FMO DATABASE

FMODB ID: 89RKY

Calculation Name: 1BKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q01082

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	OptHSide
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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-922814.766178
FMO2-HF: Nuclear repulsion	878745.751329
FMO2-HF: Total energy	-44069.014849
FMO2-MP2: Total energy	-44197.941013

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:LYS)

Summations of interaction energy for fragment #1(A:2: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.
-83.971	-82.881	21.309	-11.654	-10.746	-0.124

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.916 / q_NPA : 0.938

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	ALA	0	0.006	0.000	3.325	0.529	2.600	0.023	-0.831	-1.264	0.004
4	A	5	LYS	1	0.846	0.903	2.527	37.111	38.213	0.538	-0.466	-1.174	0.000
5	A	6	ASP	-1	-0.800	-0.894	1.701	-134.392	-136.604	20.749	-10.337	-8.200	-0.128
6	A	7	ALA	0	-0.012	-0.007	4.594	6.282	6.411	-0.001	-0.020	-0.108	0.000
7	A	8	LEU	0	-0.006	0.009	7.504	3.934	3.934	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.034	0.011	7.745	2.997	2.997	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.036	0.021	8.350	3.080	3.080	0.000	0.000	0.000	0.000
10	A	11	TRP	0	0.006	0.001	10.182	2.922	2.922	0.000	0.000	0.000	0.000
11	A	12	CYS	0	-0.044	-0.023	12.442	2.400	2.400	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.022	-0.015	10.930	0.561	0.561	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.029	-0.012	12.804	1.467	1.467	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.828	0.916	15.947	17.465	17.465	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.013	-0.015	17.495	1.062	1.062	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.003	0.004	18.447	0.477	0.477	0.000	0.000	0.000	0.000
17	A	18	GLY	0	-0.010	-0.010	19.948	0.624	0.624	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.047	-0.038	22.422	0.499	0.499	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.029	0.008	23.472	-0.396	-0.396	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.042	-0.029	24.816	-0.138	-0.138	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.094	0.063	19.353	-0.044	-0.044	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.030	-0.023	18.404	-0.476	-0.476	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.010	0.013	13.098	-0.053	-0.053	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.011	-0.008	12.333	-2.310	-2.310	0.000	0.000	0.000	0.000
25	A	26	ASN	0	0.020	0.027	10.062	-1.732	-1.732	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.034	0.005	7.852	0.741	0.741	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.054	0.017	11.688	0.575	0.575	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.057	0.031	14.656	0.464	0.464	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.032	-0.027	14.850	0.433	0.433	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.025	-0.032	13.348	0.761	0.761	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.870	0.954	18.163	13.529	13.529	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.855	-0.937	20.880	-13.040	-13.040	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.052	0.016	22.125	0.607	0.607	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.033	0.001	23.101	0.261	0.261	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.031	0.013	18.252	0.090	0.090	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.018	0.000	17.200	-0.188	-0.188	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.011	-0.022	20.914	0.551	0.551	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.019	0.022	21.773	0.263	0.263	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.041	-0.022	16.497	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.003	0.016	21.163	0.115	0.115	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.036	0.051	24.162	-0.129	-0.129	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.892	0.955	21.985	14.478	14.478	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.025	-0.016	20.304	-0.283	-0.283	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.857	0.903	25.741	10.416	10.416	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.017	0.007	28.701	0.108	0.108	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.842	-0.892	30.478	-9.598	-9.598	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.028	-0.009	28.757	0.210	0.210	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.055	-0.032	27.042	-0.027	-0.027	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.798	-0.866	31.203	-9.050	-9.050	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.028	-0.005	25.179	-0.068	-0.068	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.852	-0.914	30.460	-9.541	-9.541	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.743	0.845	32.664	8.965	8.965	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.046	0.000	27.949	0.136	0.136	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.929	0.944	30.207	9.425	9.425	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.958	0.976	24.678	12.606	12.606	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.011	-0.003	27.583	-0.176	-0.176	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.026	-0.002	30.109	0.179	0.179	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.050	0.035	25.791	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	60	HIS	0	0.042	0.026	26.981	-0.235	-0.235	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.012	0.010	28.938	0.036	0.036	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.030	-0.040	26.354	0.320	0.320	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.002	0.012	22.106	-0.197	-0.197	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.025	0.013	25.488	0.092	0.092	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.043	-0.014	28.345	0.395	0.395	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.026	0.007	23.849	0.041	0.041	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.007	-0.015	21.342	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.047	0.019	25.497	0.013	0.013	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.002	0.013	28.222	0.192	0.192	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.009	-0.012	23.913	0.075	0.075	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.840	-0.933	26.045	-10.195	-10.195	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.070	-0.041	27.444	0.390	0.390	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.010	-0.003	29.744	0.217	0.217	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.080	-0.036	24.522	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.004	0.024	25.997	-0.182	-0.182	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.088	-0.049	20.808	-0.324	-0.324	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.015	-0.002	21.928	0.062	0.062	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.905	0.945	22.380	9.413	9.413	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.062	-0.031	17.895	0.050	0.050	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.053	-0.014	17.738	-0.238	-0.238	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.792	-0.890	21.909	-10.198	-10.198	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.030	-0.043	24.093	-0.400	-0.400	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.897	-0.937	25.234	-9.893	-9.893	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.900	-0.942	22.092	-11.867	-11.867	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.105	-0.057	18.692	-0.733	-0.733	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.049	-0.035	21.397	-0.335	-0.335	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.034	0.025	21.460	0.244	0.244	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.907	-0.954	22.268	-12.586	-12.586	0.000	0.000	0.000	0.000
88	A	89	HIS	0	-0.058	-0.044	18.419	-1.273	-1.273	0.000	0.000	0.000	0.000
89	A	90	PRO	0	-0.002	0.021	17.110	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.747	-0.865	14.665	-18.368	-18.368	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.799	-0.883	8.151	-30.218	-30.218	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.952	0.980	10.914	17.855	17.855	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.002	-0.022	11.934	0.222	0.222	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.013	0.021	13.422	0.341	0.341	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.040	-0.022	7.331	-0.397	-0.397	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.052	-0.037	11.500	0.064	0.064	0.000	0.000	0.000	0.000
97	A	98	TYR	0	0.020	0.013	13.197	0.511	0.511	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.044	0.011	12.949	0.315	0.315	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.057	-0.034	10.133	0.005	0.005	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.013	0.005	13.169	0.590	0.590	0.000	0.000	0.000	0.000
101	A	102	TYR	0	0.031	0.008	16.780	0.474	0.474	0.000	0.000	0.000	0.000
102	A	103	TYR	0	-0.004	0.011	13.075	0.309	0.309	0.000	0.000	0.000	0.000
103	A	104	HIS	0	0.006	-0.020	13.014	0.663	0.663	0.000	0.000	0.000	0.000
104	A	105	TYR	0	0.043	0.029	16.964	0.449	0.449	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.016	-0.014	19.652	0.363	0.363	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.097	-0.040	16.988	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.867	0.945	16.266	15.279	15.279	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.013	0.009	21.557	0.250	0.250	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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