FMO DATABASE

FMODB ID: QYGMY

Calculation Name: 2GBJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GBJ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptHSide
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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500919.144168
FMO2-HF: Nuclear repulsion	470575.722092
FMO2-HF: Total energy	-30343.422076
FMO2-MP2: Total energy	-30433.15332

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.
-24.434	-26.578	27.767	-5.207	-20.418	-0.056

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 : -0.045 / q_NPA : -0.007

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	3	ILE	0	-0.028	-0.003	2.765	-0.821	2.388	0.434	-1.338	-2.305	-0.001
4	A	4	PHE	0	0.010	0.002	4.900	-0.051	-0.009	-0.001	-0.008	-0.033	0.000
5	A	5	VAL	0	-0.006	0.003	8.664	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.959	0.992	11.436	0.189	0.189	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.053	0.033	14.972	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.045	-0.033	18.006	0.050	0.050	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.009	0.008	20.574	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.037	0.032	23.405	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.032	-0.030	25.849	0.017	0.017	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.010	-0.003	28.586	0.006	0.006	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.026	0.000	28.897	0.007	0.007	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.006	-0.012	28.876	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.024	0.010	27.294	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.010	0.014	24.145	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.054	0.013	21.869	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.063	-0.037	18.446	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.956	0.987	17.037	0.226	0.226	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.005	-0.007	12.420	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.002	0.023	12.060	0.051	0.051	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.032	0.012	8.512	-0.071	-0.071	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.046	-0.024	7.068	0.205	0.205	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.887	-0.932	3.534	-1.642	-1.106	0.015	-0.177	-0.374	0.000
25	A	25	VAL	0	-0.051	-0.040	2.539	0.571	2.504	1.152	-0.869	-2.216	-0.001
26	A	26	GLU	-1	-0.824	-0.914	1.893	-18.586	-20.263	10.884	-4.906	-4.301	-0.056
27	A	27	PRO	0	-0.013	-0.014	2.602	-1.696	0.202	1.586	-0.687	-2.797	-0.002
28	A	28	SER	0	0.015	0.004	3.446	1.059	0.874	0.042	0.311	-0.168	0.000
29	A	29	ASP	-1	-0.810	-0.885	5.507	-4.546	-4.546	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.013	-0.012	7.224	0.041	0.041	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.032	-0.019	8.792	-0.241	-0.241	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.932	-0.968	10.814	-0.926	-0.926	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.012	0.000	9.683	-0.098	-0.098	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.005	0.004	6.970	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.828	0.899	9.813	0.966	0.966	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.021	0.019	13.370	0.137	0.137	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.840	0.911	6.204	4.332	4.332	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.063	-0.029	11.279	0.158	0.158	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.004	0.000	13.810	0.108	0.108	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.904	-0.938	13.398	-1.020	-1.020	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.788	0.877	10.442	1.275	1.275	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.929	-0.972	16.025	-0.409	-0.409	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.024	0.000	18.940	0.066	0.066	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.060	-0.030	18.952	0.038	0.038	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.057	0.023	19.158	-0.081	-0.081	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.067	0.027	17.277	0.018	0.018	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.905	-0.943	18.676	-0.508	-0.508	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.070	-0.044	21.308	0.036	0.036	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.012	-0.007	15.124	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.865	0.919	17.275	0.344	0.344	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.050	0.027	10.783	0.032	0.032	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.047	-0.024	13.871	0.044	0.044	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.049	0.021	9.016	-0.102	-0.102	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.017	0.013	12.335	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.002	0.005	14.529	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.874	0.937	14.476	0.344	0.344	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.031	0.017	15.133	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.051	-0.014	10.134	0.042	0.042	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.797	-0.880	14.107	-0.441	-0.441	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.785	-0.899	13.532	-0.898	-0.898	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.016	0.011	13.645	-0.139	-0.139	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.841	0.931	11.445	0.486	0.486	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.016	-0.018	7.505	-0.232	-0.232	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.014	-0.011	2.929	-0.103	0.470	0.194	-0.133	-0.634	-0.001
65	A	65	SER	0	-0.026	-0.018	5.295	0.833	0.833	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.825	-0.876	5.898	-0.390	-0.390	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.086	-0.071	7.988	0.240	0.240	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.051	-0.025	7.143	0.212	0.212	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.036	0.004	3.703	0.377	0.589	0.002	-0.033	-0.181	0.000
70	A	70	GLN	0	0.012	-0.010	2.933	-3.733	-3.143	2.073	-0.713	-1.950	0.000
71	A	71	LYS	1	1.019	0.991	2.191	-2.647	-8.052	11.167	-0.811	-4.952	0.003
72	A	72	GLU	-1	-0.943	-0.982	2.977	3.313	-0.557	0.219	4.157	-0.507	0.002
73	A	73	SER	0	-0.004	0.017	5.301	-0.663	-0.663	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.006	-0.009	7.074	-0.563	-0.563	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.015	0.000	7.053	0.136	0.136	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.032	-0.024	10.434	0.084	0.084	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.037	0.023	14.139	-0.042	-0.042	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.050	-0.044	15.712	0.085	0.085	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.045	0.028	19.196	-0.043	-0.043	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.883	0.944	21.169	0.450	0.450	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.034	0.021	23.248	-0.014	-0.014	0.000	0.000	0.000	0.000

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