FMO DATABASE

FMODB ID: G65V1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-416526.526327
FMO2-HF: Nuclear repulsion	384913.164791
FMO2-HF: Total energy	-31613.361535
FMO2-MP2: Total energy	-31706.97315

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.
58.168	60.768	10.244	-5.726	-7.115	-0.068

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 : 1.009 / q_NPA : 0.984

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	0.052	0.041	3.270	-1.765	0.287	-0.004	-0.913	-1.134	0.002
4	B	206	HIS	0	0.088	0.046	1.981	-34.170	-34.909	10.225	-4.475	-5.010	-0.070
5	B	207	HIS	0	0.005	0.000	3.156	-4.048	-3.032	0.025	-0.314	-0.726	0.000
6	B	208	ASN	0	0.022	-0.012	4.617	5.168	5.334	-0.001	-0.018	-0.147	0.000
7	B	209	ALA	0	-0.002	0.009	7.392	3.907	3.907	0.000	0.000	0.000	0.000
8	B	210	LEU	0	0.007	-0.009	4.251	3.522	3.627	-0.001	-0.006	-0.098	0.000
9	B	211	GLU	-1	-0.737	-0.829	8.166	-21.009	-21.009	0.000	0.000	0.000	0.000
10	B	212	ARG	1	0.830	0.905	9.999	21.674	21.674	0.000	0.000	0.000	0.000
11	B	213	LYS	1	0.965	0.980	9.946	28.327	28.327	0.000	0.000	0.000	0.000
12	B	214	ARG	1	0.934	0.963	11.619	23.932	23.932	0.000	0.000	0.000	0.000
13	B	215	ARG	1	0.815	0.880	13.323	23.520	23.520	0.000	0.000	0.000	0.000
14	B	216	ASP	-1	-0.830	-0.907	15.771	-17.203	-17.203	0.000	0.000	0.000	0.000
15	B	217	HIS	0	0.063	0.040	14.680	0.688	0.688	0.000	0.000	0.000	0.000
16	B	218	ILE	0	-0.010	0.008	16.569	0.966	0.966	0.000	0.000	0.000	0.000
17	B	219	LYS	1	0.846	0.901	19.757	14.290	14.290	0.000	0.000	0.000	0.000
18	B	220	ASP	-1	-0.855	-0.927	21.308	-13.678	-13.678	0.000	0.000	0.000	0.000
19	B	221	SER	0	-0.027	-0.022	21.588	0.685	0.685	0.000	0.000	0.000	0.000
20	B	222	PHE	0	-0.036	-0.020	23.109	0.443	0.443	0.000	0.000	0.000	0.000
21	B	223	HIS	0	0.004	0.010	25.266	0.168	0.168	0.000	0.000	0.000	0.000
22	B	224	SER	0	0.053	0.021	26.438	0.432	0.432	0.000	0.000	0.000	0.000
23	B	225	LEU	0	-0.011	0.010	28.304	0.361	0.361	0.000	0.000	0.000	0.000
24	B	226	ARG	1	0.790	0.862	30.031	10.328	10.328	0.000	0.000	0.000	0.000
25	B	227	ASP	-1	-0.809	-0.912	31.732	-9.482	-9.482	0.000	0.000	0.000	0.000
26	B	228	SER	0	-0.044	0.000	32.329	0.216	0.216	0.000	0.000	0.000	0.000
27	B	229	VAL	0	-0.006	-0.011	34.436	0.236	0.236	0.000	0.000	0.000	0.000
28	B	230	PRO	0	0.045	0.025	36.841	-0.014	-0.014	0.000	0.000	0.000	0.000
29	B	231	SER	0	-0.067	-0.036	39.208	0.115	0.115	0.000	0.000	0.000	0.000
30	B	232	LEU	0	-0.056	-0.035	34.469	-0.043	-0.043	0.000	0.000	0.000	0.000
31	B	233	GLN	0	0.000	0.019	35.795	-0.239	-0.239	0.000	0.000	0.000	0.000
32	B	234	GLY	0	-0.006	0.009	35.553	0.223	0.223	0.000	0.000	0.000	0.000
33	B	235	GLU	-1	-0.878	-0.920	35.986	-8.013	-8.013	0.000	0.000	0.000	0.000
34	B	236	LYS	1	0.882	0.935	33.374	8.410	8.410	0.000	0.000	0.000	0.000
35	B	237	ALA	0	0.013	0.022	32.941	0.107	0.107	0.000	0.000	0.000	0.000
36	B	238	SER	0	-0.007	-0.030	30.311	-0.434	-0.434	0.000	0.000	0.000	0.000
37	B	239	ARG	1	0.951	0.956	20.805	14.031	14.031	0.000	0.000	0.000	0.000
38	B	240	ALA	0	0.032	0.024	28.554	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	241	GLN	0	0.112	0.068	31.113	-0.087	-0.087	0.000	0.000	0.000	0.000
40	B	242	ILE	0	-0.001	0.003	29.245	0.162	0.162	0.000	0.000	0.000	0.000
41	B	243	LEU	0	-0.006	-0.001	27.321	0.053	0.053	0.000	0.000	0.000	0.000
42	B	244	ASP	-1	-0.873	-0.917	31.516	-9.026	-9.026	0.000	0.000	0.000	0.000
43	B	245	LYS	1	0.864	0.908	35.082	8.371	8.371	0.000	0.000	0.000	0.000
44	B	246	ALA	0	0.008	0.022	33.026	0.200	0.200	0.000	0.000	0.000	0.000
45	B	247	THR	0	-0.049	-0.032	34.009	0.102	0.102	0.000	0.000	0.000	0.000
46	B	248	GLU	-1	-0.874	-0.925	36.079	-7.676	-7.676	0.000	0.000	0.000	0.000
47	B	249	TYR	0	0.082	0.026	37.693	0.297	0.297	0.000	0.000	0.000	0.000
48	B	250	ILE	0	-0.006	-0.006	34.139	0.173	0.173	0.000	0.000	0.000	0.000
49	B	251	GLN	0	-0.031	-0.020	38.719	0.128	0.128	0.000	0.000	0.000	0.000
50	B	252	TYR	0	0.009	-0.001	41.378	0.209	0.209	0.000	0.000	0.000	0.000
51	B	253	MET	0	0.021	0.016	41.081	0.256	0.256	0.000	0.000	0.000	0.000
52	B	254	ARG	1	0.938	0.979	36.316	8.472	8.472	0.000	0.000	0.000	0.000
53	B	255	ARG	1	0.959	0.980	43.493	6.729	6.729	0.000	0.000	0.000	0.000
54	B	256	LYS	1	0.899	0.951	45.429	7.104	7.104	0.000	0.000	0.000	0.000
55	B	257	ASN	0	0.007	-0.011	43.705	0.183	0.183	0.000	0.000	0.000	0.000
56	B	258	HIS	0	-0.021	0.009	47.229	-0.028	-0.028	0.000	0.000	0.000	0.000
57	B	259	THR	0	0.007	-0.009	49.005	0.069	0.069	0.000	0.000	0.000	0.000
58	B	260	HIS	0	0.049	0.016	49.877	0.136	0.136	0.000	0.000	0.000	0.000
59	B	261	GLN	0	-0.064	-0.030	49.880	-0.018	-0.018	0.000	0.000	0.000	0.000
60	B	262	GLN	0	0.005	-0.005	51.925	0.026	0.026	0.000	0.000	0.000	0.000
61	B	263	ASP	-1	-0.863	-0.919	55.013	-5.636	-5.636	0.000	0.000	0.000	0.000
62	B	264	ILE	0	-0.042	-0.034	52.153	0.098	0.098	0.000	0.000	0.000	0.000
63	B	265	ASP	-1	-0.838	-0.906	54.705	-5.864	-5.864	0.000	0.000	0.000	0.000
64	B	266	ASP	-1	-0.840	-0.907	57.613	-5.266	-5.266	0.000	0.000	0.000	0.000
65	B	267	LEU	0	0.022	0.003	59.096	0.106	0.106	0.000	0.000	0.000	0.000
66	B	268	LYS	1	0.836	0.930	54.119	5.950	5.950	0.000	0.000	0.000	0.000
67	B	269	ARG	1	0.800	0.883	59.462	5.389	5.389	0.000	0.000	0.000	0.000
68	B	270	GLN	0	-0.005	-0.010	63.403	0.062	0.062	0.000	0.000	0.000	0.000
69	B	271	ASN	0	0.025	0.011	62.453	0.129	0.129	0.000	0.000	0.000	0.000
70	B	272	ALA	0	0.008	0.013	64.015	0.069	0.069	0.000	0.000	0.000	0.000
71	B	273	LEU	0	-0.006	-0.006	65.985	0.063	0.063	0.000	0.000	0.000	0.000
72	B	274	LEU	0	-0.029	-0.014	68.615	0.092	0.092	0.000	0.000	0.000	0.000
73	B	275	GLU	-1	-0.927	-0.968	66.981	-4.722	-4.722	0.000	0.000	0.000	0.000
74	B	276	GLN	0	-0.100	-0.039	70.206	0.029	0.029	0.000	0.000	0.000	0.000
75	B	277	GLN	0	-0.094	-0.048	72.407	0.104	0.104	0.000	0.000	0.000	0.000
76	B	278	VAL	0	-0.022	0.013	72.774	0.081	0.081	0.000	0.000	0.000	0.000

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