FMO DATABASE

FMODB ID: LZZQ9

Calculation Name: 4NPX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NPX

Chain ID: A

ChEMBL ID:

UniProt ID: Q0PAX7

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

Total energy (hartree)

FMO2-HF: Electronic energy	-486209.927899
FMO2-HF: Nuclear repulsion	454096.09649
FMO2-HF: Total energy	-32113.831409
FMO2-MP2: Total energy	-32208.071274

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:8:PHE)

Summations of interaction energy for fragment #1(A:8:PHE)

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.
-4.969	-1.124	0.02	-1.92	-1.945	0

Interaction energy analysis for fragmet #1(A:8:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.023

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	10	LYS	1	0.821	0.890	3.060	-4.394	-0.977	0.011	-1.713	-1.715	0.001
4	A	11	THR	0	-0.020	-0.035	3.560	-1.032	-0.604	0.009	-0.207	-0.230	-0.001
5	A	12	PRO	0	0.017	-0.004	6.196	0.593	0.593	0.000	0.000	0.000	0.000
6	A	13	LYS	1	0.935	0.974	7.888	0.387	0.387	0.000	0.000	0.000	0.000
7	A	14	GLU	-1	-0.821	-0.878	8.057	0.118	0.118	0.000	0.000	0.000	0.000
8	A	15	LYS	1	0.953	0.972	5.561	-1.290	-1.290	0.000	0.000	0.000	0.000
9	A	16	PHE	0	0.025	0.014	8.601	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	17	ILE	0	0.008	0.010	11.965	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	18	GLU	-1	-0.811	-0.880	9.070	1.593	1.593	0.000	0.000	0.000	0.000
12	A	19	ILE	0	-0.049	-0.013	10.487	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	20	ILE	0	0.014	0.004	13.992	-0.056	-0.056	0.000	0.000	0.000	0.000
14	A	21	GLN	0	-0.072	-0.040	15.900	0.021	0.021	0.000	0.000	0.000	0.000
15	A	22	ASN	0	-0.099	-0.052	14.683	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.022	0.036	17.276	0.001	0.001	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.041	-0.029	19.177	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.007	-0.001	22.628	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.054	0.030	25.330	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.038	-0.011	20.979	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	28	LEU	0	-0.023	-0.011	19.336	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.895	-0.962	22.596	0.119	0.119	0.000	0.000	0.000	0.000
23	A	30	LYS	1	0.888	0.940	24.994	-0.135	-0.135	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.021	-0.003	19.961	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	32	PHE	0	-0.036	-0.026	19.697	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	33	GLU	-1	-0.960	-0.974	24.557	0.075	0.075	0.000	0.000	0.000	0.000
27	A	34	GLU	-1	-0.935	-0.959	25.748	0.046	0.046	0.000	0.000	0.000	0.000
28	A	35	PHE	0	-0.015	-0.008	21.723	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	36	PHE	0	-0.010	-0.024	24.525	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	37	ALA	0	0.005	0.009	28.012	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.895	-0.947	26.894	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	39	HIS	0	-0.011	-0.006	27.044	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.027	-0.022	28.911	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	41	ALA	0	-0.004	0.003	32.247	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	42	MET	0	-0.021	-0.013	26.451	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	43	VAL	0	-0.006	0.001	31.646	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.865	-0.928	33.987	0.003	0.003	0.000	0.000	0.000	0.000
38	A	45	LEU	0	-0.045	-0.027	34.210	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.015	0.005	31.963	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	47	GLU	-1	-0.894	-0.941	36.448	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	48	LYS	1	0.766	0.875	39.441	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	49	GLN	0	-0.084	-0.049	38.856	0.000	0.000	0.000	0.000	0.000	0.000
43	A	50	GLY	0	-0.057	-0.017	40.984	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	51	LEU	0	-0.059	-0.018	35.939	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.002	-0.042	37.199	0.004	0.004	0.000	0.000	0.000	0.000
46	A	53	GLU	-1	-0.755	-0.883	31.653	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	54	MET	0	-0.039	-0.014	33.271	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	55	ASP	-1	-0.811	-0.879	34.223	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	56	VAL	0	0.006	0.012	29.086	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	57	LYS	1	0.789	0.872	28.655	0.016	0.016	0.000	0.000	0.000	0.000
51	A	58	ASN	0	-0.006	-0.002	29.862	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	59	PHE	0	0.045	0.027	26.199	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	60	ILE	0	-0.010	-0.017	24.521	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.062	-0.032	25.803	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	62	GLU	-1	-0.970	-0.979	27.893	-0.086	-0.086	0.000	0.000	0.000	0.000
56	A	63	ASN	0	-0.080	-0.039	25.733	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	64	GLY	0	0.045	0.018	22.999	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	65	ASP	-1	-0.905	-0.952	20.032	-0.242	-0.242	0.000	0.000	0.000	0.000
59	A	66	PHE	0	-0.004	-0.005	19.289	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	67	ILE	0	-0.030	-0.005	20.193	0.005	0.005	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.872	-0.933	14.646	-0.304	-0.304	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.918	-0.953	15.085	-0.426	-0.426	0.000	0.000	0.000	0.000
63	A	70	ARG	1	0.886	0.911	15.584	0.121	0.121	0.000	0.000	0.000	0.000
64	A	71	GLN	0	-0.020	-0.002	15.549	0.017	0.017	0.000	0.000	0.000	0.000
65	A	72	ASN	0	-0.050	-0.039	10.740	0.000	0.000	0.000	0.000	0.000	0.000
66	A	73	ASP	-1	-0.820	-0.889	12.353	-0.190	-0.190	0.000	0.000	0.000	0.000
67	A	74	ILE	0	-0.014	-0.003	14.711	0.046	0.046	0.000	0.000	0.000	0.000
68	A	75	TYR	0	-0.023	-0.016	11.645	0.042	0.042	0.000	0.000	0.000	0.000
69	A	76	ILE	0	-0.026	-0.016	9.549	0.097	0.097	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.898	-0.932	12.023	0.072	0.072	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.023	0.002	15.783	0.036	0.036	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.029	0.009	12.855	0.037	0.037	0.000	0.000	0.000	0.000
73	A	80	ALA	0	-0.039	-0.028	13.278	0.060	0.060	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.895	0.945	14.322	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	82	ILE	0	0.001	0.005	16.615	0.006	0.006	0.000	0.000	0.000	0.000
76	A	83	LEU	0	-0.052	-0.028	11.496	0.031	0.031	0.000	0.000	0.000	0.000
77	A	84	GLY	0	-0.016	0.001	16.021	0.001	0.001	0.000	0.000	0.000	0.000
78	A	85	HIS	0	-0.038	-0.014	18.544	-0.044	-0.044	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.901	-0.945	19.895	0.087	0.087	0.000	0.000	0.000	0.000
80	A	87	GLY	0	0.007	0.001	22.477	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:PHE)