FMO DATABASE

FMODB ID: YQ2Z2

Calculation Name: 3IX0-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IX0

Chain ID: A

ChEMBL ID:

UniProt ID: P08118

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-559688.774065
FMO2-HF: Nuclear repulsion	521667.113651
FMO2-HF: Total energy	-38021.660414
FMO2-MP2: Total energy	-38123.670828

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:1:SER )

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

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.
-17.413	-18.634	18.658	-9.238	-8.199	-0.053

Interaction energy analysis for fragmet #1(A:1:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.027

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	3	TYR	0	-0.023	0.003	3.794	0.294	2.392	-0.022	-1.132	-0.944	0.002
4	A	4	PHE	0	0.019	0.001	6.496	-0.169	-0.169	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.035	-0.020	9.956	-0.116	-0.116	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.051	0.027	13.290	0.023	0.023	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.044	-0.015	16.925	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.923	-0.964	18.962	0.261	0.261	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.025	0.005	21.828	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	NME	0	-0.065	-0.034	23.770	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	16	ACE	0	0.062	0.022	26.092	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.835	0.899	23.390	-0.185	-0.185	0.000	0.000	0.000	0.000
13	A	42	CYS	0	0.030	0.055	13.625	0.019	0.019	0.000	0.000	0.000	0.000
14	A	19	MET	0	-0.026	-0.015	20.227	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	20	ASP	-1	-0.751	-0.842	16.528	0.201	0.201	0.000	0.000	0.000	0.000
16	A	21	LEU	0	0.063	0.002	13.671	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.827	0.932	17.661	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.018	0.016	20.140	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	24	ASN	0	-0.046	-0.017	19.934	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.957	0.967	21.352	-0.126	-0.126	0.000	0.000	0.000	0.000
21	A	26	HIS	1	0.810	0.883	18.569	-0.267	-0.267	0.000	0.000	0.000	0.000
22	A	27	PRO	0	-0.006	0.000	21.387	0.003	0.003	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.078	0.031	20.112	0.027	0.027	0.000	0.000	0.000	0.000
24	A	29	ASN	0	-0.067	-0.035	18.438	0.008	0.008	0.000	0.000	0.000	0.000
25	A	30	SER	0	-0.057	-0.008	18.816	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.840	-0.881	13.362	0.545	0.545	0.000	0.000	0.000	0.000
27	A	32	TRP	0	-0.052	-0.043	14.443	-0.077	-0.077	0.000	0.000	0.000	0.000
28	A	33	GLN	0	0.086	0.048	12.206	0.100	0.100	0.000	0.000	0.000	0.000
29	A	34	THR	0	-0.052	-0.016	11.315	-0.072	-0.072	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.908	-0.973	13.889	-0.073	-0.073	0.000	0.000	0.000	0.000
31	A	36	ASN	0	-0.096	-0.074	10.507	-0.065	-0.065	0.000	0.000	0.000	0.000
32	A	73	CYS	0	-0.100	-0.022	9.477	-0.094	-0.094	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.873	-0.936	7.260	-0.248	-0.248	0.000	0.000	0.000	0.000
34	A	39	THR	0	-0.051	-0.054	7.803	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	49	CYS	0	-0.022	-0.005	8.253	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	41	THR	0	0.011	0.001	11.548	-0.073	-0.073	0.000	0.000	0.000	0.000
37	A	43	TYR	0	0.038	0.022	12.047	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.952	-0.997	17.474	0.276	0.276	0.000	0.000	0.000	0.000
39	A	45	THR	0	0.012	0.003	17.253	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.934	-0.966	13.446	0.917	0.917	0.000	0.000	0.000	0.000
41	A	47	ILE	0	-0.018	-0.030	13.019	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	48	SER	0	0.012	0.021	8.529	0.103	0.103	0.000	0.000	0.000	0.000
43	A	51	THR	0	0.022	0.016	1.851	-0.563	-1.188	4.040	-1.629	-1.786	0.002
44	A	52	LEU	0	0.032	0.009	4.483	1.296	1.454	0.000	-0.011	-0.147	0.000
45	A	53	VAL	0	-0.065	-0.030	5.953	-0.077	-0.077	0.000	0.000	0.000	0.000
46	A	54	SER	0	0.026	0.025	5.730	-0.627	-0.627	0.000	0.000	0.000	0.000
47	A	55	THR	0	-0.036	-0.040	7.172	0.467	0.467	0.000	0.000	0.000	0.000
48	A	56	PRO	0	-0.032	0.024	9.276	-0.036	-0.036	0.000	0.000	0.000	0.000
49	A	57	VAL	0	-0.001	-0.037	10.840	0.003	0.003	0.000	0.000	0.000	0.000
50	A	58	GLY	0	0.046	0.041	13.532	0.077	0.077	0.000	0.000	0.000	0.000
51	A	59	TYR	0	-0.047	-0.032	15.401	0.023	0.023	0.000	0.000	0.000	0.000
52	A	60	ASP	-1	-0.758	-0.879	19.293	-0.290	-0.290	0.000	0.000	0.000	0.000
53	A	61	LYS	1	0.943	0.964	15.971	0.674	0.674	0.000	0.000	0.000	0.000
54	A	62	ASP	-1	-0.901	-0.926	22.207	-0.286	-0.286	0.000	0.000	0.000	0.000
55	A	63	ASN	0	-0.074	-0.052	25.794	0.020	0.020	0.000	0.000	0.000	0.000
56	A	87	CYS	0	-0.042	-0.001	21.743	0.036	0.036	0.000	0.000	0.000	0.000
57	A	65	GLN	0	-0.025	-0.027	20.545	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	66	ARG	1	0.902	0.966	13.298	0.963	0.963	0.000	0.000	0.000	0.000
59	A	67	ILE	0	-0.038	-0.025	17.640	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	68	PHE	0	0.020	0.003	11.282	0.007	0.007	0.000	0.000	0.000	0.000
61	A	69	LYS	1	0.934	0.962	15.070	0.268	0.268	0.000	0.000	0.000	0.000
62	A	70	LYS	1	0.993	0.990	14.415	0.216	0.216	0.000	0.000	0.000	0.000
63	A	71	GLU	-1	-0.938	-0.967	14.908	-0.081	-0.081	0.000	0.000	0.000	0.000
64	A	72	ASP	-1	-0.877	-0.937	15.960	-0.082	-0.082	0.000	0.000	0.000	0.000
65	A	74	LYS	1	0.950	0.986	11.171	0.142	0.142	0.000	0.000	0.000	0.000
66	A	75	TYR	0	0.007	-0.003	9.918	0.086	0.086	0.000	0.000	0.000	0.000
67	A	76	ILE	0	-0.052	-0.016	14.237	0.060	0.060	0.000	0.000	0.000	0.000
68	A	77	VAL	0	0.038	0.006	16.443	-0.049	-0.049	0.000	0.000	0.000	0.000
69	A	78	VAL	0	-0.043	-0.002	19.081	0.035	0.035	0.000	0.000	0.000	0.000
70	A	79	GLU	-1	-0.850	-0.936	22.792	-0.207	-0.207	0.000	0.000	0.000	0.000
71	A	80	LYS	1	0.882	0.939	23.904	0.324	0.324	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.936	0.965	26.776	0.175	0.175	0.000	0.000	0.000	0.000
73	A	82	ASP	-1	-0.846	-0.938	28.638	-0.134	-0.134	0.000	0.000	0.000	0.000
74	A	83	PRO	0	0.032	0.022	24.830	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.912	0.951	25.104	0.120	0.120	0.000	0.000	0.000	0.000
76	A	85	LYS	1	0.877	0.958	27.249	0.145	0.145	0.000	0.000	0.000	0.000
77	A	86	THR	0	-0.008	-0.006	22.201	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	88	SER	0	-0.019	-0.007	20.964	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	89	VAL	0	-0.058	-0.034	14.769	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	90	SER	0	-0.043	-0.031	17.597	0.017	0.017	0.000	0.000	0.000	0.000
81	A	91	GLU	-1	-0.909	-0.957	11.893	-0.858	-0.858	0.000	0.000	0.000	0.000
82	A	92	TRP	0	0.002	-0.021	9.833	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	93	ILE	0	0.032	0.014	5.515	0.110	0.110	0.000	0.000	0.000	0.000
84	A	94	ILE	-1	-0.877	-0.906	1.825	-20.223	-23.075	14.640	-6.466	-5.322	-0.057

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