FMO DATABASE

FMODB ID: 765MK

Calculation Name: 3BF2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BF2

Chain ID: A

ChEMBL ID:

UniProt ID: A1KSW9

Base Structure: X-ray

Registration Date: 2023-09-23

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1051962.254344
FMO2-HF: Nuclear repulsion	1001098.873187
FMO2-HF: Total energy	-50863.381157
FMO2-MP2: Total energy	-51012.727454

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:30:LEU)

Summations of interaction energy for fragment #1(A:30: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.
-21.699	-6.917	10.179	-7.689	-17.274	-0.04

Interaction energy analysis for fragmet #1(A:30:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.051

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	32	TYR	0	0.035	-0.004	2.680	-2.890	0.434	0.799	-1.831	-2.292	-0.005
4	A	33	ARG	1	0.861	0.936	2.527	-0.580	1.775	0.787	-0.893	-2.249	0.005
5	A	34	SER	0	0.014	0.011	3.629	-0.552	-0.405	0.005	0.188	-0.341	0.000
6	A	35	TRP	0	0.046	0.011	2.631	-1.824	-0.069	0.457	-0.593	-1.619	-0.004
7	A	36	HIS	0	0.070	0.026	6.811	-0.044	-0.044	0.000	0.000	0.000	0.000
8	A	37	ILE	0	-0.027	-0.020	8.879	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	38	GLU	-1	-0.848	-0.909	11.599	-0.205	-0.205	0.000	0.000	0.000	0.000
10	A	39	GLY	0	0.037	0.021	15.106	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	40	GLY	0	0.035	0.008	16.185	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	41	GLN	0	0.060	0.018	16.419	-0.047	-0.047	0.000	0.000	0.000	0.000
13	A	42	ALA	0	-0.038	-0.021	17.641	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	43	LEU	0	-0.001	-0.001	14.216	0.001	0.001	0.000	0.000	0.000	0.000
15	A	44	GLN	0	-0.025	0.001	13.007	-0.061	-0.061	0.000	0.000	0.000	0.000
16	A	45	PHE	0	0.093	0.059	12.177	-0.088	-0.088	0.000	0.000	0.000	0.000
17	A	46	PRO	0	0.010	0.012	12.305	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	47	LEU	0	0.010	0.002	9.252	-0.161	-0.161	0.000	0.000	0.000	0.000
19	A	48	GLU	-1	-0.886	-0.958	7.667	-0.927	-0.927	0.000	0.000	0.000	0.000
20	A	49	THR	0	-0.051	-0.029	7.943	-0.190	-0.190	0.000	0.000	0.000	0.000
21	A	50	ALA	0	0.025	0.011	7.372	-0.138	-0.138	0.000	0.000	0.000	0.000
22	A	51	LEU	0	-0.021	-0.019	3.018	-1.505	-0.809	0.196	-0.148	-0.745	-0.001
23	A	52	TYR	0	-0.014	-0.007	3.676	-1.070	-0.601	0.015	-0.184	-0.300	-0.001
24	A	53	GLN	0	-0.026	-0.002	6.447	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	54	ALA	0	-0.041	-0.011	2.428	-0.863	-0.132	1.140	-0.532	-1.339	-0.002
26	A	55	SER	0	-0.035	-0.018	2.566	-3.867	-1.750	1.998	-1.814	-2.301	-0.018
27	A	56	GLY	0	-0.028	-0.021	2.410	-0.959	-0.124	1.023	-0.804	-1.053	0.000
28	A	57	ARG	1	0.830	0.913	3.060	1.274	0.580	0.085	0.855	-0.245	0.000
29	A	58	VAL	0	0.007	0.004	5.732	-0.053	-0.053	0.000	0.000	0.000	0.000
30	A	59	ASP	-1	-0.856	-0.921	8.340	-0.313	-0.313	0.000	0.000	0.000	0.000
31	A	60	ASP	-1	-0.789	-0.898	11.203	-0.229	-0.229	0.000	0.000	0.000	0.000
32	A	61	ALA	0	-0.007	-0.001	13.172	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	62	ALA	0	-0.031	-0.016	14.707	0.026	0.026	0.000	0.000	0.000	0.000
34	A	63	GLY	0	-0.008	0.004	13.769	0.031	0.031	0.000	0.000	0.000	0.000
35	A	64	ALA	0	-0.041	-0.001	9.435	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	65	GLN	0	-0.049	-0.035	7.818	0.066	0.066	0.000	0.000	0.000	0.000
37	A	66	MET	0	-0.049	-0.019	5.799	0.166	0.166	0.000	0.000	0.000	0.000
38	A	67	THR	0	-0.026	-0.029	8.693	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	68	LEU	0	-0.004	0.013	8.009	0.052	0.052	0.000	0.000	0.000	0.000
40	A	69	ARG	1	0.848	0.885	9.915	0.110	0.110	0.000	0.000	0.000	0.000
41	A	70	ILE	0	-0.005	-0.011	12.127	0.019	0.019	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.804	-0.865	15.226	-0.120	-0.120	0.000	0.000	0.000	0.000
43	A	72	SER	0	-0.067	-0.049	18.134	0.014	0.014	0.000	0.000	0.000	0.000
44	A	73	VAL	0	0.013	-0.009	18.043	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	74	SER	0	-0.033	-0.002	20.564	0.017	0.017	0.000	0.000	0.000	0.000
46	A	75	GLN	0	0.025	0.004	22.815	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	76	ASN	0	-0.024	-0.002	25.349	0.006	0.006	0.000	0.000	0.000	0.000
48	A	77	LYS	1	0.832	0.892	28.044	0.105	0.105	0.000	0.000	0.000	0.000
49	A	78	GLU	-1	-0.845	-0.902	30.784	-0.067	-0.067	0.000	0.000	0.000	0.000
50	A	79	THR	0	-0.004	-0.010	32.859	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.029	-0.010	33.041	0.003	0.003	0.000	0.000	0.000	0.000
52	A	81	THR	0	-0.021	-0.040	35.999	0.006	0.006	0.000	0.000	0.000	0.000
53	A	82	VAL	0	0.022	-0.002	38.899	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	83	THR	0	0.001	0.014	41.912	0.000	0.000	0.000	0.000	0.000	0.000
55	A	84	ARG	1	0.905	0.958	44.535	0.046	0.046	0.000	0.000	0.000	0.000
56	A	85	ALA	0	0.023	-0.003	46.612	0.000	0.000	0.000	0.000	0.000	0.000
57	A	86	ALA	0	-0.010	-0.007	45.905	0.000	0.000	0.000	0.000	0.000	0.000
58	A	87	VAL	0	-0.055	-0.037	44.877	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	88	ILE	0	0.010	0.022	38.365	0.002	0.002	0.000	0.000	0.000	0.000
60	A	89	ASN	0	-0.036	-0.014	40.179	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	90	GLU	-1	-0.854	-0.896	35.033	-0.073	-0.073	0.000	0.000	0.000	0.000
62	A	91	TYR	0	-0.009	-0.011	33.144	0.006	0.006	0.000	0.000	0.000	0.000
63	A	92	LEU	0	-0.023	-0.012	28.109	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	93	LEU	0	0.023	0.020	26.370	0.002	0.002	0.000	0.000	0.000	0.000
65	A	94	ILE	0	-0.051	-0.039	23.808	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	95	LEU	0	0.016	0.032	17.893	0.002	0.002	0.000	0.000	0.000	0.000
67	A	96	THR	0	-0.043	-0.045	19.651	0.010	0.010	0.000	0.000	0.000	0.000
68	A	97	VAL	0	0.018	0.013	14.740	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	98	GLU	-1	-0.891	-0.923	16.483	-0.103	-0.103	0.000	0.000	0.000	0.000
70	A	99	ALA	0	0.007	0.008	12.351	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	100	GLN	0	-0.036	-0.020	13.063	0.039	0.039	0.000	0.000	0.000	0.000
72	A	101	VAL	0	0.008	0.010	7.521	-0.054	-0.054	0.000	0.000	0.000	0.000
73	A	102	LEU	0	0.004	0.009	10.260	0.075	0.075	0.000	0.000	0.000	0.000
74	A	103	LYS	1	0.931	0.951	9.092	-0.410	-0.410	0.000	0.000	0.000	0.000
75	A	104	ARG	1	0.823	0.908	11.740	0.131	0.131	0.000	0.000	0.000	0.000
76	A	105	GLY	0	0.028	0.029	14.408	0.011	0.011	0.000	0.000	0.000	0.000
77	A	106	GLU	-1	-0.883	-0.936	15.923	0.031	0.031	0.000	0.000	0.000	0.000
78	A	107	PRO	0	-0.015	-0.016	14.207	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	108	VAL	0	-0.039	-0.018	9.999	0.051	0.051	0.000	0.000	0.000	0.000
80	A	109	GLY	0	0.025	0.015	11.638	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	110	LYS	1	0.926	0.960	13.095	-0.146	-0.146	0.000	0.000	0.000	0.000
82	A	111	PRO	0	0.046	0.028	13.755	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	112	MET	0	-0.063	-0.029	8.732	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	113	THR	0	0.024	0.011	14.193	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	114	VAL	0	-0.046	-0.015	12.253	0.015	0.015	0.000	0.000	0.000	0.000
86	A	115	SER	0	0.005	0.003	15.705	0.009	0.009	0.000	0.000	0.000	0.000
87	A	116	VAL	0	-0.030	0.007	17.327	0.012	0.012	0.000	0.000	0.000	0.000
88	A	117	ARG	1	0.882	0.927	20.047	0.121	0.121	0.000	0.000	0.000	0.000
89	A	118	ARG	1	0.777	0.862	19.655	0.216	0.216	0.000	0.000	0.000	0.000
90	A	119	VAL	0	0.021	0.020	26.094	0.003	0.003	0.000	0.000	0.000	0.000
91	A	120	LEU	0	-0.036	-0.009	29.564	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	121	ALA	0	0.026	-0.008	31.627	0.008	0.008	0.000	0.000	0.000	0.000
93	A	122	TYR	0	-0.043	-0.005	33.567	0.001	0.001	0.000	0.000	0.000	0.000
94	A	123	ALA	0	0.004	0.000	36.366	0.006	0.006	0.000	0.000	0.000	0.000
95	A	124	ASP	-1	-0.910	-0.971	38.275	-0.078	-0.078	0.000	0.000	0.000	0.000
96	A	125	ASN	0	-0.129	-0.070	40.655	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	126	GLU	-1	-0.850	-0.912	35.562	-0.102	-0.102	0.000	0.000	0.000	0.000
98	A	127	ILE	0	-0.082	-0.060	36.261	0.001	0.001	0.000	0.000	0.000	0.000
99	A	128	LEU	0	-0.006	0.032	35.562	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	129	GLY	0	0.031	0.020	34.777	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	130	LYS	1	0.969	0.982	34.069	0.083	0.083	0.000	0.000	0.000	0.000
102	A	131	GLN	0	-0.013	-0.012	33.511	0.003	0.003	0.000	0.000	0.000	0.000
103	A	132	GLU	-1	-0.881	-0.946	30.879	-0.130	-0.130	0.000	0.000	0.000	0.000
104	A	133	GLU	-1	-0.826	-0.916	29.434	-0.131	-0.131	0.000	0.000	0.000	0.000
105	A	134	GLU	-1	-0.740	-0.857	28.768	-0.135	-0.135	0.000	0.000	0.000	0.000
106	A	135	ALA	0	-0.049	-0.025	27.118	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	136	ALA	0	0.004	0.003	25.069	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	137	LEU	0	0.052	0.020	23.884	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	138	TRP	0	-0.008	-0.031	23.367	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	139	ALA	0	-0.086	-0.036	20.808	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	140	GLU	-1	-0.803	-0.880	19.236	-0.267	-0.267	0.000	0.000	0.000	0.000
112	A	141	MET	0	-0.034	-0.019	18.685	-0.028	-0.028	0.000	0.000	0.000	0.000
113	A	142	ARG	1	0.885	0.930	17.543	0.250	0.250	0.000	0.000	0.000	0.000
114	A	143	GLN	0	-0.041	-0.020	14.265	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	144	ASP	-1	-0.780	-0.871	13.796	-0.373	-0.373	0.000	0.000	0.000	0.000
116	A	145	ALA	0	0.032	0.002	13.750	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	146	ALA	0	0.006	0.000	11.054	-0.034	-0.034	0.000	0.000	0.000	0.000
118	A	147	GLU	-1	-0.862	-0.924	9.403	-0.840	-0.840	0.000	0.000	0.000	0.000
119	A	148	GLN	0	-0.086	-0.055	9.025	-0.073	-0.073	0.000	0.000	0.000	0.000
120	A	149	ILE	0	0.007	0.001	8.055	0.041	0.041	0.000	0.000	0.000	0.000
121	A	150	VAL	0	0.027	0.014	3.855	-0.226	-0.015	0.002	-0.031	-0.182	0.000
122	A	151	ARG	1	0.953	0.990	4.262	-0.605	-0.415	-0.001	-0.023	-0.167	0.000
123	A	152	ARG	1	0.881	0.921	6.403	0.367	0.367	0.000	0.000	0.000	0.000
124	A	153	LEU	0	-0.032	-0.014	3.408	0.014	0.395	0.024	-0.076	-0.329	0.000
125	A	154	THR	0	-0.092	-0.055	2.100	-3.694	-1.075	3.618	-2.496	-3.741	-0.013
126	A	155	PHE	0	-0.028	-0.019	3.373	2.258	1.904	0.031	0.693	-0.371	-0.001
127	A	156	LEU	0	0.044	0.026	6.005	0.045	0.045	0.000	0.000	0.000	0.000
128	A	157	LYS	1	0.873	0.939	5.870	-2.494	-2.494	0.000	0.000	0.000	0.000
129	A	158	ALA	0	-0.040	-0.012	7.570	-0.098	-0.098	0.000	0.000	0.000	0.000
130	A	159	GLU	-1	-0.908	-0.931	9.630	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:LEU)