FMO DATABASE

FMODB ID: 859QY

Calculation Name: 1NLW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NLW

Chain ID: B

ChEMBL ID:

UniProt ID: Q05195

Base Structure: X-ray

Registration Date: 2023-06-22

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-416926.082012
FMO2-HF: Nuclear repulsion	385312.453191
FMO2-HF: Total energy	-31613.628821
FMO2-MP2: Total energy	-31707.199884

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(B:203:LYS)

Summations of interaction energy for fragment #1(B:203:LYS)

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.
53.941	54.227	14.564	-6.671	-8.178	-0.076

Interaction energy analysis for fragmet #1(B:203:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.005 / q_NPA : 0.979

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	B	205	ALA	0	0.056	0.039	3.620	-2.096	-0.424	-0.009	-0.745	-0.918	0.001
4	B	206	HIS	0	0.096	0.056	1.895	-36.730	-40.161	14.358	-5.298	-5.628	-0.074
5	B	207	HIS	0	0.005	0.005	2.662	-9.587	-7.951	0.212	-0.552	-1.295	-0.003
6	B	208	ASN	0	0.038	0.000	4.031	5.779	6.029	0.003	-0.053	-0.200	0.000
7	B	209	ALA	0	0.006	0.010	6.977	4.220	4.220	0.000	0.000	0.000	0.000
8	B	210	LEU	0	-0.007	-0.005	3.852	3.653	3.812	0.000	-0.023	-0.137	0.000
9	B	211	GLU	-1	-0.731	-0.838	7.482	-21.740	-21.740	0.000	0.000	0.000	0.000
10	B	212	ARG	1	0.767	0.854	9.329	22.515	22.515	0.000	0.000	0.000	0.000
11	B	213	LYS	1	0.975	0.990	9.970	28.456	28.456	0.000	0.000	0.000	0.000
12	B	214	ARG	1	0.945	0.971	11.082	25.053	25.053	0.000	0.000	0.000	0.000
13	B	215	ARG	1	0.831	0.887	12.604	24.416	24.416	0.000	0.000	0.000	0.000
14	B	216	ASP	-1	-0.786	-0.858	15.357	-17.320	-17.320	0.000	0.000	0.000	0.000
15	B	217	HIS	0	0.047	0.020	14.597	0.637	0.637	0.000	0.000	0.000	0.000
16	B	218	ILE	0	-0.002	0.013	15.936	1.026	1.026	0.000	0.000	0.000	0.000
17	B	219	LYS	1	0.784	0.866	19.083	15.061	15.061	0.000	0.000	0.000	0.000
18	B	220	ASP	-1	-0.784	-0.888	20.889	-13.791	-13.791	0.000	0.000	0.000	0.000
19	B	221	SER	0	-0.020	-0.003	20.932	0.689	0.689	0.000	0.000	0.000	0.000
20	B	222	PHE	0	-0.022	-0.023	22.545	0.507	0.507	0.000	0.000	0.000	0.000
21	B	223	HIS	0	-0.008	0.004	24.934	0.151	0.151	0.000	0.000	0.000	0.000
22	B	224	SER	0	0.052	0.017	25.752	0.477	0.477	0.000	0.000	0.000	0.000
23	B	225	LEU	0	-0.028	0.000	27.570	0.415	0.415	0.000	0.000	0.000	0.000
24	B	226	ARG	1	0.788	0.860	29.288	10.400	10.400	0.000	0.000	0.000	0.000
25	B	227	ASP	-1	-0.791	-0.902	31.059	-9.665	-9.665	0.000	0.000	0.000	0.000
26	B	228	SER	0	-0.040	-0.018	31.431	0.260	0.260	0.000	0.000	0.000	0.000
27	B	229	VAL	0	-0.011	-0.001	33.860	0.239	0.239	0.000	0.000	0.000	0.000
28	B	230	PRO	0	0.002	-0.008	36.292	-0.015	-0.015	0.000	0.000	0.000	0.000
29	B	231	SER	0	-0.029	-0.008	38.503	0.116	0.116	0.000	0.000	0.000	0.000
30	B	232	LEU	0	-0.054	-0.036	33.757	-0.038	-0.038	0.000	0.000	0.000	0.000
31	B	233	GLN	0	-0.014	0.020	35.005	-0.206	-0.206	0.000	0.000	0.000	0.000
32	B	234	GLY	0	-0.010	0.003	34.643	0.267	0.267	0.000	0.000	0.000	0.000
33	B	235	GLU	-1	-0.866	-0.927	35.859	-8.398	-8.398	0.000	0.000	0.000	0.000
34	B	236	LYS	1	0.876	0.938	33.038	8.431	8.431	0.000	0.000	0.000	0.000
35	B	237	ALA	0	-0.011	0.008	32.088	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	238	SER	0	-0.005	-0.026	29.636	-0.446	-0.446	0.000	0.000	0.000	0.000
37	B	239	ARG	1	0.925	0.946	20.247	14.328	14.328	0.000	0.000	0.000	0.000
38	B	240	ALA	0	0.033	0.031	27.881	-0.057	-0.057	0.000	0.000	0.000	0.000
39	B	241	GLN	0	0.126	0.081	30.444	-0.137	-0.137	0.000	0.000	0.000	0.000
40	B	242	ILE	0	0.005	0.006	28.499	0.170	0.170	0.000	0.000	0.000	0.000
41	B	243	LEU	0	0.005	0.008	26.873	0.054	0.054	0.000	0.000	0.000	0.000
42	B	244	ASP	-1	-0.877	-0.928	31.088	-9.103	-9.103	0.000	0.000	0.000	0.000
43	B	245	LYS	1	0.829	0.887	34.663	8.547	8.547	0.000	0.000	0.000	0.000
44	B	246	ALA	0	0.015	0.019	32.336	0.184	0.184	0.000	0.000	0.000	0.000
45	B	247	THR	0	-0.052	-0.034	33.767	0.121	0.121	0.000	0.000	0.000	0.000
46	B	248	GLU	-1	-0.822	-0.898	35.784	-7.824	-7.824	0.000	0.000	0.000	0.000
47	B	249	TYR	0	0.053	0.018	37.060	0.321	0.321	0.000	0.000	0.000	0.000
48	B	250	ILE	0	0.011	0.002	33.657	0.176	0.176	0.000	0.000	0.000	0.000
49	B	251	GLN	0	-0.024	-0.019	38.221	0.199	0.199	0.000	0.000	0.000	0.000
50	B	252	TYR	0	0.004	0.003	40.992	0.206	0.206	0.000	0.000	0.000	0.000
51	B	253	MET	0	0.020	0.027	40.677	0.264	0.264	0.000	0.000	0.000	0.000
52	B	254	ARG	1	0.944	0.979	35.876	8.571	8.571	0.000	0.000	0.000	0.000
53	B	255	ARG	1	0.980	0.989	43.141	6.776	6.776	0.000	0.000	0.000	0.000
54	B	256	LYS	1	0.894	0.954	44.910	7.207	7.207	0.000	0.000	0.000	0.000
55	B	257	ASN	0	0.013	-0.005	43.538	0.190	0.190	0.000	0.000	0.000	0.000
56	B	258	HIS	0	-0.020	-0.002	46.861	-0.032	-0.032	0.000	0.000	0.000	0.000
57	B	259	THR	0	-0.019	-0.023	48.515	0.138	0.138	0.000	0.000	0.000	0.000
58	B	260	HIS	0	0.040	0.006	49.682	0.105	0.105	0.000	0.000	0.000	0.000
59	B	261	GLN	0	-0.058	-0.033	49.529	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	262	GLN	0	0.000	0.003	51.591	0.016	0.016	0.000	0.000	0.000	0.000
61	B	263	ASP	-1	-0.865	-0.926	54.651	-5.658	-5.658	0.000	0.000	0.000	0.000
62	B	264	ILE	0	-0.036	-0.021	51.667	0.099	0.099	0.000	0.000	0.000	0.000
63	B	265	ASP	-1	-0.799	-0.889	54.160	-5.910	-5.910	0.000	0.000	0.000	0.000
64	B	266	ASP	-1	-0.831	-0.891	57.036	-5.255	-5.255	0.000	0.000	0.000	0.000
65	B	267	LEU	0	0.025	0.005	58.503	0.107	0.107	0.000	0.000	0.000	0.000
66	B	268	LYS	1	0.797	0.901	53.626	6.010	6.010	0.000	0.000	0.000	0.000
67	B	269	ARG	1	0.804	0.876	58.740	5.450	5.450	0.000	0.000	0.000	0.000
68	B	270	GLN	0	-0.015	-0.009	62.981	0.108	0.108	0.000	0.000	0.000	0.000
69	B	271	ASN	0	0.030	0.007	62.003	0.138	0.138	0.000	0.000	0.000	0.000
70	B	272	ALA	0	-0.007	0.003	63.784	0.065	0.065	0.000	0.000	0.000	0.000
71	B	273	LEU	0	-0.004	-0.007	65.727	0.069	0.069	0.000	0.000	0.000	0.000
72	B	274	LEU	0	-0.016	0.007	68.262	0.089	0.089	0.000	0.000	0.000	0.000
73	B	275	GLU	-1	-0.919	-0.959	66.666	-4.727	-4.727	0.000	0.000	0.000	0.000
74	B	276	GLN	0	-0.066	-0.034	69.672	0.035	0.035	0.000	0.000	0.000	0.000
75	B	277	GLN	0	-0.114	-0.055	72.036	0.117	0.117	0.000	0.000	0.000	0.000
76	B	278	VAL	0	-0.045	-0.007	72.488	0.069	0.069	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:203:LYS)