FMO DATABASE

FMODB ID: RQLV8

Calculation Name: 1BKR-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1BKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q01082

Base Structure: X-ray

Registration Date: 2025-09-02

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-924549.35733
FMO2-HF: Nuclear repulsion	880480.568916
FMO2-HF: Total energy	-44068.788415
FMO2-MP2: Total energy	-44197.561066

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: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.
-72.452	-66.368	9.272	-7.021	-8.336	-0.078

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 : 2 / q_Mulliken : 1.804 / q_NPA : 1.894

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	0.058	0.032	3.458	7.119	9.298	0.027	-0.809	-1.397	-0.003
4	A	5	LYS	1	0.807	0.894	3.194	83.197	84.393	0.040	-0.397	-0.839	-0.002
5	A	6	ASP	-1	-0.817	-0.930	2.151	-148.760	-146.051	9.205	-5.815	-6.100	-0.073
6	A	7	ALA	0	0.003	0.002	5.661	10.156	10.156	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.012	0.021	7.971	6.626	6.626	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.012	0.014	8.334	5.328	5.328	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.044	0.023	9.379	4.804	4.804	0.000	0.000	0.000	0.000
10	A	11	TRP	0	-0.008	-0.009	11.129	4.221	4.221	0.000	0.000	0.000	0.000
11	A	12	CYS	0	-0.014	-0.010	12.907	3.871	3.871	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.038	-0.015	11.376	1.788	1.788	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.025	-0.019	13.803	2.645	2.645	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.866	0.956	17.041	34.013	34.013	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.017	-0.031	18.069	1.770	1.770	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.007	0.011	19.258	0.968	0.968	0.000	0.000	0.000	0.000
17	A	18	GLY	0	-0.016	-0.012	20.757	0.991	0.991	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.020	-0.024	23.169	0.766	0.766	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.017	0.000	24.289	-0.594	-0.594	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.031	-0.025	25.404	-0.278	-0.278	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.086	0.062	19.729	-0.314	-0.314	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.033	-0.031	18.893	-0.556	-0.556	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.010	0.016	13.276	-0.334	-0.334	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.030	0.004	12.387	-3.616	-3.616	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.024	0.005	10.336	-2.719	-2.719	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.033	0.001	7.470	0.480	0.480	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.064	0.026	11.859	0.700	0.700	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.050	0.023	14.845	0.887	0.887	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.030	-0.026	14.879	1.411	1.411	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.008	-0.025	13.473	0.971	0.971	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.914	0.988	18.444	26.419	26.419	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.853	-0.935	21.136	-25.245	-25.245	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.049	0.016	22.333	1.157	1.157	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.052	-0.008	23.218	0.363	0.363	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.023	0.008	18.234	0.198	0.198	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.024	0.005	17.371	-0.488	-0.488	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.017	-0.028	21.207	1.009	1.009	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.014	0.015	21.916	0.525	0.525	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.043	-0.018	16.639	-0.127	-0.127	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.006	0.028	21.257	0.147	0.147	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.033	0.041	24.239	-0.293	-0.293	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.905	0.964	22.428	26.793	26.793	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.050	-0.044	20.471	-0.615	-0.615	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.849	0.898	25.832	20.791	20.791	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.026	0.015	28.609	0.126	0.126	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.864	-0.906	30.571	-19.130	-19.130	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.011	0.000	28.640	0.424	0.424	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.051	-0.023	27.349	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.797	-0.877	31.547	-17.556	-17.556	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.010	-0.011	25.418	-0.100	-0.100	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.900	-0.944	30.884	-18.810	-18.810	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.787	0.879	33.328	17.260	17.260	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.002	0.016	28.185	0.240	0.240	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.904	0.936	30.076	18.289	18.289	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.917	0.960	24.893	23.944	23.944	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.001	-0.004	27.646	-0.447	-0.447	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.018	0.012	30.318	0.203	0.203	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.040	0.026	25.977	0.008	0.008	0.000	0.000	0.000	0.000
59	A	60	HIS	0	0.053	0.033	27.021	-0.427	-0.427	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.028	0.016	28.956	0.017	0.017	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.026	-0.042	26.646	0.594	0.594	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.005	0.013	22.169	-0.407	-0.407	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.028	0.020	25.605	0.036	0.036	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.055	-0.026	28.382	0.767	0.767	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.030	0.005	23.890	0.092	0.092	0.000	0.000	0.000	0.000
66	A	67	PHE	0	0.004	-0.011	21.330	-0.267	-0.267	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.027	0.008	25.371	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.007	0.004	28.008	0.349	0.349	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.002	-0.004	23.551	0.140	0.140	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.850	-0.925	25.685	-21.108	-21.108	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.062	-0.043	27.260	0.755	0.755	0.000	0.000	0.000	0.000
72	A	73	HIS	0	-0.008	-0.003	29.402	0.481	0.481	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.060	-0.022	24.245	-0.068	-0.068	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.015	0.027	25.828	-0.477	-0.477	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.089	-0.047	20.744	-0.664	-0.664	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.008	-0.010	23.473	-0.184	-0.184	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.896	0.941	22.498	19.279	19.279	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.054	-0.026	17.756	0.081	0.081	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.054	-0.020	17.611	-0.793	-0.793	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.771	-0.871	21.712	-20.898	-20.898	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.047	-0.046	23.893	-0.878	-0.878	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.949	-0.962	25.844	-19.876	-19.876	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.894	-0.941	21.996	-24.708	-24.708	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.092	-0.060	18.770	-1.518	-1.518	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.044	-0.039	21.782	-0.473	-0.473	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.012	0.013	21.699	0.476	0.476	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.920	-0.964	22.438	-24.778	-24.778	0.000	0.000	0.000	0.000
88	A	89	HIS	0	-0.049	-0.044	18.458	-2.452	-2.452	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.010	0.033	17.393	-0.124	-0.124	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.760	-0.880	14.767	-39.357	-39.357	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.783	-0.870	8.483	-62.740	-62.740	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.931	0.971	10.766	40.871	40.871	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.001	-0.013	11.786	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.022	0.025	13.550	0.456	0.456	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.038	-0.025	7.212	-1.118	-1.118	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.044	-0.036	11.189	-0.347	-0.347	0.000	0.000	0.000	0.000
97	A	98	TYR	0	0.041	0.026	13.230	1.024	1.024	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.033	0.013	12.776	0.809	0.809	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.052	-0.034	9.934	-0.118	-0.118	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.025	-0.004	12.913	1.523	1.523	0.000	0.000	0.000	0.000
101	A	102	TYR	0	0.019	-0.003	16.602	1.140	1.140	0.000	0.000	0.000	0.000
102	A	103	TYR	0	-0.047	-0.015	13.251	0.346	0.346	0.000	0.000	0.000	0.000
103	A	104	HIS	0	0.002	-0.026	13.156	1.607	1.607	0.000	0.000	0.000	0.000
104	A	105	TYR	0	0.037	0.027	17.071	1.128	1.128	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.013	-0.010	19.492	0.708	0.708	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.089	-0.041	17.125	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.851	0.922	16.781	31.719	31.719	0.000	0.000	0.000	0.000
108	A	109	MET	-1	-0.924	-0.926	21.966	-23.539	-23.539	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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