FMO DATABASE

FMODB ID: ZVN1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-548460.047964
FMO2-HF: Nuclear repulsion	516223.742044
FMO2-HF: Total energy	-32236.30592
FMO2-MP2: Total energy	-32329.115341

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.
-11.143	-4.121	9.093	-4.208	-11.905	-0.021

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 : 0.011 / q_NPA : 0.006

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	-0.025	-0.004	2.702	-2.601	1.019	0.173	-1.818	-1.975	0.004
4	A	4	ASP	-1	-0.781	-0.858	3.174	-5.722	-4.448	0.125	-0.585	-0.814	-0.005
5	A	5	THR	0	0.018	-0.029	5.560	0.686	0.686	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.076	-0.040	7.064	0.478	0.478	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.014	0.002	7.564	-0.150	-0.150	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.919	0.973	6.366	0.700	0.700	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.007	-0.009	9.594	0.244	0.244	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.874	0.932	12.484	1.038	1.038	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.001	0.008	11.309	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.019	0.007	13.436	0.098	0.098	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.108	-0.055	15.794	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.012	0.004	17.541	0.047	0.047	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.869	-0.931	15.825	-0.216	-0.216	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.846	0.899	15.792	0.252	0.252	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.008	0.009	21.224	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.014	0.013	19.316	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.880	0.918	20.873	0.224	0.224	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.035	-0.002	18.806	0.033	0.033	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.002	-0.002	20.926	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.759	-0.865	23.001	-0.236	-0.236	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.032	0.012	16.810	0.018	0.018	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.011	-0.004	20.635	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.005	0.006	22.233	0.026	0.026	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.023	0.009	21.637	0.019	0.019	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.009	-0.007	19.956	0.014	0.014	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.002	0.006	21.538	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.010	-0.017	24.822	0.015	0.015	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.031	0.019	20.820	0.019	0.019	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.017	-0.014	21.714	0.022	0.022	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.882	0.941	23.393	0.110	0.110	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.932	0.988	23.630	0.049	0.049	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.025	0.001	19.648	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.024	0.031	23.518	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.040	-0.018	18.225	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.988	0.989	21.509	0.126	0.126	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.011	0.006	17.452	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.032	0.030	20.962	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	LYS	1	1.040	1.004	21.130	0.256	0.256	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.043	0.027	21.325	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.021	0.016	17.073	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.020	0.015	15.937	-0.068	-0.068	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.060	-0.043	16.579	-0.070	-0.070	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.004	-0.004	16.274	-0.056	-0.056	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.023	0.011	12.640	-0.068	-0.068	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.002	-0.010	12.178	-0.159	-0.159	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.070	-0.035	14.146	-0.062	-0.062	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.050	-0.004	9.035	0.119	0.119	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.042	0.004	11.322	-0.036	-0.036	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.013	-0.017	12.873	0.106	0.106	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.056	0.040	8.254	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.033	-0.032	9.019	0.203	0.203	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.755	-0.841	10.031	-0.381	-0.381	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.043	-0.020	8.285	0.082	0.082	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.012	-0.004	12.212	0.049	0.049	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.826	0.868	14.452	0.354	0.354	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.010	0.017	7.969	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.059	0.024	11.323	0.024	0.024	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.050	-0.022	13.938	0.014	0.014	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.002	0.003	13.220	0.030	0.030	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.039	0.021	11.676	0.010	0.010	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.801	0.897	13.546	0.068	0.068	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.077	-0.048	17.252	0.018	0.018	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.029	-0.010	14.169	0.005	0.005	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.003	0.026	16.935	0.009	0.009	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.046	-0.020	11.751	0.014	0.014	0.000	0.000	0.000	0.000
68	A	68	SER	0	0.009	-0.001	9.913	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.827	-0.934	9.320	-0.123	-0.123	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.011	0.014	5.756	-0.279	-0.279	0.000	0.000	0.000	0.000
71	A	71	TRP	0	0.077	0.042	4.645	-0.760	-0.690	-0.001	-0.004	-0.065	0.000
72	A	72	LEU	0	-0.019	-0.005	6.051	-0.424	-0.424	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.029	0.005	3.705	-0.235	-0.022	0.002	-0.049	-0.165	0.000
74	A	74	GLY	0	0.022	0.020	2.586	-3.470	-2.736	1.837	-0.891	-1.680	-0.011
75	A	75	PHE	0	-0.032	-0.020	2.761	-1.515	0.395	6.903	-1.818	-6.994	-0.009
76	A	76	ASP	-1	-0.934	-0.963	3.382	0.438	-0.361	0.054	0.957	-0.212	0.000
77	A	77	VAL	0	-0.020	-0.007	6.768	-0.106	-0.106	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.024	-0.004	9.083	-0.254	-0.254	0.000	0.000	0.000	0.000
79	A	79	MET	0	0.035	0.044	11.146	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.029	0.017	12.152	-0.050	-0.050	0.000	0.000	0.000	0.000

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