FMO DATABASE

FMODB ID: 9GJV2

Calculation Name: 4HBO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HBO

Chain ID: A

ChEMBL ID:

UniProt ID: P08563

Base Structure: X-ray

Registration Date: 2023-06-20

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	79
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-486186.130621
FMO2-HF: Nuclear repulsion	453948.086332
FMO2-HF: Total energy	-32238.044289
FMO2-MP2: Total energy	-32330.720246

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:25:GLU)

Summations of interaction energy for fragment #1(A:25:GLU)

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.
-44.168	-57.615	47.99	-21.953	-12.592	0.107

Interaction energy analysis for fragmet #1(A:25:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.888 / q_NPA : -0.910

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

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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	27	CYM	-1	-0.734	-0.786	3.883	47.001	49.035	-0.021	-1.044	-0.969	0.002
4	A	28	VAL	0	-0.028	-0.011	7.093	-3.832	-3.832	0.000	0.000	0.000	0.000
5	A	29	THR	0	-0.042	-0.036	10.574	0.282	0.282	0.000	0.000	0.000	0.000
6	A	30	SER	0	0.026	0.007	13.857	-0.706	-0.706	0.000	0.000	0.000	0.000
7	A	31	TRP	0	-0.010	-0.012	17.176	-0.330	-0.330	0.000	0.000	0.000	0.000
8	A	32	LEU	0	-0.002	0.001	20.296	-0.245	-0.245	0.000	0.000	0.000	0.000
9	A	33	TRP	0	-0.017	0.000	22.570	0.233	0.233	0.000	0.000	0.000	0.000
10	A	34	SER	0	-0.022	-0.007	25.930	-0.272	-0.272	0.000	0.000	0.000	0.000
11	A	35	GLU	-1	-0.818	-0.894	29.125	9.387	9.387	0.000	0.000	0.000	0.000
12	A	36	GLY	0	0.004	0.000	32.751	-0.144	-0.144	0.000	0.000	0.000	0.000
13	A	37	GLU	-1	-0.873	-0.935	34.730	8.907	8.907	0.000	0.000	0.000	0.000
14	A	38	GLY	0	-0.021	-0.013	33.879	0.040	0.040	0.000	0.000	0.000	0.000
15	A	39	ALA	0	-0.074	-0.017	30.620	0.311	0.311	0.000	0.000	0.000	0.000
16	A	40	VAL	0	0.008	-0.001	25.958	0.121	0.121	0.000	0.000	0.000	0.000
17	A	41	PHE	0	0.002	-0.022	23.107	0.001	0.001	0.000	0.000	0.000	0.000
18	A	42	TYR	0	0.002	0.003	18.836	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	43	ARG	1	0.929	0.974	17.806	-14.699	-14.699	0.000	0.000	0.000	0.000
20	A	44	VAL	0	0.021	0.009	14.790	0.011	0.011	0.000	0.000	0.000	0.000
21	A	45	ASP	-1	-0.847	-0.895	10.338	26.490	26.490	0.000	0.000	0.000	0.000
22	A	46	LEU	0	-0.045	-0.009	9.725	0.661	0.661	0.000	0.000	0.000	0.000
23	A	47	HIS	1	0.733	0.757	4.252	-42.566	-42.376	-0.001	-0.029	-0.160	0.000
24	A	48	PHE	0	-0.018	-0.003	4.772	-1.816	-1.592	-0.001	-0.044	-0.180	0.000
25	A	49	THR	0	-0.061	-0.065	1.429	-57.322	-73.217	48.013	-20.836	-11.283	0.105
26	A	67	MET	0	-0.001	-0.015	13.587	-0.563	-0.563	0.000	0.000	0.000	0.000
27	A	68	TYR	0	-0.042	-0.019	15.234	-1.232	-1.232	0.000	0.000	0.000	0.000
28	A	69	ASN	0	0.028	0.007	14.966	0.292	0.292	0.000	0.000	0.000	0.000
29	A	70	PRO	0	0.009	0.023	14.829	0.965	0.965	0.000	0.000	0.000	0.000
30	A	71	CYS	0	0.015	-0.008	9.973	0.624	0.624	0.000	0.000	0.000	0.000
31	A	72	GLY	0	0.000	-0.003	11.800	1.190	1.190	0.000	0.000	0.000	0.000
32	A	73	PRO	0	-0.032	-0.019	14.493	-0.677	-0.677	0.000	0.000	0.000	0.000
33	A	74	GLU	-1	-0.899	-0.939	17.530	16.455	16.455	0.000	0.000	0.000	0.000
34	A	75	PRO	0	-0.022	-0.009	17.504	-0.764	-0.764	0.000	0.000	0.000	0.000
35	A	76	PRO	0	0.031	0.006	20.490	-0.372	-0.372	0.000	0.000	0.000	0.000
36	A	77	ALA	0	0.085	0.041	23.268	0.079	0.079	0.000	0.000	0.000	0.000
37	A	78	HIS	0	-0.049	-0.029	24.317	0.111	0.111	0.000	0.000	0.000	0.000
38	A	79	VAL	0	0.032	0.027	20.947	-0.175	-0.175	0.000	0.000	0.000	0.000
39	A	80	VAL	0	0.068	0.042	18.834	0.120	0.120	0.000	0.000	0.000	0.000
40	A	81	ARG	1	0.878	0.935	21.041	-11.413	-11.413	0.000	0.000	0.000	0.000
41	A	82	ALA	0	0.009	0.011	23.674	-0.537	-0.537	0.000	0.000	0.000	0.000
42	A	83	TYR	0	0.019	0.019	15.838	-0.401	-0.401	0.000	0.000	0.000	0.000
43	A	84	ASN	0	0.030	0.001	18.611	0.517	0.517	0.000	0.000	0.000	0.000
44	A	85	GLN	0	-0.029	0.008	21.168	-0.374	-0.374	0.000	0.000	0.000	0.000
45	A	86	PRO	0	0.056	0.032	24.133	0.172	0.172	0.000	0.000	0.000	0.000
46	A	87	ALA	0	-0.028	-0.021	25.052	-0.560	-0.560	0.000	0.000	0.000	0.000
47	A	88	GLY	0	0.023	0.009	26.216	0.278	0.278	0.000	0.000	0.000	0.000
48	A	89	ASP	-1	-0.872	-0.890	28.175	9.730	9.730	0.000	0.000	0.000	0.000
49	A	90	VAL	0	0.004	-0.015	25.729	0.483	0.483	0.000	0.000	0.000	0.000
50	A	91	ARG	1	0.790	0.866	28.534	-9.844	-9.844	0.000	0.000	0.000	0.000
51	A	92	GLY	0	0.042	0.036	28.745	-0.361	-0.361	0.000	0.000	0.000	0.000
52	A	93	VAL	0	-0.017	-0.014	25.001	0.440	0.440	0.000	0.000	0.000	0.000
53	A	94	TRP	0	-0.033	-0.013	25.456	-0.431	-0.431	0.000	0.000	0.000	0.000
54	A	95	GLY	0	0.009	0.002	23.420	0.587	0.587	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.910	0.939	23.054	-12.923	-12.923	0.000	0.000	0.000	0.000
56	A	97	GLY	0	0.053	0.016	21.991	0.426	0.426	0.000	0.000	0.000	0.000
57	A	98	GLU	-1	-0.928	-0.964	18.437	14.416	14.416	0.000	0.000	0.000	0.000
58	A	99	ARG	0	-0.011	0.030	12.698	0.507	0.507	0.000	0.000	0.000	0.000
59	A	100	THR	0	-0.044	-0.046	19.422	-0.535	-0.535	0.000	0.000	0.000	0.000
60	A	101	TYR	0	-0.032	-0.044	16.246	0.666	0.666	0.000	0.000	0.000	0.000
61	A	102	ALA	0	0.011	0.022	21.623	-0.740	-0.740	0.000	0.000	0.000	0.000
62	A	103	GLU	-1	-0.864	-0.942	23.030	11.632	11.632	0.000	0.000	0.000	0.000
63	A	104	GLN	0	0.005	-0.001	23.429	0.161	0.161	0.000	0.000	0.000	0.000
64	A	105	ASP	-1	-0.755	-0.848	27.276	10.329	10.329	0.000	0.000	0.000	0.000
65	A	106	PHE	0	-0.024	-0.020	25.193	-0.089	-0.089	0.000	0.000	0.000	0.000
66	A	107	ARG	1	0.881	0.944	30.679	-9.072	-9.072	0.000	0.000	0.000	0.000
67	A	108	VAL	0	0.020	0.013	28.274	0.081	0.081	0.000	0.000	0.000	0.000
68	A	109	GLY	0	0.011	0.001	31.620	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	110	GLY	0	0.017	0.009	34.871	-0.214	-0.214	0.000	0.000	0.000	0.000
70	A	111	THR	0	0.002	-0.001	30.953	-0.234	-0.234	0.000	0.000	0.000	0.000
71	A	112	ARG	1	0.788	0.862	32.628	-9.346	-9.346	0.000	0.000	0.000	0.000
72	A	113	TRP	0	-0.002	-0.004	24.761	0.258	0.258	0.000	0.000	0.000	0.000
73	A	114	HIS	1	0.841	0.904	27.608	-10.785	-10.785	0.000	0.000	0.000	0.000
74	A	115	ARG	1	0.819	0.892	20.673	-13.614	-13.614	0.000	0.000	0.000	0.000
75	A	116	LEU	0	-0.016	0.003	20.756	-0.408	-0.408	0.000	0.000	0.000	0.000
76	A	117	LEU	0	0.037	-0.003	17.347	0.815	0.815	0.000	0.000	0.000	0.000
77	A	118	ARG	0	-0.017	0.002	14.541	-0.475	-0.475	0.000	0.000	0.000	0.000
78	A	119	MET	0	-0.017	-0.006	17.173	0.293	0.293	0.000	0.000	0.000	0.000
79	A	120	PRO	0	0.010	0.039	15.850	-1.087	-1.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:GLU)