FMO DATABASE

FMODB ID: LZM89

Calculation Name: 4XD9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XD9

Chain ID: B

ChEMBL ID:

UniProt ID: C8VMF9

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	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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467926.519767
FMO2-HF: Nuclear repulsion	435366.068811
FMO2-HF: Total energy	-32560.450956
FMO2-MP2: Total energy	-32657.075829

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:17:GLU)

Summations of interaction energy for fragment #1(B:17:GLU)

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.
-14.896	-10.75	-0.042	-2.28	-1.825	0.004

Interaction energy analysis for fragmet #1(B:17:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.932 / 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	B	19	LEU	0	0.007	-0.002	3.680	-11.069	-7.040	-0.041	-2.277	-1.711	0.004
4	B	20	PRO	0	-0.019	0.010	5.160	2.462	2.579	-0.001	-0.003	-0.114	0.000
5	B	21	ILE	0	0.056	0.035	6.254	-2.033	-2.033	0.000	0.000	0.000	0.000
6	B	22	THR	0	-0.009	0.001	8.482	-1.410	-1.410	0.000	0.000	0.000	0.000
7	B	23	VAL	0	0.000	0.001	11.024	0.306	0.306	0.000	0.000	0.000	0.000
8	B	24	SER	0	-0.054	-0.023	14.461	-0.271	-0.271	0.000	0.000	0.000	0.000
9	B	25	LYS	1	0.890	0.943	16.605	-13.036	-13.036	0.000	0.000	0.000	0.000
10	B	26	PRO	0	0.006	0.003	20.292	0.051	0.051	0.000	0.000	0.000	0.000
11	B	27	THR	0	0.005	0.017	23.375	-0.276	-0.276	0.000	0.000	0.000	0.000
12	B	28	PRO	0	-0.004	0.019	21.565	0.347	0.347	0.000	0.000	0.000	0.000
13	B	29	TYR	0	0.073	0.020	18.823	-0.271	-0.271	0.000	0.000	0.000	0.000
14	B	30	THR	0	-0.012	0.005	22.421	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	31	PHE	0	0.003	-0.027	19.190	0.212	0.212	0.000	0.000	0.000	0.000
16	B	32	ASP	-1	-0.711	-0.829	24.913	9.069	9.069	0.000	0.000	0.000	0.000
17	B	33	LEU	0	0.031	0.004	21.786	-0.079	-0.079	0.000	0.000	0.000	0.000
18	B	34	GLY	0	0.032	0.036	25.484	0.045	0.045	0.000	0.000	0.000	0.000
19	B	35	HIS	0	-0.104	-0.058	28.600	-0.372	-0.372	0.000	0.000	0.000	0.000
20	B	36	LEU	0	-0.057	-0.024	24.039	0.078	0.078	0.000	0.000	0.000	0.000
21	B	37	LEU	0	0.009	0.020	25.202	0.178	0.178	0.000	0.000	0.000	0.000
22	B	38	ALA	0	0.017	-0.018	22.085	0.259	0.259	0.000	0.000	0.000	0.000
23	B	39	ASN	0	-0.047	-0.020	24.143	-0.425	-0.425	0.000	0.000	0.000	0.000
24	B	40	ASP	-1	-0.792	-0.913	23.137	12.322	12.322	0.000	0.000	0.000	0.000
25	B	41	PRO	0	-0.036	-0.010	24.638	-0.257	-0.257	0.000	0.000	0.000	0.000
26	B	42	ASN	0	-0.058	-0.046	23.208	-0.345	-0.345	0.000	0.000	0.000	0.000
27	B	43	PRO	0	0.021	0.006	26.555	-0.100	-0.100	0.000	0.000	0.000	0.000
28	B	44	LEU	0	-0.002	0.007	26.718	0.303	0.303	0.000	0.000	0.000	0.000
29	B	45	GLU	-1	-0.907	-0.952	25.525	10.142	10.142	0.000	0.000	0.000	0.000
30	B	46	LEU	0	-0.060	-0.041	26.965	0.180	0.180	0.000	0.000	0.000	0.000
31	B	47	PRO	0	0.024	0.022	26.445	-0.380	-0.380	0.000	0.000	0.000	0.000
32	B	48	LYS	1	1.000	0.971	29.747	-8.052	-8.052	0.000	0.000	0.000	0.000
33	B	49	SER	0	-0.048	-0.015	28.486	-0.187	-0.187	0.000	0.000	0.000	0.000
34	B	50	GLU	-1	-0.920	-0.947	25.795	11.161	11.161	0.000	0.000	0.000	0.000
35	B	51	PRO	0	0.014	0.007	27.626	-0.291	-0.291	0.000	0.000	0.000	0.000
36	B	52	LEU	0	0.070	0.029	28.363	0.321	0.321	0.000	0.000	0.000	0.000
37	B	53	ASN	0	0.020	-0.011	28.155	0.205	0.205	0.000	0.000	0.000	0.000
38	B	54	ALA	0	-0.014	0.004	24.488	0.336	0.336	0.000	0.000	0.000	0.000
39	B	55	SER	0	0.056	0.034	23.555	0.560	0.560	0.000	0.000	0.000	0.000
40	B	56	LEU	0	-0.003	0.001	24.108	0.352	0.352	0.000	0.000	0.000	0.000
41	B	57	LYS	1	0.962	0.983	20.299	-12.582	-12.582	0.000	0.000	0.000	0.000
42	B	58	ALA	0	-0.005	0.004	19.701	0.552	0.552	0.000	0.000	0.000	0.000
43	B	59	THR	0	0.033	0.014	19.514	0.549	0.549	0.000	0.000	0.000	0.000
44	B	60	ALA	0	-0.004	-0.003	20.937	0.264	0.264	0.000	0.000	0.000	0.000
45	B	61	ARG	1	0.836	0.916	12.590	-17.679	-17.679	0.000	0.000	0.000	0.000
46	B	62	ASP	-1	-0.849	-0.921	16.220	16.446	16.446	0.000	0.000	0.000	0.000
47	B	63	GLY	0	0.009	-0.002	16.963	0.390	0.390	0.000	0.000	0.000	0.000
48	B	64	VAL	0	0.002	-0.003	17.511	-0.045	-0.045	0.000	0.000	0.000	0.000
49	B	65	GLN	0	-0.026	0.003	10.928	0.683	0.683	0.000	0.000	0.000	0.000
50	B	66	SER	0	-0.022	-0.022	14.597	0.559	0.559	0.000	0.000	0.000	0.000
51	B	67	LEU	0	-0.008	-0.005	16.397	0.088	0.088	0.000	0.000	0.000	0.000
52	B	68	LEU	0	0.005	0.004	13.929	-0.228	-0.228	0.000	0.000	0.000	0.000
53	B	69	ASN	0	-0.013	-0.019	11.348	0.431	0.431	0.000	0.000	0.000	0.000
54	B	70	GLN	0	0.014	0.024	14.288	0.525	0.525	0.000	0.000	0.000	0.000
55	B	71	LEU	0	-0.027	-0.008	17.654	-0.336	-0.336	0.000	0.000	0.000	0.000
56	B	72	LEU	0	-0.022	-0.018	13.341	-0.265	-0.265	0.000	0.000	0.000	0.000
57	B	73	THR	0	-0.055	-0.021	14.225	0.415	0.415	0.000	0.000	0.000	0.000
58	B	74	THR	0	-0.083	-0.067	16.174	-0.489	-0.489	0.000	0.000	0.000	0.000
59	B	75	CYS	0	-0.041	0.001	19.826	-0.763	-0.763	0.000	0.000	0.000	0.000
60	B	76	PRO	0	-0.001	0.007	20.691	0.434	0.434	0.000	0.000	0.000	0.000
61	B	77	ILE	0	0.027	0.014	17.622	-0.227	-0.227	0.000	0.000	0.000	0.000
62	B	78	THR	0	-0.023	-0.008	22.098	-0.186	-0.186	0.000	0.000	0.000	0.000
63	B	79	SER	0	-0.043	-0.014	22.601	-0.133	-0.133	0.000	0.000	0.000	0.000
64	B	80	SER	0	0.012	-0.004	24.684	-0.330	-0.330	0.000	0.000	0.000	0.000
65	B	81	GLN	0	0.047	0.024	27.761	0.352	0.352	0.000	0.000	0.000	0.000
66	B	82	GLN	0	-0.023	-0.019	30.440	0.115	0.115	0.000	0.000	0.000	0.000
67	B	83	GLY	0	0.010	0.019	26.545	0.006	0.006	0.000	0.000	0.000	0.000
68	B	84	VAL	0	-0.017	-0.017	20.129	0.054	0.054	0.000	0.000	0.000	0.000
69	B	85	LEU	0	-0.019	-0.010	23.468	0.019	0.019	0.000	0.000	0.000	0.000
70	B	86	LEU	0	0.019	0.014	19.451	0.207	0.207	0.000	0.000	0.000	0.000
71	B	87	THR	0	-0.025	-0.009	23.464	-0.571	-0.571	0.000	0.000	0.000	0.000
72	B	88	LEU	0	0.000	-0.010	24.493	0.288	0.288	0.000	0.000	0.000	0.000
73	B	89	PRO	0	-0.009	0.006	25.667	-0.324	-0.324	0.000	0.000	0.000	0.000
74	B	90	ALA	0	0.015	-0.007	28.714	-0.059	-0.059	0.000	0.000	0.000	0.000
75	B	91	PRO	0	-0.019	-0.014	31.256	0.141	0.141	0.000	0.000	0.000	0.000
76	B	92	SER	0	-0.048	-0.021	30.265	-0.211	-0.211	0.000	0.000	0.000	0.000
77	B	93	THR	0	-0.048	-0.033	31.654	-0.232	-0.232	0.000	0.000	0.000	0.000
78	B	94	ILE	0	-0.010	-0.007	34.190	-0.090	-0.090	0.000	0.000	0.000	0.000
79	B	95	LEU	0	0.006	0.005	35.596	-0.079	-0.079	0.000	0.000	0.000	0.000
80	B	96	PRO	0	-0.014	0.000	39.519	-0.108	-0.108	0.000	0.000	0.000	0.000
81	B	97	ARG	1	0.905	0.945	42.845	-6.365	-6.365	0.000	0.000	0.000	0.000
82	B	98	HIS	0	0.027	0.018	44.940	-0.077	-0.077	0.000	0.000	0.000	0.000
83	B	99	LYS	1	0.966	0.977	46.964	-6.089	-6.089	0.000	0.000	0.000	0.000
84	B	100	PRO	0	0.058	0.027	48.848	0.137	0.137	0.000	0.000	0.000	0.000
85	B	101	LEU	0	-0.007	-0.014	46.712	0.017	0.017	0.000	0.000	0.000	0.000
86	B	102	PRO	0	0.000	0.002	49.335	-0.095	-0.095	0.000	0.000	0.000	0.000
87	B	103	THR	0	0.024	-0.037	52.585	-0.009	-0.009	0.000	0.000	0.000	0.000
88	B	104	PRO	0	-0.003	0.066	53.729	-0.028	-0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:17:GLU)