FMO DATABASE

FMODB ID: 9YJ62

Calculation Name: 3A2E-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A2E

Chain ID: A

ChEMBL ID:

UniProt ID: A4ZDL6

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	105
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-811715.839255
FMO2-HF: Nuclear repulsion	769490.063383
FMO2-HF: Total energy	-42225.775872
FMO2-MP2: Total energy	-42344.748559

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:ALA )

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

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.
-32.825	-29.471	28.323	-17.31	-14.364	-0.168

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.794 / q_NPA : 0.879

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	THR	0	0.018	0.007	3.271	5.950	7.478	0.022	-0.549	-1.001	0.001
4	A	4	ALA	0	0.048	0.044	5.286	6.783	6.894	0.000	-0.007	-0.102	0.000
5	A	5	PHE	0	-0.002	-0.025	8.392	-0.735	-0.735	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.008	0.014	9.875	0.731	0.731	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.024	-0.008	12.580	1.973	1.973	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.034	0.000	14.223	-0.938	-0.938	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.004	0.020	16.864	0.797	0.797	0.000	0.000	0.000	0.000
10	A	86	CYS	0	-0.010	-0.001	17.077	0.019	0.019	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.056	0.027	21.853	0.805	0.805	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.013	-0.007	24.951	-0.179	-0.179	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.013	0.021	27.821	0.267	0.267	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.854	0.932	24.165	11.717	11.717	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.026	-0.015	23.273	0.424	0.424	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.011	0.016	27.339	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.083	0.029	29.456	-0.295	-0.295	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.001	-0.001	29.317	0.281	0.281	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.024	-0.002	28.746	0.130	0.130	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.080	0.034	28.488	-0.479	-0.479	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.004	-0.012	23.668	-0.326	-0.326	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.020	-0.022	23.907	-1.042	-1.042	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.961	0.985	22.990	10.307	10.307	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.020	-0.011	23.514	-0.359	-0.359	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.041	0.032	19.551	-0.448	-0.448	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.976	0.980	18.845	14.050	14.050	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.022	0.001	18.837	-0.611	-0.611	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.053	0.012	17.225	-0.490	-0.490	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.004	-0.025	14.937	-0.669	-0.669	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.048	-0.017	14.594	-1.500	-1.500	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.765	-0.838	15.396	-16.510	-16.510	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.016	0.007	13.383	-0.678	-0.678	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.944	1.012	9.963	21.170	21.170	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.011	-0.006	11.183	-0.863	-0.863	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.030	-0.016	13.465	-0.502	-0.502	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.022	-0.036	10.540	0.620	0.620	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.022	-0.008	8.779	0.328	0.328	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.019	0.004	10.596	0.014	0.014	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.018	-0.017	14.127	1.640	1.640	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.034	0.017	14.758	0.599	0.599	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.117	-0.080	7.738	0.488	0.488	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.838	-0.942	11.376	-19.131	-19.131	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.048	-0.007	13.858	1.143	1.143	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.866	0.909	16.113	13.181	13.181	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.022	0.021	18.414	0.594	0.594	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.005	-0.005	20.887	0.185	0.185	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.829	0.930	21.621	13.434	13.434	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.075	0.049	25.110	0.015	0.015	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.001	0.004	28.342	-0.238	-0.238	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.021	-0.019	29.800	0.184	0.184	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.046	0.001	32.317	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.038	0.023	34.710	0.064	0.064	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.068	-0.006	29.116	-0.053	-0.053	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.039	0.019	28.766	0.042	0.042	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.042	0.002	26.232	-0.210	-0.210	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.063	-0.007	22.336	-0.093	-0.093	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.021	-0.002	22.772	0.029	0.029	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.059	-0.010	18.609	-0.271	-0.271	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.861	0.924	15.129	17.744	17.744	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.012	0.008	11.287	-0.500	-0.500	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.016	0.008	10.851	0.521	0.521	0.000	0.000	0.000	0.000
62	A	71	CYS	0	-0.050	-0.032	2.796	-11.838	-10.515	0.417	-0.779	-0.960	-0.009
63	A	63	LYS	1	0.947	0.977	5.722	35.948	35.948	0.000	0.000	0.000	0.000
64	A	64	GLN	0	0.030	-0.003	7.427	-2.251	-2.251	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.004	0.015	7.925	0.937	0.937	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.043	0.010	2.695	-1.786	-1.253	0.247	-0.206	-0.573	-0.001
67	A	67	SER	0	0.067	0.048	5.861	4.516	4.516	0.000	0.000	0.000	0.000
68	A	68	GLN	0	0.059	-0.003	6.027	-3.677	-3.677	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.006	-0.002	7.441	-2.177	-2.177	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.740	-0.866	1.636	-136.688	-139.759	22.805	-12.350	-7.384	-0.134
71	A	72	THR	0	0.044	0.018	4.752	2.674	2.674	0.000	-0.003	0.003	0.000
72	A	73	ALA	0	0.006	0.040	3.763	3.711	3.882	0.005	-0.045	-0.132	0.000
73	A	99	CYS	0	-0.094	-0.020	2.074	1.804	1.510	3.321	-1.201	-1.826	-0.002
74	A	75	LEU	0	0.057	0.025	3.412	6.167	6.116	0.045	0.122	-0.116	0.000
75	A	76	SER	0	-0.052	-0.071	7.145	4.725	4.725	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.027	-0.008	5.424	3.493	3.493	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.036	0.011	7.293	2.968	2.968	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.019	-0.016	8.946	2.840	2.840	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.023	-0.018	10.501	3.406	3.406	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.866	0.931	7.837	31.060	31.060	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.027	0.010	12.959	1.410	1.410	0.000	0.000	0.000	0.000
82	A	83	PHE	0	-0.002	-0.008	14.554	1.156	1.156	0.000	0.000	0.000	0.000
83	A	84	SER	0	0.004	0.005	16.427	1.157	1.157	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.011	-0.024	12.477	0.604	0.604	0.000	0.000	0.000	0.000
85	A	87	ASN	0	-0.002	0.003	19.955	0.609	0.609	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.021	0.002	21.314	0.135	0.135	0.000	0.000	0.000	0.000
87	A	89	ALA	0	-0.002	0.027	21.923	0.625	0.625	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.030	-0.019	22.901	-0.437	-0.437	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.003	-0.005	22.035	0.093	0.093	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.017	-0.010	17.922	0.108	0.108	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.976	0.995	16.307	13.913	13.913	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.022	0.003	11.548	0.378	0.378	0.000	0.000	0.000	0.000
93	A	95	GLN	0	-0.003	0.003	9.823	-2.274	-2.274	0.000	0.000	0.000	0.000
94	A	96	LEU	0	-0.021	-0.017	6.405	0.467	0.467	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.037	-0.014	5.875	0.946	0.946	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.761	-0.901	2.397	-63.577	-60.473	1.461	-2.292	-2.273	-0.023
97	A	100	PHE	0	0.011	0.018	6.475	1.413	1.413	0.000	0.000	0.000	0.000
98	A	101	ILE	0	0.026	0.018	9.976	0.056	0.056	0.000	0.000	0.000	0.000
99	A	102	GLN	0	-0.076	-0.037	12.753	0.239	0.239	0.000	0.000	0.000	0.000
100	A	103	TYR	0	-0.031	-0.030	16.428	-0.248	-0.248	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.879	-0.939	19.317	-12.494	-12.494	0.000	0.000	0.000	0.000
102	A	105	GLN	0	-0.001	0.002	23.102	0.254	0.254	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.956	0.969	25.792	10.613	10.613	0.000	0.000	0.000	0.000
104	A	107	SER	0	0.012	0.004	25.247	-0.366	-0.366	0.000	0.000	0.000	0.000
105	A	108	PHE	-1	-0.879	-0.922	19.110	-12.415	-12.415	0.000	0.000	0.000	0.000

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