FMO DATABASE

FMODB ID: MVVMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-673960.818061
FMO2-HF: Nuclear repulsion	629952.210287
FMO2-HF: Total energy	-44008.607773
FMO2-MP2: Total energy	-44121.317977

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.
-31.02	-22.629	17.934	-11.638	-14.685	0.088

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 : 0.030 / q_NPA : -0.008

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	0.964	0.966	3.852	-0.102	1.787	-0.024	-1.049	-0.815	0.001
4	F	43	GLY	0	0.070	0.046	7.140	-0.431	-0.431	0.000	0.000	0.000	0.000
5	F	44	CYS	0	-0.181	-0.078	2.711	-2.312	1.734	4.052	-3.139	-4.958	0.016
6	F	45	GLU	-1	-0.796	-0.894	3.873	-1.919	-0.288	-0.012	-0.748	-0.872	-0.004
9	F	49	GLU	-1	-0.855	-0.925	3.862	0.943	3.649	-0.006	-0.923	-1.777	0.002
10	F	50	VAL	0	-0.031	0.002	5.819	-0.155	-0.111	-0.002	-0.002	-0.040	0.000
11	F	51	ASN	0	0.040	0.013	6.047	-0.405	-0.405	0.000	0.000	0.000	0.000
12	F	52	GLY	0	0.036	0.037	5.180	0.139	0.216	-0.002	-0.015	-0.059	0.000
13	F	54	LEU	0	-0.005	-0.013	1.794	-12.924	-17.009	13.206	-4.872	-4.249	0.053
14	F	55	LYS	1	0.871	0.916	2.510	-11.755	-10.103	0.720	-0.828	-1.544	0.020
15	F	56	CYS	0	-0.006	-0.001	4.021	1.544	1.975	0.002	-0.062	-0.371	0.000
16	F	57	SER	0	0.048	0.030	6.680	-1.313	-1.313	0.000	0.000	0.000	0.000
17	F	58	PRO	0	0.002	-0.023	9.168	0.235	0.235	0.000	0.000	0.000	0.000
18	F	59	LYS	1	0.908	0.961	12.182	-0.379	-0.379	0.000	0.000	0.000	0.000
19	F	60	LEU	0	-0.048	0.004	9.906	-0.037	-0.037	0.000	0.000	0.000	0.000
20	F	61	PHE	0	0.011	0.013	12.611	-0.044	-0.044	0.000	0.000	0.000	0.000
21	F	62	ILE	0	-0.012	-0.015	6.728	0.273	0.273	0.000	0.000	0.000	0.000
22	F	63	LEU	0	-0.010	-0.010	10.395	-0.559	-0.559	0.000	0.000	0.000	0.000
23	F	64	LEU	0	-0.010	-0.007	10.010	0.524	0.524	0.000	0.000	0.000	0.000
24	F	65	GLU	-1	-0.802	-0.894	12.180	0.867	0.867	0.000	0.000	0.000	0.000
25	F	66	ARG	1	0.779	0.887	13.555	-0.926	-0.926	0.000	0.000	0.000	0.000
26	F	67	ASN	0	-0.043	-0.028	14.497	-0.044	-0.044	0.000	0.000	0.000	0.000
27	F	68	ASP	-1	-0.854	-0.931	15.959	0.819	0.819	0.000	0.000	0.000	0.000
28	F	69	ILE	0	-0.003	-0.014	17.800	0.023	0.023	0.000	0.000	0.000	0.000
29	F	70	ARG	1	0.860	0.931	8.990	-1.446	-1.446	0.000	0.000	0.000	0.000
30	F	71	GLN	0	-0.003	-0.006	12.642	-0.278	-0.278	0.000	0.000	0.000	0.000
31	F	72	VAL	0	-0.005	0.000	8.077	0.209	0.209	0.000	0.000	0.000	0.000
32	F	73	GLY	0	0.018	0.026	7.168	-0.489	-0.489	0.000	0.000	0.000	0.000
33	F	74	VAL	0	-0.035	-0.022	7.007	0.885	0.885	0.000	0.000	0.000	0.000
34	F	76	LEU	0	0.015	0.003	9.582	-0.417	-0.417	0.000	0.000	0.000	0.000
35	F	77	PRO	0	0.019	-0.001	13.327	0.033	0.033	0.000	0.000	0.000	0.000
36	F	78	SER	0	0.032	0.012	15.845	-0.129	-0.129	0.000	0.000	0.000	0.000
37	F	79	CYS	0	-0.024	0.018	14.540	-0.043	-0.043	0.000	0.000	0.000	0.000
38	F	80	PRO	0	0.027	0.009	17.173	-0.099	-0.099	0.000	0.000	0.000	0.000
39	F	81	PRO	0	0.061	0.028	20.385	0.011	0.011	0.000	0.000	0.000	0.000
40	F	82	GLY	0	0.032	0.022	23.268	-0.032	-0.032	0.000	0.000	0.000	0.000
41	F	83	TYR	0	-0.057	-0.043	17.706	0.062	0.062	0.000	0.000	0.000	0.000
42	F	84	PHE	0	0.026	0.016	20.780	-0.035	-0.035	0.000	0.000	0.000	0.000
43	F	85	ASP	-1	-0.838	-0.930	19.369	0.777	0.777	0.000	0.000	0.000	0.000
44	F	86	ALA	0	-0.016	-0.007	19.248	0.059	0.059	0.000	0.000	0.000	0.000
45	F	87	ARG	1	0.959	0.982	18.095	-0.480	-0.480	0.000	0.000	0.000	0.000
46	F	88	ASN	0	-0.019	0.005	16.682	-0.025	-0.025	0.000	0.000	0.000	0.000
47	F	89	PRO	0	0.011	-0.003	17.991	0.006	0.006	0.000	0.000	0.000	0.000
48	F	90	ASP	-1	-0.905	-0.957	15.088	0.366	0.366	0.000	0.000	0.000	0.000
49	F	91	MET	0	-0.064	-0.021	10.134	0.219	0.219	0.000	0.000	0.000	0.000
50	F	92	ASN	0	-0.017	-0.005	13.382	-0.141	-0.141	0.000	0.000	0.000	0.000
51	F	93	LYS	1	0.887	0.930	12.762	-0.867	-0.867	0.000	0.000	0.000	0.000
52	F	95	ILE	0	-0.010	0.003	16.490	0.102	0.102	0.000	0.000	0.000	0.000
53	F	96	LYS	1	0.940	0.974	18.418	-1.126	-1.126	0.000	0.000	0.000	0.000
54	F	97	CYS	0	-0.067	-0.025	20.675	-0.093	-0.093	0.000	0.000	0.000	0.000
55	F	98	LYS	1	0.925	0.951	24.403	-0.474	-0.474	0.000	0.000	0.000	0.000
56	F	99	ILE	0	0.015	0.010	27.154	-0.031	-0.031	0.000	0.000	0.000	0.000
57	F	100	GLU	-1	-0.785	-0.867	30.445	0.346	0.346	0.000	0.000	0.000	0.000
58	F	101	HIS	0	-0.028	-0.029	33.103	-0.002	-0.002	0.000	0.000	0.000	0.000
59	F	102	CYS	0	-0.004	-0.028	29.814	0.032	0.032	0.000	0.000	0.000	0.000
60	F	103	GLU	-1	-0.849	-0.934	28.617	0.397	0.397	0.000	0.000	0.000	0.000
61	F	104	ALA	0	-0.010	-0.007	26.909	0.046	0.046	0.000	0.000	0.000	0.000
62	F	106	PHE	0	0.006	0.023	25.676	0.042	0.042	0.000	0.000	0.000	0.000
63	F	107	SER	0	-0.012	-0.020	25.417	0.018	0.018	0.000	0.000	0.000	0.000
64	F	108	HIS	0	0.022	0.025	25.015	0.005	0.005	0.000	0.000	0.000	0.000
65	F	109	ASN	0	-0.044	-0.040	27.914	-0.005	-0.005	0.000	0.000	0.000	0.000
66	F	110	PHE	0	0.000	0.019	30.221	-0.023	-0.023	0.000	0.000	0.000	0.000
67	F	112	THR	0	-0.008	-0.028	28.633	-0.022	-0.022	0.000	0.000	0.000	0.000
68	F	113	LYS	1	0.855	0.933	31.597	-0.315	-0.315	0.000	0.000	0.000	0.000
69	F	114	CYS	0	-0.031	-0.002	32.989	-0.002	-0.002	0.000	0.000	0.000	0.000
70	F	115	LYS	1	0.915	0.967	33.073	-0.298	-0.298	0.000	0.000	0.000	0.000
71	F	116	GLU	-1	-0.818	-0.902	34.410	0.257	0.257	0.000	0.000	0.000	0.000
72	F	117	GLY	0	-0.019	-0.019	37.167	0.001	0.001	0.000	0.000	0.000	0.000
73	F	118	LEU	0	-0.061	-0.031	37.292	-0.008	-0.008	0.000	0.000	0.000	0.000
74	F	119	TYR	0	0.044	0.019	39.426	0.003	0.003	0.000	0.000	0.000	0.000
75	F	120	LEU	0	-0.023	0.005	34.988	0.005	0.005	0.000	0.000	0.000	0.000
76	F	121	HIS	0	0.049	0.024	38.385	-0.016	-0.016	0.000	0.000	0.000	0.000
77	F	122	LYS	1	0.941	0.943	38.227	-0.186	-0.186	0.000	0.000	0.000	0.000
78	F	123	GLY	0	0.051	0.053	34.704	0.001	0.001	0.000	0.000	0.000	0.000
79	F	124	ARG	1	0.833	0.888	34.212	-0.290	-0.290	0.000	0.000	0.000	0.000
80	F	126	TYR	0	-0.002	-0.006	37.368	0.001	0.001	0.000	0.000	0.000	0.000
81	F	127	PRO	0	0.014	-0.001	40.945	0.002	0.002	0.000	0.000	0.000	0.000
82	F	128	ALA	0	0.012	0.002	43.104	-0.008	-0.008	0.000	0.000	0.000	0.000
83	F	129	CYS	0	-0.027	-0.019	44.246	0.005	0.005	0.000	0.000	0.000	0.000
84	F	130	PRO	0	-0.044	-0.017	43.790	-0.007	-0.007	0.000	0.000	0.000	0.000
85	F	131	GLU	-1	-0.907	-0.940	46.413	0.145	0.145	0.000	0.000	0.000	0.000
86	F	132	GLY	0	-0.013	-0.016	46.179	-0.007	-0.007	0.000	0.000	0.000	0.000
87	F	133	SER	0	-0.050	-0.012	42.681	0.009	0.009	0.000	0.000	0.000	0.000
88	F	134	SER	0	0.011	0.002	44.080	0.010	0.010	0.000	0.000	0.000	0.000
89	F	135	ALA	0	0.018	0.019	46.434	-0.003	-0.003	0.000	0.000	0.000	0.000
90	F	136	ALA	0	0.012	-0.028	47.979	-0.005	-0.005	0.000	0.000	0.000	0.000
91	F	137	ASN	0	-0.026	-0.010	48.513	-0.008	-0.008	0.000	0.000	0.000	0.000
92	F	138	GLY	0	0.046	0.039	45.329	0.004	0.004	0.000	0.000	0.000	0.000
93	F	139	THR	0	-0.005	-0.008	45.472	-0.003	-0.003	0.000	0.000	0.000	0.000
94	F	140	MET	0	-0.041	-0.003	41.027	0.006	0.006	0.000	0.000	0.000	0.000
95	F	141	GLU	-1	-0.859	-0.931	36.668	0.274	0.274	0.000	0.000	0.000	0.000
96	F	142	CYS	0	-0.076	-0.017	38.997	-0.007	-0.007	0.000	0.000	0.000	0.000

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