FMO DATABASE

FMODB ID: 3J98L

Calculation Name: 2ZAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q1JZD9

Base Structure: X-ray

Registration Date: 2023-09-21

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1025606.708872
FMO2-HF: Nuclear repulsion	978537.67011
FMO2-HF: Total energy	-47069.038762
FMO2-MP2: Total energy	-47206.125234

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:8:TRP)

Summations of interaction energy for fragment #1(A:8:TRP)

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.
-8.529	-1.691	1.125	-2.559	-5.407	0.002

Interaction energy analysis for fragmet #1(A:8:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.009

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	10	ARG	1	0.939	0.979	2.426	-1.888	2.451	1.006	-1.806	-3.539	0.005
4	A	11	ILE	0	-0.012	-0.005	4.487	0.837	0.983	-0.001	-0.018	-0.128	0.000
5	A	12	MET	0	-0.005	0.021	8.209	0.071	0.071	0.000	0.000	0.000	0.000
6	A	13	LEU	0	-0.026	-0.017	10.695	0.164	0.164	0.000	0.000	0.000	0.000
7	A	14	VAL	0	-0.018	-0.017	13.976	0.000	0.000	0.000	0.000	0.000	0.000
8	A	15	ASP	-1	-0.788	-0.918	17.077	-0.338	-0.338	0.000	0.000	0.000	0.000
9	A	16	THR	0	-0.055	-0.045	20.238	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	17	GLN	0	-0.079	-0.036	22.803	0.031	0.031	0.000	0.000	0.000	0.000
11	A	18	LEU	0	0.052	0.022	16.839	0.013	0.013	0.000	0.000	0.000	0.000
12	A	19	PRO	0	0.000	-0.004	20.231	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	20	ALA	0	0.005	0.012	22.346	0.012	0.012	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.031	-0.018	18.800	0.014	0.014	0.000	0.000	0.000	0.000
15	A	22	ALA	0	0.032	0.030	18.638	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	23	ALA	0	0.014	0.008	18.344	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	24	SER	0	-0.006	-0.026	17.724	0.016	0.016	0.000	0.000	0.000	0.000
18	A	25	ILE	0	0.013	0.006	13.413	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	26	SER	0	0.001	-0.001	13.410	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.016	-0.009	13.920	0.021	0.021	0.000	0.000	0.000	0.000
21	A	28	LEU	0	-0.016	-0.007	10.827	0.022	0.022	0.000	0.000	0.000	0.000
22	A	29	SER	0	0.015	0.013	9.158	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.039	-0.006	8.993	0.089	0.089	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.915	-0.956	9.501	-0.219	-0.219	0.000	0.000	0.000	0.000
25	A	32	GLY	0	-0.026	-0.011	6.173	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	33	PHE	0	-0.121	-0.063	4.426	-0.219	-0.027	-0.001	-0.012	-0.179	0.000
27	A	34	ASP	-1	-0.888	-0.939	3.464	-6.277	-4.740	0.027	-0.570	-0.995	-0.004
28	A	35	ILE	0	-0.026	-0.026	5.990	-0.561	-0.561	0.000	0.000	0.000	0.000
29	A	36	ILE	0	0.020	0.013	5.806	0.122	0.122	0.000	0.000	0.000	0.000
30	A	37	GLN	0	-0.008	-0.020	9.484	0.215	0.215	0.000	0.000	0.000	0.000
31	A	38	CYS	0	-0.016	0.002	13.290	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	39	GLY	0	0.059	0.021	15.908	0.034	0.034	0.000	0.000	0.000	0.000
33	A	40	ASN	0	-0.012	-0.024	19.297	0.044	0.044	0.000	0.000	0.000	0.000
34	A	41	ALA	0	0.079	0.019	19.346	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	42	ILE	0	-0.028	-0.007	20.246	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	43	GLU	-1	-0.860	-0.924	17.189	-0.600	-0.600	0.000	0.000	0.000	0.000
37	A	44	ALA	0	0.034	0.009	15.527	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	45	VAL	0	0.030	0.022	15.131	-0.071	-0.071	0.000	0.000	0.000	0.000
39	A	46	PRO	0	0.000	-0.006	15.922	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	47	VAL	0	0.012	0.004	11.170	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	48	ALA	0	0.006	0.005	11.452	-0.174	-0.174	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.026	-0.019	11.579	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	50	LYS	1	0.921	0.968	11.610	0.736	0.736	0.000	0.000	0.000	0.000
44	A	51	THR	0	-0.057	-0.033	7.135	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	52	HIS	0	-0.011	0.009	6.703	-0.466	-0.466	0.000	0.000	0.000	0.000
46	A	53	PRO	0	-0.038	-0.007	6.763	-0.295	-0.295	0.000	0.000	0.000	0.000
47	A	54	HIS	0	0.061	0.035	2.696	-0.971	-0.347	0.094	-0.153	-0.566	0.001
48	A	55	LEU	0	0.001	0.006	7.629	0.394	0.394	0.000	0.000	0.000	0.000
49	A	56	ILE	0	0.007	0.011	10.274	-0.211	-0.211	0.000	0.000	0.000	0.000
50	A	57	ILE	0	-0.003	0.007	12.999	0.129	0.129	0.000	0.000	0.000	0.000
51	A	58	THR	0	0.025	-0.002	15.528	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	59	GLU	-1	-0.829	-0.890	18.671	-0.287	-0.287	0.000	0.000	0.000	0.000
53	A	60	ALA	0	0.012	-0.004	22.055	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	61	ASN	0	-0.098	-0.067	24.652	0.018	0.018	0.000	0.000	0.000	0.000
55	A	62	MET	0	-0.006	0.023	21.138	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	63	PRO	0	0.009	0.003	26.486	0.015	0.015	0.000	0.000	0.000	0.000
57	A	64	LYS	1	0.908	0.954	27.666	0.176	0.176	0.000	0.000	0.000	0.000
58	A	65	ILE	0	0.015	0.002	24.173	0.008	0.008	0.000	0.000	0.000	0.000
59	A	66	SER	0	0.001	0.007	25.236	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	67	GLY	0	0.070	0.019	22.388	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	68	MET	0	0.003	-0.007	22.616	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	69	ASP	-1	-0.825	-0.898	24.956	-0.221	-0.221	0.000	0.000	0.000	0.000
63	A	70	LEU	0	-0.017	-0.011	17.591	0.000	0.000	0.000	0.000	0.000	0.000
64	A	71	PHE	0	0.007	0.002	20.103	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	72	ASN	0	0.030	-0.001	21.359	0.008	0.008	0.000	0.000	0.000	0.000
66	A	73	SER	0	-0.058	-0.038	21.656	0.021	0.021	0.000	0.000	0.000	0.000
67	A	74	LEU	0	-0.018	-0.004	16.001	0.002	0.002	0.000	0.000	0.000	0.000
68	A	75	LYS	1	0.911	0.971	19.174	0.273	0.273	0.000	0.000	0.000	0.000
69	A	76	LYS	1	0.921	0.970	21.434	0.217	0.217	0.000	0.000	0.000	0.000
70	A	77	ASN	0	0.001	0.015	18.436	0.038	0.038	0.000	0.000	0.000	0.000
71	A	78	PRO	0	0.030	-0.001	18.792	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	79	GLN	0	-0.014	-0.003	14.511	0.007	0.007	0.000	0.000	0.000	0.000
73	A	80	THR	0	0.025	-0.012	13.677	-0.038	-0.038	0.000	0.000	0.000	0.000
74	A	81	ALA	0	-0.047	-0.003	15.411	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	82	SER	0	0.010	-0.011	15.981	0.030	0.030	0.000	0.000	0.000	0.000
76	A	83	ILE	0	-0.041	0.009	11.193	0.028	0.028	0.000	0.000	0.000	0.000
77	A	84	PRO	0	-0.017	0.003	12.126	0.026	0.026	0.000	0.000	0.000	0.000
78	A	85	VAL	0	0.038	0.005	14.016	-0.104	-0.104	0.000	0.000	0.000	0.000
79	A	86	ILE	0	-0.004	0.000	15.099	0.065	0.065	0.000	0.000	0.000	0.000
80	A	87	ALA	0	0.011	0.015	17.879	-0.036	-0.036	0.000	0.000	0.000	0.000
81	A	88	LEU	0	-0.016	-0.011	18.834	0.019	0.019	0.000	0.000	0.000	0.000
82	A	89	SER	0	-0.021	-0.043	22.005	0.001	0.001	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.015	0.007	25.723	0.005	0.005	0.000	0.000	0.000	0.000
84	A	91	ARG	1	0.861	0.944	28.372	0.192	0.192	0.000	0.000	0.000	0.000
85	A	92	ALA	0	0.005	0.001	28.430	0.008	0.008	0.000	0.000	0.000	0.000
86	A	93	THR	0	0.024	0.032	30.009	0.011	0.011	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.076	0.024	31.801	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	95	LYS	1	0.946	0.968	32.652	0.103	0.103	0.000	0.000	0.000	0.000
89	A	96	GLU	-1	-0.730	-0.843	28.803	-0.208	-0.208	0.000	0.000	0.000	0.000
90	A	97	GLU	-1	-0.928	-0.960	27.080	-0.169	-0.169	0.000	0.000	0.000	0.000
91	A	98	ALA	0	0.015	-0.007	28.099	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	99	GLN	0	0.021	0.020	29.531	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	100	LEU	0	-0.027	-0.032	24.594	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	101	LEU	0	-0.012	-0.012	23.934	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	102	ASP	-1	-0.924	-0.958	26.031	-0.115	-0.115	0.000	0.000	0.000	0.000
96	A	103	MET	0	-0.101	-0.044	25.262	0.003	0.003	0.000	0.000	0.000	0.000
97	A	104	GLY	0	-0.004	0.002	23.516	0.000	0.000	0.000	0.000	0.000	0.000
98	A	105	PHE	0	-0.109	-0.047	20.225	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	106	ILE	0	-0.035	-0.019	16.216	0.018	0.018	0.000	0.000	0.000	0.000
100	A	107	ASP	-1	-0.821	-0.913	18.680	-0.226	-0.226	0.000	0.000	0.000	0.000
101	A	108	PHE	0	0.011	0.005	20.591	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	109	ILE	0	-0.063	-0.031	18.116	0.015	0.015	0.000	0.000	0.000	0.000
103	A	110	ALA	0	0.024	0.011	22.650	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	111	LYS	1	0.837	0.935	22.195	0.341	0.341	0.000	0.000	0.000	0.000
105	A	112	PRO	0	0.040	0.002	25.867	0.013	0.013	0.000	0.000	0.000	0.000
106	A	113	VAL	0	0.023	0.009	19.177	0.005	0.005	0.000	0.000	0.000	0.000
107	A	114	ASN	0	0.018	0.021	21.031	0.000	0.000	0.000	0.000	0.000	0.000
108	A	115	ALA	0	0.082	0.022	17.046	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	116	ILE	0	0.049	0.032	16.426	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	117	ARG	1	0.929	0.962	17.178	0.183	0.183	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.016	0.000	14.937	0.006	0.006	0.000	0.000	0.000	0.000
112	A	119	SER	0	0.045	0.025	12.536	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	120	ALA	0	0.000	-0.004	12.578	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	121	ARG	1	0.852	0.918	14.636	0.237	0.237	0.000	0.000	0.000	0.000
115	A	122	ILE	0	0.056	0.043	9.724	0.028	0.028	0.000	0.000	0.000	0.000
116	A	123	LYS	1	0.936	0.964	9.035	0.333	0.333	0.000	0.000	0.000	0.000
117	A	124	ARG	1	0.804	0.917	11.004	0.152	0.152	0.000	0.000	0.000	0.000
118	A	125	VAL	0	0.098	0.048	13.262	0.064	0.064	0.000	0.000	0.000	0.000
119	A	126	LEU	0	0.006	0.006	6.791	0.053	0.053	0.000	0.000	0.000	0.000
120	A	127	LYS	1	0.899	0.939	10.490	0.217	0.217	0.000	0.000	0.000	0.000
121	A	128	LEU	0	-0.083	-0.040	11.808	0.068	0.068	0.000	0.000	0.000	0.000
122	A	129	LEU	0	-0.003	0.003	13.192	0.028	0.028	0.000	0.000	0.000	0.000
123	A	130	TYR	0	-0.049	-0.018	9.368	0.066	0.066	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:8:TRP)