FMO DATABASE

FMODB ID: 7GN4K

Calculation Name: 2CLY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CLY

Chain ID: B

ChEMBL ID:

UniProt ID: P13619

Base Structure: X-ray

Registration Date: 2023-03-13

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-731622.275633
FMO2-HF: Nuclear repulsion	684010.292598
FMO2-HF: Total energy	-47611.983035
FMO2-MP2: Total energy	-47752.751994

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:4:LYS)

Summations of interaction energy for fragment #1(B:4:LYS)

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.
-117.735	-114.212	15.029	-10.434	-8.119	-0.134

Interaction energy analysis for fragmet #1(B:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.895

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

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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	6	ALA	0	0.014	0.019	3.833	0.188	2.151	-0.022	-0.971	-0.971	0.002
4	B	7	LEU	0	0.008	-0.025	6.760	0.371	0.371	0.000	0.000	0.000	0.000
5	B	8	LYS	1	0.966	0.995	9.542	16.711	16.711	0.000	0.000	0.000	0.000
6	B	9	THR	0	0.033	0.011	12.213	0.246	0.246	0.000	0.000	0.000	0.000
7	B	10	ILE	0	0.003	-0.005	14.039	0.782	0.782	0.000	0.000	0.000	0.000
8	B	11	ASP	-1	-0.877	-0.935	17.373	-12.748	-12.748	0.000	0.000	0.000	0.000
9	B	12	TRP	0	0.032	-0.012	17.374	0.735	0.735	0.000	0.000	0.000	0.000
10	B	13	VAL	0	-0.017	0.008	22.490	0.290	0.290	0.000	0.000	0.000	0.000
11	B	14	ALA	0	0.074	0.042	23.925	0.434	0.434	0.000	0.000	0.000	0.000
12	B	15	PHE	0	-0.042	-0.023	22.650	0.217	0.217	0.000	0.000	0.000	0.000
13	B	16	GLY	0	-0.031	-0.030	24.804	0.250	0.250	0.000	0.000	0.000	0.000
14	B	17	GLU	-1	-0.965	-0.978	27.729	-9.575	-9.575	0.000	0.000	0.000	0.000
15	B	18	ILE	0	-0.021	-0.004	24.884	0.244	0.244	0.000	0.000	0.000	0.000
16	B	19	ILE	0	-0.063	-0.014	26.128	0.060	0.060	0.000	0.000	0.000	0.000
17	B	20	PRO	0	0.044	0.025	30.229	0.315	0.315	0.000	0.000	0.000	0.000
18	B	21	ARG	1	1.038	1.001	32.966	7.894	7.894	0.000	0.000	0.000	0.000
19	B	22	ASN	0	-0.048	-0.019	34.823	-0.114	-0.114	0.000	0.000	0.000	0.000
20	B	23	GLN	0	0.017	-0.006	30.726	-0.130	-0.130	0.000	0.000	0.000	0.000
21	B	24	LYS	1	0.946	0.984	30.085	9.294	9.294	0.000	0.000	0.000	0.000
22	B	25	ALA	0	-0.025	-0.008	29.533	-0.304	-0.304	0.000	0.000	0.000	0.000
23	B	26	VAL	0	0.078	0.030	26.204	-0.298	-0.298	0.000	0.000	0.000	0.000
24	B	27	ALA	0	0.050	0.039	25.471	-0.451	-0.451	0.000	0.000	0.000	0.000
25	B	28	ASN	0	-0.017	-0.026	24.726	-0.119	-0.119	0.000	0.000	0.000	0.000
26	B	29	SER	0	0.030	0.027	24.638	-0.496	-0.496	0.000	0.000	0.000	0.000
27	B	30	LEU	0	0.039	0.006	20.835	-0.577	-0.577	0.000	0.000	0.000	0.000
28	B	31	LYS	1	0.850	0.931	20.261	13.136	13.136	0.000	0.000	0.000	0.000
29	B	32	SER	0	0.017	0.020	20.197	-0.443	-0.443	0.000	0.000	0.000	0.000
30	B	33	TRP	0	0.000	0.019	18.467	-0.661	-0.661	0.000	0.000	0.000	0.000
31	B	34	ASN	0	0.046	0.022	14.664	-0.846	-0.846	0.000	0.000	0.000	0.000
32	B	35	GLU	-1	-0.797	-0.880	15.747	-15.420	-15.420	0.000	0.000	0.000	0.000
33	B	36	THR	0	-0.023	-0.025	17.027	-0.523	-0.523	0.000	0.000	0.000	0.000
34	B	37	LEU	0	-0.032	-0.022	13.713	-0.864	-0.864	0.000	0.000	0.000	0.000
35	B	38	THR	0	-0.044	-0.031	12.259	-2.048	-2.048	0.000	0.000	0.000	0.000
36	B	39	SER	0	-0.026	-0.027	12.825	-0.940	-0.940	0.000	0.000	0.000	0.000
37	B	40	ARG	1	0.912	0.962	13.593	19.109	19.109	0.000	0.000	0.000	0.000
38	B	41	LEU	0	0.017	0.003	7.889	-0.329	-0.329	0.000	0.000	0.000	0.000
39	B	42	ALA	0	-0.018	0.014	9.301	-2.321	-2.321	0.000	0.000	0.000	0.000
40	B	43	THR	0	-0.094	-0.053	11.370	0.702	0.702	0.000	0.000	0.000	0.000
41	B	44	LEU	0	-0.069	-0.042	10.835	1.161	1.161	0.000	0.000	0.000	0.000
42	B	45	PRO	0	0.010	0.020	8.659	-2.835	-2.835	0.000	0.000	0.000	0.000
43	B	46	GLU	-1	-0.842	-0.922	1.936	-136.534	-134.974	15.051	-9.463	-7.148	-0.136
44	B	47	LYS	1	0.939	0.976	6.169	37.703	37.703	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.020	0.010	8.888	0.472	0.472	0.000	0.000	0.000	0.000
46	B	49	PRO	0	-0.003	-0.003	12.422	-0.716	-0.716	0.000	0.000	0.000	0.000
47	B	50	ALA	0	0.004	0.006	14.710	0.087	0.087	0.000	0.000	0.000	0.000
48	B	51	ILE	0	0.028	0.002	16.005	0.509	0.509	0.000	0.000	0.000	0.000
49	B	52	ASP	-1	-0.858	-0.915	19.625	-12.534	-12.534	0.000	0.000	0.000	0.000
50	B	53	TRP	0	0.056	0.003	19.350	0.968	0.968	0.000	0.000	0.000	0.000
51	B	54	ALA	0	0.004	0.011	24.015	0.577	0.577	0.000	0.000	0.000	0.000
52	B	55	TYR	0	0.047	0.028	26.132	0.623	0.623	0.000	0.000	0.000	0.000
53	B	56	TYR	0	0.016	0.005	23.688	0.304	0.304	0.000	0.000	0.000	0.000
54	B	57	LYS	1	0.827	0.885	27.965	10.879	10.879	0.000	0.000	0.000	0.000
55	B	58	ALA	0	-0.051	-0.026	29.904	0.371	0.371	0.000	0.000	0.000	0.000
56	B	59	ASN	0	-0.103	-0.029	31.108	0.613	0.613	0.000	0.000	0.000	0.000
57	B	60	VAL	0	0.020	0.006	31.781	-0.127	-0.127	0.000	0.000	0.000	0.000
58	B	61	ALA	0	0.001	-0.005	33.874	0.261	0.261	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.923	0.965	34.908	8.350	8.350	0.000	0.000	0.000	0.000
60	B	63	ALA	0	0.064	0.009	34.477	-0.212	-0.212	0.000	0.000	0.000	0.000
61	B	64	GLY	0	0.034	0.044	32.287	-0.177	-0.177	0.000	0.000	0.000	0.000
62	B	65	LEU	0	-0.015	-0.004	29.839	-0.160	-0.160	0.000	0.000	0.000	0.000
63	B	66	VAL	0	0.081	0.037	26.464	-0.338	-0.338	0.000	0.000	0.000	0.000
64	B	67	ASP	-1	-0.870	-0.904	26.426	-10.939	-10.939	0.000	0.000	0.000	0.000
65	B	68	ASP	-1	-0.856	-0.913	26.556	-11.242	-11.242	0.000	0.000	0.000	0.000
66	B	69	PHE	0	-0.007	-0.020	24.558	-0.319	-0.319	0.000	0.000	0.000	0.000
67	B	70	GLU	-1	-0.888	-0.944	21.557	-13.973	-13.973	0.000	0.000	0.000	0.000
68	B	71	LYS	1	0.890	0.939	21.462	10.377	10.377	0.000	0.000	0.000	0.000
69	B	72	LYS	1	0.835	0.891	21.740	10.603	10.603	0.000	0.000	0.000	0.000
70	B	73	PHE	0	-0.037	0.001	15.719	-0.481	-0.481	0.000	0.000	0.000	0.000
71	B	74	ASN	0	-0.017	-0.024	17.191	-1.869	-1.869	0.000	0.000	0.000	0.000
72	B	75	ALA	0	-0.071	-0.042	17.233	0.503	0.503	0.000	0.000	0.000	0.000
73	B	76	LEU	0	0.048	0.057	18.218	0.721	0.721	0.000	0.000	0.000	0.000
74	B	77	LYS	1	0.878	0.924	14.793	18.466	18.466	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.032	0.011	13.760	0.946	0.946	0.000	0.000	0.000	0.000
76	B	79	PRO	0	-0.022	0.004	13.536	-1.232	-1.232	0.000	0.000	0.000	0.000
77	B	80	ILE	0	0.020	0.002	8.258	-0.744	-0.744	0.000	0.000	0.000	0.000
78	B	81	PRO	0	-0.027	-0.013	11.296	1.193	1.193	0.000	0.000	0.000	0.000
79	B	82	GLU	-1	-0.810	-0.893	12.953	-15.677	-15.677	0.000	0.000	0.000	0.000
80	B	83	ASP	-1	-0.804	-0.893	13.012	-18.465	-18.465	0.000	0.000	0.000	0.000
81	B	84	LYS	1	0.780	0.870	14.926	14.910	14.910	0.000	0.000	0.000	0.000
82	B	85	TYR	0	-0.044	-0.032	15.385	1.157	1.157	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.032	-0.021	15.696	0.498	0.498	0.000	0.000	0.000	0.000
84	B	87	ALA	0	0.045	0.027	18.585	0.271	0.271	0.000	0.000	0.000	0.000
85	B	88	GLN	0	-0.099	-0.043	18.212	-0.190	-0.190	0.000	0.000	0.000	0.000
86	B	89	VAL	0	0.067	0.038	18.773	0.302	0.302	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.827	-0.918	21.429	-12.084	-12.084	0.000	0.000	0.000	0.000
88	B	91	ALA	0	-0.063	-0.046	24.919	0.464	0.464	0.000	0.000	0.000	0.000
89	B	92	GLU	-1	-0.985	-0.987	21.139	-13.572	-13.572	0.000	0.000	0.000	0.000
90	B	93	GLU	-1	-0.876	-0.937	25.059	-10.591	-10.591	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.894	0.945	26.851	9.779	9.779	0.000	0.000	0.000	0.000
92	B	95	GLU	-1	-0.922	-0.951	27.388	-10.046	-10.046	0.000	0.000	0.000	0.000
93	B	96	ASP	-1	-0.826	-0.905	26.712	-10.873	-10.873	0.000	0.000	0.000	0.000
94	B	97	VAL	0	-0.072	-0.047	30.041	0.412	0.412	0.000	0.000	0.000	0.000
95	B	98	LYS	1	0.758	0.882	32.540	8.518	8.518	0.000	0.000	0.000	0.000
96	B	99	SER	0	-0.006	-0.027	29.993	0.318	0.318	0.000	0.000	0.000	0.000
97	B	100	CYS	0	0.043	0.000	29.626	0.392	0.392	0.000	0.000	0.000	0.000
98	B	101	ALA	0	0.035	0.045	31.967	0.274	0.274	0.000	0.000	0.000	0.000
99	B	102	GLU	-1	-0.870	-0.907	34.836	-7.441	-7.441	0.000	0.000	0.000	0.000
100	B	103	PHE	0	0.048	0.017	35.304	0.278	0.278	0.000	0.000	0.000	0.000
101	B	104	LEU	0	-0.014	-0.002	31.791	0.234	0.234	0.000	0.000	0.000	0.000
102	B	105	THR	0	-0.077	-0.059	36.487	0.174	0.174	0.000	0.000	0.000	0.000
103	B	106	GLN	0	-0.030	-0.020	39.304	0.247	0.247	0.000	0.000	0.000	0.000
104	B	107	SER	0	-0.019	-0.025	38.543	0.251	0.251	0.000	0.000	0.000	0.000
105	B	108	LYS	1	0.971	0.992	35.118	8.424	8.424	0.000	0.000	0.000	0.000
106	B	109	THR	0	0.010	0.015	41.091	0.140	0.140	0.000	0.000	0.000	0.000
107	B	110	ARG	1	0.924	0.962	41.169	7.299	7.299	0.000	0.000	0.000	0.000
108	B	111	ILE	0	-0.061	-0.009	41.202	0.102	0.102	0.000	0.000	0.000	0.000
109	B	112	GLN	0	0.023	0.006	43.980	0.204	0.204	0.000	0.000	0.000	0.000
110	B	113	GLU	-1	-0.918	-0.945	46.524	-6.144	-6.144	0.000	0.000	0.000	0.000
111	B	114	TYR	0	0.012	-0.004	45.435	0.081	0.081	0.000	0.000	0.000	0.000
112	B	115	GLU	-1	-0.871	-0.941	45.292	-6.650	-6.650	0.000	0.000	0.000	0.000
113	B	116	LYS	1	0.921	0.953	49.106	5.830	5.830	0.000	0.000	0.000	0.000
114	B	117	GLU	-1	-0.887	-0.928	51.885	-5.400	-5.400	0.000	0.000	0.000	0.000
115	B	118	LEU	0	-0.013	-0.018	49.281	0.098	0.098	0.000	0.000	0.000	0.000
116	B	119	GLU	-1	-0.838	-0.897	53.169	-5.524	-5.524	0.000	0.000	0.000	0.000
117	B	120	LYS	1	0.787	0.870	54.637	5.534	5.534	0.000	0.000	0.000	0.000
118	B	121	MET	0	-0.017	-0.005	56.223	0.069	0.069	0.000	0.000	0.000	0.000
119	B	122	ARG	1	0.788	0.900	54.757	5.541	5.541	0.000	0.000	0.000	0.000
120	B	123	ASN	0	-0.077	-0.032	57.997	0.095	0.095	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:LYS)