FMO DATABASE

FMODB ID: Z64KN

Calculation Name: 3FCD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-943891.397945
FMO2-HF: Nuclear repulsion	896495.558243
FMO2-HF: Total energy	-47395.839703
FMO2-MP2: Total energy	-47532.150913

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: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.
-5.96	-1.228	6.068	-3.285	-7.513	-0.009

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 : -0.055 / q_NPA : -0.041

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	0.028	0.011	3.739	-2.743	0.107	-0.021	-1.266	-1.564	-0.001
4	A	7	ILE	0	-0.005	-0.001	4.058	-0.203	0.196	0.002	-0.053	-0.348	0.000
5	A	8	THR	0	-0.008	0.006	6.034	0.097	0.097	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.014	0.012	9.471	0.053	0.053	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.003	-0.018	12.562	0.026	0.026	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.008	-0.006	14.654	0.007	0.007	0.000	0.000	0.000	0.000
9	A	12	HIS	1	0.765	0.867	17.491	0.042	0.042	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.017	-0.007	21.364	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	14	PRO	0	0.050	0.014	24.278	0.008	0.008	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.761	-0.882	27.657	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	16	MET	0	-0.049	-0.037	22.050	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	17	GLN	0	0.015	0.011	26.328	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.965	-0.981	28.691	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.016	-0.008	23.524	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.041	-0.034	22.937	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	21	THR	0	0.000	0.013	25.226	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.030	-0.007	24.364	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	23	PHE	0	0.018	-0.016	19.813	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	24	CYS	0	-0.033	-0.012	22.427	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.882	-0.934	23.933	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	26	THR	0	-0.108	-0.039	26.566	0.000	0.000	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.094	-0.056	21.608	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.003	0.023	22.301	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	29	PHE	0	-0.069	-0.050	15.558	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.890	-0.951	19.176	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.031	-0.011	19.163	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.863	0.939	16.592	0.013	0.013	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.002	-0.007	18.123	0.026	0.026	0.000	0.000	0.000	0.000
31	A	34	ARG	1	0.968	0.983	20.112	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	35	HIS	0	-0.003	0.004	22.417	0.006	0.006	0.000	0.000	0.000	0.000
33	A	36	SER	0	-0.022	0.004	23.421	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	37	ASN	0	0.000	-0.005	23.978	0.005	0.005	0.000	0.000	0.000	0.000
35	A	38	TYR	0	0.052	0.029	15.176	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.003	-0.008	19.522	0.008	0.008	0.000	0.000	0.000	0.000
37	A	40	TYR	0	-0.077	-0.064	11.744	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.035	-0.012	16.269	0.017	0.017	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.829	-0.883	13.184	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.029	0.033	14.793	0.024	0.024	0.000	0.000	0.000	0.000
41	A	44	SER	0	-0.031	-0.037	14.865	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	45	GLY	0	-0.003	0.002	13.414	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.061	-0.009	10.500	-0.077	-0.077	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.030	0.011	10.152	0.076	0.076	0.000	0.000	0.000	0.000
45	A	48	LEU	0	-0.028	-0.019	11.617	-0.062	-0.062	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.790	0.890	9.449	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	50	LEU	0	0.008	-0.003	15.178	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	51	LEU	0	-0.012	-0.017	18.748	0.020	0.020	0.000	0.000	0.000	0.000
49	A	52	GLU	-1	-0.868	-0.928	21.056	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	53	GLU	-1	-0.858	-0.930	23.227	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	54	PRO	0	-0.034	0.001	26.574	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	64	ALA	0	-0.019	-0.009	20.679	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	65	ARG	1	0.863	0.923	19.318	0.045	0.045	0.000	0.000	0.000	0.000
54	A	66	VAL	0	0.049	0.033	13.103	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	67	ALA	0	0.019	0.038	14.755	0.001	0.001	0.000	0.000	0.000	0.000
56	A	68	ILE	0	0.004	0.001	8.521	-0.042	-0.042	0.000	0.000	0.000	0.000
57	A	69	CYS	0	-0.035	-0.007	9.014	0.083	0.083	0.000	0.000	0.000	0.000
58	A	70	ILE	0	-0.010	0.001	2.756	-1.157	-0.307	0.503	-0.223	-1.129	-0.001
59	A	71	ASP	-1	-0.760	-0.841	5.109	0.456	0.456	0.000	0.000	0.000	0.000
60	A	72	VAL	0	-0.036	-0.031	2.214	-0.804	-1.512	5.247	-1.431	-3.108	-0.007
61	A	73	SER	0	0.043	0.025	3.699	-1.126	-0.811	0.008	-0.094	-0.228	0.000
62	A	74	ASP	-1	-0.877	-0.935	5.456	1.114	1.114	0.000	0.000	0.000	0.000
63	A	75	ILE	0	0.019	0.005	6.264	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	76	ASP	-1	-0.811	-0.908	7.294	0.352	0.352	0.000	0.000	0.000	0.000
65	A	77	SER	0	-0.013	-0.015	8.481	-0.196	-0.196	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.056	-0.023	2.938	-0.885	-0.226	0.317	-0.158	-0.817	0.000
67	A	79	HIS	0	0.017	0.002	6.309	-0.185	-0.185	0.000	0.000	0.000	0.000
68	A	80	THR	0	0.013	0.010	8.898	-0.106	-0.106	0.000	0.000	0.000	0.000
69	A	81	LYS	1	0.905	0.950	6.615	-0.053	-0.053	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.036	-0.026	5.251	-0.073	-0.073	0.000	0.000	0.000	0.000
71	A	83	SER	0	0.027	0.020	9.381	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.018	0.014	12.662	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	85	ALA	0	-0.036	-0.016	11.983	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	86	LEU	0	-0.025	-0.019	9.904	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	87	GLU	-1	-0.948	-0.968	13.779	0.078	0.078	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.090	-0.034	16.762	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	89	LEU	0	-0.054	-0.015	13.528	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	90	PRO	0	-0.006	-0.002	18.042	0.009	0.009	0.000	0.000	0.000	0.000
79	A	91	ALA	0	0.064	0.021	19.584	0.004	0.004	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.945	-0.962	20.212	0.023	0.023	0.000	0.000	0.000	0.000
81	A	93	GLN	0	-0.069	-0.049	17.628	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	94	VAL	0	-0.004	-0.004	13.772	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	95	GLU	-1	-0.929	-0.946	14.831	0.096	0.096	0.000	0.000	0.000	0.000
84	A	96	PRO	0	-0.037	-0.024	14.225	0.026	0.026	0.000	0.000	0.000	0.000
85	A	97	LEU	0	-0.020	-0.007	10.396	0.010	0.010	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.942	0.965	14.191	-0.183	-0.183	0.000	0.000	0.000	0.000
87	A	99	ASN	0	0.010	0.009	15.308	0.066	0.066	0.000	0.000	0.000	0.000
88	A	100	MET	0	-0.022	0.003	15.784	-0.042	-0.042	0.000	0.000	0.000	0.000
89	A	101	PRO	0	-0.028	-0.025	18.146	0.013	0.013	0.000	0.000	0.000	0.000
90	A	102	TYR	0	-0.072	-0.053	15.386	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	103	GLY	0	0.028	0.013	17.403	0.004	0.004	0.000	0.000	0.000	0.000
92	A	104	GLN	0	-0.013	-0.017	10.626	0.018	0.018	0.000	0.000	0.000	0.000
93	A	105	ARG	1	0.834	0.912	11.719	-0.518	-0.518	0.000	0.000	0.000	0.000
94	A	106	GLU	-1	-0.786	-0.900	10.495	0.346	0.346	0.000	0.000	0.000	0.000
95	A	107	PHE	0	0.014	0.008	6.776	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	108	GLN	0	-0.059	-0.047	10.578	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	109	VAL	0	0.039	0.022	10.616	0.006	0.006	0.000	0.000	0.000	0.000
98	A	110	ARG	1	0.903	0.976	12.961	0.001	0.001	0.000	0.000	0.000	0.000
99	A	111	MET	0	-0.033	-0.016	12.897	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	112	PRO	0	-0.015	-0.034	15.065	0.013	0.013	0.000	0.000	0.000	0.000
101	A	113	ASP	-1	-0.869	-0.926	17.761	-0.106	-0.106	0.000	0.000	0.000	0.000
102	A	114	GLY	0	-0.080	-0.038	19.095	0.009	0.009	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.809	-0.904	16.919	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	116	TRP	0	-0.027	-0.027	14.659	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.002	-0.006	7.191	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	118	ASN	0	0.039	0.025	9.897	0.020	0.020	0.000	0.000	0.000	0.000
107	A	119	PHE	0	0.019	0.032	3.422	-0.475	-0.108	0.012	-0.060	-0.319	0.000
108	A	120	THR	0	-0.023	-0.052	6.949	0.024	0.024	0.000	0.000	0.000	0.000
109	A	121	ALA	0	0.035	0.011	7.152	0.251	0.251	0.000	0.000	0.000	0.000
110	A	122	PRO	0	0.033	0.037	9.157	-0.143	-0.143	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.039	-0.003	12.243	0.087	0.087	0.000	0.000	0.000	0.000
112	A	124	ALA	0	0.043	0.025	13.215	0.013	0.013	0.000	0.000	0.000	0.000
113	A	125	GLU	-1	-0.885	-0.959	14.884	0.475	0.475	0.000	0.000	0.000	0.000
114	A	126	GLY	0	-0.041	-0.022	17.943	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	127	HIS	0	-0.074	-0.029	18.567	-0.050	-0.050	0.000	0.000	0.000	0.000
116	A	128	HIS	0	-0.017	0.001	20.288	0.017	0.017	0.000	0.000	0.000	0.000
117	A	129	HIS	0	-0.032	-0.008	16.534	-0.032	-0.032	0.000	0.000	0.000	0.000

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