FMO DATABASE

FMODB ID: LNYR9

Calculation Name: 1BGF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BGF

Chain ID: A

ChEMBL ID:

UniProt ID: P42228

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	OptAll
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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1104275.82952
FMO2-HF: Nuclear repulsion	1053391.229518
FMO2-HF: Total energy	-50884.600002
FMO2-MP2: Total energy	-51032.631126

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
1.263	2.358	-0.015	-0.552	-0.527	0

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.016

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].
3	A	2	SER	0	0.014	0.007	3.859	0.828	1.923	-0.015	-0.552	-0.527
4	A	3	GLN	0	-0.031	-0.025	7.062	0.349	0.349	0.000	0.000	0.000
5	A	4	TRP	0	-0.006	-0.023	9.693	0.077	0.077	0.000	0.000	0.000
6	A	5	ASN	0	-0.048	-0.030	6.350	0.003	0.003	0.000	0.000	0.000
7	A	6	GLN	0	-0.007	-0.010	6.024	0.160	0.160	0.000	0.000	0.000
8	A	7	VAL	0	0.034	0.014	9.310	-0.013	-0.013	0.000	0.000	0.000
9	A	8	GLN	0	-0.052	-0.026	11.124	-0.086	-0.086	0.000	0.000	0.000
10	A	9	GLN	0	-0.081	-0.032	8.915	-0.039	-0.039	0.000	0.000	0.000
11	A	10	LEU	0	-0.034	0.005	12.170	0.022	0.022	0.000	0.000	0.000
12	A	11	GLU	-1	-0.840	-0.920	15.566	0.102	0.102	0.000	0.000	0.000
13	A	12	ILE	0	0.030	0.000	18.986	-0.001	-0.001	0.000	0.000	0.000
14	A	13	LYS	1	0.865	0.930	20.599	-0.134	-0.134	0.000	0.000	0.000
15	A	14	PHE	0	0.024	0.007	17.646	0.004	0.004	0.000	0.000	0.000
16	A	15	LEU	0	-0.031	-0.011	20.311	-0.006	-0.006	0.000	0.000	0.000
17	A	16	GLU	-1	-0.945	-0.982	22.200	0.051	0.051	0.000	0.000	0.000
18	A	17	GLN	0	0.013	0.014	23.246	0.005	0.005	0.000	0.000	0.000
19	A	18	VAL	0	-0.005	-0.002	19.671	0.002	0.002	0.000	0.000	0.000
20	A	19	ASP	-1	-0.932	-0.947	23.104	-0.005	-0.005	0.000	0.000	0.000
21	A	20	GLN	0	-0.016	-0.023	25.865	-0.011	-0.011	0.000	0.000	0.000
22	A	21	PHE	0	-0.070	-0.038	23.226	0.003	0.003	0.000	0.000	0.000
23	A	22	TYR	0	-0.037	-0.022	18.717	-0.009	-0.009	0.000	0.000	0.000
24	A	23	ASP	-1	-0.751	-0.867	25.303	-0.013	-0.013	0.000	0.000	0.000
25	A	24	ASP	-1	-0.882	-0.937	27.723	-0.033	-0.033	0.000	0.000	0.000
26	A	25	ASN	0	-0.105	-0.089	28.045	-0.009	-0.009	0.000	0.000	0.000
27	A	26	PHE	0	0.001	-0.004	18.555	-0.010	-0.010	0.000	0.000	0.000
28	A	27	PRO	0	0.063	0.048	24.245	0.005	0.005	0.000	0.000	0.000
29	A	28	MET	0	0.061	0.023	20.185	-0.016	-0.016	0.000	0.000	0.000
30	A	29	GLU	-1	-0.852	-0.936	19.927	-0.106	-0.106	0.000	0.000	0.000
31	A	30	ILE	0	-0.032	-0.013	19.884	-0.030	-0.030	0.000	0.000	0.000
32	A	31	ARG	1	0.726	0.838	12.581	0.061	0.061	0.000	0.000	0.000
33	A	32	HIS	0	0.036	0.024	15.201	-0.025	-0.025	0.000	0.000	0.000
34	A	33	LEU	0	-0.052	-0.043	15.004	-0.061	-0.061	0.000	0.000	0.000
35	A	34	LEU	0	-0.024	0.000	16.058	-0.034	-0.034	0.000	0.000	0.000
36	A	35	ALA	0	-0.018	0.013	12.132	0.002	0.002	0.000	0.000	0.000
37	A	36	GLN	0	0.025	-0.006	7.765	-0.228	-0.228	0.000	0.000	0.000
38	A	37	TRP	0	0.033	0.039	11.393	0.054	0.054	0.000	0.000	0.000
39	A	38	ILE	0	0.028	0.006	14.820	0.042	0.042	0.000	0.000	0.000
40	A	39	GLU	-1	-0.711	-0.849	9.661	-0.227	-0.227	0.000	0.000	0.000
41	A	40	THR	0	-0.057	-0.023	12.350	0.028	0.028	0.000	0.000	0.000
42	A	41	GLN	0	-0.063	-0.039	14.032	0.034	0.034	0.000	0.000	0.000
43	A	42	ASP	-1	-0.863	-0.925	17.762	0.039	0.039	0.000	0.000	0.000
44	A	43	TRP	0	-0.003	-0.033	17.613	-0.002	-0.002	0.000	0.000	0.000
45	A	44	GLU	-1	-0.749	-0.863	19.029	0.067	0.067	0.000	0.000	0.000
46	A	45	VAL	0	-0.007	0.005	22.722	0.000	0.000	0.000	0.000	0.000
47	A	46	ALA	0	-0.007	-0.003	24.034	-0.003	-0.003	0.000	0.000	0.000
48	A	47	SER	0	-0.089	-0.057	25.408	-0.002	-0.002	0.000	0.000	0.000
49	A	48	ASN	0	-0.072	-0.030	27.263	0.001	0.001	0.000	0.000	0.000
50	A	49	ASN	0	-0.004	-0.013	28.446	-0.005	-0.005	0.000	0.000	0.000
51	A	50	GLU	-1	-0.841	-0.925	29.474	-0.016	-0.016	0.000	0.000	0.000
52	A	51	THR	0	-0.010	0.009	31.074	-0.004	-0.004	0.000	0.000	0.000
53	A	52	MET	0	-0.017	-0.007	24.450	-0.005	-0.005	0.000	0.000	0.000
54	A	53	ALA	0	0.030	0.022	26.391	-0.008	-0.008	0.000	0.000	0.000
55	A	54	THR	0	-0.038	-0.035	27.371	-0.007	-0.007	0.000	0.000	0.000
56	A	55	ILE	0	0.010	0.007	25.591	-0.007	-0.007	0.000	0.000	0.000
57	A	56	LEU	0	-0.006	0.002	21.403	-0.011	-0.011	0.000	0.000	0.000
58	A	57	LEU	0	0.004	0.011	24.037	-0.013	-0.013	0.000	0.000	0.000
59	A	58	GLN	0	-0.006	-0.015	26.452	-0.003	-0.003	0.000	0.000	0.000
60	A	59	ASN	0	0.008	-0.001	22.567	-0.007	-0.007	0.000	0.000	0.000
61	A	60	LEU	0	0.007	0.019	21.216	-0.016	-0.016	0.000	0.000	0.000
62	A	61	LEU	0	-0.040	-0.034	23.354	-0.010	-0.010	0.000	0.000	0.000
63	A	62	ILE	0	-0.015	0.003	24.375	-0.003	-0.003	0.000	0.000	0.000
64	A	63	GLN	0	0.002	-0.018	18.257	-0.030	-0.030	0.000	0.000	0.000
65	A	64	LEU	0	-0.020	-0.007	21.966	-0.016	-0.016	0.000	0.000	0.000
66	A	65	ASP	-1	-0.803	-0.895	23.954	-0.105	-0.105	0.000	0.000	0.000
67	A	66	GLU	-1	-0.873	-0.917	21.085	-0.200	-0.200	0.000	0.000	0.000
68	A	67	GLN	0	0.008	-0.002	18.122	-0.021	-0.021	0.000	0.000	0.000
69	A	68	LEU	0	-0.020	-0.007	22.248	0.003	0.003	0.000	0.000	0.000
70	A	69	GLY	0	0.006	0.020	25.936	0.006	0.006	0.000	0.000	0.000
71	A	70	ARG	1	0.831	0.906	16.762	0.321	0.321	0.000	0.000	0.000
72	A	71	VAL	0	0.020	-0.001	22.476	0.005	0.005	0.000	0.000	0.000
73	A	72	SER	0	-0.053	-0.054	24.632	0.015	0.015	0.000	0.000	0.000
74	A	73	LYS	1	0.912	0.962	25.144	0.168	0.168	0.000	0.000	0.000
75	A	74	GLU	-1	-0.864	-0.918	20.538	-0.252	-0.252	0.000	0.000	0.000
76	A	75	LYS	1	0.902	0.957	25.484	0.111	0.111	0.000	0.000	0.000
77	A	76	ASN	0	0.070	0.040	23.436	0.023	0.023	0.000	0.000	0.000
78	A	77	LEU	0	0.023	-0.007	27.135	0.002	0.002	0.000	0.000	0.000
79	A	78	LEU	0	0.035	0.032	26.361	0.005	0.005	0.000	0.000	0.000
80	A	79	LEU	0	0.052	0.024	21.895	0.005	0.005	0.000	0.000	0.000
81	A	80	ILE	0	-0.019	-0.005	26.153	0.005	0.005	0.000	0.000	0.000
82	A	81	HIS	0	-0.018	-0.004	28.857	0.012	0.012	0.000	0.000	0.000
83	A	82	ASN	0	-0.019	-0.021	27.274	0.008	0.008	0.000	0.000	0.000
84	A	83	LEU	0	0.065	0.033	23.186	0.006	0.006	0.000	0.000	0.000
85	A	84	LYS	1	0.929	0.978	27.371	0.096	0.096	0.000	0.000	0.000
86	A	85	ARG	1	0.829	0.911	30.964	0.060	0.060	0.000	0.000	0.000
87	A	86	ILE	0	0.059	0.029	25.641	0.005	0.005	0.000	0.000	0.000
88	A	87	ARG	1	0.846	0.911	28.945	0.090	0.090	0.000	0.000	0.000
89	A	88	LYS	1	0.933	0.968	29.878	0.057	0.057	0.000	0.000	0.000
90	A	89	VAL	0	0.021	0.021	31.084	0.004	0.004	0.000	0.000	0.000
91	A	90	LEU	0	0.042	0.017	25.829	0.004	0.004	0.000	0.000	0.000
92	A	91	GLN	0	-0.001	-0.007	30.208	0.000	0.000	0.000	0.000	0.000
93	A	92	GLY	0	0.000	0.011	32.857	0.003	0.003	0.000	0.000	0.000
94	A	93	LYS	1	0.803	0.886	30.434	0.030	0.030	0.000	0.000	0.000
95	A	94	PHE	0	-0.010	-0.009	31.064	0.003	0.003	0.000	0.000	0.000
96	A	95	HIS	0	-0.083	-0.045	32.629	0.002	0.002	0.000	0.000	0.000
97	A	96	GLY	0	0.002	0.007	35.126	0.003	0.003	0.000	0.000	0.000
98	A	97	ASN	0	-0.025	-0.019	33.013	0.003	0.003	0.000	0.000	0.000
99	A	98	PRO	0	0.054	0.027	29.550	0.000	0.000	0.000	0.000	0.000
100	A	99	MET	0	0.028	0.022	28.512	-0.002	-0.002	0.000	0.000	0.000
101	A	100	HIS	0	0.002	0.009	28.577	0.005	0.005	0.000	0.000	0.000
102	A	101	VAL	0	-0.005	-0.001	24.962	0.002	0.002	0.000	0.000	0.000
103	A	102	ALA	0	0.017	0.024	24.113	0.000	0.000	0.000	0.000	0.000
104	A	103	VAL	0	0.032	0.025	24.146	0.009	0.009	0.000	0.000	0.000
105	A	104	VAL	0	-0.017	0.002	24.478	0.009	0.009	0.000	0.000	0.000
106	A	105	ILE	0	-0.008	0.001	19.488	0.008	0.008	0.000	0.000	0.000
107	A	106	SER	0	0.012	-0.013	20.347	0.011	0.011	0.000	0.000	0.000
108	A	107	ASN	0	-0.103	-0.059	20.914	0.027	0.027	0.000	0.000	0.000
109	A	108	CYS	0	0.002	0.028	20.023	0.012	0.012	0.000	0.000	0.000
110	A	109	LEU	0	0.023	0.005	14.873	0.017	0.017	0.000	0.000	0.000
111	A	110	ARG	1	0.929	0.951	16.910	-0.069	-0.069	0.000	0.000	0.000
112	A	111	GLU	-1	-0.756	-0.833	19.348	0.137	0.137	0.000	0.000	0.000
113	A	112	GLU	-1	-0.762	-0.847	15.071	0.051	0.051	0.000	0.000	0.000
114	A	113	ARG	1	0.821	0.899	14.095	-0.099	-0.099	0.000	0.000	0.000
115	A	114	ARG	1	0.761	0.851	16.059	-0.097	-0.097	0.000	0.000	0.000
116	A	115	ILE	0	-0.012	-0.016	17.709	0.017	0.017	0.000	0.000	0.000
117	A	116	LEU	0	-0.024	-0.018	11.629	0.015	0.015	0.000	0.000	0.000
118	A	117	ALA	0	-0.039	-0.015	15.356	0.041	0.041	0.000	0.000	0.000
119	A	118	ALA	0	-0.045	-0.016	17.324	-0.012	-0.012	0.000	0.000	0.000
120	A	119	ALA	0	-0.015	0.007	16.002	-0.031	-0.031	0.000	0.000	0.000
121	A	120	ASN	0	-0.036	-0.020	17.952	0.020	0.020	0.000	0.000	0.000
122	A	121	MET	0	0.013	0.002	11.659	0.013	0.013	0.000	0.000	0.000
123	A	122	PRO	0	-0.042	-0.006	16.450	-0.017	-0.017	0.000	0.000	0.000
124	A	123	ILE	0	0.012	0.005	16.684	0.044	0.044	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)