FMO DATABASE

FMODB ID: QYMRY

Calculation Name: 3LNO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LNO

Chain ID: A

ChEMBL ID:

UniProt ID: A0A2B0

Base Structure: X-ray

Registration Date: 2023-06-22

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-772983.102076
FMO2-HF: Nuclear repulsion	731043.771148
FMO2-HF: Total energy	-41939.330928
FMO2-MP2: Total energy	-42057.624465

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:ASN)

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

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.
-20.53	-14.598	0.797	-2.582	-4.149	-0.001

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.002

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	1	MET	0	0.003	-0.004	3.085	-3.153	-0.756	0.016	-1.130	-1.283	0.002
4	A	2	SER	0	-0.039	-0.014	2.560	-2.546	-1.312	0.608	-0.625	-1.218	0.000
5	A	3	GLN	0	0.023	0.004	3.507	-4.092	-2.699	0.020	-0.535	-0.879	-0.002
6	A	4	GLU	-1	-0.873	-0.933	5.818	0.668	0.668	0.000	0.000	0.000	0.000
7	A	5	ALA	0	-0.025	-0.001	7.400	-0.078	-0.078	0.000	0.000	0.000	0.000
8	A	6	PHE	0	-0.052	-0.028	8.112	-0.129	-0.129	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.776	-0.896	9.759	-0.391	-0.391	0.000	0.000	0.000	0.000
10	A	8	ASN	0	-0.008	0.004	11.637	-0.124	-0.124	0.000	0.000	0.000	0.000
11	A	9	LYS	1	0.798	0.879	12.780	-0.715	-0.715	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.003	-0.006	13.184	-0.076	-0.076	0.000	0.000	0.000	0.000
13	A	11	TYR	0	0.015	0.002	15.732	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.015	0.006	17.481	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	13	ASN	0	-0.043	-0.040	17.907	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.002	0.008	19.773	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.958	-0.977	22.351	0.173	0.173	0.000	0.000	0.000	0.000
18	A	16	ALA	0	-0.098	-0.039	24.520	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	17	VAL	0	0.002	0.010	24.858	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	18	ILE	0	-0.037	-0.028	27.492	0.003	0.003	0.000	0.000	0.000	0.000
21	A	19	ASP	-1	-0.836	-0.927	30.887	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	20	PRO	0	-0.020	-0.027	32.870	0.006	0.006	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.900	-0.960	36.136	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	22	LEU	0	-0.022	-0.014	34.947	0.003	0.003	0.000	0.000	0.000	0.000
25	A	23	GLY	0	-0.049	-0.012	35.865	0.006	0.006	0.000	0.000	0.000	0.000
26	A	24	VAL	0	-0.068	-0.042	31.124	0.010	0.010	0.000	0.000	0.000	0.000
27	A	25	ASP	-1	-0.734	-0.820	26.899	0.093	0.093	0.000	0.000	0.000	0.000
28	A	26	ILE	0	0.065	0.000	24.180	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	27	VAL	0	0.038	0.039	22.315	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	28	ASN	0	-0.048	-0.031	25.030	0.001	0.001	0.000	0.000	0.000	0.000
31	A	29	LEU	0	-0.001	-0.007	28.006	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	30	GLY	0	-0.009	0.010	26.473	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	31	LEU	0	-0.081	-0.049	27.145	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	32	VAL	0	0.015	0.007	20.592	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	33	TYR	0	-0.108	-0.071	21.967	0.028	0.028	0.000	0.000	0.000	0.000
36	A	34	ASP	-1	-0.884	-0.948	15.918	-0.206	-0.206	0.000	0.000	0.000	0.000
37	A	35	VAL	0	-0.031	-0.012	14.081	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	36	THR	0	-0.016	0.019	11.410	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	37	ALA	0	0.009	-0.009	9.456	0.059	0.059	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.827	-0.915	7.435	-2.028	-2.028	0.000	0.000	0.000	0.000
41	A	39	GLU	-1	-0.981	-1.004	2.811	-9.070	-8.283	0.154	-0.287	-0.654	-0.001
42	A	40	ASN	0	-0.079	-0.033	4.553	0.556	0.677	-0.001	-0.005	-0.115	0.000
43	A	41	ASN	0	-0.044	-0.014	7.353	0.617	0.617	0.000	0.000	0.000	0.000
44	A	42	ASN	0	0.011	0.020	9.414	0.408	0.408	0.000	0.000	0.000	0.000
45	A	43	ALA	0	0.018	-0.003	11.523	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	44	VAL	0	0.007	0.014	13.998	0.021	0.021	0.000	0.000	0.000	0.000
47	A	45	ILE	0	-0.017	-0.009	16.191	0.047	0.047	0.000	0.000	0.000	0.000
48	A	46	THR	0	0.011	0.013	18.666	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	47	MET	0	-0.010	-0.014	20.952	0.037	0.037	0.000	0.000	0.000	0.000
50	A	48	THR	0	-0.027	-0.011	24.259	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.001	-0.002	27.907	0.012	0.012	0.000	0.000	0.000	0.000
52	A	50	THR	0	0.020	0.003	31.235	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	51	SER	0	-0.007	-0.012	34.048	0.001	0.001	0.000	0.000	0.000	0.000
54	A	52	ILE	0	0.000	-0.003	34.199	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	53	GLY	0	-0.040	-0.016	36.061	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	54	CYS	0	-0.078	-0.013	34.932	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	55	PRO	0	0.068	0.028	36.187	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	56	MET	0	-0.007	0.003	34.814	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	57	ALA	0	0.033	0.017	31.882	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	58	GLY	0	-0.001	-0.004	30.991	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	59	GLN	0	-0.014	-0.020	31.142	0.003	0.003	0.000	0.000	0.000	0.000
62	A	60	ILE	0	0.056	0.033	28.118	0.004	0.004	0.000	0.000	0.000	0.000
63	A	61	VAL	0	0.036	0.024	25.681	0.004	0.004	0.000	0.000	0.000	0.000
64	A	62	SER	0	-0.061	-0.038	26.036	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	63	ASP	-1	-0.918	-0.960	26.934	0.010	0.010	0.000	0.000	0.000	0.000
66	A	64	VAL	0	0.005	0.010	21.977	0.016	0.016	0.000	0.000	0.000	0.000
67	A	65	LYS	1	0.933	0.974	22.161	0.211	0.211	0.000	0.000	0.000	0.000
68	A	66	LYS	1	0.973	1.004	22.665	0.004	0.004	0.000	0.000	0.000	0.000
69	A	67	VAL	0	0.005	0.010	22.316	0.017	0.017	0.000	0.000	0.000	0.000
70	A	68	LEU	0	0.021	0.009	17.889	0.030	0.030	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.040	-0.026	19.144	0.031	0.031	0.000	0.000	0.000	0.000
72	A	70	THR	0	-0.081	-0.049	20.464	0.013	0.013	0.000	0.000	0.000	0.000
73	A	71	ASN	0	-0.043	-0.035	21.226	0.013	0.013	0.000	0.000	0.000	0.000
74	A	72	VAL	0	-0.075	-0.030	14.763	0.066	0.066	0.000	0.000	0.000	0.000
75	A	73	PRO	0	0.007	0.014	16.475	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.817	-0.891	11.694	0.534	0.534	0.000	0.000	0.000	0.000
77	A	75	VAL	0	-0.047	-0.013	12.568	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	76	ASN	0	-0.045	-0.040	10.890	0.069	0.069	0.000	0.000	0.000	0.000
79	A	77	GLU	-1	-0.970	-0.980	13.910	-0.556	-0.556	0.000	0.000	0.000	0.000
80	A	78	ILE	0	-0.012	-0.004	15.335	0.025	0.025	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.943	-0.963	17.717	-0.472	-0.472	0.000	0.000	0.000	0.000
82	A	80	VAL	0	-0.054	-0.034	19.507	0.022	0.022	0.000	0.000	0.000	0.000
83	A	81	ASN	0	-0.005	0.004	20.144	0.013	0.013	0.000	0.000	0.000	0.000
84	A	82	VAL	0	0.009	-0.002	23.162	0.020	0.020	0.000	0.000	0.000	0.000
85	A	83	VAL	0	-0.020	-0.004	24.158	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	84	TRP	0	0.034	0.006	27.058	0.021	0.021	0.000	0.000	0.000	0.000
87	A	85	ASN	0	-0.062	-0.018	28.187	0.020	0.020	0.000	0.000	0.000	0.000
88	A	86	PRO	0	0.028	0.013	25.931	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	87	PRO	0	0.044	0.016	29.114	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	88	TRP	0	0.014	-0.005	29.603	0.005	0.005	0.000	0.000	0.000	0.000
91	A	89	SER	0	-0.007	-0.016	31.662	0.001	0.001	0.000	0.000	0.000	0.000
92	A	90	LYS	1	1.052	1.015	32.878	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-1.005	-0.998	33.468	0.037	0.037	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.928	0.971	26.362	0.013	0.013	0.000	0.000	0.000	0.000
95	A	93	MET	0	-0.049	0.014	29.002	0.005	0.005	0.000	0.000	0.000	0.000
96	A	94	SER	0	0.020	-0.026	27.983	0.001	0.001	0.000	0.000	0.000	0.000
97	A	95	ARG	1	0.950	0.962	29.712	-0.151	-0.151	0.000	0.000	0.000	0.000
98	A	96	MET	0	0.009	0.000	30.293	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	97	ALA	0	0.084	0.056	31.726	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	98	LYS	1	0.859	0.931	32.687	-0.076	-0.076	0.000	0.000	0.000	0.000
101	A	99	ILE	0	-0.017	-0.004	35.273	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	100	ALA	0	-0.001	-0.006	36.096	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	101	LEU	0	0.017	-0.002	35.673	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	102	GLY	0	-0.038	0.003	39.092	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	103	ILE	0	-0.060	-0.026	41.229	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.892	0.954	37.350	-0.062	-0.062	0.000	0.000	0.000	0.000

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