FMO DATABASE

FMODB ID: 17N9Z

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-416708.930728
FMO2-HF: Nuclear repulsion	385096.39762
FMO2-HF: Total energy	-31612.533109
FMO2-MP2: Total energy	-31706.215496

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.
74.609	81.025	0.186	-2.722	-3.88	-0.015

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 : 1.061 / q_NPA : 1.016

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

Sort

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	0.050	0.045	3.393	-1.607	0.471	-0.006	-0.939	-1.133	0.002
4	B	206	HIS	0	0.045	0.016	3.046	-15.581	-12.125	0.192	-1.567	-2.081	-0.017
5	B	207	HIS	0	0.009	0.001	3.669	-1.597	-0.913	0.002	-0.209	-0.477	0.000
6	B	208	ASN	0	0.030	-0.009	5.244	4.351	4.478	-0.001	-0.006	-0.120	0.000
7	B	209	ALA	0	-0.003	0.005	7.793	3.506	3.506	0.000	0.000	0.000	0.000
8	B	210	LEU	0	0.006	-0.012	4.657	3.454	3.525	-0.001	-0.001	-0.069	0.000
9	B	211	GLU	-1	-0.838	-0.908	8.665	-21.542	-21.542	0.000	0.000	0.000	0.000
10	B	212	ARG	1	0.801	0.873	10.773	20.782	20.782	0.000	0.000	0.000	0.000
11	B	213	LYS	1	0.971	0.991	10.130	27.355	27.355	0.000	0.000	0.000	0.000
12	B	214	ARG	1	0.964	0.999	12.210	23.100	23.100	0.000	0.000	0.000	0.000
13	B	215	ARG	1	0.893	0.939	13.238	22.810	22.810	0.000	0.000	0.000	0.000
14	B	216	ASP	-1	-0.838	-0.909	16.393	-16.013	-16.013	0.000	0.000	0.000	0.000
15	B	217	HIS	0	0.073	0.046	14.973	0.655	0.655	0.000	0.000	0.000	0.000
16	B	218	ILE	0	-0.001	0.008	17.591	0.869	0.869	0.000	0.000	0.000	0.000
17	B	219	LYS	1	0.868	0.934	20.511	13.678	13.678	0.000	0.000	0.000	0.000
18	B	220	ASP	-1	-0.851	-0.922	21.984	-13.379	-13.379	0.000	0.000	0.000	0.000
19	B	221	SER	0	-0.021	-0.018	22.446	0.683	0.683	0.000	0.000	0.000	0.000
20	B	222	PHE	0	-0.035	-0.020	23.481	0.392	0.392	0.000	0.000	0.000	0.000
21	B	223	HIS	0	-0.041	-0.035	26.367	0.280	0.280	0.000	0.000	0.000	0.000
22	B	224	SER	0	0.060	0.022	27.180	0.408	0.408	0.000	0.000	0.000	0.000
23	B	225	LEU	0	-0.013	0.010	29.048	0.329	0.329	0.000	0.000	0.000	0.000
24	B	226	ARG	1	0.886	0.931	30.454	10.372	10.372	0.000	0.000	0.000	0.000
25	B	227	ASP	-1	-0.813	-0.939	32.482	-9.295	-9.295	0.000	0.000	0.000	0.000
26	B	228	SER	0	-0.046	0.004	33.179	0.207	0.207	0.000	0.000	0.000	0.000
27	B	229	VAL	0	-0.024	-0.010	35.203	0.233	0.233	0.000	0.000	0.000	0.000
28	B	230	PRO	0	0.040	0.015	37.570	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	231	SER	0	-0.085	-0.044	39.999	0.130	0.130	0.000	0.000	0.000	0.000
30	B	232	LEU	0	-0.051	-0.025	34.977	-0.046	-0.046	0.000	0.000	0.000	0.000
31	B	233	GLN	0	0.019	0.023	36.498	-0.304	-0.304	0.000	0.000	0.000	0.000
32	B	234	GLY	0	-0.011	0.006	36.193	0.210	0.210	0.000	0.000	0.000	0.000
33	B	235	GLU	-1	-0.915	-0.935	36.648	-7.814	-7.814	0.000	0.000	0.000	0.000
34	B	236	LYS	1	0.868	0.923	34.029	8.326	8.326	0.000	0.000	0.000	0.000
35	B	237	ALA	0	0.028	0.025	33.747	0.084	0.084	0.000	0.000	0.000	0.000
36	B	238	SER	0	-0.019	-0.009	31.108	-0.423	-0.423	0.000	0.000	0.000	0.000
37	B	239	ARG	1	0.959	0.957	21.619	13.652	13.652	0.000	0.000	0.000	0.000
38	B	240	ALA	0	0.032	0.026	29.275	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	241	GLN	0	0.082	0.028	31.766	-0.031	-0.031	0.000	0.000	0.000	0.000
40	B	242	ILE	0	-0.008	0.002	29.778	0.150	0.150	0.000	0.000	0.000	0.000
41	B	243	LEU	0	-0.013	-0.006	27.985	0.042	0.042	0.000	0.000	0.000	0.000
42	B	244	ASP	-1	-0.871	-0.920	32.130	-8.945	-8.945	0.000	0.000	0.000	0.000
43	B	245	LYS	1	0.948	0.961	35.680	8.275	8.275	0.000	0.000	0.000	0.000
44	B	246	ALA	0	0.016	0.029	33.651	0.194	0.194	0.000	0.000	0.000	0.000
45	B	247	THR	0	-0.048	-0.026	34.591	0.083	0.083	0.000	0.000	0.000	0.000
46	B	248	GLU	-1	-0.939	-0.972	36.624	-7.468	-7.468	0.000	0.000	0.000	0.000
47	B	249	TYR	0	0.096	0.032	38.365	0.180	0.180	0.000	0.000	0.000	0.000
48	B	250	ILE	0	0.000	0.000	34.679	0.170	0.170	0.000	0.000	0.000	0.000
49	B	251	GLN	0	-0.044	-0.033	39.261	0.061	0.061	0.000	0.000	0.000	0.000
50	B	252	TYR	0	0.026	0.010	41.877	0.210	0.210	0.000	0.000	0.000	0.000
51	B	253	MET	0	0.001	-0.003	41.555	0.251	0.251	0.000	0.000	0.000	0.000
52	B	254	ARG	1	0.936	0.977	36.937	8.354	8.354	0.000	0.000	0.000	0.000
53	B	255	ARG	1	0.954	0.980	43.973	6.676	6.676	0.000	0.000	0.000	0.000
54	B	256	LYS	1	0.895	0.953	46.268	6.998	6.998	0.000	0.000	0.000	0.000
55	B	257	ASN	0	0.024	0.000	43.936	0.238	0.238	0.000	0.000	0.000	0.000
56	B	258	HIS	0	-0.014	0.009	47.732	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	259	THR	0	-0.011	-0.008	49.450	0.124	0.124	0.000	0.000	0.000	0.000
58	B	260	HIS	0	0.049	0.016	49.945	0.149	0.149	0.000	0.000	0.000	0.000
59	B	261	GLN	0	-0.061	-0.014	50.334	-0.036	-0.036	0.000	0.000	0.000	0.000
60	B	262	GLN	0	0.014	-0.006	52.373	0.084	0.084	0.000	0.000	0.000	0.000
61	B	263	ASP	-1	-0.838	-0.906	55.444	-5.620	-5.620	0.000	0.000	0.000	0.000
62	B	264	ILE	0	-0.063	-0.040	52.546	0.098	0.098	0.000	0.000	0.000	0.000
63	B	265	ASP	-1	-0.930	-0.970	55.160	-5.816	-5.816	0.000	0.000	0.000	0.000
64	B	266	ASP	-1	-0.934	-0.973	58.023	-5.272	-5.272	0.000	0.000	0.000	0.000
65	B	267	LEU	0	0.012	-0.013	59.195	0.107	0.107	0.000	0.000	0.000	0.000
66	B	268	LYS	1	0.924	0.978	55.132	5.874	5.874	0.000	0.000	0.000	0.000
67	B	269	ARG	1	0.893	0.955	60.707	5.320	5.320	0.000	0.000	0.000	0.000
68	B	270	GLN	0	-0.015	-0.018	63.796	0.039	0.039	0.000	0.000	0.000	0.000
69	B	271	ASN	0	0.041	0.022	63.428	0.127	0.127	0.000	0.000	0.000	0.000
70	B	272	ALA	0	0.000	0.007	64.431	0.067	0.067	0.000	0.000	0.000	0.000
71	B	273	LEU	0	-0.011	-0.007	66.381	0.061	0.061	0.000	0.000	0.000	0.000
72	B	274	LEU	0	-0.044	-0.026	69.038	0.090	0.090	0.000	0.000	0.000	0.000
73	B	275	GLU	-1	-0.914	-0.963	67.421	-4.683	-4.683	0.000	0.000	0.000	0.000
74	B	276	GLN	0	-0.097	-0.039	70.635	0.018	0.018	0.000	0.000	0.000	0.000
75	B	277	GLN	0	-0.086	-0.036	72.849	0.108	0.108	0.000	0.000	0.000	0.000
76	B	278	VAL	0	-0.028	0.010	73.206	0.082	0.082	0.000	0.000	0.000	0.000

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