FMO DATABASE

FMODB ID: JQLN9

Calculation Name: 3CFY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CFY

Chain ID: A

ChEMBL ID:

UniProt ID: Q87PN2

Base Structure: X-ray

Registration Date: 2023-09-21

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1150223.447636
FMO2-HF: Nuclear repulsion	1099789.158024
FMO2-HF: Total energy	-50434.289613
FMO2-MP2: Total energy	-50584.938603

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:LEU)

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

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.
0.325	2.015	-0.016	-0.739	-0.935	0.001

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.025

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	3	PRO	0	-0.005	0.002	3.829	0.097	1.710	-0.015	-0.736	-0.862	0.001
4	A	4	ARG	1	0.942	0.984	6.128	-0.464	-0.464	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.009	0.001	8.681	-0.142	-0.142	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.035	-0.013	12.257	0.071	0.071	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.028	-0.014	15.146	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.007	-0.010	18.653	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.849	-0.953	21.549	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.809	-0.886	24.781	0.029	0.029	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.047	-0.009	28.042	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.180	0.098	25.297	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.199	-0.138	26.815	0.008	0.008	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.063	-0.031	26.651	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.095	0.061	22.472	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.025	0.007	22.234	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.030	-0.003	23.310	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.004	-0.012	21.133	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	19	LYN	0	0.007	0.008	18.160	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.067	-0.031	19.315	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.028	-0.025	21.512	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.022	-0.008	16.201	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.952	0.981	15.969	-0.086	-0.086	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-1.021	-0.999	15.700	0.049	0.049	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.891	-0.944	13.846	-0.236	-0.236	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.075	-0.028	8.666	0.070	0.070	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.014	-0.038	8.371	-0.231	-0.231	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.876	-0.909	8.089	0.997	0.997	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.015	-0.005	10.828	-0.066	-0.066	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.033	-0.028	10.421	0.067	0.067	0.000	0.000	0.000	0.000
31	A	31	HIS	-1	-0.869	-0.956	15.705	0.051	0.051	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.028	-0.002	19.023	0.019	0.019	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.832	-0.927	21.439	0.083	0.083	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.053	-0.030	24.789	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.056	0.007	24.071	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.931	0.950	23.838	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.910	-0.956	22.174	0.104	0.104	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.006	0.005	19.663	0.018	0.018	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.029	0.013	18.799	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.023	-0.016	19.337	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.022	-0.005	12.742	0.041	0.041	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.007	-0.017	14.809	0.036	0.036	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.865	-0.931	14.781	0.036	0.036	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.910	0.969	11.742	-0.429	-0.429	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.149	-0.089	11.361	0.062	0.062	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.959	1.003	9.964	0.020	0.020	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.038	-0.008	9.422	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.056	0.023	6.146	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.021	-0.001	9.791	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.019	0.013	13.202	0.054	0.054	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.047	-0.027	16.382	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.010	-0.016	19.174	0.019	0.019	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.756	-0.871	22.025	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.042	-0.039	25.556	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.877	0.947	28.317	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.081	0.046	25.085	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.046	-0.023	28.787	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.836	-0.921	28.300	0.038	0.038	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.074	-0.009	25.821	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.006	0.011	30.021	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.055	0.018	26.129	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.878	-0.950	25.438	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.812	-0.917	26.766	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.052	-0.025	21.107	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.029	-0.022	21.912	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.833	-0.918	23.107	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.082	-0.047	20.606	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.052	-0.028	18.013	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.002	-0.012	20.312	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.079	-0.027	22.788	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.050	-0.026	20.544	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.916	-0.943	19.164	-0.101	-0.101	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.071	-0.026	14.142	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.008	-0.004	12.159	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.051	-0.029	12.207	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.005	0.005	13.807	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.052	0.024	15.822	0.018	0.018	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.058	-0.021	18.244	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.038	0.018	20.615	0.014	0.014	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.030	-0.010	23.855	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	THR	0	0.054	0.020	25.431	0.011	0.011	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.023	-0.010	28.949	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.032	-0.024	32.581	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.050	0.038	32.667	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.015	0.007	33.679	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.041	0.002	34.027	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.897	-0.954	34.324	-0.039	-0.039	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.020	-0.016	32.054	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.018	0.025	29.981	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.019	-0.012	29.567	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	91	ASN	0	0.014	-0.006	30.587	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.029	0.014	26.943	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.049	-0.020	25.164	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.056	-0.031	26.065	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.768	0.884	26.616	0.036	0.036	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.047	0.039	23.064	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.038	0.006	21.467	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.873	-0.959	17.205	-0.254	-0.254	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.884	-0.952	21.243	-0.123	-0.123	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.015	0.012	23.241	0.008	0.008	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.093	-0.049	22.262	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.908	-0.960	26.408	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.781	0.924	27.398	0.009	0.009	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.036	-0.024	30.495	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.041	0.018	24.700	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.015	-0.023	27.336	0.004	0.004	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.074	0.032	24.468	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.875	-0.964	22.841	-0.096	-0.096	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.889	0.972	23.639	0.070	0.070	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.053	0.028	19.973	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.954	0.994	18.215	0.064	0.064	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.016	-0.011	18.179	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.046	-0.037	18.910	-0.035	-0.035	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.048	0.038	14.416	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.052	0.028	14.193	-0.057	-0.057	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.090	-0.052	14.453	-0.063	-0.063	0.000	0.000	0.000	0.000
117	A	117	HIS	1	0.818	0.883	16.087	0.171	0.171	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.070	0.056	9.813	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.905	0.951	11.295	0.226	0.226	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.936	0.973	12.792	0.202	0.202	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.100	0.064	11.847	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.899	0.956	4.628	1.999	2.076	-0.001	-0.003	-0.073	0.000
123	A	123	LEU	0	-0.066	-0.058	9.959	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.924	-0.968	12.512	-0.264	-0.264	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.898	-0.920	7.773	-1.019	-1.019	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.120	-0.064	8.016	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.050	-0.017	10.447	0.048	0.048	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.952	-0.966	13.543	-0.253	-0.253	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.045	0.016	11.083	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.104	-0.041	10.642	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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