FMO DATABASE

FMODB ID: 85J7Y

Calculation Name: 5V3S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V3S

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0U4

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1338103.2722
FMO2-HF: Nuclear repulsion	1280581.679984
FMO2-HF: Total energy	-57521.592216
FMO2-MP2: Total energy	-57689.9931

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:9:GLU)

Summations of interaction energy for fragment #1(A:9:GLU)

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.
-34.491	-29.656	0.973	-2.675	-3.132	0.011

Interaction energy analysis for fragmet #1(A:9:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.956 / q_NPA : -0.984

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	11	SER	0	-0.123	-0.095	3.189	-10.964	-7.653	0.065	-1.821	-1.553	0.008
4	A	12	LYS	1	0.906	0.945	2.351	-46.278	-45.236	0.906	-0.702	-1.247	0.003
5	A	13	ILE	0	0.028	0.029	3.796	-5.027	-4.545	0.002	-0.152	-0.332	0.000
6	A	14	ARG	1	0.929	0.977	6.573	-30.343	-30.343	0.000	0.000	0.000	0.000
7	A	15	ALA	0	0.031	0.022	8.808	-1.899	-1.899	0.000	0.000	0.000	0.000
8	A	16	TYR	0	-0.031	-0.021	7.652	-1.918	-1.918	0.000	0.000	0.000	0.000
9	A	17	ALA	0	-0.012	-0.002	10.471	-1.233	-1.233	0.000	0.000	0.000	0.000
10	A	18	GLN	0	-0.012	0.014	12.725	-0.823	-0.823	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.036	-0.032	14.542	0.710	0.710	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.006	0.010	16.509	-0.484	-0.484	0.000	0.000	0.000	0.000
13	A	21	GLU	-1	-0.867	-0.954	18.090	15.802	15.802	0.000	0.000	0.000	0.000
14	A	22	ILE	0	-0.005	-0.001	21.378	-0.380	-0.380	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.015	-0.013	25.031	0.111	0.111	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.025	-0.016	27.391	-0.279	-0.279	0.000	0.000	0.000	0.000
17	A	25	PHE	0	0.024	0.010	30.843	0.113	0.113	0.000	0.000	0.000	0.000
18	A	26	VAL	0	-0.055	-0.031	33.542	-0.148	-0.148	0.000	0.000	0.000	0.000
19	A	27	VAL	0	0.025	0.006	36.886	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	28	ASN	0	-0.002	-0.009	40.496	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	29	SER	0	-0.064	-0.048	41.718	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	30	ASN	0	-0.013	0.004	38.723	0.222	0.222	0.000	0.000	0.000	0.000
23	A	31	PHE	0	-0.007	0.003	36.151	-0.161	-0.161	0.000	0.000	0.000	0.000
24	A	32	LYS	1	0.930	0.983	34.778	-7.834	-7.834	0.000	0.000	0.000	0.000
25	A	33	VAL	0	0.010	0.013	28.846	-0.117	-0.117	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.872	-0.951	32.036	8.710	8.710	0.000	0.000	0.000	0.000
27	A	35	GLY	0	0.024	0.006	31.642	0.046	0.046	0.000	0.000	0.000	0.000
28	A	36	ALA	0	-0.027	-0.023	26.012	0.095	0.095	0.000	0.000	0.000	0.000
29	A	37	TYR	0	-0.061	-0.027	25.715	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.004	-0.004	19.151	0.121	0.121	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.844	0.931	23.241	-10.473	-10.473	0.000	0.000	0.000	0.000
32	A	40	TRP	0	0.004	0.000	18.242	0.682	0.682	0.000	0.000	0.000	0.000
33	A	41	GLY	0	0.025	0.024	15.744	-0.096	-0.096	0.000	0.000	0.000	0.000
34	A	42	LYS	1	0.805	0.887	9.883	-23.418	-23.418	0.000	0.000	0.000	0.000
35	A	43	PHE	0	0.054	0.032	16.535	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	44	HIS	0	-0.022	-0.040	14.780	0.821	0.821	0.000	0.000	0.000	0.000
37	A	45	VAL	0	-0.005	0.014	16.811	-0.754	-0.754	0.000	0.000	0.000	0.000
38	A	46	PRO	0	0.027	0.013	16.786	0.969	0.969	0.000	0.000	0.000	0.000
39	A	47	GLY	0	0.010	0.014	16.700	-0.198	-0.198	0.000	0.000	0.000	0.000
40	A	48	ASP	-1	-0.903	-0.967	12.197	22.706	22.706	0.000	0.000	0.000	0.000
41	A	49	LYS	1	0.903	0.947	10.442	-21.748	-21.748	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.880	-0.924	7.479	32.243	32.243	0.000	0.000	0.000	0.000
43	A	51	LYS	1	0.887	0.953	10.407	-19.068	-19.068	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.826	-0.891	14.112	16.056	16.056	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.020	-0.005	15.614	-0.435	-0.435	0.000	0.000	0.000	0.000
46	A	54	SER	0	-0.004	-0.004	19.390	-0.081	-0.081	0.000	0.000	0.000	0.000
47	A	55	PRO	0	0.047	0.000	21.805	-0.203	-0.203	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.057	-0.038	24.611	-0.347	-0.347	0.000	0.000	0.000	0.000
49	A	57	GLN	0	0.020	0.013	21.966	0.131	0.131	0.000	0.000	0.000	0.000
50	A	58	ILE	0	0.021	0.041	22.574	-0.098	-0.098	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.020	0.004	26.533	-0.344	-0.344	0.000	0.000	0.000	0.000
52	A	60	GLY	0	0.060	0.035	29.771	0.033	0.033	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.097	-0.056	28.825	-0.166	-0.166	0.000	0.000	0.000	0.000
54	A	62	ILE	0	-0.048	-0.035	31.342	-0.177	-0.177	0.000	0.000	0.000	0.000
55	A	63	ILE	0	-0.031	-0.012	31.325	0.175	0.175	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.950	0.959	34.146	-8.366	-8.366	0.000	0.000	0.000	0.000
57	A	65	ASP	-1	-0.794	-0.903	36.794	7.504	7.504	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.988	-0.988	38.165	7.468	7.468	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.910	-0.927	33.379	8.937	8.937	0.000	0.000	0.000	0.000
60	A	68	SER	0	-0.062	-0.065	29.771	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	69	TYR	0	-0.001	0.005	25.539	0.146	0.146	0.000	0.000	0.000	0.000
62	A	70	THR	0	0.001	0.003	22.512	-0.324	-0.324	0.000	0.000	0.000	0.000
63	A	71	ILE	0	-0.014	0.013	22.710	0.181	0.181	0.000	0.000	0.000	0.000
64	A	72	ALA	0	0.029	0.019	18.102	-0.066	-0.066	0.000	0.000	0.000	0.000
65	A	73	SER	0	-0.013	-0.004	17.364	-0.099	-0.099	0.000	0.000	0.000	0.000
66	A	74	CYS	0	-0.011	0.000	12.205	0.227	0.227	0.000	0.000	0.000	0.000
67	A	75	GLY	0	0.019	0.027	13.139	-0.551	-0.551	0.000	0.000	0.000	0.000
68	A	76	ARG	1	0.781	0.880	11.707	-16.494	-16.494	0.000	0.000	0.000	0.000
69	A	77	GLU	-1	-0.806	-0.917	6.846	24.416	24.416	0.000	0.000	0.000	0.000
70	A	78	ASN	0	-0.047	-0.011	6.720	2.296	2.296	0.000	0.000	0.000	0.000
71	A	79	ALA	0	0.042	0.005	9.277	-1.241	-1.241	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.066	-0.020	12.884	-0.210	-0.210	0.000	0.000	0.000	0.000
73	A	81	SER	0	0.050	0.021	14.534	0.806	0.806	0.000	0.000	0.000	0.000
74	A	82	GLY	0	-0.013	-0.005	15.737	-0.661	-0.661	0.000	0.000	0.000	0.000
75	A	83	THR	0	-0.002	-0.021	16.791	0.183	0.183	0.000	0.000	0.000	0.000
76	A	84	GLU	-1	-0.743	-0.827	18.975	10.901	10.901	0.000	0.000	0.000	0.000
77	A	85	GLY	0	0.021	0.007	22.642	0.143	0.143	0.000	0.000	0.000	0.000
78	A	86	GLY	0	0.058	0.032	24.765	-0.229	-0.229	0.000	0.000	0.000	0.000
79	A	87	PHE	0	-0.042	-0.021	26.893	0.196	0.196	0.000	0.000	0.000	0.000
80	A	88	SER	0	0.008	0.012	29.583	-0.198	-0.198	0.000	0.000	0.000	0.000
81	A	89	LEU	0	-0.004	0.015	32.847	0.155	0.155	0.000	0.000	0.000	0.000
82	A	90	TYR	0	0.019	-0.007	34.886	-0.135	-0.135	0.000	0.000	0.000	0.000
83	A	91	ASP	-1	-0.724	-0.814	38.178	7.246	7.246	0.000	0.000	0.000	0.000
84	A	92	GLY	0	-0.002	-0.006	41.013	-0.187	-0.187	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.938	-0.976	41.218	7.048	7.048	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.901	0.962	43.081	-6.530	-6.530	0.000	0.000	0.000	0.000
87	A	95	LEU	0	-0.002	0.004	37.048	0.123	0.123	0.000	0.000	0.000	0.000
88	A	96	VAL	0	-0.016	0.005	38.291	-0.131	-0.131	0.000	0.000	0.000	0.000
89	A	97	PHE	0	-0.042	-0.041	31.771	-0.137	-0.137	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.881	-0.935	33.924	8.143	8.143	0.000	0.000	0.000	0.000
91	A	99	TYR	0	-0.055	-0.058	26.500	0.005	0.005	0.000	0.000	0.000	0.000
92	A	100	TYR	0	-0.057	-0.077	27.332	0.045	0.045	0.000	0.000	0.000	0.000
93	A	101	TRP	0	-0.039	-0.031	21.448	-0.386	-0.386	0.000	0.000	0.000	0.000
94	A	102	ASP	-1	-0.846	-0.928	24.041	11.829	11.829	0.000	0.000	0.000	0.000
95	A	103	CYS	0	-0.041	-0.017	20.436	-0.214	-0.214	0.000	0.000	0.000	0.000
96	A	104	PRO	0	0.062	0.047	19.598	0.890	0.890	0.000	0.000	0.000	0.000
97	A	105	TRP	0	-0.030	-0.019	13.027	0.723	0.723	0.000	0.000	0.000	0.000
98	A	106	SER	0	-0.040	-0.025	17.720	0.271	0.271	0.000	0.000	0.000	0.000
99	A	107	GLY	0	0.018	0.000	20.429	-0.482	-0.482	0.000	0.000	0.000	0.000
100	A	108	SER	0	-0.025	-0.003	23.095	0.323	0.323	0.000	0.000	0.000	0.000
101	A	109	ASN	0	0.015	-0.007	21.966	0.217	0.217	0.000	0.000	0.000	0.000
102	A	110	SER	0	-0.022	-0.009	24.890	-0.526	-0.526	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.765	-0.873	26.836	10.484	10.484	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.892	-0.942	29.147	8.225	8.225	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.057	-0.018	31.933	0.171	0.171	0.000	0.000	0.000	0.000
106	A	114	THR	0	0.020	0.016	34.074	-0.220	-0.220	0.000	0.000	0.000	0.000
107	A	115	VAL	0	-0.019	-0.016	37.146	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	116	LYS	1	0.909	0.933	39.417	-7.499	-7.499	0.000	0.000	0.000	0.000
109	A	117	ASP	-1	-0.776	-0.872	41.788	6.453	6.453	0.000	0.000	0.000	0.000
110	A	118	LYS	1	0.922	0.941	42.455	-7.069	-7.069	0.000	0.000	0.000	0.000
111	A	119	GLU	-1	-0.940	-0.941	44.922	5.991	5.991	0.000	0.000	0.000	0.000
112	A	120	ASN	0	-0.057	-0.062	46.456	-0.151	-0.151	0.000	0.000	0.000	0.000
113	A	121	TYR	0	-0.057	-0.040	41.668	0.007	0.007	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.057	-0.025	41.463	-0.103	-0.103	0.000	0.000	0.000	0.000
115	A	123	VAL	0	0.009	0.006	36.593	0.118	0.118	0.000	0.000	0.000	0.000
116	A	124	ILE	0	-0.037	-0.023	36.214	-0.075	-0.075	0.000	0.000	0.000	0.000
117	A	125	LYS	1	0.881	0.961	30.033	-9.584	-9.584	0.000	0.000	0.000	0.000
118	A	126	LYS	1	0.880	0.945	31.586	-8.726	-8.726	0.000	0.000	0.000	0.000
119	A	127	GLY	0	0.083	0.044	28.120	0.279	0.279	0.000	0.000	0.000	0.000
120	A	128	GLY	0	0.020	0.002	26.853	-0.326	-0.326	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.028	-0.016	27.864	-0.131	-0.131	0.000	0.000	0.000	0.000
122	A	130	SER	0	-0.012	-0.026	27.678	0.155	0.155	0.000	0.000	0.000	0.000
123	A	131	PRO	0	-0.047	0.001	24.482	-0.201	-0.201	0.000	0.000	0.000	0.000
124	A	132	SER	0	0.002	-0.015	23.927	0.089	0.089	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.006	-0.006	20.247	0.163	0.163	0.000	0.000	0.000	0.000
126	A	134	ALA	0	0.002	0.009	17.204	-0.203	-0.203	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.033	0.005	19.098	-0.534	-0.534	0.000	0.000	0.000	0.000
128	A	136	GLY	0	-0.020	-0.002	20.028	-0.537	-0.537	0.000	0.000	0.000	0.000
129	A	137	ASN	0	0.006	-0.003	21.275	0.158	0.158	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.021	-0.013	23.532	-0.413	-0.413	0.000	0.000	0.000	0.000
131	A	139	PHE	0	-0.032	-0.014	26.637	0.094	0.094	0.000	0.000	0.000	0.000
132	A	140	ILE	0	0.006	-0.011	29.590	-0.215	-0.215	0.000	0.000	0.000	0.000
133	A	141	THR	0	0.005	0.019	32.394	0.045	0.045	0.000	0.000	0.000	0.000
134	A	142	VAL	0	-0.001	-0.011	35.322	-0.124	-0.124	0.000	0.000	0.000	0.000
135	A	143	VAL	0	0.034	0.027	37.961	0.006	0.006	0.000	0.000	0.000	0.000
136	A	144	LYS	1	0.896	0.939	41.501	-6.837	-6.837	0.000	0.000	0.000	0.000
137	A	145	LYS	1	0.819	0.914	44.096	-6.542	-6.542	0.000	0.000	0.000	0.000
138	A	146	SER	0	0.053	0.035	47.247	-0.039	-0.039	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.015	-0.012	49.972	-0.033	-0.033	0.000	0.000	0.000	0.000
140	A	148	GLU	-1	-0.946	-0.960	53.342	5.772	5.772	0.000	0.000	0.000	0.000
141	A	149	HIS	0	-0.024	-0.016	49.475	-0.044	-0.044	0.000	0.000	0.000	0.000
142	A	150	HIS	0	-0.026	-0.037	47.312	-0.059	-0.059	0.000	0.000	0.000	0.000
143	A	151	HIS	0	-0.040	-0.010	52.246	-0.059	-0.059	0.000	0.000	0.000	0.000
144	A	152	HIS	0	0.031	0.005	50.147	-0.100	-0.100	0.000	0.000	0.000	0.000
145	A	153	HIS	0	-0.019	-0.004	52.448	0.041	0.041	0.000	0.000	0.000	0.000
146	A	154	HIS	0	0.002	0.013	55.373	-0.035	-0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLU)