FMO DATABASE

FMODB ID: 7GKGK

Calculation Name: 3BK6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BK6

Chain ID: A

ChEMBL ID:

UniProt ID: O59180

Base Structure: X-ray

Registration Date: 2023-03-14

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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1412118.189539
FMO2-HF: Nuclear repulsion	1344632.046208
FMO2-HF: Total energy	-67486.143332
FMO2-MP2: Total energy	-67682.142239

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:55:MET)

Summations of interaction energy for fragment #1(A:55:MET)

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.
-2.324	1.642	1.839	-2.133	-3.671	-0.008

Interaction energy analysis for fragmet #1(A:55:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.000

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	57	PHE	0	0.000	-0.003	2.751	-2.576	1.390	1.839	-2.133	-3.671	-0.008
4	A	58	GLU	-1	-0.919	-0.955	5.786	-0.192	-0.192	0.000	0.000	0.000	0.000
5	A	59	LYS	1	0.918	0.945	9.377	0.365	0.365	0.000	0.000	0.000	0.000
6	A	60	ALA	0	0.033	0.023	11.653	0.005	0.005	0.000	0.000	0.000	0.000
7	A	61	VAL	0	0.004	0.012	13.008	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	62	ILE	0	-0.005	-0.011	16.403	0.043	0.043	0.000	0.000	0.000	0.000
9	A	63	VAL	0	0.003	0.001	18.994	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	64	ASP	-1	-0.772	-0.843	22.507	0.059	0.059	0.000	0.000	0.000	0.000
11	A	65	LEU	0	0.005	-0.012	22.848	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	66	ARG	1	0.895	0.930	25.409	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	67	THR	0	-0.020	-0.005	25.976	0.006	0.006	0.000	0.000	0.000	0.000
14	A	68	GLN	0	-0.012	0.002	20.916	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	69	VAL	0	0.002	-0.009	25.435	0.003	0.003	0.000	0.000	0.000	0.000
16	A	70	LEU	0	-0.053	-0.019	24.978	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	71	ASP	-1	-0.823	-0.888	27.219	-0.078	-0.078	0.000	0.000	0.000	0.000
18	A	72	VAL	0	-0.036	-0.009	28.823	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	73	PRO	0	-0.011	-0.008	29.716	0.000	0.000	0.000	0.000	0.000	0.000
20	A	74	VAL	0	0.020	0.002	32.153	0.007	0.007	0.000	0.000	0.000	0.000
21	A	75	GLN	0	-0.067	-0.046	35.371	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	76	GLU	-1	-0.793	-0.854	37.670	-0.064	-0.064	0.000	0.000	0.000	0.000
23	A	77	THR	0	-0.019	-0.020	40.613	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	78	ILE	0	0.000	0.002	43.212	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	79	THR	0	0.014	0.019	46.691	0.001	0.001	0.000	0.000	0.000	0.000
26	A	80	LYS	1	0.813	0.888	48.724	0.021	0.021	0.000	0.000	0.000	0.000
27	A	81	ASP	-1	-0.818	-0.912	51.238	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	82	ASN	0	-0.110	-0.049	52.068	0.000	0.000	0.000	0.000	0.000	0.000
29	A	83	VAL	0	-0.023	-0.006	50.282	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	84	PRO	0	-0.011	0.000	47.491	0.000	0.000	0.000	0.000	0.000	0.000
31	A	85	VAL	0	-0.016	-0.024	44.273	0.001	0.001	0.000	0.000	0.000	0.000
32	A	86	ARG	1	0.815	0.887	40.636	0.071	0.071	0.000	0.000	0.000	0.000
33	A	87	VAL	0	0.023	0.010	39.511	0.003	0.003	0.000	0.000	0.000	0.000
34	A	88	ASN	0	-0.014	-0.014	34.861	0.000	0.000	0.000	0.000	0.000	0.000
35	A	89	ALA	0	0.040	0.014	34.712	0.006	0.006	0.000	0.000	0.000	0.000
36	A	90	VAL	0	0.000	0.012	31.162	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	91	VAL	0	0.009	0.013	29.743	0.008	0.008	0.000	0.000	0.000	0.000
38	A	92	TYR	0	-0.039	-0.045	29.748	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	93	PHE	0	-0.023	-0.033	23.579	0.007	0.007	0.000	0.000	0.000	0.000
40	A	94	ARG	1	0.861	0.923	26.509	-0.059	-0.059	0.000	0.000	0.000	0.000
41	A	95	VAL	0	0.031	0.017	21.388	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	96	VAL	0	-0.038	-0.020	24.597	0.011	0.011	0.000	0.000	0.000	0.000
43	A	97	ASP	-1	-0.808	-0.889	24.461	0.132	0.132	0.000	0.000	0.000	0.000
44	A	98	PRO	0	0.025	-0.002	19.219	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	99	VAL	0	0.023	0.024	19.980	0.008	0.008	0.000	0.000	0.000	0.000
46	A	100	LYS	1	0.878	0.921	21.449	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	101	ALA	0	-0.001	0.015	20.815	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	102	VAL	0	-0.036	-0.020	16.035	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	103	THR	0	-0.051	-0.034	19.097	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	104	GLN	0	-0.052	-0.021	21.429	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	105	VAL	0	-0.011	-0.005	21.980	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	106	LYS	1	0.959	0.996	15.048	0.154	0.154	0.000	0.000	0.000	0.000
53	A	107	ASN	0	0.025	-0.021	18.153	0.009	0.009	0.000	0.000	0.000	0.000
54	A	108	TYR	0	0.103	0.051	18.237	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	109	ILE	0	0.020	0.035	19.986	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	110	MET	0	-0.025	-0.016	20.335	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	111	ALA	0	0.012	0.017	23.734	0.002	0.002	0.000	0.000	0.000	0.000
58	A	112	THR	0	0.052	0.012	25.749	0.003	0.003	0.000	0.000	0.000	0.000
59	A	113	SER	0	0.009	0.028	26.428	0.001	0.001	0.000	0.000	0.000	0.000
60	A	114	GLN	0	0.018	0.008	27.584	0.008	0.008	0.000	0.000	0.000	0.000
61	A	115	ILE	0	0.008	0.019	29.886	0.002	0.002	0.000	0.000	0.000	0.000
62	A	116	SER	0	0.013	-0.001	30.682	0.006	0.006	0.000	0.000	0.000	0.000
63	A	117	GLN	0	-0.025	-0.011	29.366	0.001	0.001	0.000	0.000	0.000	0.000
64	A	118	THR	0	-0.043	-0.021	33.549	0.002	0.002	0.000	0.000	0.000	0.000
65	A	119	THR	0	-0.018	-0.021	35.600	0.004	0.004	0.000	0.000	0.000	0.000
66	A	120	LEU	0	0.008	0.011	36.595	0.003	0.003	0.000	0.000	0.000	0.000
67	A	121	ARG	1	0.885	0.938	36.129	0.064	0.064	0.000	0.000	0.000	0.000
68	A	122	SER	0	-0.014	-0.005	39.857	0.002	0.002	0.000	0.000	0.000	0.000
69	A	123	VAL	0	0.018	0.012	41.389	0.002	0.002	0.000	0.000	0.000	0.000
70	A	124	ILE	0	0.000	-0.009	41.097	0.001	0.001	0.000	0.000	0.000	0.000
71	A	125	GLY	0	0.018	0.017	44.205	0.001	0.001	0.000	0.000	0.000	0.000
72	A	126	GLN	0	-0.088	-0.049	44.603	0.004	0.004	0.000	0.000	0.000	0.000
73	A	127	ALA	0	0.001	0.021	46.906	0.003	0.003	0.000	0.000	0.000	0.000
74	A	128	HIS	0	0.009	-0.008	48.742	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	129	LEU	0	-0.033	-0.036	49.513	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	130	ASP	-1	-0.858	-0.921	50.221	-0.024	-0.024	0.000	0.000	0.000	0.000
77	A	131	GLU	-1	-0.742	-0.861	48.934	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	132	LEU	0	-0.009	-0.012	44.744	0.000	0.000	0.000	0.000	0.000	0.000
79	A	133	LEU	0	-0.093	-0.039	46.410	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	134	SER	0	-0.034	-0.035	49.072	0.000	0.000	0.000	0.000	0.000	0.000
81	A	135	GLU	-1	-0.834	-0.884	49.465	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	136	ARG	1	0.849	0.920	41.780	0.038	0.038	0.000	0.000	0.000	0.000
83	A	137	ASP	-1	-0.903	-0.942	44.324	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	138	LYS	1	0.845	0.907	44.510	0.013	0.013	0.000	0.000	0.000	0.000
85	A	139	LEU	0	0.033	0.017	43.455	0.000	0.000	0.000	0.000	0.000	0.000
86	A	140	ASN	0	0.037	0.017	40.420	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	141	MET	0	-0.002	0.007	40.025	0.002	0.002	0.000	0.000	0.000	0.000
88	A	142	GLN	0	-0.014	-0.017	41.451	0.003	0.003	0.000	0.000	0.000	0.000
89	A	143	LEU	0	0.000	-0.002	37.639	0.000	0.000	0.000	0.000	0.000	0.000
90	A	144	GLN	0	-0.068	-0.035	35.952	0.000	0.000	0.000	0.000	0.000	0.000
91	A	145	ARG	1	0.821	0.878	36.966	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	146	ILE	0	-0.023	-0.002	37.449	0.003	0.003	0.000	0.000	0.000	0.000
93	A	147	ILE	0	-0.002	-0.006	32.342	0.001	0.001	0.000	0.000	0.000	0.000
94	A	148	ASP	-1	-0.800	-0.890	32.971	0.019	0.019	0.000	0.000	0.000	0.000
95	A	149	GLU	-1	-0.815	-0.873	33.204	0.015	0.015	0.000	0.000	0.000	0.000
96	A	150	ALA	0	-0.024	-0.014	33.599	0.003	0.003	0.000	0.000	0.000	0.000
97	A	151	THR	0	0.001	-0.004	28.107	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	152	ASH	0	-0.051	-0.033	28.916	0.007	0.007	0.000	0.000	0.000	0.000
99	A	153	PRO	0	-0.034	-0.015	29.795	0.011	0.011	0.000	0.000	0.000	0.000
100	A	154	TRP	0	0.001	-0.020	24.813	0.005	0.005	0.000	0.000	0.000	0.000
101	A	155	GLY	0	-0.004	0.001	24.857	0.007	0.007	0.000	0.000	0.000	0.000
102	A	156	ILE	0	-0.026	-0.009	23.283	0.008	0.008	0.000	0.000	0.000	0.000
103	A	157	LYS	1	0.984	1.001	27.166	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	158	VAL	0	0.003	-0.019	29.967	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	159	THR	0	-0.061	-0.026	31.938	0.003	0.003	0.000	0.000	0.000	0.000
106	A	160	ALA	0	0.032	0.009	33.746	0.000	0.000	0.000	0.000	0.000	0.000
107	A	161	VAL	0	-0.007	-0.006	33.637	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	162	GLU	-1	-0.899	-0.917	35.801	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	163	ILE	0	0.015	-0.001	36.894	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	164	LYS	1	0.803	0.892	32.744	0.079	0.079	0.000	0.000	0.000	0.000
111	A	165	ASP	-1	-0.819	-0.901	37.511	-0.063	-0.063	0.000	0.000	0.000	0.000
112	A	166	VAL	0	-0.024	-0.033	40.193	0.000	0.000	0.000	0.000	0.000	0.000
113	A	167	GLU	-1	-0.947	-0.966	41.126	-0.070	-0.070	0.000	0.000	0.000	0.000
114	A	168	LEU	0	0.014	-0.005	44.554	0.002	0.002	0.000	0.000	0.000	0.000
115	A	169	PRO	0	0.024	0.012	47.986	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	170	ALA	0	0.051	0.023	49.792	0.002	0.002	0.000	0.000	0.000	0.000
117	A	171	GLY	0	-0.031	-0.015	51.171	0.001	0.001	0.000	0.000	0.000	0.000
118	A	172	MET	0	0.031	0.013	52.842	0.002	0.002	0.000	0.000	0.000	0.000
119	A	173	GLN	0	0.063	0.025	49.994	0.000	0.000	0.000	0.000	0.000	0.000
120	A	174	LYS	1	0.956	0.972	53.615	0.042	0.042	0.000	0.000	0.000	0.000
121	A	175	ALA	0	-0.034	-0.005	56.663	0.002	0.002	0.000	0.000	0.000	0.000
122	A	176	MET	0	0.047	0.019	52.762	0.002	0.002	0.000	0.000	0.000	0.000
123	A	177	ALA	0	0.008	0.016	56.656	0.002	0.002	0.000	0.000	0.000	0.000
124	A	178	ARG	1	0.995	0.988	58.446	0.031	0.031	0.000	0.000	0.000	0.000
125	A	179	GLN	0	-0.015	0.001	61.131	0.000	0.000	0.000	0.000	0.000	0.000
126	A	180	ALA	0	0.033	0.014	59.644	0.001	0.001	0.000	0.000	0.000	0.000
127	A	181	GLU	-1	-0.984	-0.986	61.691	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	182	ALA	0	0.013	0.000	63.616	0.001	0.001	0.000	0.000	0.000	0.000
129	A	183	GLU	-1	-0.824	-0.897	64.420	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	184	ARG	1	0.933	0.969	63.151	0.019	0.019	0.000	0.000	0.000	0.000
131	A	185	GLU	-1	-0.832	-0.899	65.885	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	186	ARG	1	0.844	0.915	69.214	0.017	0.017	0.000	0.000	0.000	0.000
133	A	187	ARG	1	0.998	0.981	64.351	0.014	0.014	0.000	0.000	0.000	0.000
134	A	188	ALA	0	-0.013	0.013	69.481	0.001	0.001	0.000	0.000	0.000	0.000
135	A	189	ARG	1	0.852	0.904	71.062	0.016	0.016	0.000	0.000	0.000	0.000
136	A	190	ILE	0	-0.008	-0.005	71.562	0.001	0.001	0.000	0.000	0.000	0.000
137	A	191	THR	0	-0.044	-0.034	71.491	0.001	0.001	0.000	0.000	0.000	0.000
138	A	192	LEU	0	-0.011	0.009	73.964	0.001	0.001	0.000	0.000	0.000	0.000
139	A	193	ALA	0	0.045	0.021	76.434	0.001	0.001	0.000	0.000	0.000	0.000
140	A	194	GLU	-1	-0.869	-0.917	76.770	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	195	ALA	0	0.000	0.006	76.885	0.001	0.001	0.000	0.000	0.000	0.000
142	A	196	GLU	-1	-0.915	-0.966	78.904	-0.009	-0.009	0.000	0.000	0.000	0.000
143	A	197	ARG	1	0.855	0.917	80.509	0.010	0.010	0.000	0.000	0.000	0.000
144	A	198	GLN	0	-0.025	-0.025	78.108	0.001	0.001	0.000	0.000	0.000	0.000
145	A	199	ALA	0	-0.002	0.001	82.650	0.000	0.000	0.000	0.000	0.000	0.000
146	A	200	ALA	0	-0.008	-0.012	84.265	0.000	0.000	0.000	0.000	0.000	0.000
147	A	201	GLU	-1	-0.875	-0.913	86.177	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	202	LYS	1	0.805	0.871	84.879	0.004	0.004	0.000	0.000	0.000	0.000
149	A	203	LEU	0	-0.017	-0.007	86.948	0.000	0.000	0.000	0.000	0.000	0.000
150	A	204	ARG	1	0.751	0.846	89.869	0.005	0.005	0.000	0.000	0.000	0.000
151	A	205	GLU	-1	-0.772	-0.858	89.763	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	206	ALA	0	-0.034	-0.019	91.089	0.000	0.000	0.000	0.000	0.000	0.000
153	A	207	ALA	0	-0.023	-0.016	93.061	0.000	0.000	0.000	0.000	0.000	0.000
154	A	208	GLU	-1	-0.816	-0.892	94.917	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	209	ILE	0	-0.003	-0.003	93.238	0.000	0.000	0.000	0.000	0.000	0.000
156	A	210	ILE	0	-0.061	-0.032	97.032	0.000	0.000	0.000	0.000	0.000	0.000
157	A	211	SER	0	-0.024	-0.017	98.757	0.000	0.000	0.000	0.000	0.000	0.000
158	A	212	GLU	-1	-0.958	-0.963	100.710	-0.003	-0.003	0.000	0.000	0.000	0.000
159	A	213	HIS	0	-0.042	-0.019	99.980	0.000	0.000	0.000	0.000	0.000	0.000
160	A	214	PRO	0	0.046	0.021	100.875	0.000	0.000	0.000	0.000	0.000	0.000
161	A	215	MET	0	-0.043	-0.025	101.960	0.000	0.000	0.000	0.000	0.000	0.000
162	A	216	ALA	0	0.018	0.006	97.157	0.000	0.000	0.000	0.000	0.000	0.000
163	A	217	LEU	0	-0.012	-0.009	95.333	0.000	0.000	0.000	0.000	0.000	0.000
164	A	218	GLN	0	0.010	0.025	97.677	0.000	0.000	0.000	0.000	0.000	0.000
165	A	219	LEU	0	0.025	-0.005	98.997	0.000	0.000	0.000	0.000	0.000	0.000
166	A	220	ARG	1	0.970	0.990	91.435	0.002	0.002	0.000	0.000	0.000	0.000
167	A	221	THR	0	-0.004	-0.016	95.101	0.000	0.000	0.000	0.000	0.000	0.000
168	A	222	LEU	0	-0.046	-0.018	96.792	0.000	0.000	0.000	0.000	0.000	0.000
169	A	223	GLN	0	-0.036	-0.009	94.543	0.000	0.000	0.000	0.000	0.000	0.000
170	A	224	THR	0	-0.053	-0.012	92.624	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:55:MET)