FMO DATABASE

FMODB ID: Q18KY

Calculation Name: 4LRV-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LRV

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	108
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-860501.924509
FMO2-HF: Nuclear repulsion	818193.212003
FMO2-HF: Total energy	-42308.712506
FMO2-MP2: Total energy	-42433.091549

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:2:SER )

Summations of interaction energy for fragment #1(A:2: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.
-11.508	-3.627	3.777	-5.885	-5.771	-0.037

Interaction energy analysis for fragmet #1(A:2:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.064

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	4	LEU	0	0.015	0.020	3.067	-0.709	2.306	0.019	-1.570	-1.464	0.005
4	A	5	PRO	0	0.029	0.025	3.266	-0.299	0.400	0.065	-0.316	-0.446	-0.003
5	A	6	ASN	0	0.045	0.007	5.320	-0.081	-0.081	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.952	0.993	6.523	-0.372	-0.372	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.016	0.005	7.167	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.058	0.037	11.618	0.016	0.016	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.022	0.025	15.155	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.029	0.009	17.393	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	ARG	1	1.023	1.012	20.770	0.016	0.016	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.017	-0.014	23.923	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.028	0.002	19.395	0.004	0.004	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.808	-0.909	20.405	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.956	-0.985	22.734	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	GLN	0	0.042	0.017	24.844	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.002	0.009	19.521	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.941	0.972	24.011	0.011	0.011	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.916	0.960	26.674	0.018	0.018	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.057	0.040	24.245	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.943	0.996	25.605	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.055	-0.016	27.875	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.001	0.003	31.222	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.035	-0.030	28.122	0.000	0.000	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.042	0.016	29.170	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.049	-0.026	23.121	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.024	0.004	21.138	0.000	0.000	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.050	0.008	20.648	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.002	-0.020	16.283	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.018	0.025	16.900	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.017	0.003	19.064	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.015	0.008	15.993	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.856	0.936	13.996	0.062	0.062	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.003	-0.007	15.923	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.035	-0.002	18.854	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.037	0.007	11.557	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	38	PHE	0	-0.001	-0.020	12.456	0.002	0.002	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.941	0.977	17.289	0.036	0.036	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.033	-0.033	18.202	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.057	-0.022	14.347	0.004	0.004	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-1.004	-0.980	17.759	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.022	-0.025	20.553	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.939	-0.984	22.066	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.015	0.015	18.484	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.883	0.924	17.958	0.027	0.027	0.000	0.000	0.000	0.000
46	A	47	TYR	0	-0.081	-0.047	16.103	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.023	-0.082	18.271	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.013	0.004	17.714	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.815	-0.849	19.494	-0.061	-0.061	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.863	0.921	22.447	0.059	0.059	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.751	-0.872	18.886	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.071	-0.061	22.422	0.001	0.001	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.907	0.990	20.827	0.057	0.057	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.929	0.954	20.690	0.044	0.044	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.037	-0.017	15.358	0.002	0.002	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.851	-0.928	19.128	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.044	-0.010	20.054	0.004	0.004	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.041	-0.031	20.838	0.005	0.005	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.014	-0.007	18.335	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	VAL	0	-0.033	-0.009	13.549	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.009	-0.006	14.210	0.022	0.022	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.871	-0.947	10.576	0.141	0.141	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.840	0.904	2.489	-0.023	0.358	0.587	-0.327	-0.641	0.002
64	A	65	ILE	0	0.043	0.022	8.403	-0.057	-0.057	0.000	0.000	0.000	0.000
65	A	66	THR	0	0.041	0.027	10.254	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	67	TRP	0	-0.017	-0.013	11.288	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.004	0.014	7.394	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.008	0.019	11.526	0.016	0.016	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.871	-0.950	11.407	-0.112	-0.112	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.089	-0.046	12.204	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.011	0.015	5.253	0.016	0.016	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.088	0.032	6.574	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.033	0.021	7.661	0.186	0.186	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.002	-0.017	8.321	0.066	0.066	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.830	-0.958	2.428	-9.258	-5.495	3.106	-3.669	-3.200	-0.041
76	A	77	LEU	0	-0.038	-0.003	5.826	0.378	0.378	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.043	0.011	8.367	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.004	-0.012	7.491	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.933	0.976	5.380	-1.309	-1.286	0.000	-0.003	-0.020	0.000
80	A	81	MET	0	-0.033	-0.027	8.790	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.030	-0.001	12.219	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.056	-0.054	11.205	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.025	0.024	11.459	-0.057	-0.057	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.021	-0.023	11.980	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.054	-0.002	11.583	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.830	-0.916	10.034	-0.484	-0.484	0.000	0.000	0.000	0.000
87	A	88	GLN	0	0.031	0.007	5.559	0.054	0.054	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.923	0.944	8.664	0.213	0.213	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.012	0.000	12.198	0.045	0.045	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.064	0.037	6.486	0.040	0.040	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.032	-0.015	9.479	0.052	0.052	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.899	0.964	11.124	0.163	0.163	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.044	0.039	12.071	0.026	0.026	0.000	0.000	0.000	0.000
94	A	95	TRP	0	0.010	-0.005	10.133	0.023	0.023	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.005	-0.021	12.275	0.031	0.031	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.002	0.004	15.285	0.018	0.018	0.000	0.000	0.000	0.000
97	A	98	HIS	0	0.057	0.050	14.366	0.010	0.010	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.049	-0.010	14.882	0.012	0.012	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.960	-0.999	17.546	-0.043	-0.043	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.831	-0.883	20.280	-0.034	-0.034	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.065	0.028	20.271	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.106	-0.059	21.477	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.005	0.001	23.363	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.027	0.006	25.214	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.067	-0.035	25.464	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.859	0.926	27.340	0.028	0.028	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.007	-0.003	31.882	0.000	0.000	0.000	0.000	0.000	0.000
108	A	1	NME	0	0.024	0.032	35.425	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER )