FMO DATABASE

FMODB ID: 855RY

Calculation Name: 4ZWS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZWS

Chain ID: D

ChEMBL ID:

UniProt ID: P04537

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-654119.869259
FMO2-HF: Nuclear repulsion	615072.230071
FMO2-HF: Total energy	-39047.639188
FMO2-MP2: Total energy	-39160.927557

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(D:2:ARG)

Summations of interaction energy for fragment #1(D:2:ARG)

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.
-166.24	-167.227	47.145	-21.984	-24.173	-0.246

Interaction energy analysis for fragmet #1(D:2:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.782 / q_NPA : 0.862

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	D	4	GLU	-1	-0.786	-0.893	1.761	-116.310	-120.719	28.567	-11.731	-12.427	-0.121
4	D	5	ASP	-1	-0.830	-0.895	1.756	-110.586	-109.417	18.253	-9.402	-10.019	-0.120
5	D	6	LEU	0	-0.044	-0.018	3.623	10.316	10.966	0.003	-0.143	-0.510	0.000
6	D	7	GLN	0	-0.002	-0.009	5.921	1.765	1.765	0.000	0.000	0.000	0.000
7	D	8	GLU	-1	-0.764	-0.872	6.196	-29.049	-29.049	0.000	0.000	0.000	0.000
8	D	9	GLU	-1	-0.803	-0.888	7.998	-22.669	-22.669	0.000	0.000	0.000	0.000
9	D	10	LEU	0	0.008	-0.002	9.805	3.108	3.108	0.000	0.000	0.000	0.000
10	D	11	LYS	1	0.808	0.900	9.673	31.817	31.817	0.000	0.000	0.000	0.000
11	D	12	LYS	1	0.876	0.932	12.139	23.638	23.638	0.000	0.000	0.000	0.000
12	D	13	ASP	-1	-0.818	-0.890	13.228	-19.541	-19.541	0.000	0.000	0.000	0.000
13	D	14	VAL	0	-0.003	-0.014	15.583	1.387	1.387	0.000	0.000	0.000	0.000
14	D	15	PHE	0	-0.008	0.015	17.733	1.044	1.044	0.000	0.000	0.000	0.000
15	D	16	ILE	0	0.015	0.020	19.512	0.274	0.274	0.000	0.000	0.000	0.000
16	D	17	ASP	-1	-0.759	-0.838	23.184	-12.062	-12.062	0.000	0.000	0.000	0.000
17	D	18	SER	0	0.019	-0.003	24.872	0.511	0.511	0.000	0.000	0.000	0.000
18	D	19	THR	0	-0.066	-0.054	27.553	0.493	0.493	0.000	0.000	0.000	0.000
19	D	20	LYS	1	0.841	0.911	25.257	12.470	12.470	0.000	0.000	0.000	0.000
20	D	21	LEU	0	0.065	0.031	28.001	-0.249	-0.249	0.000	0.000	0.000	0.000
21	D	22	GLN	0	0.021	0.005	28.646	-0.138	-0.138	0.000	0.000	0.000	0.000
22	D	23	TYR	0	0.023	0.019	22.079	-0.090	-0.090	0.000	0.000	0.000	0.000
23	D	24	GLU	-1	-0.770	-0.865	22.766	-14.320	-14.320	0.000	0.000	0.000	0.000
24	D	25	ALA	0	-0.011	-0.009	24.213	-0.325	-0.325	0.000	0.000	0.000	0.000
25	D	26	ALA	0	-0.020	-0.005	25.738	-0.083	-0.083	0.000	0.000	0.000	0.000
26	D	27	ASN	0	-0.013	-0.016	19.516	-0.147	-0.147	0.000	0.000	0.000	0.000
27	D	28	ASN	0	0.024	0.019	20.693	-0.994	-0.994	0.000	0.000	0.000	0.000
28	D	29	VAL	0	0.016	0.002	20.382	-0.421	-0.421	0.000	0.000	0.000	0.000
29	D	30	MET	0	0.005	0.005	19.285	-0.308	-0.308	0.000	0.000	0.000	0.000
30	D	31	LEU	0	-0.019	-0.003	15.698	-0.635	-0.635	0.000	0.000	0.000	0.000
31	D	32	TYR	0	0.016	0.008	15.698	-0.580	-0.580	0.000	0.000	0.000	0.000
32	D	33	SER	0	0.005	0.001	16.764	-0.356	-0.356	0.000	0.000	0.000	0.000
33	D	34	LYS	1	0.782	0.880	11.492	21.009	21.009	0.000	0.000	0.000	0.000
34	D	35	TRP	0	0.029	-0.021	8.058	-0.830	-0.830	0.000	0.000	0.000	0.000
35	D	36	LEU	0	0.006	0.020	12.778	-0.179	-0.179	0.000	0.000	0.000	0.000
36	D	37	ASN	0	0.003	-0.009	13.688	0.583	0.583	0.000	0.000	0.000	0.000
37	D	38	LYS	1	0.805	0.917	6.782	25.787	25.787	0.000	0.000	0.000	0.000
38	D	39	HIS	0	0.060	0.031	10.307	0.816	0.816	0.000	0.000	0.000	0.000
39	D	40	SER	0	-0.026	-0.014	12.200	0.386	0.386	0.000	0.000	0.000	0.000
40	D	41	SER	0	-0.019	-0.028	10.614	0.579	0.579	0.000	0.000	0.000	0.000
41	D	42	ILE	0	0.018	0.019	7.434	0.265	0.265	0.000	0.000	0.000	0.000
42	D	43	LYS	1	0.923	0.958	10.717	14.167	14.167	0.000	0.000	0.000	0.000
43	D	44	LYS	1	0.937	0.980	14.227	14.194	14.194	0.000	0.000	0.000	0.000
44	D	45	GLU	-1	-0.804	-0.864	9.681	-15.934	-15.934	0.000	0.000	0.000	0.000
45	D	46	MET	0	-0.016	-0.005	12.105	0.187	0.187	0.000	0.000	0.000	0.000
46	D	47	LEU	0	0.008	0.011	14.269	0.516	0.516	0.000	0.000	0.000	0.000
47	D	48	ARG	1	0.790	0.857	13.047	15.469	15.469	0.000	0.000	0.000	0.000
48	D	49	ILE	0	0.044	0.025	12.183	0.419	0.419	0.000	0.000	0.000	0.000
49	D	50	GLU	-1	-0.872	-0.929	16.723	-11.719	-11.719	0.000	0.000	0.000	0.000
50	D	51	ALA	0	-0.064	-0.034	19.664	0.549	0.549	0.000	0.000	0.000	0.000
51	D	52	GLN	0	-0.011	-0.017	17.196	0.007	0.007	0.000	0.000	0.000	0.000
52	D	53	LYS	1	0.893	0.944	19.660	12.395	12.395	0.000	0.000	0.000	0.000
53	D	54	LYS	1	0.862	0.954	21.820	10.447	10.447	0.000	0.000	0.000	0.000
54	D	55	VAL	0	-0.006	0.000	24.249	0.266	0.266	0.000	0.000	0.000	0.000
55	D	56	ALA	0	-0.021	-0.006	26.223	0.365	0.365	0.000	0.000	0.000	0.000
56	D	96	VAL	0	0.006	-0.017	17.602	0.140	0.140	0.000	0.000	0.000	0.000
57	D	97	ASP	-1	-0.825	-0.880	13.157	-18.126	-18.126	0.000	0.000	0.000	0.000
58	D	98	THR	0	-0.016	-0.008	11.136	0.505	0.505	0.000	0.000	0.000	0.000
59	D	99	SER	0	-0.016	-0.037	9.897	-1.302	-1.302	0.000	0.000	0.000	0.000
60	D	100	LEU	0	-0.027	-0.014	10.076	-0.672	-0.672	0.000	0.000	0.000	0.000
61	D	101	GLN	0	0.067	0.017	12.014	-0.393	-0.393	0.000	0.000	0.000	0.000
62	D	102	TYR	0	0.046	0.028	2.971	-2.505	-1.224	0.315	-0.631	-0.965	-0.005
63	D	103	TRP	0	0.030	-0.008	6.769	-1.185	-1.185	0.000	0.000	0.000	0.000
64	D	104	GLY	0	0.036	0.017	8.791	0.024	0.024	0.000	0.000	0.000	0.000
65	D	105	ILE	0	0.021	0.021	8.091	0.071	0.071	0.000	0.000	0.000	0.000
66	D	106	LEU	0	-0.024	-0.005	3.777	-0.826	-0.504	0.007	-0.077	-0.252	0.000
67	D	107	LEU	0	-0.010	-0.003	7.832	0.280	0.280	0.000	0.000	0.000	0.000
68	D	108	ASP	-1	-0.877	-0.935	11.121	-16.232	-16.232	0.000	0.000	0.000	0.000
69	D	109	PHE	0	-0.028	-0.012	8.504	-0.060	-0.060	0.000	0.000	0.000	0.000
70	D	110	CYS	0	-0.036	-0.028	8.726	0.169	0.169	0.000	0.000	0.000	0.000
71	D	111	SER	0	-0.034	-0.018	11.284	1.157	1.157	0.000	0.000	0.000	0.000
72	D	112	GLY	0	0.050	0.032	14.216	0.794	0.794	0.000	0.000	0.000	0.000
73	D	113	ALA	0	-0.005	-0.003	11.816	0.512	0.512	0.000	0.000	0.000	0.000
74	D	114	LEU	0	-0.054	-0.033	13.977	0.798	0.798	0.000	0.000	0.000	0.000
75	D	115	ASP	-1	-0.933	-0.964	16.481	-12.863	-12.863	0.000	0.000	0.000	0.000
76	D	116	ALA	0	0.014	0.007	16.397	0.615	0.615	0.000	0.000	0.000	0.000
77	D	117	ILE	0	-0.003	-0.009	14.779	0.635	0.635	0.000	0.000	0.000	0.000
78	D	118	LYS	1	0.909	0.964	18.929	12.538	12.538	0.000	0.000	0.000	0.000
79	D	119	SER	0	0.007	0.000	21.590	0.725	0.725	0.000	0.000	0.000	0.000
80	D	120	ARG	1	0.779	0.869	19.678	15.136	15.136	0.000	0.000	0.000	0.000
81	D	121	GLY	0	0.002	-0.003	22.673	0.385	0.385	0.000	0.000	0.000	0.000
82	D	122	PHE	0	-0.027	-0.016	24.917	0.490	0.490	0.000	0.000	0.000	0.000
83	D	123	ALA	0	0.040	0.032	25.472	0.405	0.405	0.000	0.000	0.000	0.000
84	D	124	ILE	0	-0.001	0.003	24.292	0.368	0.368	0.000	0.000	0.000	0.000
85	D	125	LYS	1	0.816	0.889	28.263	9.113	9.113	0.000	0.000	0.000	0.000
86	D	126	HIS	0	0.041	0.004	29.545	0.472	0.472	0.000	0.000	0.000	0.000
87	D	127	ILE	0	0.007	-0.002	28.080	0.264	0.264	0.000	0.000	0.000	0.000
88	D	128	GLN	0	-0.024	-0.019	32.230	0.058	0.058	0.000	0.000	0.000	0.000
89	D	129	ASP	-1	-0.813	-0.888	34.354	-8.408	-8.408	0.000	0.000	0.000	0.000
90	D	130	MET	0	-0.011	-0.002	33.120	0.156	0.156	0.000	0.000	0.000	0.000
91	D	131	ARG	1	0.863	0.926	31.233	9.999	9.999	0.000	0.000	0.000	0.000
92	D	132	ALA	0	-0.048	-0.027	37.715	0.192	0.192	0.000	0.000	0.000	0.000
93	D	133	PHE	0	-0.057	-0.018	40.118	0.232	0.232	0.000	0.000	0.000	0.000
94	D	134	GLU	-1	-0.933	-0.971	38.964	-7.803	-7.803	0.000	0.000	0.000	0.000
95	D	135	ALA	0	-0.087	-0.015	41.874	0.122	0.122	0.000	0.000	0.000	0.000
96	D	136	GLY	0	-0.003	-0.002	43.938	0.076	0.076	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:ARG)