FMO DATABASE

FMODB ID: P3N3L

Calculation Name: 1NKD-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NKD

Chain ID: A

ChEMBL ID:

UniProt ID: P03051

Base Structure: X-ray

Registration Date: 2017-12-04

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20171117

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	60
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-304221.74942
FMO2-HF: Nuclear repulsion	279845.903348
FMO2-HF: Total energy	-24375.846072
FMO2-MP2: Total energy	-24444.550469

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:1:MET)

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

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.
-51.989	-36.114	10.104	-8.802	-17.179	-0.091

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.929

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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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	3	LYS	1	0.972	0.968	2.464	36.566	38.937	1.353	-1.477	-2.247	-0.010
4	A	4	GLN	0	0.057	0.020	5.023	0.219	0.449	-0.001	-0.011	-0.218	0.000
5	A	5	GLU	-1	-0.798	-0.890	2.563	-74.649	-69.213	1.591	-3.113	-3.915	-0.036
6	A	6	LYS	1	0.972	0.985	2.851	36.116	38.964	2.021	-1.769	-3.101	0.000
7	A	7	THR	0	-0.060	-0.028	3.777	4.565	3.369	0.065	1.372	-0.241	0.000
8	A	8	ALA	0	0.042	0.024	6.777	2.174	2.174	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.031	0.029	2.274	0.383	0.745	1.762	-0.378	-1.746	-0.005
10	A	10	ASN	0	-0.057	-0.058	6.098	1.116	1.138	-0.001	-0.004	-0.018	0.000
11	A	11	MET	0	0.029	0.029	8.128	1.824	1.824	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.046	0.027	8.964	1.283	1.283	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.880	0.944	5.272	26.176	26.176	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.025	-0.020	10.624	1.099	1.099	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.049	0.023	13.573	0.872	0.872	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.920	0.956	12.590	18.123	18.123	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.007	-0.009	14.957	0.625	0.625	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.047	-0.028	16.802	0.636	0.636	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.008	-0.005	18.110	0.604	0.604	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.025	0.037	19.512	0.381	0.381	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.018	0.004	21.130	0.483	0.483	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.074	-0.035	23.057	0.417	0.417	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.053	0.024	24.074	0.326	0.326	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.933	-0.966	24.339	-10.542	-10.542	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.920	0.956	26.804	10.091	10.091	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.030	-0.024	27.848	0.290	0.290	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.047	0.013	28.321	0.328	0.328	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-1.019	-0.997	30.337	-8.776	-8.776	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.089	-0.046	33.218	0.256	0.256	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.004	0.007	35.116	0.222	0.222	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.889	-0.962	36.694	-7.137	-7.137	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.066	-0.019	38.289	0.008	0.008	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.056	-0.033	33.521	-0.068	-0.068	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.830	-0.900	33.705	-7.900	-7.900	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.944	-0.969	33.623	-8.354	-8.354	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.043	-0.040	31.288	-0.219	-0.219	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.004	-0.002	29.463	-0.419	-0.419	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.843	-0.908	28.723	-9.048	-9.048	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.086	-0.047	27.336	-0.404	-0.404	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.082	-0.039	24.241	-0.544	-0.544	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.912	-0.945	24.046	-10.618	-10.618	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.016	0.010	23.565	-0.470	-0.470	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.029	-0.016	21.128	-0.613	-0.613	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.052	-0.037	18.017	-0.832	-0.832	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.876	-0.928	18.508	-12.833	-12.833	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.018	-0.003	18.296	-1.183	-1.183	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.019	-0.016	15.872	-1.038	-1.038	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.826	-0.912	14.038	-17.775	-17.775	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.921	-0.938	13.465	-16.288	-16.288	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.007	-0.004	11.914	-1.643	-1.643	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.025	-0.024	7.075	-3.056	-3.056	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.867	0.920	8.591	13.858	13.858	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.002	0.014	9.609	-2.289	-2.289	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.041	-0.022	6.753	-2.161	-2.161	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.059	-0.033	4.184	-5.667	-5.471	-0.001	-0.011	-0.184	0.000
56	A	56	ALA	0	-0.030	-0.020	5.271	-3.580	-3.580	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.955	0.993	7.201	26.768	26.768	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.013	-0.031	2.577	-3.797	-2.223	0.890	-0.689	-1.775	-0.004
59	A	59	GLY	0	0.021	0.043	2.488	-27.241	-22.952	2.368	-3.109	-3.547	-0.035
60	A	0	NME	0	-0.054	-0.038	3.169	1.346	1.089	0.057	0.387	-0.187	-0.001

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