FMO DATABASE

FMODB ID: ZVYVN

Calculation Name: 5NLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q13618

Base Structure: X-ray

Registration Date: 2023-09-20

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1356689.922344
FMO2-HF: Nuclear repulsion	1294626.249542
FMO2-HF: Total energy	-62063.672803
FMO2-MP2: Total energy	-62237.52428

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:51:THR)

Summations of interaction energy for fragment #1(A:51:THR)

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.
-0.284	1.344	-0.015	-0.865	-0.747	0.004

Interaction energy analysis for fragmet #1(A:51:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.020

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	53	SER	0	0.019	-0.010	3.890	-0.093	1.535	-0.015	-0.865	-0.747	0.004
4	A	54	TYR	0	-0.013	0.013	7.024	-0.450	-0.450	0.000	0.000	0.000	0.000
5	A	55	THR	0	-0.003	-0.013	10.583	0.003	0.003	0.000	0.000	0.000	0.000
6	A	56	LEU	0	0.009	0.012	14.153	-0.035	-0.035	0.000	0.000	0.000	0.000
7	A	57	GLU	-1	-0.867	-0.936	17.594	0.150	0.150	0.000	0.000	0.000	0.000
8	A	58	ASP	-1	-0.889	-0.938	20.471	0.176	0.176	0.000	0.000	0.000	0.000
9	A	59	HIS	0	0.005	0.001	20.107	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	60	THR	0	0.007	-0.003	21.546	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	61	LYS	1	0.917	0.947	23.722	-0.183	-0.183	0.000	0.000	0.000	0.000
12	A	62	GLN	0	0.017	0.015	23.896	0.011	0.011	0.000	0.000	0.000	0.000
13	A	63	ALA	0	-0.006	-0.007	23.753	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	64	PHE	0	-0.007	-0.005	25.877	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	65	GLY	0	0.001	0.011	28.695	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	66	ILE	0	-0.012	-0.017	26.552	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	67	MET	0	-0.010	0.006	27.241	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	68	ASN	0	0.039	0.021	31.229	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	69	GLU	-1	-0.918	-0.947	33.678	0.134	0.134	0.000	0.000	0.000	0.000
20	A	70	LEU	0	0.011	0.000	30.714	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	71	ARG	1	0.893	0.947	34.856	-0.125	-0.125	0.000	0.000	0.000	0.000
22	A	72	LEU	0	-0.029	-0.006	37.197	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	73	SER	0	-0.076	-0.031	38.187	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	74	GLN	0	-0.041	-0.043	40.208	0.001	0.001	0.000	0.000	0.000	0.000
25	A	75	GLN	0	-0.011	0.004	36.301	0.006	0.006	0.000	0.000	0.000	0.000
26	A	76	LEU	0	-0.005	-0.020	32.285	0.005	0.005	0.000	0.000	0.000	0.000
27	A	77	CYS	0	-0.108	-0.025	35.274	0.005	0.005	0.000	0.000	0.000	0.000
28	A	78	ASP	-1	-0.720	-0.843	34.640	0.158	0.158	0.000	0.000	0.000	0.000
29	A	79	VAL	0	-0.046	-0.016	37.744	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	80	THR	0	0.018	-0.001	40.259	0.001	0.001	0.000	0.000	0.000	0.000
31	A	81	LEU	0	-0.017	0.000	41.493	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	82	GLN	0	0.034	0.006	45.403	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	83	VAL	0	0.006	0.011	46.941	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	84	LYS	1	0.853	0.915	49.587	-0.061	-0.061	0.000	0.000	0.000	0.000
35	A	85	TYR	0	0.021	0.006	53.313	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	86	GLN	0	-0.032	-0.015	55.295	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	87	ASP	-1	-0.882	-0.939	59.039	0.043	0.043	0.000	0.000	0.000	0.000
38	A	88	ALA	0	-0.044	-0.011	55.567	0.000	0.000	0.000	0.000	0.000	0.000
39	A	89	PRO	0	0.000	-0.001	56.487	0.000	0.000	0.000	0.000	0.000	0.000
40	A	90	ALA	0	-0.027	-0.019	53.671	0.002	0.002	0.000	0.000	0.000	0.000
41	A	91	ALA	0	-0.009	0.003	49.822	0.000	0.000	0.000	0.000	0.000	0.000
42	A	92	GLN	0	0.018	-0.003	48.053	0.003	0.003	0.000	0.000	0.000	0.000
43	A	93	PHE	0	-0.031	-0.007	43.336	0.000	0.000	0.000	0.000	0.000	0.000
44	A	94	MET	0	0.003	0.013	41.573	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	95	ALA	0	0.013	-0.006	38.069	0.000	0.000	0.000	0.000	0.000	0.000
46	A	96	HIS	0	0.075	0.057	33.318	0.000	0.000	0.000	0.000	0.000	0.000
47	A	97	LYS	1	0.863	0.915	34.111	-0.150	-0.150	0.000	0.000	0.000	0.000
48	A	98	VAL	0	0.018	-0.001	28.453	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	99	VAL	0	0.019	0.022	30.324	0.005	0.005	0.000	0.000	0.000	0.000
50	A	100	LEU	0	0.034	0.019	31.918	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	101	ALA	0	-0.010	0.005	32.068	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	102	SER	0	-0.069	-0.037	28.969	0.003	0.003	0.000	0.000	0.000	0.000
53	A	103	SER	0	-0.012	0.008	30.444	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	104	SER	0	-0.037	-0.018	33.302	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	105	PRO	0	0.022	-0.007	34.482	0.007	0.007	0.000	0.000	0.000	0.000
56	A	106	VAL	0	0.023	0.030	35.657	0.001	0.001	0.000	0.000	0.000	0.000
57	A	107	PHE	0	-0.007	-0.007	36.949	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	108	LYS	1	0.851	0.905	30.205	-0.139	-0.139	0.000	0.000	0.000	0.000
59	A	109	ALA	0	-0.007	-0.018	34.836	0.003	0.003	0.000	0.000	0.000	0.000
60	A	110	MET	0	-0.039	0.005	37.517	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	111	PHE	0	0.016	-0.017	36.350	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	112	THR	0	-0.012	0.023	34.783	0.008	0.008	0.000	0.000	0.000	0.000
63	A	113	ASN	0	-0.046	-0.030	35.384	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	114	GLY	0	-0.023	0.000	37.197	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	115	LEU	0	0.031	0.027	40.482	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	116	ARG	1	0.860	0.915	42.820	-0.070	-0.070	0.000	0.000	0.000	0.000
67	A	117	GLU	-1	-0.833	-0.916	42.017	0.079	0.079	0.000	0.000	0.000	0.000
68	A	118	GLN	0	-0.008	0.000	37.804	0.005	0.005	0.000	0.000	0.000	0.000
69	A	119	GLY	0	-0.003	-0.026	39.084	0.008	0.008	0.000	0.000	0.000	0.000
70	A	120	MET	0	-0.058	-0.005	40.962	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	121	GLU	-1	-0.877	-0.925	40.604	0.118	0.118	0.000	0.000	0.000	0.000
72	A	122	VAL	0	-0.081	-0.051	42.991	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	123	VAL	0	-0.029	-0.012	44.314	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	124	SER	0	-0.048	-0.030	46.547	0.000	0.000	0.000	0.000	0.000	0.000
75	A	125	ILE	0	0.012	-0.005	44.644	0.002	0.002	0.000	0.000	0.000	0.000
76	A	126	GLU	-1	-0.872	-0.921	48.414	0.056	0.056	0.000	0.000	0.000	0.000
77	A	127	GLY	0	0.010	0.017	49.231	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	128	ILE	0	-0.009	-0.014	49.299	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	129	HIS	0	0.034	0.015	51.149	0.003	0.003	0.000	0.000	0.000	0.000
80	A	130	PRO	0	0.052	0.010	48.797	0.002	0.002	0.000	0.000	0.000	0.000
81	A	131	LYS	1	0.989	0.997	48.027	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	132	VAL	0	0.012	0.003	46.764	0.003	0.003	0.000	0.000	0.000	0.000
83	A	133	MET	0	0.006	0.013	44.449	0.004	0.004	0.000	0.000	0.000	0.000
84	A	134	GLU	-1	-0.877	-0.911	43.239	0.080	0.080	0.000	0.000	0.000	0.000
85	A	135	ARG	1	0.778	0.868	42.657	-0.071	-0.071	0.000	0.000	0.000	0.000
86	A	136	LEU	0	0.002	0.002	41.063	0.004	0.004	0.000	0.000	0.000	0.000
87	A	137	ILE	0	0.003	0.003	38.627	0.006	0.006	0.000	0.000	0.000	0.000
88	A	138	GLU	-1	-0.841	-0.930	37.798	0.092	0.092	0.000	0.000	0.000	0.000
89	A	139	PHE	0	0.005	0.027	34.674	0.006	0.006	0.000	0.000	0.000	0.000
90	A	140	ALA	0	-0.058	-0.028	34.758	0.008	0.008	0.000	0.000	0.000	0.000
91	A	141	TYR	0	-0.008	-0.035	33.328	0.008	0.008	0.000	0.000	0.000	0.000
92	A	142	THR	0	-0.069	-0.062	33.169	0.007	0.007	0.000	0.000	0.000	0.000
93	A	143	ALA	0	-0.045	-0.010	31.560	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	144	SER	0	-0.016	-0.010	33.725	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	145	ILE	0	0.044	0.013	37.179	0.002	0.002	0.000	0.000	0.000	0.000
96	A	146	SER	0	-0.001	0.017	40.751	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	147	MET	0	-0.024	-0.020	42.458	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	148	GLY	0	0.016	-0.006	46.631	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	149	GLU	-1	-0.823	-0.910	50.321	0.039	0.039	0.000	0.000	0.000	0.000
100	A	150	LYS	1	0.902	0.959	52.699	-0.038	-0.038	0.000	0.000	0.000	0.000
101	A	151	CYS	0	0.003	-0.003	49.663	0.000	0.000	0.000	0.000	0.000	0.000
102	A	152	VAL	0	0.047	0.037	47.260	0.002	0.002	0.000	0.000	0.000	0.000
103	A	153	LEU	0	0.044	0.040	48.795	0.001	0.001	0.000	0.000	0.000	0.000
104	A	154	HIS	0	0.018	0.000	49.996	0.002	0.002	0.000	0.000	0.000	0.000
105	A	155	VAL	0	-0.018	-0.024	44.850	0.002	0.002	0.000	0.000	0.000	0.000
106	A	156	MET	0	0.040	0.030	45.234	0.003	0.003	0.000	0.000	0.000	0.000
107	A	157	ASN	0	-0.003	-0.008	45.624	0.001	0.001	0.000	0.000	0.000	0.000
108	A	158	GLY	0	0.018	0.010	45.975	0.001	0.001	0.000	0.000	0.000	0.000
109	A	159	ALA	0	-0.019	-0.013	41.378	0.002	0.002	0.000	0.000	0.000	0.000
110	A	160	VAL	0	-0.005	-0.009	41.983	0.003	0.003	0.000	0.000	0.000	0.000
111	A	161	MET	0	-0.021	0.020	43.631	0.001	0.001	0.000	0.000	0.000	0.000
112	A	162	TYR	0	-0.017	-0.036	41.023	0.000	0.000	0.000	0.000	0.000	0.000
113	A	163	GLN	0	0.003	0.001	37.953	0.009	0.009	0.000	0.000	0.000	0.000
114	A	164	ILE	0	-0.018	-0.012	36.092	0.007	0.007	0.000	0.000	0.000	0.000
115	A	165	ASP	-1	-0.783	-0.902	36.363	0.063	0.063	0.000	0.000	0.000	0.000
116	A	166	SER	0	-0.016	-0.006	33.947	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	167	VAL	0	0.028	0.007	36.082	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	168	VAL	0	0.025	0.021	38.851	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	169	ARG	1	0.746	0.845	37.837	-0.046	-0.046	0.000	0.000	0.000	0.000
120	A	170	ALA	0	0.008	0.003	38.691	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	171	CYS	0	-0.072	-0.041	40.526	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	172	SER	0	-0.062	-0.072	42.660	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	173	ASP	-1	-0.806	-0.881	40.695	0.034	0.034	0.000	0.000	0.000	0.000
124	A	174	PHE	0	-0.012	0.018	43.934	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	175	LEU	0	-0.001	-0.017	45.538	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	176	VAL	0	-0.063	-0.016	46.624	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	177	GLN	0	-0.082	-0.032	46.553	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	178	GLN	0	-0.032	-0.035	49.908	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	179	LEU	0	-0.029	-0.004	53.362	0.000	0.000	0.000	0.000	0.000	0.000
130	A	180	ASP	-1	-0.863	-0.919	54.918	0.024	0.024	0.000	0.000	0.000	0.000
131	A	181	PRO	0	-0.053	-0.046	58.576	0.000	0.000	0.000	0.000	0.000	0.000
132	A	182	SER	0	0.006	-0.001	60.823	0.000	0.000	0.000	0.000	0.000	0.000
133	A	183	ASN	0	0.010	-0.014	58.176	0.000	0.000	0.000	0.000	0.000	0.000
134	A	184	ALA	0	0.016	0.020	57.317	0.001	0.001	0.000	0.000	0.000	0.000
135	A	185	ILE	0	-0.002	-0.004	57.688	0.001	0.001	0.000	0.000	0.000	0.000
136	A	186	GLY	0	0.044	0.015	58.748	0.000	0.000	0.000	0.000	0.000	0.000
137	A	187	ILE	0	0.019	0.012	52.797	0.001	0.001	0.000	0.000	0.000	0.000
138	A	188	ALA	0	0.019	0.008	54.155	0.001	0.001	0.000	0.000	0.000	0.000
139	A	189	ASN	0	-0.042	-0.018	55.149	0.000	0.000	0.000	0.000	0.000	0.000
140	A	190	PHE	0	0.006	-0.001	52.494	0.001	0.001	0.000	0.000	0.000	0.000
141	A	191	ALA	0	0.011	0.009	50.618	0.001	0.001	0.000	0.000	0.000	0.000
142	A	192	GLU	-1	-0.892	-0.936	50.955	0.023	0.023	0.000	0.000	0.000	0.000
143	A	193	GLN	0	-0.050	-0.024	53.070	0.000	0.000	0.000	0.000	0.000	0.000
144	A	194	ILE	0	-0.089	-0.053	47.715	0.001	0.001	0.000	0.000	0.000	0.000
145	A	195	GLY	0	0.055	0.042	48.355	0.003	0.003	0.000	0.000	0.000	0.000
146	A	196	CYS	0	-0.045	-0.022	43.346	-0.002	-0.002	0.000	0.000	0.000	0.000
147	A	197	VAL	0	0.070	0.063	46.666	0.000	0.000	0.000	0.000	0.000	0.000
148	A	198	GLU	-1	-0.799	-0.878	43.045	0.036	0.036	0.000	0.000	0.000	0.000
149	A	199	LEU	0	-0.009	-0.029	46.241	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	200	HIS	0	0.014	-0.008	48.741	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	201	GLN	0	0.001	0.003	48.040	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	202	ARG	1	0.783	0.885	42.969	-0.028	-0.028	0.000	0.000	0.000	0.000
153	A	203	ALA	0	-0.005	0.015	50.064	0.000	0.000	0.000	0.000	0.000	0.000
154	A	204	ARG	1	0.962	0.991	53.390	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:51:THR)