FMO DATABASE

FMODB ID: QY4GY

Calculation Name: 5D0Q-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: G

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-26

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	OptH
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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-375609.296068
FMO2-HF: Nuclear repulsion	344011.302235
FMO2-HF: Total energy	-31597.993833
FMO2-MP2: Total energy	-31687.82491

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(G:29:SER)

Summations of interaction energy for fragment #1(G:29: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.
-8.478	-3.982	4.959	-4.153	-5.303	-0.007

Interaction energy analysis for fragmet #1(G:29:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.003

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	G	31	TYR	0	0.030	-0.002	2.146	-4.433	-1.692	2.252	-2.439	-2.554	-0.012
4	G	32	LYS	1	0.943	0.987	2.257	-0.997	-0.679	2.691	-0.959	-2.050	0.003
5	G	33	ARG	1	0.926	0.961	3.235	-3.767	-2.330	0.016	-0.755	-0.699	0.002
6	G	34	GLN	0	0.021	0.030	7.365	0.148	0.148	0.000	0.000	0.000	0.000
7	G	35	VAL	0	0.093	0.047	9.806	-0.048	-0.048	0.000	0.000	0.000	0.000
8	G	36	SER	0	-0.043	-0.030	11.560	0.088	0.088	0.000	0.000	0.000	0.000
9	G	37	GLY	0	0.040	0.026	13.019	-0.052	-0.052	0.000	0.000	0.000	0.000
10	G	38	ASP	-1	-0.945	-0.984	14.298	0.372	0.372	0.000	0.000	0.000	0.000
11	G	39	GLU	-1	-0.862	-0.951	15.536	0.472	0.472	0.000	0.000	0.000	0.000
12	G	40	ALA	0	0.046	0.032	18.166	-0.021	-0.021	0.000	0.000	0.000	0.000
13	G	41	TYR	0	-0.005	0.006	18.103	-0.004	-0.004	0.000	0.000	0.000	0.000
14	G	42	LEU	0	-0.035	-0.029	18.718	-0.015	-0.015	0.000	0.000	0.000	0.000
15	G	43	GLU	-1	-0.976	-0.975	22.271	0.222	0.222	0.000	0.000	0.000	0.000
16	G	44	ALA	0	-0.041	-0.008	25.205	-0.015	-0.015	0.000	0.000	0.000	0.000
17	G	45	ALA	0	-0.010	-0.009	27.899	-0.002	-0.002	0.000	0.000	0.000	0.000
18	G	46	PRO	0	-0.006	0.001	31.502	0.001	0.001	0.000	0.000	0.000	0.000
19	G	47	LEU	0	0.004	-0.012	32.449	-0.006	-0.006	0.000	0.000	0.000	0.000
20	G	48	ALA	0	-0.042	-0.011	35.249	-0.002	-0.002	0.000	0.000	0.000	0.000
21	G	49	GLU	-1	-0.896	-0.959	38.449	0.071	0.071	0.000	0.000	0.000	0.000
22	G	50	LEU	0	-0.048	-0.006	41.339	-0.001	-0.001	0.000	0.000	0.000	0.000
23	G	51	HIS	0	-0.004	-0.009	44.524	-0.003	-0.003	0.000	0.000	0.000	0.000
24	G	52	ALA	0	-0.019	-0.008	48.008	-0.001	-0.001	0.000	0.000	0.000	0.000
25	G	53	PRO	0	-0.003	-0.008	51.218	-0.001	-0.001	0.000	0.000	0.000	0.000
26	G	54	ALA	0	0.011	0.004	54.214	0.000	0.000	0.000	0.000	0.000	0.000
27	G	55	GLY	0	-0.023	-0.008	57.793	-0.001	-0.001	0.000	0.000	0.000	0.000
28	G	56	MET	0	-0.019	-0.008	54.294	0.000	0.000	0.000	0.000	0.000	0.000
29	G	57	ILE	0	-0.001	0.002	51.806	0.001	0.001	0.000	0.000	0.000	0.000
30	G	58	LEU	0	0.020	0.009	48.504	-0.001	-0.001	0.000	0.000	0.000	0.000
31	G	59	PRO	0	-0.007	-0.007	48.151	0.000	0.000	0.000	0.000	0.000	0.000
32	G	60	VAL	0	0.017	0.003	45.108	0.002	0.002	0.000	0.000	0.000	0.000
33	G	61	THR	0	0.003	-0.005	39.975	-0.001	-0.001	0.000	0.000	0.000	0.000
34	G	62	SER	0	-0.030	-0.007	43.020	-0.001	-0.001	0.000	0.000	0.000	0.000
35	G	63	GLY	0	-0.019	0.002	43.035	0.000	0.000	0.000	0.000	0.000	0.000
36	G	64	ASP	-1	-0.886	-0.951	37.677	0.069	0.069	0.000	0.000	0.000	0.000
37	G	65	TYR	0	-0.059	-0.038	34.450	-0.001	-0.001	0.000	0.000	0.000	0.000
38	G	66	ALA	0	0.046	0.039	36.299	0.002	0.002	0.000	0.000	0.000	0.000
39	G	67	ILE	0	-0.030	-0.019	30.774	0.003	0.003	0.000	0.000	0.000	0.000
40	G	68	PRO	0	-0.016	-0.004	32.996	-0.002	-0.002	0.000	0.000	0.000	0.000
41	G	69	VAL	0	0.028	0.023	32.992	0.007	0.007	0.000	0.000	0.000	0.000
42	G	70	THR	0	-0.007	-0.011	29.429	0.000	0.000	0.000	0.000	0.000	0.000
43	G	71	ASN	0	0.020	-0.004	29.987	0.002	0.002	0.000	0.000	0.000	0.000
44	G	72	GLY	0	0.002	0.080	26.929	0.009	0.009	0.000	0.000	0.000	0.000
45	G	73	SER	0	-0.020	-0.066	24.948	-0.009	-0.009	0.000	0.000	0.000	0.000
46	G	74	GLY	0	-0.012	-0.017	22.057	-0.001	-0.001	0.000	0.000	0.000	0.000
47	G	75	ALA	0	-0.024	-0.011	16.565	0.002	0.002	0.000	0.000	0.000	0.000
48	G	76	VAL	0	0.051	0.017	18.270	-0.012	-0.012	0.000	0.000	0.000	0.000
49	G	77	GLY	0	0.068	0.036	16.721	0.025	0.025	0.000	0.000	0.000	0.000
50	G	78	LYS	1	0.777	0.884	10.757	-0.621	-0.621	0.000	0.000	0.000	0.000
51	G	79	ALA	0	-0.011	0.001	11.763	0.061	0.061	0.000	0.000	0.000	0.000
52	G	80	LEU	0	-0.029	-0.011	13.583	0.010	0.010	0.000	0.000	0.000	0.000
53	G	81	ASP	-1	-0.813	-0.915	10.461	0.530	0.530	0.000	0.000	0.000	0.000
54	G	82	ILE	0	-0.025	-0.007	11.118	-0.050	-0.050	0.000	0.000	0.000	0.000
55	G	83	ARG	1	0.866	0.937	8.215	-0.507	-0.507	0.000	0.000	0.000	0.000
56	G	84	PRO	0	0.059	0.037	12.411	0.005	0.005	0.000	0.000	0.000	0.000
57	G	85	PRO	0	-0.028	-0.019	15.571	0.003	0.003	0.000	0.000	0.000	0.000
58	G	86	ALA	0	-0.015	-0.005	16.632	-0.017	-0.017	0.000	0.000	0.000	0.000
59	G	87	GLN	0	0.025	0.008	18.416	0.017	0.017	0.000	0.000	0.000	0.000
60	G	88	PRO	0	-0.013	0.011	20.520	-0.007	-0.007	0.000	0.000	0.000	0.000
61	G	189	ALA	0	0.007	-0.013	19.176	0.007	0.007	0.000	0.000	0.000	0.000
62	G	190	ASP	-1	-0.873	-0.928	17.176	0.283	0.283	0.000	0.000	0.000	0.000
63	G	191	ALA	0	0.055	0.008	19.784	0.003	0.003	0.000	0.000	0.000	0.000
64	G	192	ALA	0	0.013	-0.002	18.675	-0.007	-0.007	0.000	0.000	0.000	0.000
65	G	193	SER	0	-0.001	0.006	15.007	0.018	0.018	0.000	0.000	0.000	0.000
66	G	194	MET	0	-0.025	-0.007	16.805	0.001	0.001	0.000	0.000	0.000	0.000
67	G	195	GLN	0	-0.010	-0.002	19.386	-0.025	-0.025	0.000	0.000	0.000	0.000
68	G	196	ARG	1	0.901	0.945	12.859	-0.283	-0.283	0.000	0.000	0.000	0.000
69	G	197	TYR	0	-0.054	-0.039	10.409	0.028	0.028	0.000	0.000	0.000	0.000
70	G	198	SER	0	0.036	0.009	16.226	-0.021	-0.021	0.000	0.000	0.000	0.000
71	G	199	THR	0	0.001	0.002	18.172	-0.021	-0.021	0.000	0.000	0.000	0.000
72	G	200	GLU	-1	-1.005	-1.001	13.452	0.104	0.104	0.000	0.000	0.000	0.000
73	G	201	MET	0	0.012	0.022	16.800	-0.020	-0.020	0.000	0.000	0.000	0.000
74	G	202	MET	0	0.061	0.038	19.694	-0.016	-0.016	0.000	0.000	0.000	0.000
75	G	203	ASN	0	-0.030	-0.032	18.547	-0.015	-0.015	0.000	0.000	0.000	0.000
76	G	204	VAL	0	0.002	0.010	18.886	-0.012	-0.012	0.000	0.000	0.000	0.000
77	G	205	ILE	0	-0.035	-0.031	21.468	-0.011	-0.011	0.000	0.000	0.000	0.000
78	G	206	SER	0	-0.019	-0.013	24.167	-0.005	-0.005	0.000	0.000	0.000	0.000
79	G	207	ALA	0	0.008	0.018	22.629	-0.004	-0.004	0.000	0.000	0.000	0.000
80	G	208	GLY	0	-0.020	-0.016	24.659	-0.009	-0.009	0.000	0.000	0.000	0.000
81	G	209	LEU	0	-0.061	-0.032	26.563	-0.002	-0.002	0.000	0.000	0.000	0.000
82	G	210	ASP	-1	-0.930	-0.965	27.944	-0.018	-0.018	0.000	0.000	0.000	0.000
83	G	211	LYS	1	0.950	0.996	26.112	0.027	0.027	0.000	0.000	0.000	0.000
84	G	212	SER	0	-0.072	-0.041	29.676	-0.003	-0.003	0.000	0.000	0.000	0.000
85	G	213	ALA	0	0.023	0.025	32.378	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:29:SER)