FMO DATABASE

FMODB ID: ZLMVN

Calculation Name: 1BKB-A-Xray547

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: 2025-10-05

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	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1121213.301514
FMO2-HF: Nuclear repulsion	1068187.208949
FMO2-HF: Total energy	-53026.092565
FMO2-MP2: Total energy	-53180.267406

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.
-161.084	-156.652	2.635	-2.718	-4.348	-0.029

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 : 2 / q_Mulliken : 1.817 / q_NPA : 1.901

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	0.003	-0.010	2.258	-20.938	-16.963	2.637	-2.545	-4.066	-0.028
4	A	7	MET	0	0.051	0.028	4.560	8.081	8.217	-0.001	-0.028	-0.107	0.000
127	A	130	ASP	-1	-0.929	-0.960	4.008	-94.790	-94.469	-0.001	-0.145	-0.175	-0.001
5	A	8	SER	0	-0.024	-0.010	8.400	-3.773	-3.773	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.004	0.001	11.182	0.011	0.011	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.945	0.984	13.071	32.038	32.038	0.000	0.000	0.000	0.000
8	A	11	TYR	0	0.016	-0.004	15.811	-0.781	-0.781	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.033	-0.005	19.622	0.462	0.462	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.868	-0.936	23.365	-22.236	-22.236	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.008	-0.009	26.319	0.292	0.292	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.055	-0.042	27.463	0.575	0.575	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.897	-0.945	26.819	-22.291	-22.291	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.050	-0.009	24.274	0.097	0.097	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.941	0.955	28.294	20.093	20.093	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.882	-0.930	28.729	-19.014	-19.014	0.000	0.000	0.000	0.000
17	A	20	GLY	0	-0.034	-0.016	27.712	0.161	0.161	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.048	-0.036	24.936	-0.669	-0.669	0.000	0.000	0.000	0.000
19	A	22	TYR	0	0.015	-0.005	20.005	0.004	0.004	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.025	0.000	19.935	-0.070	-0.070	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.021	-0.004	14.689	0.265	0.265	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.047	-0.022	18.014	1.111	1.111	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.895	-0.955	18.563	-29.487	-29.487	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.016	-0.003	14.365	-0.494	-0.494	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.752	-0.860	13.892	-36.665	-36.665	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.032	0.004	14.174	1.303	1.303	0.000	0.000	0.000	0.000
27	A	30	CYS	0	-0.031	-0.016	16.904	1.116	1.116	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.963	0.987	20.675	22.664	22.664	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.014	-0.018	23.617	0.520	0.520	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.055	-0.040	26.604	0.317	0.317	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.868	-0.927	29.847	-17.784	-17.784	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.046	-0.028	29.586	-0.725	-0.725	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.928	-0.942	32.768	-16.386	-16.386	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.890	0.944	32.093	18.583	18.583	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.040	0.025	36.490	0.461	0.461	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.938	0.956	37.844	15.219	15.219	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.041	0.032	40.018	0.298	0.298	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.015	0.014	40.401	0.351	0.351	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.956	0.975	41.547	12.780	12.780	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.022	0.001	42.707	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.014	0.019	38.701	-0.226	-0.226	0.000	0.000	0.000	0.000
42	A	45	SER	0	0.073	0.034	33.362	0.334	0.334	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.030	-0.018	36.024	0.253	0.253	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.871	0.936	33.320	17.647	17.647	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.037	0.014	30.389	0.508	0.508	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.949	0.983	31.227	18.299	18.299	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.024	0.014	25.845	0.486	0.486	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.019	-0.005	28.357	-0.302	-0.302	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.024	0.004	24.118	0.119	0.119	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.006	-0.002	24.605	0.421	0.421	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.042	0.014	20.419	-0.631	-0.631	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.051	-0.027	18.022	1.044	1.044	0.000	0.000	0.000	0.000
53	A	56	PHE	0	-0.019	-0.024	14.130	0.382	0.382	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.790	-0.877	18.271	-28.230	-28.230	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.017	0.026	20.267	1.081	1.081	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.017	-0.007	22.457	1.130	1.130	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.914	0.955	23.851	18.903	18.903	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.852	0.899	19.316	29.300	29.300	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.030	-0.031	25.341	0.929	0.929	0.000	0.000	0.000	0.000
60	A	63	LEU	0	0.036	0.030	23.092	-0.307	-0.307	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.009	-0.012	26.902	0.890	0.890	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.011	0.006	25.492	-0.213	-0.213	0.000	0.000	0.000	0.000
63	A	66	PRO	0	-0.014	-0.020	28.678	0.697	0.697	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.026	-0.018	29.400	-0.560	-0.560	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.823	-0.910	29.464	-20.655	-20.655	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.047	-0.015	25.777	-0.629	-0.629	0.000	0.000	0.000	0.000
67	A	70	GLN	0	-0.006	-0.009	20.700	-0.093	-0.093	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.015	-0.009	21.253	-0.274	-0.274	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.850	-0.921	13.385	-43.948	-43.948	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.041	-0.020	17.735	1.145	1.145	0.000	0.000	0.000	0.000
71	A	74	PRO	0	-0.022	0.000	14.563	-1.724	-1.724	0.000	0.000	0.000	0.000
72	A	75	ILE	0	-0.004	-0.016	12.504	2.273	2.273	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.033	-0.016	13.796	-1.685	-1.685	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.859	-0.903	13.489	-38.186	-38.186	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.897	0.948	15.676	26.219	26.219	0.000	0.000	0.000	0.000
76	A	79	PHE	0	-0.025	-0.014	14.895	-0.254	-0.254	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.047	0.018	19.591	-0.267	-0.267	0.000	0.000	0.000	0.000
78	A	81	ALA	0	-0.021	-0.016	19.578	-0.821	-0.821	0.000	0.000	0.000	0.000
79	A	82	GLN	0	0.045	0.023	21.654	1.060	1.060	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.016	-0.008	22.927	-0.996	-0.996	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.043	-0.017	21.489	0.950	0.950	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.035	-0.040	24.331	0.895	0.895	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.029	0.009	24.526	-0.833	-0.833	0.000	0.000	0.000	0.000
84	A	87	SER	0	0.009	0.011	24.528	0.654	0.654	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.020	0.004	26.418	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.907	-0.949	22.954	-22.977	-22.977	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.043	-0.028	19.216	-1.386	-1.386	0.000	0.000	0.000	0.000
88	A	91	ILE	0	-0.014	0.008	20.868	1.283	1.283	0.000	0.000	0.000	0.000
89	A	92	GLN	0	0.025	0.031	19.882	-0.582	-0.582	0.000	0.000	0.000	0.000
90	A	93	LEU	0	0.001	-0.009	18.053	1.271	1.271	0.000	0.000	0.000	0.000
91	A	94	MET	0	0.022	0.015	19.358	-0.816	-0.816	0.000	0.000	0.000	0.000
92	A	95	ASP	-1	-0.763	-0.859	15.806	-31.965	-31.965	0.000	0.000	0.000	0.000
93	A	96	MET	0	-0.021	-0.009	18.804	0.013	0.013	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.753	0.846	14.242	34.905	34.905	0.000	0.000	0.000	0.000
95	A	98	ASP	-1	-0.813	-0.900	15.289	-34.320	-34.320	0.000	0.000	0.000	0.000
96	A	99	TYR	0	-0.027	-0.011	18.939	0.163	0.163	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.776	0.891	12.325	37.033	37.033	0.000	0.000	0.000	0.000
98	A	101	THR	0	-0.025	-0.025	17.269	1.018	1.018	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.042	-0.014	13.655	-2.129	-2.129	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.918	-0.957	14.838	-28.354	-28.354	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.009	-0.010	15.078	-2.282	-2.282	0.000	0.000	0.000	0.000
102	A	105	PRO	0	-0.013	0.006	16.078	1.524	1.524	0.000	0.000	0.000	0.000
103	A	106	MET	0	0.044	0.002	19.104	-0.095	-0.095	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.920	0.970	16.818	32.062	32.062	0.000	0.000	0.000	0.000
105	A	108	TYR	0	-0.066	-0.039	14.439	-0.984	-0.984	0.000	0.000	0.000	0.000
106	A	109	VAL	0	0.037	0.008	19.703	-0.562	-0.562	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.845	-0.894	22.728	-24.128	-24.128	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.817	-0.896	25.430	-20.831	-20.831	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.910	-0.970	28.714	-19.583	-19.583	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.076	-0.033	26.156	0.407	0.407	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.856	0.909	25.344	22.498	22.498	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.018	0.001	28.469	0.251	0.251	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.872	0.933	30.683	18.395	18.395	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.012	0.023	25.519	-0.121	-0.121	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.011	0.001	28.993	0.493	0.493	0.000	0.000	0.000	0.000
116	A	119	PRO	0	0.007	0.003	28.135	-0.484	-0.484	0.000	0.000	0.000	0.000
117	A	120	GLY	0	-0.013	-0.010	28.144	0.691	0.691	0.000	0.000	0.000	0.000
118	A	121	ALA	0	-0.062	-0.019	28.940	0.251	0.251	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.896	-0.946	25.998	-21.589	-21.589	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.010	-0.017	22.228	0.646	0.646	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.810	-0.885	22.287	-24.530	-24.530	0.000	0.000	0.000	0.000
122	A	125	VAL	0	-0.017	-0.008	16.742	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	126	TRP	0	-0.082	-0.070	17.197	-0.193	-0.193	0.000	0.000	0.000	0.000
124	A	127	GLN	0	0.026	0.016	9.936	-2.543	-2.543	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.026	-0.018	12.086	0.991	0.991	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.011	-0.009	6.927	-1.310	-1.310	0.000	0.000	0.000	0.000
128	A	131	ARG	1	0.813	0.911	7.180	44.794	44.794	0.000	0.000	0.000	0.000
129	A	132	TYR	0	0.022	0.000	10.211	1.126	1.126	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.769	0.870	14.040	27.144	27.144	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.016	0.022	17.733	0.107	0.107	0.000	0.000	0.000	0.000
132	A	135	ILE	0	0.009	-0.006	20.280	0.596	0.596	0.000	0.000	0.000	0.000
133	A	136	ARG	1	0.945	0.962	23.356	21.698	21.698	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.010	0.008	25.904	-0.355	-0.355	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.808	0.896	28.224	18.413	18.413	0.000	0.000	0.000	0.000
136	A	139	GLY	-1	-0.787	-0.865	25.565	-22.088	-22.088	0.000	0.000	0.000	0.000

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