FMO DATABASE

FMODB ID: LZ889

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

Total energy (hartree)

FMO2-HF: Electronic energy	-280938.18098
FMO2-HF: Nuclear repulsion	254248.022324
FMO2-HF: Total energy	-26690.158656
FMO2-MP2: Total energy	-26767.540677

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.
-17.449	-13.229	0.414	-1.432	-3.203	0

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 : 1.012 / q_NPA : 0.999

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	-0.765	-0.874	3.670	-34.272	-32.073	0.013	-0.928	-1.284	0.002
4	A	53	LYS	1	0.887	0.926	3.134	33.467	34.206	0.036	-0.145	-0.631	-0.001
5	A	54	ILE	0	0.009	0.033	2.690	-4.778	-3.496	0.365	-0.359	-1.288	-0.001
6	A	55	LYS	1	0.897	0.928	5.666	30.639	30.639	0.000	0.000	0.000	0.000
7	A	56	HIS	0	-0.052	-0.033	8.019	0.015	0.015	0.000	0.000	0.000	0.000
8	A	57	VAL	0	0.021	0.010	7.022	-0.725	-0.725	0.000	0.000	0.000	0.000
9	A	58	GLN	0	-0.069	-0.032	9.472	-0.131	-0.131	0.000	0.000	0.000	0.000
10	A	59	ASN	0	0.041	0.010	11.139	0.209	0.209	0.000	0.000	0.000	0.000
11	A	60	GLN	0	0.014	0.024	12.261	-0.291	-0.291	0.000	0.000	0.000	0.000
12	A	61	VAL	0	-0.009	-0.010	12.205	1.047	1.047	0.000	0.000	0.000	0.000
13	A	62	ASP	-1	-0.831	-0.926	14.773	-18.366	-18.366	0.000	0.000	0.000	0.000
14	A	63	GLU	-1	-0.956	-0.965	17.105	-15.260	-15.260	0.000	0.000	0.000	0.000
15	A	64	VAL	0	-0.013	-0.010	17.663	0.880	0.880	0.000	0.000	0.000	0.000
16	A	65	ILE	0	-0.037	-0.017	17.606	0.769	0.769	0.000	0.000	0.000	0.000
17	A	66	ASP	-1	-0.919	-0.947	20.781	-11.925	-11.925	0.000	0.000	0.000	0.000
18	A	67	VAL	0	0.027	0.008	22.726	0.712	0.712	0.000	0.000	0.000	0.000
19	A	68	MET	0	-0.042	-0.022	22.900	0.706	0.706	0.000	0.000	0.000	0.000
20	A	69	GLN	0	-0.039	-0.020	24.386	0.428	0.428	0.000	0.000	0.000	0.000
21	A	70	GLU	-1	-0.809	-0.902	26.628	-9.595	-9.595	0.000	0.000	0.000	0.000
22	A	71	ASN	0	-0.080	-0.051	26.699	0.678	0.678	0.000	0.000	0.000	0.000
23	A	72	ILE	0	-0.020	-0.012	28.357	0.358	0.358	0.000	0.000	0.000	0.000
24	A	73	THR	0	0.003	-0.001	30.810	0.316	0.316	0.000	0.000	0.000	0.000
25	A	74	LYS	1	0.935	0.972	29.448	10.683	10.683	0.000	0.000	0.000	0.000
26	A	75	VAL	0	-0.079	-0.041	32.248	0.298	0.298	0.000	0.000	0.000	0.000
27	A	76	ILE	0	-0.003	0.002	34.078	0.257	0.257	0.000	0.000	0.000	0.000
28	A	77	GLU	-1	-0.897	-0.937	36.820	-8.133	-8.133	0.000	0.000	0.000	0.000
29	A	78	ARG	1	0.914	0.941	37.152	8.656	8.656	0.000	0.000	0.000	0.000
30	A	79	GLY	0	-0.006	-0.002	38.936	0.178	0.178	0.000	0.000	0.000	0.000
31	A	80	GLU	-1	-0.786	-0.885	40.549	-7.377	-7.377	0.000	0.000	0.000	0.000
32	A	81	ARG	1	0.771	0.865	42.370	7.454	7.454	0.000	0.000	0.000	0.000
33	A	82	LEU	0	-0.060	-0.032	40.963	0.153	0.153	0.000	0.000	0.000	0.000
34	A	83	ASP	-1	-0.855	-0.920	44.459	-6.990	-6.990	0.000	0.000	0.000	0.000
35	A	84	GLU	-1	-0.860	-0.909	46.784	-6.408	-6.408	0.000	0.000	0.000	0.000
36	A	85	LEU	0	-0.056	-0.037	46.342	0.179	0.179	0.000	0.000	0.000	0.000
37	A	86	GLN	0	-0.051	-0.007	48.536	0.087	0.087	0.000	0.000	0.000	0.000
38	A	87	ASP	-1	-0.828	-0.902	50.446	-5.992	-5.992	0.000	0.000	0.000	0.000
39	A	88	LYS	1	0.808	0.895	50.429	6.435	6.435	0.000	0.000	0.000	0.000
40	A	89	SER	0	-0.054	-0.050	51.973	0.132	0.132	0.000	0.000	0.000	0.000
41	A	90	GLU	-1	-0.877	-0.923	54.407	-5.716	-5.716	0.000	0.000	0.000	0.000
42	A	91	SER	0	0.014	-0.007	56.227	0.159	0.159	0.000	0.000	0.000	0.000
43	A	92	LEU	0	-0.048	-0.017	57.035	0.138	0.138	0.000	0.000	0.000	0.000
44	A	93	SER	0	0.030	0.019	57.910	0.107	0.107	0.000	0.000	0.000	0.000
45	A	94	ASP	-1	-0.858	-0.908	59.845	-5.134	-5.134	0.000	0.000	0.000	0.000
46	A	95	ASN	0	-0.086	-0.060	62.182	0.199	0.199	0.000	0.000	0.000	0.000
47	A	96	ALA	0	0.003	0.006	62.401	0.110	0.110	0.000	0.000	0.000	0.000
48	A	97	THR	0	-0.021	-0.021	63.120	0.107	0.107	0.000	0.000	0.000	0.000
49	A	98	ALA	0	-0.016	-0.012	65.689	0.106	0.106	0.000	0.000	0.000	0.000
50	A	99	PHE	0	0.024	0.012	67.303	0.105	0.105	0.000	0.000	0.000	0.000
51	A	100	SER	0	0.060	0.038	67.463	0.114	0.114	0.000	0.000	0.000	0.000
52	A	101	ASN	0	0.007	0.004	69.131	0.098	0.098	0.000	0.000	0.000	0.000
53	A	102	ARG	1	0.926	0.953	71.853	4.405	4.405	0.000	0.000	0.000	0.000
54	A	103	SER	0	0.010	0.005	71.746	0.081	0.081	0.000	0.000	0.000	0.000
55	A	104	LYS	1	0.847	0.907	69.805	4.647	4.647	0.000	0.000	0.000	0.000
56	A	105	GLN	0	-0.029	0.010	75.626	0.055	0.055	0.000	0.000	0.000	0.000
57	A	106	LEU	0	0.103	0.060	77.238	0.064	0.064	0.000	0.000	0.000	0.000
58	A	107	ARG	1	0.932	0.957	77.519	4.151	4.151	0.000	0.000	0.000	0.000
59	A	108	ARG	1	0.853	0.910	76.790	4.154	4.154	0.000	0.000	0.000	0.000
60	A	109	GLN	0	0.028	0.012	81.814	0.008	0.008	0.000	0.000	0.000	0.000
61	A	110	MET	0	-0.038	-0.023	81.935	0.048	0.048	0.000	0.000	0.000	0.000
62	A	111	TRP	0	-0.055	-0.016	84.493	0.019	0.019	0.000	0.000	0.000	0.000
63	A	112	TRP	0	0.004	0.020	86.169	0.033	0.033	0.000	0.000	0.000	0.000

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