FMO DATABASE

FMODB ID: K3VR3

Calculation Name: 3A2E-A-Xray372

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: 2023-03-14

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	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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-811438.965259
FMO2-HF: Nuclear repulsion	769212.713362
FMO2-HF: Total energy	-42226.251897
FMO2-MP2: Total energy	-42345.155766

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.
-22.588	-20.268	21.76	-11.717	-12.365	-0.086

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 : 0 / q_Mulliken : -0.027 / q_NPA : -0.016

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	A	3	THR	0	-0.005	-0.013	2.981	-1.040	0.991	0.054	-0.866	-1.220	0.005
4	A	4	ALA	0	0.036	0.035	5.194	-0.008	0.113	-0.001	-0.008	-0.113	0.000
5	A	5	PHE	0	-0.010	-0.025	8.524	-0.011	-0.011	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.003	0.012	9.936	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.001	0.001	12.699	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.022	-0.001	14.328	0.005	0.005	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.010	0.015	16.968	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.008	-0.001	17.000	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.051	0.029	21.824	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.013	0.000	24.885	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.016	0.022	27.765	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.848	0.923	23.865	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.024	-0.016	23.027	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.010	0.010	27.292	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.080	0.030	29.416	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.006	0.005	29.276	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.012	0.007	28.680	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.072	0.020	28.462	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.003	-0.008	23.704	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.007	0.003	23.879	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.949	0.976	22.973	0.028	0.028	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.022	-0.019	23.510	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.041	0.029	19.592	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.922	0.952	18.876	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.018	0.003	18.840	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.022	0.005	17.806	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.014	-0.019	14.709	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.036	-0.013	14.599	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.735	-0.799	15.423	-0.128	-0.128	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.016	0.003	13.534	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.951	0.999	10.249	0.104	0.104	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.025	-0.005	11.124	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.045	-0.012	13.418	-0.041	-0.041	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.002	-0.016	10.506	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.013	-0.007	8.860	0.007	0.007	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.032	-0.011	10.626	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.025	-0.014	14.162	0.034	0.034	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.032	0.015	14.807	0.021	0.021	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.097	-0.062	7.770	0.039	0.039	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.771	-0.879	11.321	-0.062	-0.062	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.040	-0.010	13.808	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.894	0.927	16.083	0.065	0.065	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.014	0.010	18.417	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.033	0.003	20.894	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.774	0.890	21.424	0.070	0.070	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.076	0.052	25.111	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.006	0.004	28.339	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.002	-0.007	29.790	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.038	0.000	32.304	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.037	0.024	34.695	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.071	-0.002	29.102	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.045	0.020	28.679	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.025	-0.003	26.402	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.054	-0.002	22.361	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.018	-0.015	22.755	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.049	0.003	18.599	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.778	0.844	15.157	0.059	0.059	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.012	0.012	11.241	0.015	0.015	0.000	0.000	0.000	0.000
61	A	61	THR	0	0.005	0.008	10.282	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.054	-0.023	2.710	-1.299	-0.179	0.601	-0.684	-1.037	-0.008
63	A	63	LYS	1	0.865	0.925	5.731	0.185	0.185	0.000	0.000	0.000	0.000
64	A	64	GLN	0	0.014	-0.008	7.343	-0.114	-0.114	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.008	0.014	7.849	0.005	0.005	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.030	0.019	2.944	-0.451	0.038	0.169	-0.147	-0.511	0.000
67	A	67	SER	0	0.062	0.041	6.009	0.239	0.239	0.000	0.000	0.000	0.000
68	A	68	GLN	0	0.066	0.011	6.068	-0.286	-0.286	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.042	0.010	7.118	0.076	0.076	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.821	-0.914	1.767	-16.753	-20.035	16.760	-7.670	-5.808	-0.076
71	A	72	THR	0	0.012	0.001	4.763	0.534	0.540	-0.001	-0.001	-0.003	0.000
72	A	73	ALA	0	0.004	0.017	3.813	0.174	0.395	0.004	-0.061	-0.164	0.000
73	A	74	CYS	0	-0.043	0.006	2.158	-0.771	-0.771	3.021	-1.136	-1.885	0.002
74	A	75	LEU	0	0.041	0.016	3.404	-0.156	-0.244	0.046	0.171	-0.129	0.000
75	A	76	SER	0	-0.040	-0.042	7.140	0.046	0.046	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.002	0.014	5.421	0.074	0.074	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.024	0.011	7.278	0.006	0.006	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.019	-0.021	8.896	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.029	-0.018	10.811	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.874	0.933	7.573	-0.113	-0.113	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.024	0.011	12.912	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	PHE	0	-0.001	-0.012	14.494	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.009	0.002	16.333	0.002	0.002	0.000	0.000	0.000	0.000
84	A	85	ILE	0	0.006	-0.020	12.467	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	87	ASN	0	0.002	0.003	19.883	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.018	0.004	21.241	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	89	ALA	0	0.002	0.029	21.779	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	90	ILE	0	-0.024	-0.012	22.850	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	91	GLY	0	-0.008	-0.013	21.985	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.015	-0.006	17.887	0.005	0.005	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.959	0.988	16.377	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.023	0.004	11.316	0.004	0.004	0.000	0.000	0.000	0.000
93	A	95	GLN	0	-0.006	0.003	9.955	0.007	0.007	0.000	0.000	0.000	0.000
94	A	96	LEU	0	-0.009	-0.015	6.210	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.025	-0.012	6.037	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.736	-0.868	2.418	-2.946	-1.244	1.107	-1.315	-1.495	-0.009
97	A	100	PHE	0	0.013	0.020	6.503	0.000	0.000	0.000	0.000	0.000	0.000
98	A	101	ILE	0	0.024	0.014	9.992	-0.026	-0.026	0.000	0.000	0.000	0.000
99	A	102	GLN	0	-0.097	-0.057	12.791	0.006	0.006	0.000	0.000	0.000	0.000
100	A	103	TYR	0	-0.042	-0.040	16.469	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.860	-0.922	19.282	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	105	GLN	0	0.018	0.011	23.065	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.956	0.970	25.797	0.016	0.016	0.000	0.000	0.000	0.000
104	A	107	SER	0	0.041	0.027	25.270	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	108	PHE	0	0.009	0.009	18.883	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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