FMO DATABASE

FMODB ID: Z6YVN

Calculation Name: 2Y3W-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y3W

Chain ID: C

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-926708.233318
FMO2-HF: Nuclear repulsion	881856.14386
FMO2-HF: Total energy	-44852.089457
FMO2-MP2: Total energy	-44984.728229

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(C:2:THR)

Summations of interaction energy for fragment #1(C:2:THR)

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.
2.715	-3.418	18.497	-6.991	-5.372	-0.035

Interaction energy analysis for fragmet #1(C:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.049

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	C	4	LEU	0	-0.028	-0.011	3.752	2.150	3.788	-0.018	-0.735	-0.885	0.002
4	C	5	LEU	0	-0.010	-0.009	6.494	-0.432	-0.432	0.000	0.000	0.000	0.000
5	C	6	PHE	0	-0.002	-0.015	9.045	-0.056	-0.056	0.000	0.000	0.000	0.000
6	C	7	ASN	0	0.036	0.021	10.696	0.200	0.200	0.000	0.000	0.000	0.000
7	C	8	LYS	1	0.823	0.905	12.975	-0.042	-0.042	0.000	0.000	0.000	0.000
8	C	9	ARG	1	0.942	0.985	16.744	-0.052	-0.052	0.000	0.000	0.000	0.000
9	C	10	LEU	0	0.016	0.011	18.389	-0.024	-0.024	0.000	0.000	0.000	0.000
10	C	11	GLN	0	-0.008	-0.011	21.954	0.019	0.019	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.043	0.019	22.023	0.004	0.004	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.033	-0.010	25.295	-0.005	-0.005	0.000	0.000	0.000	0.000
13	C	14	VAL	0	0.028	0.009	25.732	0.002	0.002	0.000	0.000	0.000	0.000
14	C	22	ARG	1	1.002	0.998	31.721	-0.076	-0.076	0.000	0.000	0.000	0.000
15	C	23	ARG	1	0.906	0.950	29.156	-0.046	-0.046	0.000	0.000	0.000	0.000
16	C	24	SER	0	0.013	0.015	26.097	-0.007	-0.007	0.000	0.000	0.000	0.000
17	C	25	VAL	0	-0.014	-0.009	22.900	0.000	0.000	0.000	0.000	0.000	0.000
18	C	26	ILE	0	0.033	0.028	19.654	0.008	0.008	0.000	0.000	0.000	0.000
19	C	27	ARG	1	0.745	0.832	14.477	-0.236	-0.236	0.000	0.000	0.000	0.000
20	C	28	VAL	0	0.008	0.007	14.496	0.051	0.051	0.000	0.000	0.000	0.000
21	C	29	SER	0	-0.004	-0.018	9.015	-0.098	-0.098	0.000	0.000	0.000	0.000
22	C	30	ILE	0	-0.009	-0.002	9.024	0.078	0.078	0.000	0.000	0.000	0.000
23	C	31	GLU	-1	-0.912	-0.947	4.215	2.908	3.187	0.001	-0.062	-0.217	0.000
24	C	32	LEU	0	0.013	0.006	3.799	-1.047	-0.138	0.000	-0.465	-0.444	-0.001
25	C	33	GLN	0	0.054	0.038	1.733	-0.647	-9.606	18.514	-5.729	-3.826	-0.036
26	C	44	LEU	0	-0.028	-0.016	6.866	0.058	0.058	0.000	0.000	0.000	0.000
27	C	45	VAL	0	-0.016	-0.010	6.572	-0.156	-0.156	0.000	0.000	0.000	0.000
28	C	46	VAL	0	0.007	0.012	8.398	0.079	0.079	0.000	0.000	0.000	0.000
29	C	47	ARG	1	0.947	0.969	10.188	-0.774	-0.774	0.000	0.000	0.000	0.000
30	C	48	LEU	0	-0.009	-0.003	12.621	-0.048	-0.048	0.000	0.000	0.000	0.000
31	C	49	THR	0	0.025	-0.006	14.339	0.035	0.035	0.000	0.000	0.000	0.000
32	C	50	ASP	-1	-0.773	-0.878	17.200	0.137	0.137	0.000	0.000	0.000	0.000
33	C	51	ASP	-1	-0.842	-0.894	18.612	0.185	0.185	0.000	0.000	0.000	0.000
34	C	52	THR	0	-0.156	-0.091	20.842	-0.020	-0.020	0.000	0.000	0.000	0.000
35	C	53	ASP	-1	-0.862	-0.943	22.507	0.157	0.157	0.000	0.000	0.000	0.000
36	C	54	LEU	0	-0.030	-0.012	19.416	0.020	0.020	0.000	0.000	0.000	0.000
37	C	55	TYR	0	-0.040	-0.028	19.630	0.029	0.029	0.000	0.000	0.000	0.000
38	C	56	PHE	0	-0.004	0.031	19.665	0.008	0.008	0.000	0.000	0.000	0.000
39	C	57	LEU	0	-0.015	-0.030	13.768	0.040	0.040	0.000	0.000	0.000	0.000
40	C	58	TYR	0	-0.038	0.009	16.765	-0.030	-0.030	0.000	0.000	0.000	0.000
41	C	59	ASN	0	-0.007	0.000	12.486	0.019	0.019	0.000	0.000	0.000	0.000
42	C	60	LEU	0	0.052	0.007	12.622	-0.078	-0.078	0.000	0.000	0.000	0.000
43	C	61	ILE	0	-0.015	-0.005	9.288	0.094	0.094	0.000	0.000	0.000	0.000
44	C	62	ILE	0	0.009	0.012	10.968	-0.088	-0.088	0.000	0.000	0.000	0.000
45	C	63	SER	0	-0.014	-0.022	11.274	0.064	0.064	0.000	0.000	0.000	0.000
46	C	64	GLU	-1	-0.875	-0.934	12.323	0.152	0.152	0.000	0.000	0.000	0.000
47	C	65	GLU	-1	-0.874	-0.931	14.343	0.209	0.209	0.000	0.000	0.000	0.000
48	C	66	ASP	-1	-0.858	-0.936	15.009	0.343	0.343	0.000	0.000	0.000	0.000
49	C	67	PHE	0	-0.061	-0.041	15.193	-0.024	-0.024	0.000	0.000	0.000	0.000
50	C	68	GLN	0	-0.010	-0.008	17.123	-0.043	-0.043	0.000	0.000	0.000	0.000
51	C	69	SER	0	0.040	0.013	20.381	-0.025	-0.025	0.000	0.000	0.000	0.000
52	C	70	LEU	0	-0.068	-0.011	17.343	-0.012	-0.012	0.000	0.000	0.000	0.000
53	C	71	LYS	1	0.872	0.954	20.620	-0.077	-0.077	0.000	0.000	0.000	0.000
54	C	72	VAL	0	-0.044	-0.016	22.117	-0.016	-0.016	0.000	0.000	0.000	0.000
55	C	73	GLN	0	-0.097	-0.066	22.756	-0.010	-0.010	0.000	0.000	0.000	0.000
56	C	74	GLN	0	-0.049	-0.041	22.256	0.001	0.001	0.000	0.000	0.000	0.000
57	C	75	GLY	0	0.027	0.027	25.450	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	76	LEU	0	0.001	0.007	20.105	-0.012	-0.012	0.000	0.000	0.000	0.000
59	C	77	LEU	0	-0.013	0.003	22.926	-0.009	-0.009	0.000	0.000	0.000	0.000
60	C	78	ILE	0	-0.049	-0.025	18.564	-0.005	-0.005	0.000	0.000	0.000	0.000
61	C	79	ASP	-1	-0.840	-0.948	17.282	0.082	0.082	0.000	0.000	0.000	0.000
62	C	80	PHE	0	0.035	0.012	9.041	-0.017	-0.017	0.000	0.000	0.000	0.000
63	C	81	THR	0	-0.005	-0.011	12.825	-0.002	-0.002	0.000	0.000	0.000	0.000
64	C	82	SER	0	-0.029	-0.018	13.910	-0.039	-0.039	0.000	0.000	0.000	0.000
65	C	83	PHE	0	-0.018	0.004	13.803	-0.009	-0.009	0.000	0.000	0.000	0.000
66	C	84	PRO	0	0.043	0.019	11.032	0.019	0.019	0.000	0.000	0.000	0.000
67	C	85	GLN	0	0.023	0.022	13.096	-0.020	-0.020	0.000	0.000	0.000	0.000
68	C	86	LYS	1	0.986	1.012	15.583	0.002	0.002	0.000	0.000	0.000	0.000
69	C	87	PHE	0	-0.016	-0.023	14.101	0.010	0.010	0.000	0.000	0.000	0.000
70	C	88	ILE	0	0.036	0.006	12.131	0.013	0.013	0.000	0.000	0.000	0.000
71	C	89	ASP	-1	-0.894	-0.960	16.466	-0.074	-0.074	0.000	0.000	0.000	0.000
72	C	90	LEU	0	-0.054	-0.025	19.884	0.004	0.004	0.000	0.000	0.000	0.000
73	C	91	LEU	0	-0.027	-0.009	15.855	0.006	0.006	0.000	0.000	0.000	0.000
74	C	92	GLU	-1	-0.773	-0.875	18.600	-0.028	-0.028	0.000	0.000	0.000	0.000
75	C	93	GLN	0	0.003	0.010	21.413	0.003	0.003	0.000	0.000	0.000	0.000
76	C	94	CYS	0	-0.056	-0.015	22.841	0.004	0.004	0.000	0.000	0.000	0.000
77	C	95	ILE	0	-0.024	-0.007	19.919	0.002	0.002	0.000	0.000	0.000	0.000
78	C	96	CYS	0	-0.113	-0.062	24.341	-0.007	-0.007	0.000	0.000	0.000	0.000
79	C	97	GLU	-1	-0.907	-0.950	27.135	0.005	0.005	0.000	0.000	0.000	0.000
80	C	98	GLN	0	-0.040	-0.019	24.601	0.014	0.014	0.000	0.000	0.000	0.000
81	C	99	ASP	-1	-0.932	-0.957	29.274	0.021	0.021	0.000	0.000	0.000	0.000
82	C	100	LYS	1	0.865	0.942	32.244	-0.001	-0.001	0.000	0.000	0.000	0.000
83	C	101	GLU	-1	-0.893	-0.958	34.337	0.014	0.014	0.000	0.000	0.000	0.000
84	C	102	ASN	0	-0.116	-0.064	35.840	0.006	0.006	0.000	0.000	0.000	0.000
85	C	103	PRO	0	0.002	0.008	30.377	-0.004	-0.004	0.000	0.000	0.000	0.000
86	C	104	ARG	1	0.988	1.011	31.287	-0.002	-0.002	0.000	0.000	0.000	0.000
87	C	105	PHE	0	0.026	0.034	25.062	0.006	0.006	0.000	0.000	0.000	0.000
88	C	106	LEU	0	0.003	-0.001	26.981	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	107	LEU	0	0.033	0.014	20.410	0.005	0.005	0.000	0.000	0.000	0.000
90	C	108	GLN	0	-0.046	-0.026	24.567	-0.006	-0.006	0.000	0.000	0.000	0.000
91	C	109	LEU	0	0.003	0.001	21.554	0.014	0.014	0.000	0.000	0.000	0.000
92	C	110	SER	0	0.016	0.012	24.869	-0.010	-0.010	0.000	0.000	0.000	0.000
93	C	111	SER	0	0.013	0.025	26.135	0.005	0.005	0.000	0.000	0.000	0.000
94	C	119	SER	0	-0.004	-0.015	25.631	0.005	0.005	0.000	0.000	0.000	0.000
95	C	120	PRO	0	0.033	-0.005	22.623	0.005	0.005	0.000	0.000	0.000	0.000
96	C	121	SER	0	-0.035	-0.003	22.430	-0.024	-0.024	0.000	0.000	0.000	0.000
97	C	122	ASN	0	-0.040	-0.034	22.232	0.024	0.024	0.000	0.000	0.000	0.000
98	C	123	LEU	0	0.019	0.022	17.918	-0.012	-0.012	0.000	0.000	0.000	0.000
99	C	124	ASN	0	0.004	-0.002	21.643	0.006	0.006	0.000	0.000	0.000	0.000
100	C	125	ILE	0	-0.004	0.011	19.994	-0.002	-0.002	0.000	0.000	0.000	0.000
101	C	126	VAL	0	-0.032	-0.019	24.011	-0.004	-0.004	0.000	0.000	0.000	0.000
102	C	127	GLU	-1	-0.897	-0.956	27.765	0.021	0.021	0.000	0.000	0.000	0.000
103	C	128	THR	0	-0.069	-0.048	30.089	-0.001	-0.001	0.000	0.000	0.000	0.000
104	C	137	LEU	0	0.043	0.023	19.130	-0.003	-0.003	0.000	0.000	0.000	0.000
105	C	138	SER	0	-0.077	-0.063	22.088	0.000	0.000	0.000	0.000	0.000	0.000
106	C	139	LEU	0	0.033	0.026	15.904	0.007	0.007	0.000	0.000	0.000	0.000
107	C	140	LYS	1	0.985	0.991	19.996	-0.185	-0.185	0.000	0.000	0.000	0.000
108	C	141	LEU	0	-0.010	0.002	15.865	0.020	0.020	0.000	0.000	0.000	0.000
109	C	142	LEU	0	0.022	0.002	16.186	-0.046	-0.046	0.000	0.000	0.000	0.000
110	C	143	PRO	0	-0.007	0.011	17.950	0.029	0.029	0.000	0.000	0.000	0.000
111	C	144	GLY	0	-0.040	-0.028	16.844	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:THR)