FMO DATABASE

FMODB ID: 7234K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-641125.792955
FMO2-HF: Nuclear repulsion	604247.315194
FMO2-HF: Total energy	-36878.477761
FMO2-MP2: Total energy	-36983.874399

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.
-5.944	-1.419	1.566	-2.415	-3.676	-0.019

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 : -0.051 / q_NPA : -0.039

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	29	THR	0	-0.011	-0.047	2.621	-2.681	0.446	1.003	-1.831	-2.300	-0.015
4	A	30	PRO	0	0.046	0.024	5.278	0.166	0.242	-0.001	-0.002	-0.072	0.000
5	A	31	GLU	-1	-0.791	-0.871	7.261	-0.960	-0.960	0.000	0.000	0.000	0.000
6	A	32	GLU	-1	-0.847	-0.894	6.352	-3.375	-3.375	0.000	0.000	0.000	0.000
7	A	33	TYR	0	0.052	0.022	2.681	-1.099	0.223	0.564	-0.582	-1.304	-0.004
8	A	34	LEU	0	0.009	0.020	7.721	0.318	0.318	0.000	0.000	0.000	0.000
9	A	35	LYS	1	0.873	0.924	11.147	0.839	0.839	0.000	0.000	0.000	0.000
10	A	36	ASN	0	0.004	0.021	7.863	0.212	0.212	0.000	0.000	0.000	0.000
11	A	37	TYR	0	-0.011	0.005	11.479	0.172	0.172	0.000	0.000	0.000	0.000
12	A	38	ALA	0	0.004	-0.010	13.187	0.078	0.078	0.000	0.000	0.000	0.000
13	A	39	LEU	0	-0.014	0.001	14.793	0.059	0.059	0.000	0.000	0.000	0.000
14	A	40	SER	0	-0.020	-0.021	13.942	0.073	0.073	0.000	0.000	0.000	0.000
15	A	41	VAL	0	-0.010	-0.019	16.634	0.043	0.043	0.000	0.000	0.000	0.000
16	A	42	CYS	0	-0.066	-0.019	18.945	0.013	0.013	0.000	0.000	0.000	0.000
17	A	43	ILE	0	0.056	0.019	18.301	0.021	0.021	0.000	0.000	0.000	0.000
18	A	44	ALA	0	-0.018	-0.003	20.501	0.017	0.017	0.000	0.000	0.000	0.000
19	A	45	GLU	-1	-0.841	-0.898	22.348	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	46	GLY	0	0.004	0.011	24.509	0.004	0.004	0.000	0.000	0.000	0.000
21	A	47	TYR	0	0.024	0.017	23.663	0.002	0.002	0.000	0.000	0.000	0.000
22	A	48	SER	0	0.005	-0.013	27.431	0.004	0.004	0.000	0.000	0.000	0.000
23	A	49	ALA	0	0.040	0.020	27.771	0.007	0.007	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.978	0.968	26.988	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	51	GLU	-1	-0.932	-0.949	24.814	0.083	0.083	0.000	0.000	0.000	0.000
26	A	52	VAL	0	0.075	0.039	22.282	0.011	0.011	0.000	0.000	0.000	0.000
27	A	53	LYS	1	0.777	0.884	22.029	0.011	0.011	0.000	0.000	0.000	0.000
28	A	54	ASN	0	-0.038	-0.035	22.104	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	55	ASP	-1	-0.901	-0.929	18.640	0.177	0.177	0.000	0.000	0.000	0.000
30	A	56	ALA	0	0.050	0.019	17.520	0.017	0.017	0.000	0.000	0.000	0.000
31	A	57	ALA	0	-0.013	-0.020	17.152	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	58	ALA	0	-0.061	-0.031	17.168	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	59	ALA	0	0.048	0.034	13.350	0.031	0.031	0.000	0.000	0.000	0.000
34	A	60	ALA	0	-0.003	-0.013	12.813	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.912	0.962	13.446	-0.170	-0.170	0.000	0.000	0.000	0.000
36	A	62	GLY	0	0.068	0.040	11.529	0.000	0.000	0.000	0.000	0.000	0.000
37	A	63	TYR	0	-0.035	-0.031	7.932	0.025	0.025	0.000	0.000	0.000	0.000
38	A	64	THR	0	-0.064	-0.031	9.263	-0.121	-0.121	0.000	0.000	0.000	0.000
39	A	65	GLU	-1	-1.004	-0.997	10.821	0.350	0.350	0.000	0.000	0.000	0.000
40	A	66	PHE	0	-0.046	-0.021	5.389	0.163	0.163	0.000	0.000	0.000	0.000
41	A	67	GLY	0	-0.012	0.013	5.782	-0.251	-0.251	0.000	0.000	0.000	0.000
42	A	68	ASP	-1	-0.859	-0.941	7.520	-0.391	-0.391	0.000	0.000	0.000	0.000
43	A	69	TYR	0	-0.142	-0.101	9.611	0.134	0.134	0.000	0.000	0.000	0.000
44	A	70	SER	0	0.029	-0.016	12.601	0.045	0.045	0.000	0.000	0.000	0.000
45	A	71	LEU	0	0.087	0.036	15.911	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	72	GLU	-1	-0.835	-0.893	17.652	-0.125	-0.125	0.000	0.000	0.000	0.000
47	A	73	ALA	0	0.018	0.028	15.925	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	74	HIS	0	0.019	-0.012	12.115	-0.041	-0.041	0.000	0.000	0.000	0.000
49	A	75	THR	0	-0.098	-0.052	16.979	0.016	0.016	0.000	0.000	0.000	0.000
50	A	76	ALA	0	0.014	0.006	20.433	0.010	0.010	0.000	0.000	0.000	0.000
51	A	77	VAL	0	0.025	0.012	16.136	0.006	0.006	0.000	0.000	0.000	0.000
52	A	78	ARG	1	0.830	0.900	19.242	0.079	0.079	0.000	0.000	0.000	0.000
53	A	79	ALA	0	-0.039	-0.027	20.916	0.015	0.015	0.000	0.000	0.000	0.000
54	A	80	LEU	0	0.043	0.026	20.929	0.009	0.009	0.000	0.000	0.000	0.000
55	A	81	ALA	0	0.026	0.001	20.708	0.006	0.006	0.000	0.000	0.000	0.000
56	A	82	LYS	1	0.828	0.901	22.768	0.082	0.082	0.000	0.000	0.000	0.000
57	A	83	GLU	-1	-0.898	-0.935	26.132	-0.148	-0.148	0.000	0.000	0.000	0.000
58	A	84	PHE	0	0.034	-0.007	24.592	0.005	0.005	0.000	0.000	0.000	0.000
59	A	85	LEU	0	-0.036	-0.019	24.477	0.010	0.010	0.000	0.000	0.000	0.000
60	A	86	ALA	0	-0.047	-0.015	27.839	0.011	0.011	0.000	0.000	0.000	0.000
61	A	87	LYS	1	0.828	0.939	27.160	0.169	0.169	0.000	0.000	0.000	0.000
62	A	88	PRO	0	-0.024	-0.018	31.960	0.002	0.002	0.000	0.000	0.000	0.000
63	A	89	TYR	0	-0.069	-0.080	27.511	0.001	0.001	0.000	0.000	0.000	0.000
64	A	90	ASP	-1	-0.888	-0.929	33.644	-0.069	-0.069	0.000	0.000	0.000	0.000
65	A	91	SER	0	-0.021	-0.009	34.316	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	92	MET	0	-0.014	-0.045	31.569	0.002	0.002	0.000	0.000	0.000	0.000
67	A	93	SER	0	-0.027	-0.004	33.994	0.003	0.003	0.000	0.000	0.000	0.000
68	A	94	GLY	0	0.003	0.016	37.246	0.005	0.005	0.000	0.000	0.000	0.000
69	A	95	GLU	-1	-0.917	-0.954	32.094	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	96	PRO	0	0.001	-0.009	30.627	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	97	MET	0	-0.035	-0.026	29.332	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	98	THR	0	0.052	0.025	25.009	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	99	MET	0	-0.010	0.011	20.053	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	100	ALA	0	0.033	0.005	23.415	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.902	0.983	25.011	0.071	0.071	0.000	0.000	0.000	0.000
76	A	103	ILE	0	0.036	0.018	20.069	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	104	ASP	-1	-0.791	-0.859	20.863	-0.230	-0.230	0.000	0.000	0.000	0.000
78	A	105	LEU	0	-0.030	-0.003	19.676	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	106	VAL	0	-0.013	0.004	15.573	-0.038	-0.038	0.000	0.000	0.000	0.000
80	A	107	HIS	0	-0.081	-0.056	17.716	-0.105	-0.105	0.000	0.000	0.000	0.000
81	A	108	SER	0	-0.060	-0.004	20.119	0.001	0.001	0.000	0.000	0.000	0.000
82	A	109	GLN	0	0.011	-0.016	21.004	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	110	GLU	-1	-0.818	-0.927	22.622	-0.242	-0.242	0.000	0.000	0.000	0.000
84	A	111	LEU	0	0.010	0.007	15.963	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	112	GLN	0	0.003	0.001	16.922	-0.064	-0.064	0.000	0.000	0.000	0.000
86	A	113	ALA	0	-0.014	-0.003	19.137	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	114	ILE	0	-0.032	-0.009	18.056	0.006	0.006	0.000	0.000	0.000	0.000
88	A	115	ILE	0	0.023	0.006	14.188	0.004	0.004	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.869	0.914	16.618	0.546	0.546	0.000	0.000	0.000	0.000
90	A	117	LYS	1	0.883	0.959	19.030	0.244	0.244	0.000	0.000	0.000	0.000
91	A	118	TYR	0	-0.026	-0.023	16.900	0.028	0.028	0.000	0.000	0.000	0.000
92	A	119	GLN	0	-0.017	0.021	12.921	0.100	0.100	0.000	0.000	0.000	0.000

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