FMO DATABASE

FMODB ID: LZLQ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-306280.4808
FMO2-HF: Nuclear repulsion	283193.22683
FMO2-HF: Total energy	-23087.253969
FMO2-MP2: Total energy	-23154.191283

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.
-5.26	-3.285	1.958	-0.629	-3.304	-0.012

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 : -0.025 / q_NPA : -0.024

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	0.029	0.006	2.597	-0.812	0.399	1.908	-0.464	-2.656	-0.012
4	A	5	LYS	1	0.870	0.943	4.005	0.688	0.764	0.004	-0.028	-0.051	0.000
5	A	6	VAL	0	0.026	0.019	7.722	0.161	0.161	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.039	-0.019	10.391	0.087	0.087	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.022	0.015	13.396	0.018	0.018	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.000	-0.010	16.844	0.017	0.017	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.932	0.967	20.303	0.246	0.246	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.041	0.009	23.372	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.903	-0.956	26.443	-0.111	-0.111	0.000	0.000	0.000	0.000
12	A	13	GLY	0	-0.007	0.007	25.035	0.011	0.011	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.017	0.010	23.829	0.005	0.005	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.946	0.980	17.030	0.085	0.085	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.024	-0.021	16.549	0.003	0.003	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.898	-0.965	12.993	-0.192	-0.192	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.021	0.025	11.773	0.044	0.044	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.002	-0.008	9.317	-0.136	-0.136	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.878	-0.947	8.136	-1.102	-1.102	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.043	-0.024	6.681	0.142	0.142	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.045	-0.011	6.349	-1.105	-1.105	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.935	-0.974	7.333	-1.591	-1.591	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.021	-0.010	8.842	0.196	0.196	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.958	0.990	11.420	0.594	0.594	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.003	0.002	14.466	0.040	0.040	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.944	-0.989	17.497	-0.464	-0.464	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.032	-0.019	20.558	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.034	0.026	23.676	0.006	0.006	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.004	0.010	21.232	0.015	0.015	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.027	-0.003	14.726	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.925	0.970	16.525	0.470	0.470	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.013	-0.016	11.108	-0.089	-0.089	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.061	0.034	12.210	0.154	0.154	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.018	-0.014	10.901	-0.290	-0.290	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.015	-0.026	7.324	0.068	0.068	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.069	-0.034	11.573	0.146	0.146	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.941	-0.954	14.610	-0.516	-0.516	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.947	-0.954	15.954	-0.444	-0.444	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.951	-1.002	15.562	-0.702	-0.702	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.010	0.013	15.263	0.116	0.116	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.013	-0.002	16.958	-0.050	-0.050	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.080	-0.046	15.816	0.064	0.064	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.007	-0.013	20.355	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.034	0.017	23.348	0.012	0.012	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.044	-0.005	18.458	0.018	0.018	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.040	0.014	18.424	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.004	-0.013	12.154	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.026	0.002	14.900	0.038	0.038	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.910	0.939	12.254	-0.237	-0.237	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.054	0.032	7.287	-0.096	-0.096	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.887	-0.951	8.297	1.093	1.093	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.027	-0.005	4.148	-0.243	0.061	0.035	-0.061	-0.279	0.000
53	A	54	ARG	1	0.894	0.960	5.233	-0.340	-0.162	-0.001	-0.012	-0.165	0.000
54	A	55	SER	0	-0.045	-0.028	7.011	0.282	0.282	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.082	0.060	4.067	-0.322	-0.129	0.013	-0.063	-0.142	0.000
56	A	57	VAL	0	-0.046	-0.016	4.773	-1.182	-1.169	-0.001	-0.001	-0.011	0.000
57	A	58	ILE	0	0.022	0.009	5.935	0.302	0.302	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.059	-0.030	9.111	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.018	-0.012	12.906	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.035	-0.019	15.558	0.047	0.047	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.914	-0.957	19.096	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.979	-0.988	22.148	-0.197	-0.197	0.000	0.000	0.000	0.000

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