FMO DATABASE

FMODB ID: 944Y2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-673912.868477
FMO2-HF: Nuclear repulsion	629904.981736
FMO2-HF: Total energy	-44007.886741
FMO2-MP2: Total energy	-44120.655307

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.
-34.55	-24.851	15.675	-11.617	-13.755	0.102

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 : 0.047 / q_NPA : -0.006

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	0.970	0.969	3.789	-1.207	0.952	-0.028	-1.242	-0.889	0.004
4	F	43	GLY	0	0.073	0.045	7.215	-0.133	-0.133	0.000	0.000	0.000	0.000
5	F	44	CYS	0	-0.141	-0.059	2.778	-1.051	2.583	3.970	-2.979	-4.625	0.023
6	F	45	GLU	-1	-0.797	-0.886	3.819	-3.540	-1.692	-0.019	-0.833	-0.996	-0.003
9	F	49	GLU	-1	-0.865	-0.931	3.804	-0.836	2.278	-0.027	-1.074	-2.013	0.006
10	F	50	VAL	0	-0.023	-0.008	5.840	-0.030	0.006	-0.002	-0.002	-0.032	0.000
11	F	51	ASN	0	0.035	0.009	6.657	-0.558	-0.558	0.000	0.000	0.000	0.000
12	F	52	GLY	0	0.042	0.038	5.079	0.379	0.379	0.000	0.000	0.000	0.000
13	F	54	LEU	0	0.014	-0.001	1.811	-12.822	-16.274	11.299	-4.439	-3.408	0.052
14	F	55	LYS	1	0.892	0.923	2.607	-10.742	-8.772	0.483	-0.997	-1.455	0.020
15	F	56	CYS	0	-0.055	-0.011	4.114	-0.691	-0.301	-0.001	-0.051	-0.337	0.000
16	F	57	SER	0	0.044	0.012	6.628	-0.825	-0.825	0.000	0.000	0.000	0.000
17	F	58	PRO	0	-0.005	-0.006	9.003	0.346	0.346	0.000	0.000	0.000	0.000
18	F	59	LYS	1	0.911	0.955	11.855	0.069	0.069	0.000	0.000	0.000	0.000
19	F	60	LEU	0	-0.072	-0.009	10.108	0.009	0.009	0.000	0.000	0.000	0.000
20	F	61	PHE	0	0.052	0.030	12.296	0.021	0.021	0.000	0.000	0.000	0.000
21	F	62	ILE	0	-0.036	-0.019	6.406	0.238	0.238	0.000	0.000	0.000	0.000
22	F	63	LEU	0	-0.015	-0.014	10.118	-0.452	-0.452	0.000	0.000	0.000	0.000
23	F	64	LEU	0	-0.040	-0.028	9.939	0.410	0.410	0.000	0.000	0.000	0.000
24	F	65	GLU	-1	-0.847	-0.912	11.990	0.879	0.879	0.000	0.000	0.000	0.000
25	F	66	ARG	1	0.822	0.915	13.484	-1.079	-1.079	0.000	0.000	0.000	0.000
26	F	67	ASN	0	-0.033	-0.031	14.592	-0.041	-0.041	0.000	0.000	0.000	0.000
27	F	68	ASP	-1	-0.875	-0.934	16.314	0.861	0.861	0.000	0.000	0.000	0.000
28	F	69	ILE	0	-0.012	-0.017	17.614	0.011	0.011	0.000	0.000	0.000	0.000
29	F	70	ARG	1	0.889	0.947	8.970	-1.594	-1.594	0.000	0.000	0.000	0.000
30	F	71	GLN	0	0.003	0.005	12.785	-0.330	-0.330	0.000	0.000	0.000	0.000
31	F	72	VAL	0	0.001	0.005	7.801	0.329	0.329	0.000	0.000	0.000	0.000
32	F	73	GLY	0	0.019	0.022	6.941	-0.554	-0.554	0.000	0.000	0.000	0.000
33	F	74	VAL	0	-0.018	-0.018	7.113	0.329	0.329	0.000	0.000	0.000	0.000
34	F	76	LEU	0	0.008	-0.006	9.404	-0.455	-0.455	0.000	0.000	0.000	0.000
35	F	77	PRO	0	0.000	-0.007	13.148	0.017	0.017	0.000	0.000	0.000	0.000
36	F	78	SER	0	0.048	0.024	15.656	-0.072	-0.072	0.000	0.000	0.000	0.000
37	F	79	CYS	0	-0.009	0.028	14.665	-0.040	-0.040	0.000	0.000	0.000	0.000
38	F	80	PRO	0	0.008	-0.003	17.125	-0.088	-0.088	0.000	0.000	0.000	0.000
39	F	81	PRO	0	0.047	0.027	20.208	0.005	0.005	0.000	0.000	0.000	0.000
40	F	82	GLY	0	0.030	0.018	22.958	-0.020	-0.020	0.000	0.000	0.000	0.000
41	F	83	TYR	0	-0.060	-0.049	17.820	0.034	0.034	0.000	0.000	0.000	0.000
42	F	84	PHE	0	0.044	0.023	20.917	-0.043	-0.043	0.000	0.000	0.000	0.000
43	F	85	ASP	-1	-0.928	-0.979	19.738	0.668	0.668	0.000	0.000	0.000	0.000
44	F	86	ALA	0	-0.004	-0.007	19.386	0.056	0.056	0.000	0.000	0.000	0.000
45	F	87	ARG	1	1.003	1.022	18.563	-0.350	-0.350	0.000	0.000	0.000	0.000
46	F	88	ASN	0	-0.018	-0.015	16.657	0.069	0.069	0.000	0.000	0.000	0.000
47	F	89	PRO	0	0.002	0.001	17.570	0.001	0.001	0.000	0.000	0.000	0.000
48	F	90	ASP	-1	-0.892	-0.953	15.018	0.330	0.330	0.000	0.000	0.000	0.000
49	F	91	MET	0	-0.053	-0.018	10.543	0.215	0.215	0.000	0.000	0.000	0.000
50	F	92	ASN	0	-0.027	-0.007	13.056	-0.119	-0.119	0.000	0.000	0.000	0.000
51	F	93	LYS	1	0.916	0.948	12.726	-0.931	-0.931	0.000	0.000	0.000	0.000
52	F	95	ILE	0	-0.027	-0.012	16.328	0.142	0.142	0.000	0.000	0.000	0.000
53	F	96	LYS	1	0.952	0.980	18.891	-1.091	-1.091	0.000	0.000	0.000	0.000
54	F	97	CYS	0	-0.024	-0.005	20.868	-0.077	-0.077	0.000	0.000	0.000	0.000
55	F	98	LYS	1	0.920	0.952	24.551	-0.505	-0.505	0.000	0.000	0.000	0.000
56	F	99	ILE	0	0.011	-0.005	27.147	-0.031	-0.031	0.000	0.000	0.000	0.000
57	F	100	GLU	-1	-0.870	-0.905	30.163	0.338	0.338	0.000	0.000	0.000	0.000
58	F	101	HIS	0	-0.018	-0.034	33.072	-0.004	-0.004	0.000	0.000	0.000	0.000
59	F	102	CYS	0	0.037	0.023	29.971	0.024	0.024	0.000	0.000	0.000	0.000
60	F	103	GLU	-1	-0.863	-0.938	28.720	0.360	0.360	0.000	0.000	0.000	0.000
61	F	104	ALA	0	0.000	-0.007	26.663	0.043	0.043	0.000	0.000	0.000	0.000
62	F	106	PHE	0	-0.013	0.019	25.915	0.035	0.035	0.000	0.000	0.000	0.000
63	F	107	SER	0	-0.018	-0.027	25.579	0.025	0.025	0.000	0.000	0.000	0.000
64	F	108	HIS	0	0.033	0.047	25.194	-0.004	-0.004	0.000	0.000	0.000	0.000
65	F	109	ASN	0	-0.042	-0.051	28.036	0.004	0.004	0.000	0.000	0.000	0.000
66	F	110	PHE	0	0.000	-0.003	30.608	-0.010	-0.010	0.000	0.000	0.000	0.000
67	F	112	THR	0	-0.014	-0.018	28.918	-0.018	-0.018	0.000	0.000	0.000	0.000
68	F	113	LYS	1	0.912	0.953	31.403	-0.276	-0.276	0.000	0.000	0.000	0.000
69	F	114	CYS	0	-0.007	0.033	32.081	0.012	0.012	0.000	0.000	0.000	0.000
70	F	115	LYS	1	0.956	0.979	32.960	-0.280	-0.280	0.000	0.000	0.000	0.000
71	F	116	GLU	-1	-0.870	-0.937	34.414	0.216	0.216	0.000	0.000	0.000	0.000
72	F	117	GLY	0	-0.041	-0.017	37.122	0.004	0.004	0.000	0.000	0.000	0.000
73	F	118	LEU	0	-0.092	-0.051	36.852	-0.006	-0.006	0.000	0.000	0.000	0.000
74	F	119	TYR	0	0.067	0.028	39.112	-0.001	-0.001	0.000	0.000	0.000	0.000
75	F	120	LEU	0	-0.018	-0.009	34.805	0.010	0.010	0.000	0.000	0.000	0.000
76	F	121	HIS	0	0.023	0.013	38.505	-0.015	-0.015	0.000	0.000	0.000	0.000
77	F	122	LYS	1	0.973	0.962	38.257	-0.167	-0.167	0.000	0.000	0.000	0.000
78	F	123	GLY	0	0.027	0.037	34.832	0.003	0.003	0.000	0.000	0.000	0.000
79	F	124	ARG	1	0.851	0.915	33.677	-0.294	-0.294	0.000	0.000	0.000	0.000
80	F	126	TYR	0	-0.004	-0.014	37.491	0.004	0.004	0.000	0.000	0.000	0.000
81	F	127	PRO	0	0.019	0.001	40.977	-0.001	-0.001	0.000	0.000	0.000	0.000
82	F	128	ALA	0	0.011	0.003	42.811	-0.008	-0.008	0.000	0.000	0.000	0.000
83	F	129	CYS	0	-0.044	-0.021	44.205	0.003	0.003	0.000	0.000	0.000	0.000
84	F	130	PRO	0	-0.026	-0.008	43.574	-0.006	-0.006	0.000	0.000	0.000	0.000
85	F	131	GLU	-1	-0.911	-0.956	45.948	0.138	0.138	0.000	0.000	0.000	0.000
86	F	132	GLY	0	0.005	0.002	45.912	-0.007	-0.007	0.000	0.000	0.000	0.000
87	F	133	SER	0	-0.059	0.000	42.492	0.008	0.008	0.000	0.000	0.000	0.000
88	F	134	SER	0	0.024	0.007	44.155	0.009	0.009	0.000	0.000	0.000	0.000
89	F	135	ALA	0	0.015	-0.001	46.341	-0.003	-0.003	0.000	0.000	0.000	0.000
90	F	136	ALA	0	-0.003	-0.032	47.923	-0.006	-0.006	0.000	0.000	0.000	0.000
91	F	137	ASN	0	-0.005	-0.006	48.234	-0.009	-0.009	0.000	0.000	0.000	0.000
92	F	138	GLY	0	0.030	0.061	45.356	0.004	0.004	0.000	0.000	0.000	0.000
93	F	139	THR	0	-0.004	-0.019	45.564	-0.004	-0.004	0.000	0.000	0.000	0.000
94	F	140	MET	0	-0.044	-0.024	40.722	0.007	0.007	0.000	0.000	0.000	0.000
95	F	141	GLU	-1	-0.837	-0.917	36.875	0.216	0.216	0.000	0.000	0.000	0.000
96	F	142	CYS	0	-0.094	-0.021	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)