FMO DATABASE

FMODB ID: YVG22

Calculation Name: 3DFG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DFG

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P9X1

Base Structure: X-ray

Registration Date: 2023-09-23

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1160081.146807
FMO2-HF: Nuclear repulsion	1106006.616454
FMO2-HF: Total energy	-54074.530354
FMO2-MP2: Total energy	-54235.735272

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:17:GLN)

Summations of interaction energy for fragment #1(A:17:GLN)

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.
-21.802	-13.579	4.589	-4.711	-8.104	-0.009

Interaction energy analysis for fragmet #1(A:17:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.003

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	19	PRO	0	0.067	0.016	3.221	0.722	2.640	0.072	-0.960	-1.032	0.000
4	A	20	VAL	0	0.070	0.034	5.923	0.897	0.897	0.000	0.000	0.000	0.000
5	A	21	GLN	0	0.032	0.026	2.183	-4.101	-1.688	2.984	-2.002	-3.396	-0.016
6	A	22	ARG	1	0.871	0.943	2.448	-10.962	-7.294	1.524	-1.684	-3.508	0.007
7	A	23	ALA	0	0.010	0.000	4.024	-1.621	-1.397	0.009	-0.065	-0.168	0.000
8	A	24	LEU	0	0.032	0.025	6.885	-0.386	-0.386	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.015	0.004	5.112	-0.778	-0.778	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.081	-0.045	6.022	-0.700	-0.700	0.000	0.000	0.000	0.000
11	A	27	LEU	0	-0.013	-0.020	8.714	-0.447	-0.447	0.000	0.000	0.000	0.000
12	A	28	VAL	0	-0.022	0.005	8.436	-0.276	-0.276	0.000	0.000	0.000	0.000
13	A	29	HIS	0	-0.057	-0.005	10.438	-0.228	-0.228	0.000	0.000	0.000	0.000
14	A	30	ARG	1	0.796	0.849	11.951	-1.195	-1.195	0.000	0.000	0.000	0.000
15	A	31	GLU	-1	-0.740	-0.812	13.949	0.701	0.701	0.000	0.000	0.000	0.000
16	A	32	HIS	0	-0.067	-0.034	12.194	0.265	0.265	0.000	0.000	0.000	0.000
17	A	33	SER	0	0.045	0.030	15.590	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.911	0.932	16.170	-0.406	-0.406	0.000	0.000	0.000	0.000
19	A	35	LYS	1	0.892	0.942	16.562	-0.514	-0.514	0.000	0.000	0.000	0.000
20	A	36	GLU	-1	-0.814	-0.876	14.796	1.294	1.294	0.000	0.000	0.000	0.000
21	A	37	LEU	0	0.009	-0.002	10.541	0.246	0.246	0.000	0.000	0.000	0.000
22	A	38	ASN	0	0.027	0.028	12.128	0.361	0.361	0.000	0.000	0.000	0.000
23	A	39	ARG	1	1.004	1.002	13.578	-1.074	-1.074	0.000	0.000	0.000	0.000
24	A	40	LYS	1	0.801	0.885	10.644	-1.698	-1.698	0.000	0.000	0.000	0.000
25	A	41	LEU	0	-0.032	-0.014	7.424	0.545	0.545	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.028	0.002	9.873	0.094	0.094	0.000	0.000	0.000	0.000
27	A	43	ALA	0	-0.055	-0.010	12.296	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	44	ARG	1	0.868	0.923	6.326	-4.373	-4.373	0.000	0.000	0.000	0.000
29	A	45	GLY	0	0.017	0.009	9.123	0.269	0.269	0.000	0.000	0.000	0.000
30	A	46	ILE	0	-0.088	-0.024	6.250	-0.088	-0.088	0.000	0.000	0.000	0.000
31	A	47	GLU	-1	-0.829	-0.925	10.677	0.691	0.691	0.000	0.000	0.000	0.000
32	A	48	PRO	0	0.031	0.007	13.750	0.073	0.073	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.905	-0.948	15.891	0.428	0.428	0.000	0.000	0.000	0.000
34	A	50	ALA	0	-0.001	0.000	11.661	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	51	ALA	0	-0.038	-0.023	11.284	0.087	0.087	0.000	0.000	0.000	0.000
36	A	52	GLN	0	0.006	-0.004	12.363	0.128	0.128	0.000	0.000	0.000	0.000
37	A	53	ALA	0	0.019	0.012	13.710	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	54	ALA	0	-0.031	-0.018	9.177	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	55	VAL	0	-0.016	-0.010	11.242	0.015	0.015	0.000	0.000	0.000	0.000
40	A	56	GLU	-1	-0.797	-0.895	13.344	0.472	0.472	0.000	0.000	0.000	0.000
41	A	57	ARG	1	0.779	0.880	11.345	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	58	LEU	0	0.007	-0.008	9.031	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.048	-0.014	13.460	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	60	GLY	0	0.007	0.010	17.029	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	61	GLU	-1	-0.878	-0.920	13.125	-0.068	-0.068	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.016	0.022	16.911	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	63	TRP	0	0.001	-0.011	12.531	0.036	0.036	0.000	0.000	0.000	0.000
48	A	64	GLN	0	-0.088	-0.068	14.583	0.036	0.036	0.000	0.000	0.000	0.000
49	A	65	ASP	-1	-0.772	-0.894	16.332	0.283	0.283	0.000	0.000	0.000	0.000
50	A	66	ASP	-1	-0.768	-0.899	19.869	0.677	0.677	0.000	0.000	0.000	0.000
51	A	67	VAL	0	0.003	0.014	21.579	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	68	ARG	1	0.801	0.867	17.236	-0.427	-0.427	0.000	0.000	0.000	0.000
53	A	69	PHE	0	-0.035	-0.009	18.413	0.012	0.012	0.000	0.000	0.000	0.000
54	A	70	ALA	0	0.041	0.022	20.878	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	71	ALA	0	0.059	0.028	24.317	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	72	SER	0	-0.108	-0.068	20.965	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	73	VAL	0	0.000	0.001	21.803	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	74	VAL	0	0.009	0.006	23.971	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	75	ARG	1	1.014	1.014	22.748	-0.311	-0.311	0.000	0.000	0.000	0.000
60	A	76	ASN	0	-0.003	-0.013	21.282	-0.048	-0.048	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.810	0.895	21.119	-0.549	-0.549	0.000	0.000	0.000	0.000
62	A	78	ALA	0	0.037	0.029	27.256	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	79	SER	0	-0.042	-0.025	27.775	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	80	SER	0	-0.042	-0.035	26.927	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	81	GLY	0	0.011	0.000	29.152	0.008	0.008	0.000	0.000	0.000	0.000
66	A	82	TYR	0	-0.044	-0.018	26.908	0.002	0.002	0.000	0.000	0.000	0.000
67	A	83	GLY	0	0.035	0.015	31.505	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	84	PRO	0	0.026	-0.002	32.548	0.021	0.021	0.000	0.000	0.000	0.000
69	A	85	LEU	0	-0.007	-0.004	33.333	0.011	0.011	0.000	0.000	0.000	0.000
70	A	86	HIS	0	-0.018	-0.001	26.574	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	87	ILE	0	0.013	0.005	27.947	0.031	0.031	0.000	0.000	0.000	0.000
72	A	88	ARG	1	0.948	0.979	28.543	-0.224	-0.224	0.000	0.000	0.000	0.000
73	A	89	ALA	0	0.006	0.012	29.910	0.014	0.014	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.794	-0.859	23.042	0.584	0.584	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.003	0.005	24.614	0.050	0.050	0.000	0.000	0.000	0.000
76	A	92	GLY	0	0.083	0.051	25.824	0.018	0.018	0.000	0.000	0.000	0.000
77	A	93	THR	0	-0.100	-0.052	24.277	0.030	0.030	0.000	0.000	0.000	0.000
78	A	94	HIS	0	-0.014	-0.007	19.220	0.098	0.098	0.000	0.000	0.000	0.000
79	A	95	GLY	0	-0.059	-0.033	22.727	0.021	0.021	0.000	0.000	0.000	0.000
80	A	96	LEU	0	-0.013	0.016	23.347	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.812	-0.904	26.814	0.290	0.290	0.000	0.000	0.000	0.000
82	A	98	SER	0	0.018	-0.019	30.516	0.006	0.006	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.876	-0.924	33.438	0.209	0.209	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.021	0.014	27.910	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	101	VAL	0	-0.045	-0.031	28.979	0.004	0.004	0.000	0.000	0.000	0.000
86	A	102	SER	0	-0.060	-0.050	30.592	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.022	0.024	30.861	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	104	ALA	0	0.013	0.011	28.047	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	105	MET	0	-0.078	-0.040	29.819	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	106	ALA	0	-0.020	-0.002	32.544	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	107	THR	0	-0.063	-0.031	29.555	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	108	PHE	0	-0.073	-0.033	32.383	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	109	GLU	-1	-0.889	-0.948	33.564	0.134	0.134	0.000	0.000	0.000	0.000
94	A	110	GLY	0	-0.046	-0.008	35.748	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	111	ASP	-1	-0.813	-0.909	37.277	0.143	0.143	0.000	0.000	0.000	0.000
96	A	112	TRP	0	0.027	-0.020	31.668	0.007	0.007	0.000	0.000	0.000	0.000
97	A	113	THR	0	-0.016	-0.020	38.208	0.004	0.004	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.765	-0.863	40.530	0.129	0.129	0.000	0.000	0.000	0.000
99	A	115	ASN	0	-0.029	-0.006	33.965	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	116	ALA	0	-0.033	-0.011	37.682	0.006	0.006	0.000	0.000	0.000	0.000
101	A	117	LEU	0	-0.004	-0.012	39.267	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	118	ASP	-1	-0.783	-0.866	36.887	0.157	0.157	0.000	0.000	0.000	0.000
103	A	119	LEU	0	-0.067	-0.027	34.717	0.002	0.002	0.000	0.000	0.000	0.000
104	A	120	ILE	0	-0.070	-0.041	37.914	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	121	ARG	1	0.836	0.905	41.014	-0.130	-0.130	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.822	0.890	34.286	-0.188	-0.188	0.000	0.000	0.000	0.000
107	A	123	ARG	1	0.844	0.943	37.355	-0.185	-0.185	0.000	0.000	0.000	0.000
108	A	124	PHE	0	-0.044	-0.054	40.253	0.001	0.001	0.000	0.000	0.000	0.000
109	A	125	GLY	0	0.061	0.056	43.436	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	126	GLU	-1	-0.882	-0.966	45.173	0.109	0.109	0.000	0.000	0.000	0.000
111	A	127	ASP	-1	-0.929	-0.952	47.435	0.091	0.091	0.000	0.000	0.000	0.000
112	A	128	GLY	0	-0.073	-0.036	46.235	0.002	0.002	0.000	0.000	0.000	0.000
113	A	129	PRO	0	-0.082	-0.040	45.588	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	130	VAL	0	0.068	0.033	47.729	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	131	ASP	-1	-0.812	-0.889	50.371	0.118	0.118	0.000	0.000	0.000	0.000
116	A	132	LEU	0	0.023	-0.014	50.351	0.006	0.006	0.000	0.000	0.000	0.000
117	A	133	ALA	0	-0.003	0.001	48.103	0.007	0.007	0.000	0.000	0.000	0.000
118	A	134	GLN	0	0.016	-0.015	45.897	0.012	0.012	0.000	0.000	0.000	0.000
119	A	135	ARG	1	0.927	0.967	45.413	-0.112	-0.112	0.000	0.000	0.000	0.000
120	A	136	ARG	1	0.941	0.971	45.904	-0.128	-0.128	0.000	0.000	0.000	0.000
121	A	137	LYS	1	0.834	0.919	39.694	-0.188	-0.188	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.034	0.020	41.186	0.012	0.012	0.000	0.000	0.000	0.000
123	A	139	ALA	0	0.027	0.007	41.265	0.008	0.008	0.000	0.000	0.000	0.000
124	A	140	ASP	-1	-0.764	-0.846	39.037	0.233	0.233	0.000	0.000	0.000	0.000
125	A	141	LEU	0	-0.045	-0.023	35.107	0.016	0.016	0.000	0.000	0.000	0.000
126	A	142	LEU	0	0.023	0.011	36.389	0.016	0.016	0.000	0.000	0.000	0.000
127	A	143	ALA	0	0.013	0.011	37.318	0.008	0.008	0.000	0.000	0.000	0.000
128	A	144	ARG	1	0.805	0.870	33.906	-0.242	-0.242	0.000	0.000	0.000	0.000
129	A	145	ARG	1	0.806	0.911	30.406	-0.280	-0.280	0.000	0.000	0.000	0.000
130	A	146	GLY	0	0.045	0.033	33.049	0.010	0.010	0.000	0.000	0.000	0.000
131	A	147	PHE	0	-0.011	-0.007	34.782	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	148	ASP	-1	-0.779	-0.854	37.736	0.177	0.177	0.000	0.000	0.000	0.000
133	A	149	GLY	0	0.035	-0.001	40.706	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	150	ASN	0	-0.008	-0.012	44.119	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	151	SER	0	0.033	-0.015	41.399	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	152	ILE	0	-0.017	0.002	40.190	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	153	ARG	1	0.908	0.974	43.675	-0.146	-0.146	0.000	0.000	0.000	0.000
138	A	154	LEU	0	0.035	0.029	46.215	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	155	ALA	0	0.041	0.017	43.515	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	156	THR	0	-0.064	-0.046	44.834	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	157	ARG	1	0.896	0.962	46.596	-0.122	-0.122	0.000	0.000	0.000	0.000
142	A	158	PHE	0	-0.025	-0.009	49.633	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:GLN)