FMO DATABASE

FMODB ID: 4962N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-776985.040511
FMO2-HF: Nuclear repulsion	735045.061954
FMO2-HF: Total energy	-41939.978556
FMO2-MP2: Total energy	-42058.287093

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.
-22.71	-15.908	2.677	-3.494	-5.985	-0.005

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 : 0.029 / q_NPA : -0.004

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	-0.005	-0.007	3.501	-1.494	0.179	-0.007	-0.758	-0.909	0.000
4	A	2	SER	0	-0.031	-0.007	2.758	-3.912	-2.196	0.503	-0.796	-1.423	0.007
5	A	3	GLN	0	-0.029	-0.024	2.959	-5.739	-3.497	0.238	-1.039	-1.441	-0.006
6	A	4	GLU	-1	-0.813	-0.902	5.752	0.477	0.576	-0.001	-0.005	-0.092	0.000
7	A	5	ALA	0	0.003	0.002	8.062	-0.187	-0.187	0.000	0.000	0.000	0.000
8	A	6	PHE	0	-0.033	-0.014	7.729	-0.276	-0.276	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.801	-0.905	9.444	-0.332	-0.332	0.000	0.000	0.000	0.000
10	A	8	ASN	0	-0.079	-0.038	11.492	-0.204	-0.204	0.000	0.000	0.000	0.000
11	A	9	LYS	1	0.803	0.898	12.583	-0.649	-0.649	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.004	-0.002	12.092	-0.105	-0.105	0.000	0.000	0.000	0.000
13	A	11	TYR	0	0.021	-0.006	15.279	-0.053	-0.053	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.015	0.003	17.194	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	13	ASN	0	-0.038	-0.036	17.382	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	14	LEU	0	0.006	0.005	19.435	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.905	-0.948	21.898	0.173	0.173	0.000	0.000	0.000	0.000
18	A	16	ALA	0	-0.084	-0.036	23.794	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	17	VAL	0	-0.020	-0.004	23.551	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	18	ILE	0	-0.043	-0.025	26.443	0.003	0.003	0.000	0.000	0.000	0.000
21	A	19	ASP	-1	-0.800	-0.902	30.022	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	20	PRO	0	-0.024	-0.041	32.073	0.006	0.006	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.881	-0.933	35.305	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	22	LEU	0	-0.030	-0.012	34.336	0.003	0.003	0.000	0.000	0.000	0.000
25	A	23	GLY	0	0.009	0.010	35.258	0.006	0.006	0.000	0.000	0.000	0.000
26	A	24	VAL	0	-0.065	-0.038	30.859	0.009	0.009	0.000	0.000	0.000	0.000
27	A	25	ASP	-1	-0.729	-0.834	26.729	0.097	0.097	0.000	0.000	0.000	0.000
28	A	26	ILE	0	0.055	0.004	23.631	0.000	0.000	0.000	0.000	0.000	0.000
29	A	27	VAL	0	0.030	0.037	22.014	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	28	ASN	0	-0.032	-0.020	24.804	0.000	0.000	0.000	0.000	0.000	0.000
31	A	29	LEU	0	-0.002	-0.004	27.909	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	30	GLY	0	-0.009	0.000	26.427	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	31	LEU	0	-0.071	-0.031	27.058	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	32	VAL	0	0.016	0.008	20.264	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	33	TYR	0	-0.133	-0.099	21.859	0.023	0.023	0.000	0.000	0.000	0.000
36	A	34	ASP	-1	-0.844	-0.926	15.483	-0.123	-0.123	0.000	0.000	0.000	0.000
37	A	35	VAL	0	-0.057	-0.027	13.982	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	36	THR	0	-0.002	0.005	11.385	0.038	0.038	0.000	0.000	0.000	0.000
39	A	37	ALA	0	-0.018	-0.023	8.632	0.033	0.033	0.000	0.000	0.000	0.000
40	A	38	ASP	-1	-0.784	-0.870	6.673	-2.526	-2.526	0.000	0.000	0.000	0.000
41	A	39	GLU	-1	-0.972	-0.997	2.279	-8.122	-7.635	1.944	-0.816	-1.615	-0.002
42	A	40	ASN	0	-0.103	-0.047	3.282	-0.828	-0.243	0.000	-0.080	-0.505	-0.004
43	A	41	ASN	0	-0.045	-0.016	6.019	0.867	0.867	0.000	0.000	0.000	0.000
44	A	42	ASN	0	-0.006	-0.011	7.996	0.564	0.564	0.000	0.000	0.000	0.000
45	A	43	ALA	0	0.012	-0.005	9.969	-0.127	-0.127	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.014	0.001	12.387	0.022	0.022	0.000	0.000	0.000	0.000
47	A	45	ILE	0	-0.013	-0.002	15.381	0.062	0.062	0.000	0.000	0.000	0.000
48	A	46	THR	0	0.004	0.012	18.055	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	47	MET	0	-0.010	-0.009	20.485	0.039	0.039	0.000	0.000	0.000	0.000
50	A	48	THR	0	-0.027	-0.020	23.854	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.013	-0.004	27.550	0.011	0.011	0.000	0.000	0.000	0.000
52	A	50	THR	0	0.042	0.013	30.808	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	51	SER	0	-0.031	-0.021	33.918	0.001	0.001	0.000	0.000	0.000	0.000
54	A	52	ILE	0	-0.005	-0.013	34.012	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	53	GLY	0	0.001	0.005	35.664	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	54	CYS	0	-0.086	-0.017	34.147	0.001	0.001	0.000	0.000	0.000	0.000
57	A	55	PRO	0	0.038	0.010	35.119	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	56	MET	0	-0.022	-0.004	33.566	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	57	ALA	0	0.033	0.012	30.929	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	58	GLY	0	0.006	-0.001	29.579	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	59	GLN	0	0.009	0.005	29.517	0.000	0.000	0.000	0.000	0.000	0.000
62	A	60	ILE	0	0.062	0.033	26.929	0.001	0.001	0.000	0.000	0.000	0.000
63	A	61	VAL	0	0.016	0.012	24.535	0.002	0.002	0.000	0.000	0.000	0.000
64	A	62	SER	0	-0.063	-0.040	24.562	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	63	ASP	-1	-0.812	-0.907	25.292	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	64	VAL	0	0.019	0.013	20.610	0.015	0.015	0.000	0.000	0.000	0.000
67	A	65	LYS	1	0.908	0.953	20.311	0.244	0.244	0.000	0.000	0.000	0.000
68	A	66	LYS	1	0.809	0.918	21.063	0.003	0.003	0.000	0.000	0.000	0.000
69	A	67	VAL	0	0.000	0.008	21.958	0.010	0.010	0.000	0.000	0.000	0.000
70	A	68	LEU	0	0.009	0.010	16.871	0.030	0.030	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.029	-0.034	18.023	0.029	0.029	0.000	0.000	0.000	0.000
72	A	70	THR	0	-0.081	-0.044	19.100	0.008	0.008	0.000	0.000	0.000	0.000
73	A	71	ASN	0	-0.048	-0.028	20.216	0.001	0.001	0.000	0.000	0.000	0.000
74	A	72	VAL	0	-0.088	-0.042	13.778	0.083	0.083	0.000	0.000	0.000	0.000
75	A	73	PRO	0	0.020	0.018	15.267	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.816	-0.898	11.070	0.532	0.532	0.000	0.000	0.000	0.000
77	A	75	VAL	0	-0.031	-0.004	11.037	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	76	ASN	0	-0.048	-0.028	9.794	0.103	0.103	0.000	0.000	0.000	0.000
79	A	77	GLU	-1	-0.966	-0.979	12.930	-0.507	-0.507	0.000	0.000	0.000	0.000
80	A	78	ILE	0	0.014	0.003	13.885	0.015	0.015	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.863	-0.914	16.179	-0.442	-0.442	0.000	0.000	0.000	0.000
82	A	80	VAL	0	-0.043	-0.037	18.178	0.036	0.036	0.000	0.000	0.000	0.000
83	A	81	ASN	0	-0.041	-0.017	19.267	0.031	0.031	0.000	0.000	0.000	0.000
84	A	82	VAL	0	-0.007	-0.004	22.423	0.019	0.019	0.000	0.000	0.000	0.000
85	A	83	VAL	0	-0.012	-0.001	24.248	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	84	TRP	0	0.032	0.011	26.987	0.018	0.018	0.000	0.000	0.000	0.000
87	A	85	ASN	0	-0.044	-0.020	28.194	0.018	0.018	0.000	0.000	0.000	0.000
88	A	86	PRO	0	0.069	0.037	25.848	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	87	PRO	0	0.030	0.020	28.798	0.001	0.001	0.000	0.000	0.000	0.000
90	A	88	TRP	0	0.049	0.025	29.570	0.005	0.005	0.000	0.000	0.000	0.000
91	A	89	SER	0	-0.047	-0.058	31.449	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	90	LYS	1	1.007	1.008	32.716	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.868	-0.933	33.405	0.039	0.039	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.853	0.952	26.516	0.001	0.001	0.000	0.000	0.000	0.000
95	A	93	MET	0	-0.038	0.029	28.895	0.007	0.007	0.000	0.000	0.000	0.000
96	A	94	SER	0	0.026	-0.022	28.232	0.002	0.002	0.000	0.000	0.000	0.000
97	A	95	ARG	1	0.930	0.949	29.922	-0.144	-0.144	0.000	0.000	0.000	0.000
98	A	96	MET	0	0.016	0.015	30.360	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	97	ALA	0	0.080	0.047	31.574	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	98	LYS	1	0.790	0.883	32.028	-0.083	-0.083	0.000	0.000	0.000	0.000
101	A	99	ILE	0	-0.010	-0.006	35.753	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	100	ALA	0	-0.007	-0.001	35.795	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	101	LEU	0	0.005	-0.014	35.538	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	102	GLY	0	-0.013	0.016	39.038	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	103	ILE	0	-0.054	-0.014	41.260	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.803	0.899	36.298	-0.063	-0.063	0.000	0.000	0.000	0.000

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