FMO DATABASE

FMODB ID: 39YYL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-282027.038605
FMO2-HF: Nuclear repulsion	255337.406437
FMO2-HF: Total energy	-26689.632168
FMO2-MP2: Total energy	-26767.136508

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.
-21.226	-16.531	0.167	-1.631	-3.231	-0.001

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 : 0.995 / q_NPA : 0.994

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	-0.770	-0.879	3.532	-36.356	-33.394	0.021	-1.238	-1.745	0.001
4	A	53	LYS	1	0.895	0.943	3.190	34.378	35.106	0.022	-0.131	-0.619	-0.001
5	A	54	ILE	0	0.008	0.028	2.968	-3.784	-2.779	0.124	-0.262	-0.867	-0.001
6	A	55	LYS	1	0.984	0.956	5.976	29.755	29.755	0.000	0.000	0.000	0.000
7	A	56	HIS	0	-0.008	-0.013	8.274	0.241	0.241	0.000	0.000	0.000	0.000
8	A	57	VAL	0	0.006	-0.019	6.423	-1.587	-1.587	0.000	0.000	0.000	0.000
9	A	58	GLN	0	-0.151	-0.031	9.312	-1.088	-1.088	0.000	0.000	0.000	0.000
10	A	59	ASN	0	0.006	-0.002	10.708	0.100	0.100	0.000	0.000	0.000	0.000
11	A	60	GLN	0	0.018	0.019	11.826	-0.535	-0.535	0.000	0.000	0.000	0.000
12	A	61	VAL	0	-0.017	-0.029	12.035	1.202	1.202	0.000	0.000	0.000	0.000
13	A	62	ASP	-1	-0.823	-0.915	14.725	-18.755	-18.755	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.931	-0.943	16.749	-15.226	-15.226	0.000	0.000	0.000	0.000
15	A	64	VAL	0	-0.007	-0.007	17.380	0.897	0.897	0.000	0.000	0.000	0.000
16	A	65	ILE	0	-0.068	-0.041	17.444	0.774	0.774	0.000	0.000	0.000	0.000
17	A	66	ASP	-1	-0.898	-0.940	20.581	-12.093	-12.093	0.000	0.000	0.000	0.000
18	A	67	VAL	0	0.010	0.006	22.412	0.723	0.723	0.000	0.000	0.000	0.000
19	A	68	MET	0	-0.051	-0.039	22.704	0.720	0.720	0.000	0.000	0.000	0.000
20	A	69	GLN	0	-0.004	0.000	24.064	0.346	0.346	0.000	0.000	0.000	0.000
21	A	70	GLU	-1	-0.858	-0.924	26.449	-9.922	-9.922	0.000	0.000	0.000	0.000
22	A	71	ASN	0	-0.048	-0.035	26.707	0.702	0.702	0.000	0.000	0.000	0.000
23	A	72	ILE	0	-0.034	-0.015	27.971	0.378	0.378	0.000	0.000	0.000	0.000
24	A	73	THR	0	0.045	0.022	30.690	0.337	0.337	0.000	0.000	0.000	0.000
25	A	74	LYS	1	0.923	0.977	29.543	10.674	10.674	0.000	0.000	0.000	0.000
26	A	75	VAL	0	-0.070	-0.041	32.174	0.314	0.314	0.000	0.000	0.000	0.000
27	A	76	ILE	0	0.010	0.014	34.031	0.253	0.253	0.000	0.000	0.000	0.000
28	A	77	GLU	-1	-0.872	-0.926	36.658	-8.195	-8.195	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.883	0.917	37.213	8.669	8.669	0.000	0.000	0.000	0.000
30	A	79	GLY	0	-0.019	-0.013	38.737	0.194	0.194	0.000	0.000	0.000	0.000
31	A	80	GLU	-1	-0.794	-0.884	40.455	-7.422	-7.422	0.000	0.000	0.000	0.000
32	A	81	ARG	1	0.786	0.877	42.145	7.487	7.487	0.000	0.000	0.000	0.000
33	A	82	LEU	0	-0.067	-0.040	40.771	0.164	0.164	0.000	0.000	0.000	0.000
34	A	83	ASP	-1	-0.852	-0.923	44.417	-6.990	-6.990	0.000	0.000	0.000	0.000
35	A	84	GLU	-1	-0.862	-0.902	46.480	-6.448	-6.448	0.000	0.000	0.000	0.000
36	A	85	LEU	0	-0.091	-0.058	45.931	0.179	0.179	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.062	-0.018	48.142	0.077	0.077	0.000	0.000	0.000	0.000
38	A	87	ASP	-1	-0.818	-0.890	50.087	-6.046	-6.046	0.000	0.000	0.000	0.000
39	A	88	LYS	1	0.816	0.889	50.402	6.442	6.442	0.000	0.000	0.000	0.000
40	A	89	SER	0	-0.095	-0.070	51.766	0.135	0.135	0.000	0.000	0.000	0.000
41	A	90	GLU	-1	-0.840	-0.915	54.193	-5.772	-5.772	0.000	0.000	0.000	0.000
42	A	91	SER	0	0.051	0.030	55.911	0.147	0.147	0.000	0.000	0.000	0.000
43	A	92	LEU	0	-0.043	0.006	56.878	0.136	0.136	0.000	0.000	0.000	0.000
44	A	93	SER	0	0.062	0.034	57.583	0.116	0.116	0.000	0.000	0.000	0.000
45	A	94	ASP	-1	-0.868	-0.919	59.549	-5.181	-5.181	0.000	0.000	0.000	0.000
46	A	95	ASN	0	-0.107	-0.096	61.884	0.201	0.201	0.000	0.000	0.000	0.000
47	A	96	ALA	0	-0.035	-0.009	61.943	0.106	0.106	0.000	0.000	0.000	0.000
48	A	97	THR	0	-0.028	-0.021	62.758	0.107	0.107	0.000	0.000	0.000	0.000
49	A	98	ALA	0	-0.008	-0.007	65.331	0.108	0.108	0.000	0.000	0.000	0.000
50	A	99	PHE	0	0.025	0.015	66.876	0.108	0.108	0.000	0.000	0.000	0.000
51	A	100	SER	0	0.053	0.022	67.315	0.116	0.116	0.000	0.000	0.000	0.000
52	A	101	ASN	0	-0.013	-0.021	68.765	0.103	0.103	0.000	0.000	0.000	0.000
53	A	102	ARG	1	0.940	0.966	71.483	4.426	4.426	0.000	0.000	0.000	0.000
54	A	103	SER	0	0.022	0.016	71.499	0.075	0.075	0.000	0.000	0.000	0.000
55	A	104	LYS	1	0.837	0.919	69.565	4.654	4.654	0.000	0.000	0.000	0.000
56	A	105	GLN	0	-0.041	-0.019	75.319	0.060	0.060	0.000	0.000	0.000	0.000
57	A	106	LEU	0	0.084	0.059	76.756	0.061	0.061	0.000	0.000	0.000	0.000
58	A	107	ARG	1	0.996	0.998	76.744	4.184	4.184	0.000	0.000	0.000	0.000
59	A	108	ARG	1	0.881	0.920	76.056	4.203	4.203	0.000	0.000	0.000	0.000
60	A	109	GLN	0	0.006	0.009	81.325	0.007	0.007	0.000	0.000	0.000	0.000
61	A	110	MET	0	-0.039	-0.024	81.794	0.052	0.052	0.000	0.000	0.000	0.000
62	A	111	TRP	0	-0.084	-0.012	83.932	0.041	0.041	0.000	0.000	0.000	0.000
63	A	112	TRP	0	0.016	0.011	85.597	0.022	0.022	0.000	0.000	0.000	0.000

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