FMO DATABASE

FMODB ID: 3J9LL

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	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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1151778.566987
FMO2-HF: Nuclear repulsion	1101343.374614
FMO2-HF: Total energy	-50435.192373
FMO2-MP2: Total energy	-50585.888018

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.
0.079	1.692	-0.016	-0.737	-0.86	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 : -0.019 / q_NPA : -0.024

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

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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	-0.001	0.002	3.829	0.136	1.749	-0.016	-0.737	-0.860	0.001
4	A	4	ARG	1	0.884	0.959	6.143	-0.483	-0.483	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.005	0.001	8.701	-0.148	-0.148	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.027	-0.010	12.275	0.074	0.074	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.044	-0.011	15.165	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.005	-0.004	18.673	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.791	-0.897	21.568	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.827	-0.904	24.801	0.033	0.033	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.027	0.001	28.062	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.103	0.051	24.436	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.137	-0.091	26.838	0.007	0.007	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.062	-0.033	26.481	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.064	0.051	22.640	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.022	0.002	22.255	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.017	0.003	23.342	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.006	-0.012	21.218	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	19	LYN	0	0.012	0.009	18.259	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.077	-0.035	19.349	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.057	-0.037	21.549	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.010	-0.003	16.209	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.847	0.926	16.008	-0.072	-0.072	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.921	-0.955	15.698	0.069	0.069	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.827	-0.881	13.873	-0.231	-0.231	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.074	-0.032	8.723	0.072	0.072	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.046	-0.081	8.419	-0.229	-0.229	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.852	-0.890	8.082	0.976	0.976	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.013	-0.004	10.858	-0.066	-0.066	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.045	-0.029	10.385	0.071	0.071	0.000	0.000	0.000	0.000
31	A	31	HIS	-1	-0.839	-0.955	15.728	0.053	0.053	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.021	0.000	19.005	0.020	0.020	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.846	-0.930	21.460	0.089	0.089	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.077	-0.050	24.814	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.058	-0.003	24.091	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.837	0.888	23.855	-0.079	-0.079	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.870	-0.922	22.451	0.104	0.104	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.021	0.022	19.680	0.019	0.019	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.034	0.016	18.816	0.010	0.010	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.015	0.017	19.352	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.015	-0.007	12.578	0.040	0.040	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.006	-0.012	14.826	0.038	0.038	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.787	-0.876	14.794	0.037	0.037	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.874	0.953	12.352	-0.419	-0.419	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.092	-0.052	11.421	0.056	0.056	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.913	0.971	9.981	0.016	0.016	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.020	-0.002	9.435	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.057	0.024	6.721	0.100	0.100	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.018	0.001	9.801	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.021	0.010	13.214	0.057	0.057	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.038	-0.020	16.397	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.001	-0.010	19.190	0.021	0.021	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.724	-0.855	22.041	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.038	-0.031	25.572	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.891	0.953	28.332	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.044	0.024	25.102	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.035	-0.018	28.837	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.827	-0.904	28.214	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.078	-0.014	26.597	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.010	0.009	30.036	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.046	0.013	26.143	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.866	-0.937	25.451	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.802	-0.908	26.777	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.045	-0.021	21.111	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.034	-0.019	22.203	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.820	-0.913	23.115	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.070	-0.048	20.706	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.054	-0.028	18.026	0.003	0.003	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.011	-0.013	20.317	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.089	-0.030	22.792	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.075	-0.051	20.509	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.941	-0.957	19.556	-0.120	-0.120	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.056	-0.019	14.171	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.007	0.002	12.223	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.059	-0.035	12.211	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.001	-0.001	13.813	0.009	0.009	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.039	0.015	15.828	0.020	0.020	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.057	-0.016	18.383	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.035	0.015	20.625	0.014	0.014	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.027	-0.006	23.836	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	THR	0	0.042	0.023	25.445	0.010	0.010	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.012	-0.005	28.964	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.041	-0.027	32.596	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.051	0.039	32.679	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.011	0.005	33.691	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.048	0.006	34.036	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.896	-0.950	34.331	-0.040	-0.040	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.013	0.005	32.301	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.019	0.026	29.989	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.022	-0.014	29.573	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.030	-0.036	30.592	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.025	0.017	26.962	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.057	-0.023	24.971	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.055	-0.030	26.068	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.774	0.870	26.514	0.036	0.036	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.044	0.039	23.068	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.045	0.001	21.471	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.774	-0.895	17.266	-0.270	-0.270	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.862	-0.923	21.247	-0.129	-0.129	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.017	0.013	23.248	0.008	0.008	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.086	-0.043	22.160	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.919	-0.966	26.418	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.705	0.853	27.233	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.031	-0.020	30.508	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.057	0.022	24.732	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.021	-0.030	27.371	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.072	0.034	24.567	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.797	-0.917	22.913	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.917	0.986	23.639	0.072	0.072	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.043	0.026	20.012	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.877	0.946	18.312	0.076	0.076	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.034	-0.023	18.179	-0.034	-0.034	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.052	-0.056	18.909	-0.037	-0.037	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.055	0.040	14.445	-0.026	-0.026	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.046	0.025	14.194	-0.059	-0.059	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.084	-0.051	14.451	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	117	HIS	1	0.779	0.864	16.089	0.172	0.172	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.056	0.052	9.362	-0.032	-0.032	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.896	0.947	11.293	0.245	0.245	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.869	0.936	12.785	0.198	0.198	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.096	0.059	11.878	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.823	0.905	5.219	1.909	1.909	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.069	-0.050	9.948	-0.030	-0.030	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.910	-0.962	12.505	-0.285	-0.285	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.852	-0.894	7.848	-1.225	-1.225	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.105	-0.059	8.654	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.037	-0.009	10.379	0.049	0.049	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.951	-0.966	13.434	-0.255	-0.255	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.032	0.009	10.571	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.098	-0.036	10.160	-0.008	-0.008	0.000	0.000	0.000	0.000

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