FMO DATABASE

FMODB ID: Q163Y

Calculation Name: 2ZXX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZXX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4E9

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	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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-327294.308173
FMO2-HF: Nuclear repulsion	298070.780018
FMO2-HF: Total energy	-29223.528155
FMO2-MP2: Total energy	-29309.691043

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:88:LYS)

Summations of interaction energy for fragment #1(A:88:LYS)

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.
25.787	33.339	4.505	-4.316	-7.741	-0.011

Interaction energy analysis for fragmet #1(A:88:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.957 / q_NPA : 0.962

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	90	ASN	0	-0.018	0.012	2.946	7.909	11.028	0.096	-1.464	-1.751	0.001
4	A	91	PRO	0	0.047	0.007	4.443	-1.541	-1.368	-0.001	-0.021	-0.151	0.000
5	A	92	SER	0	-0.041	-0.020	6.060	0.614	0.614	0.000	0.000	0.000	0.000
6	A	93	SER	0	-0.026	-0.016	2.480	-6.224	-4.729	2.407	-1.331	-2.571	-0.013
7	A	94	GLN	0	0.037	0.017	4.451	5.160	5.284	-0.001	-0.019	-0.104	0.000
8	A	95	TYR	0	0.073	0.052	2.617	-1.192	0.590	1.905	-1.219	-2.468	0.001
9	A	96	TRP	0	0.003	-0.021	2.999	3.468	4.327	0.099	-0.262	-0.696	0.000
10	A	97	LYS	1	0.890	0.945	6.679	22.247	22.247	0.000	0.000	0.000	0.000
11	A	98	GLU	-1	-0.920	-0.966	8.080	-28.462	-28.462	0.000	0.000	0.000	0.000
12	A	99	VAL	0	0.051	0.017	6.836	1.970	1.970	0.000	0.000	0.000	0.000
13	A	100	ALA	0	-0.042	-0.014	9.652	1.448	1.448	0.000	0.000	0.000	0.000
14	A	101	GLU	-1	-0.759	-0.850	11.998	-13.518	-13.518	0.000	0.000	0.000	0.000
15	A	102	GLN	0	-0.048	-0.030	10.854	0.051	0.051	0.000	0.000	0.000	0.000
16	A	103	ARG	1	0.960	0.975	10.071	19.551	19.551	0.000	0.000	0.000	0.000
17	A	104	ARG	1	0.896	0.941	15.332	14.124	14.124	0.000	0.000	0.000	0.000
18	A	105	LYS	1	0.866	0.910	17.493	15.565	15.565	0.000	0.000	0.000	0.000
19	A	106	ALA	0	0.027	0.017	18.274	0.559	0.559	0.000	0.000	0.000	0.000
20	A	107	LEU	0	0.011	0.008	19.456	0.518	0.518	0.000	0.000	0.000	0.000
21	A	108	TYR	0	-0.005	0.002	21.272	0.537	0.537	0.000	0.000	0.000	0.000
22	A	109	GLU	-1	-0.832	-0.899	23.332	-10.238	-10.238	0.000	0.000	0.000	0.000
23	A	110	ALA	0	-0.001	0.003	23.635	0.394	0.394	0.000	0.000	0.000	0.000
24	A	111	LEU	0	-0.012	-0.017	24.434	0.349	0.349	0.000	0.000	0.000	0.000
25	A	112	LYS	1	0.812	0.895	26.823	10.590	10.590	0.000	0.000	0.000	0.000
26	A	113	GLU	-1	-0.785	-0.891	28.819	-8.387	-8.387	0.000	0.000	0.000	0.000
27	A	114	ASN	0	-0.038	-0.015	29.066	0.402	0.402	0.000	0.000	0.000	0.000
28	A	115	GLU	-1	-0.847	-0.916	30.995	-7.968	-7.968	0.000	0.000	0.000	0.000
29	A	116	LYS	1	0.823	0.904	33.272	8.422	8.422	0.000	0.000	0.000	0.000
30	A	117	LEU	0	-0.013	-0.014	32.165	0.260	0.260	0.000	0.000	0.000	0.000
31	A	118	HIS	0	-0.034	-0.014	33.163	0.306	0.306	0.000	0.000	0.000	0.000
32	A	119	LYS	1	0.884	0.945	37.032	7.831	7.831	0.000	0.000	0.000	0.000
33	A	120	GLU	-1	-0.873	-0.923	37.960	-7.279	-7.279	0.000	0.000	0.000	0.000
34	A	121	ILE	0	-0.016	-0.009	37.603	0.177	0.177	0.000	0.000	0.000	0.000
35	A	122	GLU	-1	-0.917	-0.956	41.145	-6.802	-6.802	0.000	0.000	0.000	0.000
36	A	123	GLN	0	-0.027	-0.012	43.095	0.136	0.136	0.000	0.000	0.000	0.000
37	A	124	LYS	1	0.879	0.932	41.637	7.064	7.064	0.000	0.000	0.000	0.000
38	A	125	ASP	-1	-0.870	-0.938	44.247	-6.376	-6.376	0.000	0.000	0.000	0.000
39	A	126	SER	0	-0.098	-0.052	46.948	0.173	0.173	0.000	0.000	0.000	0.000
40	A	127	GLU	-1	-0.797	-0.898	49.106	-5.501	-5.501	0.000	0.000	0.000	0.000
41	A	128	ILE	0	-0.021	-0.015	47.135	0.142	0.142	0.000	0.000	0.000	0.000
42	A	129	ALA	0	-0.036	-0.019	51.035	0.116	0.116	0.000	0.000	0.000	0.000
43	A	130	ARG	1	0.768	0.858	52.899	5.473	5.473	0.000	0.000	0.000	0.000
44	A	131	LEU	0	0.032	0.009	52.863	0.113	0.113	0.000	0.000	0.000	0.000
45	A	132	ARG	1	0.916	0.960	50.027	5.798	5.798	0.000	0.000	0.000	0.000
46	A	133	LYS	1	0.770	0.872	56.444	4.900	4.900	0.000	0.000	0.000	0.000
47	A	134	GLU	-1	-0.832	-0.897	58.887	-5.037	-5.037	0.000	0.000	0.000	0.000
48	A	135	ASN	0	-0.023	-0.014	58.988	0.057	0.057	0.000	0.000	0.000	0.000
49	A	136	LYS	1	0.941	0.970	59.878	5.005	5.005	0.000	0.000	0.000	0.000
50	A	137	ASP	-1	-0.816	-0.886	62.326	-4.678	-4.678	0.000	0.000	0.000	0.000
51	A	138	LEU	0	-0.006	0.000	63.539	0.075	0.075	0.000	0.000	0.000	0.000
52	A	139	ALA	0	-0.007	-0.001	64.872	0.019	0.019	0.000	0.000	0.000	0.000
53	A	140	GLU	-1	-0.858	-0.925	66.139	-4.231	-4.231	0.000	0.000	0.000	0.000
54	A	141	VAL	0	-0.031	-0.019	67.251	0.049	0.049	0.000	0.000	0.000	0.000
55	A	142	ALA	0	0.004	0.002	65.161	0.010	0.010	0.000	0.000	0.000	0.000
56	A	143	GLU	-1	-0.941	-0.964	67.113	-4.376	-4.376	0.000	0.000	0.000	0.000
57	A	144	HIS	0	0.005	-0.001	69.701	0.047	0.047	0.000	0.000	0.000	0.000
58	A	145	VAL	0	-0.020	-0.015	66.878	0.030	0.030	0.000	0.000	0.000	0.000
59	A	146	GLN	0	-0.035	-0.020	66.801	0.000	0.000	0.000	0.000	0.000	0.000
60	A	147	TYR	0	0.003	0.010	69.810	0.043	0.043	0.000	0.000	0.000	0.000
61	A	148	MET	0	-0.033	-0.027	72.482	0.063	0.063	0.000	0.000	0.000	0.000
62	A	149	ALA	0	0.002	0.001	69.655	0.023	0.023	0.000	0.000	0.000	0.000
63	A	150	GLU	-1	-0.828	-0.878	71.699	-3.982	-3.982	0.000	0.000	0.000	0.000
64	A	151	VAL	0	-0.018	-0.025	73.725	0.045	0.045	0.000	0.000	0.000	0.000
65	A	152	ILE	0	-0.036	-0.016	73.138	0.047	0.047	0.000	0.000	0.000	0.000
66	A	153	GLU	-1	-0.901	-0.945	71.369	-4.276	-4.276	0.000	0.000	0.000	0.000
67	A	154	ARG	1	0.804	0.874	74.795	3.948	3.948	0.000	0.000	0.000	0.000
68	A	155	LEU	0	-0.087	-0.034	78.109	0.060	0.060	0.000	0.000	0.000	0.000
69	A	156	SER	0	-0.066	-0.036	75.775	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	157	ASN	0	-0.052	-0.007	77.614	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:88:LYS)