FMO DATABASE

FMODB ID: JLJJ9

Calculation Name: 2NPS-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2NPS

Chain ID: A

ChEMBL ID:
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UniProt ID: G3V7P1

Base Structure: X-ray

Registration Date: 2023-09-20

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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-282585.070879
FMO2-HF: Nuclear repulsion	255896.296261
FMO2-HF: Total energy	-26688.774618
FMO2-MP2: Total energy	-26766.398601

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:50:ARG)

Summations of interaction energy for fragment #1(A:50:ARG)

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.
-25.462	-22.494	0.387	0.097	-3.451	-0.007

Interaction energy analysis for fragmet #1(A:50:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.969

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	52	ASP	-1	-0.841	-0.928	2.976	-38.528	-37.067	0.188	0.374	-2.023	-0.006
4	A	53	LYS	1	0.902	0.939	3.276	34.316	34.904	0.010	-0.084	-0.513	0.000
5	A	54	ILE	0	-0.017	0.028	2.905	-3.006	-2.087	0.189	-0.193	-0.915	-0.001
6	A	55	LYS	1	1.126	1.039	5.800	26.055	26.055	0.000	0.000	0.000	0.000
7	A	56	HIS	0	-0.024	-0.034	7.922	0.793	0.793	0.000	0.000	0.000	0.000
8	A	57	VAL	0	0.016	-0.009	6.938	-1.764	-1.764	0.000	0.000	0.000	0.000
9	A	58	GLN	0	-0.110	-0.001	9.317	-0.786	-0.786	0.000	0.000	0.000	0.000
10	A	59	ASN	0	-0.040	-0.024	10.748	1.014	1.014	0.000	0.000	0.000	0.000
11	A	60	GLN	0	0.062	0.033	11.570	-0.824	-0.824	0.000	0.000	0.000	0.000
12	A	61	VAL	0	-0.024	-0.025	12.042	1.130	1.130	0.000	0.000	0.000	0.000
13	A	62	ASP	-1	-0.873	-0.946	14.765	-17.977	-17.977	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.932	-0.948	16.779	-15.387	-15.387	0.000	0.000	0.000	0.000
15	A	64	VAL	0	-0.013	-0.007	17.075	0.866	0.866	0.000	0.000	0.000	0.000
16	A	65	ILE	0	-0.087	-0.050	17.389	0.741	0.741	0.000	0.000	0.000	0.000
17	A	66	ASP	-1	-0.884	-0.936	20.629	-12.097	-12.097	0.000	0.000	0.000	0.000
18	A	67	VAL	0	-0.006	0.003	22.015	0.682	0.682	0.000	0.000	0.000	0.000
19	A	68	MET	0	-0.060	-0.046	22.672	0.714	0.714	0.000	0.000	0.000	0.000
20	A	69	GLN	0	0.025	0.009	23.832	0.388	0.388	0.000	0.000	0.000	0.000
21	A	70	GLU	-1	-0.885	-0.933	26.499	-10.153	-10.153	0.000	0.000	0.000	0.000
22	A	71	ASN	0	-0.052	-0.037	27.299	0.610	0.610	0.000	0.000	0.000	0.000
23	A	72	ILE	0	-0.015	-0.012	28.094	0.389	0.389	0.000	0.000	0.000	0.000
24	A	73	THR	0	0.033	0.022	30.741	0.377	0.377	0.000	0.000	0.000	0.000
25	A	74	LYS	1	0.951	0.989	30.780	10.281	10.281	0.000	0.000	0.000	0.000
26	A	75	VAL	0	-0.068	-0.038	32.137	0.317	0.317	0.000	0.000	0.000	0.000
27	A	76	ILE	0	0.008	0.013	34.021	0.249	0.249	0.000	0.000	0.000	0.000
28	A	77	GLU	-1	-0.864	-0.929	36.712	-8.230	-8.230	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.893	0.927	36.849	8.612	8.612	0.000	0.000	0.000	0.000
30	A	79	GLY	0	-0.023	-0.016	38.782	0.189	0.189	0.000	0.000	0.000	0.000
31	A	80	GLU	-1	-0.808	-0.890	40.506	-7.340	-7.340	0.000	0.000	0.000	0.000
32	A	81	ARG	1	0.781	0.879	41.839	7.467	7.467	0.000	0.000	0.000	0.000
33	A	82	LEU	0	-0.082	-0.049	40.867	0.156	0.156	0.000	0.000	0.000	0.000
34	A	83	ASP	-1	-0.862	-0.931	44.574	-6.874	-6.874	0.000	0.000	0.000	0.000
35	A	84	GLU	-1	-0.911	-0.935	46.518	-6.517	-6.517	0.000	0.000	0.000	0.000
36	A	85	LEU	0	-0.113	-0.066	45.810	0.178	0.178	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.064	-0.023	48.122	0.086	0.086	0.000	0.000	0.000	0.000
38	A	87	ASP	-1	-0.781	-0.878	50.084	-6.071	-6.071	0.000	0.000	0.000	0.000
39	A	88	LYS	1	0.896	0.936	51.547	6.299	6.299	0.000	0.000	0.000	0.000
40	A	89	SER	0	-0.113	-0.061	52.006	0.140	0.140	0.000	0.000	0.000	0.000
41	A	90	GLU	-1	-0.824	-0.925	53.896	-5.777	-5.777	0.000	0.000	0.000	0.000
42	A	91	SER	0	0.041	0.030	55.910	0.136	0.136	0.000	0.000	0.000	0.000
43	A	92	LEU	0	-0.075	-0.013	56.823	0.130	0.130	0.000	0.000	0.000	0.000
44	A	93	SER	0	0.045	0.024	57.477	0.136	0.136	0.000	0.000	0.000	0.000
45	A	94	ASP	-1	-0.860	-0.918	59.515	-5.206	-5.206	0.000	0.000	0.000	0.000
46	A	95	ASN	0	-0.062	-0.064	61.852	0.191	0.191	0.000	0.000	0.000	0.000
47	A	96	ALA	0	-0.044	-0.014	61.872	0.106	0.106	0.000	0.000	0.000	0.000
48	A	97	THR	0	-0.018	-0.013	62.735	0.108	0.108	0.000	0.000	0.000	0.000
49	A	98	ALA	0	-0.010	-0.008	65.298	0.107	0.107	0.000	0.000	0.000	0.000
50	A	99	PHE	0	0.011	0.009	66.505	0.112	0.112	0.000	0.000	0.000	0.000
51	A	100	SER	0	0.036	0.011	67.276	0.112	0.112	0.000	0.000	0.000	0.000
52	A	101	ASN	0	-0.031	-0.035	68.519	0.102	0.102	0.000	0.000	0.000	0.000
53	A	102	ARG	1	0.926	0.959	71.440	4.442	4.442	0.000	0.000	0.000	0.000
54	A	103	SER	0	0.032	0.026	71.499	0.077	0.077	0.000	0.000	0.000	0.000
55	A	104	LYS	1	0.863	0.941	69.870	4.630	4.630	0.000	0.000	0.000	0.000
56	A	105	GLN	0	-0.027	-0.016	75.256	0.075	0.075	0.000	0.000	0.000	0.000
57	A	106	LEU	0	0.086	0.058	76.818	0.061	0.061	0.000	0.000	0.000	0.000
58	A	107	ARG	1	0.992	1.002	76.591	4.184	4.184	0.000	0.000	0.000	0.000
59	A	108	ARG	1	0.887	0.918	75.931	4.196	4.196	0.000	0.000	0.000	0.000
60	A	109	GLN	0	0.021	0.016	81.190	0.001	0.001	0.000	0.000	0.000	0.000
61	A	110	MET	0	-0.044	-0.026	81.490	0.053	0.053	0.000	0.000	0.000	0.000
62	A	111	TRP	0	-0.084	-0.008	83.854	0.041	0.041	0.000	0.000	0.000	0.000
63	A	112	TRP	0	0.008	0.003	85.459	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:50:ARG)