FMO DATABASE

FMODB ID: LZZL9

Calculation Name: 4CDK-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CDK

Chain ID: F

ChEMBL ID:

UniProt ID: Q2MKA7

Base Structure: X-ray

Registration Date: 2023-06-21

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-674418.524001
FMO2-HF: Nuclear repulsion	630411.717097
FMO2-HF: Total energy	-44006.806904
FMO2-MP2: Total energy	-44119.680793

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(F:40:CYS)

Summations of interaction energy for fragment #1(F:40:CYS)

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.
-36.839	-28.057	17.212	-11.493	-14.502	0.101

Interaction energy analysis for fragmet #1(F:40:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / 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

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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	F	42	LYS	1	0.961	0.964	3.523	-0.860	0.939	-0.017	-0.864	-0.918	0.003
4	F	43	GLY	0	0.063	0.043	7.084	-0.122	-0.122	0.000	0.000	0.000	0.000
5	F	44	CYS	0	-0.173	-0.076	2.718	-2.168	0.712	5.493	-3.266	-5.106	0.026
6	F	45	GLU	-1	-0.827	-0.899	3.819	-3.720	-1.666	-0.021	-0.940	-1.093	-0.004
9	F	49	GLU	-1	-0.886	-0.942	3.804	-2.181	0.868	-0.009	-1.052	-1.989	0.005
10	F	50	VAL	0	-0.034	-0.006	5.830	0.051	0.101	-0.002	-0.002	-0.046	0.000
11	F	51	ASN	0	0.011	-0.006	6.556	-0.447	-0.447	0.000	0.000	0.000	0.000
12	F	52	GLY	0	0.039	0.033	5.079	0.480	0.480	0.000	0.000	0.000	0.000
13	F	54	LEU	0	0.025	0.002	1.810	-13.087	-16.531	11.284	-4.333	-3.508	0.051
14	F	55	LYS	1	0.925	0.949	2.607	-11.153	-9.158	0.485	-0.987	-1.493	0.020
15	F	56	CYS	0	-0.050	-0.009	4.114	-0.547	-0.148	-0.001	-0.049	-0.349	0.000
16	F	57	SER	0	0.020	0.010	6.628	-0.873	-0.873	0.000	0.000	0.000	0.000
17	F	58	PRO	0	0.024	0.000	9.003	0.341	0.341	0.000	0.000	0.000	0.000
18	F	59	LYS	1	0.915	0.958	11.855	0.007	0.007	0.000	0.000	0.000	0.000
19	F	60	LEU	0	-0.079	-0.015	10.156	0.000	0.000	0.000	0.000	0.000	0.000
20	F	61	PHE	0	0.054	0.035	12.296	0.035	0.035	0.000	0.000	0.000	0.000
21	F	62	ILE	0	-0.020	-0.019	6.358	0.273	0.273	0.000	0.000	0.000	0.000
22	F	63	LEU	0	-0.020	-0.016	10.118	-0.463	-0.463	0.000	0.000	0.000	0.000
23	F	64	LEU	0	-0.038	-0.024	9.905	0.434	0.434	0.000	0.000	0.000	0.000
24	F	65	GLU	-1	-0.870	-0.910	11.943	0.871	0.871	0.000	0.000	0.000	0.000
25	F	66	ARG	1	0.867	0.935	13.439	-1.079	-1.079	0.000	0.000	0.000	0.000
26	F	67	ASN	0	-0.017	-0.034	14.223	0.014	0.014	0.000	0.000	0.000	0.000
27	F	68	ASP	-1	-0.879	-0.926	16.286	0.750	0.750	0.000	0.000	0.000	0.000
28	F	69	ILE	0	-0.006	-0.017	17.410	0.018	0.018	0.000	0.000	0.000	0.000
29	F	70	ARG	1	0.942	0.973	9.463	-1.168	-1.168	0.000	0.000	0.000	0.000
30	F	71	GLN	0	-0.032	-0.021	12.956	-0.286	-0.286	0.000	0.000	0.000	0.000
31	F	72	VAL	0	0.005	0.011	7.610	0.301	0.301	0.000	0.000	0.000	0.000
32	F	73	GLY	0	0.010	0.020	6.944	-0.536	-0.536	0.000	0.000	0.000	0.000
33	F	74	VAL	0	-0.006	-0.013	7.104	0.308	0.308	0.000	0.000	0.000	0.000
34	F	76	LEU	0	0.002	-0.008	9.404	-0.487	-0.487	0.000	0.000	0.000	0.000
35	F	77	PRO	0	-0.001	-0.002	13.148	0.025	0.025	0.000	0.000	0.000	0.000
36	F	78	SER	0	0.051	0.018	15.656	-0.073	-0.073	0.000	0.000	0.000	0.000
37	F	79	CYS	0	0.007	0.036	14.675	-0.042	-0.042	0.000	0.000	0.000	0.000
38	F	80	PRO	0	-0.007	-0.007	17.102	-0.094	-0.094	0.000	0.000	0.000	0.000
39	F	81	PRO	0	0.045	0.032	20.208	0.004	0.004	0.000	0.000	0.000	0.000
40	F	82	GLY	0	0.034	0.012	22.954	-0.021	-0.021	0.000	0.000	0.000	0.000
41	F	83	TYR	0	-0.049	-0.039	18.200	0.040	0.040	0.000	0.000	0.000	0.000
42	F	84	PHE	0	0.025	0.014	20.917	-0.046	-0.046	0.000	0.000	0.000	0.000
43	F	85	ASP	-1	-0.931	-0.978	19.732	0.746	0.746	0.000	0.000	0.000	0.000
44	F	86	ALA	0	-0.014	-0.018	19.386	0.053	0.053	0.000	0.000	0.000	0.000
45	F	87	ARG	1	1.005	1.024	18.864	-0.402	-0.402	0.000	0.000	0.000	0.000
46	F	88	ASN	0	-0.010	-0.015	16.471	0.038	0.038	0.000	0.000	0.000	0.000
47	F	89	PRO	0	-0.019	-0.009	17.570	0.000	0.000	0.000	0.000	0.000	0.000
48	F	90	ASP	-1	-0.886	-0.950	14.884	0.408	0.408	0.000	0.000	0.000	0.000
49	F	91	MET	0	-0.055	-0.027	10.398	0.220	0.220	0.000	0.000	0.000	0.000
50	F	92	ASN	0	-0.006	0.007	13.051	-0.115	-0.115	0.000	0.000	0.000	0.000
51	F	93	LYS	1	0.949	0.970	12.726	-1.062	-1.062	0.000	0.000	0.000	0.000
52	F	95	ILE	0	-0.028	-0.009	16.328	0.138	0.138	0.000	0.000	0.000	0.000
53	F	96	LYS	1	0.955	0.970	18.925	-1.039	-1.039	0.000	0.000	0.000	0.000
54	F	97	CYS	0	-0.035	-0.002	20.868	-0.076	-0.076	0.000	0.000	0.000	0.000
55	F	98	LYS	1	0.920	0.952	24.551	-0.526	-0.526	0.000	0.000	0.000	0.000
56	F	99	ILE	0	-0.008	-0.014	27.147	-0.034	-0.034	0.000	0.000	0.000	0.000
57	F	100	GLU	-1	-0.934	-0.950	30.163	0.338	0.338	0.000	0.000	0.000	0.000
58	F	101	HIS	0	-0.014	-0.032	33.072	-0.001	-0.001	0.000	0.000	0.000	0.000
59	F	102	CYS	0	0.037	0.022	29.971	0.025	0.025	0.000	0.000	0.000	0.000
60	F	103	GLU	-1	-0.850	-0.930	28.730	0.367	0.367	0.000	0.000	0.000	0.000
61	F	104	ALA	0	0.004	-0.009	26.671	0.043	0.043	0.000	0.000	0.000	0.000
62	F	106	PHE	0	-0.001	0.019	25.915	0.036	0.036	0.000	0.000	0.000	0.000
63	F	107	SER	0	-0.014	-0.025	25.579	0.024	0.024	0.000	0.000	0.000	0.000
64	F	108	HIS	0	0.024	0.046	24.937	-0.008	-0.008	0.000	0.000	0.000	0.000
65	F	109	ASN	0	-0.032	-0.049	28.036	0.007	0.007	0.000	0.000	0.000	0.000
66	F	110	PHE	0	-0.010	-0.001	30.547	-0.011	-0.011	0.000	0.000	0.000	0.000
67	F	112	THR	0	-0.026	-0.025	29.504	-0.017	-0.017	0.000	0.000	0.000	0.000
68	F	113	LYS	1	0.950	0.983	31.331	-0.286	-0.286	0.000	0.000	0.000	0.000
69	F	114	CYS	0	-0.009	0.023	32.081	0.011	0.011	0.000	0.000	0.000	0.000
70	F	115	LYS	1	0.996	1.004	32.815	-0.293	-0.293	0.000	0.000	0.000	0.000
71	F	116	GLU	-1	-0.889	-0.950	34.414	0.222	0.222	0.000	0.000	0.000	0.000
72	F	117	GLY	0	-0.046	-0.020	37.122	0.003	0.003	0.000	0.000	0.000	0.000
73	F	118	LEU	0	-0.098	-0.044	36.874	-0.006	-0.006	0.000	0.000	0.000	0.000
74	F	119	TYR	0	0.064	0.019	39.112	0.001	0.001	0.000	0.000	0.000	0.000
75	F	120	LEU	0	-0.021	-0.016	34.767	0.010	0.010	0.000	0.000	0.000	0.000
76	F	121	HIS	0	0.030	0.017	38.505	-0.016	-0.016	0.000	0.000	0.000	0.000
77	F	122	LYS	1	0.968	0.959	38.257	-0.177	-0.177	0.000	0.000	0.000	0.000
78	F	123	GLY	0	0.026	0.037	34.833	0.003	0.003	0.000	0.000	0.000	0.000
79	F	124	ARG	1	0.909	0.960	33.126	-0.304	-0.304	0.000	0.000	0.000	0.000
80	F	126	TYR	0	-0.003	-0.014	37.491	0.003	0.003	0.000	0.000	0.000	0.000
81	F	127	PRO	0	0.010	-0.005	40.977	-0.001	-0.001	0.000	0.000	0.000	0.000
82	F	128	ALA	0	0.033	0.014	42.811	-0.008	-0.008	0.000	0.000	0.000	0.000
83	F	129	CYS	0	-0.037	-0.028	44.198	0.004	0.004	0.000	0.000	0.000	0.000
84	F	130	PRO	0	-0.052	-0.014	43.545	-0.006	-0.006	0.000	0.000	0.000	0.000
85	F	131	GLU	-1	-0.891	-0.942	45.941	0.144	0.144	0.000	0.000	0.000	0.000
86	F	132	GLY	0	0.002	-0.002	45.939	-0.007	-0.007	0.000	0.000	0.000	0.000
87	F	133	SER	0	-0.084	-0.017	42.188	0.005	0.005	0.000	0.000	0.000	0.000
88	F	134	SER	0	0.026	-0.020	44.155	0.009	0.009	0.000	0.000	0.000	0.000
89	F	135	ALA	0	-0.004	-0.012	46.341	-0.002	-0.002	0.000	0.000	0.000	0.000
90	F	136	ALA	0	-0.019	-0.036	47.923	-0.005	-0.005	0.000	0.000	0.000	0.000
91	F	137	ASN	0	0.034	0.023	48.262	-0.007	-0.007	0.000	0.000	0.000	0.000
92	F	138	GLY	0	0.034	0.079	45.356	0.004	0.004	0.000	0.000	0.000	0.000
93	F	139	THR	0	-0.001	-0.017	45.564	-0.005	-0.005	0.000	0.000	0.000	0.000
94	F	140	MET	0	-0.039	-0.023	40.725	0.007	0.007	0.000	0.000	0.000	0.000
95	F	141	GLU	-1	-0.885	-0.953	37.828	0.212	0.212	0.000	0.000	0.000	0.000
96	F	142	CYS	0	-0.082	-0.003	39.657	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:40:CYS)