FMO DATABASE

FMODB ID: 6Y2VZ

Calculation Name: 3ZBD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZBD

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6V2

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	OptHSide
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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-891774.067245
FMO2-HF: Nuclear repulsion	846797.396923
FMO2-HF: Total energy	-44976.670323
FMO2-MP2: Total energy	-45105.854963

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:HIS)

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

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.
-5.069	-1.978	0.832	-1.508	-2.415	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.017

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	-2	HIS	0	-0.005	-0.010	2.831	-5.625	-2.534	0.832	-1.508	-2.415	-0.008
4	A	-1	HIS	0	0.011	0.017	6.041	0.354	0.354	0.000	0.000	0.000	0.000
5	A	0	HIS	0	-0.047	-0.032	9.583	-0.109	-0.109	0.000	0.000	0.000	0.000
6	A	1	MET	0	0.011	0.016	12.488	0.104	0.104	0.000	0.000	0.000	0.000
7	A	2	SER	0	-0.004	-0.011	14.826	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	3	SER	0	-0.100	-0.069	16.961	0.051	0.051	0.000	0.000	0.000	0.000
9	A	4	LYS	1	0.860	0.932	20.420	-0.105	-0.105	0.000	0.000	0.000	0.000
10	A	5	GLN	0	-0.021	-0.017	22.059	0.002	0.002	0.000	0.000	0.000	0.000
11	A	6	PHE	0	-0.068	-0.033	26.026	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	7	LYS	1	0.885	0.936	30.071	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	8	ILE	0	-0.053	-0.020	31.365	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	9	LEU	0	-0.009	0.009	35.313	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	10	VAL	0	0.008	0.004	36.182	0.008	0.008	0.000	0.000	0.000	0.000
16	A	11	ASN	0	-0.018	-0.031	38.859	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	12	GLU	-1	-0.825	-0.917	39.990	0.104	0.104	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.923	-0.960	42.875	0.071	0.071	0.000	0.000	0.000	0.000
19	A	14	TYR	0	-0.054	-0.033	46.065	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	15	GLN	0	-0.005	-0.006	46.376	0.002	0.002	0.000	0.000	0.000	0.000
21	A	16	VAL	0	-0.055	-0.033	43.782	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	17	ASN	0	-0.034	-0.017	46.457	0.008	0.008	0.000	0.000	0.000	0.000
23	A	18	VAL	0	0.002	-0.005	41.682	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	19	PRO	0	-0.024	0.000	42.190	0.002	0.002	0.000	0.000	0.000	0.000
25	A	20	SER	0	0.008	-0.004	40.461	0.003	0.003	0.000	0.000	0.000	0.000
26	A	21	LEU	0	-0.015	-0.026	38.244	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	22	PRO	0	0.034	0.027	38.678	0.010	0.010	0.000	0.000	0.000	0.000
28	A	23	ILE	0	0.039	0.012	31.861	0.001	0.001	0.000	0.000	0.000	0.000
29	A	24	ARG	1	0.924	0.961	33.613	-0.175	-0.175	0.000	0.000	0.000	0.000
30	A	25	ASP	-1	-0.842	-0.932	33.972	0.140	0.140	0.000	0.000	0.000	0.000
31	A	26	VAL	0	0.020	0.023	32.720	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	27	LEU	0	-0.020	-0.013	28.313	0.005	0.005	0.000	0.000	0.000	0.000
33	A	28	GLN	0	-0.013	-0.005	30.123	0.014	0.014	0.000	0.000	0.000	0.000
34	A	29	GLU	-1	-0.774	-0.857	32.054	0.107	0.107	0.000	0.000	0.000	0.000
35	A	30	ILE	0	0.028	0.021	27.743	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	31	LYS	1	0.844	0.921	26.873	-0.200	-0.200	0.000	0.000	0.000	0.000
37	A	32	TYR	0	-0.021	-0.011	28.757	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	33	CYS	0	0.021	0.016	31.396	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	34	TYR	0	-0.020	0.004	21.679	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	35	ARG	1	0.909	0.949	24.716	-0.099	-0.099	0.000	0.000	0.000	0.000
41	A	36	ASN	0	-0.044	-0.035	28.806	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	37	GLY	0	0.003	0.023	31.568	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	38	PHE	0	0.014	-0.012	29.807	0.005	0.005	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.879	-0.924	35.163	0.047	0.047	0.000	0.000	0.000	0.000
45	A	40	GLY	0	-0.010	-0.015	38.695	0.005	0.005	0.000	0.000	0.000	0.000
46	A	41	TYR	0	-0.102	-0.096	36.770	0.005	0.005	0.000	0.000	0.000	0.000
47	A	42	VAL	0	0.005	0.012	38.715	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	43	PHE	0	-0.010	-0.015	32.660	0.009	0.009	0.000	0.000	0.000	0.000
49	A	44	VAL	0	0.009	0.014	36.718	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	45	PRO	0	0.031	0.017	35.748	0.012	0.012	0.000	0.000	0.000	0.000
51	A	46	GLU	-1	-0.855	-0.926	34.551	0.166	0.166	0.000	0.000	0.000	0.000
52	A	47	TYR	0	-0.042	-0.055	36.172	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	CYS	0	-0.061	-0.012	39.260	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	49	ARG	1	0.784	0.861	36.466	-0.175	-0.175	0.000	0.000	0.000	0.000
55	A	50	ASP	-1	-0.914	-0.951	41.063	0.119	0.119	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.046	-0.004	43.649	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	52	VAL	0	-0.055	-0.025	40.747	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	53	ASP	-1	-0.875	-0.921	44.148	0.101	0.101	0.000	0.000	0.000	0.000
59	A	54	CYS	0	-0.057	-0.050	43.965	0.003	0.003	0.000	0.000	0.000	0.000
60	A	55	ASP	-1	-0.850	-0.912	46.054	0.092	0.092	0.000	0.000	0.000	0.000
61	A	56	ARG	1	0.806	0.885	44.515	-0.119	-0.119	0.000	0.000	0.000	0.000
62	A	57	LYS	1	0.957	0.976	43.251	-0.111	-0.111	0.000	0.000	0.000	0.000
63	A	58	ASP	-1	-0.855	-0.899	41.954	0.139	0.139	0.000	0.000	0.000	0.000
64	A	59	HIS	0	-0.030	-0.017	40.011	0.013	0.013	0.000	0.000	0.000	0.000
65	A	60	TYR	0	-0.038	-0.030	34.694	0.007	0.007	0.000	0.000	0.000	0.000
66	A	61	VAL	0	0.065	0.034	35.996	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	62	ILE	0	-0.006	-0.004	31.094	0.017	0.017	0.000	0.000	0.000	0.000
68	A	63	GLY	0	0.033	0.020	31.457	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	64	VAL	0	0.022	0.006	27.996	0.010	0.010	0.000	0.000	0.000	0.000
70	A	65	LEU	0	-0.031	-0.017	25.854	0.000	0.000	0.000	0.000	0.000	0.000
71	A	66	GLY	0	0.017	0.008	23.781	0.019	0.019	0.000	0.000	0.000	0.000
72	A	67	ASN	0	0.034	0.017	23.631	-0.039	-0.039	0.000	0.000	0.000	0.000
73	A	68	GLY	0	-0.004	-0.001	21.387	0.031	0.031	0.000	0.000	0.000	0.000
74	A	69	VAL	0	0.000	0.010	18.692	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	70	SER	0	-0.010	-0.013	21.348	0.035	0.035	0.000	0.000	0.000	0.000
76	A	71	ASP	-1	-0.877	-0.944	21.215	0.417	0.417	0.000	0.000	0.000	0.000
77	A	72	LEU	0	-0.019	0.001	23.910	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	73	LYS	1	0.947	0.963	24.269	-0.352	-0.352	0.000	0.000	0.000	0.000
79	A	74	PRO	0	-0.021	-0.006	28.277	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	75	VAL	0	-0.005	0.014	31.178	0.017	0.017	0.000	0.000	0.000	0.000
81	A	76	LEU	0	0.048	0.031	33.648	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	77	LEU	0	0.061	0.016	36.682	0.005	0.005	0.000	0.000	0.000	0.000
83	A	78	THR	0	0.000	0.007	39.154	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	79	GLU	-1	-0.927	-0.952	32.210	0.260	0.260	0.000	0.000	0.000	0.000
85	A	80	PRO	0	0.052	0.021	34.419	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	81	SER	0	-0.042	-0.011	28.609	0.006	0.006	0.000	0.000	0.000	0.000
87	A	82	VAL	0	0.056	0.015	29.101	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	83	MET	0	-0.049	-0.020	24.355	0.000	0.000	0.000	0.000	0.000	0.000
89	A	84	LEU	0	-0.035	-0.009	28.255	0.005	0.005	0.000	0.000	0.000	0.000
90	A	85	GLN	0	-0.016	-0.002	28.227	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.077	0.026	31.274	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	87	PHE	0	-0.048	-0.019	32.967	0.014	0.014	0.000	0.000	0.000	0.000
93	A	88	ILE	0	-0.014	0.007	31.361	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	89	VAL	0	-0.001	-0.016	35.400	0.004	0.004	0.000	0.000	0.000	0.000
95	A	90	ARG	1	0.855	0.926	38.856	-0.093	-0.093	0.000	0.000	0.000	0.000
96	A	91	ALA	0	0.011	0.001	41.377	0.000	0.000	0.000	0.000	0.000	0.000
97	A	92	ASN	0	-0.020	-0.016	43.631	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	93	CYS	0	-0.040	0.009	44.832	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	94	ASN	0	-0.003	0.000	45.380	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	95	GLY	0	0.081	0.025	42.709	0.005	0.005	0.000	0.000	0.000	0.000
101	A	96	VAL	0	0.001	0.012	39.359	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	97	LEU	0	-0.035	-0.025	37.277	0.004	0.004	0.000	0.000	0.000	0.000
103	A	98	GLU	-1	-0.871	-0.926	33.546	0.094	0.094	0.000	0.000	0.000	0.000
104	A	99	ASP	-1	-0.885	-0.941	29.348	0.047	0.047	0.000	0.000	0.000	0.000
105	A	100	PHE	0	0.013	0.014	28.456	0.012	0.012	0.000	0.000	0.000	0.000
106	A	101	ASP	-1	-0.801	-0.871	21.970	0.122	0.122	0.000	0.000	0.000	0.000
107	A	102	LEU	0	-0.002	-0.001	24.298	0.028	0.028	0.000	0.000	0.000	0.000
108	A	103	LYS	1	0.892	0.926	17.782	-0.422	-0.422	0.000	0.000	0.000	0.000
109	A	104	ILE	0	-0.016	-0.009	22.249	0.002	0.002	0.000	0.000	0.000	0.000
110	A	105	ALA	0	-0.036	-0.002	21.240	0.058	0.058	0.000	0.000	0.000	0.000

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