FMO DATABASE

FMODB ID: GNVK1

Calculation Name: 4JPB-W-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 4JPB

Chain ID: W

ChEMBL ID:

UniProt ID: Q56310

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1291207.495823
FMO2-HF: Nuclear repulsion	1236794.916252
FMO2-HF: Total energy	-54412.579571
FMO2-MP2: Total energy	-54574.330151

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(W:8:LEU)

Summations of interaction energy for fragment #1(W:8:LEU)

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.
-9.215	-3.906	6.536	-4.89	-6.954	-0.015

Interaction energy analysis for fragmet #1(W:8:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.002

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	W	10	GLU	-1	-0.873	-0.918	3.037	-3.882	0.189	0.234	-2.106	-2.199	-0.002
4	W	11	PHE	0	-0.007	-0.009	4.569	-0.079	-0.019	-0.001	-0.007	-0.052	0.000
5	W	12	GLU	-1	-0.821	-0.875	7.488	-0.309	-0.309	0.000	0.000	0.000	0.000
6	W	13	VAL	0	0.008	0.010	10.831	-0.003	-0.003	0.000	0.000	0.000	0.000
7	W	14	LEU	0	0.005	0.002	13.614	0.029	0.029	0.000	0.000	0.000	0.000
8	W	15	SER	0	-0.003	-0.003	16.939	0.021	0.021	0.000	0.000	0.000	0.000
9	W	16	PHE	0	0.015	-0.012	18.581	0.003	0.003	0.000	0.000	0.000	0.000
10	W	17	GLU	-1	-0.908	-0.961	22.290	-0.005	-0.005	0.000	0.000	0.000	0.000
11	W	18	ILE	0	-0.049	-0.042	24.999	-0.008	-0.008	0.000	0.000	0.000	0.000
12	W	19	ASP	-1	-0.772	-0.873	27.536	-0.001	-0.001	0.000	0.000	0.000	0.000
13	W	20	GLU	-1	-0.965	-0.962	28.132	0.026	0.026	0.000	0.000	0.000	0.000
14	W	21	GLN	0	0.011	-0.001	23.760	0.008	0.008	0.000	0.000	0.000	0.000
15	W	22	ALA	0	-0.008	-0.005	20.827	-0.012	-0.012	0.000	0.000	0.000	0.000
16	W	23	LEU	0	-0.037	-0.017	19.283	0.013	0.013	0.000	0.000	0.000	0.000
17	W	24	ALA	0	0.067	0.021	15.768	-0.006	-0.006	0.000	0.000	0.000	0.000
18	W	25	PHE	0	-0.012	-0.005	16.165	0.013	0.013	0.000	0.000	0.000	0.000
19	W	26	ASP	-1	-0.764	-0.862	13.120	-0.432	-0.432	0.000	0.000	0.000	0.000
20	W	27	VAL	0	0.009	-0.012	13.754	0.038	0.038	0.000	0.000	0.000	0.000
21	W	28	ASP	-1	-0.949	-0.966	13.684	-0.604	-0.604	0.000	0.000	0.000	0.000
22	W	29	ASN	0	-0.034	-0.017	16.746	-0.004	-0.004	0.000	0.000	0.000	0.000
23	W	30	ILE	0	-0.063	-0.026	18.830	0.040	0.040	0.000	0.000	0.000	0.000
24	W	31	GLU	-1	-0.867	-0.911	21.354	-0.212	-0.212	0.000	0.000	0.000	0.000
25	W	32	MET	0	-0.052	-0.045	24.342	0.006	0.006	0.000	0.000	0.000	0.000
26	W	33	VAL	0	-0.008	-0.007	23.416	0.004	0.004	0.000	0.000	0.000	0.000
27	W	34	ILE	0	-0.014	0.006	26.374	0.004	0.004	0.000	0.000	0.000	0.000
28	W	35	GLU	-1	-0.933	-0.969	30.128	-0.060	-0.060	0.000	0.000	0.000	0.000
29	W	36	LYS	1	0.886	0.940	32.554	0.046	0.046	0.000	0.000	0.000	0.000
30	W	37	SER	0	-0.044	-0.009	34.515	0.004	0.004	0.000	0.000	0.000	0.000
31	W	38	ASP	-1	-0.902	-0.968	37.837	-0.049	-0.049	0.000	0.000	0.000	0.000
32	W	39	ILE	0	-0.038	-0.017	35.719	-0.005	-0.005	0.000	0.000	0.000	0.000
33	W	40	THR	0	-0.012	0.005	39.633	0.004	0.004	0.000	0.000	0.000	0.000
34	W	41	PRO	0	0.022	0.021	41.252	-0.003	-0.003	0.000	0.000	0.000	0.000
35	W	42	VAL	0	0.047	0.015	40.628	0.000	0.000	0.000	0.000	0.000	0.000
36	W	43	PRO	0	-0.019	-0.004	42.823	0.001	0.001	0.000	0.000	0.000	0.000
37	W	44	LYS	1	0.921	0.956	44.787	0.031	0.031	0.000	0.000	0.000	0.000
38	W	45	SER	0	0.017	0.008	39.615	-0.001	-0.001	0.000	0.000	0.000	0.000
39	W	46	ARG	1	0.882	0.927	32.982	0.067	0.067	0.000	0.000	0.000	0.000
40	W	47	HIS	0	0.063	0.027	35.258	-0.003	-0.003	0.000	0.000	0.000	0.000
41	W	48	PHE	0	0.021	0.005	33.017	0.002	0.002	0.000	0.000	0.000	0.000
42	W	49	VAL	0	-0.059	-0.017	34.303	-0.005	-0.005	0.000	0.000	0.000	0.000
43	W	50	GLU	-1	-0.750	-0.860	35.557	-0.042	-0.042	0.000	0.000	0.000	0.000
44	W	51	GLY	0	-0.033	-0.027	36.830	0.004	0.004	0.000	0.000	0.000	0.000
45	W	52	VAL	0	-0.040	-0.008	36.862	-0.006	-0.006	0.000	0.000	0.000	0.000
46	W	53	ILE	0	0.037	0.025	33.020	0.005	0.005	0.000	0.000	0.000	0.000
47	W	54	ASN	0	-0.022	-0.016	37.215	-0.008	-0.008	0.000	0.000	0.000	0.000
48	W	55	LEU	0	0.051	0.022	31.303	0.002	0.002	0.000	0.000	0.000	0.000
49	W	56	ARG	1	0.929	0.950	33.540	0.099	0.099	0.000	0.000	0.000	0.000
50	W	57	GLY	0	-0.006	-0.004	35.862	-0.003	-0.003	0.000	0.000	0.000	0.000
51	W	58	ARG	1	0.851	0.914	29.669	0.140	0.140	0.000	0.000	0.000	0.000
52	W	59	ILE	0	-0.003	-0.006	36.620	0.002	0.002	0.000	0.000	0.000	0.000
53	W	60	ILE	0	0.011	0.017	30.958	-0.005	-0.005	0.000	0.000	0.000	0.000
54	W	61	PRO	0	0.010	0.012	32.410	0.007	0.007	0.000	0.000	0.000	0.000
55	W	62	VAL	0	0.017	0.006	32.217	-0.007	-0.007	0.000	0.000	0.000	0.000
56	W	63	VAL	0	-0.018	-0.018	29.703	0.008	0.008	0.000	0.000	0.000	0.000
57	W	64	ASN	0	0.029	-0.010	31.094	-0.002	-0.002	0.000	0.000	0.000	0.000
58	W	65	LEU	0	0.044	0.019	23.864	0.003	0.003	0.000	0.000	0.000	0.000
59	W	66	ALA	0	0.060	0.039	28.391	0.004	0.004	0.000	0.000	0.000	0.000
60	W	67	LYS	1	0.805	0.909	29.789	0.044	0.044	0.000	0.000	0.000	0.000
61	W	68	ILE	0	-0.034	-0.001	27.493	0.003	0.003	0.000	0.000	0.000	0.000
62	W	69	LEU	0	-0.034	-0.011	23.843	0.002	0.002	0.000	0.000	0.000	0.000
63	W	70	GLY	0	-0.001	-0.010	27.692	0.008	0.008	0.000	0.000	0.000	0.000
64	W	71	ILE	0	-0.064	-0.018	25.996	0.008	0.008	0.000	0.000	0.000	0.000
65	W	72	SER	0	0.023	0.013	29.927	-0.003	-0.003	0.000	0.000	0.000	0.000
66	W	73	PHE	0	0.021	-0.017	31.150	-0.002	-0.002	0.000	0.000	0.000	0.000
67	W	74	ASP	-1	-0.790	-0.903	33.250	-0.015	-0.015	0.000	0.000	0.000	0.000
68	W	75	GLU	-1	-0.891	-0.961	35.364	-0.037	-0.037	0.000	0.000	0.000	0.000
69	W	76	GLN	0	-0.049	-0.017	37.216	-0.006	-0.006	0.000	0.000	0.000	0.000
70	W	77	LYS	1	0.752	0.865	33.038	0.009	0.009	0.000	0.000	0.000	0.000
71	W	78	MET	0	-0.022	0.021	30.333	-0.004	-0.004	0.000	0.000	0.000	0.000
72	W	79	LYS	1	0.897	0.944	31.889	0.037	0.037	0.000	0.000	0.000	0.000
73	W	80	SER	0	-0.020	0.008	28.071	-0.004	-0.004	0.000	0.000	0.000	0.000
74	W	81	ILE	0	-0.011	-0.010	29.169	0.004	0.004	0.000	0.000	0.000	0.000
75	W	82	ILE	0	-0.002	0.010	22.394	-0.007	-0.007	0.000	0.000	0.000	0.000
76	W	83	VAL	0	-0.009	0.007	25.865	0.006	0.006	0.000	0.000	0.000	0.000
77	W	84	ALA	0	0.010	0.017	22.463	-0.015	-0.015	0.000	0.000	0.000	0.000
78	W	85	ARG	1	0.798	0.891	23.312	0.201	0.201	0.000	0.000	0.000	0.000
79	W	86	THR	0	0.003	0.011	21.061	-0.020	-0.020	0.000	0.000	0.000	0.000
80	W	87	LYS	1	0.862	0.929	22.522	0.217	0.217	0.000	0.000	0.000	0.000
81	W	88	ASP	-1	-0.888	-0.945	25.145	-0.152	-0.152	0.000	0.000	0.000	0.000
82	W	89	VAL	0	-0.019	0.000	27.623	0.010	0.010	0.000	0.000	0.000	0.000
83	W	90	GLU	-1	-0.756	-0.856	27.118	-0.159	-0.159	0.000	0.000	0.000	0.000
84	W	91	VAL	0	-0.036	-0.027	27.631	0.014	0.014	0.000	0.000	0.000	0.000
85	W	92	GLY	0	0.028	0.018	27.672	-0.010	-0.010	0.000	0.000	0.000	0.000
86	W	93	PHE	0	-0.009	-0.014	25.399	0.013	0.013	0.000	0.000	0.000	0.000
87	W	94	LEU	0	-0.021	0.000	28.019	-0.003	-0.003	0.000	0.000	0.000	0.000
88	W	95	VAL	0	-0.006	-0.022	25.241	0.004	0.004	0.000	0.000	0.000	0.000
89	W	96	ASP	-1	-0.852	-0.934	28.295	-0.033	-0.033	0.000	0.000	0.000	0.000
90	W	97	ARG	1	0.913	0.954	26.348	0.041	0.041	0.000	0.000	0.000	0.000
91	W	98	VAL	0	0.030	0.014	22.022	0.001	0.001	0.000	0.000	0.000	0.000
92	W	99	LEU	0	-0.095	-0.052	20.785	0.009	0.009	0.000	0.000	0.000	0.000
93	W	100	GLY	0	0.029	0.020	19.483	0.007	0.007	0.000	0.000	0.000	0.000
94	W	101	VAL	0	-0.013	0.000	13.904	-0.001	-0.001	0.000	0.000	0.000	0.000
95	W	102	LEU	0	-0.007	0.004	12.190	0.032	0.032	0.000	0.000	0.000	0.000
96	W	103	ARG	1	0.760	0.863	7.205	0.581	0.581	0.000	0.000	0.000	0.000
97	W	104	ILE	0	-0.021	-0.029	7.208	0.124	0.124	0.000	0.000	0.000	0.000
98	W	105	THR	0	0.092	0.043	1.839	-2.179	-1.811	4.764	-2.046	-3.086	-0.011
99	W	106	GLU	-1	-0.903	-0.941	3.644	-0.890	-0.495	0.008	-0.114	-0.289	-0.001
100	W	107	ASN	0	-0.046	-0.039	2.177	-1.341	-0.926	1.531	-0.617	-1.328	-0.001
101	W	108	GLN	0	-0.064	-0.028	5.740	-0.175	-0.175	0.000	0.000	0.000	0.000
102	W	109	LEU	0	-0.001	-0.007	7.791	-0.177	-0.177	0.000	0.000	0.000	0.000
103	W	110	ASP	-1	-0.819	-0.870	9.398	0.461	0.461	0.000	0.000	0.000	0.000
104	W	111	LEU	0	0.036	0.013	10.382	-0.083	-0.083	0.000	0.000	0.000	0.000
105	W	112	THR	0	-0.039	-0.030	14.148	-0.023	-0.023	0.000	0.000	0.000	0.000
106	W	113	ASN	0	-0.057	-0.040	17.690	-0.027	-0.027	0.000	0.000	0.000	0.000
107	W	114	VAL	0	-0.030	-0.015	20.129	-0.011	-0.011	0.000	0.000	0.000	0.000
108	W	115	SER	0	-0.029	-0.025	22.380	-0.016	-0.016	0.000	0.000	0.000	0.000
109	W	116	ASP	-1	-0.800	-0.883	22.736	0.077	0.077	0.000	0.000	0.000	0.000
110	W	117	LYS	1	0.818	0.909	24.805	-0.018	-0.018	0.000	0.000	0.000	0.000
111	W	118	PHE	0	-0.012	-0.005	21.604	-0.008	-0.008	0.000	0.000	0.000	0.000
112	W	119	GLY	0	0.075	0.042	22.696	-0.015	-0.015	0.000	0.000	0.000	0.000
113	W	120	LYS	1	0.933	0.943	16.863	0.017	0.017	0.000	0.000	0.000	0.000
114	W	121	LYS	1	0.837	0.924	19.087	0.027	0.027	0.000	0.000	0.000	0.000
115	W	122	SER	0	-0.029	0.004	18.220	-0.020	-0.020	0.000	0.000	0.000	0.000
116	W	123	LYS	1	0.855	0.916	12.282	0.336	0.336	0.000	0.000	0.000	0.000
117	W	124	GLY	0	0.011	0.010	13.020	0.035	0.035	0.000	0.000	0.000	0.000
118	W	125	LEU	0	-0.042	-0.021	14.269	-0.046	-0.046	0.000	0.000	0.000	0.000
119	W	126	VAL	0	0.032	0.014	11.145	0.044	0.044	0.000	0.000	0.000	0.000
120	W	127	LYS	1	0.815	0.894	12.433	-0.464	-0.464	0.000	0.000	0.000	0.000
121	W	128	THR	0	0.013	-0.002	12.503	0.029	0.029	0.000	0.000	0.000	0.000
122	W	129	ASP	-1	-0.901	-0.952	14.484	0.072	0.072	0.000	0.000	0.000	0.000
123	W	130	GLY	0	-0.028	-0.004	16.228	-0.002	-0.002	0.000	0.000	0.000	0.000
124	W	131	ARG	1	0.948	0.969	17.575	-0.043	-0.043	0.000	0.000	0.000	0.000
125	W	132	LEU	0	-0.043	-0.023	17.271	-0.002	-0.002	0.000	0.000	0.000	0.000
126	W	133	ILE	0	0.014	0.013	15.843	-0.021	-0.021	0.000	0.000	0.000	0.000
127	W	134	ILE	0	-0.019	-0.012	16.038	0.017	0.017	0.000	0.000	0.000	0.000
128	W	135	TYR	0	-0.062	-0.052	10.152	-0.029	-0.029	0.000	0.000	0.000	0.000
129	W	136	LEU	0	-0.008	-0.022	15.316	0.021	0.021	0.000	0.000	0.000	0.000
130	W	137	ASP	-1	-0.834	-0.915	15.978	-0.280	-0.280	0.000	0.000	0.000	0.000
131	W	138	ILE	0	0.000	0.001	17.447	0.027	0.027	0.000	0.000	0.000	0.000
132	W	139	ASP	-1	-0.789	-0.917	18.614	-0.270	-0.270	0.000	0.000	0.000	0.000
133	W	140	LYS	1	0.866	0.946	19.673	0.117	0.117	0.000	0.000	0.000	0.000
134	W	141	ILE	0	-0.004	-0.013	21.599	0.023	0.023	0.000	0.000	0.000	0.000
135	W	142	ILE	0	0.027	0.009	23.584	0.017	0.017	0.000	0.000	0.000	0.000
136	W	143	GLU	-1	-0.904	-0.969	22.864	-0.157	-0.157	0.000	0.000	0.000	0.000
137	W	144	GLU	-1	-0.938	-0.950	25.681	-0.048	-0.048	0.000	0.000	0.000	0.000
138	W	145	ILE	0	-0.039	-0.002	27.540	0.011	0.011	0.000	0.000	0.000	0.000
139	W	146	THR	0	-0.023	0.000	28.926	0.005	0.005	0.000	0.000	0.000	0.000
140	W	147	VAL	0	-0.017	0.001	30.916	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(W:8:LEU)