FMO DATABASE

FMODB ID: 94NJ2

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	OptHSide
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	-467861.311413
FMO2-HF: Nuclear repulsion	435300.667575
FMO2-HF: Total energy	-32560.643837
FMO2-MP2: Total energy	-32657.249751

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.
-13.591	-9.506	-0.041	-2.211	-1.834	0.003

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 : -0.940 / q_NPA : -0.971

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	B	19	LEU	0	0.005	0.005	3.689	-10.753	-6.787	-0.040	-2.208	-1.719	0.003
4	B	20	PRO	0	-0.013	0.008	5.160	2.767	2.886	-0.001	-0.003	-0.115	0.000
5	B	21	ILE	0	0.053	0.026	6.461	-2.033	-2.033	0.000	0.000	0.000	0.000
6	B	22	THR	0	-0.014	0.004	8.690	-1.372	-1.372	0.000	0.000	0.000	0.000
7	B	23	VAL	0	-0.013	-0.004	11.217	0.285	0.285	0.000	0.000	0.000	0.000
8	B	24	SER	0	-0.030	-0.011	14.507	-0.078	-0.078	0.000	0.000	0.000	0.000
9	B	25	LYS	1	0.827	0.907	16.600	-13.356	-13.356	0.000	0.000	0.000	0.000
10	B	26	PRO	0	0.007	0.001	20.288	0.064	0.064	0.000	0.000	0.000	0.000
11	B	27	THR	0	0.000	0.013	23.372	-0.281	-0.281	0.000	0.000	0.000	0.000
12	B	28	PRO	0	-0.013	0.007	21.568	0.341	0.341	0.000	0.000	0.000	0.000
13	B	29	TYR	0	0.013	-0.024	19.057	-0.183	-0.183	0.000	0.000	0.000	0.000
14	B	30	THR	0	-0.028	-0.007	22.635	-0.017	-0.017	0.000	0.000	0.000	0.000
15	B	31	PHE	0	0.019	-0.019	19.342	0.219	0.219	0.000	0.000	0.000	0.000
16	B	32	ASP	-1	-0.697	-0.795	25.097	9.085	9.085	0.000	0.000	0.000	0.000
17	B	33	LEU	0	0.032	0.008	22.042	-0.087	-0.087	0.000	0.000	0.000	0.000
18	B	34	GLY	0	0.036	0.036	25.632	0.043	0.043	0.000	0.000	0.000	0.000
19	B	35	HIS	0	-0.104	-0.063	28.741	-0.381	-0.381	0.000	0.000	0.000	0.000
20	B	36	LEU	0	-0.060	-0.027	23.907	0.072	0.072	0.000	0.000	0.000	0.000
21	B	37	LEU	0	0.005	0.013	25.355	0.170	0.170	0.000	0.000	0.000	0.000
22	B	38	ALA	0	0.018	-0.009	22.303	0.256	0.256	0.000	0.000	0.000	0.000
23	B	39	ASN	0	-0.046	-0.018	24.331	-0.420	-0.420	0.000	0.000	0.000	0.000
24	B	40	ASP	-1	-0.714	-0.841	22.588	12.687	12.687	0.000	0.000	0.000	0.000
25	B	41	PRO	0	-0.024	-0.007	24.902	-0.251	-0.251	0.000	0.000	0.000	0.000
26	B	42	ASN	0	-0.042	-0.038	23.149	-0.361	-0.361	0.000	0.000	0.000	0.000
27	B	43	PRO	0	0.025	0.006	26.560	-0.097	-0.097	0.000	0.000	0.000	0.000
28	B	44	LEU	0	-0.016	-0.002	26.751	0.312	0.312	0.000	0.000	0.000	0.000
29	B	45	GLU	-1	-0.919	-0.954	25.390	10.158	10.158	0.000	0.000	0.000	0.000
30	B	46	LEU	0	-0.045	-0.036	26.965	0.179	0.179	0.000	0.000	0.000	0.000
31	B	47	PRO	0	0.032	0.023	26.425	-0.381	-0.381	0.000	0.000	0.000	0.000
32	B	48	LYS	1	0.975	0.969	29.747	-8.049	-8.049	0.000	0.000	0.000	0.000
33	B	49	SER	0	-0.074	-0.056	28.409	-0.213	-0.213	0.000	0.000	0.000	0.000
34	B	50	GLU	-1	-0.866	-0.895	25.832	11.079	11.079	0.000	0.000	0.000	0.000
35	B	51	PRO	0	0.004	-0.002	27.669	-0.271	-0.271	0.000	0.000	0.000	0.000
36	B	52	LEU	0	0.064	0.028	28.363	0.326	0.326	0.000	0.000	0.000	0.000
37	B	53	ASN	0	0.019	-0.012	28.222	0.169	0.169	0.000	0.000	0.000	0.000
38	B	54	ALA	0	-0.011	0.004	24.528	0.339	0.339	0.000	0.000	0.000	0.000
39	B	55	SER	0	0.061	0.038	23.555	0.583	0.583	0.000	0.000	0.000	0.000
40	B	56	LEU	0	-0.001	0.002	24.108	0.355	0.355	0.000	0.000	0.000	0.000
41	B	57	LYS	1	0.959	0.981	20.329	-12.564	-12.564	0.000	0.000	0.000	0.000
42	B	58	ALA	0	-0.003	0.007	19.703	0.559	0.559	0.000	0.000	0.000	0.000
43	B	59	THR	0	0.023	0.005	19.514	0.557	0.557	0.000	0.000	0.000	0.000
44	B	60	ALA	0	-0.002	0.000	20.983	0.263	0.263	0.000	0.000	0.000	0.000
45	B	61	ARG	1	0.820	0.909	12.417	-17.865	-17.865	0.000	0.000	0.000	0.000
46	B	62	ASP	-1	-0.811	-0.907	16.286	16.568	16.568	0.000	0.000	0.000	0.000
47	B	63	GLY	0	0.033	0.012	17.166	0.411	0.411	0.000	0.000	0.000	0.000
48	B	64	VAL	0	-0.006	-0.010	17.605	-0.042	-0.042	0.000	0.000	0.000	0.000
49	B	65	GLN	0	-0.032	-0.005	10.774	0.668	0.668	0.000	0.000	0.000	0.000
50	B	66	SER	0	-0.028	-0.022	14.775	0.607	0.607	0.000	0.000	0.000	0.000
51	B	67	LEU	0	0.000	-0.002	16.593	0.078	0.078	0.000	0.000	0.000	0.000
52	B	68	LEU	0	0.003	0.005	14.165	-0.233	-0.233	0.000	0.000	0.000	0.000
53	B	69	ASN	0	0.004	-0.008	12.043	0.657	0.657	0.000	0.000	0.000	0.000
54	B	70	GLN	0	0.007	0.027	14.444	0.566	0.566	0.000	0.000	0.000	0.000
55	B	71	LEU	0	-0.027	-0.009	17.811	-0.349	-0.349	0.000	0.000	0.000	0.000
56	B	72	LEU	0	-0.017	-0.018	13.568	-0.271	-0.271	0.000	0.000	0.000	0.000
57	B	73	THR	0	-0.056	-0.031	14.417	0.425	0.425	0.000	0.000	0.000	0.000
58	B	74	THR	0	-0.082	-0.064	16.285	-0.493	-0.493	0.000	0.000	0.000	0.000
59	B	75	CYS	0	-0.038	0.006	19.930	-0.774	-0.774	0.000	0.000	0.000	0.000
60	B	76	PRO	0	-0.004	0.004	20.765	0.429	0.429	0.000	0.000	0.000	0.000
61	B	77	ILE	0	0.019	0.011	17.654	-0.238	-0.238	0.000	0.000	0.000	0.000
62	B	78	THR	0	-0.018	-0.003	22.130	-0.172	-0.172	0.000	0.000	0.000	0.000
63	B	79	SER	0	-0.001	0.000	22.564	0.092	0.092	0.000	0.000	0.000	0.000
64	B	80	SER	0	-0.033	-0.020	24.661	-0.317	-0.317	0.000	0.000	0.000	0.000
65	B	81	GLN	0	0.038	0.018	27.725	0.292	0.292	0.000	0.000	0.000	0.000
66	B	82	GLN	0	-0.024	-0.018	30.359	0.096	0.096	0.000	0.000	0.000	0.000
67	B	83	GLY	0	0.018	0.023	26.522	0.001	0.001	0.000	0.000	0.000	0.000
68	B	84	VAL	0	-0.017	-0.017	20.112	0.041	0.041	0.000	0.000	0.000	0.000
69	B	85	LEU	0	-0.018	-0.007	23.489	0.017	0.017	0.000	0.000	0.000	0.000
70	B	86	LEU	0	0.028	0.018	19.459	0.205	0.205	0.000	0.000	0.000	0.000
71	B	87	THR	0	-0.034	-0.016	23.527	-0.573	-0.573	0.000	0.000	0.000	0.000
72	B	88	LEU	0	0.006	-0.004	24.476	0.289	0.289	0.000	0.000	0.000	0.000
73	B	89	PRO	0	-0.007	0.005	25.795	-0.322	-0.322	0.000	0.000	0.000	0.000
74	B	90	ALA	0	0.014	-0.007	28.835	-0.060	-0.060	0.000	0.000	0.000	0.000
75	B	91	PRO	0	-0.022	-0.016	31.391	0.137	0.137	0.000	0.000	0.000	0.000
76	B	92	SER	0	-0.048	-0.032	30.396	-0.205	-0.205	0.000	0.000	0.000	0.000
77	B	93	THR	0	-0.064	-0.052	31.837	-0.225	-0.225	0.000	0.000	0.000	0.000
78	B	94	ILE	0	-0.012	-0.010	34.363	-0.091	-0.091	0.000	0.000	0.000	0.000
79	B	95	LEU	0	0.007	0.009	35.737	-0.081	-0.081	0.000	0.000	0.000	0.000
80	B	96	PRO	0	-0.013	0.000	39.684	-0.108	-0.108	0.000	0.000	0.000	0.000
81	B	97	ARG	1	0.903	0.944	43.001	-6.359	-6.359	0.000	0.000	0.000	0.000
82	B	98	HIS	0	0.032	0.020	45.091	-0.084	-0.084	0.000	0.000	0.000	0.000
83	B	99	LYS	1	0.956	0.973	47.109	-6.071	-6.071	0.000	0.000	0.000	0.000
84	B	100	PRO	0	0.066	0.030	48.989	0.137	0.137	0.000	0.000	0.000	0.000
85	B	101	LEU	0	-0.011	-0.016	46.805	0.017	0.017	0.000	0.000	0.000	0.000
86	B	102	PRO	0	0.005	0.001	49.544	-0.091	-0.091	0.000	0.000	0.000	0.000
87	B	103	THR	0	0.009	0.000	52.711	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	104	PRO	0	0.011	0.031	53.952	-0.019	-0.019	0.000	0.000	0.000	0.000

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