FMO DATABASE

FMODB ID: N938Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1338774.451284
FMO2-HF: Nuclear repulsion	1281251.934044
FMO2-HF: Total energy	-57522.51724
FMO2-MP2: Total energy	-57690.952505

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.
-35.557	-30.903	0.297	-2.245	-2.706	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 : -0.983

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	-0.077	-0.075	3.190	-10.912	-7.634	0.062	-1.817	-1.523	0.009
4	A	12	LYS	1	0.845	0.910	2.693	-46.388	-45.288	0.236	-0.361	-0.974	0.002
5	A	13	ILE	0	0.034	0.026	4.317	-4.709	-4.433	-0.001	-0.067	-0.209	0.000
6	A	14	ARG	1	0.914	0.964	6.577	-30.719	-30.719	0.000	0.000	0.000	0.000
7	A	15	ALA	0	0.042	0.028	8.812	-1.854	-1.854	0.000	0.000	0.000	0.000
8	A	16	TYR	0	-0.042	-0.055	7.599	-1.823	-1.823	0.000	0.000	0.000	0.000
9	A	17	ALA	0	-0.004	0.002	10.468	-1.252	-1.252	0.000	0.000	0.000	0.000
10	A	18	GLN	0	-0.030	-0.003	12.726	-0.947	-0.947	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.015	-0.026	14.512	0.811	0.811	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.004	0.015	16.506	-0.503	-0.503	0.000	0.000	0.000	0.000
13	A	21	GLU	-1	-0.829	-0.942	17.934	16.038	16.038	0.000	0.000	0.000	0.000
14	A	22	ILE	0	0.006	0.005	21.377	-0.394	-0.394	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.007	-0.009	25.028	0.124	0.124	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.031	-0.021	27.390	-0.286	-0.286	0.000	0.000	0.000	0.000
17	A	25	PHE	0	0.021	0.006	30.841	0.098	0.098	0.000	0.000	0.000	0.000
18	A	26	VAL	0	-0.055	-0.030	33.541	-0.148	-0.148	0.000	0.000	0.000	0.000
19	A	27	VAL	0	0.030	0.011	36.884	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	28	ASN	0	-0.024	-0.027	40.495	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	29	SER	0	-0.030	-0.050	41.591	-0.250	-0.250	0.000	0.000	0.000	0.000
22	A	30	ASN	0	-0.038	-0.004	38.794	0.259	0.259	0.000	0.000	0.000	0.000
23	A	31	PHE	0	0.004	0.001	36.239	-0.161	-0.161	0.000	0.000	0.000	0.000
24	A	32	LYS	1	0.865	0.937	34.766	-7.959	-7.959	0.000	0.000	0.000	0.000
25	A	33	VAL	0	0.012	0.015	28.770	-0.115	-0.115	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.809	-0.899	32.044	8.722	8.722	0.000	0.000	0.000	0.000
27	A	35	GLY	0	0.017	0.002	31.627	0.035	0.035	0.000	0.000	0.000	0.000
28	A	36	ALA	0	-0.027	-0.030	26.040	0.098	0.098	0.000	0.000	0.000	0.000
29	A	37	TYR	0	-0.055	-0.026	25.702	0.067	0.067	0.000	0.000	0.000	0.000
30	A	38	LEU	0	0.002	-0.001	19.277	0.111	0.111	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.804	0.901	23.223	-10.495	-10.495	0.000	0.000	0.000	0.000
32	A	40	TRP	0	0.004	-0.005	18.311	0.652	0.652	0.000	0.000	0.000	0.000
33	A	41	GLY	0	0.020	0.020	15.725	-0.118	-0.118	0.000	0.000	0.000	0.000
34	A	42	LYS	1	0.795	0.895	10.188	-23.501	-23.501	0.000	0.000	0.000	0.000
35	A	43	PHE	0	0.059	0.039	16.518	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	44	HIS	0	-0.034	-0.045	14.814	0.880	0.880	0.000	0.000	0.000	0.000
37	A	45	VAL	0	0.005	0.014	16.798	-0.774	-0.774	0.000	0.000	0.000	0.000
38	A	46	PRO	0	0.013	0.009	16.784	0.961	0.961	0.000	0.000	0.000	0.000
39	A	47	GLY	0	-0.003	0.009	16.647	-0.180	-0.180	0.000	0.000	0.000	0.000
40	A	48	ASP	-1	-0.889	-0.945	12.355	23.063	23.063	0.000	0.000	0.000	0.000
41	A	49	LYS	1	0.895	0.949	10.422	-21.315	-21.315	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.817	-0.860	7.528	33.656	33.656	0.000	0.000	0.000	0.000
43	A	51	LYS	1	0.834	0.916	10.400	-20.551	-20.551	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.811	-0.865	14.104	16.548	16.548	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.036	-0.011	15.600	-0.441	-0.441	0.000	0.000	0.000	0.000
46	A	54	SER	0	0.007	-0.013	19.376	-0.094	-0.094	0.000	0.000	0.000	0.000
47	A	55	PRO	0	0.044	-0.004	21.788	-0.188	-0.188	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.018	-0.017	24.595	-0.324	-0.324	0.000	0.000	0.000	0.000
49	A	57	GLN	0	-0.004	0.017	21.665	-0.055	-0.055	0.000	0.000	0.000	0.000
50	A	58	ILE	0	0.024	0.041	22.472	-0.109	-0.109	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.019	0.008	26.521	-0.408	-0.408	0.000	0.000	0.000	0.000
52	A	60	GLY	0	0.048	0.025	29.758	0.025	0.025	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.077	-0.048	28.824	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	62	ILE	0	-0.038	-0.030	31.333	-0.173	-0.173	0.000	0.000	0.000	0.000
55	A	63	ILE	0	-0.042	-0.014	31.343	0.183	0.183	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.904	0.926	34.142	-8.631	-8.631	0.000	0.000	0.000	0.000
57	A	65	ASP	-1	-0.803	-0.902	36.793	7.564	7.564	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.975	-0.981	38.160	7.513	7.513	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.886	-0.912	33.377	8.987	8.987	0.000	0.000	0.000	0.000
60	A	68	SER	0	-0.028	-0.039	30.023	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	69	TYR	0	-0.037	-0.016	25.961	0.236	0.236	0.000	0.000	0.000	0.000
62	A	70	THR	0	0.000	0.001	22.530	-0.330	-0.330	0.000	0.000	0.000	0.000
63	A	71	ILE	0	-0.011	0.016	22.701	0.188	0.188	0.000	0.000	0.000	0.000
64	A	72	ALA	0	0.019	0.017	18.138	-0.070	-0.070	0.000	0.000	0.000	0.000
65	A	73	SER	0	-0.012	-0.016	17.325	-0.095	-0.095	0.000	0.000	0.000	0.000
66	A	74	CYS	0	-0.021	-0.014	12.184	0.274	0.274	0.000	0.000	0.000	0.000
67	A	75	GLY	0	0.010	0.028	13.127	-0.535	-0.535	0.000	0.000	0.000	0.000
68	A	76	ARG	1	0.787	0.853	11.693	-17.157	-17.157	0.000	0.000	0.000	0.000
69	A	77	GLU	-1	-0.801	-0.912	6.839	24.273	24.273	0.000	0.000	0.000	0.000
70	A	78	ASN	0	-0.062	-0.023	7.499	1.623	1.623	0.000	0.000	0.000	0.000
71	A	79	ALA	0	0.038	0.005	9.277	-1.231	-1.231	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.048	0.000	12.884	-0.231	-0.231	0.000	0.000	0.000	0.000
73	A	81	SER	0	0.045	0.021	14.534	0.826	0.826	0.000	0.000	0.000	0.000
74	A	82	GLY	0	-0.019	-0.007	15.734	-0.651	-0.651	0.000	0.000	0.000	0.000
75	A	83	THR	0	0.003	-0.012	16.777	0.175	0.175	0.000	0.000	0.000	0.000
76	A	84	GLU	-1	-0.742	-0.845	18.962	10.778	10.778	0.000	0.000	0.000	0.000
77	A	85	GLY	0	0.046	0.021	22.628	0.156	0.156	0.000	0.000	0.000	0.000
78	A	86	GLY	0	0.048	0.026	24.751	-0.251	-0.251	0.000	0.000	0.000	0.000
79	A	87	PHE	0	-0.033	-0.015	26.449	0.199	0.199	0.000	0.000	0.000	0.000
80	A	88	SER	0	-0.011	0.003	29.571	-0.108	-0.108	0.000	0.000	0.000	0.000
81	A	89	LEU	0	-0.019	0.010	32.836	0.160	0.160	0.000	0.000	0.000	0.000
82	A	90	TYR	0	0.045	0.003	34.877	-0.250	-0.250	0.000	0.000	0.000	0.000
83	A	91	ASP	-1	-0.710	-0.786	38.169	7.254	7.254	0.000	0.000	0.000	0.000
84	A	92	GLY	0	-0.002	-0.001	41.005	-0.186	-0.186	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.930	-0.972	41.207	7.087	7.087	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.853	0.941	43.066	-6.652	-6.652	0.000	0.000	0.000	0.000
87	A	95	LEU	0	-0.014	-0.004	37.030	0.147	0.147	0.000	0.000	0.000	0.000
88	A	96	VAL	0	-0.020	0.004	38.251	-0.130	-0.130	0.000	0.000	0.000	0.000
89	A	97	PHE	0	-0.027	-0.034	31.711	-0.130	-0.130	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.799	-0.886	33.912	8.050	8.050	0.000	0.000	0.000	0.000
91	A	99	TYR	0	-0.060	-0.068	26.365	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	100	TYR	0	-0.043	-0.041	27.548	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	101	TRP	0	-0.026	-0.029	21.359	-0.375	-0.375	0.000	0.000	0.000	0.000
94	A	102	ASP	-1	-0.853	-0.930	24.029	11.842	11.842	0.000	0.000	0.000	0.000
95	A	103	CYS	0	-0.038	-0.007	20.459	-0.270	-0.270	0.000	0.000	0.000	0.000
96	A	104	PRO	0	0.066	0.044	19.588	0.928	0.928	0.000	0.000	0.000	0.000
97	A	105	TRP	0	-0.017	-0.011	13.183	0.733	0.733	0.000	0.000	0.000	0.000
98	A	106	SER	0	-0.063	-0.033	17.720	0.252	0.252	0.000	0.000	0.000	0.000
99	A	107	GLY	0	0.029	0.003	20.429	-0.467	-0.467	0.000	0.000	0.000	0.000
100	A	108	SER	0	-0.041	-0.005	23.089	0.255	0.255	0.000	0.000	0.000	0.000
101	A	109	ASN	0	0.012	-0.016	22.075	0.234	0.234	0.000	0.000	0.000	0.000
102	A	110	SER	0	-0.005	0.013	24.885	-0.536	-0.536	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.749	-0.849	26.828	10.536	10.536	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.884	-0.938	29.139	8.226	8.226	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.067	-0.019	31.924	0.196	0.196	0.000	0.000	0.000	0.000
106	A	114	THR	0	0.037	0.024	34.066	-0.222	-0.222	0.000	0.000	0.000	0.000
107	A	115	VAL	0	-0.021	-0.017	37.138	0.001	0.001	0.000	0.000	0.000	0.000
108	A	116	LYS	1	0.822	0.880	39.229	-7.791	-7.791	0.000	0.000	0.000	0.000
109	A	117	ASP	-1	-0.752	-0.859	41.779	6.465	6.465	0.000	0.000	0.000	0.000
110	A	118	LYS	1	0.912	0.932	42.149	-7.119	-7.119	0.000	0.000	0.000	0.000
111	A	119	GLU	-1	-0.904	-0.927	44.916	6.045	6.045	0.000	0.000	0.000	0.000
112	A	120	ASN	0	-0.030	-0.039	46.473	-0.142	-0.142	0.000	0.000	0.000	0.000
113	A	121	TYR	0	-0.055	-0.048	41.679	0.013	0.013	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.046	-0.017	41.652	-0.107	-0.107	0.000	0.000	0.000	0.000
115	A	123	VAL	0	0.010	0.005	36.544	0.128	0.128	0.000	0.000	0.000	0.000
116	A	124	ILE	0	-0.040	-0.025	36.309	-0.069	-0.069	0.000	0.000	0.000	0.000
117	A	125	LYS	1	0.857	0.940	29.967	-9.645	-9.645	0.000	0.000	0.000	0.000
118	A	126	LYS	1	0.873	0.941	31.640	-8.721	-8.721	0.000	0.000	0.000	0.000
119	A	127	GLY	0	0.088	0.045	28.122	0.282	0.282	0.000	0.000	0.000	0.000
120	A	128	GLY	0	0.020	0.000	26.851	-0.313	-0.313	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.019	-0.007	27.863	-0.136	-0.136	0.000	0.000	0.000	0.000
122	A	130	SER	0	-0.019	-0.045	27.642	0.155	0.155	0.000	0.000	0.000	0.000
123	A	131	PRO	0	-0.038	0.003	24.456	-0.209	-0.209	0.000	0.000	0.000	0.000
124	A	132	SER	0	-0.002	-0.013	24.047	0.080	0.080	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.005	-0.005	20.281	0.162	0.162	0.000	0.000	0.000	0.000
126	A	134	ALA	0	-0.004	0.012	17.233	-0.199	-0.199	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.010	0.013	19.100	-0.535	-0.535	0.000	0.000	0.000	0.000
128	A	136	GLY	0	-0.023	-0.001	20.033	-0.524	-0.524	0.000	0.000	0.000	0.000
129	A	137	ASN	0	0.005	-0.003	21.278	0.349	0.349	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.022	-0.019	23.535	-0.423	-0.423	0.000	0.000	0.000	0.000
131	A	139	PHE	0	-0.020	-0.007	26.637	0.105	0.105	0.000	0.000	0.000	0.000
132	A	140	ILE	0	-0.001	-0.009	29.591	-0.226	-0.226	0.000	0.000	0.000	0.000
133	A	141	THR	0	0.003	0.022	32.393	-0.027	-0.027	0.000	0.000	0.000	0.000
134	A	142	VAL	0	-0.012	-0.017	35.397	-0.119	-0.119	0.000	0.000	0.000	0.000
135	A	143	VAL	0	0.026	0.019	37.958	0.011	0.011	0.000	0.000	0.000	0.000
136	A	144	LYS	1	0.857	0.914	41.499	-6.939	-6.939	0.000	0.000	0.000	0.000
137	A	145	LYS	1	0.778	0.897	44.092	-6.618	-6.618	0.000	0.000	0.000	0.000
138	A	146	SER	0	0.081	0.039	47.245	0.005	0.005	0.000	0.000	0.000	0.000
139	A	147	LEU	0	-0.016	-0.003	49.970	-0.041	-0.041	0.000	0.000	0.000	0.000
140	A	148	GLU	-1	-0.934	-0.955	53.204	5.818	5.818	0.000	0.000	0.000	0.000
141	A	149	HIS	0	-0.027	-0.021	49.203	-0.044	-0.044	0.000	0.000	0.000	0.000
142	A	150	HIS	0	-0.019	-0.030	47.160	-0.068	-0.068	0.000	0.000	0.000	0.000
143	A	151	HIS	0	-0.070	-0.024	52.245	-0.091	-0.091	0.000	0.000	0.000	0.000
144	A	152	HIS	0	0.040	0.010	50.224	-0.084	-0.084	0.000	0.000	0.000	0.000
145	A	153	HIS	0	-0.023	-0.008	52.645	0.050	0.050	0.000	0.000	0.000	0.000
146	A	154	HIS	0	-0.001	0.012	55.368	-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)