FMO DATABASE

FMODB ID: 43Q8N

Calculation Name: 1BM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BM8

Chain ID: A

ChEMBL ID:

UniProt ID: P39678

Base Structure: X-ray

Registration Date: 2023-03-13

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-797384.525937
FMO2-HF: Nuclear repulsion	758073.154629
FMO2-HF: Total energy	-39311.371308
FMO2-MP2: Total energy	-39429.227747

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:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-5.437	0.43	0.261	-2.397	-3.729	0.006

Interaction energy analysis for fragmet #1(A:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.026

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	TYR	0	0.010	0.023	2.967	-3.297	0.852	0.184	-1.778	-2.555	0.008
4	A	7	SER	0	0.043	0.034	5.366	-1.287	-1.291	-0.001	0.000	0.006	0.000
5	A	8	ALA	0	-0.014	-0.005	8.988	0.228	0.228	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.898	0.935	11.376	-0.493	-0.493	0.000	0.000	0.000	0.000
7	A	10	TYR	0	-0.063	-0.051	11.167	0.004	0.004	0.000	0.000	0.000	0.000
8	A	11	SER	0	0.010	0.005	17.281	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.000	0.001	20.336	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.015	-0.009	17.532	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.840	-0.900	15.118	0.445	0.445	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.017	-0.034	11.409	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.020	0.012	8.747	0.259	0.259	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.816	-0.911	7.503	0.051	0.051	0.000	0.000	0.000	0.000
15	A	18	PHE	0	0.054	0.033	3.594	-0.911	-0.470	0.011	-0.210	-0.242	-0.001
16	A	19	ILE	0	-0.013	-0.007	2.858	0.879	1.862	0.066	-0.310	-0.739	0.000
17	A	20	HIS	0	0.024	0.008	3.944	-0.855	-0.557	0.001	-0.099	-0.199	-0.001
18	A	21	SER	0	0.026	0.005	6.666	0.178	0.178	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.035	-0.017	9.307	0.071	0.071	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.014	-0.008	9.739	0.146	0.146	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.062	-0.023	7.878	-0.210	-0.210	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.050	-0.021	7.955	0.268	0.268	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.041	-0.005	8.815	-0.122	-0.122	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.878	0.943	11.439	0.210	0.210	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.763	0.874	13.088	0.065	0.065	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.896	0.930	12.051	-0.701	-0.701	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.884	0.945	16.080	-0.079	-0.079	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.733	-0.861	19.178	0.014	0.014	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.877	-0.918	16.211	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	33	TRP	0	-0.056	-0.040	16.914	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.012	-0.006	13.052	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	35	ASN	0	-0.004	-0.002	14.642	0.025	0.025	0.000	0.000	0.000	0.000
33	A	36	ALA	0	0.088	0.025	15.300	-0.054	-0.054	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.023	-0.020	17.631	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	38	HIS	0	0.010	-0.003	12.355	-0.060	-0.060	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.044	0.039	13.415	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.029	-0.017	14.548	0.005	0.005	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.862	0.906	14.644	0.170	0.170	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.074	0.061	11.608	0.015	0.015	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.027	-0.001	13.252	0.012	0.012	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.008	-0.003	15.257	0.028	0.028	0.000	0.000	0.000	0.000
42	A	45	PHE	0	0.006	0.015	17.660	0.034	0.034	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.075	0.024	20.234	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.991	0.984	22.750	0.044	0.044	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.060	0.025	23.807	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.921	0.974	24.140	0.114	0.114	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.924	0.967	18.970	0.132	0.132	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.010	0.003	23.076	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.966	0.990	25.937	0.070	0.070	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.038	0.021	23.049	0.003	0.003	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.024	-0.008	21.251	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.928	-0.989	25.106	-0.035	-0.035	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.875	0.972	28.287	0.052	0.052	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.909	-1.005	25.392	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.005	0.008	22.364	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.017	-0.005	25.530	0.006	0.006	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.859	0.955	28.210	0.072	0.072	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.907	-0.943	25.083	-0.069	-0.069	0.000	0.000	0.000	0.000
59	A	62	THR	0	0.009	0.012	25.948	0.007	0.007	0.000	0.000	0.000	0.000
60	A	63	HIS	0	-0.055	-0.057	24.239	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.852	-0.916	23.439	0.033	0.033	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.900	0.954	23.593	0.010	0.010	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.024	0.025	22.130	0.013	0.013	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.002	-0.019	23.348	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.028	0.026	25.873	0.003	0.003	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.002	-0.001	23.458	0.011	0.011	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.015	-0.003	22.264	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.049	0.038	19.522	0.027	0.027	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.830	0.903	11.446	-0.185	-0.185	0.000	0.000	0.000	0.000
70	A	73	TYR	0	0.074	0.034	16.010	-0.051	-0.051	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.021	0.013	17.657	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.007	0.007	18.874	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.047	-0.018	20.443	0.022	0.022	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.033	-0.012	15.230	-0.037	-0.037	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.022	0.005	19.009	0.016	0.016	0.000	0.000	0.000	0.000
76	A	79	PRO	0	0.058	0.036	19.377	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.080	0.038	15.036	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	81	ASN	0	0.007	-0.008	18.263	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.064	0.030	20.782	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.003	-0.003	15.973	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.947	0.981	15.816	0.152	0.152	0.000	0.000	0.000	0.000
82	A	85	GLN	0	0.057	0.031	17.619	0.000	0.000	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.042	-0.016	18.523	0.000	0.000	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.004	-0.012	14.664	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.919	-0.956	16.659	-0.170	-0.170	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.940	0.991	18.936	0.111	0.111	0.000	0.000	0.000	0.000
87	A	90	PHE	0	-0.090	-0.063	18.682	0.016	0.016	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.006	0.001	18.123	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.003	-0.003	12.949	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	93	TYR	0	0.020	0.000	12.497	-0.078	-0.078	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.884	-0.957	12.495	-0.281	-0.281	0.000	0.000	0.000	0.000
92	A	95	GLN	0	-0.023	0.006	9.443	-0.052	-0.052	0.000	0.000	0.000	0.000
93	A	96	LEU	0	-0.019	-0.017	7.795	-0.185	-0.185	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.977	1.003	9.307	0.183	0.183	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.031	0.021	5.759	0.011	0.011	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.007	0.015	7.161	0.031	0.031	0.000	0.000	0.000	0.000
97	A	100	PHE	0	-0.062	-0.046	8.321	0.200	0.200	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.920	-0.974	10.392	-0.261	-0.261	0.000	0.000	0.000	0.000
99	A	102	PHE	0	-0.012	0.014	6.343	0.117	0.117	0.000	0.000	0.000	0.000

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