FMO DATABASE

FMODB ID: 2NL8R

Calculation Name: 5A7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5A7L

Chain ID: A

ChEMBL ID:

UniProt ID: O48503

Base Structure: X-ray

Registration Date: 2023-09-22

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-546436.566892
FMO2-HF: Nuclear repulsion	514200.69154
FMO2-HF: Total energy	-32235.875352
FMO2-MP2: Total energy	-32328.695244

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:MET)

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

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.
-14.266	-8.784	9.845	-4.17	-11.159	-0.016

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.001

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	A	3	THR	0	-0.037	-0.005	2.764	-2.093	0.859	0.101	-1.367	-1.686	0.005
4	A	4	ASP	-1	-0.842	-0.909	2.875	-9.849	-8.344	0.315	-0.742	-1.079	-0.008
5	A	5	THR	0	-0.002	-0.042	5.022	0.853	0.962	-0.001	-0.002	-0.106	0.000
6	A	6	SER	0	-0.053	-0.018	6.830	0.550	0.550	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.042	0.010	7.424	-0.085	-0.085	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.934	0.999	6.170	0.944	0.944	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.009	-0.003	9.570	0.281	0.281	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.917	0.956	12.141	1.237	1.237	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.002	0.011	11.393	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.007	-0.001	12.939	0.121	0.121	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.100	-0.052	15.615	0.041	0.041	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.005	0.003	17.304	0.058	0.058	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.887	-0.940	16.331	-0.291	-0.291	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.845	0.905	17.109	0.283	0.283	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.041	-0.002	21.102	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.019	-0.001	19.358	0.021	0.021	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.973	0.980	20.602	0.286	0.286	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.054	0.000	18.398	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.007	-0.004	20.641	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.816	-0.907	22.938	-0.271	-0.271	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.028	0.014	16.683	0.021	0.021	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.022	-0.013	20.453	0.014	0.014	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.005	0.012	21.758	0.032	0.032	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.020	0.005	21.013	0.023	0.023	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.003	-0.005	19.678	0.019	0.019	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.015	0.018	21.315	0.024	0.024	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.013	-0.023	24.600	0.017	0.017	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.036	0.017	20.827	0.025	0.025	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.034	-0.020	21.298	0.030	0.030	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.906	0.956	23.054	0.132	0.132	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.932	0.989	23.434	0.046	0.046	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.013	-0.024	19.024	0.020	0.020	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.038	0.038	23.179	0.011	0.011	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.026	-0.016	18.406	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.962	0.977	21.582	0.148	0.148	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.018	0.007	16.965	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.028	0.023	20.277	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	LYS	1	1.069	1.007	20.669	0.312	0.312	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.016	-0.004	20.883	-0.057	-0.057	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.067	0.037	16.763	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.028	0.027	15.785	-0.077	-0.077	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.040	-0.029	16.070	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	45	GLN	0	0.023	0.006	16.046	-0.080	-0.080	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.042	0.029	12.183	-0.099	-0.099	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.017	-0.007	11.792	-0.208	-0.208	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.113	-0.076	13.359	-0.116	-0.116	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.041	0.022	9.716	-0.179	-0.179	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.040	0.008	11.434	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.042	-0.026	12.894	0.109	0.109	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.042	0.024	7.872	-0.108	-0.108	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.035	-0.028	8.412	0.236	0.236	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.772	-0.863	9.896	-0.401	-0.401	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.084	0.000	7.805	0.039	0.039	0.000	0.000	0.000	0.000
56	A	56	ASN	0	0.009	0.016	11.909	0.061	0.061	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.795	0.871	13.704	0.395	0.395	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.016	0.030	7.653	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.064	0.033	11.113	0.031	0.031	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.055	-0.024	13.759	0.011	0.011	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.004	-0.008	12.867	0.028	0.028	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.030	0.027	11.609	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.908	0.957	13.522	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.082	-0.033	17.080	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.036	-0.015	14.040	0.008	0.008	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.006	0.032	17.046	0.010	0.010	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.051	-0.014	11.797	0.016	0.016	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.012	0.010	10.352	0.018	0.018	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.862	-0.964	9.648	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.018	0.009	6.385	-0.281	-0.281	0.000	0.000	0.000	0.000
71	A	71	TRP	0	0.064	0.030	5.199	-0.434	-0.370	-0.001	0.000	-0.063	0.000
72	A	72	LEU	0	-0.029	-0.009	6.187	-0.465	-0.465	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.038	-0.025	3.389	-0.353	-0.086	0.007	-0.061	-0.213	0.000
74	A	74	GLY	0	-0.009	0.005	2.524	-3.922	-3.391	2.106	-0.972	-1.666	-0.012
75	A	75	PHE	0	-0.031	-0.021	3.154	-0.651	0.126	7.297	-1.883	-6.191	-0.001
76	A	76	ASP	-1	-0.939	-0.963	3.928	-0.056	-0.779	0.021	0.857	-0.155	0.000
77	A	77	VAL	0	-0.023	-0.005	6.867	-0.147	-0.147	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.033	0.001	9.575	-0.276	-0.276	0.000	0.000	0.000	0.000
79	A	79	MET	0	0.021	0.016	11.446	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.024	0.006	12.707	-0.029	-0.029	0.000	0.000	0.000	0.000

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