FMO DATABASE

FMODB ID: JL269

Calculation Name: 3A7M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7M

Chain ID: A

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:

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-805631.530487
FMO2-HF: Nuclear repulsion	759962.579027
FMO2-HF: Total energy	-45668.951461
FMO2-MP2: Total energy	-45802.789886

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:2:THR)

Summations of interaction energy for fragment #1(A: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.
-13.539	-8.451	4.452	-4.212	-5.328	0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.010

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	4	THR	0	0.011	0.000	2.900	-4.892	-2.010	0.257	-1.352	-1.787	0.012
4	A	5	VAL	0	0.024	0.017	1.985	-2.884	-2.454	3.869	-2.152	-2.147	0.003
5	A	6	GLU	-1	-0.926	-0.968	2.721	-6.541	-4.765	0.326	-0.708	-1.394	-0.004
6	A	7	PHE	0	-0.028	-0.016	5.439	0.423	0.423	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.033	0.015	7.051	-0.083	-0.083	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.027	-0.028	7.197	-0.312	-0.312	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.963	0.995	6.692	1.362	1.362	0.000	0.000	0.000	0.000
10	A	11	TRP	0	0.121	0.049	11.139	0.000	0.000	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.048	-0.010	10.863	-0.095	-0.095	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.950	0.967	12.899	0.496	0.496	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.007	0.015	14.526	0.001	0.001	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.035	0.008	16.949	0.012	0.012	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.053	-0.019	15.570	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.011	-0.017	18.143	0.005	0.005	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.009	-0.004	20.485	0.017	0.017	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.025	0.026	22.252	0.008	0.008	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.046	-0.036	22.829	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.022	0.005	24.200	0.006	0.006	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.012	0.003	26.692	0.007	0.007	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.898	-0.958	27.224	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.035	-0.014	27.780	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.023	0.022	30.851	0.002	0.002	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.050	-0.034	31.557	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.851	0.936	31.111	0.071	0.071	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.002	0.013	35.084	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.950	-0.970	32.916	-0.090	-0.090	0.000	0.000	0.000	0.000
29	A	30	TRP	0	-0.002	-0.047	33.126	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.905	-0.947	33.827	-0.097	-0.097	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.012	-0.006	29.866	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.032	-0.012	29.264	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.004	0.002	29.219	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.041	-0.014	29.010	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	36	GLN	0	-0.026	-0.024	24.710	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.914	-0.948	24.647	-0.135	-0.135	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.049	0.029	24.805	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.039	0.001	21.721	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	40	TYR	0	-0.099	-0.081	20.427	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.033	0.010	20.659	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	42	GLN	0	0.021	0.033	19.505	0.019	0.019	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.080	-0.053	16.284	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.004	-0.017	16.612	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.873	-0.924	18.576	-0.091	-0.091	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.057	-0.036	13.904	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.087	-0.063	12.793	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	48	MET	0	-0.072	-0.027	14.466	0.069	0.069	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.913	-0.939	16.357	-0.196	-0.196	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.831	0.930	9.735	0.739	0.739	0.000	0.000	0.000	0.000
50	A	51	GLN	0	0.021	0.017	11.964	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.018	-0.022	11.328	0.021	0.021	0.000	0.000	0.000	0.000
52	A	53	PRO	0	-0.053	-0.022	7.586	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.039	0.008	7.937	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.012	0.010	8.770	-0.234	-0.234	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.023	0.005	9.363	0.364	0.364	0.000	0.000	0.000	0.000
56	A	57	THR	0	0.061	0.030	10.839	-0.195	-0.195	0.000	0.000	0.000	0.000
57	A	58	ARG	1	1.060	1.005	13.269	-0.505	-0.505	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.011	0.014	13.107	-0.057	-0.057	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.005	0.007	8.376	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.031	-0.018	12.162	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.890	-0.957	15.026	0.446	0.446	0.000	0.000	0.000	0.000
62	A	63	MET	0	-0.050	-0.018	11.685	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.002	-0.006	11.529	-0.092	-0.092	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.012	0.019	14.314	-0.099	-0.099	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.016	-0.007	17.694	-0.064	-0.064	0.000	0.000	0.000	0.000
66	A	67	TYR	0	0.028	0.017	13.068	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	68	ILE	0	0.006	0.000	16.230	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.954	0.964	19.017	-0.186	-0.186	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.005	0.009	19.754	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.042	-0.020	19.054	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.009	0.001	22.012	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.856	-0.937	24.465	0.081	0.081	0.000	0.000	0.000	0.000
73	A	74	ASN	0	-0.023	-0.009	23.990	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.816	-0.874	24.270	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.020	0.013	27.700	0.001	0.001	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.022	-0.025	29.603	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.001	0.011	28.600	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.896	0.938	29.190	0.043	0.043	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.026	0.016	33.449	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.009	0.020	33.498	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	LEU	0	0.029	0.003	33.597	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	GLN	0	-0.046	-0.026	36.695	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	GLN	0	0.026	0.016	39.130	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.934	0.974	39.379	0.040	0.040	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.018	-0.007	38.567	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.879	-0.931	42.479	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.923	-0.981	44.398	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.042	-0.024	42.946	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.033	-0.018	45.954	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.092	-0.041	48.301	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.047	-0.015	48.944	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.021	0.008	47.777	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.023	0.030	52.067	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.046	-0.036	52.583	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	SER	0	0.031	0.005	53.741	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	THR	0	0.068	-0.002	55.641	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.978	0.993	53.843	0.022	0.022	0.000	0.000	0.000	0.000
98	A	99	GLN	0	0.078	0.032	49.254	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.974	1.007	53.555	0.013	0.013	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.008	-0.008	56.246	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.019	-0.007	52.072	0.001	0.001	0.000	0.000	0.000	0.000
102	A	103	ASN	0	0.010	0.010	50.475	0.003	0.003	0.000	0.000	0.000	0.000
103	A	104	ASN	0	-0.057	-0.033	53.053	0.003	0.003	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.005	0.000	54.853	0.002	0.002	0.000	0.000	0.000	0.000
105	A	106	TYR	0	0.049	0.024	46.108	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.040	0.026	52.249	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.912	0.958	53.384	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	109	LEU	0	-0.013	0.000	50.764	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.048	0.013	49.739	0.001	0.001	0.000	0.000	0.000	0.000
110	A	111	GLY	0	-0.053	-0.011	51.569	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.078	-0.030	54.329	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.010	-0.001	54.662	0.002	0.002	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.002	-0.004	52.705	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.005	-0.010	56.754	0.001	0.001	0.000	0.000	0.000	0.000
115	A	116	PRO	0	-0.025	0.010	57.101	-0.001	-0.001	0.000	0.000	0.000	0.000

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