FMO DATABASE

FMODB ID: 2J7GR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-643963.407888
FMO2-HF: Nuclear repulsion	607084.602925
FMO2-HF: Total energy	-36878.804963
FMO2-MP2: Total energy	-36984.077674

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.
-5.653	-1.863	0.824	-1.892	-2.72	-0.013

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 : -0.045 / q_NPA : -0.037

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	0.013	-0.032	2.619	-3.997	-1.266	0.718	-1.549	-1.899	-0.012
4	A	30	PRO	0	0.035	0.012	5.205	0.396	0.460	-0.001	-0.001	-0.061	0.000
5	A	31	GLU	-1	-0.802	-0.876	7.274	-0.831	-0.831	0.000	0.000	0.000	0.000
6	A	32	GLU	-1	-0.841	-0.889	6.997	-2.447	-2.447	0.000	0.000	0.000	0.000
7	A	33	TYR	0	0.027	0.021	2.939	-0.308	0.687	0.107	-0.342	-0.760	-0.001
8	A	34	LEU	0	0.027	0.020	8.268	0.273	0.273	0.000	0.000	0.000	0.000
9	A	35	LYS	1	0.869	0.934	11.462	0.595	0.595	0.000	0.000	0.000	0.000
10	A	36	ASN	0	0.008	0.011	7.768	0.120	0.120	0.000	0.000	0.000	0.000
11	A	37	TYR	0	-0.035	-0.016	11.776	0.125	0.125	0.000	0.000	0.000	0.000
12	A	38	ALA	0	0.002	-0.006	13.702	0.050	0.050	0.000	0.000	0.000	0.000
13	A	39	LEU	0	0.007	0.008	14.489	0.033	0.033	0.000	0.000	0.000	0.000
14	A	40	SER	0	-0.023	-0.016	13.895	0.055	0.055	0.000	0.000	0.000	0.000
15	A	41	VAL	0	-0.011	-0.024	16.570	0.019	0.019	0.000	0.000	0.000	0.000
16	A	42	CYS	0	-0.058	-0.022	19.317	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	43	ILE	0	0.042	0.015	17.996	0.005	0.005	0.000	0.000	0.000	0.000
18	A	44	ALA	0	-0.015	0.001	20.138	0.004	0.004	0.000	0.000	0.000	0.000
19	A	45	GLU	-1	-0.849	-0.899	22.030	0.039	0.039	0.000	0.000	0.000	0.000
20	A	46	GLY	0	0.027	0.001	24.416	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	47	TYR	0	0.036	0.029	23.338	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	48	SER	0	0.007	-0.007	27.489	0.004	0.004	0.000	0.000	0.000	0.000
23	A	49	ALA	0	0.037	0.014	27.603	0.004	0.004	0.000	0.000	0.000	0.000
24	A	50	LYS	1	0.971	0.972	26.843	-0.093	-0.093	0.000	0.000	0.000	0.000
25	A	51	GLU	-1	-0.914	-0.947	24.619	0.158	0.158	0.000	0.000	0.000	0.000
26	A	52	VAL	0	0.079	0.040	22.249	0.017	0.017	0.000	0.000	0.000	0.000
27	A	53	LYS	1	0.758	0.877	21.932	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	54	ASN	0	-0.046	-0.035	22.170	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	55	ASP	-1	-0.909	-0.941	18.438	0.328	0.328	0.000	0.000	0.000	0.000
30	A	56	ALA	0	0.059	0.034	17.474	0.030	0.030	0.000	0.000	0.000	0.000
31	A	57	ALA	0	-0.009	-0.018	17.238	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	58	ALA	0	-0.066	-0.038	16.969	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	59	ALA	0	0.040	0.027	13.224	0.039	0.039	0.000	0.000	0.000	0.000
34	A	60	ALA	0	-0.010	-0.010	12.673	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.918	0.974	14.069	-0.274	-0.274	0.000	0.000	0.000	0.000
36	A	62	GLY	0	0.070	0.043	11.391	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	63	TYR	0	-0.036	-0.040	7.806	0.076	0.076	0.000	0.000	0.000	0.000
38	A	64	THR	0	-0.052	-0.032	9.690	-0.161	-0.161	0.000	0.000	0.000	0.000
39	A	65	GLU	-1	-1.014	-1.001	10.953	0.452	0.452	0.000	0.000	0.000	0.000
40	A	66	PHE	0	-0.054	-0.023	5.506	0.173	0.173	0.000	0.000	0.000	0.000
41	A	67	GLY	0	0.015	0.013	5.912	-0.286	-0.286	0.000	0.000	0.000	0.000
42	A	68	ASP	-1	-0.898	-0.955	7.253	-0.497	-0.497	0.000	0.000	0.000	0.000
43	A	69	TYR	0	-0.112	-0.077	9.923	0.119	0.119	0.000	0.000	0.000	0.000
44	A	70	SER	0	0.017	-0.021	12.662	0.051	0.051	0.000	0.000	0.000	0.000
45	A	71	LEU	0	0.069	0.028	16.024	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	72	GLU	-1	-0.848	-0.901	18.065	-0.087	-0.087	0.000	0.000	0.000	0.000
47	A	73	ALA	0	0.032	0.040	16.116	0.002	0.002	0.000	0.000	0.000	0.000
48	A	74	HIS	0	0.044	0.010	12.395	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	75	THR	0	-0.092	-0.048	17.266	0.024	0.024	0.000	0.000	0.000	0.000
50	A	76	ALA	0	0.004	0.002	20.591	0.009	0.009	0.000	0.000	0.000	0.000
51	A	77	VAL	0	0.027	0.012	16.540	0.007	0.007	0.000	0.000	0.000	0.000
52	A	78	ARG	1	0.834	0.904	19.615	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	79	ALA	0	-0.043	-0.022	21.457	0.014	0.014	0.000	0.000	0.000	0.000
54	A	80	LEU	0	0.026	0.016	21.124	0.006	0.006	0.000	0.000	0.000	0.000
55	A	81	ALA	0	0.027	0.011	21.148	0.005	0.005	0.000	0.000	0.000	0.000
56	A	82	LYS	1	0.860	0.918	23.166	0.007	0.007	0.000	0.000	0.000	0.000
57	A	83	GLU	-1	-0.896	-0.933	26.600	-0.089	-0.089	0.000	0.000	0.000	0.000
58	A	84	PHE	0	0.028	-0.013	24.517	0.001	0.001	0.000	0.000	0.000	0.000
59	A	85	LEU	0	-0.042	-0.012	24.828	0.008	0.008	0.000	0.000	0.000	0.000
60	A	86	ALA	0	-0.032	-0.005	28.005	0.006	0.006	0.000	0.000	0.000	0.000
61	A	87	LYS	1	0.840	0.943	27.006	0.100	0.100	0.000	0.000	0.000	0.000
62	A	88	PRO	0	-0.031	-0.013	31.835	0.005	0.005	0.000	0.000	0.000	0.000
63	A	89	TYR	0	-0.058	-0.081	27.252	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	90	ASP	-1	-0.908	-0.937	33.529	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	91	SER	0	-0.016	-0.029	34.013	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	92	MET	0	-0.022	-0.021	31.734	0.000	0.000	0.000	0.000	0.000	0.000
67	A	93	SER	0	-0.022	-0.020	34.117	0.000	0.000	0.000	0.000	0.000	0.000
68	A	94	GLY	0	0.018	0.024	37.228	0.004	0.004	0.000	0.000	0.000	0.000
69	A	95	GLU	-1	-0.929	-0.959	31.907	0.032	0.032	0.000	0.000	0.000	0.000
70	A	96	PRO	0	0.000	0.001	30.626	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	97	MET	0	-0.023	-0.021	29.219	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	98	THR	0	0.004	0.005	24.625	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	99	MET	0	0.013	0.006	19.916	0.001	0.001	0.000	0.000	0.000	0.000
74	A	100	ALA	0	0.022	0.018	23.082	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.892	0.966	24.282	0.008	0.008	0.000	0.000	0.000	0.000
76	A	103	ILE	0	0.024	0.015	19.742	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	104	ASP	-1	-0.806	-0.875	20.439	-0.128	-0.128	0.000	0.000	0.000	0.000
78	A	105	LEU	0	-0.020	0.000	19.610	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	106	VAL	0	0.000	0.010	15.420	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	107	HIS	0	-0.082	-0.063	17.582	-0.091	-0.091	0.000	0.000	0.000	0.000
81	A	108	SER	0	-0.046	-0.008	20.120	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	109	GLN	0	0.011	-0.006	21.068	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	110	GLU	-1	-0.821	-0.925	22.719	-0.164	-0.164	0.000	0.000	0.000	0.000
84	A	111	LEU	0	0.025	0.011	16.235	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	112	GLN	0	-0.002	-0.001	16.463	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	113	ALA	0	-0.012	-0.009	19.115	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	114	ILE	0	-0.038	-0.015	18.261	0.004	0.004	0.000	0.000	0.000	0.000
88	A	115	ILE	0	0.011	0.004	14.150	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	116	LYS	1	0.878	0.914	16.600	0.476	0.476	0.000	0.000	0.000	0.000
90	A	117	LYS	1	0.878	0.962	18.822	0.201	0.201	0.000	0.000	0.000	0.000
91	A	118	TYR	0	-0.009	-0.012	16.786	0.031	0.031	0.000	0.000	0.000	0.000
92	A	119	GLN	0	-0.018	0.013	12.579	0.089	0.089	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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