FMO DATABASE

FMODB ID: GNGY1

Calculation Name: 1Z0P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z0P

Chain ID: A

ChEMBL ID:

UniProt ID: Q99YR7

Base Structure: X-ray

Registration Date: 2023-06-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-472758.885867
FMO2-HF: Nuclear repulsion	440841.148734
FMO2-HF: Total energy	-31917.737133
FMO2-MP2: Total energy	-32011.129033

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:1:MET)

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

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.
-18.607	-12.056	5.074	-2.923	-8.702	-0.015

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.024

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	3	TYR	0	0.097	0.035	3.068	-3.670	-1.423	0.136	-1.184	-1.199	-0.001
4	A	4	GLU	-1	-0.888	-0.956	5.745	-0.755	-0.755	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.890	0.948	2.265	-5.045	-3.667	1.646	-0.750	-2.274	0.003
6	A	6	GLU	-1	-0.913	-0.958	2.374	-8.782	-6.352	2.636	-1.441	-3.625	-0.014
7	A	7	PHE	0	0.017	0.025	3.301	1.004	0.542	0.061	0.733	-0.332	-0.001
8	A	8	LEU	0	-0.023	-0.029	6.755	0.207	0.207	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.879	0.951	2.353	-0.059	0.899	0.595	-0.281	-1.272	-0.002
10	A	10	ASP	-1	-0.857	-0.926	5.386	-2.901	-2.901	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.087	-0.041	6.970	0.257	0.257	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.826	-0.920	8.788	0.923	0.923	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.864	-0.941	7.132	-0.370	-0.370	0.000	0.000	0.000	0.000
14	A	14	TRP	0	-0.017	-0.007	10.268	0.039	0.039	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.010	0.002	12.667	0.027	0.027	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.941	0.973	10.934	-0.395	-0.395	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.002	0.013	13.685	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.037	-0.022	16.124	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.021	0.040	17.675	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.013	-0.002	17.015	0.014	0.014	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.051	-0.025	19.944	0.001	0.001	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.064	-0.077	21.954	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.064	0.038	22.916	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.014	0.025	25.046	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.001	0.010	26.629	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.023	0.002	28.049	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.015	0.002	29.371	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.028	-0.020	30.396	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.066	-0.042	32.368	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.013	-0.014	33.827	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.948	-0.958	35.327	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.035	-0.017	37.209	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.030	0.032	38.510	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.142	-0.076	39.053	0.009	0.009	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-1.008	-1.012	41.331	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.914	-0.959	43.121	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.013	0.013	44.093	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.981	-1.015	43.136	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.931	-0.962	41.554	-0.041	-0.041	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.940	0.972	38.899	0.067	0.067	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.050	0.036	37.274	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	LYS	1	1.037	1.020	36.482	0.011	0.011	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.860	-0.938	36.398	-0.043	-0.043	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.129	-0.084	33.305	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.027	0.024	32.034	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.028	0.012	31.722	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.880	0.959	29.431	0.077	0.077	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.048	-0.048	27.446	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.861	-0.947	26.913	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.001	0.015	27.777	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.876	0.928	23.841	0.106	0.106	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.019	-0.002	22.446	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.873	-0.921	23.118	0.067	0.067	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.003	0.001	23.014	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.056	-0.057	18.489	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.858	-0.941	18.945	0.144	0.144	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.014	0.001	20.411	0.047	0.047	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.062	-0.045	16.728	0.036	0.036	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.015	0.005	14.605	0.054	0.054	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.069	0.043	16.172	0.075	0.075	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.816	0.911	16.529	-0.191	-0.191	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.015	0.002	10.799	0.066	0.066	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.843	-0.924	12.445	0.779	0.779	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.069	-0.033	14.806	0.097	0.097	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.011	-0.002	6.102	-0.126	-0.126	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.780	0.897	9.444	-0.705	-0.705	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.070	-0.051	11.402	0.054	0.054	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.056	-0.016	13.177	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.853	0.943	14.103	-0.553	-0.553	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.006	0.011	16.213	0.023	0.023	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.062	0.009	16.391	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	HIS	0	-0.048	-0.054	18.382	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.858	-0.902	20.470	0.334	0.334	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.013	0.006	21.566	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.026	-0.013	19.704	0.019	0.019	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.882	-0.932	20.543	0.422	0.422	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.997	-0.995	21.863	0.216	0.216	0.000	0.000	0.000	0.000

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