FMO DATABASE

FMODB ID: 89NLY

Calculation Name: 2C0D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C0D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8I5Q6

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	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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1777493.015424
FMO2-HF: Nuclear repulsion	1710676.960052
FMO2-HF: Total energy	-66816.055372
FMO2-MP2: Total energy	-67011.113758

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:21:LEU)

Summations of interaction energy for fragment #1(A:21:LEU)

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.
-11.59	-3.646	8.484	-4.734	-11.695	-0.028

Interaction energy analysis for fragmet #1(A:21:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / 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	A	23	THR	0	-0.038	-0.016	3.865	1.102	2.350	-0.010	-0.538	-0.700	0.003
4	A	24	LYS	1	0.859	0.931	2.846	-2.525	-1.693	0.136	-0.228	-0.740	0.000
5	A	25	LYS	1	0.866	0.920	4.992	-0.308	-0.288	-0.001	-0.008	-0.011	0.000
6	A	26	ALA	0	0.022	0.010	4.475	-0.402	-0.247	-0.001	-0.009	-0.145	0.000
7	A	27	TYR	0	-0.085	-0.105	4.323	0.140	0.327	-0.001	-0.014	-0.172	0.000
8	A	28	ASN	0	0.046	0.018	5.737	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	29	PHE	0	0.013	0.002	8.997	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	30	THR	0	0.012	0.003	11.523	0.039	0.039	0.000	0.000	0.000	0.000
11	A	31	ALA	0	-0.020	-0.002	14.723	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	32	GLN	0	0.025	0.010	16.658	0.012	0.012	0.000	0.000	0.000	0.000
13	A	33	GLY	0	0.015	0.008	18.182	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	34	LEU	0	-0.028	0.010	19.752	0.022	0.022	0.000	0.000	0.000	0.000
15	A	35	ASN	0	0.035	-0.002	21.802	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	36	LYS	1	0.991	0.989	23.442	0.140	0.140	0.000	0.000	0.000	0.000
17	A	37	ASN	0	-0.033	-0.007	25.563	0.012	0.012	0.000	0.000	0.000	0.000
18	A	38	ASN	0	-0.043	-0.021	26.711	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	39	GLU	-1	-0.848	-0.909	26.895	-0.125	-0.125	0.000	0.000	0.000	0.000
20	A	40	ILE	0	-0.029	-0.022	23.605	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	41	ILE	0	-0.025	-0.007	20.921	0.011	0.011	0.000	0.000	0.000	0.000
22	A	42	ASN	0	0.009	-0.008	19.832	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	43	VAL	0	-0.009	-0.001	15.136	0.011	0.011	0.000	0.000	0.000	0.000
24	A	44	ASP	-1	-0.824	-0.913	15.514	-0.339	-0.339	0.000	0.000	0.000	0.000
25	A	45	LEU	0	-0.002	0.007	8.873	0.022	0.022	0.000	0.000	0.000	0.000
26	A	46	SER	0	-0.034	-0.038	13.223	0.028	0.028	0.000	0.000	0.000	0.000
27	A	47	SER	0	-0.023	-0.009	14.189	0.044	0.044	0.000	0.000	0.000	0.000
28	A	48	PHE	0	0.050	0.018	14.600	0.030	0.030	0.000	0.000	0.000	0.000
29	A	49	ILE	0	0.004	0.008	12.457	0.014	0.014	0.000	0.000	0.000	0.000
30	A	50	GLY	0	-0.052	-0.030	15.634	0.022	0.022	0.000	0.000	0.000	0.000
31	A	51	GLN	0	-0.125	-0.060	17.792	0.034	0.034	0.000	0.000	0.000	0.000
32	A	52	LYS	1	0.840	0.906	17.298	0.217	0.217	0.000	0.000	0.000	0.000
33	A	53	TYR	0	-0.063	-0.040	13.518	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	54	CYS	0	-0.045	-0.007	11.389	0.027	0.027	0.000	0.000	0.000	0.000
35	A	55	CYS	0	-0.017	0.001	11.417	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	56	LEU	0	-0.006	0.006	6.587	0.036	0.036	0.000	0.000	0.000	0.000
37	A	57	LEU	0	0.041	0.009	9.563	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	58	PHE	0	0.031	0.012	6.385	0.019	0.019	0.000	0.000	0.000	0.000
39	A	59	TYR	0	-0.006	-0.009	11.067	0.052	0.052	0.000	0.000	0.000	0.000
40	A	60	PRO	0	0.002	0.020	14.232	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	61	LEU	0	0.051	0.003	16.649	0.020	0.020	0.000	0.000	0.000	0.000
42	A	62	ASN	0	-0.044	-0.014	19.349	0.029	0.029	0.000	0.000	0.000	0.000
43	A	63	TYR	0	0.043	0.009	21.133	0.003	0.003	0.000	0.000	0.000	0.000
44	A	64	THR	0	-0.005	-0.001	22.718	0.006	0.006	0.000	0.000	0.000	0.000
45	A	65	PHE	0	0.035	0.011	19.075	0.005	0.005	0.000	0.000	0.000	0.000
46	A	66	VAL	0	-0.026	0.023	20.280	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	67	CYS	0	-0.013	-0.012	19.896	0.017	0.017	0.000	0.000	0.000	0.000
48	A	68	PRO	0	0.058	0.026	21.245	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	69	THR	0	0.030	0.004	23.384	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	70	GLU	-1	-0.709	-0.820	16.923	-0.258	-0.258	0.000	0.000	0.000	0.000
51	A	71	ILE	0	-0.006	0.010	17.601	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.012	-0.001	20.721	0.005	0.005	0.000	0.000	0.000	0.000
53	A	73	GLU	-1	-0.977	-0.998	22.498	-0.106	-0.106	0.000	0.000	0.000	0.000
54	A	74	PHE	0	0.027	-0.012	15.781	0.005	0.005	0.000	0.000	0.000	0.000
55	A	75	ASN	0	0.082	0.053	20.899	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	76	LYS	1	0.910	0.973	23.296	0.101	0.101	0.000	0.000	0.000	0.000
57	A	77	HIS	1	0.826	0.909	22.480	0.119	0.119	0.000	0.000	0.000	0.000
58	A	78	ILE	0	0.068	0.054	21.173	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	79	LYS	1	1.011	0.990	23.438	0.078	0.078	0.000	0.000	0.000	0.000
60	A	80	ASP	-1	-0.913	-0.951	22.991	-0.085	-0.085	0.000	0.000	0.000	0.000
61	A	81	PHE	0	-0.028	-0.027	16.378	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	82	GLU	-1	-0.918	-0.967	20.849	-0.128	-0.128	0.000	0.000	0.000	0.000
63	A	83	ASN	0	-0.047	-0.024	23.331	0.005	0.005	0.000	0.000	0.000	0.000
64	A	84	LYS	1	0.811	0.898	19.751	0.089	0.089	0.000	0.000	0.000	0.000
65	A	85	ASN	0	-0.045	-0.028	19.848	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	86	VAL	0	-0.018	-0.011	15.265	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	87	GLU	-1	-0.898	-0.934	16.011	-0.213	-0.213	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.040	-0.013	14.663	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	89	LEU	0	0.004	-0.007	12.740	0.018	0.018	0.000	0.000	0.000	0.000
70	A	90	GLY	0	0.022	0.016	13.121	-0.043	-0.043	0.000	0.000	0.000	0.000
71	A	91	ILE	0	-0.026	-0.006	9.625	0.005	0.005	0.000	0.000	0.000	0.000
72	A	92	SER	0	0.016	-0.007	13.043	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	93	VAL	0	-0.001	0.001	13.491	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	94	ASP	-1	-0.875	-0.905	15.777	-0.245	-0.245	0.000	0.000	0.000	0.000
75	A	95	SER	0	0.024	0.005	19.287	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	96	VAL	0	0.119	0.039	21.566	0.003	0.003	0.000	0.000	0.000	0.000
77	A	97	TYR	0	-0.018	0.007	23.089	0.009	0.009	0.000	0.000	0.000	0.000
78	A	98	SER	0	0.024	0.002	22.655	0.012	0.012	0.000	0.000	0.000	0.000
79	A	99	HIS	0	0.013	0.010	17.810	0.022	0.022	0.000	0.000	0.000	0.000
80	A	100	LEU	0	0.016	0.005	23.096	0.008	0.008	0.000	0.000	0.000	0.000
81	A	101	ALA	0	-0.025	-0.021	26.490	0.010	0.010	0.000	0.000	0.000	0.000
82	A	102	TRP	0	0.008	-0.013	19.766	0.004	0.004	0.000	0.000	0.000	0.000
83	A	103	LYS	1	0.849	0.923	23.838	0.173	0.173	0.000	0.000	0.000	0.000
84	A	104	ASN	0	-0.048	-0.020	27.001	0.011	0.011	0.000	0.000	0.000	0.000
85	A	105	MET	0	-0.048	0.017	28.302	0.008	0.008	0.000	0.000	0.000	0.000
86	A	106	PRO	0	0.004	0.001	30.633	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	107	ILE	0	0.064	0.020	29.009	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	108	GLU	-1	-0.848	-0.928	31.061	-0.083	-0.083	0.000	0.000	0.000	0.000
89	A	109	LYS	1	0.806	0.898	32.653	0.083	0.083	0.000	0.000	0.000	0.000
90	A	110	GLY	0	0.028	0.024	28.605	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	111	GLY	0	-0.005	-0.005	26.847	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	112	ILE	0	-0.069	-0.035	22.259	0.001	0.001	0.000	0.000	0.000	0.000
93	A	113	GLY	0	0.044	0.028	26.026	0.002	0.002	0.000	0.000	0.000	0.000
94	A	114	ASN	0	0.012	-0.018	26.700	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	115	VAL	0	-0.027	-0.005	22.007	0.005	0.005	0.000	0.000	0.000	0.000
96	A	116	GLU	-1	-0.950	-0.995	24.674	-0.122	-0.122	0.000	0.000	0.000	0.000
97	A	117	PHE	0	-0.020	-0.020	17.403	0.000	0.000	0.000	0.000	0.000	0.000
98	A	118	THR	0	-0.005	-0.003	18.019	0.012	0.012	0.000	0.000	0.000	0.000
99	A	119	LEU	0	-0.051	-0.002	17.528	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	120	VAL	0	0.041	0.000	13.854	0.020	0.020	0.000	0.000	0.000	0.000
101	A	121	SER	0	-0.008	-0.018	15.896	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	122	ASP	-1	-0.775	-0.890	11.449	-0.622	-0.622	0.000	0.000	0.000	0.000
103	A	123	ILE	0	0.011	0.015	14.651	0.000	0.000	0.000	0.000	0.000	0.000
104	A	124	ASN	0	-0.039	-0.027	14.643	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	125	LYS	1	0.910	0.964	12.649	0.328	0.328	0.000	0.000	0.000	0.000
106	A	126	ASP	-1	-0.745	-0.795	10.790	-0.710	-0.710	0.000	0.000	0.000	0.000
107	A	127	ILE	0	0.008	0.012	7.971	-0.161	-0.161	0.000	0.000	0.000	0.000
108	A	128	SER	0	0.006	-0.033	6.933	-0.258	-0.258	0.000	0.000	0.000	0.000
109	A	129	LYS	1	0.809	0.907	6.409	0.491	0.491	0.000	0.000	0.000	0.000
110	A	130	ASN	0	-0.061	-0.031	5.231	-0.165	-0.165	0.000	0.000	0.000	0.000
111	A	131	TYR	0	-0.049	-0.031	2.411	-3.111	-1.370	1.717	-1.148	-2.310	-0.007
112	A	132	ASN	0	-0.057	-0.027	1.970	-0.232	-0.721	4.950	-0.944	-3.517	-0.012
113	A	133	VAL	0	0.002	0.000	4.287	0.202	0.293	-0.001	-0.005	-0.086	0.000
114	A	134	LEU	0	-0.033	-0.002	7.017	0.149	0.149	0.000	0.000	0.000	0.000
115	A	135	TYR	0	0.014	0.007	9.844	0.016	0.016	0.000	0.000	0.000	0.000
116	A	136	ASP	-1	-0.853	-0.930	12.855	-0.209	-0.209	0.000	0.000	0.000	0.000
117	A	137	ASN	0	-0.065	-0.046	13.548	-0.020	-0.020	0.000	0.000	0.000	0.000
118	A	138	SER	0	-0.030	-0.010	14.877	0.016	0.016	0.000	0.000	0.000	0.000
119	A	139	PHE	0	0.015	-0.016	14.891	0.003	0.003	0.000	0.000	0.000	0.000
120	A	140	ALA	0	0.022	0.025	10.758	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	141	LEU	0	0.038	0.007	9.198	0.069	0.069	0.000	0.000	0.000	0.000
122	A	142	ARG	1	0.807	0.908	11.002	0.184	0.184	0.000	0.000	0.000	0.000
123	A	143	GLY	0	0.002	0.002	7.707	0.028	0.028	0.000	0.000	0.000	0.000
124	A	144	LEU	0	-0.049	-0.026	7.977	0.050	0.050	0.000	0.000	0.000	0.000
125	A	145	PHE	0	0.012	-0.001	2.452	-1.105	-0.304	1.061	-0.394	-1.468	-0.001
126	A	146	ILE	0	0.014	0.021	7.315	0.095	0.095	0.000	0.000	0.000	0.000
127	A	147	ILE	0	-0.013	-0.001	6.831	-0.088	-0.088	0.000	0.000	0.000	0.000
128	A	148	ASP	-1	-0.725	-0.859	9.134	-0.094	-0.094	0.000	0.000	0.000	0.000
129	A	149	LYS	1	0.991	0.995	11.978	0.062	0.062	0.000	0.000	0.000	0.000
130	A	150	ASN	0	0.037	0.029	12.844	0.004	0.004	0.000	0.000	0.000	0.000
131	A	151	GLY	0	0.016	0.016	10.337	0.014	0.014	0.000	0.000	0.000	0.000
132	A	152	CYS	0	-0.067	-0.024	7.567	-0.116	-0.116	0.000	0.000	0.000	0.000
133	A	153	VAL	0	0.039	0.028	2.621	-0.910	0.066	0.327	-0.278	-1.025	0.001
134	A	154	ARG	1	0.781	0.853	5.635	0.285	0.285	0.000	0.000	0.000	0.000
135	A	155	HIS	0	0.020	0.009	6.769	0.244	0.244	0.000	0.000	0.000	0.000
136	A	156	GLN	0	0.045	0.022	2.904	-4.032	-1.650	0.307	-1.168	-1.521	-0.012
137	A	157	THR	0	-0.067	-0.018	6.018	0.268	0.268	0.000	0.000	0.000	0.000
138	A	158	VAL	0	0.010	-0.018	6.574	-0.162	-0.162	0.000	0.000	0.000	0.000
139	A	159	ASN	0	-0.058	-0.015	9.252	0.090	0.090	0.000	0.000	0.000	0.000
140	A	160	ASP	-1	-0.844	-0.932	12.964	-0.155	-0.155	0.000	0.000	0.000	0.000
141	A	161	LEU	0	0.012	0.000	14.442	-0.015	-0.015	0.000	0.000	0.000	0.000
142	A	162	PRO	0	-0.014	-0.003	16.449	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	163	ILE	0	-0.034	0.009	17.718	0.013	0.013	0.000	0.000	0.000	0.000
144	A	164	GLY	0	0.022	0.018	17.173	-0.025	-0.025	0.000	0.000	0.000	0.000
145	A	165	ARG	1	0.745	0.823	11.827	0.377	0.377	0.000	0.000	0.000	0.000
146	A	166	ASN	0	0.060	0.030	17.157	0.010	0.010	0.000	0.000	0.000	0.000
147	A	167	VAL	0	0.033	0.015	18.508	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	168	GLN	0	0.004	-0.013	19.484	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	169	GLU	-1	-0.798	-0.864	17.552	-0.025	-0.025	0.000	0.000	0.000	0.000
150	A	170	VAL	0	0.001	0.001	14.205	0.005	0.005	0.000	0.000	0.000	0.000
151	A	171	LEU	0	-0.022	-0.013	16.061	0.001	0.001	0.000	0.000	0.000	0.000
152	A	172	ARG	1	0.874	0.912	18.745	0.039	0.039	0.000	0.000	0.000	0.000
153	A	173	THR	0	-0.010	-0.004	12.360	0.025	0.025	0.000	0.000	0.000	0.000
154	A	174	ILE	0	-0.015	-0.015	14.433	0.011	0.011	0.000	0.000	0.000	0.000
155	A	175	ASP	-1	-0.810	-0.881	15.853	-0.049	-0.049	0.000	0.000	0.000	0.000
156	A	176	SER	0	-0.030	-0.015	16.474	0.020	0.020	0.000	0.000	0.000	0.000
157	A	177	ILE	0	-0.037	-0.012	11.410	0.019	0.019	0.000	0.000	0.000	0.000
158	A	178	ILE	0	0.016	0.004	15.416	0.013	0.013	0.000	0.000	0.000	0.000
159	A	179	HIS	0	-0.008	-0.003	18.308	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	180	VAL	0	-0.015	-0.002	15.807	0.012	0.012	0.000	0.000	0.000	0.000
161	A	181	ASP	-1	-0.818	-0.878	15.866	-0.016	-0.016	0.000	0.000	0.000	0.000
162	A	182	THR	0	-0.111	-0.055	18.591	0.002	0.002	0.000	0.000	0.000	0.000
163	A	183	SER	0	-0.012	0.005	21.952	0.007	0.007	0.000	0.000	0.000	0.000
164	A	184	GLY	0	-0.014	-0.004	20.132	0.005	0.005	0.000	0.000	0.000	0.000
165	A	185	GLU	-1	-0.932	-0.967	21.185	0.102	0.102	0.000	0.000	0.000	0.000
166	A	186	VAL	0	-0.024	-0.019	18.291	0.015	0.015	0.000	0.000	0.000	0.000
167	A	187	CYS	0	-0.097	-0.050	19.003	-0.007	-0.007	0.000	0.000	0.000	0.000
168	A	188	PRO	0	0.037	0.033	20.021	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:LEU)