FMO DATABASE

FMODB ID: Z62ZN

Calculation Name: 5WXL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WXL

Chain ID: B

ChEMBL ID:

UniProt ID: P36160

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:

Apendix: None

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-412893.13282
FMO2-HF: Nuclear repulsion	382319.726028
FMO2-HF: Total energy	-30573.406793
FMO2-MP2: Total energy	-30662.453225

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:16:GLY)

Summations of interaction energy for fragment #1(B:16: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.
-4.254	-2.223	2.602	-2.376	-2.257	-0.017

Interaction energy analysis for fragmet #1(B:16:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.021

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	18	GLU	-1	-0.796	-0.878	3.885	-2.327	-1.465	-0.007	-0.366	-0.489	0.001
4	B	19	ALA	0	-0.028	-0.001	6.805	0.373	0.373	0.000	0.000	0.000	0.000
5	B	20	VAL	0	-0.023	-0.011	9.204	0.087	0.087	0.000	0.000	0.000	0.000
6	B	21	TYR	0	-0.039	-0.072	11.521	0.091	0.091	0.000	0.000	0.000	0.000
7	B	22	ASP	-1	-0.736	-0.821	15.785	-0.117	-0.117	0.000	0.000	0.000	0.000
8	B	23	LEU	0	0.022	-0.004	18.427	0.017	0.017	0.000	0.000	0.000	0.000
9	B	24	GLY	0	0.034	0.032	21.387	0.011	0.011	0.000	0.000	0.000	0.000
10	B	25	ASN	0	-0.098	-0.069	22.102	0.022	0.022	0.000	0.000	0.000	0.000
11	B	26	LEU	0	-0.075	-0.032	22.247	0.002	0.002	0.000	0.000	0.000	0.000
12	B	27	ALA	0	0.011	0.010	18.702	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	28	ALA	0	0.003	-0.014	13.845	-0.028	-0.028	0.000	0.000	0.000	0.000
14	B	29	PHE	0	-0.032	-0.012	12.625	0.068	0.068	0.000	0.000	0.000	0.000
15	B	30	ASP	-1	-0.768	-0.863	6.795	-1.024	-1.024	0.000	0.000	0.000	0.000
16	B	31	SER	0	-0.023	-0.016	6.376	0.081	0.081	0.000	0.000	0.000	0.000
17	B	32	ASN	0	-0.069	-0.047	2.446	-1.346	-0.215	2.610	-1.996	-1.745	-0.018
18	B	33	VAL	0	-0.026	-0.012	4.314	0.074	0.112	-0.001	-0.014	-0.023	0.000
19	B	34	LEU	0	0.012	0.007	6.424	-0.237	-0.237	0.000	0.000	0.000	0.000
20	B	35	ASP	-1	-0.809	-0.894	9.866	0.352	0.352	0.000	0.000	0.000	0.000
21	B	36	LYS	1	0.994	0.990	12.604	-0.279	-0.279	0.000	0.000	0.000	0.000
22	B	37	ASN	0	-0.068	-0.055	16.113	-0.062	-0.062	0.000	0.000	0.000	0.000
23	B	38	ASP	-1	-0.825	-0.895	12.989	0.100	0.100	0.000	0.000	0.000	0.000
24	B	39	LEU	0	-0.012	-0.013	13.386	-0.037	-0.037	0.000	0.000	0.000	0.000
25	B	40	ASP	-1	-0.826	-0.882	17.562	0.092	0.092	0.000	0.000	0.000	0.000
26	B	41	SER	0	-0.014	-0.009	20.777	-0.013	-0.013	0.000	0.000	0.000	0.000
27	B	42	SER	0	-0.053	-0.039	24.097	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	43	ASN	0	-0.065	-0.035	18.949	-0.022	-0.022	0.000	0.000	0.000	0.000
29	B	44	ALA	0	0.022	-0.007	22.625	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	45	ARG	1	0.831	0.902	20.733	0.016	0.016	0.000	0.000	0.000	0.000
31	B	46	ARG	1	0.839	0.909	18.770	-0.049	-0.049	0.000	0.000	0.000	0.000
32	B	47	GLU	-1	-0.821	-0.895	18.725	-0.018	-0.018	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.852	-0.919	19.910	-0.050	-0.050	0.000	0.000	0.000	0.000
34	B	49	LYS	1	0.838	0.927	12.025	-0.083	-0.083	0.000	0.000	0.000	0.000
35	B	50	ILE	0	0.048	0.018	14.970	-0.030	-0.030	0.000	0.000	0.000	0.000
36	B	51	LYS	1	0.944	0.985	16.205	0.055	0.055	0.000	0.000	0.000	0.000
37	B	52	SER	0	-0.038	-0.017	14.064	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	53	LEU	0	0.026	0.015	9.820	-0.041	-0.041	0.000	0.000	0.000	0.000
39	B	54	THR	0	-0.009	-0.007	12.740	-0.062	-0.062	0.000	0.000	0.000	0.000
40	B	55	ARG	1	0.794	0.872	14.666	0.306	0.306	0.000	0.000	0.000	0.000
41	B	56	ASP	-1	-0.808	-0.897	11.446	-0.383	-0.383	0.000	0.000	0.000	0.000
42	B	57	ASN	0	-0.015	-0.028	9.648	-0.146	-0.146	0.000	0.000	0.000	0.000
43	B	58	VAL	0	-0.006	-0.005	12.909	0.003	0.003	0.000	0.000	0.000	0.000
44	B	59	GLN	0	-0.052	-0.014	14.567	0.038	0.038	0.000	0.000	0.000	0.000
45	B	60	LEU	0	0.004	0.010	9.475	0.036	0.036	0.000	0.000	0.000	0.000
46	B	61	LEU	0	0.027	0.016	14.144	0.024	0.024	0.000	0.000	0.000	0.000
47	B	62	ILE	0	-0.017	-0.014	16.850	0.034	0.034	0.000	0.000	0.000	0.000
48	B	63	ASN	0	-0.009	-0.010	15.812	0.063	0.063	0.000	0.000	0.000	0.000
49	B	64	GLN	0	0.006	0.020	14.159	0.079	0.079	0.000	0.000	0.000	0.000
50	B	65	LEU	0	0.000	0.008	18.581	0.035	0.035	0.000	0.000	0.000	0.000
51	B	66	LEU	0	-0.059	-0.039	21.802	0.027	0.027	0.000	0.000	0.000	0.000
52	B	67	SER	0	-0.068	-0.033	20.811	0.005	0.005	0.000	0.000	0.000	0.000
53	B	68	LEU	0	-0.016	0.010	22.927	0.009	0.009	0.000	0.000	0.000	0.000
54	B	69	PRO	0	-0.011	-0.009	25.095	0.010	0.010	0.000	0.000	0.000	0.000
55	B	70	MET	0	0.020	0.014	28.414	0.003	0.003	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.892	0.940	30.987	0.106	0.106	0.000	0.000	0.000	0.000
57	B	72	THR	0	0.003	0.006	34.316	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	73	THR	0	-0.013	-0.003	37.066	0.002	0.002	0.000	0.000	0.000	0.000
59	B	87	MET	0	0.027	0.026	36.304	0.003	0.003	0.000	0.000	0.000	0.000
60	B	88	THR	0	-0.030	-0.036	31.733	0.001	0.001	0.000	0.000	0.000	0.000
61	B	89	LEU	0	-0.021	-0.007	31.733	0.000	0.000	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.042	0.026	25.965	0.000	0.000	0.000	0.000	0.000	0.000
63	B	91	GLN	0	-0.046	-0.034	28.961	0.016	0.016	0.000	0.000	0.000	0.000
64	B	92	LEU	0	0.019	0.010	25.061	-0.010	-0.010	0.000	0.000	0.000	0.000
65	B	93	PRO	0	-0.028	0.001	23.018	0.011	0.011	0.000	0.000	0.000	0.000
66	B	94	ASP	-1	-0.891	-0.957	26.294	-0.095	-0.095	0.000	0.000	0.000	0.000
67	B	95	PRO	0	-0.081	-0.038	24.307	-0.013	-0.013	0.000	0.000	0.000	0.000
68	B	96	THR	0	0.015	-0.007	20.212	0.003	0.003	0.000	0.000	0.000	0.000
69	B	97	THR	0	-0.099	-0.066	20.386	0.007	0.007	0.000	0.000	0.000	0.000
70	B	98	ASP	-1	-0.927	-0.957	21.987	-0.030	-0.030	0.000	0.000	0.000	0.000
71	B	99	LEU	0	-0.013	-0.011	24.053	0.007	0.007	0.000	0.000	0.000	0.000
72	B	100	PRO	0	-0.043	-0.009	26.871	0.001	0.001	0.000	0.000	0.000	0.000
73	B	101	ARG	1	0.864	0.912	30.371	0.021	0.021	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.809	-0.888	33.619	-0.017	-0.017	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.857	0.909	35.840	0.023	0.023	0.000	0.000	0.000	0.000
76	B	104	PRO	0	0.049	0.024	37.921	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	105	LEU	0	0.012	0.014	36.766	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.003	0.009	40.281	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:16:GLY)