FMO DATABASE

FMODB ID: G5J71

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	OptH
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	-921709.69496
FMO2-HF: Nuclear repulsion	877641.448964
FMO2-HF: Total energy	-44068.245995
FMO2-MP2: Total energy	-44197.16994

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.
-43.282	-36.941	8.657	-7.01	-7.986	-0.066

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 : 0.984 / q_NPA : 0.988

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	0.049	0.021	3.497	1.740	4.288	0.006	-1.175	-1.379	0.004
4	A	5	LYS	1	0.923	0.962	2.583	35.187	36.162	0.481	-0.383	-1.073	0.000
5	A	6	ASP	-1	-0.840	-0.923	2.043	-91.812	-89.094	8.171	-5.444	-5.444	-0.070
6	A	7	ALA	0	-0.018	-0.010	4.922	5.554	5.654	-0.001	-0.008	-0.090	0.000
7	A	8	LEU	0	-0.017	0.004	7.508	3.724	3.724	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.037	0.008	7.967	2.785	2.785	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.033	0.020	9.050	2.673	2.673	0.000	0.000	0.000	0.000
10	A	11	TRP	0	-0.001	0.000	10.736	2.518	2.518	0.000	0.000	0.000	0.000
11	A	12	CYS	0	-0.028	-0.016	12.563	2.184	2.184	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.019	-0.017	11.537	0.588	0.588	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.038	-0.021	13.380	1.282	1.282	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.886	0.955	16.641	17.462	17.462	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.004	-0.004	17.834	0.941	0.941	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.007	0.006	19.364	0.433	0.433	0.000	0.000	0.000	0.000
17	A	18	GLY	0	-0.012	-0.010	20.747	0.548	0.548	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.053	-0.044	23.000	0.484	0.484	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.036	0.013	24.067	-0.351	-0.351	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.065	-0.048	25.114	-0.117	-0.117	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.084	0.053	19.645	-0.038	-0.038	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.034	-0.027	18.874	-0.523	-0.523	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.011	0.003	13.219	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.009	0.004	12.591	-2.034	-2.034	0.000	0.000	0.000	0.000
25	A	26	ASN	0	0.012	0.019	10.563	-1.435	-1.435	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.026	0.001	7.631	0.490	0.490	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.060	0.027	11.687	0.505	0.505	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.061	0.025	14.654	0.464	0.464	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.037	-0.020	15.228	0.357	0.357	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.003	-0.016	13.323	0.669	0.669	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.934	0.985	18.161	12.950	12.950	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.887	-0.948	20.880	-12.407	-12.407	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.057	0.016	22.131	0.553	0.553	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.036	-0.004	23.195	0.215	0.215	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.035	0.015	18.257	0.073	0.073	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.028	0.004	17.299	-0.191	-0.191	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.008	-0.017	20.918	0.497	0.497	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.018	0.020	21.758	0.232	0.232	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.042	-0.023	16.621	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.003	0.016	21.166	0.081	0.081	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.039	0.057	24.169	-0.140	-0.140	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.929	0.968	22.344	13.379	13.379	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.088	-0.053	20.404	-0.226	-0.226	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.844	0.898	25.746	10.170	10.170	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.017	0.011	28.708	0.121	0.121	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.839	-0.895	30.481	-9.311	-9.311	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.032	-0.010	28.720	0.213	0.213	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.044	-0.022	27.081	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.818	-0.897	31.206	-8.801	-8.801	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.018	-0.014	25.371	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.887	-0.946	30.456	-9.439	-9.439	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.796	0.906	32.882	8.489	8.489	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.046	0.002	27.906	0.131	0.131	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.944	0.952	30.429	9.021	9.021	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.967	0.986	24.970	11.963	11.963	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.001	0.006	27.674	-0.146	-0.146	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.030	-0.008	30.127	0.240	0.240	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.046	0.033	25.800	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	60	HIS	0	0.077	0.043	26.986	-0.143	-0.143	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.002	0.009	28.946	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.015	-0.034	26.338	0.304	0.304	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.003	0.009	22.130	-0.180	-0.180	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.018	0.016	25.497	0.085	0.085	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.050	-0.018	28.358	0.353	0.353	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.023	0.009	23.841	0.037	0.037	0.000	0.000	0.000	0.000
66	A	67	PHE	0	0.011	-0.010	21.292	-0.068	-0.068	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.032	0.003	25.515	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.002	0.011	28.241	0.179	0.179	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.011	0.000	23.921	0.083	0.083	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.869	-0.950	26.059	-9.987	-9.987	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.066	-0.042	27.450	0.325	0.325	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.010	0.002	29.776	0.198	0.198	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.074	-0.034	24.570	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	75	GLY	0	-0.002	0.022	26.042	-0.187	-0.187	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.079	-0.041	20.948	-0.293	-0.293	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.002	-0.006	22.721	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.894	0.956	22.366	9.228	9.228	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.062	-0.031	17.880	0.041	0.041	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.057	-0.018	17.782	-0.234	-0.234	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.803	-0.890	21.844	-9.953	-9.953	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.052	-0.053	24.111	-0.352	-0.352	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.940	-0.969	25.245	-9.675	-9.675	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.885	-0.933	22.145	-11.453	-11.453	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.107	-0.061	18.805	-0.673	-0.673	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.062	-0.029	21.403	-0.294	-0.294	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.024	0.013	21.403	0.231	0.231	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.906	-0.955	22.269	-12.023	-12.023	0.000	0.000	0.000	0.000
88	A	89	HIS	0	-0.073	-0.047	18.471	-1.099	-1.099	0.000	0.000	0.000	0.000
89	A	90	PRO	0	-0.002	0.014	17.169	-0.064	-0.064	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.771	-0.878	15.255	-17.516	-17.516	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.869	-0.950	8.225	-27.443	-27.443	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.964	0.982	10.736	17.593	17.593	0.000	0.000	0.000	0.000
93	A	94	SER	0	-0.003	-0.017	11.823	0.171	0.171	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.021	0.019	13.405	0.309	0.309	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.039	-0.022	7.342	-0.378	-0.378	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.045	-0.024	11.485	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	98	TYR	0	0.043	0.032	13.164	0.389	0.389	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.047	0.011	12.973	0.294	0.294	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.067	-0.037	10.235	-0.078	-0.078	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.033	-0.002	13.201	0.594	0.594	0.000	0.000	0.000	0.000
101	A	102	TYR	0	0.030	-0.005	16.798	0.475	0.475	0.000	0.000	0.000	0.000
102	A	103	TYR	0	-0.028	0.003	12.594	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.032	-0.047	12.852	0.373	0.373	0.000	0.000	0.000	0.000
104	A	105	TYR	0	0.035	0.028	17.050	0.442	0.442	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.024	-0.012	19.753	0.360	0.360	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.088	-0.019	17.087	0.034	0.034	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.889	0.942	16.898	14.887	14.887	0.000	0.000	0.000	0.000
108	A	109	MET	0	0.001	0.019	21.672	0.263	0.263	0.000	0.000	0.000	0.000

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