FMO DATABASE

FMODB ID: LZ379

Calculation Name: 1ZPW-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZPW

Chain ID: X

ChEMBL ID:

UniProt ID: Q746F4

Base Structure: X-ray

Registration Date: 2023-09-19

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547067.44613
FMO2-HF: Nuclear repulsion	514662.225354
FMO2-HF: Total energy	-32405.220776
FMO2-MP2: Total energy	-32501.67213

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(X:2:GLY)

Summations of interaction energy for fragment #1(X:2:GLY)

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.
0.563	2.213	0.159	-0.644	-1.166	0.001

Interaction energy analysis for fragmet #1(X:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.004

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	X	4	ARG	1	0.900	0.956	3.808	2.214	3.244	-0.009	-0.480	-0.541	0.001
4	X	5	LEU	0	0.070	0.037	6.276	-0.145	-0.145	0.000	0.000	0.000	0.000
5	X	6	TYR	0	-0.007	-0.013	6.596	-0.108	-0.108	0.000	0.000	0.000	0.000
6	X	7	ALA	0	0.051	0.040	11.602	0.061	0.061	0.000	0.000	0.000	0.000
7	X	8	VAL	0	-0.035	-0.031	14.611	-0.023	-0.023	0.000	0.000	0.000	0.000
8	X	9	ALA	0	0.019	0.013	16.910	0.037	0.037	0.000	0.000	0.000	0.000
9	X	10	TYR	0	-0.037	-0.032	20.496	-0.002	-0.002	0.000	0.000	0.000	0.000
10	X	11	ASP	-1	-0.902	-0.948	23.148	-0.148	-0.148	0.000	0.000	0.000	0.000
11	X	12	ILE	0	-0.043	-0.015	24.614	-0.005	-0.005	0.000	0.000	0.000	0.000
12	X	13	PRO	0	0.091	0.045	28.488	0.005	0.005	0.000	0.000	0.000	0.000
13	X	14	ASP	-1	-0.838	-0.917	31.705	-0.129	-0.129	0.000	0.000	0.000	0.000
14	X	15	ASP	-1	-0.789	-0.901	31.324	-0.135	-0.135	0.000	0.000	0.000	0.000
15	X	16	THR	0	-0.023	-0.013	31.547	-0.008	-0.008	0.000	0.000	0.000	0.000
16	X	17	ARG	1	0.772	0.848	28.469	0.152	0.152	0.000	0.000	0.000	0.000
17	X	18	ARG	1	0.832	0.919	27.198	0.135	0.135	0.000	0.000	0.000	0.000
18	X	19	VAL	0	-0.014	0.005	26.731	-0.016	-0.016	0.000	0.000	0.000	0.000
19	X	20	LYS	1	0.913	0.953	26.631	0.152	0.152	0.000	0.000	0.000	0.000
20	X	21	LEU	0	0.018	0.015	20.710	-0.021	-0.021	0.000	0.000	0.000	0.000
21	X	22	ALA	0	0.013	0.001	22.182	-0.029	-0.029	0.000	0.000	0.000	0.000
22	X	23	ASN	0	-0.017	-0.021	22.446	-0.015	-0.015	0.000	0.000	0.000	0.000
23	X	24	LEU	0	-0.036	-0.005	18.636	-0.010	-0.010	0.000	0.000	0.000	0.000
24	X	25	LEU	0	-0.009	-0.007	17.193	-0.043	-0.043	0.000	0.000	0.000	0.000
25	X	26	LYS	1	0.971	0.995	17.581	0.189	0.189	0.000	0.000	0.000	0.000
26	X	27	SER	0	-0.109	-0.042	17.571	-0.008	-0.008	0.000	0.000	0.000	0.000
27	X	28	TYR	0	-0.086	-0.102	12.237	-0.016	-0.016	0.000	0.000	0.000	0.000
28	X	29	GLY	0	0.018	-0.001	13.354	-0.109	-0.109	0.000	0.000	0.000	0.000
29	X	30	GLU	-1	-0.906	-0.938	15.721	-0.229	-0.229	0.000	0.000	0.000	0.000
30	X	31	ARG	1	0.802	0.911	18.896	0.187	0.187	0.000	0.000	0.000	0.000
31	X	32	VAL	0	0.044	0.025	19.558	0.015	0.015	0.000	0.000	0.000	0.000
32	X	33	GLN	0	0.008	-0.001	22.418	0.019	0.019	0.000	0.000	0.000	0.000
33	X	34	LEU	0	0.002	-0.009	24.840	-0.016	-0.016	0.000	0.000	0.000	0.000
34	X	35	SER	0	0.007	0.009	24.933	0.000	0.000	0.000	0.000	0.000	0.000
35	X	36	VAL	0	0.012	0.005	19.444	-0.018	-0.018	0.000	0.000	0.000	0.000
36	X	37	PHE	0	-0.001	-0.010	17.759	0.038	0.038	0.000	0.000	0.000	0.000
37	X	38	GLU	-1	-0.901	-0.938	15.283	-0.320	-0.320	0.000	0.000	0.000	0.000
38	X	39	CYS	0	-0.025	-0.018	12.549	0.056	0.056	0.000	0.000	0.000	0.000
39	X	40	TYR	0	0.053	0.025	8.231	-0.170	-0.170	0.000	0.000	0.000	0.000
40	X	41	LEU	0	-0.041	-0.019	7.609	0.132	0.132	0.000	0.000	0.000	0.000
41	X	42	ASP	-1	-0.806	-0.910	3.124	-3.793	-3.329	0.169	-0.147	-0.486	0.000
42	X	43	GLU	-1	-0.888	-0.961	4.434	-1.014	-0.858	-0.001	-0.017	-0.139	0.000
43	X	44	ARG	1	0.983	0.999	6.440	1.252	1.252	0.000	0.000	0.000	0.000
44	X	45	LEU	0	-0.020	-0.015	7.537	0.315	0.315	0.000	0.000	0.000	0.000
45	X	46	LEU	0	0.017	0.023	8.473	0.324	0.324	0.000	0.000	0.000	0.000
46	X	47	GLU	-1	-0.961	-0.989	10.235	-0.365	-0.365	0.000	0.000	0.000	0.000
47	X	48	ASP	-1	-0.886	-0.913	12.084	-0.385	-0.385	0.000	0.000	0.000	0.000
48	X	49	LEU	0	0.053	0.036	13.169	0.114	0.114	0.000	0.000	0.000	0.000
49	X	50	ARG	1	0.956	0.971	11.675	0.842	0.842	0.000	0.000	0.000	0.000
50	X	51	ARG	1	0.899	0.962	15.472	0.510	0.510	0.000	0.000	0.000	0.000
51	X	52	ARG	1	0.881	0.937	17.166	0.451	0.451	0.000	0.000	0.000	0.000
52	X	53	ALA	0	0.048	0.017	18.900	0.040	0.040	0.000	0.000	0.000	0.000
53	X	54	ARG	1	0.936	0.959	18.303	0.385	0.385	0.000	0.000	0.000	0.000
54	X	55	ARG	1	0.895	0.958	21.288	0.298	0.298	0.000	0.000	0.000	0.000
55	X	56	LEU	0	-0.052	-0.016	23.015	0.022	0.022	0.000	0.000	0.000	0.000
56	X	57	LEU	0	-0.032	-0.006	21.682	0.013	0.013	0.000	0.000	0.000	0.000
57	X	58	ASP	-1	-0.851	-0.919	26.144	-0.145	-0.145	0.000	0.000	0.000	0.000
58	X	59	LEU	0	-0.065	-0.064	23.133	-0.004	-0.004	0.000	0.000	0.000	0.000
59	X	60	GLY	0	0.004	0.019	27.547	0.001	0.001	0.000	0.000	0.000	0.000
60	X	61	GLN	0	-0.007	-0.007	30.229	0.004	0.004	0.000	0.000	0.000	0.000
61	X	62	ASP	-1	-0.741	-0.829	26.207	-0.184	-0.184	0.000	0.000	0.000	0.000
62	X	63	ALA	0	-0.008	-0.007	24.529	-0.006	-0.006	0.000	0.000	0.000	0.000
63	X	64	LEU	0	-0.007	-0.006	17.409	-0.008	-0.008	0.000	0.000	0.000	0.000
64	X	65	ARG	1	0.889	0.942	18.675	0.227	0.227	0.000	0.000	0.000	0.000
65	X	66	ILE	0	0.015	0.001	12.382	-0.011	-0.011	0.000	0.000	0.000	0.000
66	X	67	TYR	0	0.019	0.009	14.119	0.010	0.010	0.000	0.000	0.000	0.000
67	X	68	PRO	0	0.006	0.008	9.059	-0.054	-0.054	0.000	0.000	0.000	0.000
68	X	69	VAL	0	0.009	0.000	10.728	0.130	0.130	0.000	0.000	0.000	0.000
69	X	70	ALA	0	-0.048	-0.039	10.464	-0.018	-0.018	0.000	0.000	0.000	0.000
70	X	71	GLY	0	0.030	0.025	12.278	0.025	0.025	0.000	0.000	0.000	0.000
71	X	72	GLN	0	-0.071	-0.038	15.288	-0.010	-0.010	0.000	0.000	0.000	0.000
72	X	73	VAL	0	0.031	0.015	16.212	-0.012	-0.012	0.000	0.000	0.000	0.000
73	X	74	GLU	-1	-0.940	-0.966	18.825	-0.011	-0.011	0.000	0.000	0.000	0.000
74	X	75	VAL	0	-0.001	-0.005	22.512	-0.017	-0.017	0.000	0.000	0.000	0.000
75	X	76	LEU	0	-0.012	-0.007	24.888	0.014	0.014	0.000	0.000	0.000	0.000
76	X	77	GLY	0	-0.015	-0.004	28.551	-0.008	-0.008	0.000	0.000	0.000	0.000
77	X	78	VAL	0	-0.023	-0.015	29.669	0.001	0.001	0.000	0.000	0.000	0.000
78	X	79	GLY	0	0.010	0.002	26.583	-0.007	-0.007	0.000	0.000	0.000	0.000
79	X	80	PRO	0	-0.038	-0.020	21.996	0.012	0.012	0.000	0.000	0.000	0.000
80	X	81	LEU	0	0.024	0.010	23.209	-0.002	-0.002	0.000	0.000	0.000	0.000
81	X	82	PRO	0	0.013	0.021	19.456	-0.018	-0.018	0.000	0.000	0.000	0.000
82	X	83	GLU	-1	-0.960	-0.969	13.611	-0.024	-0.024	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(X:2:GLY)