FMO DATABASE

FMODB ID: 22RGR

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	OptAll
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	-731230.792164
FMO2-HF: Nuclear repulsion	683617.825192
FMO2-HF: Total energy	-47612.966972
FMO2-MP2: Total energy	-47753.504411

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.
-120.561	-129.45	32.135	-14.075	-9.171	-0.156

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 : 0.813 / q_NPA : 0.870

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	0.015	0.018	3.879	0.342	2.216	-0.016	-0.956	-0.901	0.001
4	B	7	LEU	0	0.004	-0.014	6.705	0.865	0.865	0.000	0.000	0.000	0.000
5	B	8	LYS	1	0.872	0.929	9.694	16.153	16.153	0.000	0.000	0.000	0.000
6	B	9	THR	0	0.011	0.003	12.353	0.365	0.365	0.000	0.000	0.000	0.000
7	B	10	ILE	0	-0.007	-0.002	14.283	0.833	0.833	0.000	0.000	0.000	0.000
8	B	11	ASP	-1	-0.838	-0.897	17.584	-12.642	-12.642	0.000	0.000	0.000	0.000
9	B	12	TRP	0	0.028	-0.030	17.116	0.576	0.576	0.000	0.000	0.000	0.000
10	B	13	VAL	0	-0.001	0.015	22.348	0.324	0.324	0.000	0.000	0.000	0.000
11	B	14	ALA	0	0.019	0.007	23.831	0.369	0.369	0.000	0.000	0.000	0.000
12	B	15	PHE	0	-0.031	-0.021	22.250	0.136	0.136	0.000	0.000	0.000	0.000
13	B	16	GLY	0	-0.025	-0.010	24.489	0.130	0.130	0.000	0.000	0.000	0.000
14	B	17	GLU	-1	-0.956	-0.989	27.802	-9.543	-9.543	0.000	0.000	0.000	0.000
15	B	18	ILE	0	-0.010	0.001	25.196	0.254	0.254	0.000	0.000	0.000	0.000
16	B	19	ILE	0	-0.046	-0.004	26.295	0.055	0.055	0.000	0.000	0.000	0.000
17	B	20	PRO	0	0.032	0.024	30.427	0.328	0.328	0.000	0.000	0.000	0.000
18	B	21	ARG	1	1.006	0.981	33.269	7.919	7.919	0.000	0.000	0.000	0.000
19	B	22	ASN	0	-0.021	-0.015	35.121	-0.084	-0.084	0.000	0.000	0.000	0.000
20	B	23	GLN	0	0.018	0.001	30.588	-0.079	-0.079	0.000	0.000	0.000	0.000
21	B	24	LYS	1	0.942	0.981	30.058	9.355	9.355	0.000	0.000	0.000	0.000
22	B	25	ALA	0	-0.005	-0.008	29.522	-0.290	-0.290	0.000	0.000	0.000	0.000
23	B	26	VAL	0	0.044	0.021	26.324	-0.297	-0.297	0.000	0.000	0.000	0.000
24	B	27	ALA	0	0.062	0.040	25.242	-0.501	-0.501	0.000	0.000	0.000	0.000
25	B	28	ASN	0	-0.011	-0.012	24.552	-0.105	-0.105	0.000	0.000	0.000	0.000
26	B	29	SER	0	0.052	0.029	24.720	-0.276	-0.276	0.000	0.000	0.000	0.000
27	B	30	LEU	0	-0.016	-0.005	20.126	-0.520	-0.520	0.000	0.000	0.000	0.000
28	B	31	LYS	1	0.822	0.920	20.177	13.422	13.422	0.000	0.000	0.000	0.000
29	B	32	SER	0	0.037	0.020	19.937	-0.631	-0.631	0.000	0.000	0.000	0.000
30	B	33	TRP	0	0.019	0.020	18.211	-0.598	-0.598	0.000	0.000	0.000	0.000
31	B	34	ASN	0	0.030	0.010	14.435	-0.832	-0.832	0.000	0.000	0.000	0.000
32	B	35	GLU	-1	-0.801	-0.887	15.419	-15.654	-15.654	0.000	0.000	0.000	0.000
33	B	36	THR	0	-0.027	-0.017	16.966	-0.452	-0.452	0.000	0.000	0.000	0.000
34	B	37	LEU	0	-0.026	-0.013	13.315	-0.818	-0.818	0.000	0.000	0.000	0.000
35	B	38	THR	0	-0.024	-0.017	12.009	-2.157	-2.157	0.000	0.000	0.000	0.000
36	B	39	SER	0	-0.018	-0.022	12.755	-1.063	-1.063	0.000	0.000	0.000	0.000
37	B	40	ARG	1	0.855	0.928	13.785	20.205	20.205	0.000	0.000	0.000	0.000
38	B	41	LEU	0	0.013	-0.002	7.859	-0.735	-0.735	0.000	0.000	0.000	0.000
39	B	42	ALA	0	-0.020	-0.002	9.561	-1.971	-1.971	0.000	0.000	0.000	0.000
40	B	43	THR	0	-0.037	-0.019	11.463	0.987	0.987	0.000	0.000	0.000	0.000
41	B	44	LEU	0	-0.051	-0.024	10.357	2.242	2.242	0.000	0.000	0.000	0.000
42	B	45	PRO	0	0.005	0.024	8.204	-3.049	-3.049	0.000	0.000	0.000	0.000
43	B	46	GLU	-1	-0.808	-0.896	1.724	-140.015	-150.778	32.151	-13.119	-8.270	-0.157
44	B	47	LYS	1	0.920	0.961	6.058	36.855	36.855	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.028	0.016	8.838	0.556	0.556	0.000	0.000	0.000	0.000
46	B	49	PRO	0	0.002	0.009	12.071	-1.046	-1.046	0.000	0.000	0.000	0.000
47	B	50	ALA	0	0.000	-0.005	14.392	0.246	0.246	0.000	0.000	0.000	0.000
48	B	51	ILE	0	0.010	0.007	16.042	0.582	0.582	0.000	0.000	0.000	0.000
49	B	52	ASP	-1	-0.834	-0.909	19.647	-12.647	-12.647	0.000	0.000	0.000	0.000
50	B	53	TRP	0	0.043	-0.004	19.518	0.941	0.941	0.000	0.000	0.000	0.000
51	B	54	ALA	0	0.005	0.013	24.234	0.557	0.557	0.000	0.000	0.000	0.000
52	B	55	TYR	0	0.014	0.006	26.127	0.590	0.590	0.000	0.000	0.000	0.000
53	B	56	TYR	0	0.020	0.000	23.784	0.306	0.306	0.000	0.000	0.000	0.000
54	B	57	LYS	1	0.843	0.903	28.156	10.996	10.996	0.000	0.000	0.000	0.000
55	B	58	ALA	0	-0.028	-0.002	30.057	0.359	0.359	0.000	0.000	0.000	0.000
56	B	59	ASN	0	-0.093	-0.044	30.982	0.548	0.548	0.000	0.000	0.000	0.000
57	B	60	VAL	0	0.003	0.006	31.867	-0.101	-0.101	0.000	0.000	0.000	0.000
58	B	61	ALA	0	0.029	0.013	33.913	0.247	0.247	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.922	0.956	34.672	8.352	8.352	0.000	0.000	0.000	0.000
60	B	63	ALA	0	0.055	0.017	34.100	-0.285	-0.285	0.000	0.000	0.000	0.000
61	B	64	GLY	0	0.035	0.022	32.672	-0.201	-0.201	0.000	0.000	0.000	0.000
62	B	65	LEU	0	-0.012	0.002	29.919	-0.226	-0.226	0.000	0.000	0.000	0.000
63	B	66	VAL	0	0.041	0.018	26.692	-0.361	-0.361	0.000	0.000	0.000	0.000
64	B	67	ASP	-1	-0.805	-0.872	26.486	-11.022	-11.022	0.000	0.000	0.000	0.000
65	B	68	ASP	-1	-0.847	-0.907	26.660	-11.276	-11.276	0.000	0.000	0.000	0.000
66	B	69	PHE	0	0.012	-0.011	24.641	-0.353	-0.353	0.000	0.000	0.000	0.000
67	B	70	GLU	-1	-0.899	-0.942	21.890	-13.753	-13.753	0.000	0.000	0.000	0.000
68	B	71	LYS	1	0.817	0.886	21.555	10.393	10.393	0.000	0.000	0.000	0.000
69	B	72	LYS	1	0.814	0.903	22.749	10.973	10.973	0.000	0.000	0.000	0.000
70	B	73	PHE	0	-0.010	0.009	15.573	-0.412	-0.412	0.000	0.000	0.000	0.000
71	B	74	ASN	0	-0.030	-0.025	17.417	-1.894	-1.894	0.000	0.000	0.000	0.000
72	B	75	ALA	0	-0.013	-0.013	17.610	0.555	0.555	0.000	0.000	0.000	0.000
73	B	76	LEU	0	-0.002	0.009	18.433	0.051	0.051	0.000	0.000	0.000	0.000
74	B	77	LYS	1	0.908	0.949	14.861	18.209	18.209	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.021	0.010	13.855	0.749	0.749	0.000	0.000	0.000	0.000
76	B	79	PRO	0	-0.025	0.001	13.451	-1.319	-1.319	0.000	0.000	0.000	0.000
77	B	80	ILE	0	0.015	0.001	8.085	-0.584	-0.584	0.000	0.000	0.000	0.000
78	B	81	PRO	0	-0.029	-0.007	11.181	1.266	1.266	0.000	0.000	0.000	0.000
79	B	82	GLU	-1	-0.797	-0.894	12.958	-15.806	-15.806	0.000	0.000	0.000	0.000
80	B	83	ASP	-1	-0.792	-0.864	13.457	-18.237	-18.237	0.000	0.000	0.000	0.000
81	B	84	LYS	1	0.785	0.875	15.236	15.055	15.055	0.000	0.000	0.000	0.000
82	B	85	TYR	0	-0.054	-0.039	15.391	1.078	1.078	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.029	-0.037	15.736	0.458	0.458	0.000	0.000	0.000	0.000
84	B	87	ALA	0	0.024	0.020	18.549	0.236	0.236	0.000	0.000	0.000	0.000
85	B	88	GLN	0	-0.071	-0.042	18.314	-0.226	-0.226	0.000	0.000	0.000	0.000
86	B	89	VAL	0	0.019	0.016	18.841	0.162	0.162	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.831	-0.923	21.721	-12.075	-12.075	0.000	0.000	0.000	0.000
88	B	91	ALA	0	-0.048	-0.033	24.878	0.525	0.525	0.000	0.000	0.000	0.000
89	B	92	GLU	-1	-0.872	-0.917	20.849	-13.891	-13.891	0.000	0.000	0.000	0.000
90	B	93	GLU	-1	-0.914	-0.960	24.985	-10.609	-10.609	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.897	0.943	27.064	9.799	9.799	0.000	0.000	0.000	0.000
92	B	95	GLU	-1	-0.889	-0.918	27.324	-10.180	-10.180	0.000	0.000	0.000	0.000
93	B	96	ASP	-1	-0.812	-0.893	26.692	-10.664	-10.664	0.000	0.000	0.000	0.000
94	B	97	VAL	0	-0.094	-0.047	29.867	0.418	0.418	0.000	0.000	0.000	0.000
95	B	98	LYS	1	0.778	0.865	32.794	8.524	8.524	0.000	0.000	0.000	0.000
96	B	99	SER	0	-0.004	-0.021	30.029	0.302	0.302	0.000	0.000	0.000	0.000
97	B	100	CYS	0	-0.017	-0.009	29.411	0.397	0.397	0.000	0.000	0.000	0.000
98	B	101	ALA	0	0.018	0.006	32.034	0.263	0.263	0.000	0.000	0.000	0.000
99	B	102	GLU	-1	-0.841	-0.892	34.760	-7.420	-7.420	0.000	0.000	0.000	0.000
100	B	103	PHE	0	0.050	0.023	35.538	0.251	0.251	0.000	0.000	0.000	0.000
101	B	104	LEU	0	0.011	0.004	31.815	0.211	0.211	0.000	0.000	0.000	0.000
102	B	105	THR	0	-0.058	-0.035	36.513	0.171	0.171	0.000	0.000	0.000	0.000
103	B	106	GLN	0	-0.043	-0.042	39.352	0.255	0.255	0.000	0.000	0.000	0.000
104	B	107	SER	0	-0.014	-0.019	38.704	0.253	0.253	0.000	0.000	0.000	0.000
105	B	108	LYS	1	0.941	0.985	35.150	8.426	8.426	0.000	0.000	0.000	0.000
106	B	109	THR	0	0.032	0.014	41.218	0.146	0.146	0.000	0.000	0.000	0.000
107	B	110	ARG	1	0.896	0.958	41.014	7.341	7.341	0.000	0.000	0.000	0.000
108	B	111	ILE	0	-0.035	-0.001	41.516	0.104	0.104	0.000	0.000	0.000	0.000
109	B	112	GLN	0	0.035	0.016	44.327	0.174	0.174	0.000	0.000	0.000	0.000
110	B	113	GLU	-1	-0.941	-0.970	46.700	-6.145	-6.145	0.000	0.000	0.000	0.000
111	B	114	TYR	0	-0.017	-0.015	45.526	0.082	0.082	0.000	0.000	0.000	0.000
112	B	115	GLU	-1	-0.905	-0.956	45.431	-6.639	-6.639	0.000	0.000	0.000	0.000
113	B	116	LYS	1	0.935	0.968	49.374	5.853	5.853	0.000	0.000	0.000	0.000
114	B	117	GLU	-1	-0.820	-0.891	52.333	-5.393	-5.393	0.000	0.000	0.000	0.000
115	B	118	LEU	0	-0.007	-0.020	49.508	0.110	0.110	0.000	0.000	0.000	0.000
116	B	119	GLU	-1	-0.795	-0.860	53.362	-5.493	-5.493	0.000	0.000	0.000	0.000
117	B	120	LYS	1	0.775	0.865	54.982	5.539	5.539	0.000	0.000	0.000	0.000
118	B	121	MET	0	-0.034	-0.018	56.067	0.069	0.069	0.000	0.000	0.000	0.000
119	B	122	ARG	1	0.756	0.869	54.996	5.521	5.521	0.000	0.000	0.000	0.000
120	B	123	ASN	0	-0.071	-0.023	58.118	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)