-0.039	0.000	0.000	0.000	0.000
43	B	44	ILE	0	-0.005	-0.033	18.616	-0.020	-0.020	0.000	0.000	0.000	0.000
44	B	45	GLU	-1	-0.917	-0.967	19.476	-0.107	-0.107	0.000	0.000	0.000	0.000
45	B	46	THR	0	0.005	0.018	16.146	-0.019	-0.019	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.107	-0.070	13.507	-0.040	-0.040	0.000	0.000	0.000	0.000
47	B	48	MET	0	-0.053	-0.019	15.494	0.051	0.051	0.000	0.000	0.000	0.000
48	B	49	GLU	-1	-0.958	-0.946	18.060	-0.148	-0.148	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.905	0.947	11.917	0.515	0.515	0.000	0.000	0.000	0.000
50	B	51	GLN	0	0.006	0.005	11.624	0.122	0.122	0.000	0.000	0.000	0.000
51	B	52	THR	0	-0.032	-0.022	10.635	-0.067	-0.067	0.000	0.000	0.000	0.000
52	B	53	PRO	0	-0.033	-0.013	6.146	0.013	0.013	0.000	0.000	0.000	0.000
53	B	54	PRO	0	0.063	0.031	6.342	0.061	0.061	0.000	0.000	0.000	0.000
54	B	55	GLY	0	0.000	0.001	7.121	-0.077	-0.077	0.000	0.000	0.000	0.000
55	B	56	ILE	0	-0.031	-0.010	8.064	0.343	0.343	0.000	0.000	0.000	0.000
56	B	57	THR	0	0.047	0.025	9.203	-0.271	-0.271	0.000	0.000	0.000	0.000
57	B	58	ARG	1	1.018	0.991	11.575	-0.352	-0.352	0.000	0.000	0.000	0.000
58	B	59	SER	0	0.027	0.019	11.853	-0.039	-0.039	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.010	0.008	6.482	-0.020	-0.020	0.000	0.000	0.000	0.000
60	B	61	GLN	0	-0.006	-0.011	10.708	-0.123	-0.123	0.000	0.000	0.000	0.000
61	B	62	ASP	-1	-0.906	-0.955	13.390	0.274	0.274	0.000	0.000	0.000	0.000
62	B	63	MET	0	-0.039	-0.011	11.234	-0.060	-0.060	0.000	0.000	0.000	0.000
63	B	64	VAL	0	0.001	-0.003	11.071	-0.080	-0.080	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.019	0.010	13.699	-0.080	-0.080	0.000	0.000	0.000	0.000
65	B	66	GLY	0	-0.011	-0.002	16.906	-0.044	-0.044	0.000	0.000	0.000	0.000
66	B	67	TYR	0	0.059	0.030	12.633	-0.042	-0.042	0.000	0.000	0.000	0.000
67	B	68	ILE	0	0.003	0.018	16.761	-0.031	-0.031	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.927	0.972	19.324	-0.162	-0.162	0.000	0.000	0.000	0.000
69	B	70	GLN	0	0.049	0.019	20.290	-0.020	-0.020	0.000	0.000	0.000	0.000
70	B	71	THR	0	-0.025	-0.035	20.045	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	72	LEU	0	-0.036	-0.034	22.599	-0.007	-0.007	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.901	-0.947	25.045	0.030	0.030	0.000	0.000	0.000	0.000
73	B	74	ASN	0	-0.054	-0.038	24.024	0.005	0.005	0.000	0.000	0.000	0.000
74	B	75	GLU	-1	-0.935	-0.970	26.559	-0.052	-0.052	0.000	0.000	0.000	0.000
75	B	76	GLN	0	-0.024	-0.009	28.301	0.003	0.003	0.000	0.000	0.000	0.000
76	B	77	LEU	0	-0.038	-0.015	29.854	0.000	0.000	0.000	0.000	0.000	0.000
77	B	78	LEU	0	0.024	0.017	29.368	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	79	LYS	1	0.982	0.989	32.210	0.016	0.016	0.000	0.000	0.000	0.000
79	B	80	GLY	0	-0.006	0.006	34.315	0.002	0.002	0.000	0.000	0.000	0.000
80	B	81	LEU	0	0.023	-0.003	33.910	0.000	0.000	0.000	0.000	0.000	0.000
81	B	82	LEU	0	-0.019	-0.011	33.484	-0.001	-0.001	0.000	0.000	0.000	0.000
82	B	83	GLN	0	-0.052	-0.017	37.479	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	84	GLN	0	0.030	0.015	39.889	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	85	ARG	1	0.864	0.943	40.268	0.040	0.040	0.000	0.000	0.000	0.000
85	B	86	LEU	0	-0.032	-0.014	41.377	0.000	0.000	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.877	-0.948	43.090	-0.018	-0.018	0.000	0.000	0.000	0.000
87	B	88	GLU	-1	-0.900	-0.959	44.320	-0.030	-0.030	0.000	0.000	0.000	0.000
88	B	89	LEU	0	0.006	-0.001	43.722	0.000	0.000	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.017	-0.007	46.770	0.001	0.001	0.000	0.000	0.000	0.000
90	B	91	SER	0	-0.071	-0.020	48.954	0.002	0.002	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.036	-0.025	50.003	0.001	0.001	0.000	0.000	0.000	0.000
92	B	93	ILE	0	-0.019	-0.008	50.263	0.001	0.001	0.000	0.000	0.000	0.000
93	B	94	GLY	0	-0.003	0.003	53.766	0.001	0.001	0.000	0.000	0.000	0.000
94	B	95	GLN	0	0.050	0.014	55.806	0.001	0.001	0.000	0.000	0.000	0.000
95	B	96	SER	0	-0.017	0.004	57.360	0.001	0.001	0.000	0.000	0.000	0.000
96	B	97	THR	0	0.075	0.065	58.837	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	98	ARG	1	0.899	0.923	60.803	0.018	0.018	0.000	0.000	0.000	0.000
98	B	99	GLN	0	0.128	0.073	60.873	0.001	0.001	0.000	0.000	0.000	0.000
99	B	100	LYS	1	1.042	1.031	63.281	0.018	0.018	0.000	0.000	0.000	0.000
100	B	101	SER	0	-0.014	0.003	66.018	0.001	0.001	0.000	0.000	0.000	0.000
101	B	102	LEU	0	0.032	0.013	64.085	0.000	0.000	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.058	-0.061	65.106	0.000	0.000	0.000	0.000	0.000	0.000
103	B	104	ASN	0	-0.073	-0.031	68.202	0.000	0.000	0.000	0.000	0.000	0.000
104	B	105	ALA	0	-0.050	-0.034	70.345	0.000	0.000	0.000	0.000	0.000	0.000
105	B	106	TYR	0	0.021	0.021	69.964	0.000	0.000	0.000	0.000	0.000	0.000
106	B	107	GLY	0	0.025	0.022	71.933	0.000	0.000	0.000	0.000	0.000	0.000
107	B	108	ARG	1	0.932	0.955	73.746	0.014	0.014	0.000	0.000	0.000	0.000
108	B	109	LEU	0	0.011	0.012	75.290	0.000	0.000	0.000	0.000	0.000	0.000
109	B	110	SER	0	-0.038	-0.048	74.115	0.000	0.000	0.000	0.000	0.000	0.000
110	B	111	GLY	0	-0.025	0.012	76.758	0.000	0.000	0.000	0.000	0.000	0.000
111	B	112	MET	0	-0.051	-0.019	79.593	0.001	0.001	0.000	0.000	0.000	0.000
112	B	113	LEU	0	0.018	-0.006	82.525	0.000	0.000	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.027	-0.019	85.992	0.000	0.000	0.000	0.000	0.000	0.000
114	B	115	VAL	0	-0.045	-0.014	83.063	0.000	0.000	0.000	0.000	0.000	0.000
115	B	116	PRO	0	-0.010	0.013	86.387	0.000	0.000	0.000	0.000	0.000	0.000
116	B	117	ASP	-1	-0.867	-0.947	86.987	-0.014	-0.014	0.000	0.000	0.000	0.000
117	B	118	ALA	0	-0.077	-0.022	87.982	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:THR)