FMO DATABASE

FMODB ID: MVK5Z

Calculation Name: 1GXP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GXP

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFJ5

Base Structure: X-ray

Registration Date: 2023-09-20

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-840140.859975
FMO2-HF: Nuclear repulsion	797538.158817
FMO2-HF: Total energy	-42602.701159
FMO2-MP2: Total energy	-42725.605168

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:127:ALA)

Summations of interaction energy for fragment #1(A:127:ALA)

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.
-5.305	-1.814	2.642	-2.675	-3.459	-0.014

Interaction energy analysis for fragmet #1(A:127:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.032

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	129	GLU	-1	-0.910	-0.952	3.881	-2.187	-1.007	-0.015	-0.575	-0.591	0.001
4	A	130	GLU	-1	-0.955	-0.969	6.618	0.147	0.147	0.000	0.000	0.000	0.000
5	A	131	VAL	0	-0.033	-0.017	7.205	0.176	0.176	0.000	0.000	0.000	0.000
6	A	132	ILE	0	-0.043	-0.013	6.023	0.089	0.089	0.000	0.000	0.000	0.000
7	A	133	GLU	-1	-0.841	-0.943	10.147	0.183	0.183	0.000	0.000	0.000	0.000
8	A	134	MET	0	-0.056	-0.027	12.542	0.029	0.029	0.000	0.000	0.000	0.000
9	A	135	GLN	0	-0.002	-0.009	16.134	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	136	GLY	0	0.028	0.029	18.518	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	137	LEU	0	-0.054	-0.019	13.875	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	138	SER	0	-0.010	-0.008	12.800	0.026	0.026	0.000	0.000	0.000	0.000
13	A	139	LEU	0	-0.017	-0.017	5.703	0.007	0.007	0.000	0.000	0.000	0.000
14	A	140	ASP	-1	-0.722	-0.820	7.914	-0.144	-0.144	0.000	0.000	0.000	0.000
15	A	141	PRO	0	-0.028	-0.017	2.879	-0.430	0.010	0.109	-0.154	-0.395	0.000
16	A	142	THR	0	-0.045	-0.030	4.718	-0.301	-0.256	-0.001	-0.004	-0.039	0.000
17	A	143	SER	0	-0.095	-0.075	7.486	0.020	0.020	0.000	0.000	0.000	0.000
18	A	144	HIS	0	-0.057	-0.019	4.996	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	145	ARG	1	0.857	0.920	7.492	0.071	0.071	0.000	0.000	0.000	0.000
20	A	146	VAL	0	0.021	-0.010	9.669	0.083	0.083	0.000	0.000	0.000	0.000
21	A	147	MET	0	0.002	0.006	12.110	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	148	ALA	0	0.008	0.018	15.527	0.038	0.038	0.000	0.000	0.000	0.000
23	A	149	GLY	0	0.006	-0.003	18.361	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	150	GLU	-1	-0.994	-0.999	18.554	0.038	0.038	0.000	0.000	0.000	0.000
25	A	151	GLU	-1	-0.929	-0.956	19.539	0.058	0.058	0.000	0.000	0.000	0.000
26	A	152	PRO	0	-0.040	-0.020	16.570	0.021	0.021	0.000	0.000	0.000	0.000
27	A	153	LEU	0	-0.034	-0.019	15.292	0.001	0.001	0.000	0.000	0.000	0.000
28	A	154	GLU	-1	-0.814	-0.898	14.906	0.032	0.032	0.000	0.000	0.000	0.000
29	A	155	MET	0	-0.052	-0.029	12.395	0.046	0.046	0.000	0.000	0.000	0.000
30	A	156	GLY	0	0.023	0.023	13.652	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	157	PRO	0	0.044	0.012	9.981	0.038	0.038	0.000	0.000	0.000	0.000
32	A	158	THR	0	-0.016	-0.011	9.179	0.004	0.004	0.000	0.000	0.000	0.000
33	A	159	GLU	-1	-0.806	-0.911	10.340	0.223	0.223	0.000	0.000	0.000	0.000
34	A	160	PHE	0	0.070	0.040	4.732	0.096	0.150	-0.001	-0.006	-0.048	0.000
35	A	161	LYS	1	0.909	0.955	5.720	0.224	0.224	0.000	0.000	0.000	0.000
36	A	162	LEU	0	-0.032	-0.013	6.734	0.388	0.388	0.000	0.000	0.000	0.000
37	A	163	LEU	0	0.035	0.022	9.543	0.125	0.125	0.000	0.000	0.000	0.000
38	A	164	HIS	0	0.054	0.028	2.569	-1.925	-0.153	2.550	-1.936	-2.386	-0.015
39	A	165	PHE	0	-0.025	0.006	6.344	0.655	0.655	0.000	0.000	0.000	0.000
40	A	166	PHE	0	0.012	-0.016	7.323	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	167	MET	0	0.013	0.004	9.154	-0.074	-0.074	0.000	0.000	0.000	0.000
42	A	168	THR	0	0.003	-0.012	5.782	0.010	0.010	0.000	0.000	0.000	0.000
43	A	169	HIS	1	0.749	0.874	7.450	-1.830	-1.830	0.000	0.000	0.000	0.000
44	A	170	PRO	0	0.078	0.050	11.868	-0.110	-0.110	0.000	0.000	0.000	0.000
45	A	171	GLU	-1	-0.775	-0.843	14.720	0.287	0.287	0.000	0.000	0.000	0.000
46	A	172	ARG	1	0.925	0.979	15.340	-0.489	-0.489	0.000	0.000	0.000	0.000
47	A	173	VAL	0	-0.040	-0.026	17.166	0.024	0.024	0.000	0.000	0.000	0.000
48	A	174	TYR	0	-0.004	-0.005	12.984	0.029	0.029	0.000	0.000	0.000	0.000
49	A	175	SER	0	0.038	0.001	17.586	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	176	ARG	1	0.798	0.876	17.528	-0.141	-0.141	0.000	0.000	0.000	0.000
51	A	177	GLU	-1	-0.798	-0.890	17.235	0.216	0.216	0.000	0.000	0.000	0.000
52	A	178	GLN	0	0.078	0.059	15.973	0.021	0.021	0.000	0.000	0.000	0.000
53	A	179	LEU	0	0.008	0.005	12.754	0.052	0.052	0.000	0.000	0.000	0.000
54	A	180	LEU	0	-0.031	-0.012	12.564	0.032	0.032	0.000	0.000	0.000	0.000
55	A	181	ASN	0	-0.003	-0.023	13.344	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	182	HIS	0	-0.065	-0.034	9.777	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	183	VAL	0	-0.031	0.000	8.334	0.111	0.111	0.000	0.000	0.000	0.000
58	A	184	TRP	0	-0.028	-0.034	9.243	-0.097	-0.097	0.000	0.000	0.000	0.000
59	A	185	GLY	0	-0.014	0.017	11.159	-0.065	-0.065	0.000	0.000	0.000	0.000
60	A	186	THR	0	0.004	-0.013	11.819	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	187	ASN	0	-0.028	-0.013	15.603	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	188	VAL	0	-0.008	-0.002	18.414	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	189	TYR	0	-0.010	-0.002	17.724	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	190	VAL	0	-0.040	-0.018	17.057	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	191	GLU	-1	-0.775	-0.880	20.202	0.108	0.108	0.000	0.000	0.000	0.000
66	A	192	ASP	-1	-0.778	-0.900	20.786	0.172	0.172	0.000	0.000	0.000	0.000
67	A	193	ARG	1	0.883	0.908	20.722	-0.102	-0.102	0.000	0.000	0.000	0.000
68	A	194	THR	0	-0.042	-0.024	18.502	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	195	VAL	0	0.008	0.015	16.176	0.004	0.004	0.000	0.000	0.000	0.000
70	A	196	ASP	-1	-0.760	-0.828	18.202	0.177	0.177	0.000	0.000	0.000	0.000
71	A	197	VAL	0	-0.027	-0.010	20.531	0.002	0.002	0.000	0.000	0.000	0.000
72	A	198	HIS	0	-0.006	-0.015	15.016	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	199	ILE	0	0.041	0.026	15.636	0.016	0.016	0.000	0.000	0.000	0.000
74	A	200	ARG	1	0.924	0.966	17.685	-0.102	-0.102	0.000	0.000	0.000	0.000
75	A	201	ARG	1	0.813	0.902	17.042	-0.114	-0.114	0.000	0.000	0.000	0.000
76	A	202	LEU	0	0.039	0.024	12.932	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	203	ARG	1	0.824	0.883	16.407	-0.205	-0.205	0.000	0.000	0.000	0.000
78	A	204	LYS	1	0.797	0.873	19.510	-0.108	-0.108	0.000	0.000	0.000	0.000
79	A	205	ALA	0	0.017	0.005	16.537	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	206	LEU	0	0.021	0.011	14.944	0.006	0.006	0.000	0.000	0.000	0.000
81	A	207	GLU	-1	-0.838	-0.897	18.867	0.106	0.106	0.000	0.000	0.000	0.000
82	A	208	PRO	0	-0.006	0.012	20.829	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	209	GLY	0	0.073	0.048	21.185	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	210	GLY	0	-0.039	-0.005	22.184	0.003	0.003	0.000	0.000	0.000	0.000
85	A	211	HIS	0	0.008	-0.009	18.145	0.010	0.010	0.000	0.000	0.000	0.000
86	A	212	ASP	-1	-0.880	-0.943	19.065	0.202	0.202	0.000	0.000	0.000	0.000
87	A	213	ARG	1	0.861	0.914	20.544	-0.143	-0.143	0.000	0.000	0.000	0.000
88	A	214	MET	0	-0.010	0.016	16.569	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	215	VAL	0	0.012	0.021	15.671	0.038	0.038	0.000	0.000	0.000	0.000
90	A	216	GLN	0	0.015	0.023	18.253	-0.041	-0.041	0.000	0.000	0.000	0.000
91	A	217	THR	0	0.019	0.001	20.593	0.018	0.018	0.000	0.000	0.000	0.000
92	A	218	VAL	0	-0.006	0.005	21.811	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	219	ARG	1	1.002	0.984	24.269	-0.112	-0.112	0.000	0.000	0.000	0.000
94	A	220	GLY	0	-0.016	-0.011	27.374	0.000	0.000	0.000	0.000	0.000	0.000
95	A	221	THR	0	-0.018	0.008	22.726	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	222	GLY	0	-0.020	-0.019	20.770	0.008	0.008	0.000	0.000	0.000	0.000
97	A	223	TYR	0	-0.080	-0.056	17.666	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	224	ARG	1	0.898	0.950	17.521	-0.238	-0.238	0.000	0.000	0.000	0.000
99	A	225	PHE	0	0.041	0.033	14.430	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	226	SER	0	-0.077	-0.072	16.398	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	227	THR	0	0.055	0.014	17.865	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	228	ARG	1	0.812	0.898	20.185	-0.282	-0.282	0.000	0.000	0.000	0.000
103	A	229	PHE	0	0.030	0.020	21.941	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:127:ALA)