FMO DATABASE

FMODB ID: 767VK

Calculation Name: 3ZIT-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIT

Chain ID: B

ChEMBL ID:

UniProt ID: Q819J1

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-524404.700289
FMO2-HF: Nuclear repulsion	492876.180372
FMO2-HF: Total energy	-31528.519917
FMO2-MP2: Total energy	-31620.123279

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-11.234	-5.409	6.566	-3.728	-8.663	-0.029

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.008

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	B	3	LYS	1	0.820	0.891	3.206	-0.668	1.493	0.080	-1.076	-1.165	0.001
4	B	4	ILE	0	0.046	0.017	5.705	0.395	0.395	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.810	-0.827	2.597	-4.676	-2.631	1.218	-1.602	-1.661	-0.017
6	B	6	VAL	0	0.000	-0.006	6.826	0.278	0.278	0.000	0.000	0.000	0.000
7	B	7	TYR	0	-0.027	-0.032	4.731	0.166	0.239	-0.001	-0.001	-0.071	0.000
8	B	8	ALA	0	0.032	-0.019	11.194	0.016	0.016	0.000	0.000	0.000	0.000
9	B	9	GLN	0	-0.006	-0.003	14.846	0.023	0.023	0.000	0.000	0.000	0.000
10	B	10	PRO	0	-0.031	-0.031	17.813	-0.014	-0.014	0.000	0.000	0.000	0.000
11	B	11	ASP	-1	-0.924	-0.957	21.418	0.068	0.068	0.000	0.000	0.000	0.000
12	B	12	CYS	0	0.025	0.038	17.285	0.008	0.008	0.000	0.000	0.000	0.000
13	B	13	PRO	0	0.047	0.018	21.345	-0.009	-0.009	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.041	0.013	20.513	-0.010	-0.010	0.000	0.000	0.000	0.000
15	B	16	VAL	0	-0.013	0.005	18.102	-0.020	-0.020	0.000	0.000	0.000	0.000
16	B	17	ILE	0	0.011	0.004	20.511	-0.015	-0.015	0.000	0.000	0.000	0.000
17	B	18	VAL	0	0.022	0.011	14.722	-0.013	-0.013	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.852	0.918	14.958	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.815	-0.895	17.426	-0.089	-0.089	0.000	0.000	0.000	0.000
20	B	21	PHE	0	0.015	0.017	17.905	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	22	LEU	0	0.003	0.004	13.050	-0.016	-0.016	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.808	0.881	16.989	0.059	0.059	0.000	0.000	0.000	0.000
23	B	24	HIS	0	-0.010	0.008	19.190	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.072	-0.051	18.591	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.086	-0.043	18.984	-0.022	-0.022	0.000	0.000	0.000	0.000
26	B	27	VAL	0	0.014	0.017	12.688	-0.033	-0.033	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.011	-0.005	13.182	0.027	0.027	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.077	-0.054	10.034	-0.131	-0.131	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.787	-0.869	7.566	-0.204	-0.204	0.000	0.000	0.000	0.000
30	B	31	GLU	-1	-0.798	-0.890	9.214	-0.091	-0.091	0.000	0.000	0.000	0.000
31	B	32	PHE	0	0.033	0.014	5.979	0.116	0.116	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.770	-0.876	11.166	0.106	0.106	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.066	0.026	12.086	0.020	0.020	0.000	0.000	0.000	0.000
34	B	35	LYS	1	0.829	0.915	14.564	-0.110	-0.110	0.000	0.000	0.000	0.000
35	B	36	LYS	1	0.821	0.906	16.446	-0.105	-0.105	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.776	-0.887	10.453	0.415	0.415	0.000	0.000	0.000	0.000
37	B	38	ALA	0	0.011	-0.011	13.339	0.008	0.008	0.000	0.000	0.000	0.000
38	B	39	ALA	0	0.018	0.016	10.660	0.009	0.009	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.007	0.001	9.024	0.024	0.024	0.000	0.000	0.000	0.000
40	B	41	ARG	1	0.863	0.924	10.056	-0.218	-0.218	0.000	0.000	0.000	0.000
41	B	42	ASN	0	0.007	-0.003	11.646	-0.012	-0.012	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.884	0.955	5.248	-0.283	-0.283	0.000	0.000	0.000	0.000
43	B	44	LEU	0	-0.069	-0.032	7.888	0.123	0.123	0.000	0.000	0.000	0.000
44	B	45	LEU	0	-0.029	-0.020	9.844	0.062	0.062	0.000	0.000	0.000	0.000
45	B	46	TYR	0	-0.060	-0.030	10.515	-0.036	-0.036	0.000	0.000	0.000	0.000
46	B	47	ASP	-1	-0.908	-0.943	5.292	0.533	0.533	0.000	0.000	0.000	0.000
47	B	48	TYR	0	-0.091	-0.088	2.508	-3.332	-1.535	2.324	-1.138	-2.983	-0.013
48	B	49	ASP	-1	-0.882	-0.910	7.887	0.402	0.402	0.000	0.000	0.000	0.000
49	B	50	SER	0	0.000	0.003	11.587	-0.109	-0.109	0.000	0.000	0.000	0.000
50	B	51	TYR	0	-0.049	-0.056	13.133	-0.061	-0.061	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.084	-0.032	15.268	-0.054	-0.054	0.000	0.000	0.000	0.000
52	B	53	THR	0	0.011	0.024	14.588	0.024	0.024	0.000	0.000	0.000	0.000
53	B	54	PRO	0	0.011	-0.023	14.948	-0.016	-0.016	0.000	0.000	0.000	0.000
54	B	55	THR	0	0.007	0.014	9.897	0.032	0.032	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.045	-0.014	9.445	-0.059	-0.059	0.000	0.000	0.000	0.000
56	B	57	VAL	0	0.016	0.018	3.789	-0.413	0.102	0.150	-0.140	-0.525	0.001
57	B	58	ILE	0	0.016	-0.001	6.227	-0.612	-0.612	0.000	0.000	0.000	0.000
58	B	59	ASP	-1	-0.802	-0.899	3.978	-1.967	-1.805	0.000	-0.034	-0.128	0.000
59	B	60	GLY	0	-0.008	0.003	2.554	-2.837	-2.095	2.704	-1.713	-1.732	0.001
60	B	61	GLU	-1	-0.844	-0.899	2.985	2.808	1.138	0.091	1.976	-0.398	-0.002
61	B	62	VAL	0	0.002	-0.003	6.370	0.028	0.028	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.011	0.010	8.465	-0.180	-0.180	0.000	0.000	0.000	0.000
63	B	64	ALA	0	0.035	0.018	11.859	-0.041	-0.041	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.022	0.019	13.455	-0.044	-0.044	0.000	0.000	0.000	0.000
65	B	66	PHE	0	-0.043	-0.037	16.249	-0.015	-0.015	0.000	0.000	0.000	0.000
66	B	67	GLN	0	-0.019	-0.019	15.378	-0.034	-0.034	0.000	0.000	0.000	0.000
67	B	68	ILE	0	0.021	0.007	17.498	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	69	GLU	-1	-0.886	-0.938	18.635	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	70	LYS	1	0.836	0.916	12.364	-0.076	-0.076	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.019	-0.016	12.915	-0.024	-0.024	0.000	0.000	0.000	0.000
71	B	72	GLN	0	-0.038	-0.045	15.135	-0.042	-0.042	0.000	0.000	0.000	0.000
72	B	73	GLN	0	-0.017	-0.010	16.495	-0.022	-0.022	0.000	0.000	0.000	0.000
73	B	74	LEU	0	-0.030	-0.010	10.104	-0.026	-0.026	0.000	0.000	0.000	0.000
74	B	75	LEU	0	-0.033	-0.026	11.311	-0.098	-0.098	0.000	0.000	0.000	0.000
75	B	76	ASN	0	-0.094	-0.041	13.797	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	77	ILE	0	-0.010	0.005	16.464	0.003	0.003	0.000	0.000	0.000	0.000
77	B	78	GLU	-1	-0.931	-0.935	18.913	-0.080	-0.080	0.000	0.000	0.000	0.000

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