FMO DATABASE

FMODB ID: 66V7Z

Calculation Name: 4D3G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3G

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G229

Base Structure: X-ray

Registration Date: 2023-06-19

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479664.801469
FMO2-HF: Nuclear repulsion	448331.507114
FMO2-HF: Total energy	-31333.294355
FMO2-MP2: Total energy	-31421.703616

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-30.364	-18.997	6.238	-7.758	-9.842	-0.054

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.001

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	A	2	LYS	1	0.941	0.976	3.830	-3.968	-0.819	-0.020	-1.585	-1.543	0.009
4	A	3	MET	0	0.006	0.005	6.556	0.080	0.080	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.006	0.008	9.775	-0.138	-0.138	0.000	0.000	0.000	0.000
6	A	5	ILE	0	-0.012	-0.009	13.166	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.024	0.003	16.353	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.022	-0.013	19.130	0.002	0.002	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.005	0.001	22.649	0.003	0.003	0.000	0.000	0.000	0.000
10	A	9	GLN	0	0.107	0.040	24.963	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.782	-0.884	28.545	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.041	0.015	30.008	0.002	0.002	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.764	-0.876	28.233	0.027	0.027	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.085	-0.071	26.248	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	GLN	0	-0.061	-0.042	26.238	0.007	0.007	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.773	-0.890	27.725	0.051	0.051	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.013	0.010	21.030	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.042	-0.035	22.889	0.019	0.019	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.911	-0.952	23.454	0.101	0.101	0.000	0.000	0.000	0.000
20	A	19	GLN	0	-0.056	-0.052	23.285	0.017	0.017	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.005	0.002	17.569	0.019	0.019	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.008	0.011	18.967	0.036	0.036	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.889	0.952	20.631	-0.098	-0.098	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.008	0.006	17.479	0.008	0.008	0.000	0.000	0.000	0.000
25	A	24	ASN	0	-0.057	-0.017	15.580	0.019	0.019	0.000	0.000	0.000	0.000
26	A	25	PHE	0	0.034	0.015	12.235	0.074	0.074	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.964	0.981	13.983	-0.264	-0.264	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.029	0.020	14.346	0.034	0.034	0.000	0.000	0.000	0.000
29	A	28	THR	0	-0.066	-0.041	16.626	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	29	LYS	1	0.958	0.990	18.189	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.002	-0.006	18.446	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.005	-0.002	22.353	0.004	0.004	0.000	0.000	0.000	0.000
33	A	32	THR	0	-0.016	-0.027	25.639	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	33	THR	0	0.022	0.032	27.900	0.002	0.002	0.000	0.000	0.000	0.000
35	A	41	ASN	0	-0.073	-0.063	27.624	0.002	0.002	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.032	-0.016	25.087	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	43	THR	0	0.026	0.014	19.904	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.026	-0.014	18.737	0.003	0.003	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.006	-0.001	14.364	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.057	-0.038	13.421	0.030	0.030	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.061	0.046	9.078	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.033	-0.014	9.028	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	49	ASN	0	0.025	-0.001	3.949	-0.625	-0.551	0.000	-0.053	-0.020	0.000
44	A	50	ASP	-1	-0.909	-0.957	2.593	-7.545	-3.649	0.560	-2.117	-2.338	-0.020
45	A	51	ASP	-1	-0.877	-0.939	4.711	-0.177	0.018	-0.001	-0.014	-0.180	0.000
46	A	52	ARG	1	0.835	0.920	7.265	-0.116	-0.116	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.006	-0.004	8.540	0.085	0.085	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.858	-0.937	11.120	0.035	0.035	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.948	-0.971	13.296	0.259	0.259	0.000	0.000	0.000	0.000
50	A	56	ILE	0	0.002	-0.010	13.457	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.004	-0.008	14.751	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.001	0.011	17.291	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.020	-0.007	18.445	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.010	-0.017	17.454	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.017	0.000	21.453	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	62	GLN	0	-0.060	-0.024	23.353	0.001	0.001	0.000	0.000	0.000	0.000
57	A	63	THR	0	-0.081	-0.020	24.158	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	64	CYS	0	-0.119	-0.061	25.426	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	65	GLY	0	0.046	0.019	25.889	0.000	0.000	0.000	0.000	0.000	0.000
60	A	66	ASN	0	-0.030	-0.025	27.776	0.000	0.000	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.922	0.981	29.948	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	93	VAL	0	-0.012	-0.026	34.081	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	94	GLY	0	0.049	0.045	30.965	0.004	0.004	0.000	0.000	0.000	0.000
64	A	95	GLY	0	-0.034	-0.020	28.135	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	96	ALA	0	0.010	0.004	22.869	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	97	THR	0	-0.040	-0.018	21.444	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	98	VAL	0	-0.001	0.000	15.864	0.001	0.001	0.000	0.000	0.000	0.000
68	A	99	PHE	0	-0.022	0.005	15.427	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.027	0.007	9.649	0.041	0.041	0.000	0.000	0.000	0.000
70	A	101	MET	0	-0.044	-0.027	10.385	-0.068	-0.068	0.000	0.000	0.000	0.000
71	A	102	PRO	0	-0.001	-0.004	6.548	0.358	0.358	0.000	0.000	0.000	0.000
72	A	103	VAL	0	0.007	0.002	2.911	-0.911	-0.266	0.095	-0.174	-0.565	0.001
73	A	104	ASP	-1	-0.878	-0.924	3.159	-5.122	-3.320	0.543	-0.832	-1.513	-0.005
74	A	105	ALA	0	-0.057	-0.043	2.016	-14.664	-13.792	5.034	-2.827	-3.078	-0.037
75	A	106	PHE	0	0.000	0.007	3.392	1.501	2.168	0.028	-0.154	-0.541	-0.002
76	A	107	HIS	0	0.002	-0.004	4.547	0.538	0.605	-0.001	-0.002	-0.064	0.000
77	A	108	GLN	0	-0.024	-0.015	8.025	0.220	0.220	0.000	0.000	0.000	0.000
78	A	109	PHE	0	0.023	0.024	11.044	0.054	0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)