FMO DATABASE

FMODB ID: MN86Z

Calculation Name: 3D6R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1082120.096312
FMO2-HF: Nuclear repulsion	1030638.735518
FMO2-HF: Total energy	-51481.360794
FMO2-MP2: Total energy	-51627.52351

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(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.
-2.405	-0.029	1.739	-1.432	-2.683	-0.005

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 : 0.004 / q_NPA : -0.010

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

Sort

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	0.027	0.015	3.349	-1.594	0.329	0.030	-0.928	-1.024	-0.001
4	B	86	ALA	0	-0.033	-0.011	5.717	0.674	0.674	0.000	0.000	0.000	0.000
5	B	87	PRO	0	0.040	0.012	7.196	0.062	0.062	0.000	0.000	0.000	0.000
6	B	88	ARG	1	0.932	0.978	6.304	-1.255	-1.255	0.000	0.000	0.000	0.000
7	B	89	TYR	0	-0.005	-0.013	9.251	-0.006	-0.006	0.000	0.000	0.000	0.000
8	B	90	ILE	0	-0.021	-0.001	9.361	0.155	0.155	0.000	0.000	0.000	0.000
9	B	91	THR	0	-0.021	-0.014	13.383	-0.069	-0.069	0.000	0.000	0.000	0.000
10	B	92	ASP	-1	-0.728	-0.817	17.053	0.263	0.263	0.000	0.000	0.000	0.000
11	B	93	MET	0	-0.095	-0.042	19.686	-0.011	-0.011	0.000	0.000	0.000	0.000
12	B	94	SER	0	-0.007	-0.025	21.662	0.010	0.010	0.000	0.000	0.000	0.000
13	B	95	ILE	0	0.061	0.001	23.979	-0.012	-0.012	0.000	0.000	0.000	0.000
14	B	96	GLU	-1	-0.824	-0.885	25.329	0.080	0.080	0.000	0.000	0.000	0.000
15	B	97	GLU	-1	-0.750	-0.835	25.666	0.144	0.144	0.000	0.000	0.000	0.000
16	B	98	ILE	0	-0.027	-0.012	22.050	-0.011	-0.011	0.000	0.000	0.000	0.000
17	B	99	SER	0	-0.043	-0.035	26.011	-0.013	-0.013	0.000	0.000	0.000	0.000
18	B	100	ARG	1	0.777	0.900	28.853	-0.091	-0.091	0.000	0.000	0.000	0.000
19	B	101	GLU	-1	-0.858	-0.908	31.700	0.033	0.033	0.000	0.000	0.000	0.000
20	B	102	TRP	0	-0.093	-0.052	31.034	0.002	0.002	0.000	0.000	0.000	0.000
21	B	103	TYR	0	-0.041	-0.045	35.152	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	104	MET	0	-0.053	0.005	35.913	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	105	LEU	0	0.006	0.000	39.082	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	106	MET	0	-0.076	-0.042	41.427	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	107	PRO	0	0.035	0.006	39.030	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	108	ARG	1	0.877	0.950	37.664	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	109	GLN	0	0.035	-0.009	34.754	0.006	0.006	0.000	0.000	0.000	0.000
28	B	110	LYS	1	0.942	0.974	33.093	0.027	0.027	0.000	0.000	0.000	0.000
29	B	111	ILE	0	0.034	0.024	31.097	0.003	0.003	0.000	0.000	0.000	0.000
30	B	112	THR	0	-0.031	-0.014	27.544	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	113	GLY	0	0.050	0.036	27.235	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	114	GLY	0	0.014	0.001	26.075	0.008	0.008	0.000	0.000	0.000	0.000
33	B	115	LEU	0	-0.051	-0.015	22.640	0.010	0.010	0.000	0.000	0.000	0.000
34	B	116	MET	0	-0.026	-0.005	26.845	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	117	VAL	0	0.018	0.010	28.093	0.006	0.006	0.000	0.000	0.000	0.000
36	B	118	LYS	1	0.910	0.949	30.331	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	119	MET	0	0.022	0.008	32.112	0.003	0.003	0.000	0.000	0.000	0.000
38	B	120	ASP	-1	-0.735	-0.864	34.513	0.016	0.016	0.000	0.000	0.000	0.000
39	B	121	GLN	0	-0.018	-0.018	37.623	0.002	0.002	0.000	0.000	0.000	0.000
40	B	122	ALA	0	-0.011	-0.009	39.833	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	123	ILE	0	-0.065	-0.022	36.333	0.002	0.002	0.000	0.000	0.000	0.000
42	B	124	MET	0	0.004	0.011	39.116	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	125	ASP	-1	-0.854	-0.899	39.764	0.021	0.021	0.000	0.000	0.000	0.000
44	B	126	LYS	1	0.872	0.947	36.088	-0.043	-0.043	0.000	0.000	0.000	0.000
45	B	127	ARG	1	0.847	0.914	31.255	-0.077	-0.077	0.000	0.000	0.000	0.000
46	B	128	ILE	0	-0.019	-0.020	29.682	0.003	0.003	0.000	0.000	0.000	0.000
47	B	129	THR	0	-0.017	-0.009	25.389	0.002	0.002	0.000	0.000	0.000	0.000
48	B	130	LEU	0	-0.001	0.008	23.930	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	131	LYS	1	0.863	0.916	21.848	-0.145	-0.145	0.000	0.000	0.000	0.000
50	B	132	ALA	0	0.006	-0.017	18.931	-0.024	-0.024	0.000	0.000	0.000	0.000
51	B	133	ASN	0	0.019	0.030	17.684	0.047	0.047	0.000	0.000	0.000	0.000
52	B	134	PHE	0	0.014	-0.003	12.722	-0.040	-0.040	0.000	0.000	0.000	0.000
53	B	135	SER	0	0.035	0.022	12.226	0.079	0.079	0.000	0.000	0.000	0.000
54	B	136	VAL	0	-0.040	-0.009	7.441	-0.021	-0.021	0.000	0.000	0.000	0.000
55	B	137	LEU	0	0.049	0.025	7.378	-0.022	-0.022	0.000	0.000	0.000	0.000
56	B	138	PHE	0	-0.006	-0.017	2.240	-0.689	-0.298	1.710	-0.504	-1.598	-0.004
57	B	139	ASP	-1	-0.825	-0.903	5.277	1.344	1.406	-0.001	0.000	-0.061	0.000
58	B	140	GLN	0	0.018	0.017	7.660	0.007	0.007	0.000	0.000	0.000	0.000
59	B	141	LEU	0	-0.050	-0.026	10.582	-0.036	-0.036	0.000	0.000	0.000	0.000
60	B	142	GLU	-1	-0.957	-0.984	12.196	-0.399	-0.399	0.000	0.000	0.000	0.000
61	B	143	THR	0	-0.006	0.002	13.912	0.009	0.009	0.000	0.000	0.000	0.000
62	B	144	LEU	0	-0.038	-0.021	16.250	0.043	0.043	0.000	0.000	0.000	0.000
63	B	145	VAL	0	-0.039	-0.030	18.207	-0.010	-0.010	0.000	0.000	0.000	0.000
64	B	146	SER	0	-0.025	-0.043	20.651	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	147	LEU	0	0.001	0.014	21.350	0.019	0.019	0.000	0.000	0.000	0.000
66	B	148	ARG	1	0.789	0.855	23.308	-0.071	-0.071	0.000	0.000	0.000	0.000
67	B	149	ALA	0	0.006	-0.002	25.989	0.009	0.009	0.000	0.000	0.000	0.000
68	B	150	PHE	0	-0.002	-0.008	25.937	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	151	THR	0	0.003	-0.019	30.261	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	152	ASP	-1	-0.819	-0.905	32.524	0.082	0.082	0.000	0.000	0.000	0.000
71	B	153	ASP	-1	-0.866	-0.905	33.771	0.064	0.064	0.000	0.000	0.000	0.000
72	B	154	GLY	0	0.010	0.007	31.691	0.002	0.002	0.000	0.000	0.000	0.000
73	B	155	ALA	0	-0.022	-0.004	32.437	0.002	0.002	0.000	0.000	0.000	0.000
74	B	156	ILE	0	-0.022	-0.005	29.725	0.002	0.002	0.000	0.000	0.000	0.000
75	B	157	VAL	0	0.000	-0.003	32.076	-0.005	-0.005	0.000	0.000	0.000	0.000
76	B	158	ALA	0	-0.012	-0.027	30.531	-0.008	-0.008	0.000	0.000	0.000	0.000
77	B	159	GLU	-1	-0.774	-0.837	27.050	0.049	0.049	0.000	0.000	0.000	0.000
78	B	160	ILE	0	-0.021	0.002	24.540	-0.010	-0.010	0.000	0.000	0.000	0.000
79	B	161	SER	0	0.026	0.003	24.854	0.007	0.007	0.000	0.000	0.000	0.000
80	B	162	PRO	0	0.035	0.018	22.765	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	163	ILE	0	-0.019	-0.002	25.551	0.010	0.010	0.000	0.000	0.000	0.000
82	B	164	PRO	0	0.013	-0.003	28.010	-0.009	-0.009	0.000	0.000	0.000	0.000
83	B	165	SER	0	-0.026	-0.011	29.014	-0.005	-0.005	0.000	0.000	0.000	0.000
84	B	166	MET	0	-0.057	-0.017	28.321	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	167	PRO	0	0.014	0.003	26.061	0.000	0.000	0.000	0.000	0.000	0.000
86	B	168	GLY	0	-0.003	0.002	21.970	0.005	0.005	0.000	0.000	0.000	0.000
87	B	169	HIS	0	0.019	0.020	19.967	-0.010	-0.010	0.000	0.000	0.000	0.000
88	B	170	SER	0	0.036	0.006	20.317	-0.021	-0.021	0.000	0.000	0.000	0.000
89	B	171	THR	0	0.058	-0.004	16.739	0.012	0.012	0.000	0.000	0.000	0.000
90	B	172	GLU	-1	-0.925	-0.959	19.241	-0.129	-0.129	0.000	0.000	0.000	0.000
91	B	173	ASP	-1	-0.782	-0.870	22.747	-0.106	-0.106	0.000	0.000	0.000	0.000
92	B	174	VAL	0	0.008	0.007	18.927	0.020	0.020	0.000	0.000	0.000	0.000
93	B	175	LYS	1	0.889	0.946	16.725	0.169	0.169	0.000	0.000	0.000	0.000
94	B	176	ASN	0	0.025	0.022	22.728	0.017	0.017	0.000	0.000	0.000	0.000
95	B	177	ALA	0	-0.035	-0.020	24.712	0.011	0.011	0.000	0.000	0.000	0.000
96	B	178	ILE	0	0.004	-0.011	20.974	0.012	0.012	0.000	0.000	0.000	0.000
97	B	179	GLY	0	0.034	0.028	25.370	0.008	0.008	0.000	0.000	0.000	0.000
98	B	180	ILE	0	-0.049	-0.036	27.773	0.006	0.006	0.000	0.000	0.000	0.000
99	B	181	LEU	0	-0.030	0.003	26.981	0.005	0.005	0.000	0.000	0.000	0.000
100	B	182	ILE	0	-0.004	-0.006	25.802	0.006	0.006	0.000	0.000	0.000	0.000
101	B	183	GLY	0	0.047	0.029	30.164	0.002	0.002	0.000	0.000	0.000	0.000
102	B	184	GLY	0	-0.040	-0.033	33.025	0.001	0.001	0.000	0.000	0.000	0.000
103	B	185	LEU	0	-0.013	-0.023	30.842	0.003	0.003	0.000	0.000	0.000	0.000
104	B	186	GLU	-1	-0.877	-0.942	31.826	0.004	0.004	0.000	0.000	0.000	0.000
105	B	187	TRP	0	-0.061	-0.014	35.621	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	188	ASN	0	-0.076	-0.034	38.083	-0.002	-0.002	0.000	0.000	0.000	0.000
107	B	189	ASP	-1	-0.807	-0.894	38.636	0.011	0.011	0.000	0.000	0.000	0.000
108	B	190	ASN	0	-0.094	-0.053	34.717	0.008	0.008	0.000	0.000	0.000	0.000
109	B	191	SER	0	0.020	0.010	33.175	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	192	ILE	0	0.008	-0.004	27.550	0.008	0.008	0.000	0.000	0.000	0.000
111	B	193	ARG	1	0.897	0.953	26.262	-0.098	-0.098	0.000	0.000	0.000	0.000
112	B	194	ALA	0	0.027	0.004	21.792	0.000	0.000	0.000	0.000	0.000	0.000
113	B	195	SER	0	-0.015	-0.036	19.379	0.006	0.006	0.000	0.000	0.000	0.000
114	B	196	GLU	-1	-0.851	-0.937	16.945	0.187	0.187	0.000	0.000	0.000	0.000
115	B	197	ASN	0	-0.033	-0.036	14.343	0.081	0.081	0.000	0.000	0.000	0.000
116	B	198	ILE	0	-0.023	-0.009	14.997	-0.016	-0.016	0.000	0.000	0.000	0.000
117	B	199	GLN	0	-0.077	-0.039	17.044	-0.045	-0.045	0.000	0.000	0.000	0.000
118	B	200	ARG	1	0.799	0.894	7.114	-0.994	-0.994	0.000	0.000	0.000	0.000
119	B	201	PHE	0	-0.055	-0.018	8.464	0.009	0.009	0.000	0.000	0.000	0.000
120	B	202	ALA	0	-0.006	0.010	12.893	-0.101	-0.101	0.000	0.000	0.000	0.000
121	B	218	GLN	0	-0.051	-0.038	49.071	0.001	0.001	0.000	0.000	0.000	0.000
122	B	219	LYS	1	0.810	0.874	42.131	-0.013	-0.013	0.000	0.000	0.000	0.000
123	B	220	ARG	1	0.959	0.984	45.049	-0.025	-0.025	0.000	0.000	0.000	0.000
124	B	221	TYR	0	0.022	0.000	48.785	0.001	0.001	0.000	0.000	0.000	0.000
125	B	222	MET	0	-0.023	0.017	51.826	0.001	0.001	0.000	0.000	0.000	0.000
126	B	223	ALA	0	0.050	0.027	52.846	-0.001	-0.001	0.000	0.000	0.000	0.000
127	B	224	ARG	1	0.947	0.957	54.758	-0.019	-0.019	0.000	0.000	0.000	0.000

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