FMO DATABASE

FMODB ID: QY2ZY

Calculation Name: 3FCD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FCD

Chain ID: A

ChEMBL ID:

UniProt ID: Q93AH5

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-945871.758933
FMO2-HF: Nuclear repulsion	898475.233603
FMO2-HF: Total energy	-47396.52533
FMO2-MP2: Total energy	-47532.817375

3D Structure Molmil

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:4:ILE)

Summations of interaction energy for fragment #1(A:4:ILE)

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.
-9.238	-2.236	5.812	-4.058	-8.758	-0.011

Interaction energy analysis for fragmet #1(A:4:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.033

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	6	GLN	0	0.021	-0.003	3.712	-1.918	0.276	-0.006	-0.982	-1.207	-0.001
4	A	7	ILE	0	-0.008	-0.014	3.807	-0.259	0.251	0.008	-0.082	-0.436	0.000
5	A	8	THR	0	0.011	0.036	6.019	0.072	0.072	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.020	0.008	9.490	0.055	0.055	0.000	0.000	0.000	0.000
7	A	10	PHE	0	-0.008	-0.011	12.454	0.024	0.024	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.013	0.003	14.608	0.005	0.005	0.000	0.000	0.000	0.000
9	A	12	HIS	1	0.773	0.864	17.287	0.002	0.002	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.014	-0.009	21.395	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	14	PRO	0	0.029	0.014	24.577	0.007	0.007	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.777	-0.888	27.717	0.007	0.007	0.000	0.000	0.000	0.000
13	A	16	MET	0	-0.016	-0.014	21.651	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	17	GLN	0	-0.023	0.000	26.023	0.001	0.001	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.946	-0.959	28.507	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.014	-0.008	23.360	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.020	-0.018	22.454	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	21	THR	0	-0.006	-0.015	24.878	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.024	0.007	23.970	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	23	PHE	0	0.011	-0.025	19.710	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	24	CYS	0	-0.060	-0.034	22.125	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.918	-0.960	23.817	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	26	THR	0	-0.086	-0.041	26.278	0.000	0.000	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.083	-0.041	21.755	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.003	0.016	21.805	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	29	PHE	0	-0.030	-0.032	15.187	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.816	-0.894	18.994	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.002	-0.015	18.997	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.737	0.880	16.261	0.028	0.028	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.009	-0.012	17.989	0.025	0.025	0.000	0.000	0.000	0.000
31	A	34	ARG	1	0.883	0.940	19.899	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	35	HIS	0	-0.007	0.002	22.102	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	36	SER	0	-0.001	0.004	23.345	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	37	ASN	0	0.021	0.003	24.140	0.002	0.002	0.000	0.000	0.000	0.000
35	A	38	TYR	0	0.034	0.031	14.980	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.005	-0.012	19.554	0.004	0.004	0.000	0.000	0.000	0.000
37	A	40	TYR	0	-0.058	-0.045	11.901	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.026	0.006	15.907	0.012	0.012	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.797	-0.880	12.979	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.008	0.025	14.764	0.020	0.020	0.000	0.000	0.000	0.000
41	A	44	SER	0	-0.020	-0.026	14.840	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	45	GLY	0	0.008	0.011	13.096	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.065	-0.020	10.364	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.034	0.015	10.103	0.071	0.071	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.055	-0.036	11.345	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.812	0.871	9.296	-0.141	-0.141	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.005	-0.002	15.143	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	51	LEU	0	-0.021	-0.020	18.707	0.021	0.021	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.831	-0.911	21.145	0.013	0.013	0.000	0.000	0.000	0.000
50	A	53	GLU	-1	-0.787	-0.877	22.719	0.024	0.024	0.000	0.000	0.000	0.000
51	A	54	PRO	0	-0.024	0.003	26.451	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	64	ALA	0	-0.033	-0.023	21.204	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	65	ARG	1	0.764	0.854	19.365	0.012	0.012	0.000	0.000	0.000	0.000
54	A	66	VAL	0	0.018	0.015	13.218	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	67	ALA	0	0.007	0.022	14.787	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	68	ILE	0	-0.001	0.000	8.464	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	69	CYS	0	-0.064	-0.024	8.861	0.077	0.077	0.000	0.000	0.000	0.000
58	A	70	ILE	0	0.013	0.013	2.550	-1.245	-0.459	1.064	-0.334	-1.516	-0.002
59	A	71	ASP	-1	-0.736	-0.821	5.114	0.402	0.601	-0.001	-0.020	-0.178	0.000
60	A	72	VAL	0	-0.050	-0.032	2.147	-2.681	-1.090	3.775	-2.064	-3.302	-0.010
61	A	73	SER	0	0.045	0.031	3.567	-3.240	-2.500	0.028	-0.315	-0.453	0.003
62	A	74	ASP	-1	-0.844	-0.905	4.807	1.061	1.197	-0.001	-0.003	-0.132	0.000
63	A	75	ILE	0	0.040	0.023	6.129	-0.097	-0.097	0.000	0.000	0.000	0.000
64	A	76	ASP	-1	-0.754	-0.837	7.140	0.356	0.356	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.023	-0.036	8.524	-0.203	-0.203	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.061	-0.018	2.641	-0.824	-0.358	0.932	-0.195	-1.204	-0.001
67	A	79	HIS	0	0.025	-0.002	6.282	-0.185	-0.185	0.000	0.000	0.000	0.000
68	A	80	THR	0	-0.015	-0.005	8.855	-0.108	-0.108	0.000	0.000	0.000	0.000
69	A	81	LYS	1	0.885	0.940	6.810	0.016	0.016	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.022	-0.014	5.102	-0.071	-0.071	0.000	0.000	0.000	0.000
71	A	83	SER	0	0.006	0.009	9.428	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.031	0.016	12.831	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	85	ALA	0	-0.041	-0.015	11.679	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	86	LEU	0	-0.008	-0.014	10.119	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	87	GLU	-1	-0.924	-0.976	13.870	0.086	0.086	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.115	-0.053	16.687	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	89	LEU	0	-0.034	0.002	13.319	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	90	PRO	0	-0.010	-0.007	17.903	0.006	0.006	0.000	0.000	0.000	0.000
79	A	91	ALA	0	0.035	0.009	19.492	0.006	0.006	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.895	-0.932	20.791	0.038	0.038	0.000	0.000	0.000	0.000
81	A	93	GLN	0	-0.121	-0.081	17.716	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	94	VAL	0	0.007	0.001	13.423	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	95	GLU	-1	-0.863	-0.907	14.648	0.145	0.145	0.000	0.000	0.000	0.000
84	A	96	PRO	0	-0.020	-0.016	14.104	0.025	0.025	0.000	0.000	0.000	0.000
85	A	97	LEU	0	-0.062	-0.028	10.435	0.008	0.008	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.861	0.927	13.924	-0.220	-0.220	0.000	0.000	0.000	0.000
87	A	99	ASN	0	0.022	0.015	14.880	0.078	0.078	0.000	0.000	0.000	0.000
88	A	100	MET	0	-0.005	0.007	15.844	-0.050	-0.050	0.000	0.000	0.000	0.000
89	A	101	PRO	0	-0.009	-0.016	18.151	0.014	0.014	0.000	0.000	0.000	0.000
90	A	102	TYR	0	-0.078	-0.062	15.138	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	103	GLY	0	0.006	0.011	17.362	0.003	0.003	0.000	0.000	0.000	0.000
92	A	104	GLN	0	-0.025	-0.024	10.218	0.035	0.035	0.000	0.000	0.000	0.000
93	A	105	ARG	1	0.771	0.842	11.965	-0.571	-0.571	0.000	0.000	0.000	0.000
94	A	106	GLU	-1	-0.774	-0.841	10.483	0.457	0.457	0.000	0.000	0.000	0.000
95	A	107	PHE	0	0.030	0.014	6.876	-0.040	-0.040	0.000	0.000	0.000	0.000
96	A	108	GLN	0	-0.036	-0.028	10.338	0.012	0.012	0.000	0.000	0.000	0.000
97	A	109	VAL	0	0.022	0.007	10.417	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	110	ARG	1	0.856	0.937	12.868	-0.022	-0.022	0.000	0.000	0.000	0.000
99	A	111	MET	0	-0.030	-0.010	13.034	-0.021	-0.021	0.000	0.000	0.000	0.000
100	A	112	PRO	0	-0.009	-0.028	15.256	0.008	0.008	0.000	0.000	0.000	0.000
101	A	113	ASP	-1	-0.879	-0.931	17.121	-0.061	-0.061	0.000	0.000	0.000	0.000
102	A	114	GLY	0	-0.008	0.010	19.091	0.006	0.006	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.772	-0.869	17.330	0.006	0.006	0.000	0.000	0.000	0.000
104	A	116	TRP	0	-0.014	-0.015	14.685	0.001	0.001	0.000	0.000	0.000	0.000
105	A	117	LEU	0	0.006	0.004	7.185	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	118	ASN	0	0.010	-0.004	9.951	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	119	PHE	0	0.014	0.008	3.450	-0.487	-0.107	0.013	-0.063	-0.330	0.000
108	A	120	THR	0	-0.015	-0.051	6.759	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	121	ALA	0	0.046	0.022	6.770	0.383	0.383	0.000	0.000	0.000	0.000
110	A	122	PRO	0	0.060	0.033	8.852	-0.202	-0.202	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.057	-0.015	12.048	0.082	0.082	0.000	0.000	0.000	0.000
112	A	124	ALA	0	0.041	0.027	13.180	0.023	0.023	0.000	0.000	0.000	0.000
113	A	125	GLU	-1	-0.862	-0.941	14.567	0.457	0.457	0.000	0.000	0.000	0.000
114	A	126	GLY	0	-0.049	-0.019	17.726	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	127	HIS	0	-0.077	-0.040	18.472	-0.041	-0.041	0.000	0.000	0.000	0.000
116	A	128	HIS	0	0.001	0.007	20.408	0.009	0.009	0.000	0.000	0.000	0.000
117	A	129	HIS	0	-0.047	-0.021	16.732	-0.016	-0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ILE)