FMO DATABASE

FMODB ID: 399KL

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	OptHSide
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	-483854.936635
FMO2-HF: Nuclear repulsion	451741.45109
FMO2-HF: Total energy	-32113.485546
FMO2-MP2: Total energy	-32207.721766

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.
-8.364	-3.552	0.741	-2.638	-2.916	-0.003

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 : -0.011 / q_NPA : -0.017

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	0.818	0.877	2.402	-5.131	-1.869	0.579	-1.738	-2.104	0.006
4	A	11	THR	0	0.006	-0.014	2.920	-4.114	-2.564	0.162	-0.900	-0.812	-0.009
5	A	12	PRO	0	0.046	0.008	5.672	0.706	0.706	0.000	0.000	0.000	0.000
6	A	13	LYS	1	0.987	1.008	7.382	0.381	0.381	0.000	0.000	0.000	0.000
7	A	14	GLU	-1	-0.821	-0.887	7.206	0.229	0.229	0.000	0.000	0.000	0.000
8	A	15	LYS	1	0.960	0.979	5.089	-1.046	-1.046	0.000	0.000	0.000	0.000
9	A	16	PHE	0	0.015	0.005	8.001	-0.050	-0.050	0.000	0.000	0.000	0.000
10	A	17	ILE	0	0.017	0.006	11.417	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	18	GLU	-1	-0.833	-0.879	8.926	1.836	1.836	0.000	0.000	0.000	0.000
12	A	19	ILE	0	-0.064	-0.019	10.056	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	20	ILE	0	0.038	0.020	13.491	-0.051	-0.051	0.000	0.000	0.000	0.000
14	A	21	GLN	0	-0.068	-0.038	15.314	0.031	0.031	0.000	0.000	0.000	0.000
15	A	22	ASN	0	-0.110	-0.057	14.533	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.006	0.030	17.307	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.019	-0.016	18.935	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.012	-0.010	22.366	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.030	0.024	25.285	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.003	0.001	20.624	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	28	LEU	0	-0.001	-0.009	18.876	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.926	-0.966	22.326	0.114	0.114	0.000	0.000	0.000	0.000
23	A	30	LYS	1	0.870	0.932	24.416	-0.132	-0.132	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.013	-0.011	19.504	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	32	PHE	0	-0.046	-0.032	19.459	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	33	GLU	-1	-0.966	-0.970	24.263	0.071	0.071	0.000	0.000	0.000	0.000
27	A	34	GLU	-1	-0.936	-0.965	25.448	0.038	0.038	0.000	0.000	0.000	0.000
28	A	35	PHE	0	-0.021	-0.006	21.428	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	36	PHE	0	-0.014	-0.029	24.446	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	37	ALA	0	0.004	0.013	27.627	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.868	-0.939	26.876	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	39	HIS	0	-0.050	-0.022	26.734	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.019	-0.017	28.775	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	41	ALA	0	-0.002	0.005	32.056	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	42	MET	0	-0.017	-0.013	26.361	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	43	VAL	0	0.010	0.008	31.644	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.877	-0.930	33.943	0.000	0.000	0.000	0.000	0.000	0.000
38	A	45	LEU	0	-0.043	-0.028	34.167	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.006	0.002	31.819	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	47	GLU	-1	-0.883	-0.941	36.353	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	48	LYS	1	0.759	0.892	39.299	0.003	0.003	0.000	0.000	0.000	0.000
42	A	49	GLN	0	-0.089	-0.057	38.691	0.000	0.000	0.000	0.000	0.000	0.000
43	A	50	GLY	0	-0.056	-0.013	40.816	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	51	LEU	0	-0.046	-0.014	35.590	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.030	-0.052	37.313	0.004	0.004	0.000	0.000	0.000	0.000
46	A	53	GLU	-1	-0.757	-0.878	31.215	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	54	MET	0	-0.066	-0.037	33.190	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	55	ASP	-1	-0.819	-0.885	34.050	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	56	VAL	0	-0.002	0.011	29.081	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	57	LYS	1	0.848	0.893	28.182	0.022	0.022	0.000	0.000	0.000	0.000
51	A	58	ASN	0	0.024	0.003	29.500	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	59	PHE	0	0.032	0.035	25.656	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	60	ILE	0	-0.035	-0.033	24.161	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.075	-0.033	25.727	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	62	GLU	-1	-0.966	-0.971	28.021	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	63	ASN	0	-0.085	-0.034	25.582	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	64	GLY	0	0.030	0.002	22.808	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	65	ASP	-1	-0.875	-0.936	19.943	-0.262	-0.262	0.000	0.000	0.000	0.000
59	A	66	PHE	0	-0.026	-0.015	19.448	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	67	ILE	0	-0.011	-0.011	19.986	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.959	-0.972	14.656	-0.399	-0.399	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.908	-0.956	15.079	-0.480	-0.480	0.000	0.000	0.000	0.000
63	A	70	ARG	1	0.905	0.926	15.420	0.150	0.150	0.000	0.000	0.000	0.000
64	A	71	GLN	0	-0.040	-0.014	15.451	0.011	0.011	0.000	0.000	0.000	0.000
65	A	72	ASN	0	-0.028	-0.029	10.674	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	73	ASP	-1	-0.828	-0.887	12.185	-0.258	-0.258	0.000	0.000	0.000	0.000
67	A	74	ILE	0	-0.022	-0.008	14.453	0.045	0.045	0.000	0.000	0.000	0.000
68	A	75	TYR	0	-0.029	-0.023	11.219	0.052	0.052	0.000	0.000	0.000	0.000
69	A	76	ILE	0	-0.036	-0.025	9.437	0.085	0.085	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.873	-0.903	11.893	0.065	0.065	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.042	0.010	15.458	0.040	0.040	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.028	0.006	12.563	0.044	0.044	0.000	0.000	0.000	0.000
73	A	80	ALA	0	-0.047	-0.023	13.073	0.062	0.062	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.882	0.924	14.145	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	82	ILE	0	0.006	0.011	16.090	0.011	0.011	0.000	0.000	0.000	0.000
76	A	83	LEU	0	-0.059	-0.045	11.035	0.035	0.035	0.000	0.000	0.000	0.000
77	A	84	GLY	0	-0.010	0.008	15.594	0.005	0.005	0.000	0.000	0.000	0.000
78	A	85	HIS	0	-0.046	-0.028	18.088	-0.044	-0.044	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.920	-0.940	19.491	0.078	0.078	0.000	0.000	0.000	0.000
80	A	87	GLY	0	0.031	0.018	22.077	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)