FMO DATABASE

FMODB ID: 85ZGY

Calculation Name: 3BDW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDW

Chain ID: B

ChEMBL ID:

UniProt ID: Q13241

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	-1027936.679658
FMO2-HF: Nuclear repulsion	978166.598693
FMO2-HF: Total energy	-49770.080965
FMO2-MP2: Total energy	-49909.962657

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:113:ALA)

Summations of interaction energy for fragment #1(B:113:ALA)

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.
-4.385	-2.767	-0.024	-0.773	-0.821	0.003

Interaction energy analysis for fragmet #1(B:113:ALA)

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 : -0.005

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	115	HIS	0	0.042	0.022	3.835	-1.106	0.412	-0.023	-0.763	-0.732	0.003
4	B	116	CYS	0	-0.055	-0.021	6.758	0.108	0.108	0.000	0.000	0.000	0.000
5	B	117	GLY	0	0.039	0.016	10.533	-0.113	-0.113	0.000	0.000	0.000	0.000
6	B	118	HIS	0	0.000	-0.007	12.182	-0.065	-0.065	0.000	0.000	0.000	0.000
7	B	119	CYS	0	-0.096	-0.030	12.658	0.055	0.055	0.000	0.000	0.000	0.000
8	B	120	PRO	0	0.029	-0.001	11.112	-0.047	-0.047	0.000	0.000	0.000	0.000
9	B	121	GLU	-1	-0.938	-0.956	4.609	-2.647	-2.547	-0.001	-0.010	-0.089	0.000
10	B	122	GLU	-1	-0.937	-0.962	6.547	-1.065	-1.065	0.000	0.000	0.000	0.000
11	B	123	TRP	0	-0.083	-0.039	8.852	0.211	0.211	0.000	0.000	0.000	0.000
12	B	124	ILE	0	-0.016	-0.008	11.041	0.012	0.012	0.000	0.000	0.000	0.000
13	B	125	THR	0	0.014	-0.010	13.296	-0.009	-0.009	0.000	0.000	0.000	0.000
14	B	126	TYR	0	0.003	0.001	15.551	0.020	0.020	0.000	0.000	0.000	0.000
15	B	127	SER	0	0.021	0.016	18.788	0.023	0.023	0.000	0.000	0.000	0.000
16	B	128	ASN	0	-0.036	-0.008	20.769	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	129	SER	0	0.046	0.015	20.031	-0.010	-0.010	0.000	0.000	0.000	0.000
18	B	131	TYR	0	-0.016	-0.033	16.284	0.009	0.009	0.000	0.000	0.000	0.000
19	B	132	TYR	0	0.052	0.037	13.062	0.008	0.008	0.000	0.000	0.000	0.000
20	B	133	ILE	0	0.008	-0.005	15.934	0.024	0.024	0.000	0.000	0.000	0.000
21	B	134	GLY	0	0.048	0.020	16.716	-0.020	-0.020	0.000	0.000	0.000	0.000
22	B	135	LYS	1	0.855	0.907	14.749	0.181	0.181	0.000	0.000	0.000	0.000
23	B	136	GLU	-1	-0.903	-0.933	19.192	-0.231	-0.231	0.000	0.000	0.000	0.000
24	B	137	ARG	1	0.872	0.923	21.993	0.085	0.085	0.000	0.000	0.000	0.000
25	B	138	ARG	1	0.942	0.978	22.645	0.161	0.161	0.000	0.000	0.000	0.000
26	B	139	THR	0	0.052	0.057	27.424	0.008	0.008	0.000	0.000	0.000	0.000
27	B	140	TRP	0	0.032	0.010	29.190	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	141	GLU	-1	-0.868	-0.954	29.694	-0.089	-0.089	0.000	0.000	0.000	0.000
29	B	142	GLU	-1	-0.870	-0.942	27.778	-0.121	-0.121	0.000	0.000	0.000	0.000
30	B	143	SER	0	-0.039	-0.031	25.347	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	144	LEU	0	0.003	0.003	25.021	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	145	LEU	0	0.004	0.002	26.079	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	146	ALA	0	-0.012	0.005	22.299	-0.014	-0.014	0.000	0.000	0.000	0.000
34	B	147	CYS	0	-0.097	-0.044	19.093	-0.013	-0.013	0.000	0.000	0.000	0.000
35	B	148	THR	0	-0.004	-0.009	21.538	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	149	SER	0	-0.045	-0.004	21.418	-0.014	-0.014	0.000	0.000	0.000	0.000
37	B	150	LYS	1	0.888	0.959	16.748	0.259	0.259	0.000	0.000	0.000	0.000
38	B	151	ASN	0	-0.030	-0.012	17.824	0.005	0.005	0.000	0.000	0.000	0.000
39	B	152	SER	0	-0.042	-0.021	19.681	0.005	0.005	0.000	0.000	0.000	0.000
40	B	153	SER	0	-0.002	0.004	21.697	0.010	0.010	0.000	0.000	0.000	0.000
41	B	154	LEU	0	0.026	0.001	23.296	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	155	LEU	0	-0.012	0.013	23.514	0.005	0.005	0.000	0.000	0.000	0.000
43	B	156	SER	0	0.018	0.017	25.202	0.005	0.005	0.000	0.000	0.000	0.000
44	B	157	ILE	0	-0.002	-0.018	26.863	0.000	0.000	0.000	0.000	0.000	0.000
45	B	158	ASP	-1	-0.870	-0.914	27.407	-0.040	-0.040	0.000	0.000	0.000	0.000
46	B	159	ASN	0	-0.005	-0.017	29.826	0.000	0.000	0.000	0.000	0.000	0.000
47	B	160	GLU	-1	-0.876	-0.962	31.130	-0.008	-0.008	0.000	0.000	0.000	0.000
48	B	161	GLU	-1	-0.966	-0.974	28.095	0.032	0.032	0.000	0.000	0.000	0.000
49	B	162	GLU	-1	-0.731	-0.849	25.040	-0.035	-0.035	0.000	0.000	0.000	0.000
50	B	163	MET	0	0.011	0.026	26.182	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	164	LYS	1	0.964	0.990	27.747	-0.024	-0.024	0.000	0.000	0.000	0.000
52	B	165	PHE	0	0.029	0.034	19.080	0.004	0.004	0.000	0.000	0.000	0.000
53	B	166	LEU	0	0.044	0.001	21.960	0.000	0.000	0.000	0.000	0.000	0.000
54	B	167	SER	0	-0.156	-0.094	24.199	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	168	ILE	0	-0.039	-0.015	22.223	0.002	0.002	0.000	0.000	0.000	0.000
56	B	169	ILE	0	0.004	0.020	18.392	0.001	0.001	0.000	0.000	0.000	0.000
57	B	170	SER	0	-0.050	-0.053	20.706	-0.024	-0.024	0.000	0.000	0.000	0.000
58	B	171	PRO	0	0.002	0.037	23.152	0.003	0.003	0.000	0.000	0.000	0.000
59	B	172	SER	0	-0.025	-0.035	26.286	0.004	0.004	0.000	0.000	0.000	0.000
60	B	173	SER	0	0.025	-0.004	24.857	-0.013	-0.013	0.000	0.000	0.000	0.000
61	B	174	TRP	0	-0.027	0.008	26.882	0.013	0.013	0.000	0.000	0.000	0.000
62	B	175	ILE	0	0.000	0.007	27.234	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	176	GLY	0	-0.012	-0.001	28.996	0.000	0.000	0.000	0.000	0.000	0.000
64	B	177	VAL	0	-0.063	-0.047	30.451	0.004	0.004	0.000	0.000	0.000	0.000
65	B	178	PHE	0	-0.053	-0.032	34.125	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	179	ARG	1	0.915	0.962	36.998	0.038	0.038	0.000	0.000	0.000	0.000
67	B	180	ASN	0	0.020	0.003	40.430	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	181	SER	0	-0.022	-0.017	42.689	0.000	0.000	0.000	0.000	0.000	0.000
69	B	182	SER	0	0.083	0.030	44.926	0.000	0.000	0.000	0.000	0.000	0.000
70	B	183	HIS	0	-0.052	-0.029	46.284	0.000	0.000	0.000	0.000	0.000	0.000
71	B	184	HIS	0	0.040	0.041	44.790	0.000	0.000	0.000	0.000	0.000	0.000
72	B	185	PRO	0	0.007	-0.005	43.507	0.000	0.000	0.000	0.000	0.000	0.000
73	B	186	TRP	0	0.031	0.030	37.481	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	187	VAL	0	-0.016	0.005	37.765	0.003	0.003	0.000	0.000	0.000	0.000
75	B	188	THR	0	-0.023	-0.010	33.408	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	189	MET	0	0.031	0.007	30.720	0.002	0.002	0.000	0.000	0.000	0.000
77	B	190	ASN	0	-0.033	-0.018	30.603	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	191	GLY	0	0.008	0.022	33.789	0.003	0.003	0.000	0.000	0.000	0.000
79	B	192	LEU	0	-0.029	-0.012	35.494	0.004	0.004	0.000	0.000	0.000	0.000
80	B	193	ALA	0	0.040	0.013	38.345	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	194	PHE	0	-0.018	-0.017	33.333	0.001	0.001	0.000	0.000	0.000	0.000
82	B	195	LYS	1	0.967	0.966	38.012	0.021	0.021	0.000	0.000	0.000	0.000
83	B	196	HIS	0	-0.014	0.021	33.918	0.005	0.005	0.000	0.000	0.000	0.000
84	B	197	GLU	-1	-0.933	-0.962	38.113	-0.015	-0.015	0.000	0.000	0.000	0.000
85	B	198	ILE	0	-0.040	-0.026	36.956	0.000	0.000	0.000	0.000	0.000	0.000
86	B	199	LYS	1	0.926	0.965	37.028	0.021	0.021	0.000	0.000	0.000	0.000
87	B	200	ASP	-1	-0.887	-0.972	39.563	-0.027	-0.027	0.000	0.000	0.000	0.000
88	B	201	SER	0	-0.051	-0.036	41.345	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	202	ASP	-1	-0.851	-0.889	43.696	-0.024	-0.024	0.000	0.000	0.000	0.000
90	B	203	ASN	0	-0.010	-0.004	46.717	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	204	ALA	0	-0.065	-0.025	44.661	0.000	0.000	0.000	0.000	0.000	0.000
92	B	205	GLU	-1	-0.908	-0.974	43.502	-0.043	-0.043	0.000	0.000	0.000	0.000
93	B	206	LEU	0	-0.073	-0.017	39.455	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	207	ASN	0	0.046	0.016	39.614	0.004	0.004	0.000	0.000	0.000	0.000
95	B	208	CYS	0	0.046	0.015	34.233	-0.005	-0.005	0.000	0.000	0.000	0.000
96	B	209	ALA	0	0.028	0.019	33.838	0.003	0.003	0.000	0.000	0.000	0.000
97	B	210	VAL	0	0.019	0.000	30.201	-0.007	-0.007	0.000	0.000	0.000	0.000
98	B	211	LEU	0	-0.019	0.004	27.231	0.007	0.007	0.000	0.000	0.000	0.000
99	B	212	GLN	0	-0.031	-0.038	29.325	-0.007	-0.007	0.000	0.000	0.000	0.000
100	B	213	VAL	0	-0.028	-0.029	29.482	0.004	0.004	0.000	0.000	0.000	0.000
101	B	214	ASN	0	0.010	0.006	29.957	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	215	ARG	1	0.979	0.986	31.661	0.010	0.010	0.000	0.000	0.000	0.000
103	B	216	LEU	0	0.035	0.039	32.625	-0.005	-0.005	0.000	0.000	0.000	0.000
104	B	217	LYS	1	0.843	0.938	34.584	0.036	0.036	0.000	0.000	0.000	0.000
105	B	218	SER	0	0.057	0.026	35.719	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	219	ALA	0	0.004	-0.022	34.897	0.002	0.002	0.000	0.000	0.000	0.000
107	B	220	GLN	0	0.083	0.042	36.992	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	222	GLY	0	0.037	0.012	34.187	-0.006	-0.006	0.000	0.000	0.000	0.000
109	B	223	SER	0	-0.045	-0.007	33.800	0.000	0.000	0.000	0.000	0.000	0.000
110	B	224	SER	0	0.004	0.001	29.364	-0.006	-0.006	0.000	0.000	0.000	0.000
111	B	225	ILE	0	-0.034	-0.033	28.120	0.006	0.006	0.000	0.000	0.000	0.000
112	B	226	ILE	0	-0.031	0.012	22.517	-0.009	-0.009	0.000	0.000	0.000	0.000
113	B	227	TYR	0	0.022	0.001	21.087	0.002	0.002	0.000	0.000	0.000	0.000
114	B	228	HIS	0	0.073	0.033	20.692	-0.029	-0.029	0.000	0.000	0.000	0.000
115	B	230	LYS	1	0.792	0.863	19.844	0.052	0.052	0.000	0.000	0.000	0.000
116	B	231	HIS	0	0.010	0.015	17.532	0.019	0.019	0.000	0.000	0.000	0.000
117	B	232	LYS	1	0.995	0.999	21.302	0.123	0.123	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:113:ALA)