FMO DATABASE

FMODB ID: R5GM8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-481518.796287
FMO2-HF: Nuclear repulsion	450184.577491
FMO2-HF: Total energy	-31334.218795
FMO2-MP2: Total energy	-31422.63562

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.
-32.233	-24.998	14.744	-9.705	-12.274	-0.093

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 : -0.038 / q_NPA : -0.010

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	0.822	0.890	3.246	-2.592	0.442	0.015	-1.487	-1.562	0.007
4	A	3	MET	0	-0.006	0.000	6.687	0.267	0.267	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.013	0.015	10.198	-0.119	-0.119	0.000	0.000	0.000	0.000
6	A	5	ILE	0	-0.018	-0.008	13.282	0.012	0.012	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.020	-0.007	16.520	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.006	0.014	19.355	0.016	0.016	0.000	0.000	0.000	0.000
9	A	8	VAL	0	-0.016	-0.022	22.929	0.010	0.010	0.000	0.000	0.000	0.000
10	A	9	GLN	0	0.070	0.042	25.419	0.005	0.005	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.772	-0.869	29.057	-0.081	-0.081	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.040	-0.007	30.565	0.005	0.005	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.688	-0.792	27.938	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.042	-0.038	26.532	0.006	0.006	0.000	0.000	0.000	0.000
15	A	14	GLN	0	-0.053	-0.032	26.776	0.000	0.000	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.788	-0.896	27.498	0.008	0.008	0.000	0.000	0.000	0.000
17	A	16	LEU	0	0.025	0.019	21.117	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.020	-0.013	22.773	0.012	0.012	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.835	-0.899	23.077	0.096	0.096	0.000	0.000	0.000	0.000
20	A	19	GLN	0	0.026	0.006	22.443	0.025	0.025	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.005	0.007	17.483	0.021	0.021	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.012	0.002	18.815	0.037	0.037	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.777	0.870	20.315	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.040	-0.016	17.395	0.019	0.019	0.000	0.000	0.000	0.000
25	A	24	ASN	0	-0.049	-0.022	15.390	0.033	0.033	0.000	0.000	0.000	0.000
26	A	25	PHE	0	0.038	0.019	11.628	0.069	0.069	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.915	0.961	14.024	-0.149	-0.149	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.004	-0.013	15.148	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	28	THR	0	-0.066	-0.046	17.011	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	LYS	1	0.868	0.938	18.824	0.031	0.031	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.007	0.010	19.525	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	31	ALA	0	0.026	0.003	22.956	0.011	0.011	0.000	0.000	0.000	0.000
33	A	32	THR	0	-0.011	-0.020	26.581	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.020	-0.036	28.431	0.007	0.007	0.000	0.000	0.000	0.000
35	A	41	ASN	0	-0.060	-0.017	27.044	0.008	0.008	0.000	0.000	0.000	0.000
36	A	42	THR	0	-0.042	-0.036	25.526	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	43	THR	0	0.002	0.006	20.343	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.019	-0.016	19.067	0.001	0.001	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.002	0.005	15.029	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.033	-0.012	13.759	0.072	0.072	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.057	0.046	9.416	-0.082	-0.082	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.040	-0.023	8.460	0.091	0.091	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.001	-0.025	4.153	0.848	0.989	-0.001	-0.036	-0.104	0.000
44	A	50	ASP	-1	-0.792	-0.894	2.095	-11.415	-9.903	5.756	-3.421	-3.847	-0.042
45	A	51	ASP	-1	-0.885	-0.922	4.489	0.919	1.113	-0.001	-0.022	-0.171	0.000
46	A	52	ARG	1	0.804	0.865	6.964	-0.134	-0.134	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.001	0.000	7.843	0.073	0.073	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.871	-0.943	10.436	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.821	-0.866	12.941	0.286	0.286	0.000	0.000	0.000	0.000
50	A	56	ILE	0	-0.007	-0.003	12.556	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.020	-0.014	13.933	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.021	-0.015	16.580	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	59	VAL	0	0.006	-0.003	18.292	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.016	-0.006	17.367	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.016	-0.003	20.712	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	62	GLN	0	-0.032	-0.002	21.679	0.004	0.004	0.000	0.000	0.000	0.000
57	A	63	THR	0	-0.073	-0.029	23.498	0.007	0.007	0.000	0.000	0.000	0.000
58	A	64	CYS	0	-0.143	-0.086	24.912	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	65	GLY	0	0.071	0.036	25.088	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	66	ASN	0	-0.047	-0.016	27.376	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.808	0.895	28.999	0.023	0.023	0.000	0.000	0.000	0.000
62	A	93	VAL	0	0.042	0.016	34.625	0.000	0.000	0.000	0.000	0.000	0.000
63	A	94	GLY	0	0.015	0.008	30.982	0.006	0.006	0.000	0.000	0.000	0.000
64	A	95	GLY	0	-0.009	-0.017	28.171	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	96	ALA	0	0.028	0.007	23.174	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	97	THR	0	-0.061	-0.031	21.916	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	98	VAL	0	0.004	0.002	16.840	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	99	PHE	0	-0.009	0.004	15.499	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.026	0.005	9.473	0.034	0.034	0.000	0.000	0.000	0.000
70	A	101	MET	0	-0.021	-0.005	10.531	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	102	PRO	0	0.033	0.005	6.618	0.270	0.270	0.000	0.000	0.000	0.000
72	A	103	VAL	0	-0.004	-0.009	3.495	-0.139	0.313	0.010	-0.094	-0.368	0.000
73	A	104	ASP	-1	-0.907	-0.935	2.851	-7.966	-6.525	2.153	-1.098	-2.497	-0.012
74	A	105	ALA	0	-0.029	-0.022	1.932	-15.179	-15.177	6.807	-3.500	-3.309	-0.045
75	A	106	PHE	0	0.006	0.000	3.619	1.788	2.194	0.006	-0.047	-0.364	-0.001
76	A	107	HIS	0	-0.001	-0.002	4.852	0.509	0.562	-0.001	0.000	-0.052	0.000
77	A	108	GLN	0	-0.017	-0.008	8.334	0.206	0.206	0.000	0.000	0.000	0.000
78	A	109	PHE	0	0.017	0.021	11.318	0.100	0.100	0.000	0.000	0.000	0.000

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