FMO DATABASE

FMODB ID: MVYVZ

Calculation Name: 4NKJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NKJ

Chain ID: A

ChEMBL ID:

UniProt ID: S5DRP1

Base Structure: X-ray

Registration Date: 2023-09-19

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-919618.128353
FMO2-HF: Nuclear repulsion	865027.988199
FMO2-HF: Total energy	-54590.140154
FMO2-MP2: Total energy	-54748.930078

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:4:VAL)

Summations of interaction energy for fragment #1(A:4:VAL)

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.
-4.691	-1.908	3.153	-2.472	-3.462	-0.016

Interaction energy analysis for fragmet #1(A:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.025

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	A	6	ALA	0	0.033	0.006	2.426	-4.683	-1.975	1.615	-1.974	-2.348	-0.017
4	A	7	ASP	-1	-0.840	-0.928	5.154	-0.107	-0.025	-0.001	-0.003	-0.078	0.000
5	A	8	LEU	0	0.017	0.012	7.271	-0.002	-0.002	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.969	0.978	10.662	0.238	0.238	0.000	0.000	0.000	0.000
7	A	10	SER	0	0.063	0.052	9.323	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	11	THR	0	0.048	0.007	9.211	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.055	-0.026	11.694	0.092	0.092	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.915	-0.967	14.705	-0.319	-0.319	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.002	-0.002	13.479	0.035	0.035	0.000	0.000	0.000	0.000
12	A	15	ILE	0	0.001	-0.005	15.043	0.043	0.043	0.000	0.000	0.000	0.000
13	A	16	ASN	0	0.003	0.006	17.468	0.049	0.049	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.832	0.925	18.766	0.361	0.361	0.000	0.000	0.000	0.000
15	A	18	ILE	0	0.027	0.012	17.567	0.024	0.024	0.000	0.000	0.000	0.000
16	A	19	THR	0	0.012	0.010	21.053	0.031	0.031	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.949	0.974	23.364	0.216	0.216	0.000	0.000	0.000	0.000
18	A	21	ASN	0	-0.030	-0.023	22.517	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.046	0.034	25.249	0.013	0.013	0.000	0.000	0.000	0.000
20	A	23	ASN	0	0.018	-0.002	27.061	0.015	0.015	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.025	0.002	28.755	0.015	0.015	0.000	0.000	0.000	0.000
22	A	25	LEU	0	0.024	0.000	29.006	0.009	0.009	0.000	0.000	0.000	0.000
23	A	26	SER	0	-0.003	0.009	31.173	0.012	0.012	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.924	-0.980	33.124	-0.115	-0.115	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.044	-0.035	32.705	0.008	0.008	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.846	-0.936	35.159	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.004	0.010	37.014	0.007	0.007	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.916	0.962	38.425	0.101	0.101	0.000	0.000	0.000	0.000
29	A	32	ASN	0	-0.009	0.002	38.029	0.010	0.010	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.008	0.001	39.824	0.006	0.006	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.019	-0.013	43.161	0.003	0.003	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.946	0.988	43.006	0.086	0.086	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.002	-0.008	43.983	0.003	0.003	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.007	0.004	47.171	0.003	0.003	0.000	0.000	0.000	0.000
35	A	38	GLY	0	-0.004	0.006	49.144	0.003	0.003	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.012	0.002	50.434	0.002	0.002	0.000	0.000	0.000	0.000
37	A	40	MET	0	-0.026	-0.012	49.555	0.003	0.003	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.903	-0.955	53.132	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.967	-0.976	55.067	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.008	-0.002	54.363	0.002	0.002	0.000	0.000	0.000	0.000
41	A	44	HIS	0	-0.015	-0.004	57.419	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	ASN	0	-0.032	-0.027	59.274	0.001	0.001	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.870	-0.933	59.970	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	47	ILE	0	-0.025	-0.019	59.998	0.002	0.002	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.036	-0.020	63.091	0.001	0.001	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.766	-0.889	65.420	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.022	-0.023	66.102	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.942	-0.975	67.861	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.857	-0.939	69.671	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.894	0.954	71.051	0.034	0.034	0.000	0.000	0.000	0.000
51	A	54	VAL	0	-0.066	-0.035	71.288	0.001	0.001	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.896	-0.941	73.929	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	56	ASP	-1	-0.760	-0.910	75.885	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.022	0.015	76.914	0.001	0.001	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.871	0.925	78.249	0.026	0.026	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.006	-0.015	80.207	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.843	-0.900	81.420	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.049	-0.020	82.267	0.001	0.001	0.000	0.000	0.000	0.000
59	A	62	ILE	0	-0.077	-0.038	83.559	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.019	-0.004	85.617	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	SER	0	0.043	0.012	87.035	0.001	0.001	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.056	-0.036	86.830	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	ILE	0	-0.056	-0.022	89.270	0.001	0.001	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.861	-0.934	91.415	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.040	-0.013	93.501	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.018	-0.016	94.796	0.000	0.000	0.000	0.000	0.000	0.000
67	A	70	VAL	0	0.030	0.025	96.144	0.001	0.001	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.030	-0.005	97.912	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.036	-0.025	98.102	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.033	-0.023	100.281	0.000	0.000	0.000	0.000	0.000	0.000
71	A	74	ASN	0	-0.069	-0.040	101.305	0.001	0.001	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.972	-0.971	104.012	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	76	GLY	0	-0.005	0.009	105.878	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	ILE	0	-0.029	-0.019	104.244	0.000	0.000	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.068	-0.022	102.200	0.000	0.000	0.000	0.000	0.000	0.000
76	A	79	ASN	0	0.015	-0.001	105.492	0.000	0.000	0.000	0.000	0.000	0.000
77	A	80	SER	0	0.003	-0.001	106.701	0.000	0.000	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.890	-0.918	102.024	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	82	ASP	-1	-0.790	-0.892	102.235	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.898	-0.961	102.167	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	84	HIS	1	0.731	0.826	98.983	0.015	0.015	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.043	0.039	97.540	0.000	0.000	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.083	0.047	97.355	0.000	0.000	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.091	-0.055	96.013	0.000	0.000	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.045	-0.019	91.811	0.000	0.000	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.812	-0.915	92.512	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.882	0.941	92.372	0.015	0.015	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.896	0.939	89.437	0.017	0.017	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.061	0.027	88.065	0.000	0.000	0.000	0.000	0.000	0.000
90	A	93	LYS	1	1.015	1.006	87.472	0.017	0.017	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.856	0.935	86.376	0.018	0.018	0.000	0.000	0.000	0.000
92	A	95	MET	0	-0.076	-0.028	83.798	0.000	0.000	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.044	0.038	83.053	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.040	-0.015	80.118	0.000	0.000	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.031	0.027	76.560	0.001	0.001	0.000	0.000	0.000	0.000
96	A	99	SER	0	-0.085	-0.074	78.317	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.038	-0.012	80.750	0.000	0.000	0.000	0.000	0.000	0.000
98	A	101	VAL	0	0.005	0.001	83.947	0.000	0.000	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.914	-0.945	86.743	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	103	ILE	0	-0.073	-0.041	90.436	0.000	0.000	0.000	0.000	0.000	0.000
101	A	104	GLY	0	0.000	0.008	93.391	0.000	0.000	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.018	-0.030	94.381	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.022	-0.007	97.330	0.000	0.000	0.000	0.000	0.000	0.000
104	A	107	SER	0	0.031	0.015	93.769	0.000	0.000	0.000	0.000	0.000	0.000
105	A	108	PHE	0	-0.062	-0.024	89.288	0.000	0.000	0.000	0.000	0.000	0.000
106	A	109	GLU	-1	-0.876	-0.924	84.344	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	110	THR	0	0.002	-0.013	83.273	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	LYN	0	-0.086	0.003	77.411	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	HIS	1	0.873	0.931	78.231	0.025	0.025	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.849	0.927	73.954	0.028	0.028	0.000	0.000	0.000	0.000
111	A	114	CYS	0	0.086	0.111	66.639	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.046	-0.032	71.399	0.000	0.000	0.000	0.000	0.000	0.000
113	A	116	GLN	0	0.013	0.012	67.223	0.000	0.000	0.000	0.000	0.000	0.000
114	A	117	THR	0	-0.005	-0.023	64.039	0.000	0.000	0.000	0.000	0.000	0.000
115	A	119	LEU	0	-0.099	-0.057	68.851	0.000	0.000	0.000	0.000	0.000	0.000
116	A	120	ASP	-1	-0.959	-0.989	65.287	-0.039	-0.039	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.846	0.948	58.180	0.045	0.045	0.000	0.000	0.000	0.000
118	A	122	ILE	0	0.020	0.008	62.698	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.084	-0.044	64.484	0.000	0.000	0.000	0.000	0.000	0.000
120	A	124	ALA	0	-0.053	-0.021	64.232	0.000	0.000	0.000	0.000	0.000	0.000
121	A	125	GLY	0	0.121	0.066	61.567	0.000	0.000	0.000	0.000	0.000	0.000
122	A	126	THR	0	-0.107	-0.061	55.740	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.063	0.048	53.099	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	128	ASN	0	-0.064	-0.032	49.697	0.000	0.000	0.000	0.000	0.000	0.000
125	A	129	ALA	0	0.032	0.011	49.416	0.000	0.000	0.000	0.000	0.000	0.000
126	A	130	GLY	0	0.000	-0.019	46.442	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	131	GLU	-1	-0.995	-0.980	42.158	-0.092	-0.092	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.031	-0.008	40.317	0.000	0.000	0.000	0.000	0.000	0.000
129	A	133	SER	0	-0.022	-0.013	36.392	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	134	LEU	0	0.009	-0.006	32.878	0.001	0.001	0.000	0.000	0.000	0.000
131	A	135	PRO	0	-0.032	0.006	29.548	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	136	THR	0	0.017	0.008	26.816	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	137	PHE	0	-0.033	-0.035	23.640	0.001	0.001	0.000	0.000	0.000	0.000
134	A	138	ASP	-1	-0.876	-0.920	20.365	-0.298	-0.298	0.000	0.000	0.000	0.000
135	A	139	SER	0	-0.015	-0.026	15.010	0.003	0.003	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.034	-0.010	14.761	0.011	0.011	0.000	0.000	0.000	0.000
137	A	141	ASN	0	-0.011	-0.009	11.396	-0.075	-0.075	0.000	0.000	0.000	0.000
138	A	142	ILE	0	-0.003	0.001	7.886	0.069	0.069	0.000	0.000	0.000	0.000
139	A	143	THR	0	0.003	0.005	7.179	-0.246	-0.246	0.000	0.000	0.000	0.000
140	A	144	ALA	0	-0.004	-0.012	2.463	-0.175	-0.325	1.539	-0.478	-0.910	0.001
141	A	145	ALA	0	-0.020	0.001	4.273	0.367	0.510	0.000	-0.017	-0.126	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:4:VAL)