FMO DATABASE

FMODB ID: K93G3

Calculation Name: 2Y3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y3V

Chain ID: A

ChEMBL ID:

UniProt ID: Q7ZVT3

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1591726.922874
FMO2-HF: Nuclear repulsion	1528317.59295
FMO2-HF: Total energy	-63409.329924
FMO2-MP2: Total energy	-63595.538399

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:-1:PRO)

Summations of interaction energy for fragment #1(A:-1:PRO)

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.
-2.317	0.767	0	-1.308	-1.776	0.002

Interaction energy analysis for fragmet #1(A:-1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.017

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].	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	1	MET	0	-0.004	0.002	3.228	-2.083	0.726	-1.250	-1.559	0.002
4	A	2	THR	0	0.001	-0.017	5.414	0.132	0.132	0.000	0.000	0.000
5	A	3	GLU	-1	-0.936	-0.957	9.196	0.096	0.096	0.000	0.000	0.000
6	A	4	LEU	0	-0.035	-0.017	12.398	-0.004	-0.004	0.000	0.000	0.000
7	A	5	LEU	0	-0.017	-0.009	15.492	0.006	0.006	0.000	0.000	0.000
8	A	6	PHE	0	0.004	-0.005	18.488	-0.001	-0.001	0.000	0.000	0.000
9	A	7	ASN	0	0.032	0.017	20.047	-0.007	-0.007	0.000	0.000	0.000
10	A	8	LYS	1	0.821	0.909	21.999	-0.007	-0.007	0.000	0.000	0.000
11	A	9	ARG	1	0.827	0.892	24.065	0.009	0.009	0.000	0.000	0.000
12	A	10	LEU	0	-0.005	-0.003	27.203	0.001	0.001	0.000	0.000	0.000
13	A	11	GLN	0	0.008	0.009	30.631	-0.002	-0.002	0.000	0.000	0.000
14	A	12	VAL	0	-0.026	-0.016	29.878	0.001	0.001	0.000	0.000	0.000
15	A	13	LEU	0	-0.020	-0.012	33.329	-0.001	-0.001	0.000	0.000	0.000
16	A	14	VAL	0	-0.013	-0.005	32.256	0.000	0.000	0.000	0.000	0.000
17	A	15	LYS	1	0.916	0.967	34.717	0.004	0.004	0.000	0.000	0.000
18	A	16	SER	0	0.011	0.016	34.763	-0.001	-0.001	0.000	0.000	0.000
19	A	17	LYS	1	0.868	0.934	36.902	0.006	0.006	0.000	0.000	0.000
20	A	18	ASP	-1	-0.810	-0.910	39.290	-0.007	-0.007	0.000	0.000	0.000
21	A	19	THR	0	-0.006	0.010	38.045	0.000	0.000	0.000	0.000	0.000
22	A	20	ASP	-1	-0.884	-0.945	41.108	-0.003	-0.003	0.000	0.000	0.000
23	A	21	GLU	-1	-0.973	-1.006	38.775	-0.002	-0.002	0.000	0.000	0.000
24	A	22	ARG	1	0.964	0.990	33.414	0.008	0.008	0.000	0.000	0.000
25	A	23	ARG	1	0.890	0.951	37.023	0.001	0.001	0.000	0.000	0.000
26	A	24	SER	0	-0.005	0.000	33.323	0.000	0.000	0.000	0.000	0.000
27	A	25	VAL	0	0.024	0.018	30.763	0.001	0.001	0.000	0.000	0.000
28	A	26	ILE	0	0.032	0.016	26.745	-0.001	-0.001	0.000	0.000	0.000
29	A	27	ARG	1	0.836	0.925	19.437	0.022	0.022	0.000	0.000	0.000
30	A	28	VAL	0	0.020	0.001	23.376	-0.002	-0.002	0.000	0.000	0.000
31	A	29	SER	0	-0.018	-0.021	17.590	0.001	0.001	0.000	0.000	0.000
32	A	30	ILE	0	-0.018	-0.010	18.442	-0.002	-0.002	0.000	0.000	0.000
33	A	31	GLU	-1	-0.908	-0.962	13.119	-0.050	-0.050	0.000	0.000	0.000
34	A	32	LEU	0	-0.008	0.006	13.269	0.006	0.006	0.000	0.000	0.000
35	A	33	GLN	0	0.007	0.009	8.468	-0.061	-0.061	0.000	0.000	0.000
36	A	34	LEU	0	-0.054	-0.031	4.331	-0.241	0.034	-0.058	-0.217	0.000
37	A	35	PRO	0	0.002	0.029	7.508	-0.158	-0.158	0.000	0.000	0.000
38	A	36	SER	0	0.000	-0.012	6.834	0.087	0.087	0.000	0.000	0.000
39	A	37	SER	0	-0.002	0.000	7.706	-0.044	-0.044	0.000	0.000	0.000
40	A	38	PRO	0	0.008	0.000	8.401	0.060	0.060	0.000	0.000	0.000
41	A	39	VAL	0	-0.053	-0.029	9.571	0.000	0.000	0.000	0.000	0.000
42	A	40	HIS	0	0.009	0.020	11.933	-0.020	-0.020	0.000	0.000	0.000
43	A	41	ARG	1	0.901	0.953	12.223	-0.046	-0.046	0.000	0.000	0.000
44	A	42	LYS	1	0.938	0.960	10.514	-0.213	-0.213	0.000	0.000	0.000
45	A	43	ASP	-1	-0.809	-0.906	11.344	0.032	0.032	0.000	0.000	0.000
46	A	44	LEU	0	-0.044	-0.027	13.401	0.004	0.004	0.000	0.000	0.000
47	A	45	VAL	0	-0.009	0.002	12.332	-0.010	-0.010	0.000	0.000	0.000
48	A	46	VAL	0	0.006	0.006	15.646	0.003	0.003	0.000	0.000	0.000
49	A	47	ARG	1	0.947	0.971	16.177	0.033	0.033	0.000	0.000	0.000
50	A	48	LEU	0	-0.007	-0.011	19.872	0.004	0.004	0.000	0.000	0.000
51	A	49	THR	0	0.024	-0.007	21.428	-0.003	-0.003	0.000	0.000	0.000
52	A	50	ASP	-1	-0.802	-0.893	24.469	-0.009	-0.009	0.000	0.000	0.000
53	A	51	ASP	-1	-0.831	-0.893	26.292	-0.014	-0.014	0.000	0.000	0.000
54	A	52	THR	0	-0.129	-0.071	28.124	0.000	0.000	0.000	0.000	0.000
55	A	53	ASP	-1	-0.811	-0.918	29.161	-0.015	-0.015	0.000	0.000	0.000
56	A	54	LEU	0	-0.030	-0.019	24.714	-0.001	-0.001	0.000	0.000	0.000
57	A	55	TYR	0	-0.060	-0.024	25.134	-0.003	-0.003	0.000	0.000	0.000
58	A	56	PHE	0	-0.039	0.006	26.289	-0.001	-0.001	0.000	0.000	0.000
59	A	57	LEU	0	-0.023	-0.021	19.051	-0.002	-0.002	0.000	0.000	0.000
60	A	58	TYR	0	0.006	0.019	22.931	0.000	0.000	0.000	0.000	0.000
61	A	59	ASN	0	-0.062	-0.033	17.616	0.002	0.002	0.000	0.000	0.000
62	A	60	LEU	0	0.032	0.016	18.790	0.001	0.001	0.000	0.000	0.000
63	A	61	ILE	0	-0.013	0.001	12.333	-0.001	-0.001	0.000	0.000	0.000
64	A	62	ILE	0	-0.020	-0.008	16.377	0.001	0.001	0.000	0.000	0.000
65	A	63	SER	0	0.052	0.029	15.173	0.014	0.014	0.000	0.000	0.000
66	A	64	GLU	-1	-0.844	-0.950	15.997	0.084	0.084	0.000	0.000	0.000
67	A	65	GLU	-1	-0.939	-0.981	17.469	0.020	0.020	0.000	0.000	0.000
68	A	66	ASP	-1	-0.829	-0.909	18.187	0.000	0.000	0.000	0.000	0.000
69	A	67	PHE	0	-0.028	-0.019	20.397	-0.003	-0.003	0.000	0.000	0.000
70	A	68	GLN	0	0.022	0.013	22.313	0.000	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.007	-0.002	23.864	-0.003	-0.003	0.000	0.000	0.000
72	A	70	LEU	0	-0.004	0.004	23.817	-0.002	-0.002	0.000	0.000	0.000
73	A	71	LYS	1	0.805	0.899	26.224	-0.026	-0.026	0.000	0.000	0.000
74	A	72	VAL	0	-0.034	-0.018	28.072	-0.001	-0.001	0.000	0.000	0.000
75	A	73	GLN	0	-0.056	-0.032	28.068	-0.001	-0.001	0.000	0.000	0.000
76	A	74	GLN	0	-0.006	-0.020	28.830	-0.001	-0.001	0.000	0.000	0.000
77	A	75	GLY	0	-0.002	0.024	32.215	0.000	0.000	0.000	0.000	0.000
78	A	76	LEU	0	-0.004	0.007	27.363	0.001	0.001	0.000	0.000	0.000
79	A	77	LEU	0	0.007	-0.014	31.045	0.001	0.001	0.000	0.000	0.000
80	A	78	ILE	0	-0.015	0.014	26.647	0.001	0.001	0.000	0.000	0.000
81	A	79	ASP	-1	-0.840	-0.905	24.492	0.044	0.044	0.000	0.000	0.000
82	A	80	PHE	0	0.035	0.005	16.312	-0.002	-0.002	0.000	0.000	0.000
83	A	81	THR	0	-0.057	-0.049	20.262	0.002	0.002	0.000	0.000	0.000
84	A	82	SER	0	0.000	0.002	21.609	-0.001	-0.001	0.000	0.000	0.000
85	A	83	PHE	0	0.011	-0.002	21.466	-0.004	-0.004	0.000	0.000	0.000
86	A	84	PRO	0	0.042	0.019	19.490	-0.006	-0.006	0.000	0.000	0.000
87	A	85	GLN	0	-0.006	-0.004	22.018	-0.002	-0.002	0.000	0.000	0.000
88	A	86	LYS	1	0.951	0.983	24.575	-0.028	-0.028	0.000	0.000	0.000
89	A	87	PHE	0	0.002	0.003	22.561	-0.003	-0.003	0.000	0.000	0.000
90	A	88	ILE	0	0.028	0.003	21.567	-0.003	-0.003	0.000	0.000	0.000
91	A	89	ASP	-1	-0.876	-0.941	25.966	0.018	0.018	0.000	0.000	0.000
92	A	90	LEU	0	-0.025	-0.009	29.283	-0.002	-0.002	0.000	0.000	0.000
93	A	91	LEU	0	-0.012	-0.007	25.365	-0.002	-0.002	0.000	0.000	0.000
94	A	92	GLU	-1	-0.784	-0.885	28.276	0.007	0.007	0.000	0.000	0.000
95	A	93	GLN	0	-0.024	-0.006	31.031	-0.001	-0.001	0.000	0.000	0.000
96	A	94	CYS	0	-0.044	-0.014	32.087	-0.001	-0.001	0.000	0.000	0.000
97	A	95	ILE	0	-0.024	-0.005	29.144	-0.001	-0.001	0.000	0.000	0.000
98	A	96	CYS	0	-0.078	-0.045	33.657	0.000	0.000	0.000	0.000	0.000
99	A	97	GLU	-1	-0.865	-0.937	36.583	0.004	0.004	0.000	0.000	0.000
100	A	98	GLN	0	0.000	0.011	33.555	-0.001	-0.001	0.000	0.000	0.000
101	A	99	ASP	-1	-0.923	-0.963	37.903	0.000	0.000	0.000	0.000	0.000
102	A	100	LYS	1	0.824	0.910	40.623	-0.004	-0.004	0.000	0.000	0.000
103	A	101	GLU	-1	-0.895	-0.940	43.470	0.000	0.000	0.000	0.000	0.000
104	A	102	ASN	0	-0.058	-0.043	45.066	0.000	0.000	0.000	0.000	0.000
105	A	103	PRO	0	-0.009	0.018	39.811	0.000	0.000	0.000	0.000	0.000
106	A	104	ARG	1	0.906	0.979	40.888	-0.006	-0.006	0.000	0.000	0.000
107	A	105	PHE	0	-0.005	-0.001	35.984	0.000	0.000	0.000	0.000	0.000
108	A	106	LEU	0	-0.001	0.006	36.121	0.000	0.000	0.000	0.000	0.000
109	A	107	LEU	0	0.035	0.013	28.902	0.001	0.001	0.000	0.000	0.000
110	A	108	GLN	0	0.006	0.001	32.864	-0.001	-0.001	0.000	0.000	0.000
111	A	109	LEU	0	0.017	0.011	28.017	0.000	0.000	0.000	0.000	0.000
112	A	110	SER	0	0.017	0.000	31.670	0.000	0.000	0.000	0.000	0.000
113	A	111	SER	0	0.012	0.028	32.122	0.000	0.000	0.000	0.000	0.000
114	A	112	SER	0	-0.068	-0.034	33.412	0.000	0.000	0.000	0.000	0.000
115	A	113	SER	0	0.005	-0.016	34.010	0.000	0.000	0.000	0.000	0.000
116	A	114	SER	0	-0.012	-0.010	35.988	0.000	0.000	0.000	0.000	0.000
117	A	115	ALA	0	0.029	0.002	34.791	-0.001	-0.001	0.000	0.000	0.000
118	A	116	PHE	0	-0.088	-0.033	34.447	-0.001	-0.001	0.000	0.000	0.000
119	A	117	ASP	-1	-0.876	-0.939	33.228	-0.011	-0.011	0.000	0.000	0.000
120	A	118	HIS	0	-0.007	0.004	24.691	0.001	0.001	0.000	0.000	0.000
121	A	119	SER	0	-0.025	-0.024	28.758	0.000	0.000	0.000	0.000	0.000
122	A	120	PRO	0	-0.019	-0.033	26.338	0.000	0.000	0.000	0.000	0.000
123	A	121	SER	0	-0.025	-0.002	27.322	0.001	0.001	0.000	0.000	0.000
124	A	122	ASN	0	-0.031	-0.022	27.773	0.000	0.000	0.000	0.000	0.000
125	A	123	LEU	0	0.010	0.010	25.740	0.000	0.000	0.000	0.000	0.000
126	A	124	ASN	0	0.011	0.019	29.008	0.002	0.002	0.000	0.000	0.000
127	A	125	ILE	0	0.044	0.025	28.703	-0.001	-0.001	0.000	0.000	0.000
128	A	126	VAL	0	-0.031	-0.024	32.721	0.001	0.001	0.000	0.000	0.000
129	A	127	GLU	-1	-0.814	-0.888	36.476	0.006	0.006	0.000	0.000	0.000
130	A	128	THR	0	-0.068	-0.069	39.268	0.000	0.000	0.000	0.000	0.000
131	A	129	ASN	0	0.001	-0.014	42.494	0.000	0.000	0.000	0.000	0.000
132	A	130	ALA	0	0.019	0.010	45.716	0.000	0.000	0.000	0.000	0.000
133	A	131	PHE	0	-0.063	-0.018	48.119	0.000	0.000	0.000	0.000	0.000
134	A	132	LYS	1	0.948	0.954	41.918	-0.004	-0.004	0.000	0.000	0.000
135	A	133	HIS	0	0.066	0.044	40.802	0.001	0.001	0.000	0.000	0.000
136	A	134	LEU	0	-0.036	-0.021	39.853	0.000	0.000	0.000	0.000	0.000
137	A	135	THR	0	-0.004	0.001	33.912	0.000	0.000	0.000	0.000	0.000
138	A	136	HIS	0	-0.058	-0.033	33.502	0.001	0.001	0.000	0.000	0.000
139	A	137	LEU	0	-0.004	0.000	26.354	0.001	0.001	0.000	0.000	0.000
140	A	138	SER	0	-0.052	-0.031	30.000	-0.002	-0.002	0.000	0.000	0.000
141	A	139	LEU	0	0.015	0.020	23.387	0.001	0.001	0.000	0.000	0.000
142	A	140	LYS	1	0.998	1.003	25.491	0.007	0.007	0.000	0.000	0.000
143	A	141	LEU	0	0.000	0.002	23.070	-0.001	-0.001	0.000	0.000	0.000
144	A	142	LEU	0	0.010	-0.003	20.283	0.001	0.001	0.000	0.000	0.000
145	A	143	PRO	0	0.021	0.030	22.543	-0.002	-0.002	0.000	0.000	0.000
146	A	144	GLY	0	-0.011	-0.017	20.466	-0.003	-0.003	0.000	0.000	0.000
147	A	145	SER	0	-0.018	-0.013	18.481	0.002	0.002	0.000	0.000	0.000
148	A	146	ASP	-1	-0.823	-0.926	20.671	-0.032	-0.032	0.000	0.000	0.000
149	A	147	THR	0	-0.084	-0.049	15.010	-0.002	-0.002	0.000	0.000	0.000
150	A	148	ASP	-1	-0.864	-0.934	15.821	-0.070	-0.070	0.000	0.000	0.000
151	A	149	ILE	0	0.079	0.035	17.116	-0.004	-0.004	0.000	0.000	0.000
152	A	150	LYS	1	0.959	0.991	15.478	0.053	0.053	0.000	0.000	0.000
153	A	151	LYS	1	0.893	0.939	10.382	0.133	0.133	0.000	0.000	0.000
154	A	152	TYR	0	0.043	0.012	14.876	-0.001	-0.001	0.000	0.000	0.000
155	A	153	LEU	0	0.051	0.026	16.703	0.002	0.002	0.000	0.000	0.000
156	A	154	ALA	0	-0.061	-0.017	15.170	0.004	0.004	0.000	0.000	0.000
157	A	155	SER	0	-0.104	-0.052	13.745	-0.001	-0.001	0.000	0.000	0.000
158	A	156	CYS	0	-0.059	-0.021	15.403	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:PRO)