FMO DATABASE

FMODB ID: 2NLZR

Calculation Name: 3FAC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FAC

Chain ID: A

ChEMBL ID:

UniProt ID: Q3J4G5

Base Structure: X-ray

Registration Date: 2023-09-22

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	109
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861738.55473
FMO2-HF: Nuclear repulsion	817342.167517
FMO2-HF: Total energy	-44396.387213
FMO2-MP2: Total energy	-44521.453847

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.
-24.911	-13.57	4.255	-5.359	-10.24	-0.021

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 : 0.046 / q_NPA : 0.018

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	GLY	0	0.021	0.021	3.667	-0.827	0.977	-0.010	-0.883	-0.912	0.002
4	A	4	THR	0	-0.024	-0.019	5.590	0.121	0.121	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.136	-0.103	9.195	0.147	0.147	0.000	0.000	0.000	0.000
6	A	6	HIS	0	0.096	0.028	12.254	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.372	-0.201	14.674	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.090	0.051	13.626	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.007	-0.037	14.707	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.008	-0.031	12.215	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.835	-0.905	8.278	-0.634	-0.634	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.069	-0.025	6.312	0.287	0.287	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.873	-0.951	2.827	-8.398	-6.784	0.177	-0.883	-0.908	-0.010
14	A	14	VAL	0	-0.033	-0.025	3.216	1.914	2.657	0.017	-0.202	-0.558	0.000
15	A	15	GLU	-1	-0.856	-0.909	2.516	-13.551	-10.335	1.189	-2.015	-2.391	-0.023
16	A	16	LEU	0	-0.067	-0.043	3.811	0.060	0.843	0.154	-0.171	-0.766	0.001
17	A	17	LEU	0	-0.034	-0.014	6.401	-0.154	-0.154	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.030	-0.018	9.984	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.019	0.017	6.222	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.041	-0.005	2.806	-1.288	-0.280	0.668	-0.336	-1.340	0.002
21	A	21	ALA	0	-0.023	0.003	8.042	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.919	-0.958	11.248	0.451	0.451	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.036	0.014	10.333	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.914	0.967	12.203	-0.309	-0.309	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.980	0.981	15.128	-0.246	-0.246	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.056	0.019	17.759	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.785	-0.896	20.325	0.082	0.082	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.043	-0.028	22.795	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.022	-0.006	24.954	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.044	0.018	19.856	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	CYS	0	0.006	-0.029	19.880	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.934	0.973	20.595	-0.035	-0.035	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.876	0.929	22.999	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.837	0.943	16.867	0.028	0.028	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.058	0.030	18.981	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.047	-0.021	13.349	0.023	0.023	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.023	0.021	11.533	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.054	-0.030	11.094	0.059	0.059	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.064	0.034	7.751	0.033	0.033	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.022	-0.018	9.841	-0.152	-0.152	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.066	0.032	7.729	0.179	0.179	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.972	1.003	9.648	0.318	0.318	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.021	0.010	11.008	-0.201	-0.201	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.037	-0.027	12.351	-0.058	-0.058	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.846	-0.921	7.776	-0.967	-0.967	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.046	-0.008	6.825	-0.765	-0.765	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.889	0.939	6.505	1.978	1.978	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.024	-0.024	8.253	-0.293	-0.293	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.025	0.000	7.505	0.166	0.166	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.837	0.896	10.536	0.653	0.653	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.092	0.043	13.560	-0.062	-0.062	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.019	-0.004	15.935	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.886	-0.943	16.974	-0.282	-0.282	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.034	-0.033	18.457	0.042	0.042	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.016	0.017	14.294	0.021	0.021	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.022	-0.004	18.688	0.027	0.027	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.040	-0.005	19.794	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.022	-0.015	21.328	0.024	0.024	0.000	0.000	0.000	0.000
59	A	59	GLN	0	0.049	0.019	22.472	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.007	-0.006	23.341	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.042	0.032	27.343	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.033	-0.011	26.810	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.896	0.944	26.438	0.090	0.090	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.012	0.043	23.294	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.028	0.008	20.903	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.833	0.927	18.578	0.192	0.192	0.000	0.000	0.000	0.000
67	A	67	HIS	0	0.026	0.031	17.753	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	68	TRP	0	0.085	0.034	15.388	0.016	0.016	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.035	-0.020	15.930	0.014	0.014	0.000	0.000	0.000	0.000
70	A	70	CYS	0	-0.008	-0.045	15.643	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.917	0.963	17.502	0.194	0.194	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.001	-0.027	19.807	0.025	0.025	0.000	0.000	0.000	0.000
73	A	73	CYM	-1	-0.568	-0.566	16.658	-0.179	-0.179	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.007	0.012	19.262	0.023	0.023	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.016	-0.002	12.943	0.021	0.021	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.056	-0.062	13.387	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.064	0.033	10.902	0.103	0.103	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.091	0.051	10.363	0.042	0.042	0.000	0.000	0.000	0.000
79	A	79	HIS	0	-0.057	-0.014	12.187	0.015	0.015	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.032	0.039	14.395	0.036	0.036	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.893	0.946	13.632	-0.087	-0.087	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.985	0.969	18.107	0.019	0.019	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.071	-0.031	20.583	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ASN	0	0.068	0.024	18.081	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.002	-0.010	18.270	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.855	-0.930	17.510	-0.306	-0.306	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.919	-0.962	13.947	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.017	-0.021	10.839	0.053	0.053	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.096	-0.057	11.817	0.105	0.105	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.051	0.012	6.318	-0.162	-0.162	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.045	-0.030	9.496	0.396	0.396	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.077	0.005	6.875	-0.071	-0.071	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.012	-0.006	6.943	0.216	0.216	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.055	-0.010	6.319	-0.129	-0.129	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.045	-0.014	2.346	-2.654	-1.512	2.047	-0.669	-2.521	0.008
96	A	96	GLU	-1	-0.903	-0.968	4.006	0.034	0.418	0.000	-0.029	-0.354	0.000
97	A	97	GLY	0	-0.018	-0.008	3.758	-0.765	-0.462	0.004	-0.108	-0.199	-0.001
98	A	98	VAL	0	-0.027	0.000	3.661	-0.147	0.197	0.009	-0.063	-0.291	0.000
99	A	99	ASN	0	-0.004	0.006	6.294	-0.060	-0.060	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.010	-0.012	10.036	0.037	0.037	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.951	0.976	11.475	-0.199	-0.199	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.899	-0.959	10.496	0.279	0.279	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.059	-0.023	8.102	0.025	0.025	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.018	0.005	11.880	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.941	-0.977	15.545	0.234	0.234	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.055	-0.027	13.599	0.036	0.036	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.017	0.002	16.835	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	108	TRP	0	0.053	0.023	18.719	0.014	0.014	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.078	-0.036	19.076	-0.016	-0.016	0.000	0.000	0.000	0.000

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