FMO DATABASE

FMODB ID: MVMRZ

Calculation Name: 5N76-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N76

Chain ID: A

ChEMBL ID:

UniProt ID: P72320

Base Structure: X-ray

Registration Date: 2023-06-21

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-305793.62886
FMO2-HF: Nuclear repulsion	282705.886906
FMO2-HF: Total energy	-23087.741955
FMO2-MP2: Total energy	-23154.697379

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:CYS)

Summations of interaction energy for fragment #1(A:2:CYS)

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.
-6.315	-3.02	0.987	-1.638	-2.647	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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	4	ALA	0	0.009	-0.006	2.737	-1.141	1.618	0.970	-1.532	-2.198	-0.006
4	A	5	LYS	1	0.874	0.931	4.276	0.739	0.791	0.000	-0.020	-0.033	0.000
5	A	6	VAL	0	0.043	0.035	8.012	0.285	0.285	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.066	-0.034	10.630	0.014	0.014	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.055	0.038	13.562	0.063	0.063	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.051	-0.047	17.053	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.955	1.003	20.694	0.232	0.232	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.054	0.020	23.940	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.887	-0.944	26.699	-0.128	-0.128	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.003	0.006	25.727	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.013	-0.014	24.249	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.811	0.894	17.234	0.199	0.199	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.015	-0.016	17.452	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.818	-0.889	13.543	-0.328	-0.328	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.015	0.020	12.035	0.029	0.029	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.005	-0.005	9.692	-0.082	-0.082	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.876	-0.947	8.428	-1.880	-1.880	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.028	-0.009	6.746	0.177	0.177	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.044	-0.015	6.538	-1.104	-1.104	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.915	-0.969	7.448	-0.668	-0.668	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.027	-0.020	8.696	0.043	0.043	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.837	0.916	11.208	0.434	0.434	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.022	0.012	14.414	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.819	-0.894	17.466	-0.220	-0.220	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.032	-0.018	20.733	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.031	0.037	23.806	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.009	-0.006	21.350	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.026	0.000	14.757	0.015	0.015	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.779	0.875	16.124	0.322	0.322	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.006	-0.016	11.333	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.042	0.033	11.777	0.063	0.063	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.018	-0.029	11.038	-0.276	-0.276	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.017	-0.023	7.898	0.061	0.061	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.096	-0.040	11.914	0.099	0.099	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.952	-0.959	14.995	-0.607	-0.607	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.829	-0.884	15.955	-0.695	-0.695	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.859	-0.939	15.720	-0.563	-0.563	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.082	-0.039	15.515	0.140	0.140	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.003	-0.010	16.920	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.046	-0.030	16.082	0.031	0.031	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.025	0.002	20.583	0.017	0.017	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.025	0.010	23.538	0.002	0.002	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.056	-0.011	19.151	0.015	0.015	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.038	0.016	18.413	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.005	-0.014	12.126	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.002	0.010	14.901	0.038	0.038	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.819	0.884	11.693	-0.458	-0.458	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.058	0.025	7.041	-0.105	-0.105	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.833	-0.884	8.159	1.263	1.263	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.030	0.001	4.244	-0.250	0.010	0.019	-0.051	-0.228	0.000
53	A	54	ARG	1	0.905	0.957	5.871	-0.763	-0.626	-0.001	-0.004	-0.131	0.000
54	A	55	SER	0	-0.056	-0.047	7.745	-0.231	-0.231	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.052	0.037	4.163	-0.537	-0.443	0.000	-0.029	-0.067	0.000
56	A	57	VAL	0	-0.058	-0.018	4.966	-0.745	-0.752	-0.001	-0.002	0.010	0.000
57	A	58	ILE	0	0.016	0.003	5.846	0.382	0.382	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.006	-0.005	9.370	-0.093	-0.093	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.010	0.000	13.121	0.057	0.057	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.040	-0.018	15.757	0.023	0.023	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.899	-0.954	19.357	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.985	-0.993	22.187	-0.039	-0.039	0.000	0.000	0.000	0.000

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