FMO DATABASE

FMODB ID: JLY79

Calculation Name: 3CNW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CNW

Chain ID: A

ChEMBL ID:

UniProt ID: Q81AY6

Base Structure: X-ray

Registration Date: 2023-06-22

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1316113.200839
FMO2-HF: Nuclear repulsion	1260105.375375
FMO2-HF: Total energy	-56007.825464
FMO2-MP2: Total energy	-56172.911704

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:3:MET)

Summations of interaction energy for fragment #1(A:3:MET)

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.
-20.367	-10.297	8.42	-6.49	-12	-0.043

Interaction energy analysis for fragmet #1(A:3:MET)

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 : -0.022

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	5	HIS	0	0.034	0.009	2.963	-1.939	1.228	0.253	-1.536	-1.885	0.001
4	A	6	THR	0	-0.029	-0.010	6.025	0.223	0.223	0.000	0.000	0.000	0.000
5	A	7	THR	0	0.027	0.002	9.596	0.232	0.232	0.000	0.000	0.000	0.000
6	A	8	THR	0	-0.011	0.015	12.673	-0.067	-0.067	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.010	0.001	16.263	0.035	0.035	0.000	0.000	0.000	0.000
8	A	10	MET	0	-0.060	-0.025	19.388	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.913	-0.949	22.880	-0.139	-0.139	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.007	-0.005	24.421	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	13	PHE	0	0.024	0.000	28.309	0.013	0.013	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.076	0.025	31.133	0.002	0.002	0.000	0.000	0.000	0.000
13	A	15	SER	0	-0.005	0.024	30.233	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.045	0.011	26.908	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.924	-0.975	27.359	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.027	-0.014	29.350	0.000	0.000	0.000	0.000	0.000	0.000
17	A	19	VAL	0	0.029	0.015	24.900	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	TRP	0	0.008	0.000	20.192	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.049	-0.022	25.664	0.009	0.009	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.044	-0.001	26.446	0.002	0.002	0.000	0.000	0.000	0.000
21	A	23	ILE	0	0.002	-0.004	21.305	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.005	0.006	21.692	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	25	GLY	0	-0.007	0.003	21.915	0.022	0.022	0.000	0.000	0.000	0.000
24	A	26	PHE	0	-0.009	-0.014	15.647	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	27	ASN	0	0.002	-0.014	20.424	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.058	0.023	23.006	0.002	0.002	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.008	0.031	17.919	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	30	PRO	0	0.009	0.007	22.537	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.953	-0.963	25.636	-0.097	-0.097	0.000	0.000	0.000	0.000
30	A	32	TRP	0	-0.057	-0.048	19.315	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.045	0.001	18.783	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	34	PRO	0	-0.005	-0.001	23.168	0.008	0.008	0.000	0.000	0.000	0.000
33	A	35	TYR	0	0.030	0.006	17.537	0.003	0.003	0.000	0.000	0.000	0.000
34	A	36	ILE	0	-0.032	-0.019	18.730	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.034	0.024	22.541	0.027	0.027	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.050	-0.024	24.885	0.026	0.026	0.000	0.000	0.000	0.000
37	A	39	SER	0	0.056	0.012	22.513	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	40	LYS	1	0.943	0.980	23.211	0.064	0.064	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.024	0.034	21.633	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.031	-0.032	22.362	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.944	-0.975	20.781	0.117	0.117	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.027	-0.015	22.998	0.016	0.016	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.013	0.006	23.275	0.004	0.004	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.919	0.952	18.592	-0.149	-0.149	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.001	0.016	17.466	0.006	0.006	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.811	0.890	15.300	0.193	0.193	0.000	0.000	0.000	0.000
47	A	49	HIS	0	-0.065	-0.038	18.572	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	50	LEU	0	0.000	-0.016	17.397	0.015	0.015	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.024	0.026	20.962	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	52	ASN	0	0.061	0.034	19.968	0.030	0.030	0.000	0.000	0.000	0.000
51	A	53	PRO	0	-0.016	-0.022	22.046	0.025	0.025	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.963	-0.964	23.306	-0.314	-0.314	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.072	-0.033	24.998	0.014	0.014	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.917	-0.953	20.168	-0.320	-0.320	0.000	0.000	0.000	0.000
55	A	57	THR	0	-0.080	-0.050	20.025	0.020	0.020	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.003	-0.010	15.142	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.029	-0.013	16.287	0.044	0.044	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.795	-0.893	13.367	-0.386	-0.386	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.943	0.956	13.046	-0.122	-0.122	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.046	-0.007	13.133	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.925	-0.956	10.060	0.470	0.470	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.037	-0.026	13.094	0.045	0.045	0.000	0.000	0.000	0.000
63	A	65	PHE	0	0.020	0.014	15.507	-0.050	-0.050	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.006	0.009	18.697	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.830	-0.911	21.247	0.031	0.031	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.941	0.970	24.323	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.988	-1.003	21.188	0.205	0.205	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.850	0.935	21.758	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	71	TYR	0	0.032	0.001	15.536	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	TYR	0	-0.020	-0.003	15.525	0.019	0.019	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.010	-0.004	10.160	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	74	TYR	0	0.009	-0.003	11.355	0.054	0.054	0.000	0.000	0.000	0.000
73	A	75	SER	0	0.011	-0.008	8.404	-0.097	-0.097	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.019	0.015	8.756	0.037	0.037	0.000	0.000	0.000	0.000
75	A	77	MET	0	-0.100	-0.045	10.135	0.046	0.046	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.020	-0.027	12.859	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.014	0.017	13.371	0.018	0.018	0.000	0.000	0.000	0.000
78	A	80	PRO	0	0.044	0.035	14.815	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	81	PHE	0	-0.005	-0.007	11.753	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	82	PRO	0	0.045	0.041	11.846	0.031	0.031	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.007	-0.002	6.608	-0.301	-0.301	0.000	0.000	0.000	0.000
82	A	84	THR	0	-0.007	0.001	5.017	0.545	0.545	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.024	-0.021	2.210	-1.461	-1.623	2.724	-0.828	-1.734	0.000
84	A	86	TYR	0	0.021	0.039	2.796	-2.283	-1.163	0.508	-0.695	-0.933	-0.008
85	A	87	LEU	0	0.010	-0.008	4.440	0.483	0.610	-0.001	-0.004	-0.122	0.000
86	A	88	SER	0	-0.030	-0.001	6.261	-0.191	-0.191	0.000	0.000	0.000	0.000
87	A	89	THR	0	-0.025	-0.009	9.603	0.129	0.129	0.000	0.000	0.000	0.000
88	A	90	ILE	0	0.041	0.030	12.552	-0.083	-0.083	0.000	0.000	0.000	0.000
89	A	91	GLN	0	0.014	-0.010	16.115	0.047	0.047	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.005	0.018	18.728	-0.041	-0.041	0.000	0.000	0.000	0.000
91	A	93	LYS	1	0.853	0.925	17.578	0.091	0.091	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.929	-0.976	23.640	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.035	0.022	26.228	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.064	-0.028	28.285	0.013	0.013	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.920	-0.952	30.889	-0.059	-0.059	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.055	-0.025	32.418	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	ASN	0	-0.021	-0.033	33.962	0.004	0.004	0.000	0.000	0.000	0.000
98	A	100	THR	0	-0.018	0.011	30.595	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.017	-0.027	26.409	0.009	0.009	0.000	0.000	0.000	0.000
100	A	102	LEU	0	0.014	0.017	21.379	-0.021	-0.021	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.020	-0.001	19.891	0.024	0.024	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.862	-0.945	16.474	-0.196	-0.196	0.000	0.000	0.000	0.000
103	A	105	TRP	0	0.017	0.010	13.223	0.058	0.058	0.000	0.000	0.000	0.000
104	A	106	SER	0	-0.003	-0.007	10.545	-0.051	-0.051	0.000	0.000	0.000	0.000
105	A	107	GLY	0	0.018	0.010	8.145	0.157	0.157	0.000	0.000	0.000	0.000
106	A	108	THR	0	-0.014	-0.023	2.279	-0.050	-0.126	2.641	-0.535	-2.030	-0.001
107	A	109	PHE	0	0.006	-0.011	2.814	-0.955	0.517	0.342	-0.502	-1.312	-0.003
108	A	110	THR	0	-0.027	-0.011	2.631	-8.653	-4.548	1.944	-2.331	-3.718	-0.032
109	A	111	PRO	0	0.002	-0.001	3.628	0.718	1.035	0.009	-0.059	-0.266	0.000
110	A	112	VAL	0	-0.021	-0.020	6.701	0.290	0.290	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.956	-0.990	9.757	-0.480	-0.480	0.000	0.000	0.000	0.000
112	A	114	VAL	0	-0.041	-0.007	9.812	0.079	0.079	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.025	-0.025	9.807	-0.183	-0.183	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.837	-0.946	5.257	-4.668	-4.668	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.931	-0.975	7.928	-1.791	-1.791	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.897	-0.933	11.279	-0.886	-0.886	0.000	0.000	0.000	0.000
117	A	119	ALA	0	0.008	0.015	8.043	0.124	0.124	0.000	0.000	0.000	0.000
118	A	120	ILE	0	-0.020	-0.017	7.607	0.124	0.124	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.024	-0.016	10.524	0.260	0.260	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.006	0.019	12.575	0.140	0.140	0.000	0.000	0.000	0.000
121	A	123	PHE	0	0.035	0.003	9.668	0.137	0.137	0.000	0.000	0.000	0.000
122	A	124	HIS	0	-0.057	-0.005	12.828	0.227	0.227	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.005	-0.003	14.255	0.127	0.127	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.007	0.001	14.469	0.091	0.091	0.000	0.000	0.000	0.000
125	A	127	TYR	0	-0.015	-0.033	10.435	0.023	0.023	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.033	-0.023	16.719	0.095	0.095	0.000	0.000	0.000	0.000
127	A	129	ASP	-1	-0.857	-0.940	19.507	-0.299	-0.299	0.000	0.000	0.000	0.000
128	A	130	GLY	0	0.043	0.007	20.227	0.044	0.044	0.000	0.000	0.000	0.000
129	A	131	LEU	0	-0.017	-0.020	18.408	0.041	0.041	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.880	0.954	22.042	0.308	0.308	0.000	0.000	0.000	0.000
131	A	133	ALA	0	0.026	0.017	24.715	0.026	0.026	0.000	0.000	0.000	0.000
132	A	134	LEU	0	0.008	0.015	23.366	0.024	0.024	0.000	0.000	0.000	0.000
133	A	135	GLN	0	-0.044	-0.037	26.187	0.011	0.011	0.000	0.000	0.000	0.000
134	A	136	GLN	0	-0.040	-0.036	28.008	0.012	0.012	0.000	0.000	0.000	0.000
135	A	137	ALA	0	0.019	0.020	29.504	0.012	0.012	0.000	0.000	0.000	0.000
136	A	138	PHE	0	-0.020	-0.022	28.640	0.014	0.014	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.065	-0.017	32.257	0.009	0.009	0.000	0.000	0.000	0.000
138	A	140	ASP	-1	-0.950	-0.949	34.154	-0.121	-0.121	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.046	-0.025	36.418	0.008	0.008	0.000	0.000	0.000	0.000
140	A	142	GLU	-1	-0.970	-0.991	38.224	-0.075	-0.075	0.000	0.000	0.000	0.000
141	A	143	HIS	0	-0.028	-0.027	41.440	0.006	0.006	0.000	0.000	0.000	0.000
142	A	144	HIS	0	-0.069	-0.017	41.826	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)