FMO DATABASE

FMODB ID: M9VKZ

Calculation Name: 1BKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1BKB

Chain ID: A

ChEMBL ID:

UniProt ID: P56635

Base Structure: X-ray

Registration Date: 2023-09-27

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	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1121849.11619
FMO2-HF: Nuclear repulsion	1068823.431399
FMO2-HF: Total energy	-53025.684791
FMO2-MP2: Total energy	-53179.952198

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:LYS)

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

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.
-77.345	-73.4	0.88	-1.934	-2.89	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.971

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	VAL	0	-0.018	-0.013	2.659	-14.922	-11.126	0.882	-1.921	-2.756	-0.014
4	A	7	MET	0	0.026	0.003	4.892	4.097	4.215	-0.001	-0.012	-0.105	0.000
5	A	8	SER	0	-0.019	-0.006	8.605	-0.919	-0.919	0.000	0.000	0.000	0.000
6	A	9	THR	0	0.005	0.017	11.359	0.102	0.102	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.980	0.997	13.208	16.723	16.723	0.000	0.000	0.000	0.000
8	A	11	TYR	0	-0.007	-0.017	15.282	-0.416	-0.416	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.020	0.002	19.801	0.229	0.229	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.848	-0.923	23.537	-10.899	-10.899	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.017	0.002	26.450	0.093	0.093	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.077	-0.055	27.595	0.186	0.186	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.932	-0.962	27.259	-10.972	-10.972	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.067	-0.012	24.292	-0.067	-0.067	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.933	0.941	28.251	10.166	10.166	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.906	-0.947	28.952	-9.779	-9.779	0.000	0.000	0.000	0.000
17	A	20	GLY	0	-0.034	-0.020	28.309	0.117	0.117	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.049	-0.021	25.249	-0.384	-0.384	0.000	0.000	0.000	0.000
19	A	22	TYR	0	0.019	-0.005	20.429	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.030	0.004	20.483	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	24	VAL	0	0.004	0.007	15.315	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.045	-0.016	18.545	0.536	0.536	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.910	-0.962	18.836	-15.019	-15.019	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.013	-0.007	14.930	-0.289	-0.289	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.820	-0.915	14.623	-19.385	-19.385	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.031	0.007	15.048	0.849	0.849	0.000	0.000	0.000	0.000
27	A	30	CYS	0	-0.027	-0.024	17.781	0.551	0.551	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.957	0.991	21.558	11.973	11.973	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.016	-0.018	24.516	0.280	0.280	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.043	-0.029	27.247	0.155	0.155	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.863	-0.937	30.597	-9.074	-9.074	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.022	-0.009	29.786	-0.315	-0.315	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.941	-0.949	33.040	-8.199	-8.199	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.908	0.955	32.870	9.212	9.212	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.054	0.031	36.961	0.233	0.233	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.963	0.964	38.074	7.554	7.554	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.023	0.024	39.775	0.145	0.145	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.016	0.019	40.281	0.178	0.178	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.971	0.983	41.522	6.284	6.284	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.017	-0.001	42.366	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.001	0.011	38.488	-0.111	-0.111	0.000	0.000	0.000	0.000
42	A	45	SER	0	0.056	0.026	33.247	0.136	0.136	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.012	-0.003	36.074	0.095	0.095	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.875	0.935	32.799	8.638	8.638	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.032	0.007	30.813	0.248	0.248	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.951	0.989	31.456	9.323	9.323	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.010	-0.005	26.547	0.215	0.215	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.010	0.007	29.170	-0.174	-0.174	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.023	-0.001	24.983	0.061	0.061	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.025	-0.013	25.239	0.175	0.175	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.051	0.021	21.219	-0.339	-0.339	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.046	-0.025	18.666	0.504	0.504	0.000	0.000	0.000	0.000
53	A	56	PHE	0	-0.005	-0.010	14.912	0.032	0.032	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.785	-0.845	18.967	-14.892	-14.892	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.008	0.015	21.062	0.635	0.635	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.017	-0.005	23.188	0.667	0.667	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.926	0.962	24.713	9.768	9.768	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.844	0.889	20.054	15.195	15.195	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.028	-0.030	26.029	0.483	0.483	0.000	0.000	0.000	0.000
60	A	63	LEU	0	0.036	0.023	23.712	-0.229	-0.229	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.008	-0.005	27.533	0.441	0.441	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.002	0.010	25.264	-0.093	-0.093	0.000	0.000	0.000	0.000
63	A	66	PRO	0	-0.012	-0.020	28.338	0.307	0.307	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.022	-0.026	29.334	-0.281	-0.281	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.849	-0.914	29.511	-10.135	-10.135	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.038	-0.001	25.420	-0.239	-0.239	0.000	0.000	0.000	0.000
67	A	70	GLN	0	-0.010	-0.015	19.958	0.005	0.005	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.027	-0.010	21.605	-0.116	-0.116	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.871	-0.947	13.771	-21.868	-21.868	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.055	-0.020	17.949	0.480	0.480	0.000	0.000	0.000	0.000
71	A	74	PRO	0	-0.030	-0.005	14.997	-0.883	-0.883	0.000	0.000	0.000	0.000
72	A	75	ILE	0	-0.002	-0.005	13.041	1.330	1.330	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.040	-0.027	14.296	-1.080	-1.080	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.860	-0.884	14.183	-20.817	-20.817	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.908	0.950	16.587	13.721	13.721	0.000	0.000	0.000	0.000
76	A	79	PHE	0	-0.009	-0.005	15.464	0.105	0.105	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.031	0.019	20.259	0.120	0.120	0.000	0.000	0.000	0.000
78	A	81	ALA	0	-0.008	-0.003	20.097	-0.465	-0.465	0.000	0.000	0.000	0.000
79	A	82	GLN	0	0.040	0.023	22.140	0.665	0.665	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.035	-0.017	23.629	-0.532	-0.532	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.035	-0.013	21.869	0.573	0.573	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.032	-0.035	24.616	0.499	0.499	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.023	0.006	24.954	-0.513	-0.513	0.000	0.000	0.000	0.000
84	A	87	SER	0	0.022	0.030	24.586	0.455	0.455	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.006	-0.008	26.936	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.894	-0.950	23.252	-12.561	-12.561	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.047	-0.033	19.659	-0.766	-0.766	0.000	0.000	0.000	0.000
88	A	91	ILE	0	-0.011	0.006	21.087	0.742	0.742	0.000	0.000	0.000	0.000
89	A	92	GLN	0	0.040	0.038	20.233	-0.364	-0.364	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.010	-0.016	18.708	0.822	0.822	0.000	0.000	0.000	0.000
91	A	94	MET	0	0.025	0.020	19.559	-0.583	-0.583	0.000	0.000	0.000	0.000
92	A	95	ASP	-1	-0.758	-0.870	16.118	-17.992	-17.992	0.000	0.000	0.000	0.000
93	A	96	MET	0	-0.023	-0.006	19.148	0.055	0.055	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.736	0.831	14.636	19.615	19.615	0.000	0.000	0.000	0.000
95	A	98	ASP	-1	-0.797	-0.903	15.613	-19.131	-19.131	0.000	0.000	0.000	0.000
96	A	99	TYR	0	-0.031	-0.023	19.078	0.217	0.217	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.820	0.924	12.319	21.663	21.663	0.000	0.000	0.000	0.000
98	A	101	THR	0	-0.032	-0.026	17.257	0.732	0.732	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.040	-0.013	13.809	-1.284	-1.284	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.943	-0.967	15.139	-16.289	-16.289	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.024	-0.013	15.531	-1.331	-1.331	0.000	0.000	0.000	0.000
102	A	105	PRO	0	-0.004	0.008	16.510	0.981	0.981	0.000	0.000	0.000	0.000
103	A	106	MET	0	0.081	0.020	19.415	0.015	0.015	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.915	0.965	17.564	17.474	17.474	0.000	0.000	0.000	0.000
105	A	108	TYR	0	-0.068	-0.032	14.955	-0.673	-0.673	0.000	0.000	0.000	0.000
106	A	109	VAL	0	0.033	0.016	20.407	-0.360	-0.360	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.877	-0.933	23.353	-12.664	-12.664	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.796	-0.891	25.757	-10.997	-10.997	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.913	-0.963	28.977	-10.489	-10.489	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.086	-0.043	26.939	0.285	0.285	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.858	0.911	25.962	12.063	12.063	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.001	0.010	29.191	0.129	0.129	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.874	0.929	31.329	9.782	9.782	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.003	0.022	25.961	-0.117	-0.117	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.021	0.002	29.396	0.261	0.261	0.000	0.000	0.000	0.000
116	A	119	PRO	0	0.001	0.001	28.665	-0.244	-0.244	0.000	0.000	0.000	0.000
117	A	120	GLY	0	0.002	-0.005	28.611	0.405	0.405	0.000	0.000	0.000	0.000
118	A	121	ALA	0	-0.054	-0.014	29.148	0.101	0.101	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.882	-0.932	26.575	-11.676	-11.676	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.003	-0.004	22.687	0.396	0.396	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.874	-0.918	22.932	-13.113	-13.113	0.000	0.000	0.000	0.000
122	A	125	VAL	0	-0.016	-0.013	17.230	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	126	TRP	0	-0.071	-0.057	17.921	-0.079	-0.079	0.000	0.000	0.000	0.000
124	A	127	GLN	0	0.025	0.010	9.673	1.549	1.549	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.020	-0.013	12.783	0.562	0.562	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.009	-0.009	7.622	-0.603	-0.603	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.911	-0.951	5.125	-56.420	-56.389	-0.001	-0.001	-0.029	0.000
128	A	131	ARG	1	0.857	0.942	8.076	24.958	24.958	0.000	0.000	0.000	0.000
129	A	132	TYR	0	0.045	0.008	11.216	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.792	0.879	14.867	14.859	14.859	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.006	0.017	18.502	0.133	0.133	0.000	0.000	0.000	0.000
132	A	135	ILE	0	0.027	0.005	21.268	0.446	0.446	0.000	0.000	0.000	0.000
133	A	136	ARG	1	0.968	0.967	24.020	11.522	11.522	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.002	0.001	26.461	-0.228	-0.228	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.807	0.888	28.258	9.927	9.927	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.094	0.064	26.421	-0.083	-0.083	0.000	0.000	0.000	0.000

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