FMO DATABASE

FMODB ID: YVRJ2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1378810.502616
FMO2-HF: Nuclear repulsion	1321134.166153
FMO2-HF: Total energy	-57676.336464
FMO2-MP2: Total energy	-57844.112046

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.
-37.437	-36.809	23.827	-13.824	-10.629	-0.093

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 : 0.021 / q_NPA : 0.000

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	0.019	0.033	3.824	-0.447	1.061	-0.019	-0.860	-0.629	0.003
4	B	45	SER	0	0.064	0.028	2.654	-5.031	-3.410	1.557	-1.532	-1.646	0.023
5	B	46	ARG	1	0.891	0.950	3.250	-1.197	-0.346	0.022	-0.383	-0.490	0.002
6	B	47	ILE	0	0.036	0.020	5.779	-0.939	-0.874	-0.001	-0.003	-0.060	0.000
7	B	48	LEU	0	-0.016	-0.014	8.021	-0.342	-0.342	0.000	0.000	0.000	0.000
8	B	49	ARG	1	0.869	0.945	4.701	-3.461	-3.394	-0.001	-0.004	-0.061	0.000
9	B	50	ALA	0	-0.011	0.013	9.663	-0.276	-0.276	0.000	0.000	0.000	0.000
10	B	51	GLN	0	-0.042	-0.025	11.534	-0.148	-0.148	0.000	0.000	0.000	0.000
11	B	52	GLY	0	-0.023	0.001	12.995	-0.070	-0.070	0.000	0.000	0.000	0.000
12	B	53	THR	0	-0.035	-0.033	13.965	-0.099	-0.099	0.000	0.000	0.000	0.000
13	B	54	ARG	1	0.846	0.911	9.345	-0.477	-0.477	0.000	0.000	0.000	0.000
14	B	55	ARG	1	0.923	0.959	14.929	-0.366	-0.366	0.000	0.000	0.000	0.000
15	B	56	GLU	-1	-0.728	-0.849	13.371	0.487	0.487	0.000	0.000	0.000	0.000
16	B	57	GLY	0	-0.005	0.008	17.075	-0.037	-0.037	0.000	0.000	0.000	0.000
17	B	58	TYR	0	0.006	-0.009	19.418	0.038	0.038	0.000	0.000	0.000	0.000
18	B	59	THR	0	-0.012	0.001	20.130	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	60	GLU	-1	-0.886	-0.956	22.869	0.260	0.260	0.000	0.000	0.000	0.000
20	B	61	PHE	0	-0.027	-0.010	20.652	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	62	SER	0	-0.025	-0.017	21.107	0.003	0.003	0.000	0.000	0.000	0.000
22	B	63	LEU	0	0.013	0.000	15.809	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	64	ARG	1	0.926	0.962	19.780	-0.248	-0.248	0.000	0.000	0.000	0.000
24	B	65	VAL	0	0.011	0.008	20.395	0.021	0.021	0.000	0.000	0.000	0.000
25	B	66	GLU	-1	-0.886	-0.960	23.062	0.161	0.161	0.000	0.000	0.000	0.000
26	B	67	GLY	0	-0.008	-0.017	26.711	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	68	ASP	-1	-1.013	-0.990	25.686	0.136	0.136	0.000	0.000	0.000	0.000
28	B	69	PRO	0	-0.033	-0.011	23.316	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	70	ASP	-1	-0.828	-0.922	24.202	0.106	0.106	0.000	0.000	0.000	0.000
30	B	71	PHE	0	-0.079	-0.041	22.468	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	72	TYR	0	-0.052	-0.054	17.561	0.015	0.015	0.000	0.000	0.000	0.000
32	B	73	LYS	1	0.957	0.961	22.455	-0.096	-0.096	0.000	0.000	0.000	0.000
33	B	74	PRO	0	0.019	-0.003	22.016	0.014	0.014	0.000	0.000	0.000	0.000
34	B	75	GLY	0	-0.001	0.008	22.015	-0.009	-0.009	0.000	0.000	0.000	0.000
35	B	76	THR	0	-0.036	-0.003	23.694	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	77	SER	0	-0.021	-0.009	22.944	0.013	0.013	0.000	0.000	0.000	0.000
37	B	78	TYR	0	0.036	0.032	21.550	-0.016	-0.016	0.000	0.000	0.000	0.000
38	B	79	ARG	1	0.934	0.966	22.532	-0.161	-0.161	0.000	0.000	0.000	0.000
39	B	80	VAL	0	0.006	0.016	17.981	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	81	THR	0	-0.059	-0.035	21.393	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	82	LEU	0	0.046	0.027	18.084	0.015	0.015	0.000	0.000	0.000	0.000
42	B	83	SER	0	-0.035	-0.029	21.628	-0.028	-0.028	0.000	0.000	0.000	0.000
43	B	84	ALA	0	-0.016	0.000	23.967	0.018	0.018	0.000	0.000	0.000	0.000
44	B	85	ALA	0	0.000	0.009	26.099	-0.017	-0.017	0.000	0.000	0.000	0.000
45	B	86	PRO	0	0.028	0.028	28.842	0.005	0.005	0.000	0.000	0.000	0.000
46	B	87	PRO	0	-0.015	-0.013	32.098	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	88	SER	0	-0.033	-0.025	26.376	0.003	0.003	0.000	0.000	0.000	0.000
48	B	89	TYR	0	-0.008	-0.014	27.209	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	90	PHE	0	-0.036	-0.020	21.909	0.008	0.008	0.000	0.000	0.000	0.000
50	B	91	ARG	1	0.864	0.900	23.338	-0.269	-0.269	0.000	0.000	0.000	0.000
51	B	92	GLY	0	0.088	0.045	20.446	-0.020	-0.020	0.000	0.000	0.000	0.000
52	B	93	PHE	0	-0.033	-0.019	16.735	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	94	THR	0	-0.007	-0.010	12.373	0.093	0.093	0.000	0.000	0.000	0.000
54	B	95	LEU	0	0.001	-0.009	13.255	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	96	ILE	0	0.016	0.018	6.327	-0.011	-0.011	0.000	0.000	0.000	0.000
56	B	97	ALA	0	0.020	0.003	10.275	-0.081	-0.081	0.000	0.000	0.000	0.000
57	B	98	LEU	0	0.043	0.024	5.700	0.129	0.129	0.000	0.000	0.000	0.000
58	B	99	ARG	1	0.864	0.925	8.721	-0.062	-0.062	0.000	0.000	0.000	0.000
59	B	100	GLU	-1	-0.854	-0.922	8.862	-0.052	-0.052	0.000	0.000	0.000	0.000
60	B	101	ASN	0	-0.085	-0.066	8.757	-0.207	-0.207	0.000	0.000	0.000	0.000
61	B	102	ARG	1	0.767	0.850	9.391	-0.030	-0.030	0.000	0.000	0.000	0.000
62	B	103	GLU	-1	-0.835	-0.899	7.174	-1.389	-1.389	0.000	0.000	0.000	0.000
63	B	104	GLY	0	0.011	-0.013	4.039	0.004	0.220	-0.001	-0.109	-0.107	0.000
64	B	105	ASP	-1	-0.909	-0.955	1.807	-26.501	-30.117	22.245	-11.286	-7.343	-0.120
65	B	106	LYS	1	0.821	0.896	3.190	2.616	2.321	0.027	0.389	-0.121	-0.001
66	B	107	GLU	-1	-0.835	-0.902	4.632	0.411	0.370	-0.001	-0.009	0.052	0.000
67	B	108	GLU	-1	-0.975	-0.986	4.447	-0.671	-0.419	-0.001	-0.027	-0.224	0.000
68	B	109	ASP	-1	-0.913	-0.977	6.056	1.462	1.462	0.000	0.000	0.000	0.000
69	B	110	HIS	0	-0.008	0.007	8.462	-0.007	-0.007	0.000	0.000	0.000	0.000
70	B	111	ALA	0	-0.015	-0.006	10.416	-0.053	-0.053	0.000	0.000	0.000	0.000
71	B	112	GLY	0	0.054	0.029	12.423	0.045	0.045	0.000	0.000	0.000	0.000
72	B	113	THR	0	-0.016	-0.001	14.426	0.030	0.030	0.000	0.000	0.000	0.000
73	B	114	PHE	0	-0.026	-0.006	12.595	-0.031	-0.031	0.000	0.000	0.000	0.000
74	B	115	GLN	0	0.020	0.003	17.528	-0.019	-0.019	0.000	0.000	0.000	0.000
75	B	116	ILE	0	-0.012	-0.002	19.220	0.013	0.013	0.000	0.000	0.000	0.000
76	B	117	ILE	0	-0.068	-0.016	22.417	-0.023	-0.023	0.000	0.000	0.000	0.000
77	B	118	ASP	-1	-0.818	-0.923	24.946	0.197	0.197	0.000	0.000	0.000	0.000
78	B	119	GLU	-1	-0.852	-0.943	24.953	0.212	0.212	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.959	-0.967	25.981	0.169	0.169	0.000	0.000	0.000	0.000
80	B	121	GLU	-1	-0.888	-0.918	25.339	0.244	0.244	0.000	0.000	0.000	0.000
81	B	122	THR	0	-0.104	-0.044	20.522	0.034	0.034	0.000	0.000	0.000	0.000
82	B	123	GLN	0	0.068	0.032	19.026	-0.068	-0.068	0.000	0.000	0.000	0.000
83	B	124	PHE	0	0.029	0.005	15.718	0.042	0.042	0.000	0.000	0.000	0.000
84	B	125	MET	0	-0.030	-0.006	12.856	0.010	0.010	0.000	0.000	0.000	0.000
85	B	126	SER	0	0.017	0.008	14.347	0.023	0.023	0.000	0.000	0.000	0.000
86	B	127	ASN	0	-0.030	-0.029	12.710	-0.036	-0.036	0.000	0.000	0.000	0.000
87	B	129	PRO	0	0.045	0.029	10.796	0.068	0.068	0.000	0.000	0.000	0.000
88	B	130	VAL	0	0.034	0.025	8.501	-0.038	-0.038	0.000	0.000	0.000	0.000
89	B	131	ALA	0	-0.029	-0.014	9.949	0.043	0.043	0.000	0.000	0.000	0.000
90	B	132	VAL	0	-0.024	-0.012	11.857	-0.125	-0.125	0.000	0.000	0.000	0.000
91	B	133	THR	0	-0.049	-0.036	14.835	0.105	0.105	0.000	0.000	0.000	0.000
92	B	134	GLU	-1	-0.876	-0.951	16.931	0.437	0.437	0.000	0.000	0.000	0.000
93	B	135	SER	0	-0.034	-0.015	20.525	0.011	0.011	0.000	0.000	0.000	0.000
94	B	136	THR	0	0.025	0.002	22.976	-0.021	-0.021	0.000	0.000	0.000	0.000
95	B	137	PRO	0	-0.002	0.027	23.762	0.008	0.008	0.000	0.000	0.000	0.000
96	B	138	ARG	1	0.863	0.899	25.044	-0.243	-0.243	0.000	0.000	0.000	0.000
97	B	139	ARG	1	0.861	0.937	26.645	-0.168	-0.168	0.000	0.000	0.000	0.000
98	B	140	ARG	1	0.871	0.944	24.144	-0.307	-0.307	0.000	0.000	0.000	0.000
99	B	141	THR	0	0.043	0.007	27.047	0.009	0.009	0.000	0.000	0.000	0.000
100	B	142	ARG	1	0.900	0.928	25.551	-0.205	-0.205	0.000	0.000	0.000	0.000
101	B	143	ILE	0	-0.021	0.023	19.665	-0.012	-0.012	0.000	0.000	0.000	0.000
102	B	144	GLN	0	-0.001	-0.006	22.904	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	145	VAL	0	0.033	0.024	18.308	0.002	0.002	0.000	0.000	0.000	0.000
104	B	146	PHE	0	0.012	-0.001	21.742	-0.013	-0.013	0.000	0.000	0.000	0.000
105	B	147	TRP	0	-0.018	-0.018	14.688	0.010	0.010	0.000	0.000	0.000	0.000
106	B	148	ILE	0	-0.012	-0.019	19.170	-0.027	-0.027	0.000	0.000	0.000	0.000
107	B	149	ALA	0	0.003	0.015	18.561	0.016	0.016	0.000	0.000	0.000	0.000
108	B	150	PRO	0	-0.015	0.002	15.702	-0.012	-0.012	0.000	0.000	0.000	0.000
109	B	151	PRO	0	0.025	0.004	18.126	-0.008	-0.008	0.000	0.000	0.000	0.000
110	B	152	ALA	0	0.033	0.021	19.776	0.001	0.001	0.000	0.000	0.000	0.000
111	B	153	GLY	0	-0.028	-0.006	20.677	-0.009	-0.009	0.000	0.000	0.000	0.000
112	B	154	THR	0	-0.048	-0.029	14.698	-0.024	-0.024	0.000	0.000	0.000	0.000
113	B	155	GLY	0	0.061	0.046	15.445	-0.022	-0.022	0.000	0.000	0.000	0.000
114	B	156	CYS	0	-0.053	-0.015	14.926	0.038	0.038	0.000	0.000	0.000	0.000
115	B	157	VAL	0	0.037	0.023	12.460	-0.008	-0.008	0.000	0.000	0.000	0.000
116	B	158	ILE	0	-0.019	-0.021	10.361	-0.033	-0.033	0.000	0.000	0.000	0.000
117	B	159	LEU	0	-0.005	0.003	11.205	0.149	0.149	0.000	0.000	0.000	0.000
118	B	160	LYS	1	0.905	0.942	6.956	-1.324	-1.324	0.000	0.000	0.000	0.000
119	B	161	ALA	0	0.035	0.016	12.083	0.098	0.098	0.000	0.000	0.000	0.000
120	B	162	SER	0	-0.031	0.020	12.392	-0.020	-0.020	0.000	0.000	0.000	0.000
121	B	163	ILE	0	0.036	0.019	14.406	-0.072	-0.072	0.000	0.000	0.000	0.000
122	B	164	VAL	0	0.036	0.031	17.956	0.003	0.003	0.000	0.000	0.000	0.000
123	B	165	GLN	0	0.020	0.026	20.066	-0.054	-0.054	0.000	0.000	0.000	0.000
124	B	166	LYS	1	0.893	0.926	23.563	-0.256	-0.256	0.000	0.000	0.000	0.000
125	B	167	ARG	1	0.996	0.996	22.858	-0.237	-0.237	0.000	0.000	0.000	0.000
126	B	168	ILE	0	0.023	0.019	19.560	0.024	0.024	0.000	0.000	0.000	0.000
127	B	169	ILE	0	0.066	0.044	14.466	-0.021	-0.021	0.000	0.000	0.000	0.000
128	B	170	TYR	0	-0.010	-0.001	16.033	0.011	0.011	0.000	0.000	0.000	0.000
129	B	171	PHE	0	0.035	0.002	9.867	0.128	0.128	0.000	0.000	0.000	0.000
130	B	172	GLN	0	-0.034	-0.003	12.069	-0.135	-0.135	0.000	0.000	0.000	0.000
131	B	173	ASP	-1	-0.843	-0.932	8.574	0.967	0.967	0.000	0.000	0.000	0.000
132	B	174	GLU	-1	-0.784	-0.851	11.182	0.082	0.082	0.000	0.000	0.000	0.000
133	B	175	GLY	0	0.005	0.004	14.736	-0.003	-0.003	0.000	0.000	0.000	0.000
134	B	176	SER	0	-0.018	-0.014	17.934	0.006	0.006	0.000	0.000	0.000	0.000
135	B	177	LEU	0	-0.067	-0.018	15.494	-0.017	-0.017	0.000	0.000	0.000	0.000
136	B	178	THR	0	-0.014	-0.014	12.659	0.141	0.141	0.000	0.000	0.000	0.000
137	B	179	LYS	1	0.931	0.972	14.959	-0.300	-0.300	0.000	0.000	0.000	0.000
138	B	180	LYS	1	0.937	0.977	14.980	-0.026	-0.026	0.000	0.000	0.000	0.000
139	B	181	LEU	0	-0.040	-0.003	16.260	-0.021	-0.021	0.000	0.000	0.000	0.000
140	B	183	GLU	-1	-0.756	-0.882	19.521	0.025	0.025	0.000	0.000	0.000	0.000
141	B	184	GLN	0	-0.068	-0.035	22.134	-0.010	-0.010	0.000	0.000	0.000	0.000
142	B	185	ASP	-1	-0.959	-0.961	25.218	0.001	0.001	0.000	0.000	0.000	0.000

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