FMO DATABASE

FMODB ID: YZYL2

Calculation Name: 3V4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V4H

Chain ID: A

ChEMBL ID:

UniProt ID: Q8CLE0

Base Structure: X-ray

Registration Date: 2023-06-21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1265075.575914
FMO2-HF: Nuclear repulsion	1208702.621946
FMO2-HF: Total energy	-56372.953968
FMO2-MP2: Total energy	-56535.941019

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:ASP)

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

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.
-15.373	-3.206	7.195	-8.892	-10.469	0.06

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.878 / q_NPA : -0.932

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	PHE	0	-0.013	0.000	2.367	-1.861	1.130	1.759	-1.646	-3.105	0.001
4	A	7	ILE	0	0.003	0.001	6.098	-2.703	-2.703	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.958	0.994	9.834	-19.610	-19.610	0.000	0.000	0.000	0.000
6	A	9	ILE	0	0.044	0.009	12.275	-0.920	-0.920	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.845	-0.928	15.774	14.803	14.803	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.040	-0.022	18.908	-0.439	-0.439	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.062	-0.028	17.189	-0.453	-0.453	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.927	-0.965	15.423	18.085	18.085	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.003	-0.007	12.717	-0.439	-0.439	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.919	-0.983	12.217	20.232	20.232	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.016	0.006	6.653	0.211	0.211	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.033	-0.006	8.735	-2.945	-2.945	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.757	-0.858	5.210	51.784	51.907	-0.001	-0.001	-0.120	0.000
16	A	19	ALA	0	-0.067	-0.041	7.659	-4.224	-4.224	0.000	0.000	0.000	0.000
17	A	20	ASN	0	0.003	-0.007	7.766	-4.366	-4.366	0.000	0.000	0.000	0.000
18	A	21	HIS	1	0.766	0.862	5.990	-35.622	-35.622	0.000	0.000	0.000	0.000
19	A	22	LYS	1	0.894	0.961	8.501	-26.692	-26.692	0.000	0.000	0.000	0.000
20	A	23	ASN	0	-0.015	-0.018	11.257	-0.965	-0.965	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.824	-0.870	8.850	25.987	25.987	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.013	-0.016	10.166	0.969	0.969	0.000	0.000	0.000	0.000
23	A	26	GLN	0	0.033	0.017	5.168	3.444	3.497	-0.001	-0.002	-0.049	0.000
24	A	27	VAL	0	-0.043	-0.017	5.769	-3.908	-3.908	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.013	-0.004	5.397	5.237	5.237	0.000	0.000	0.000	0.000
26	A	29	ALA	0	-0.001	-0.004	7.792	-0.098	-0.098	0.000	0.000	0.000	0.000
27	A	30	TRP	0	0.015	-0.013	8.358	-1.148	-1.148	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.068	-0.026	11.884	-0.812	-0.812	0.000	0.000	0.000	0.000
29	A	32	TRP	0	0.006	-0.019	14.983	0.150	0.150	0.000	0.000	0.000	0.000
30	A	33	ASP	-1	-0.898	-0.912	17.634	13.309	13.309	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.038	0.028	20.563	-0.375	-0.375	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.003	0.011	23.457	0.011	0.011	0.000	0.000	0.000	0.000
33	A	36	GLN	0	-0.028	-0.027	26.689	-0.308	-0.308	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.024	0.025	29.978	0.004	0.004	0.000	0.000	0.000	0.000
35	A	50	LYS	1	0.907	0.969	30.164	-9.839	-9.839	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.043	-0.027	27.052	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	52	SER	0	-0.003	0.001	28.265	-0.152	-0.152	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.044	-0.032	22.770	0.219	0.219	0.000	0.000	0.000	0.000
39	A	54	SER	0	-0.003	-0.024	21.165	0.051	0.051	0.000	0.000	0.000	0.000
40	A	55	ASP	-1	-0.816	-0.903	20.994	12.783	12.783	0.000	0.000	0.000	0.000
41	A	56	PHE	0	-0.034	-0.010	11.821	0.302	0.302	0.000	0.000	0.000	0.000
42	A	57	CYS	0	0.009	0.012	16.058	-0.731	-0.731	0.000	0.000	0.000	0.000
43	A	58	PHE	0	-0.017	-0.032	11.025	1.311	1.311	0.000	0.000	0.000	0.000
44	A	59	ALA	0	0.054	0.046	11.512	-1.529	-1.529	0.000	0.000	0.000	0.000
45	A	60	HIS	1	0.743	0.862	10.254	-18.355	-18.355	0.000	0.000	0.000	0.000
46	A	61	TYR	0	0.049	0.001	9.794	-0.540	-0.540	0.000	0.000	0.000	0.000
47	A	62	ILE	0	-0.021	-0.004	13.324	0.031	0.031	0.000	0.000	0.000	0.000
48	A	63	ASP	-1	-0.807	-0.910	13.102	22.754	22.754	0.000	0.000	0.000	0.000
49	A	64	LYS	1	0.902	0.955	16.233	-18.708	-18.708	0.000	0.000	0.000	0.000
50	A	65	ALA	0	0.012	0.011	15.638	-1.003	-1.003	0.000	0.000	0.000	0.000
51	A	66	SER	0	0.016	0.009	17.550	-0.441	-0.441	0.000	0.000	0.000	0.000
52	A	67	PRO	0	0.015	0.018	19.105	-0.702	-0.702	0.000	0.000	0.000	0.000
53	A	68	ASN	0	-0.009	-0.002	20.649	-1.181	-1.181	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.003	-0.011	16.239	-0.493	-0.493	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.041	0.028	20.878	-0.481	-0.481	0.000	0.000	0.000	0.000
56	A	71	SER	0	-0.029	-0.024	23.699	-0.699	-0.699	0.000	0.000	0.000	0.000
57	A	72	TYR	0	-0.028	-0.032	23.271	-0.539	-0.539	0.000	0.000	0.000	0.000
58	A	73	CYS	0	-0.046	0.001	23.676	-0.376	-0.376	0.000	0.000	0.000	0.000
59	A	74	LEU	0	-0.019	-0.015	25.529	-0.431	-0.431	0.000	0.000	0.000	0.000
60	A	75	LEU	0	-0.070	-0.041	28.651	-0.373	-0.373	0.000	0.000	0.000	0.000
61	A	76	GLY	0	0.030	0.040	28.377	-0.288	-0.288	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.865	0.946	26.247	-11.485	-11.485	0.000	0.000	0.000	0.000
63	A	78	HIS	0	-0.039	-0.018	25.784	0.233	0.233	0.000	0.000	0.000	0.000
64	A	79	ILE	0	0.003	-0.002	19.596	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	80	LYS	1	0.907	0.961	22.754	-11.152	-11.152	0.000	0.000	0.000	0.000
66	A	81	ASN	0	-0.017	-0.014	18.629	-0.362	-0.362	0.000	0.000	0.000	0.000
67	A	82	VAL	0	0.034	0.031	14.601	0.366	0.366	0.000	0.000	0.000	0.000
68	A	83	GLN	0	-0.027	-0.012	10.947	-1.574	-1.574	0.000	0.000	0.000	0.000
69	A	84	PHE	0	0.030	0.017	8.082	1.200	1.200	0.000	0.000	0.000	0.000
70	A	85	VAL	0	0.013	-0.001	5.803	-1.694	-1.694	0.000	0.000	0.000	0.000
71	A	86	LEU	0	-0.011	0.012	4.629	3.792	3.833	-0.001	-0.030	-0.010	0.000
72	A	87	ARG	1	0.800	0.867	2.127	-93.591	-86.126	4.335	-5.993	-5.807	0.074
73	A	88	LYS	1	0.886	0.965	2.412	-28.116	-26.794	1.105	-1.191	-1.236	-0.015
74	A	89	ALA	0	0.012	0.005	4.319	4.742	4.914	-0.001	-0.029	-0.142	0.000
75	A	90	GLY	0	-0.019	-0.010	5.832	5.499	5.499	0.000	0.000	0.000	0.000
76	A	91	GLY	0	-0.043	-0.006	8.373	-1.977	-1.977	0.000	0.000	0.000	0.000
77	A	92	ASP	-1	-0.789	-0.909	10.604	23.509	23.509	0.000	0.000	0.000	0.000
78	A	93	PRO	0	-0.101	-0.045	5.797	1.634	1.634	0.000	0.000	0.000	0.000
79	A	94	LEU	0	0.040	0.018	7.243	0.346	0.346	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.838	-0.929	6.397	34.354	34.354	0.000	0.000	0.000	0.000
81	A	96	TYR	0	-0.027	-0.011	5.169	-2.142	-2.142	0.000	0.000	0.000	0.000
82	A	97	LEU	0	0.019	0.010	8.455	-2.304	-2.304	0.000	0.000	0.000	0.000
83	A	98	THR	0	-0.052	-0.016	9.209	1.604	1.604	0.000	0.000	0.000	0.000
84	A	99	ILE	0	0.041	0.012	11.815	-1.519	-1.519	0.000	0.000	0.000	0.000
85	A	100	LYS	1	0.889	0.958	13.766	-17.661	-17.661	0.000	0.000	0.000	0.000
86	A	101	PHE	0	0.037	0.004	14.209	-0.723	-0.723	0.000	0.000	0.000	0.000
87	A	102	THR	0	-0.037	-0.029	18.844	0.121	0.121	0.000	0.000	0.000	0.000
88	A	103	ASP	-1	-0.924	-0.964	22.067	10.867	10.867	0.000	0.000	0.000	0.000
89	A	104	VAL	0	0.004	0.007	19.120	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	105	ILE	0	0.029	0.013	22.473	-0.236	-0.236	0.000	0.000	0.000	0.000
91	A	106	ILE	0	-0.002	0.003	20.236	0.269	0.269	0.000	0.000	0.000	0.000
92	A	107	THR	0	0.002	-0.009	22.511	-0.321	-0.321	0.000	0.000	0.000	0.000
93	A	108	ARG	1	0.923	0.954	21.875	-12.754	-12.754	0.000	0.000	0.000	0.000
94	A	109	VAL	0	0.023	0.009	20.115	0.663	0.663	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.920	-0.931	20.262	12.484	12.484	0.000	0.000	0.000	0.000
96	A	111	MET	0	-0.022	-0.019	19.569	0.826	0.826	0.000	0.000	0.000	0.000
97	A	112	ALA	0	-0.015	-0.015	19.896	-0.728	-0.728	0.000	0.000	0.000	0.000
98	A	113	GLY	0	0.028	0.005	19.719	0.976	0.976	0.000	0.000	0.000	0.000
99	A	114	SER	0	-0.052	-0.015	21.333	-0.732	-0.732	0.000	0.000	0.000	0.000
100	A	115	LEU	0	0.030	0.001	22.237	0.343	0.343	0.000	0.000	0.000	0.000
101	A	116	GLU	-1	-0.986	-0.973	21.638	13.050	13.050	0.000	0.000	0.000	0.000
102	A	117	ASP	-1	-0.859	-0.919	18.133	16.468	16.468	0.000	0.000	0.000	0.000
103	A	118	GLU	-1	-0.882	-0.911	12.698	24.604	24.604	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.099	-0.083	13.968	1.580	1.580	0.000	0.000	0.000	0.000
105	A	120	ARG	1	0.914	0.981	11.484	-23.955	-23.955	0.000	0.000	0.000	0.000
106	A	121	PRO	0	0.070	0.048	16.538	0.439	0.439	0.000	0.000	0.000	0.000
107	A	122	ARG	1	0.840	0.883	12.325	-20.406	-20.406	0.000	0.000	0.000	0.000
108	A	123	GLU	-1	-0.761	-0.898	15.143	15.311	15.311	0.000	0.000	0.000	0.000
109	A	124	GLU	-1	-0.821	-0.883	14.960	17.051	17.051	0.000	0.000	0.000	0.000
110	A	125	ILE	0	-0.060	-0.033	15.415	-0.949	-0.949	0.000	0.000	0.000	0.000
111	A	126	ARG	1	0.829	0.894	16.526	-13.413	-13.413	0.000	0.000	0.000	0.000
112	A	127	PHE	0	-0.061	-0.030	15.363	-0.280	-0.280	0.000	0.000	0.000	0.000
113	A	128	SER	0	0.094	0.040	20.652	-0.076	-0.076	0.000	0.000	0.000	0.000
114	A	129	PHE	0	-0.040	-0.035	19.982	0.464	0.464	0.000	0.000	0.000	0.000
115	A	130	THR	0	0.035	0.027	23.446	-0.236	-0.236	0.000	0.000	0.000	0.000
116	A	131	LYS	1	0.918	0.974	23.987	-11.307	-11.307	0.000	0.000	0.000	0.000
117	A	132	MET	0	-0.033	0.010	17.865	0.298	0.298	0.000	0.000	0.000	0.000
118	A	133	THR	0	0.011	-0.009	18.307	-0.855	-0.855	0.000	0.000	0.000	0.000
119	A	134	GLN	0	-0.021	-0.006	14.705	1.474	1.474	0.000	0.000	0.000	0.000
120	A	135	ASP	-1	-0.847	-0.875	14.924	15.093	15.093	0.000	0.000	0.000	0.000
121	A	136	TYR	0	0.000	-0.007	11.742	1.337	1.337	0.000	0.000	0.000	0.000
122	A	137	VAL	0	-0.016	-0.010	12.318	-1.416	-1.416	0.000	0.000	0.000	0.000
123	A	138	MET	0	-0.023	-0.006	13.117	0.724	0.724	0.000	0.000	0.000	0.000
124	A	139	GLN	0	0.042	0.010	13.257	-0.059	-0.059	0.000	0.000	0.000	0.000
125	A	140	ASN	0	-0.070	-0.043	16.099	0.030	0.030	0.000	0.000	0.000	0.000
126	A	141	ALA	0	0.075	0.022	18.536	0.390	0.390	0.000	0.000	0.000	0.000
127	A	142	GLU	-1	-0.927	-0.950	19.553	13.334	13.334	0.000	0.000	0.000	0.000
128	A	143	GLY	0	-0.005	0.012	16.841	0.992	0.992	0.000	0.000	0.000	0.000
129	A	144	HIS	0	0.022	0.019	16.810	0.186	0.186	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.901	0.957	15.710	-15.513	-15.513	0.000	0.000	0.000	0.000
131	A	146	SER	0	-0.008	-0.014	17.170	-0.561	-0.561	0.000	0.000	0.000	0.000
132	A	147	GLY	0	-0.046	-0.043	18.386	-0.776	-0.776	0.000	0.000	0.000	0.000
133	A	148	VAL	0	-0.016	-0.010	16.550	0.975	0.975	0.000	0.000	0.000	0.000
134	A	149	ILE	0	-0.025	0.007	17.535	-0.860	-0.860	0.000	0.000	0.000	0.000
135	A	150	SER	0	0.005	-0.054	17.811	0.694	0.694	0.000	0.000	0.000	0.000
136	A	151	ALA	0	-0.055	-0.014	19.660	-0.666	-0.666	0.000	0.000	0.000	0.000
137	A	152	ASN	0	0.004	-0.002	20.498	0.524	0.524	0.000	0.000	0.000	0.000
138	A	153	TYR	0	0.005	-0.006	22.791	-0.620	-0.620	0.000	0.000	0.000	0.000
139	A	154	ASP	-1	-0.839	-0.893	24.723	10.727	10.727	0.000	0.000	0.000	0.000
140	A	155	VAL	0	-0.073	-0.076	26.880	-0.671	-0.671	0.000	0.000	0.000	0.000

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