FMO DATABASE

FMODB ID: VQYJ1

Calculation Name: 3COO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3COO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HCB6

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1380135.358607
FMO2-HF: Nuclear repulsion	1322458.019696
FMO2-HF: Total energy	-57677.338911
FMO2-MP2: Total energy	-57845.039855

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:42:GLY)

Summations of interaction energy for fragment #1(B:42:GLY)

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.
-35.272	-35.416	26.118	-14.611	-11.362	-0.1

Interaction energy analysis for fragmet #1(B:42:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.003

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	44	CYS	0	0.017	0.020	3.824	-0.338	1.121	-0.019	-0.825	-0.615	0.002
4	B	45	SER	0	0.066	0.029	2.737	-5.531	-3.391	1.458	-1.736	-1.861	0.020
5	B	46	ARG	1	0.882	0.929	3.357	-0.580	0.421	0.019	-0.487	-0.534	0.002
6	B	47	ILE	0	0.023	0.020	5.779	-0.932	-0.869	-0.001	-0.003	-0.058	0.000
7	B	48	LEU	0	-0.003	-0.014	7.420	-0.336	-0.336	0.000	0.000	0.000	0.000
8	B	49	ARG	1	0.872	0.941	4.727	-3.658	-3.590	-0.001	-0.007	-0.060	0.000
9	B	50	ALA	0	-0.009	0.017	9.663	-0.265	-0.265	0.000	0.000	0.000	0.000
10	B	51	GLN	0	-0.041	-0.027	11.534	-0.139	-0.139	0.000	0.000	0.000	0.000
11	B	52	GLY	0	-0.027	0.000	12.998	-0.071	-0.071	0.000	0.000	0.000	0.000
12	B	53	THR	0	-0.046	-0.039	13.965	-0.097	-0.097	0.000	0.000	0.000	0.000
13	B	54	ARG	1	0.793	0.859	9.585	-0.501	-0.501	0.000	0.000	0.000	0.000
14	B	55	ARG	1	0.826	0.880	14.944	-0.382	-0.382	0.000	0.000	0.000	0.000
15	B	56	GLU	-1	-0.703	-0.830	13.767	0.527	0.527	0.000	0.000	0.000	0.000
16	B	57	GLY	0	-0.001	0.009	17.087	-0.038	-0.038	0.000	0.000	0.000	0.000
17	B	58	TYR	0	0.017	-0.001	19.426	0.036	0.036	0.000	0.000	0.000	0.000
18	B	59	THR	0	-0.018	-0.006	20.609	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	60	GLU	-1	-0.785	-0.871	22.876	0.262	0.262	0.000	0.000	0.000	0.000
20	B	61	PHE	0	-0.016	-0.008	20.676	-0.008	-0.008	0.000	0.000	0.000	0.000
21	B	62	SER	0	-0.046	-0.019	21.109	0.002	0.002	0.000	0.000	0.000	0.000
22	B	63	LEU	0	0.008	0.003	15.689	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	64	ARG	1	0.924	0.963	19.776	-0.246	-0.246	0.000	0.000	0.000	0.000
24	B	65	VAL	0	0.032	0.019	20.454	0.019	0.019	0.000	0.000	0.000	0.000
25	B	66	GLU	-1	-0.806	-0.904	23.061	0.162	0.162	0.000	0.000	0.000	0.000
26	B	67	GLY	0	0.004	-0.013	26.710	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	68	ASP	-1	-0.947	-0.959	24.928	0.154	0.154	0.000	0.000	0.000	0.000
28	B	69	PRO	0	-0.040	-0.015	23.322	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	70	ASP	-1	-0.851	-0.931	24.194	0.100	0.100	0.000	0.000	0.000	0.000
30	B	71	PHE	0	-0.065	-0.027	22.469	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	72	TYR	0	-0.044	-0.053	17.410	0.015	0.015	0.000	0.000	0.000	0.000
32	B	73	LYS	1	0.956	0.967	22.457	-0.093	-0.093	0.000	0.000	0.000	0.000
33	B	74	PRO	0	0.018	-0.006	22.024	0.013	0.013	0.000	0.000	0.000	0.000
34	B	75	GLY	0	0.003	0.011	22.017	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	76	THR	0	-0.050	-0.011	23.696	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	77	SER	0	-0.019	-0.006	22.945	0.012	0.012	0.000	0.000	0.000	0.000
37	B	78	TYR	0	0.027	0.021	21.574	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	79	ARG	1	0.897	0.946	22.531	-0.156	-0.156	0.000	0.000	0.000	0.000
39	B	80	VAL	0	-0.001	0.011	17.988	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	81	THR	0	-0.060	-0.036	21.391	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	82	LEU	0	0.041	0.026	17.987	0.015	0.015	0.000	0.000	0.000	0.000
42	B	83	SER	0	-0.017	-0.021	21.624	-0.027	-0.027	0.000	0.000	0.000	0.000
43	B	84	ALA	0	-0.027	-0.003	23.967	0.017	0.017	0.000	0.000	0.000	0.000
44	B	85	ALA	0	0.012	0.011	26.100	-0.017	-0.017	0.000	0.000	0.000	0.000
45	B	86	PRO	0	0.032	0.029	28.844	0.004	0.004	0.000	0.000	0.000	0.000
46	B	87	PRO	0	-0.015	-0.009	32.099	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	88	SER	0	-0.033	-0.030	26.479	0.004	0.004	0.000	0.000	0.000	0.000
48	B	89	TYR	0	-0.004	-0.010	27.261	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	90	PHE	0	-0.017	-0.013	21.829	0.007	0.007	0.000	0.000	0.000	0.000
50	B	91	ARG	1	0.878	0.908	23.344	-0.265	-0.265	0.000	0.000	0.000	0.000
51	B	92	GLY	0	0.079	0.039	20.448	-0.021	-0.021	0.000	0.000	0.000	0.000
52	B	93	PHE	0	-0.052	-0.036	16.844	-0.014	-0.014	0.000	0.000	0.000	0.000
53	B	94	THR	0	-0.017	-0.001	12.392	0.089	0.089	0.000	0.000	0.000	0.000
54	B	95	LEU	0	-0.001	-0.005	13.222	-0.011	-0.011	0.000	0.000	0.000	0.000
55	B	96	ILE	0	0.022	0.024	6.345	-0.009	-0.009	0.000	0.000	0.000	0.000
56	B	97	ALA	0	0.017	0.004	10.303	-0.072	-0.072	0.000	0.000	0.000	0.000
57	B	98	LEU	0	0.030	0.017	6.048	0.099	0.099	0.000	0.000	0.000	0.000
58	B	99	ARG	1	0.881	0.943	8.723	-0.021	-0.021	0.000	0.000	0.000	0.000
59	B	100	GLU	-1	-0.783	-0.878	8.850	-0.043	-0.043	0.000	0.000	0.000	0.000
60	B	101	ASN	0	-0.091	-0.077	8.230	-0.215	-0.215	0.000	0.000	0.000	0.000
61	B	102	ARG	1	0.790	0.877	8.904	-0.052	-0.052	0.000	0.000	0.000	0.000
62	B	103	GLU	-1	-0.826	-0.899	6.854	-1.380	-1.380	0.000	0.000	0.000	0.000
63	B	104	GLY	0	0.023	-0.006	3.681	-0.128	0.277	0.002	-0.232	-0.174	-0.001
64	B	105	ASP	-1	-0.908	-0.955	1.830	-24.771	-29.844	24.624	-11.797	-7.755	-0.122
65	B	106	LYS	1	0.807	0.890	3.116	2.749	2.319	0.038	0.513	-0.121	-0.001
66	B	107	GLU	-1	-0.846	-0.896	4.582	0.450	0.427	-0.001	-0.011	0.035	0.000
67	B	108	GLU	-1	-0.955	-0.977	4.453	-0.575	-0.329	-0.001	-0.026	-0.219	0.000
68	B	109	ASP	-1	-0.906	-0.974	5.619	1.365	1.365	0.000	0.000	0.000	0.000
69	B	110	HIS	0	-0.011	0.011	8.465	0.010	0.010	0.000	0.000	0.000	0.000
70	B	111	ALA	0	-0.019	-0.011	10.403	-0.045	-0.045	0.000	0.000	0.000	0.000
71	B	112	GLY	0	0.061	0.034	12.425	0.047	0.047	0.000	0.000	0.000	0.000
72	B	113	THR	0	-0.039	-0.018	14.427	0.020	0.020	0.000	0.000	0.000	0.000
73	B	114	PHE	0	-0.005	0.006	12.469	-0.026	-0.026	0.000	0.000	0.000	0.000
74	B	115	GLN	0	0.016	0.002	17.526	-0.021	-0.021	0.000	0.000	0.000	0.000
75	B	116	ILE	0	-0.006	-0.003	19.230	0.012	0.012	0.000	0.000	0.000	0.000
76	B	117	ILE	0	-0.071	-0.011	22.414	-0.022	-0.022	0.000	0.000	0.000	0.000
77	B	118	ASP	-1	-0.803	-0.906	24.935	0.190	0.190	0.000	0.000	0.000	0.000
78	B	119	GLU	-1	-0.853	-0.940	24.910	0.202	0.202	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.952	-0.962	25.977	0.164	0.164	0.000	0.000	0.000	0.000
80	B	121	GLU	-1	-0.851	-0.874	25.230	0.242	0.242	0.000	0.000	0.000	0.000
81	B	122	THR	0	-0.104	-0.049	20.560	0.033	0.033	0.000	0.000	0.000	0.000
82	B	123	GLN	0	0.017	0.015	19.058	-0.058	-0.058	0.000	0.000	0.000	0.000
83	B	124	PHE	0	0.029	0.005	15.651	0.040	0.040	0.000	0.000	0.000	0.000
84	B	125	MET	0	-0.017	0.005	12.743	0.015	0.015	0.000	0.000	0.000	0.000
85	B	126	SER	0	0.026	0.009	14.342	0.020	0.020	0.000	0.000	0.000	0.000
86	B	127	ASN	0	-0.030	-0.028	12.696	-0.033	-0.033	0.000	0.000	0.000	0.000
87	B	129	PRO	0	0.047	0.028	10.792	0.067	0.067	0.000	0.000	0.000	0.000
88	B	130	VAL	0	0.031	0.023	8.489	-0.037	-0.037	0.000	0.000	0.000	0.000
89	B	131	ALA	0	-0.037	-0.020	9.927	0.039	0.039	0.000	0.000	0.000	0.000
90	B	132	VAL	0	-0.013	-0.009	11.853	-0.120	-0.120	0.000	0.000	0.000	0.000
91	B	133	THR	0	-0.043	-0.031	14.831	0.104	0.104	0.000	0.000	0.000	0.000
92	B	134	GLU	-1	-0.838	-0.924	16.926	0.428	0.428	0.000	0.000	0.000	0.000
93	B	135	SER	0	-0.036	-0.029	20.520	0.013	0.013	0.000	0.000	0.000	0.000
94	B	136	THR	0	0.031	0.003	22.971	-0.020	-0.020	0.000	0.000	0.000	0.000
95	B	137	PRO	0	0.012	0.030	23.778	0.008	0.008	0.000	0.000	0.000	0.000
96	B	138	ARG	1	0.857	0.891	25.038	-0.232	-0.232	0.000	0.000	0.000	0.000
97	B	139	ARG	1	0.857	0.943	26.639	-0.164	-0.164	0.000	0.000	0.000	0.000
98	B	140	ARG	1	0.853	0.926	24.137	-0.298	-0.298	0.000	0.000	0.000	0.000
99	B	141	THR	0	0.055	0.009	27.042	0.008	0.008	0.000	0.000	0.000	0.000
100	B	142	ARG	1	0.806	0.872	25.524	-0.197	-0.197	0.000	0.000	0.000	0.000
101	B	143	ILE	0	-0.019	0.025	19.643	-0.011	-0.011	0.000	0.000	0.000	0.000
102	B	144	GLN	0	-0.029	-0.031	22.904	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	145	VAL	0	0.037	0.021	18.287	0.001	0.001	0.000	0.000	0.000	0.000
104	B	146	PHE	0	0.019	0.001	21.739	-0.011	-0.011	0.000	0.000	0.000	0.000
105	B	147	TRP	0	-0.013	-0.009	14.719	0.008	0.008	0.000	0.000	0.000	0.000
106	B	148	ILE	0	-0.012	-0.022	19.172	-0.026	-0.026	0.000	0.000	0.000	0.000
107	B	149	ALA	0	0.007	0.015	18.562	0.013	0.013	0.000	0.000	0.000	0.000
108	B	150	PRO	0	-0.013	0.004	15.789	-0.011	-0.011	0.000	0.000	0.000	0.000
109	B	151	PRO	0	0.033	0.004	18.205	-0.006	-0.006	0.000	0.000	0.000	0.000
110	B	152	ALA	0	0.025	0.017	19.779	0.000	0.000	0.000	0.000	0.000	0.000
111	B	153	GLY	0	-0.031	-0.009	20.682	-0.009	-0.009	0.000	0.000	0.000	0.000
112	B	154	THR	0	-0.037	-0.026	14.755	-0.026	-0.026	0.000	0.000	0.000	0.000
113	B	155	GLY	0	0.040	0.027	15.450	-0.024	-0.024	0.000	0.000	0.000	0.000
114	B	156	CYS	0	-0.064	-0.021	14.973	0.033	0.033	0.000	0.000	0.000	0.000
115	B	157	VAL	0	0.032	0.016	12.316	-0.009	-0.009	0.000	0.000	0.000	0.000
116	B	158	ILE	0	-0.031	-0.023	10.417	-0.028	-0.028	0.000	0.000	0.000	0.000
117	B	159	LEU	0	-0.001	0.008	11.205	0.142	0.142	0.000	0.000	0.000	0.000
118	B	160	LYS	1	0.891	0.927	6.983	-1.196	-1.196	0.000	0.000	0.000	0.000
119	B	161	ALA	0	0.049	0.021	12.078	0.091	0.091	0.000	0.000	0.000	0.000
120	B	162	SER	0	-0.028	0.010	12.379	-0.012	-0.012	0.000	0.000	0.000	0.000
121	B	163	ILE	0	0.036	0.014	14.406	-0.075	-0.075	0.000	0.000	0.000	0.000
122	B	164	VAL	0	0.026	0.029	17.956	0.003	0.003	0.000	0.000	0.000	0.000
123	B	165	GLN	0	0.044	0.045	20.066	-0.050	-0.050	0.000	0.000	0.000	0.000
124	B	166	LYS	1	0.843	0.896	23.589	-0.252	-0.252	0.000	0.000	0.000	0.000
125	B	167	ARG	1	0.990	0.988	22.825	-0.239	-0.239	0.000	0.000	0.000	0.000
126	B	168	ILE	0	0.021	0.023	19.457	0.023	0.023	0.000	0.000	0.000	0.000
127	B	169	ILE	0	0.054	0.036	14.475	-0.020	-0.020	0.000	0.000	0.000	0.000
128	B	170	TYR	0	-0.009	-0.003	16.033	0.016	0.016	0.000	0.000	0.000	0.000
129	B	171	PHE	0	0.051	0.013	9.895	0.134	0.134	0.000	0.000	0.000	0.000
130	B	172	GLN	0	-0.033	-0.017	12.078	-0.132	-0.132	0.000	0.000	0.000	0.000
131	B	173	ASP	-1	-0.828	-0.898	8.304	1.071	1.071	0.000	0.000	0.000	0.000
132	B	174	GLU	-1	-0.781	-0.850	11.192	0.081	0.081	0.000	0.000	0.000	0.000
133	B	175	GLY	0	0.010	0.007	14.743	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	176	SER	0	-0.021	-0.020	17.937	0.004	0.004	0.000	0.000	0.000	0.000
135	B	177	LEU	0	-0.065	-0.023	15.549	-0.018	-0.018	0.000	0.000	0.000	0.000
136	B	178	THR	0	-0.010	-0.003	12.858	0.136	0.136	0.000	0.000	0.000	0.000
137	B	179	LYS	1	0.880	0.947	14.958	-0.270	-0.270	0.000	0.000	0.000	0.000
138	B	180	LYS	1	0.843	0.912	14.689	-0.014	-0.014	0.000	0.000	0.000	0.000
139	B	181	LEU	0	-0.021	-0.002	16.254	-0.022	-0.022	0.000	0.000	0.000	0.000
140	B	183	GLU	-1	-0.749	-0.870	19.512	0.019	0.019	0.000	0.000	0.000	0.000
141	B	184	GLN	0	-0.063	-0.035	22.137	-0.009	-0.009	0.000	0.000	0.000	0.000
142	B	185	ASP	-1	-0.949	-0.959	25.223	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:42:GLY)