FMO DATABASE

FMODB ID: 76N3K

Calculation Name: 3D6R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D6R

Chain ID: B

ChEMBL ID:

UniProt ID: P69270

Base Structure: X-ray

Registration Date: 2023-09-22

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1080479.412161
FMO2-HF: Nuclear repulsion	1028997.821573
FMO2-HF: Total energy	-51481.590588
FMO2-MP2: Total energy	-51627.725232

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(B:83:SER)

Summations of interaction energy for fragment #1(B:83:SER)

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.
-3.638	-1.468	1.023	-1.146	-2.046	-0.001

Interaction energy analysis for fragmet #1(B:83:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.013

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	B	85	PRO	0	0.030	0.014	3.543	-2.165	-0.689	0.011	-0.685	-0.802	0.001
4	B	86	ALA	0	-0.034	-0.010	5.858	0.550	0.550	0.000	0.000	0.000	0.000
5	B	87	PRO	0	0.030	0.007	7.286	-0.145	-0.145	0.000	0.000	0.000	0.000
6	B	88	ARG	1	0.940	0.984	6.397	0.057	0.057	0.000	0.000	0.000	0.000
7	B	89	TYR	0	0.010	-0.004	9.233	-0.057	-0.057	0.000	0.000	0.000	0.000
8	B	90	ILE	0	-0.025	-0.008	9.515	0.100	0.100	0.000	0.000	0.000	0.000
9	B	91	THR	0	-0.013	-0.013	13.557	-0.013	-0.013	0.000	0.000	0.000	0.000
10	B	92	ASP	-1	-0.733	-0.809	17.232	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	93	MET	0	-0.081	-0.022	19.850	0.024	0.024	0.000	0.000	0.000	0.000
12	B	94	SER	0	0.013	-0.023	21.850	0.006	0.006	0.000	0.000	0.000	0.000
13	B	95	ILE	0	0.045	0.001	24.159	-0.014	-0.014	0.000	0.000	0.000	0.000
14	B	96	GLU	-1	-0.831	-0.889	25.487	-0.021	-0.021	0.000	0.000	0.000	0.000
15	B	97	GLU	-1	-0.743	-0.825	25.717	-0.020	-0.020	0.000	0.000	0.000	0.000
16	B	98	ILE	0	-0.007	-0.001	22.082	-0.012	-0.012	0.000	0.000	0.000	0.000
17	B	99	SER	0	-0.035	-0.027	26.022	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	100	ARG	1	0.775	0.894	28.925	0.024	0.024	0.000	0.000	0.000	0.000
19	B	101	GLU	-1	-0.849	-0.895	31.863	-0.048	-0.048	0.000	0.000	0.000	0.000
20	B	102	TRP	0	-0.083	-0.053	31.030	0.004	0.004	0.000	0.000	0.000	0.000
21	B	103	TYR	0	-0.054	-0.054	35.215	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	104	MET	0	-0.057	-0.005	35.936	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	105	LEU	0	0.003	0.003	39.322	0.002	0.002	0.000	0.000	0.000	0.000
24	B	106	MET	0	-0.074	-0.043	41.618	0.002	0.002	0.000	0.000	0.000	0.000
25	B	107	PRO	0	0.041	0.010	39.090	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	108	ARG	1	0.875	0.945	37.348	0.079	0.079	0.000	0.000	0.000	0.000
27	B	109	GLN	0	0.042	0.011	34.506	0.001	0.001	0.000	0.000	0.000	0.000
28	B	110	LYS	1	0.934	0.969	32.625	0.140	0.140	0.000	0.000	0.000	0.000
29	B	111	ILE	0	0.037	0.017	30.938	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	112	THR	0	-0.031	-0.014	26.815	0.003	0.003	0.000	0.000	0.000	0.000
31	B	113	GLY	0	0.062	0.039	26.760	-0.014	-0.014	0.000	0.000	0.000	0.000
32	B	114	GLY	0	0.016	0.003	25.626	0.019	0.019	0.000	0.000	0.000	0.000
33	B	115	LEU	0	-0.052	-0.017	22.408	0.005	0.005	0.000	0.000	0.000	0.000
34	B	116	MET	0	-0.011	0.009	26.614	0.014	0.014	0.000	0.000	0.000	0.000
35	B	117	VAL	0	0.031	0.011	27.767	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	118	LYS	1	0.877	0.917	30.027	0.116	0.116	0.000	0.000	0.000	0.000
37	B	119	MET	0	0.021	0.012	31.927	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	120	ASP	-1	-0.724	-0.864	34.454	-0.060	-0.060	0.000	0.000	0.000	0.000
39	B	121	GLN	0	-0.049	-0.028	37.752	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	122	ALA	0	-0.011	-0.014	40.032	0.002	0.002	0.000	0.000	0.000	0.000
41	B	123	ILE	0	-0.066	-0.019	36.045	0.005	0.005	0.000	0.000	0.000	0.000
42	B	124	MET	0	0.027	0.025	38.531	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	125	ASP	-1	-0.850	-0.900	39.500	-0.047	-0.047	0.000	0.000	0.000	0.000
44	B	126	LYS	1	0.860	0.943	35.428	0.044	0.044	0.000	0.000	0.000	0.000
45	B	127	ARG	1	0.834	0.897	30.791	0.032	0.032	0.000	0.000	0.000	0.000
46	B	128	ILE	0	-0.015	-0.015	29.117	0.006	0.006	0.000	0.000	0.000	0.000
47	B	129	THR	0	-0.010	-0.002	25.056	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	130	LEU	0	-0.009	0.006	23.553	0.004	0.004	0.000	0.000	0.000	0.000
49	B	131	LYS	1	0.822	0.882	21.757	0.024	0.024	0.000	0.000	0.000	0.000
50	B	132	ALA	0	0.009	-0.017	18.589	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	133	ASN	0	0.008	0.015	17.740	0.015	0.015	0.000	0.000	0.000	0.000
52	B	134	PHE	0	-0.005	-0.006	12.637	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	135	SER	0	0.027	0.016	12.232	0.073	0.073	0.000	0.000	0.000	0.000
54	B	136	VAL	0	-0.039	-0.017	7.347	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	137	LEU	0	0.047	0.028	7.240	0.008	0.008	0.000	0.000	0.000	0.000
56	B	138	PHE	0	-0.017	-0.023	2.326	-0.485	0.134	1.013	-0.461	-1.171	-0.002
57	B	139	ASP	-1	-0.814	-0.883	5.144	-1.961	-1.886	-0.001	0.000	-0.073	0.000
58	B	140	GLN	0	0.035	0.022	7.234	0.530	0.530	0.000	0.000	0.000	0.000
59	B	141	LEU	0	-0.040	-0.024	10.483	-0.047	-0.047	0.000	0.000	0.000	0.000
60	B	142	GLU	-1	-0.909	-0.952	11.975	-0.779	-0.779	0.000	0.000	0.000	0.000
61	B	143	THR	0	-0.042	-0.027	13.791	0.094	0.094	0.000	0.000	0.000	0.000
62	B	144	LEU	0	-0.038	-0.017	16.263	0.006	0.006	0.000	0.000	0.000	0.000
63	B	145	VAL	0	-0.032	-0.023	18.263	0.016	0.016	0.000	0.000	0.000	0.000
64	B	146	SER	0	-0.026	-0.050	20.704	0.018	0.018	0.000	0.000	0.000	0.000
65	B	147	LEU	0	-0.017	0.001	21.020	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	148	ARG	1	0.797	0.864	23.186	0.086	0.086	0.000	0.000	0.000	0.000
67	B	149	ALA	0	0.011	0.000	25.819	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	150	PHE	0	0.013	-0.004	25.811	0.008	0.008	0.000	0.000	0.000	0.000
69	B	151	THR	0	-0.014	-0.034	29.884	-0.005	-0.005	0.000	0.000	0.000	0.000
70	B	152	ASP	-1	-0.800	-0.876	31.708	-0.030	-0.030	0.000	0.000	0.000	0.000
71	B	153	ASP	-1	-0.835	-0.882	33.006	-0.028	-0.028	0.000	0.000	0.000	0.000
72	B	154	GLY	0	0.024	0.020	31.748	0.005	0.005	0.000	0.000	0.000	0.000
73	B	155	ALA	0	-0.024	-0.006	32.463	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	156	ILE	0	-0.019	-0.009	29.817	-0.003	-0.003	0.000	0.000	0.000	0.000
75	B	157	VAL	0	-0.008	-0.006	32.037	0.002	0.002	0.000	0.000	0.000	0.000
76	B	158	ALA	0	0.003	-0.019	30.396	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	159	GLU	-1	-0.789	-0.832	27.032	-0.106	-0.106	0.000	0.000	0.000	0.000
78	B	160	ILE	0	-0.008	0.002	24.320	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	161	SER	0	0.029	0.010	24.449	-0.005	-0.005	0.000	0.000	0.000	0.000
80	B	162	PRO	0	0.040	0.012	22.691	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	163	ILE	0	-0.019	0.007	25.459	0.022	0.022	0.000	0.000	0.000	0.000
82	B	164	PRO	0	-0.012	-0.021	28.132	-0.008	-0.008	0.000	0.000	0.000	0.000
83	B	165	SER	0	-0.019	-0.001	29.171	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	166	MET	0	-0.040	-0.009	28.096	0.001	0.001	0.000	0.000	0.000	0.000
85	B	167	PRO	0	0.008	-0.006	25.843	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	168	GLY	0	0.005	0.007	21.673	0.004	0.004	0.000	0.000	0.000	0.000
87	B	169	HIS	0	0.017	0.021	19.874	-0.031	-0.031	0.000	0.000	0.000	0.000
88	B	170	SER	0	0.034	0.001	19.819	-0.044	-0.044	0.000	0.000	0.000	0.000
89	B	171	THR	0	0.041	-0.010	16.131	0.023	0.023	0.000	0.000	0.000	0.000
90	B	172	GLU	-1	-0.920	-0.955	18.667	-0.312	-0.312	0.000	0.000	0.000	0.000
91	B	173	ASP	-1	-0.795	-0.864	22.177	-0.290	-0.290	0.000	0.000	0.000	0.000
92	B	174	VAL	0	0.016	0.003	18.550	0.031	0.031	0.000	0.000	0.000	0.000
93	B	175	LYS	1	0.863	0.926	16.302	0.594	0.594	0.000	0.000	0.000	0.000
94	B	176	ASN	0	0.000	0.002	22.206	0.041	0.041	0.000	0.000	0.000	0.000
95	B	177	ALA	0	-0.034	-0.013	24.355	0.025	0.025	0.000	0.000	0.000	0.000
96	B	178	ILE	0	0.008	-0.005	20.588	0.022	0.022	0.000	0.000	0.000	0.000
97	B	179	GLY	0	0.031	0.025	24.973	0.019	0.019	0.000	0.000	0.000	0.000
98	B	180	ILE	0	-0.052	-0.041	27.234	0.021	0.021	0.000	0.000	0.000	0.000
99	B	181	LEU	0	-0.033	-0.005	27.151	0.016	0.016	0.000	0.000	0.000	0.000
100	B	182	ILE	0	-0.019	-0.004	24.968	0.013	0.013	0.000	0.000	0.000	0.000
101	B	183	GLY	0	0.077	0.041	29.486	0.012	0.012	0.000	0.000	0.000	0.000
102	B	184	GLY	0	-0.048	-0.028	32.491	0.010	0.010	0.000	0.000	0.000	0.000
103	B	185	LEU	0	-0.003	-0.011	30.499	0.011	0.011	0.000	0.000	0.000	0.000
104	B	186	GLU	-1	-0.873	-0.947	30.758	-0.126	-0.126	0.000	0.000	0.000	0.000
105	B	187	TRP	0	-0.065	-0.025	34.801	0.009	0.009	0.000	0.000	0.000	0.000
106	B	188	ASN	0	-0.037	-0.007	37.513	0.006	0.006	0.000	0.000	0.000	0.000
107	B	189	ASP	-1	-0.808	-0.900	37.916	-0.064	-0.064	0.000	0.000	0.000	0.000
108	B	190	ASN	0	-0.123	-0.072	34.142	0.010	0.010	0.000	0.000	0.000	0.000
109	B	191	SER	0	0.021	0.013	32.666	-0.006	-0.006	0.000	0.000	0.000	0.000
110	B	192	ILE	0	0.024	-0.008	27.069	0.005	0.005	0.000	0.000	0.000	0.000
111	B	193	ARG	1	0.849	0.921	25.348	0.051	0.051	0.000	0.000	0.000	0.000
112	B	194	ALA	0	0.022	0.001	21.367	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	195	SER	0	0.004	-0.020	18.860	0.000	0.000	0.000	0.000	0.000	0.000
114	B	196	GLU	-1	-0.865	-0.934	16.092	-0.133	-0.133	0.000	0.000	0.000	0.000
115	B	197	ASN	0	-0.048	-0.039	13.916	-0.054	-0.054	0.000	0.000	0.000	0.000
116	B	198	ILE	0	-0.015	-0.011	14.417	-0.088	-0.088	0.000	0.000	0.000	0.000
117	B	199	GLN	0	-0.067	-0.040	16.262	-0.063	-0.063	0.000	0.000	0.000	0.000
118	B	200	ARG	1	0.792	0.886	6.070	0.825	0.825	0.000	0.000	0.000	0.000
119	B	201	PHE	0	-0.046	-0.012	7.793	-0.116	-0.116	0.000	0.000	0.000	0.000
120	B	202	ALA	0	-0.010	0.008	12.307	-0.070	-0.070	0.000	0.000	0.000	0.000
121	B	218	GLN	0	-0.035	-0.033	48.070	0.000	0.000	0.000	0.000	0.000	0.000
122	B	219	LYS	1	0.823	0.889	41.511	0.058	0.058	0.000	0.000	0.000	0.000
123	B	220	ARG	1	0.901	0.943	43.736	0.041	0.041	0.000	0.000	0.000	0.000
124	B	221	TYR	0	0.025	0.010	48.373	0.002	0.002	0.000	0.000	0.000	0.000
125	B	222	MET	0	-0.008	0.026	51.388	0.001	0.001	0.000	0.000	0.000	0.000
126	B	223	ALA	0	0.029	0.014	52.375	0.000	0.000	0.000	0.000	0.000	0.000
127	B	224	ARG	1	0.949	0.958	54.690	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:83:SER)