FMO DATABASE

FMODB ID: MV6ZZ

Calculation Name: 3ZIB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-21

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-640623.920697
FMO2-HF: Nuclear repulsion	603745.955595
FMO2-HF: Total energy	-36877.965102
FMO2-MP2: Total energy	-36983.398046

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:27:THR)

Summations of interaction energy for fragment #1(A:27:THR)

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.
-7.569	-3.994	2.426	-2.343	-3.657	-0.022

Interaction energy analysis for fragmet #1(A:27:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.031

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	29	THR	0	0.017	-0.001	2.510	-3.064	-0.627	1.927	-1.907	-2.457	-0.017
4	A	30	PRO	0	0.064	0.033	5.156	0.279	0.370	-0.001	-0.002	-0.087	0.000
5	A	31	GLU	-1	-0.801	-0.902	7.188	-1.395	-1.395	0.000	0.000	0.000	0.000
6	A	32	GLU	-1	-0.889	-0.949	6.048	-3.336	-3.336	0.000	0.000	0.000	0.000
7	A	33	TYR	0	0.066	0.031	2.468	-0.680	0.367	0.500	-0.434	-1.113	-0.005
8	A	34	LEU	0	0.002	0.016	7.579	0.408	0.408	0.000	0.000	0.000	0.000
9	A	35	LYS	1	0.934	0.955	10.988	1.092	1.092	0.000	0.000	0.000	0.000
10	A	36	ASN	0	-0.003	0.020	7.750	0.226	0.226	0.000	0.000	0.000	0.000
11	A	37	TYR	0	-0.004	0.006	11.335	0.219	0.219	0.000	0.000	0.000	0.000
12	A	38	ALA	0	0.013	-0.007	13.053	0.107	0.107	0.000	0.000	0.000	0.000
13	A	39	LEU	0	-0.001	0.004	14.782	0.076	0.076	0.000	0.000	0.000	0.000
14	A	40	SER	0	-0.024	-0.014	13.897	0.098	0.098	0.000	0.000	0.000	0.000
15	A	41	VAL	0	-0.028	-0.025	16.537	0.054	0.054	0.000	0.000	0.000	0.000
16	A	42	CYS	0	-0.066	-0.024	18.814	0.013	0.013	0.000	0.000	0.000	0.000
17	A	43	ILE	0	0.056	0.015	18.607	0.028	0.028	0.000	0.000	0.000	0.000
18	A	44	ALA	0	-0.028	-0.007	20.426	0.023	0.023	0.000	0.000	0.000	0.000
19	A	45	GLU	-1	-0.950	-0.986	22.270	-0.097	-0.097	0.000	0.000	0.000	0.000
20	A	46	GLY	0	-0.005	0.009	24.364	0.007	0.007	0.000	0.000	0.000	0.000
21	A	47	TYR	0	0.023	0.019	23.793	0.008	0.008	0.000	0.000	0.000	0.000
22	A	48	SER	0	0.006	-0.022	27.451	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	49	ALA	0	0.014	0.014	27.808	0.004	0.004	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.984	0.970	27.010	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	51	GLU	-1	-0.935	-0.953	24.653	0.125	0.125	0.000	0.000	0.000	0.000
26	A	52	VAL	0	0.078	0.040	22.198	0.011	0.011	0.000	0.000	0.000	0.000
27	A	53	LYS	1	0.829	0.924	22.051	0.032	0.032	0.000	0.000	0.000	0.000
28	A	54	ASN	0	-0.036	-0.031	22.115	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	55	ASP	-1	-0.906	-0.931	18.484	0.225	0.225	0.000	0.000	0.000	0.000
30	A	56	ALA	0	0.047	0.021	17.538	0.012	0.012	0.000	0.000	0.000	0.000
31	A	57	ALA	0	-0.009	-0.020	17.161	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	58	ALA	0	-0.057	-0.029	17.116	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	59	ALA	0	0.050	0.039	13.369	0.011	0.011	0.000	0.000	0.000	0.000
34	A	60	ALA	0	-0.013	-0.019	12.714	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.909	0.955	13.359	-0.118	-0.118	0.000	0.000	0.000	0.000
36	A	62	GLY	0	0.066	0.038	11.469	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	63	TYR	0	-0.030	-0.029	7.846	-0.103	-0.103	0.000	0.000	0.000	0.000
38	A	64	THR	0	-0.055	-0.027	9.190	-0.191	-0.191	0.000	0.000	0.000	0.000
39	A	65	GLU	-1	-0.989	-0.990	10.305	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	66	PHE	0	-0.063	-0.029	5.349	0.151	0.151	0.000	0.000	0.000	0.000
41	A	67	GLY	0	-0.017	0.011	5.788	-0.556	-0.556	0.000	0.000	0.000	0.000
42	A	68	ASP	-1	-0.859	-0.934	7.599	-1.888	-1.888	0.000	0.000	0.000	0.000
43	A	69	TYR	0	-0.133	-0.086	9.612	0.270	0.270	0.000	0.000	0.000	0.000
44	A	70	SER	0	0.077	0.035	12.563	0.055	0.055	0.000	0.000	0.000	0.000
45	A	71	LEU	0	0.090	0.038	15.671	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	72	GLU	-1	-0.880	-0.937	17.616	-0.330	-0.330	0.000	0.000	0.000	0.000
47	A	73	ALA	0	0.009	0.020	15.864	0.022	0.022	0.000	0.000	0.000	0.000
48	A	74	HIS	0	0.011	-0.018	12.149	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	75	THR	0	-0.095	-0.051	16.895	0.048	0.048	0.000	0.000	0.000	0.000
50	A	76	ALA	0	0.007	0.000	20.348	0.030	0.030	0.000	0.000	0.000	0.000
51	A	77	VAL	0	0.025	0.014	15.889	0.026	0.026	0.000	0.000	0.000	0.000
52	A	78	ARG	1	0.881	0.940	19.124	0.203	0.203	0.000	0.000	0.000	0.000
53	A	79	ALA	0	-0.051	-0.027	20.799	0.033	0.033	0.000	0.000	0.000	0.000
54	A	80	LEU	0	0.048	0.031	20.753	0.019	0.019	0.000	0.000	0.000	0.000
55	A	81	ALA	0	0.030	0.001	20.596	0.019	0.019	0.000	0.000	0.000	0.000
56	A	82	LYS	1	0.888	0.935	22.625	0.179	0.179	0.000	0.000	0.000	0.000
57	A	83	GLU	-1	-0.956	-0.962	25.996	-0.199	-0.199	0.000	0.000	0.000	0.000
58	A	84	PHE	0	0.011	-0.021	24.455	0.011	0.011	0.000	0.000	0.000	0.000
59	A	85	LEU	0	-0.028	-0.014	24.387	0.018	0.018	0.000	0.000	0.000	0.000
60	A	86	ALA	0	-0.044	-0.013	27.685	0.016	0.016	0.000	0.000	0.000	0.000
61	A	87	LYS	1	0.897	0.973	27.251	0.206	0.206	0.000	0.000	0.000	0.000
62	A	88	PRO	0	-0.035	-0.022	31.801	0.004	0.004	0.000	0.000	0.000	0.000
63	A	89	TYR	0	-0.079	-0.096	27.311	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	90	ASP	-1	-0.873	-0.924	33.540	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	91	SER	0	-0.016	0.003	34.235	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	92	MET	0	-0.048	-0.065	31.532	0.002	0.002	0.000	0.000	0.000	0.000
67	A	93	SER	0	-0.020	-0.002	34.482	0.002	0.002	0.000	0.000	0.000	0.000
68	A	94	GLY	0	0.020	0.023	37.284	0.006	0.006	0.000	0.000	0.000	0.000
69	A	95	GLU	-1	-0.928	-0.959	32.160	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	96	PRO	0	0.003	-0.007	30.606	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	97	MET	0	-0.026	-0.024	29.182	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	98	THR	0	0.059	0.025	25.000	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	99	MET	0	-0.020	0.009	20.061	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	100	ALA	0	0.039	0.010	23.443	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.909	0.987	25.034	0.078	0.078	0.000	0.000	0.000	0.000
76	A	103	ILE	0	0.037	0.019	19.932	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	104	ASP	-1	-0.783	-0.846	20.784	-0.222	-0.222	0.000	0.000	0.000	0.000
78	A	105	LEU	0	-0.044	-0.014	19.375	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	106	VAL	0	-0.028	-0.011	15.531	-0.050	-0.050	0.000	0.000	0.000	0.000
80	A	107	HIS	0	-0.089	-0.059	17.550	-0.089	-0.089	0.000	0.000	0.000	0.000
81	A	108	SER	0	-0.061	0.005	19.950	0.001	0.001	0.000	0.000	0.000	0.000
82	A	109	GLN	0	0.012	-0.017	20.852	-0.038	-0.038	0.000	0.000	0.000	0.000
83	A	110	GLU	-1	-0.822	-0.924	22.486	-0.305	-0.305	0.000	0.000	0.000	0.000
84	A	111	LEU	0	0.008	0.003	15.690	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	112	GLN	0	-0.008	-0.006	17.186	-0.103	-0.103	0.000	0.000	0.000	0.000
86	A	113	ALA	0	-0.012	0.000	19.005	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	114	ILE	0	-0.029	-0.007	17.833	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	115	ILE	0	0.024	0.005	13.846	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.856	0.910	16.515	0.711	0.711	0.000	0.000	0.000	0.000
90	A	117	LYS	1	0.893	0.968	18.945	0.383	0.383	0.000	0.000	0.000	0.000
91	A	118	TYR	0	-0.041	-0.036	16.860	0.039	0.039	0.000	0.000	0.000	0.000
92	A	119	GLN	0	-0.011	0.032	13.041	0.142	0.142	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:THR)