FMO DATABASE

FMODB ID: M3KKZ

Calculation Name: 3CZC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CZC

Chain ID: A

ChEMBL ID:

UniProt ID: Q93DB0

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-621179.43061
FMO2-HF: Nuclear repulsion	585080.485358
FMO2-HF: Total energy	-36098.945252
FMO2-MP2: Total energy	-36199.455284

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-22.526	-17.239	18.985	-9.926	-14.347	-0.093

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.030

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

Sort

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	A	3	LYS	1	0.942	0.975	3.821	-1.452	-0.169	-0.001	-0.461	-0.821	0.001
4	A	4	VAL	0	-0.004	-0.018	5.916	0.366	0.366	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.012	-0.006	9.203	0.142	0.142	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.013	-0.016	12.408	0.021	0.021	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.005	-0.002	15.471	0.047	0.047	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.059	-0.031	18.521	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.034	0.014	21.707	0.007	0.007	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.011	-0.013	22.958	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.083	0.043	23.941	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	MET	0	0.046	0.014	21.397	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.010	0.007	21.359	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.024	-0.013	21.871	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.046	0.022	18.931	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.042	-0.020	17.153	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.017	0.001	17.249	-0.055	-0.055	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.038	0.010	17.129	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.933	0.978	12.625	0.605	0.605	0.000	0.000	0.000	0.000
20	A	20	MET	0	-0.017	0.002	13.124	-0.115	-0.115	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.892	0.954	13.982	0.338	0.338	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.017	0.007	10.992	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.844	-0.917	8.523	-1.550	-1.550	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.039	-0.018	9.527	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.063	0.020	11.647	0.033	0.033	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.006	-0.001	6.675	0.067	0.067	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.846	0.916	6.696	1.670	1.670	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.070	-0.023	8.320	0.208	0.208	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.044	-0.017	8.662	0.117	0.117	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.028	-0.004	7.180	0.120	0.120	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.028	-0.007	2.433	-0.409	-0.046	1.000	-0.235	-1.128	0.000
32	A	32	SER	0	0.009	-0.011	2.509	-1.272	-0.232	0.443	-0.456	-1.029	-0.005
33	A	33	ASP	-1	-0.909	-0.955	2.107	-11.888	-10.142	11.064	-5.400	-7.410	-0.036
34	A	34	ILE	0	0.003	-0.002	2.190	-8.160	-7.660	6.481	-3.324	-3.657	-0.053
35	A	35	GLU	-1	-0.923	-0.946	4.235	0.998	1.360	-0.001	-0.038	-0.323	0.000
36	A	36	SER	0	0.012	-0.009	5.425	0.109	0.109	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.059	-0.030	9.060	0.211	0.211	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.012	-0.012	11.871	-0.055	-0.055	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.070	-0.010	15.491	0.032	0.032	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.025	0.032	18.419	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.060	0.015	20.573	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.004	-0.008	22.168	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.866	-0.946	20.147	-0.182	-0.182	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.028	0.002	17.903	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.773	0.894	18.466	0.146	0.146	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.020	-0.005	20.215	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.016	0.002	15.028	0.022	0.022	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.036	0.014	14.464	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.002	0.009	14.035	-0.062	-0.062	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.084	-0.034	11.122	0.057	0.057	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.054	-0.029	9.025	0.159	0.159	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.797	-0.871	5.666	-2.155	-2.162	-0.001	-0.012	0.021	0.000
53	A	53	ILE	0	-0.040	-0.019	7.584	0.190	0.190	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.008	0.008	10.998	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.007	0.013	13.610	0.048	0.048	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.019	0.007	16.362	0.025	0.025	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.004	0.007	20.132	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.065	-0.016	23.332	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.029	-0.007	24.303	0.014	0.014	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.033	-0.026	24.982	0.015	0.015	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.029	0.042	20.233	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	HIS	0	0.037	0.024	23.309	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.883	-0.924	24.719	-0.132	-0.132	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.081	-0.074	19.033	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.910	-0.937	20.996	-0.171	-0.171	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.024	0.012	21.619	0.018	0.018	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.827	0.919	19.942	0.144	0.144	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.006	-0.017	14.164	0.004	0.004	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.005	0.001	14.786	0.013	0.013	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.024	0.027	12.268	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.820	0.901	10.968	0.476	0.476	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.032	0.017	13.698	-0.078	-0.078	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.026	-0.026	12.678	0.031	0.031	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.020	0.010	16.830	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.053	-0.027	17.728	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.890	-0.944	21.611	-0.194	-0.194	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.034	-0.025	24.132	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.020	-0.006	19.705	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	79	MET	0	-0.063	-0.025	20.161	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.878	-0.938	22.143	-0.254	-0.254	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.829	-0.936	18.576	-0.412	-0.412	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.023	-0.011	18.502	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.762	-0.870	19.910	-0.276	-0.276	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.009	-0.006	15.066	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.960	0.980	14.910	0.234	0.234	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.031	-0.002	15.518	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.933	0.967	17.196	0.283	0.283	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.015	-0.013	10.677	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.964	-0.986	12.714	-0.291	-0.291	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.973	-0.983	14.161	-0.204	-0.204	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.021	0.001	13.138	0.027	0.027	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.051	-0.028	7.694	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.942	0.992	11.255	0.241	0.241	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)