FMO DATABASE

FMODB ID: 6N1KZ

Calculation Name: 3FDW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FDW

Chain ID: A

ChEMBL ID:

UniProt ID: Q96C24

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1220610.695075
FMO2-HF: Nuclear repulsion	1167665.854529
FMO2-HF: Total energy	-52944.840546
FMO2-MP2: Total energy	-53101.431525

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:354:ILE)

Summations of interaction energy for fragment #1(A:354: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.
-6.212	-2.71	9.991	-2.804	-10.688	-0.02

Interaction energy analysis for fragmet #1(A:354: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 : -0.026

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	356	VAL	0	-0.027	-0.008	2.980	-2.342	-0.153	0.454	-0.890	-1.752	-0.003
4	A	357	THR	0	-0.018	-0.016	3.761	0.568	0.697	0.002	0.018	-0.150	0.000
5	A	358	GLY	0	0.044	0.027	6.464	-0.093	-0.093	0.000	0.000	0.000	0.000
6	A	359	ARG	1	0.717	0.776	9.453	0.382	0.382	0.000	0.000	0.000	0.000
7	A	360	ILE	0	-0.001	-0.009	12.240	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	361	ALA	0	0.063	0.040	14.072	0.027	0.027	0.000	0.000	0.000	0.000
9	A	362	PHE	0	0.001	-0.022	17.631	0.008	0.008	0.000	0.000	0.000	0.000
10	A	363	SER	0	-0.003	-0.004	20.348	0.011	0.011	0.000	0.000	0.000	0.000
11	A	364	LEU	0	-0.036	0.009	22.206	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	365	LYS	1	0.846	0.909	25.677	0.148	0.148	0.000	0.000	0.000	0.000
13	A	366	TYR	0	-0.001	-0.027	28.898	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	367	GLU	-1	-0.768	-0.822	31.556	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	368	GLN	0	0.039	0.004	34.542	0.001	0.001	0.000	0.000	0.000	0.000
16	A	369	GLN	0	0.003	-0.004	36.188	0.002	0.002	0.000	0.000	0.000	0.000
17	A	370	THR	0	-0.022	-0.028	34.383	0.001	0.001	0.000	0.000	0.000	0.000
18	A	371	GLN	0	-0.009	-0.003	34.896	0.000	0.000	0.000	0.000	0.000	0.000
19	A	372	SER	0	0.020	0.023	30.563	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	373	LEU	0	0.001	0.005	24.892	0.000	0.000	0.000	0.000	0.000	0.000
21	A	374	VAL	0	-0.045	-0.023	26.982	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	375	VAL	0	0.001	-0.017	20.693	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	376	HIS	0	-0.022	-0.007	22.324	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	377	VAL	0	0.018	-0.002	16.317	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	378	LYS	1	0.856	0.931	19.340	0.215	0.215	0.000	0.000	0.000	0.000
26	A	379	GLU	-1	-0.874	-0.941	16.220	-0.253	-0.253	0.000	0.000	0.000	0.000
27	A	380	CYS	0	-0.093	-0.040	11.256	-0.056	-0.056	0.000	0.000	0.000	0.000
28	A	381	HIS	0	0.043	0.030	12.256	0.036	0.036	0.000	0.000	0.000	0.000
29	A	382	GLN	0	0.027	0.001	10.661	-0.076	-0.076	0.000	0.000	0.000	0.000
30	A	383	LEU	0	-0.002	0.012	6.387	-0.122	-0.122	0.000	0.000	0.000	0.000
31	A	384	ALA	0	0.049	0.036	2.356	0.171	-0.316	2.402	-0.629	-1.286	-0.001
32	A	385	TYR	0	0.011	0.010	4.262	-0.181	0.079	0.000	-0.027	-0.233	0.000
33	A	386	ALA	0	0.004	-0.014	2.322	-1.531	-0.845	3.145	-1.730	-2.100	-0.002
34	A	387	ASP	-1	-0.899	-0.952	3.082	2.312	0.324	0.042	2.284	-0.339	-0.001
35	A	388	GLU	-1	-0.746	-0.874	5.571	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	389	ALA	0	-0.043	-0.020	7.150	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	390	LYS	1	0.886	0.940	9.924	-0.180	-0.180	0.000	0.000	0.000	0.000
38	A	391	LYS	1	0.823	0.927	9.633	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	392	ARG	1	0.799	0.886	8.508	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	393	SER	0	-0.017	-0.030	4.992	0.061	0.061	0.000	0.000	0.000	0.000
41	A	394	ASN	0	-0.053	-0.027	7.110	0.013	0.013	0.000	0.000	0.000	0.000
42	A	395	PRO	0	0.054	0.040	8.434	0.011	0.011	0.000	0.000	0.000	0.000
43	A	396	TYR	0	-0.080	-0.047	9.535	0.057	0.057	0.000	0.000	0.000	0.000
44	A	397	VAL	0	0.080	0.041	10.690	-0.099	-0.099	0.000	0.000	0.000	0.000
45	A	398	LYS	1	0.841	0.926	10.944	0.537	0.537	0.000	0.000	0.000	0.000
46	A	399	THR	0	0.032	0.014	14.345	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	400	TYR	0	-0.032	-0.023	14.527	0.012	0.012	0.000	0.000	0.000	0.000
48	A	401	LEU	0	0.057	0.049	19.408	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	402	LEU	0	0.002	0.021	18.127	0.021	0.021	0.000	0.000	0.000	0.000
50	A	403	PRO	0	0.077	0.016	22.290	0.007	0.007	0.000	0.000	0.000	0.000
51	A	404	ASP	-1	-0.837	-0.890	23.021	-0.148	-0.148	0.000	0.000	0.000	0.000
52	A	405	LYS	1	0.872	0.931	15.682	0.312	0.312	0.000	0.000	0.000	0.000
53	A	406	SER	0	-0.010	-0.023	19.682	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	407	ARG	1	0.927	0.940	20.909	0.102	0.102	0.000	0.000	0.000	0.000
55	A	408	GLN	0	0.011	-0.004	21.966	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	409	GLY	0	0.109	0.090	23.291	0.004	0.004	0.000	0.000	0.000	0.000
57	A	410	LYS	1	0.882	0.957	16.086	0.188	0.188	0.000	0.000	0.000	0.000
58	A	411	ARG	1	0.816	0.907	18.812	0.189	0.189	0.000	0.000	0.000	0.000
59	A	412	LYS	1	0.877	0.927	15.824	0.169	0.169	0.000	0.000	0.000	0.000
60	A	413	THR	0	0.050	0.046	15.431	0.012	0.012	0.000	0.000	0.000	0.000
61	A	414	SER	0	-0.123	-0.106	16.912	0.008	0.008	0.000	0.000	0.000	0.000
62	A	415	ILE	0	-0.028	-0.014	12.284	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	416	LYS	1	0.885	0.965	13.278	0.248	0.248	0.000	0.000	0.000	0.000
64	A	417	ARG	1	0.919	0.944	12.384	0.065	0.065	0.000	0.000	0.000	0.000
65	A	418	ASP	-1	-0.831	-0.912	11.423	-0.080	-0.080	0.000	0.000	0.000	0.000
66	A	419	THR	0	0.009	0.005	10.887	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	420	VAL	0	0.014	0.005	7.693	-0.039	-0.039	0.000	0.000	0.000	0.000
68	A	421	ASN	0	0.010	0.014	10.165	-0.113	-0.113	0.000	0.000	0.000	0.000
69	A	422	PRO	0	-0.044	-0.011	11.437	0.051	0.051	0.000	0.000	0.000	0.000
70	A	423	LEU	0	0.109	0.059	14.344	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	424	TYR	0	-0.156	-0.115	12.581	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	425	ASP	-1	-0.800	-0.895	18.874	-0.167	-0.167	0.000	0.000	0.000	0.000
73	A	426	GLU	-1	-0.763	-0.837	19.235	-0.199	-0.199	0.000	0.000	0.000	0.000
74	A	427	THR	0	-0.017	-0.028	21.554	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	428	LEU	0	-0.038	-0.004	18.362	0.010	0.010	0.000	0.000	0.000	0.000
76	A	429	ARG	1	0.808	0.862	23.112	0.122	0.122	0.000	0.000	0.000	0.000
77	A	430	TYR	0	-0.069	-0.056	21.290	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	431	GLU	-1	-0.871	-0.926	27.371	-0.094	-0.094	0.000	0.000	0.000	0.000
79	A	432	ILE	0	-0.043	-0.022	28.612	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	433	PRO	0	0.067	0.054	31.652	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	434	GLU	-1	-0.801	-0.894	33.227	-0.106	-0.106	0.000	0.000	0.000	0.000
82	A	435	SER	0	0.011	0.004	33.557	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	436	LEU	0	0.016	0.003	32.116	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	437	LEU	0	-0.024	-0.012	27.193	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	438	ALA	0	0.031	0.004	29.021	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	439	GLN	0	-0.023	-0.011	29.950	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	440	ARG	1	0.834	0.941	25.301	0.138	0.138	0.000	0.000	0.000	0.000
88	A	441	THR	0	0.030	0.014	20.359	0.010	0.010	0.000	0.000	0.000	0.000
89	A	442	LEU	0	-0.014	-0.001	19.844	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	443	GLN	0	-0.010	-0.011	14.570	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	444	PHE	0	0.025	-0.005	14.298	0.028	0.028	0.000	0.000	0.000	0.000
92	A	445	SER	0	-0.005	-0.004	10.494	-0.052	-0.052	0.000	0.000	0.000	0.000
93	A	446	VAL	0	0.037	0.017	7.768	0.132	0.132	0.000	0.000	0.000	0.000
94	A	447	TRP	0	0.007	-0.008	6.264	-0.293	-0.293	0.000	0.000	0.000	0.000
95	A	448	HIS	0	0.093	0.065	4.692	-0.097	0.043	-0.001	-0.008	-0.131	0.000
96	A	449	HIS	0	-0.022	-0.016	6.645	0.072	0.072	0.000	0.000	0.000	0.000
97	A	450	GLY	0	0.045	0.010	8.052	0.023	0.023	0.000	0.000	0.000	0.000
98	A	451	ARG	1	0.958	0.967	8.994	-0.301	-0.301	0.000	0.000	0.000	0.000
99	A	452	PHE	0	0.007	-0.013	11.222	0.013	0.013	0.000	0.000	0.000	0.000
100	A	453	GLY	0	0.076	0.061	12.870	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	454	ARG	1	0.903	0.954	7.463	-0.183	-0.183	0.000	0.000	0.000	0.000
102	A	455	ASN	0	0.025	0.039	8.232	0.004	0.004	0.000	0.000	0.000	0.000
103	A	456	THR	0	-0.018	-0.021	2.324	-0.103	-0.360	1.897	-0.378	-1.262	0.003
104	A	457	PHE	0	-0.021	0.002	3.998	-0.466	0.020	0.001	-0.085	-0.402	0.000
105	A	458	LEU	0	0.008	-0.011	2.482	-4.134	-1.897	2.050	-1.365	-2.921	-0.016
106	A	459	GLY	0	0.050	0.026	3.979	-0.268	-0.161	-0.001	0.006	-0.112	0.000
107	A	460	GLU	-1	-0.969	-0.988	6.821	-0.464	-0.464	0.000	0.000	0.000	0.000
108	A	461	ALA	0	0.042	0.022	10.517	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	462	GLU	-1	-0.841	-0.925	13.655	-0.339	-0.339	0.000	0.000	0.000	0.000
110	A	463	ILE	0	0.022	0.016	17.369	0.010	0.010	0.000	0.000	0.000	0.000
111	A	464	GLN	0	-0.003	-0.001	21.000	0.006	0.006	0.000	0.000	0.000	0.000
112	A	465	MET	0	-0.025	-0.016	24.040	0.006	0.006	0.000	0.000	0.000	0.000
113	A	466	ASP	-1	-0.803	-0.889	26.756	-0.107	-0.107	0.000	0.000	0.000	0.000
114	A	467	SER	0	0.026	0.012	26.654	0.006	0.006	0.000	0.000	0.000	0.000
115	A	468	TRP	0	-0.044	-0.027	26.340	0.006	0.006	0.000	0.000	0.000	0.000
116	A	469	LYS	1	0.819	0.898	28.471	0.118	0.118	0.000	0.000	0.000	0.000
117	A	470	LEU	0	-0.002	0.021	31.729	0.007	0.007	0.000	0.000	0.000	0.000
118	A	471	ASP	-1	-0.874	-0.940	31.832	-0.109	-0.109	0.000	0.000	0.000	0.000
119	A	472	LYS	1	0.795	0.894	30.174	0.110	0.110	0.000	0.000	0.000	0.000
120	A	473	LYS	1	0.903	0.943	24.046	0.194	0.194	0.000	0.000	0.000	0.000
121	A	474	LEU	0	0.015	0.017	27.455	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	475	ASP	-1	-0.780	-0.884	24.834	-0.180	-0.180	0.000	0.000	0.000	0.000
123	A	476	HIS	0	-0.033	-0.022	20.911	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	477	CYM	-1	-0.695	-0.761	17.510	-0.361	-0.361	0.000	0.000	0.000	0.000
125	A	478	LEU	0	-0.043	-0.012	15.439	0.020	0.020	0.000	0.000	0.000	0.000
126	A	479	PRO	0	0.015	0.007	12.424	-0.033	-0.033	0.000	0.000	0.000	0.000
127	A	480	LEU	0	-0.043	-0.014	7.787	0.013	0.013	0.000	0.000	0.000	0.000
128	A	481	HIS	0	-0.002	-0.004	9.302	0.035	0.035	0.000	0.000	0.000	0.000
129	A	482	GLY	0	0.044	0.009	6.632	-0.316	-0.316	0.000	0.000	0.000	0.000
130	A	483	LYS	1	0.950	0.979	7.320	1.053	1.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:354:ILE)