FMO DATABASE

FMODB ID: 6YKYZ

Calculation Name: 4XQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XQ3

Chain ID: A

ChEMBL ID:

UniProt ID: D0KRQ0

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

Total energy (hartree)

FMO2-HF: Electronic energy	-501629.2597
FMO2-HF: Nuclear repulsion	470785.600512
FMO2-HF: Total energy	-30843.659188
FMO2-MP2: Total energy	-30932.97235

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:7:ASN)

Summations of interaction energy for fragment #1(A:7:ASN)

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.
-37.993	-37.279	14.112	-7.3	-7.525	0.076

Interaction energy analysis for fragmet #1(A:7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.100 / q_NPA : 0.060

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	9	LEU	0	0.019	0.018	3.745	-1.068	1.173	0.000	-1.017	-1.224	0.003
4	A	10	LYS	1	0.813	0.902	1.760	-34.982	-36.698	14.113	-6.257	-6.140	0.073
5	A	11	SER	0	0.071	0.027	4.558	-1.171	-0.982	-0.001	-0.026	-0.161	0.000
6	A	12	LEU	0	0.003	0.011	6.462	0.434	0.434	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.921	0.956	7.712	-1.036	-1.036	0.000	0.000	0.000	0.000
8	A	14	THR	0	0.023	0.005	9.018	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.029	0.023	10.962	0.014	0.014	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.035	-0.003	12.596	0.104	0.104	0.000	0.000	0.000	0.000
11	A	17	ASN	0	-0.030	-0.029	15.515	-0.083	-0.083	0.000	0.000	0.000	0.000
12	A	18	ARG	1	0.931	0.969	16.481	0.199	0.199	0.000	0.000	0.000	0.000
13	A	19	ILE	0	-0.073	-0.027	18.586	0.068	0.068	0.000	0.000	0.000	0.000
14	A	20	VAL	0	0.011	0.016	14.994	-0.055	-0.055	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.032	0.010	17.513	0.030	0.030	0.000	0.000	0.000	0.000
16	A	22	VAL	0	-0.042	-0.027	16.617	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.826	0.912	18.201	0.003	0.003	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.013	0.006	18.772	0.065	0.065	0.000	0.000	0.000	0.000
19	A	25	LYS	1	0.872	0.913	17.696	-0.463	-0.463	0.000	0.000	0.000	0.000
20	A	26	ASP	-1	-0.853	-0.880	22.064	0.168	0.168	0.000	0.000	0.000	0.000
21	A	27	GLY	0	0.011	0.007	24.069	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.030	-0.037	25.161	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.823	-0.922	22.424	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	30	TYR	0	-0.033	-0.031	22.264	0.009	0.009	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.012	0.008	21.550	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.046	0.003	21.488	0.023	0.023	0.000	0.000	0.000	0.000
27	A	33	LYS	1	0.808	0.910	20.391	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.015	0.029	12.873	0.060	0.060	0.000	0.000	0.000	0.000
29	A	35	GLU	-1	-0.790	-0.869	17.503	0.268	0.268	0.000	0.000	0.000	0.000
30	A	36	GLN	0	-0.025	-0.020	14.747	0.060	0.060	0.000	0.000	0.000	0.000
31	A	37	THR	0	0.032	0.012	10.159	-0.071	-0.071	0.000	0.000	0.000	0.000
32	A	38	ASP	-1	-0.771	-0.858	10.466	2.012	2.012	0.000	0.000	0.000	0.000
33	A	39	GLY	0	-0.010	-0.005	7.489	0.430	0.430	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.061	-0.054	8.528	0.109	0.109	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.026	-0.022	7.448	-0.452	-0.452	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.021	-0.016	11.270	-0.480	-0.480	0.000	0.000	0.000	0.000
37	A	43	LEU	0	-0.014	-0.002	12.772	0.173	0.173	0.000	0.000	0.000	0.000
38	A	44	VAL	0	-0.003	0.006	15.633	-0.077	-0.077	0.000	0.000	0.000	0.000
39	A	45	LEU	0	0.005	0.010	17.490	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	46	ARG	1	0.802	0.875	20.341	-0.193	-0.193	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.862	-0.936	23.477	0.111	0.111	0.000	0.000	0.000	0.000
42	A	48	CYS	0	-0.036	0.002	23.613	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	49	THR	0	-0.023	-0.029	25.574	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	50	GLU	-1	-0.786	-0.884	26.050	0.113	0.113	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.035	0.000	24.298	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.917	0.948	28.812	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	53	GLU	-1	-0.840	-0.902	25.757	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	54	GLY	0	-0.016	-0.001	26.142	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	55	THR	0	-0.071	-0.029	27.451	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	56	SER	0	-0.012	-0.019	27.598	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.865	-0.925	29.087	0.006	0.006	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.058	-0.036	31.130	0.009	0.009	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.004	0.022	31.343	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.019	0.012	31.277	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.851	0.910	28.714	-0.092	-0.092	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.036	-0.039	27.148	0.010	0.010	0.000	0.000	0.000	0.000
57	A	63	GLY	0	-0.012	0.006	28.190	0.018	0.018	0.000	0.000	0.000	0.000
58	A	64	ARG	1	0.836	0.890	23.138	-0.293	-0.293	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.021	0.011	22.678	0.007	0.007	0.000	0.000	0.000	0.000
60	A	66	LEU	0	0.000	0.004	18.543	0.033	0.033	0.000	0.000	0.000	0.000
61	A	67	ILE	0	0.028	0.014	18.260	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.936	0.962	17.564	-0.543	-0.543	0.000	0.000	0.000	0.000
63	A	69	GLY	0	0.091	0.031	14.499	-0.071	-0.071	0.000	0.000	0.000	0.000
64	A	70	SER	0	-0.023	-0.024	15.341	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.032	-0.009	16.778	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.016	0.029	14.565	-0.072	-0.072	0.000	0.000	0.000	0.000
67	A	73	LEU	0	-0.047	-0.011	16.499	0.026	0.026	0.000	0.000	0.000	0.000
68	A	74	PHE	0	-0.017	-0.015	13.962	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	75	ILE	0	0.022	-0.001	11.702	0.096	0.096	0.000	0.000	0.000	0.000
70	A	76	SER	0	-0.019	0.001	12.805	-0.140	-0.140	0.000	0.000	0.000	0.000
71	A	77	VAL	0	-0.008	-0.021	10.015	0.099	0.099	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.882	-0.931	12.017	-0.944	-0.944	0.000	0.000	0.000	0.000
73	A	79	TYR	0	0.030	0.028	14.891	0.024	0.024	0.000	0.000	0.000	0.000
74	A	80	GLU	-1	-0.774	-0.886	18.290	-0.109	-0.109	0.000	0.000	0.000	0.000
75	A	81	THR	0	-0.055	-0.043	17.166	0.005	0.005	0.000	0.000	0.000	0.000
76	A	82	VAL	0	-0.034	-0.003	19.553	0.003	0.003	0.000	0.000	0.000	0.000
77	A	83	MET	0	-0.023	-0.013	22.145	0.042	0.042	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.030	-0.008	23.258	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ASN)