FMO DATABASE

FMODB ID: 17GNZ

Calculation Name: 3A01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A01

Chain ID: A

ChEMBL ID:

UniProt ID: Q06453

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502113.54484
FMO2-HF: Nuclear repulsion	469782.33371
FMO2-HF: Total energy	-32331.21113
FMO2-MP2: Total energy	-32427.554822

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:170:ALA)

Summations of interaction energy for fragment #1(A:170: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.
-11.974	-8.753	-0.004	-1.721	-1.496	0.002

Interaction energy analysis for fragmet #1(A:170:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.008

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	172	ARG	1	0.918	0.950	3.500	-9.261	-6.040	-0.004	-1.721	-1.496	0.002
4	A	173	ILE	0	0.072	0.058	5.799	-0.840	-0.840	0.000	0.000	0.000	0.000
5	A	174	GLY	0	0.022	0.006	9.169	0.202	0.202	0.000	0.000	0.000	0.000
6	A	175	HIS	0	0.042	0.028	12.423	-0.106	-0.106	0.000	0.000	0.000	0.000
7	A	176	PRO	0	0.082	0.048	16.108	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	177	TYR	0	0.005	-0.025	18.293	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	178	GLN	0	0.027	-0.001	21.149	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	179	ASN	0	0.035	0.035	21.308	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	180	ARG	1	0.828	0.928	17.041	-0.352	-0.352	0.000	0.000	0.000	0.000
12	A	181	THR	0	0.052	0.026	24.116	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	182	PRO	0	0.039	0.013	27.076	0.004	0.004	0.000	0.000	0.000	0.000
14	A	183	PRO	0	-0.008	-0.004	25.591	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	184	LYS	1	0.955	0.975	28.339	-0.149	-0.149	0.000	0.000	0.000	0.000
16	A	185	ARG	1	0.950	0.973	26.675	-0.121	-0.121	0.000	0.000	0.000	0.000
17	A	186	LYS	1	0.976	1.000	31.676	-0.109	-0.109	0.000	0.000	0.000	0.000
18	A	187	LYS	1	1.031	0.979	33.956	-0.062	-0.062	0.000	0.000	0.000	0.000
19	A	188	PRO	0	-0.034	0.015	34.202	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	189	ARG	1	0.973	0.990	30.297	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	190	THR	0	0.004	-0.005	31.759	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	191	SER	0	0.015	-0.008	32.297	0.002	0.002	0.000	0.000	0.000	0.000
23	A	192	PHE	0	-0.026	0.001	28.217	0.000	0.000	0.000	0.000	0.000	0.000
24	A	193	THR	0	0.069	0.018	33.350	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	194	ARG	1	1.012	0.985	34.247	0.004	0.004	0.000	0.000	0.000	0.000
26	A	195	ILE	0	0.069	0.047	34.362	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	196	GLN	0	0.040	0.028	32.694	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	197	VAL	0	-0.009	-0.012	28.919	0.001	0.001	0.000	0.000	0.000	0.000
29	A	198	ALA	0	0.027	0.023	29.575	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	199	GLU	-1	-0.772	-0.878	30.667	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	200	LEU	0	-0.043	-0.023	26.946	0.002	0.002	0.000	0.000	0.000	0.000
32	A	201	GLU	-1	-0.757	-0.867	24.337	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	202	LYS	1	0.854	0.922	26.165	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	203	ARG	1	0.794	0.899	25.861	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	204	PHE	0	0.026	-0.002	18.110	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	205	HIS	0	0.019	0.014	22.280	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	206	LYS	1	0.936	0.960	23.044	0.003	0.003	0.000	0.000	0.000	0.000
38	A	207	GLN	0	-0.001	0.018	22.109	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	208	LYS	1	0.880	0.946	17.310	0.074	0.074	0.000	0.000	0.000	0.000
40	A	209	TYR	0	0.029	-0.002	12.525	0.026	0.026	0.000	0.000	0.000	0.000
41	A	210	LEU	0	0.008	0.015	19.529	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	211	ALA	0	0.062	0.028	22.424	0.022	0.022	0.000	0.000	0.000	0.000
43	A	212	SER	0	0.002	-0.019	23.885	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	213	ALA	0	0.069	0.040	26.374	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	214	GLU	-1	-0.715	-0.849	24.701	0.052	0.052	0.000	0.000	0.000	0.000
46	A	215	ARG	1	0.778	0.889	22.929	-0.132	-0.132	0.000	0.000	0.000	0.000
47	A	216	ALA	0	0.052	0.019	27.547	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	217	ALA	0	-0.044	-0.019	30.749	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	218	LEU	0	0.006	0.005	27.395	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	219	ALA	0	-0.029	-0.023	30.164	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	220	ARG	1	0.971	0.986	31.862	-0.056	-0.056	0.000	0.000	0.000	0.000
52	A	221	GLY	0	0.012	0.015	34.597	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	222	LEU	0	-0.014	-0.004	30.992	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	223	LYS	1	0.952	0.982	34.942	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	224	MET	0	-0.046	0.001	28.935	0.000	0.000	0.000	0.000	0.000	0.000
56	A	225	THR	0	0.036	-0.007	31.302	0.005	0.005	0.000	0.000	0.000	0.000
57	A	226	ASP	-1	-0.801	-0.903	27.056	0.113	0.113	0.000	0.000	0.000	0.000
58	A	227	ALA	0	0.040	0.015	26.524	0.005	0.005	0.000	0.000	0.000	0.000
59	A	228	GLN	0	0.044	0.053	26.083	0.006	0.006	0.000	0.000	0.000	0.000
60	A	229	VAL	0	0.062	0.041	25.756	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	230	LYS	1	0.952	0.977	21.459	-0.200	-0.200	0.000	0.000	0.000	0.000
62	A	231	THR	0	-0.030	-0.031	21.731	0.014	0.014	0.000	0.000	0.000	0.000
63	A	232	TRP	0	0.003	0.010	22.009	0.002	0.002	0.000	0.000	0.000	0.000
64	A	233	PHE	0	0.034	-0.001	20.832	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	234	GLN	0	0.032	0.035	14.185	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	235	ASN	0	0.014	0.007	17.494	0.008	0.008	0.000	0.000	0.000	0.000
67	A	236	ARG	1	0.815	0.902	19.307	0.027	0.027	0.000	0.000	0.000	0.000
68	A	237	ARG	1	0.863	0.919	14.902	-0.154	-0.154	0.000	0.000	0.000	0.000
69	A	238	THR	0	-0.039	-0.017	14.661	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	239	LYS	1	0.882	0.941	15.690	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	240	TRP	0	0.009	-0.003	14.442	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	241	ARG	1	0.939	0.973	10.099	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	242	ARG	1	0.759	0.838	12.877	0.072	0.072	0.000	0.000	0.000	0.000
74	A	243	GLN	0	0.012	0.000	14.708	0.005	0.005	0.000	0.000	0.000	0.000
75	A	244	THR	0	-0.064	-0.050	12.915	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	245	ALA	0	0.030	0.015	10.480	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	246	GLU	-1	-0.848	-0.858	12.430	-0.193	-0.193	0.000	0.000	0.000	0.000
78	A	247	GLU	-1	-0.955	-0.970	13.505	-0.444	-0.444	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:170:ALA)