FMO DATABASE

FMODB ID: GNLV1

Calculation Name: 4GKF-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1T0

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	148
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1534859.261508
FMO2-HF: Nuclear repulsion	1475562.272354
FMO2-HF: Total energy	-59296.989154
FMO2-MP2: Total energy	-59473.183068

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:14:ACE )

Summations of interaction energy for fragment #1(A:14:ACE )

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.
0.596	1.469	0.006	-0.346	-0.534	0

Interaction energy analysis for fragmet #1(A:14:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.017

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].
3	A	16	LYS	1	0.989	1.002	3.910	0.255	0.907	-0.003	-0.221	-0.428
4	A	17	THR	0	0.031	0.023	5.996	0.243	0.243	0.000	0.000	0.000
5	A	18	LEU	0	0.061	0.012	8.436	-0.141	-0.141	0.000	0.000	0.000
6	A	19	GLU	-1	-0.782	-0.886	10.634	-0.553	-0.553	0.000	0.000	0.000
7	A	20	GLN	0	0.022	0.022	3.629	-0.008	0.213	0.009	-0.125	-0.106
8	A	21	ARG	1	0.926	0.961	7.811	0.465	0.465	0.000	0.000	0.000
9	A	22	ARG	1	0.794	0.890	9.523	0.484	0.484	0.000	0.000	0.000
10	A	23	GLY	0	0.022	0.018	10.856	0.075	0.075	0.000	0.000	0.000
11	A	24	GLU	-1	-0.912	-0.953	7.118	-0.735	-0.735	0.000	0.000	0.000
12	A	25	TYR	0	0.003	-0.003	10.186	0.122	0.122	0.000	0.000	0.000
13	A	26	ALA	0	-0.006	-0.010	13.327	0.065	0.065	0.000	0.000	0.000
14	A	27	TYR	0	-0.026	-0.015	12.149	0.057	0.057	0.000	0.000	0.000
15	A	28	TYR	0	0.035	-0.004	10.095	0.073	0.073	0.000	0.000	0.000
16	A	29	VAL	0	0.000	0.006	15.395	0.038	0.038	0.000	0.000	0.000
17	A	30	ILE	0	-0.026	-0.015	18.047	0.027	0.027	0.000	0.000	0.000
18	A	31	LYS	1	0.857	0.918	16.158	0.146	0.146	0.000	0.000	0.000
19	A	32	GLU	-1	-0.791	-0.888	19.034	-0.094	-0.094	0.000	0.000	0.000
20	A	33	VAL	0	-0.019	-0.020	21.244	0.015	0.015	0.000	0.000	0.000
21	A	34	ALA	0	-0.011	-0.003	21.756	0.011	0.011	0.000	0.000	0.000
22	A	35	ASP	-1	-0.857	-0.925	20.568	-0.095	-0.095	0.000	0.000	0.000
23	A	36	LEU	0	-0.069	-0.022	23.875	0.010	0.010	0.000	0.000	0.000
24	A	37	ASN	0	-0.046	-0.018	26.999	0.006	0.006	0.000	0.000	0.000
25	A	38	ASP	-1	-0.869	-0.924	28.991	-0.056	-0.056	0.000	0.000	0.000
26	A	39	LYS	1	0.967	0.953	30.621	0.047	0.047	0.000	0.000	0.000
27	A	40	GLN	0	0.107	0.064	32.282	-0.005	-0.005	0.000	0.000	0.000
28	A	41	LEU	0	-0.037	-0.006	27.928	-0.004	-0.004	0.000	0.000	0.000
29	A	42	GLU	-1	-0.828	-0.937	26.739	-0.102	-0.102	0.000	0.000	0.000
30	A	43	GLU	-1	-0.935	-0.954	28.587	-0.073	-0.073	0.000	0.000	0.000
31	A	44	LYS	1	0.909	0.958	31.083	0.060	0.060	0.000	0.000	0.000
32	A	45	TYR	0	-0.004	-0.017	23.219	-0.009	-0.009	0.000	0.000	0.000
33	A	46	ALA	0	0.030	0.008	26.316	-0.010	-0.010	0.000	0.000	0.000
34	A	47	SER	0	-0.002	0.005	27.368	-0.007	-0.007	0.000	0.000	0.000
35	A	48	LEU	0	-0.024	-0.012	29.188	-0.002	-0.002	0.000	0.000	0.000
36	A	49	VAL	0	0.018	0.002	22.932	-0.004	-0.004	0.000	0.000	0.000
37	A	50	LYS	1	0.839	0.929	25.323	0.119	0.119	0.000	0.000	0.000
38	A	51	LYS	1	0.904	0.961	26.898	0.085	0.085	0.000	0.000	0.000
39	A	52	ALA	0	0.024	0.022	25.819	0.002	0.002	0.000	0.000	0.000
40	A	53	PRO	0	-0.009	-0.006	24.280	0.003	0.003	0.000	0.000	0.000
41	A	54	VAL	0	0.031	0.009	26.359	0.004	0.004	0.000	0.000	0.000
42	A	55	MET	0	-0.033	-0.007	29.785	0.006	0.006	0.000	0.000	0.000
43	A	56	ILE	0	0.000	0.003	26.237	0.005	0.005	0.000	0.000	0.000
44	A	57	LEU	0	-0.069	-0.025	27.124	0.004	0.004	0.000	0.000	0.000
45	A	58	SER	0	-0.059	-0.022	30.352	0.007	0.007	0.000	0.000	0.000
46	A	59	ASN	0	0.009	0.010	33.451	0.008	0.008	0.000	0.000	0.000
47	A	60	GLY	0	0.034	0.025	31.837	0.004	0.004	0.000	0.000	0.000
48	A	61	LEU	0	-0.009	-0.017	26.953	-0.001	-0.001	0.000	0.000	0.000
49	A	62	LEU	0	0.030	0.017	30.310	0.000	0.000	0.000	0.000	0.000
50	A	63	GLN	0	0.040	0.014	33.152	0.002	0.002	0.000	0.000	0.000
51	A	64	THR	0	0.014	0.010	29.741	0.002	0.002	0.000	0.000	0.000
52	A	65	LEU	0	-0.001	-0.013	27.492	0.000	0.000	0.000	0.000	0.000
53	A	66	ALA	0	-0.003	-0.004	31.511	0.003	0.003	0.000	0.000	0.000
54	A	67	PHE	0	0.006	-0.002	33.882	0.004	0.004	0.000	0.000	0.000
55	A	68	LEU	0	-0.039	-0.015	28.980	0.002	0.002	0.000	0.000	0.000
56	A	69	LEU	0	-0.022	-0.014	32.278	0.003	0.003	0.000	0.000	0.000
57	A	70	ALA	0	-0.018	-0.001	34.943	0.004	0.004	0.000	0.000	0.000
58	A	71	LYS	1	0.892	0.949	35.764	0.063	0.063	0.000	0.000	0.000
59	A	72	ALA	0	0.034	0.028	34.332	0.001	0.001	0.000	0.000	0.000
60	A	73	GLU	-1	-0.935	-0.933	36.471	-0.043	-0.043	0.000	0.000	0.000
61	A	74	THR	0	-0.084	-0.054	34.641	0.002	0.002	0.000	0.000	0.000
62	A	75	SER	0	-0.001	-0.008	37.155	-0.001	-0.001	0.000	0.000	0.000
63	A	76	PRO	0	0.022	-0.008	33.572	-0.002	-0.002	0.000	0.000	0.000
64	A	77	GLU	-1	-0.822	-0.925	33.232	-0.049	-0.049	0.000	0.000	0.000
65	A	78	LYS	1	0.927	0.964	34.324	0.044	0.044	0.000	0.000	0.000
66	A	79	ALA	0	0.046	0.025	30.354	-0.001	-0.001	0.000	0.000	0.000
67	A	80	ASN	0	0.003	-0.014	29.630	-0.009	-0.009	0.000	0.000	0.000
68	A	81	GLN	0	-0.018	0.009	29.943	-0.002	-0.002	0.000	0.000	0.000
69	A	82	ILE	0	0.019	0.027	27.738	0.002	0.002	0.000	0.000	0.000
70	A	83	LEU	0	0.006	-0.010	24.367	-0.002	-0.002	0.000	0.000	0.000
71	A	84	SER	0	-0.093	-0.042	25.478	0.000	0.000	0.000	0.000	0.000
72	A	85	ARG	1	0.944	0.976	27.201	0.054	0.054	0.000	0.000	0.000
73	A	86	VAL	0	-0.105	-0.041	21.022	0.002	0.002	0.000	0.000	0.000
74	A	87	ASN	0	-0.012	-0.009	21.928	-0.009	-0.009	0.000	0.000	0.000
75	A	88	GLU	-1	-0.901	-0.931	18.968	-0.029	-0.029	0.000	0.000	0.000
76	A	89	TYR	0	-0.057	-0.046	10.208	-0.010	-0.010	0.000	0.000	0.000
77	A	90	PRO	0	0.003	-0.026	13.043	0.018	0.018	0.000	0.000	0.000
78	A	91	PRO	0	-0.039	0.013	15.302	0.023	0.023	0.000	0.000	0.000
79	A	92	ARG	1	0.885	0.947	18.645	0.053	0.053	0.000	0.000	0.000
80	A	93	PHE	0	0.016	-0.011	19.647	0.012	0.012	0.000	0.000	0.000
81	A	94	ILE	0	0.051	0.026	24.148	0.012	0.012	0.000	0.000	0.000
82	A	95	GLU	-1	-0.827	-0.906	25.448	-0.050	-0.050	0.000	0.000	0.000
83	A	96	LYS	1	0.714	0.842	24.103	0.075	0.075	0.000	0.000	0.000
84	A	97	LEU	0	-0.045	-0.017	28.833	0.003	0.003	0.000	0.000	0.000
85	A	98	GLY	0	0.036	0.022	31.299	0.004	0.004	0.000	0.000	0.000
86	A	99	ASN	0	0.005	-0.016	33.813	-0.005	-0.005	0.000	0.000	0.000
87	A	100	ASP	-1	-0.917	-0.953	35.571	-0.054	-0.054	0.000	0.000	0.000
88	A	101	LYS	1	0.829	0.922	30.258	0.058	0.058	0.000	0.000	0.000
89	A	102	ASP	-1	-0.708	-0.852	32.651	-0.072	-0.072	0.000	0.000	0.000
90	A	103	GLU	-1	-0.867	-0.959	29.765	-0.079	-0.079	0.000	0.000	0.000
91	A	104	HIS	0	-0.044	-0.028	29.352	-0.010	-0.010	0.000	0.000	0.000
92	A	105	LEU	0	0.004	-0.001	30.252	-0.006	-0.006	0.000	0.000	0.000
93	A	106	LEU	0	0.019	0.001	24.846	-0.005	-0.005	0.000	0.000	0.000
94	A	107	LEU	0	0.016	0.018	24.396	-0.011	-0.011	0.000	0.000	0.000
95	A	108	TYR	0	0.022	0.006	25.409	-0.009	-0.009	0.000	0.000	0.000
96	A	109	LEU	0	-0.028	-0.022	25.360	-0.004	-0.004	0.000	0.000	0.000
97	A	110	HIS	0	0.045	0.044	21.500	-0.013	-0.013	0.000	0.000	0.000
98	A	111	ILE	0	0.016	0.013	21.211	-0.019	-0.019	0.000	0.000	0.000
99	A	112	VAL	0	0.003	-0.006	22.669	-0.008	-0.008	0.000	0.000	0.000
100	A	113	TYR	0	0.054	0.029	17.253	-0.010	-0.010	0.000	0.000	0.000
101	A	114	TRP	0	-0.011	-0.016	12.956	-0.012	-0.012	0.000	0.000	0.000
102	A	115	LEU	0	-0.012	-0.015	19.449	-0.006	-0.006	0.000	0.000	0.000
103	A	116	ARG	1	0.872	0.935	22.024	0.088	0.088	0.000	0.000	0.000
104	A	117	GLU	-1	-0.945	-0.963	17.293	-0.115	-0.115	0.000	0.000	0.000
105	A	118	ASN	0	-0.135	-0.071	15.395	-0.026	-0.026	0.000	0.000	0.000
106	A	119	VAL	0	-0.068	-0.028	18.628	0.001	0.001	0.000	0.000	0.000
107	A	120	ASP	-1	-0.824	-0.918	22.031	-0.063	-0.063	0.000	0.000	0.000
108	A	121	ARG	1	0.996	1.007	23.266	0.058	0.058	0.000	0.000	0.000
109	A	122	ASN	0	-0.058	-0.035	25.419	0.005	0.005	0.000	0.000	0.000
110	A	123	ILE	0	-0.002	0.009	25.226	0.003	0.003	0.000	0.000	0.000
111	A	124	ASP	-1	-0.829	-0.907	28.415	-0.067	-0.067	0.000	0.000	0.000
112	A	125	VAL	0	0.021	0.007	30.585	0.002	0.002	0.000	0.000	0.000
113	A	126	LYS	1	0.918	0.953	33.472	0.051	0.051	0.000	0.000	0.000
114	A	127	THR	0	0.014	0.011	31.744	0.001	0.001	0.000	0.000	0.000
115	A	128	LEU	0	-0.023	-0.025	29.364	0.001	0.001	0.000	0.000	0.000
116	A	129	LEU	0	-0.056	-0.016	33.287	0.000	0.000	0.000	0.000	0.000
117	A	130	SER	0	-0.052	-0.028	36.174	0.004	0.004	0.000	0.000	0.000
118	A	131	GLN	0	-0.037	-0.013	29.833	-0.001	-0.001	0.000	0.000	0.000
119	A	132	ASP	-1	-0.811	-0.892	31.803	-0.067	-0.067	0.000	0.000	0.000
120	A	133	TYR	0	0.073	0.012	32.457	-0.005	-0.005	0.000	0.000	0.000
121	A	134	SER	0	0.010	-0.001	29.319	-0.006	-0.006	0.000	0.000	0.000
122	A	135	LYS	1	0.856	0.927	26.349	0.072	0.072	0.000	0.000	0.000
123	A	136	VAL	0	0.072	0.043	27.653	-0.010	-0.010	0.000	0.000	0.000
124	A	137	LEU	0	-0.002	0.027	27.333	-0.011	-0.011	0.000	0.000	0.000
125	A	138	TRP	0	-0.002	-0.001	20.600	-0.004	-0.004	0.000	0.000	0.000
126	A	139	ALA	0	0.042	0.017	23.651	-0.017	-0.017	0.000	0.000	0.000
127	A	140	THR	0	-0.030	-0.045	24.394	-0.009	-0.009	0.000	0.000	0.000
128	A	141	LYS	1	0.912	0.951	22.886	0.127	0.127	0.000	0.000	0.000
129	A	142	GLU	-1	-0.757	-0.840	17.251	-0.309	-0.309	0.000	0.000	0.000
130	A	143	ALA	0	0.031	0.015	20.154	-0.022	-0.022	0.000	0.000	0.000
131	A	144	ILE	0	0.000	0.004	21.852	-0.012	-0.012	0.000	0.000	0.000
132	A	145	ALA	0	-0.036	-0.019	17.519	-0.011	-0.011	0.000	0.000	0.000
133	A	146	LEU	0	-0.019	-0.007	16.885	-0.033	-0.033	0.000	0.000	0.000
134	A	147	LEU	0	0.083	0.008	18.436	-0.013	-0.013	0.000	0.000	0.000
135	A	148	ASN	0	-0.025	-0.002	19.406	0.020	0.020	0.000	0.000	0.000
136	A	149	TRP	0	-0.071	-0.034	11.651	-0.013	-0.013	0.000	0.000	0.000
137	A	150	MET	0	0.005	0.012	17.095	0.001	0.001	0.000	0.000	0.000
138	A	151	ARG	1	0.944	0.990	19.167	0.197	0.197	0.000	0.000	0.000
139	A	152	ARG	1	0.884	0.930	17.176	0.277	0.277	0.000	0.000	0.000
140	A	153	PHE	0	0.058	0.015	12.159	0.001	0.001	0.000	0.000	0.000
141	A	154	ALA	0	0.033	0.022	18.300	0.020	0.020	0.000	0.000	0.000
142	A	155	VAL	0	-0.072	-0.028	21.937	0.016	0.016	0.000	0.000	0.000
143	A	156	ALA	0	-0.036	-0.018	18.524	0.010	0.010	0.000	0.000	0.000
144	A	157	MET	0	-0.078	-0.029	17.241	-0.006	-0.006	0.000	0.000	0.000
145	A	158	LEU	0	-0.044	0.002	21.244	0.010	0.010	0.000	0.000	0.000
146	A	159	LYS	1	0.871	0.938	24.562	0.083	0.083	0.000	0.000	0.000
147	A	160	GLU	-1	-0.930	-1.016	28.113	-0.099	-0.099	0.000	0.000	0.000
148	A	161	NME	0	0.029	0.042	31.372	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:ACE )