FMO DATABASE

FMODB ID: KR693

Calculation Name: 3BCY-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BCY

Chain ID: A

ChEMBL ID:

UniProt ID: P40043

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1462506.203039
FMO2-HF: Nuclear repulsion	1402209.995838
FMO2-HF: Total energy	-60296.207201
FMO2-MP2: Total energy	-60474.318797

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:15:ACE )

Summations of interaction energy for fragment #1(A:15:ACE )

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.
-2.657	-1.791	-0.005	-0.365	-0.497	0

Interaction energy analysis for fragmet #1(A:15:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.030

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].
3	A	17	GLU	-1	-0.932	-0.939	3.875	-0.128	0.738	-0.005	-0.365	-0.497
4	A	18	ASP	-1	-0.883	-0.944	6.906	-0.526	-0.526	0.000	0.000	0.000
5	A	19	GLY	0	-0.065	-0.028	10.071	0.088	0.088	0.000	0.000	0.000
6	A	20	GLU	-1	-1.000	-1.015	12.701	-0.117	-0.117	0.000	0.000	0.000
7	A	21	THR	0	0.023	0.012	15.072	0.041	0.041	0.000	0.000	0.000
8	A	22	VAL	0	-0.071	-0.014	13.767	0.014	0.014	0.000	0.000	0.000
9	A	23	LYS	1	0.982	1.011	8.352	0.334	0.334	0.000	0.000	0.000
10	A	24	VAL	0	-0.039	-0.033	8.931	0.167	0.167	0.000	0.000	0.000
11	A	25	PHE	0	-0.008	-0.010	6.985	-0.525	-0.525	0.000	0.000	0.000
12	A	26	GLU	-1	-0.866	-0.944	6.259	-1.231	-1.231	0.000	0.000	0.000
13	A	27	ASP	-1	-0.916	-0.959	6.984	-0.720	-0.720	0.000	0.000	0.000
14	A	28	LEU	0	-0.018	-0.029	9.834	-0.019	-0.019	0.000	0.000	0.000
15	A	29	GLN	0	0.024	0.028	10.453	0.019	0.019	0.000	0.000	0.000
16	A	30	GLY	0	0.007	0.001	8.136	0.079	0.079	0.000	0.000	0.000
17	A	31	PHE	0	-0.006	-0.012	9.060	0.082	0.082	0.000	0.000	0.000
18	A	32	GLU	-1	-0.918	-0.973	11.649	-0.111	-0.111	0.000	0.000	0.000
19	A	33	THR	0	-0.002	-0.004	11.129	0.071	0.071	0.000	0.000	0.000
20	A	34	PHE	0	0.003	-0.005	10.608	0.030	0.030	0.000	0.000	0.000
21	A	35	ILE	0	0.019	0.008	12.431	0.052	0.052	0.000	0.000	0.000
22	A	36	ALA	0	0.001	0.009	15.975	0.035	0.035	0.000	0.000	0.000
23	A	37	ASN	0	-0.043	-0.041	12.635	0.036	0.036	0.000	0.000	0.000
24	A	38	GLU	-1	-0.857	-0.927	14.871	-0.116	-0.116	0.000	0.000	0.000
25	A	39	THR	0	-0.093	-0.048	17.449	0.015	0.015	0.000	0.000	0.000
26	A	40	GLU	-1	-1.004	-0.994	19.406	-0.018	-0.018	0.000	0.000	0.000
27	A	41	ASP	-1	-0.945	-0.961	17.459	-0.022	-0.022	0.000	0.000	0.000
28	A	42	ASP	-1	-0.943	-0.971	20.694	-0.048	-0.048	0.000	0.000	0.000
29	A	43	ASP	-1	-0.803	-0.891	19.249	-0.077	-0.077	0.000	0.000	0.000
30	A	44	PHE	0	-0.050	-0.046	21.096	-0.016	-0.016	0.000	0.000	0.000
31	A	45	ASP	-1	-0.890	-0.914	22.142	-0.095	-0.095	0.000	0.000	0.000
32	A	46	HIS	0	-0.016	-0.014	22.182	-0.003	-0.003	0.000	0.000	0.000
33	A	47	LEU	0	0.030	0.036	17.134	-0.018	-0.018	0.000	0.000	0.000
34	A	48	HIS	0	-0.083	-0.086	17.037	0.020	0.020	0.000	0.000	0.000
35	A	49	CYS	0	-0.065	0.003	12.495	-0.019	-0.019	0.000	0.000	0.000
36	A	50	LYS	1	0.893	0.923	12.660	0.428	0.428	0.000	0.000	0.000
37	A	51	LEU	0	-0.016	0.013	11.205	-0.118	-0.118	0.000	0.000	0.000
38	A	52	ASN	0	0.015	0.005	11.429	0.180	0.180	0.000	0.000	0.000
39	A	53	TYR	0	0.023	-0.007	11.536	-0.086	-0.086	0.000	0.000	0.000
40	A	54	TYR	0	0.070	0.035	13.582	0.069	0.069	0.000	0.000	0.000
41	A	55	PRO	0	-0.014	0.007	16.175	-0.001	-0.001	0.000	0.000	0.000
42	A	56	PRO	0	0.055	0.005	17.762	0.022	0.022	0.000	0.000	0.000
43	A	57	PHE	0	-0.043	-0.031	19.306	0.016	0.016	0.000	0.000	0.000
44	A	58	VAL	0	0.054	0.035	20.045	0.014	0.014	0.000	0.000	0.000
45	A	59	LEU	0	0.057	0.040	15.582	0.012	0.012	0.000	0.000	0.000
46	A	60	HIS	1	0.764	0.846	20.066	0.139	0.139	0.000	0.000	0.000
47	A	61	GLU	-1	-0.989	-0.996	22.684	-0.098	-0.098	0.000	0.000	0.000
48	A	62	SER	0	-0.020	-0.011	21.913	0.011	0.011	0.000	0.000	0.000
49	A	63	HIS	0	-0.072	-0.042	22.388	0.002	0.002	0.000	0.000	0.000
50	A	64	GLU	-1	-0.833	-0.886	18.346	-0.115	-0.115	0.000	0.000	0.000
51	A	65	ASP	-1	-0.840	-0.924	17.877	-0.109	-0.109	0.000	0.000	0.000
52	A	66	PRO	0	0.029	-0.004	14.846	0.004	0.004	0.000	0.000	0.000
53	A	67	GLU	-1	-0.943	-0.959	18.176	-0.098	-0.098	0.000	0.000	0.000
54	A	68	LYS	1	0.826	0.923	20.556	0.079	0.079	0.000	0.000	0.000
55	A	69	ILE	0	-0.040	-0.005	19.048	0.006	0.006	0.000	0.000	0.000
56	A	70	SER	0	-0.039	-0.012	23.220	0.005	0.005	0.000	0.000	0.000
57	A	71	ASP	-1	-0.788	-0.903	25.862	-0.115	-0.115	0.000	0.000	0.000
58	A	72	ALA	0	-0.115	-0.058	27.434	-0.002	-0.002	0.000	0.000	0.000
59	A	73	ALA	0	-0.074	-0.037	24.831	0.001	0.001	0.000	0.000	0.000
60	A	74	ASN	0	0.131	0.074	24.739	-0.008	-0.008	0.000	0.000	0.000
61	A	75	SER	0	-0.004	-0.039	26.211	0.015	0.015	0.000	0.000	0.000
62	A	76	HIS	1	0.799	0.891	27.899	0.111	0.111	0.000	0.000	0.000
63	A	77	SER	0	-0.016	0.023	29.165	0.011	0.011	0.000	0.000	0.000
64	A	78	LYS	1	0.981	0.963	30.299	0.079	0.079	0.000	0.000	0.000
65	A	79	LYS	1	0.898	0.957	29.846	0.083	0.083	0.000	0.000	0.000
66	A	80	PHE	0	0.053	0.036	22.081	0.004	0.004	0.000	0.000	0.000
67	A	81	VAL	0	0.063	0.032	26.555	-0.008	-0.008	0.000	0.000	0.000
68	A	82	ARG	1	0.896	0.959	27.892	0.082	0.082	0.000	0.000	0.000
69	A	83	HIS	0	-0.030	-0.032	26.462	0.006	0.006	0.000	0.000	0.000
70	A	84	LEU	0	0.057	0.043	21.281	-0.003	-0.003	0.000	0.000	0.000
71	A	85	HIS	0	-0.016	-0.005	24.289	-0.002	-0.002	0.000	0.000	0.000
72	A	86	GLN	0	-0.034	-0.036	26.565	0.001	0.001	0.000	0.000	0.000
73	A	87	HIS	0	0.001	0.021	18.768	-0.015	-0.015	0.000	0.000	0.000
74	A	88	ILE	0	0.061	0.020	22.109	-0.007	-0.007	0.000	0.000	0.000
75	A	89	GLU	-1	-0.859	-0.918	23.284	-0.117	-0.117	0.000	0.000	0.000
76	A	90	LYS	1	0.845	0.936	25.201	0.110	0.110	0.000	0.000	0.000
77	A	91	HIS	0	-0.047	-0.034	20.080	0.005	0.005	0.000	0.000	0.000
78	A	92	LEU	0	0.072	0.063	17.427	0.004	0.004	0.000	0.000	0.000
79	A	93	LEU	0	0.024	0.001	20.206	-0.001	-0.001	0.000	0.000	0.000
80	A	94	LYS	1	0.860	0.942	21.601	0.139	0.139	0.000	0.000	0.000
81	A	95	ASP	-1	-0.831	-0.931	17.285	-0.202	-0.202	0.000	0.000	0.000
82	A	96	ILE	0	0.026	0.021	18.786	0.006	0.006	0.000	0.000	0.000
83	A	97	LYS	1	0.873	0.943	20.442	0.122	0.122	0.000	0.000	0.000
84	A	98	GLN	0	-0.050	-0.021	20.404	0.008	0.008	0.000	0.000	0.000
85	A	99	ALA	0	0.029	0.028	18.085	0.016	0.016	0.000	0.000	0.000
86	A	100	VAL	0	-0.007	-0.005	19.925	0.013	0.013	0.000	0.000	0.000
87	A	101	ARG	1	0.834	0.915	21.569	0.077	0.077	0.000	0.000	0.000
88	A	102	LYS	1	0.860	0.933	25.072	0.089	0.089	0.000	0.000	0.000
89	A	103	PRO	0	0.043	0.024	26.919	-0.006	-0.006	0.000	0.000	0.000
90	A	104	GLU	-1	-0.965	-0.992	27.845	-0.067	-0.067	0.000	0.000	0.000
91	A	105	LEU	0	-0.016	0.010	27.099	0.003	0.003	0.000	0.000	0.000
92	A	106	LYS	1	0.831	0.896	29.930	0.073	0.073	0.000	0.000	0.000
93	A	107	PHE	0	0.067	0.039	24.617	0.002	0.002	0.000	0.000	0.000
94	A	108	HIS	0	-0.068	-0.050	30.635	0.006	0.006	0.000	0.000	0.000
95	A	109	GLU	-1	-0.845	-0.893	31.299	-0.095	-0.095	0.000	0.000	0.000
96	A	110	LYS	1	0.885	0.923	30.589	0.089	0.089	0.000	0.000	0.000
97	A	111	SER	0	-0.017	0.002	30.560	0.006	0.006	0.000	0.000	0.000
98	A	112	LYS	1	0.936	0.957	30.111	0.099	0.099	0.000	0.000	0.000
99	A	113	GLU	-1	-0.945	-0.950	30.308	-0.104	-0.104	0.000	0.000	0.000
100	A	114	GLU	-1	-0.977	-0.998	30.278	-0.106	-0.106	0.000	0.000	0.000
101	A	115	THR	0	-0.021	-0.008	30.263	0.007	0.007	0.000	0.000	0.000
102	A	116	PHE	0	-0.008	-0.014	31.959	0.000	0.000	0.000	0.000	0.000
103	A	117	ASP	-1	-0.819	-0.906	28.195	-0.113	-0.113	0.000	0.000	0.000
104	A	118	LYS	1	0.962	0.995	25.588	0.147	0.147	0.000	0.000	0.000
105	A	119	ILE	0	-0.050	-0.022	26.597	0.014	0.014	0.000	0.000	0.000
106	A	120	THR	0	0.012	0.012	25.146	-0.021	-0.021	0.000	0.000	0.000
107	A	121	TRP	0	-0.034	-0.031	24.582	0.018	0.018	0.000	0.000	0.000
108	A	122	HIS	0	-0.074	-0.037	25.377	-0.012	-0.012	0.000	0.000	0.000
109	A	123	TYR	0	-0.075	-0.063	25.201	0.011	0.011	0.000	0.000	0.000
110	A	124	GLY	0	0.051	0.026	26.390	-0.011	-0.011	0.000	0.000	0.000
111	A	125	GLU	-1	-0.877	-0.960	28.438	-0.078	-0.078	0.000	0.000	0.000
112	A	126	GLU	-1	-0.924	-0.942	29.052	-0.082	-0.082	0.000	0.000	0.000
113	A	127	THR	0	-0.040	-0.022	27.928	0.005	0.005	0.000	0.000	0.000
114	A	128	GLU	-1	-0.925	-0.968	30.576	-0.050	-0.050	0.000	0.000	0.000
115	A	129	TYR	0	-0.048	-0.016	25.466	0.001	0.001	0.000	0.000	0.000
116	A	130	HIS	0	0.030	0.021	27.210	0.000	0.000	0.000	0.000	0.000
117	A	131	GLY	0	-0.007	0.004	30.662	0.002	0.002	0.000	0.000	0.000
118	A	132	ARG	1	0.765	0.870	25.706	0.066	0.066	0.000	0.000	0.000
119	A	133	PRO	0	0.028	0.017	30.417	-0.005	-0.005	0.000	0.000	0.000
120	A	134	PHE	0	-0.009	-0.026	24.575	-0.001	-0.001	0.000	0.000	0.000
121	A	135	LYS	1	0.849	0.936	27.755	0.114	0.114	0.000	0.000	0.000
122	A	136	ILE	0	-0.004	-0.001	23.206	-0.010	-0.010	0.000	0.000	0.000
123	A	137	ASP	-1	-0.825	-0.913	24.018	-0.123	-0.123	0.000	0.000	0.000
124	A	138	VAL	0	-0.021	-0.013	20.664	-0.021	-0.021	0.000	0.000	0.000
125	A	139	GLN	0	-0.013	-0.011	21.503	0.003	0.003	0.000	0.000	0.000
126	A	140	VAL	0	-0.016	-0.010	20.429	-0.027	-0.027	0.000	0.000	0.000
127	A	141	VAL	0	0.002	-0.001	20.797	0.030	0.030	0.000	0.000	0.000
128	A	142	CYS	0	-0.030	-0.001	21.054	-0.014	-0.014	0.000	0.000	0.000
129	A	143	THR	0	0.103	0.029	22.058	0.016	0.016	0.000	0.000	0.000
130	A	144	HIS	0	-0.073	-0.036	24.753	0.010	0.010	0.000	0.000	0.000
131	A	145	GLU	-1	-0.895	-0.950	23.482	-0.165	-0.165	0.000	0.000	0.000
132	A	146	ASP	-1	-0.851	-0.916	20.184	-0.233	-0.233	0.000	0.000	0.000
133	A	147	ALA	0	-0.016	-0.014	20.682	0.000	0.000	0.000	0.000	0.000
134	A	148	MET	0	-0.046	-0.011	13.497	-0.026	-0.026	0.000	0.000	0.000
135	A	149	VAL	0	-0.087	-0.050	17.150	0.037	0.037	0.000	0.000	0.000
136	A	150	PHE	0	0.010	0.001	15.876	-0.060	-0.060	0.000	0.000	0.000
137	A	151	VAL	0	-0.010	-0.011	15.978	0.061	0.061	0.000	0.000	0.000
138	A	152	ASP	-1	-0.836	-0.891	16.130	-0.347	-0.347	0.000	0.000	0.000
139	A	153	TYR	0	0.044	0.016	17.036	0.038	0.038	0.000	0.000	0.000
140	A	154	LYS	1	1.005	0.987	18.316	0.156	0.156	0.000	0.000	0.000
141	A	155	THR	0	-0.043	-0.033	20.959	0.011	0.011	0.000	0.000	0.000
142	A	156	HIS	0	-0.038	-0.022	23.372	-0.005	-0.005	0.000	0.000	0.000
143	A	157	PRO	0	0.050	0.030	26.133	0.003	0.003	0.000	0.000	0.000
144	A	158	VAL	0	-0.029	0.002	29.270	-0.002	-0.002	0.000	0.000	0.000
145	A	159	GLY	0	-0.029	-0.019	32.490	0.004	0.004	0.000	0.000	0.000
146	A	160	ALA	0	-0.040	-0.011	32.522	0.004	0.004	0.000	0.000	0.000
147	A	161	ASN	-1	-0.962	-0.977	34.559	-0.047	-0.047	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ACE )