FMO DATABASE

FMODB ID: 2LJZR

Calculation Name: 1BKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1123822.644439
FMO2-HF: Nuclear repulsion	1070795.867609
FMO2-HF: Total energy	-53026.77683
FMO2-MP2: Total energy	-53181.047591

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: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.
-133.348	-128.12	14.228	-9.685	-9.773	-0.107

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 : 0.908 / q_NPA : 0.955

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	-0.023	-0.027	2.066	-14.280	-11.698	5.379	-3.092	-4.869	-0.020
4	A	7	MET	0	0.023	0.009	4.539	4.709	4.903	-0.001	-0.045	-0.149	0.000
5	A	8	SER	0	-0.015	-0.004	8.265	-1.006	-1.006	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.018	-0.019	11.132	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.949	0.991	13.087	18.060	18.060	0.000	0.000	0.000	0.000
8	A	11	TYR	0	0.010	-0.008	16.061	-0.370	-0.370	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.026	-0.003	19.527	0.222	0.222	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.871	-0.940	22.965	-11.472	-11.472	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.004	-0.006	25.735	0.074	0.074	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.042	-0.033	26.523	0.288	0.288	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.874	-0.931	26.224	-11.963	-11.963	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.032	-0.005	23.185	0.050	0.050	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.896	0.932	27.201	11.383	11.383	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.851	-0.920	27.278	-10.687	-10.687	0.000	0.000	0.000	0.000
17	A	20	GLY	0	-0.047	-0.019	25.963	0.094	0.094	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.051	-0.037	23.644	-0.415	-0.415	0.000	0.000	0.000	0.000
19	A	22	TYR	0	0.009	-0.011	18.439	-0.100	-0.100	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.031	0.001	18.375	0.011	0.011	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.026	-0.007	13.034	0.013	0.013	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.043	-0.021	16.149	0.878	0.878	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.897	-0.955	17.117	-16.284	-16.284	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.007	0.005	12.723	-0.332	-0.332	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.750	-0.849	12.108	-23.631	-23.631	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.024	0.008	12.341	1.183	1.183	0.000	0.000	0.000	0.000
27	A	30	CYS	0	-0.034	-0.015	15.153	0.565	0.565	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.967	0.990	18.921	13.286	13.286	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.008	-0.016	21.890	0.353	0.353	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.054	-0.036	24.775	0.193	0.193	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.774	-0.868	28.117	-9.684	-9.684	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.026	-0.012	27.977	-0.408	-0.408	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.871	-0.903	30.986	-8.818	-8.818	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.872	0.935	30.591	10.056	10.056	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.022	0.017	34.929	0.264	0.264	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.904	0.935	36.890	7.659	7.659	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.040	0.032	39.204	0.173	0.173	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.036	0.027	40.020	0.203	0.203	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.969	0.981	41.484	6.480	6.480	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.031	0.001	43.101	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.015	0.028	39.028	-0.082	-0.082	0.000	0.000	0.000	0.000
42	A	45	SER	0	-0.013	-0.030	33.264	0.167	0.167	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.010	0.009	35.276	0.077	0.077	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.823	0.907	32.494	9.315	9.315	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.039	0.013	29.293	0.238	0.238	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.842	0.916	29.554	9.696	9.696	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.028	0.017	24.277	0.240	0.240	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.017	-0.009	26.296	-0.137	-0.137	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.022	0.008	22.337	0.103	0.103	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.001	0.000	22.811	0.319	0.319	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.040	0.016	18.619	-0.410	-0.410	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.050	-0.027	16.141	0.649	0.649	0.000	0.000	0.000	0.000
53	A	56	PHE	0	-0.045	-0.037	12.345	0.193	0.193	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.790	-0.878	16.773	-16.656	-16.656	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.018	0.026	18.708	0.763	0.763	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.010	-0.005	20.862	0.774	0.774	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.824	0.901	22.164	10.365	10.365	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.860	0.905	17.621	17.023	17.023	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.018	-0.022	23.756	0.467	0.467	0.000	0.000	0.000	0.000
60	A	63	LEU	0	0.032	0.023	21.336	-0.174	-0.174	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.001	-0.010	25.112	0.404	0.404	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.011	0.007	24.469	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	66	PRO	0	-0.037	-0.027	28.358	0.353	0.353	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.008	-0.008	28.790	-0.331	-0.331	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.759	-0.871	28.966	-10.577	-10.577	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.031	-0.004	25.579	-0.240	-0.240	0.000	0.000	0.000	0.000
67	A	70	GLN	0	0.003	-0.005	20.759	-0.099	-0.099	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.020	-0.012	20.360	-0.131	-0.131	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.838	-0.906	12.662	-24.771	-24.771	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.038	-0.017	17.000	0.474	0.474	0.000	0.000	0.000	0.000
71	A	74	PRO	0	-0.023	-0.001	13.428	-0.921	-0.921	0.000	0.000	0.000	0.000
72	A	75	ILE	0	0.002	-0.010	11.910	1.603	1.603	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.035	-0.021	12.534	-1.648	-1.648	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.864	-0.904	12.946	-22.022	-22.022	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.839	0.908	14.658	14.889	14.889	0.000	0.000	0.000	0.000
76	A	79	PHE	0	-0.006	-0.003	14.064	0.043	0.043	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.013	0.005	18.739	0.207	0.207	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.004	0.003	18.816	-0.422	-0.422	0.000	0.000	0.000	0.000
79	A	82	GLN	0	0.035	0.018	20.953	0.640	0.640	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.030	-0.016	22.277	-0.677	-0.677	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.031	-0.013	21.092	0.607	0.607	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.036	-0.041	23.648	0.569	0.569	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.020	0.003	23.773	-0.559	-0.559	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.016	-0.016	23.451	0.378	0.378	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.028	0.006	25.396	-0.088	-0.088	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.899	-0.940	22.131	-13.047	-13.047	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.041	-0.021	18.207	-0.968	-0.968	0.000	0.000	0.000	0.000
88	A	91	ILE	0	-0.014	0.017	19.769	0.915	0.915	0.000	0.000	0.000	0.000
89	A	92	GLN	0	0.004	0.012	18.956	-0.427	-0.427	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.007	-0.010	17.106	0.864	0.864	0.000	0.000	0.000	0.000
91	A	94	MET	0	0.033	0.020	19.046	-0.405	-0.405	0.000	0.000	0.000	0.000
92	A	95	ASP	-1	-0.770	-0.865	15.551	-18.545	-18.545	0.000	0.000	0.000	0.000
93	A	96	MET	0	-0.001	-0.013	18.482	0.247	0.247	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.758	0.858	13.701	21.075	21.075	0.000	0.000	0.000	0.000
95	A	98	ASP	-1	-0.809	-0.897	15.508	-19.547	-19.547	0.000	0.000	0.000	0.000
96	A	99	TYR	0	-0.053	-0.027	19.156	0.315	0.315	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.782	0.891	12.315	21.784	21.784	0.000	0.000	0.000	0.000
98	A	101	THR	0	0.000	-0.014	17.265	0.274	0.274	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.046	-0.012	12.833	-1.383	-1.383	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.882	-0.933	14.195	-15.786	-15.786	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.016	-0.013	14.165	-1.749	-1.749	0.000	0.000	0.000	0.000
102	A	105	PRO	0	0.003	0.011	15.029	1.096	1.096	0.000	0.000	0.000	0.000
103	A	106	MET	0	0.041	0.003	18.031	-0.180	-0.180	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.889	0.958	15.625	19.823	19.823	0.000	0.000	0.000	0.000
105	A	108	TYR	0	-0.038	-0.025	13.342	-0.639	-0.639	0.000	0.000	0.000	0.000
106	A	109	VAL	0	0.039	0.006	18.160	-0.435	-0.435	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.814	-0.887	21.161	-14.247	-14.247	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.804	-0.899	23.810	-12.138	-12.138	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.914	-0.969	27.134	-11.229	-11.229	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.081	-0.037	24.669	0.248	0.248	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.855	0.908	23.540	13.123	13.123	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.016	0.004	27.016	0.170	0.170	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.848	0.917	29.254	10.500	10.500	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.005	0.014	24.046	-0.092	-0.092	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.027	0.010	27.682	0.268	0.268	0.000	0.000	0.000	0.000
116	A	119	PRO	0	0.011	0.000	27.328	-0.289	-0.289	0.000	0.000	0.000	0.000
117	A	120	GLY	0	-0.012	-0.005	27.511	0.435	0.435	0.000	0.000	0.000	0.000
118	A	121	ALA	0	-0.040	-0.006	27.903	0.138	0.138	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.845	-0.908	25.230	-11.682	-11.682	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.024	-0.026	21.183	0.328	0.328	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.779	-0.854	21.208	-13.997	-13.997	0.000	0.000	0.000	0.000
122	A	125	VAL	0	-0.012	-0.006	15.743	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	126	TRP	0	-0.049	-0.050	15.826	0.137	0.137	0.000	0.000	0.000	0.000
124	A	127	GLN	0	0.019	0.006	7.496	2.308	2.308	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.019	-0.012	10.535	1.224	1.224	0.000	0.000	0.000	0.000
126	A	129	LEU	0	0.031	0.017	5.283	-1.302	-1.302	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.862	-0.921	1.882	-120.528	-118.101	8.851	-6.548	-4.730	-0.087
128	A	131	ARG	1	0.827	0.910	5.338	31.633	31.658	-0.001	0.000	-0.025	0.000
129	A	132	TYR	0	0.023	-0.003	9.227	0.732	0.732	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.762	0.873	12.481	16.425	16.425	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.021	0.028	16.180	0.171	0.171	0.000	0.000	0.000	0.000
132	A	135	ILE	0	0.004	-0.011	18.934	0.387	0.387	0.000	0.000	0.000	0.000
133	A	136	ARG	1	0.909	0.930	22.087	12.768	12.768	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.032	0.028	24.812	-0.305	-0.305	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.837	0.901	26.196	11.084	11.084	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.041	0.052	24.495	-0.084	-0.084	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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