FMO DATABASE

FMODB ID: LNZY9

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	OptAll
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	-1157325.660297
FMO2-HF: Nuclear repulsion	1106890.052053
FMO2-HF: Total energy	-50435.608244
FMO2-MP2: Total energy	-50586.324124

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.
-0.0079999999999999	1.343	-0.007	-0.589	-0.756	0.002

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 : -0.012 / 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

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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	-0.002	0.000	3.883	0.057	1.408	-0.007	-0.589	-0.756	0.002
4	A	4	ARG	1	0.837	0.924	5.772	0.200	0.200	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.005	0.005	8.416	-0.127	-0.127	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.021	-0.010	12.085	0.084	0.084	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.045	-0.016	14.958	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.017	0.009	18.492	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.793	-0.902	21.679	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.834	-0.921	25.084	0.006	0.006	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.004	0.012	28.117	0.009	0.009	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.049	0.014	24.448	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.137	-0.080	27.682	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.029	0.000	26.515	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.093	0.053	22.283	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.001	0.005	22.107	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.020	0.000	23.385	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.023	-0.011	21.312	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	19	LYN	0	0.026	0.015	17.691	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.064	-0.035	19.348	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.083	-0.050	21.406	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.004	-0.001	16.012	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.827	0.915	15.915	-0.085	-0.085	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.897	-0.940	15.380	0.097	0.097	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.817	-0.870	13.491	-0.243	-0.243	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.050	-0.033	8.737	0.077	0.077	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.037	-0.070	8.005	-0.242	-0.242	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.845	-0.892	8.404	0.920	0.920	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.020	-0.015	10.587	-0.114	-0.114	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.038	-0.020	10.003	0.078	0.078	0.000	0.000	0.000	0.000
31	A	31	HIS	-1	-0.833	-0.952	15.349	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.012	-0.002	18.931	0.023	0.023	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.874	-0.930	21.463	0.052	0.052	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.060	-0.052	24.255	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.074	0.014	23.710	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.849	0.892	23.541	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.876	-0.915	22.354	0.057	0.057	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.031	0.019	19.542	0.011	0.011	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.024	0.016	18.807	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.014	0.009	19.356	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.005	-0.003	12.418	0.022	0.022	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.030	0.001	14.704	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.766	-0.866	14.902	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.867	0.931	12.766	-0.274	-0.274	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.059	-0.033	11.441	0.058	0.058	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.868	0.952	10.096	0.084	0.084	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.011	0.010	9.490	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.040	0.014	6.721	0.009	0.009	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.025	-0.004	9.989	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.014	0.007	13.346	0.045	0.045	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.032	-0.010	16.440	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.016	-0.001	19.268	0.019	0.019	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.755	-0.859	22.252	-0.037	-0.037	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.005	-0.007	25.912	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.891	0.951	28.475	0.018	0.018	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.034	0.022	24.861	0.002	0.002	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.041	-0.019	28.475	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.821	-0.911	27.983	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.066	-0.010	26.661	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.026	0.020	29.835	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.025	-0.001	25.843	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.871	-0.940	25.369	-0.068	-0.068	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.820	-0.913	27.010	-0.039	-0.039	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.060	-0.027	21.326	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.035	-0.012	22.322	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.819	-0.931	23.113	-0.082	-0.082	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.052	-0.035	20.677	0.006	0.006	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.028	-0.012	18.232	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.048	-0.021	20.746	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.122	-0.058	23.383	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.077	-0.053	20.494	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.931	-0.952	19.568	-0.180	-0.180	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.036	-0.010	14.284	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.002	-0.007	12.289	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.066	-0.039	12.240	-0.065	-0.065	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.005	-0.007	13.875	0.021	0.021	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.031	0.009	15.911	0.017	0.017	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.067	-0.028	18.434	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.052	0.025	20.892	0.012	0.012	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.027	-0.025	23.353	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	THR	0	0.037	0.023	25.266	0.011	0.011	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.006	-0.001	28.892	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.045	-0.029	32.484	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.072	0.051	33.176	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.047	-0.051	33.937	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.027	0.008	34.132	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.834	-0.894	34.410	-0.055	-0.055	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.022	0.017	32.370	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.003	0.013	29.992	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.013	-0.010	29.708	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.045	-0.040	30.822	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.033	0.014	26.945	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.057	-0.018	25.251	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.063	-0.038	26.418	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.788	0.892	26.665	0.067	0.067	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.051	0.040	23.235	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.035	-0.001	21.634	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.806	-0.905	17.630	-0.303	-0.303	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.841	-0.923	21.920	-0.145	-0.145	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.000	0.006	23.729	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.074	-0.029	22.027	0.005	0.005	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.884	-0.948	26.458	-0.049	-0.049	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.692	0.839	26.617	0.030	0.030	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.040	-0.021	30.547	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.056	0.030	24.594	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.003	-0.017	27.488	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.058	0.027	24.174	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.787	-0.894	22.669	-0.103	-0.103	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.892	0.968	23.228	0.091	0.091	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.042	0.027	19.838	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.871	0.938	17.973	0.083	0.083	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.041	-0.032	17.955	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.048	-0.047	18.957	-0.038	-0.038	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.041	0.026	14.195	-0.031	-0.031	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.037	0.017	14.040	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.080	-0.048	14.433	-0.065	-0.065	0.000	0.000	0.000	0.000
117	A	117	HIS	1	0.797	0.892	16.077	0.208	0.208	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.057	0.039	9.289	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.890	0.945	11.307	0.262	0.262	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.870	0.936	12.695	0.232	0.232	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.095	0.055	12.018	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.823	0.900	5.190	1.750	1.750	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.052	-0.033	9.800	-0.030	-0.030	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.905	-0.960	12.487	-0.322	-0.322	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.864	-0.915	7.865	-1.277	-1.277	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.122	-0.059	8.770	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.051	-0.013	10.256	0.059	0.059	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.910	-0.948	13.592	-0.275	-0.275	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.009	0.008	10.315	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.097	-0.044	10.316	0.018	0.018	0.000	0.000	0.000	0.000

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