FMO DATABASE

FMODB ID: 8977Y

Calculation Name: 1GRW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GRW

Chain ID: A

ChEMBL ID:

UniProt ID: P53017

Base Structure: X-ray

Registration Date: 2023-09-23

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1007308.333013
FMO2-HF: Nuclear repulsion	958529.238371
FMO2-HF: Total energy	-48779.094642
FMO2-MP2: Total energy	-48921.184015

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-0.464	1.689	0.004	-0.91	-1.246	0.004

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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

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	5	PRO	0	0.062	0.020	3.881	-2.108	-0.498	-0.012	-0.780	-0.818	0.004
4	A	6	PRO	0	-0.029	0.001	6.759	0.709	0.709	0.000	0.000	0.000	0.000
5	A	7	GLY	0	0.033	0.027	8.697	0.063	0.063	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.828	-0.889	11.371	-0.408	-0.408	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.029	-0.005	15.089	0.053	0.053	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.029	-0.009	17.567	0.000	0.000	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.015	-0.032	21.385	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	12	GLN	0	0.002	0.013	23.926	0.010	0.010	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.118	0.053	27.700	0.004	0.004	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.039	0.046	26.187	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.031	-0.025	25.736	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.839	0.903	27.756	0.087	0.087	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.025	-0.011	29.931	0.005	0.005	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.010	0.014	32.074	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.013	-0.005	32.180	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	ASN	0	0.020	0.014	37.577	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.039	0.049	41.312	0.000	0.000	0.000	0.000	0.000	0.000
20	A	22	PRO	0	-0.016	-0.006	44.152	0.001	0.001	0.000	0.000	0.000	0.000
21	A	23	TYR	0	-0.034	-0.057	40.309	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.862	-0.939	43.922	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.875	-0.929	44.335	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.765	0.872	37.483	0.057	0.057	0.000	0.000	0.000	0.000
25	A	27	HIS	0	0.015	0.016	38.889	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	THR	0	-0.046	-0.040	34.193	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	29	TYR	0	0.016	0.027	33.469	0.004	0.004	0.000	0.000	0.000	0.000
28	A	30	HIS	0	0.029	-0.002	30.621	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.039	-0.014	25.390	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.891	0.959	25.313	0.049	0.049	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.008	-0.011	19.601	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	34	ILE	0	0.011	-0.003	20.328	0.019	0.019	0.000	0.000	0.000	0.000
33	A	35	ASN	0	0.043	0.022	13.383	-0.065	-0.065	0.000	0.000	0.000	0.000
34	A	36	SER	0	-0.045	-0.032	17.019	0.030	0.030	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.034	-0.009	12.604	0.039	0.039	0.000	0.000	0.000	0.000
36	A	38	ALA	0	0.007	-0.011	12.849	0.015	0.015	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.974	0.985	6.987	-1.202	-1.202	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.894	0.940	10.974	-0.241	-0.241	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.029	0.005	10.000	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.033	0.016	11.204	0.065	0.065	0.000	0.000	0.000	0.000
41	A	43	TYR	0	-0.014	-0.028	12.808	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.021	0.007	15.614	0.032	0.032	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.030	-0.014	18.269	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.842	0.908	17.959	0.323	0.323	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.010	-0.017	23.302	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	48	THR	0	-0.023	-0.028	26.757	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	49	ASN	0	0.033	0.019	28.687	0.005	0.005	0.000	0.000	0.000	0.000
48	A	50	MET	0	0.002	-0.004	28.121	0.004	0.004	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.940	0.979	31.107	0.088	0.088	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.808	0.902	34.336	0.093	0.093	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.008	0.004	30.922	0.002	0.002	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.034	0.028	29.861	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.050	-0.031	25.667	0.003	0.003	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.884	-0.927	27.018	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	57	PRO	0	0.016	0.011	23.454	0.004	0.004	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.016	0.003	23.648	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	59	CYS	0	-0.055	-0.045	18.677	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	60	GLY	0	0.008	0.013	18.136	0.027	0.027	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.035	-0.022	13.954	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.015	0.010	15.224	0.016	0.016	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.732	-0.844	14.859	0.127	0.127	0.000	0.000	0.000	0.000
62	A	64	PRO	0	-0.021	-0.013	13.651	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.939	0.968	16.004	-0.081	-0.081	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.813	-0.846	18.565	0.010	0.010	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.017	-0.035	20.004	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.015	0.018	21.361	0.011	0.011	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.016	-0.019	23.868	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.012	0.006	22.610	0.002	0.002	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.054	0.025	26.749	0.002	0.002	0.000	0.000	0.000	0.000
70	A	72	VAL	0	-0.029	-0.036	28.378	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.033	-0.011	30.968	0.005	0.005	0.000	0.000	0.000	0.000
72	A	74	CYS	0	-0.018	-0.027	33.323	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.825	-0.902	35.951	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.002	0.018	38.687	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.068	-0.043	39.551	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	78	ALA	0	0.050	0.031	42.539	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	PHE	0	0.001	-0.014	41.154	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.030	-0.019	43.721	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	81	GLN	0	-0.083	-0.046	45.376	0.002	0.002	0.000	0.000	0.000	0.000
80	A	82	GLU	-1	-0.803	-0.878	40.592	-0.074	-0.074	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.902	-0.935	37.523	-0.089	-0.089	0.000	0.000	0.000	0.000
82	A	84	THR	0	0.023	-0.001	37.068	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.018	-0.008	35.950	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.016	-0.018	32.586	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.738	-0.807	31.151	-0.122	-0.122	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.886	0.933	24.012	0.207	0.207	0.000	0.000	0.000	0.000
87	A	89	ILE	0	0.050	0.041	24.231	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.072	-0.054	19.662	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	91	VAL	0	0.018	0.019	18.058	0.005	0.005	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.783	-0.876	15.087	-0.404	-0.404	0.000	0.000	0.000	0.000
91	A	93	TRP	0	0.001	-0.028	11.691	0.056	0.056	0.000	0.000	0.000	0.000
92	A	94	THR	0	0.016	-0.015	7.128	-0.141	-0.141	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.039	-0.022	4.928	0.624	0.624	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.020	-0.015	6.893	-0.157	-0.157	0.000	0.000	0.000	0.000
95	A	97	PRO	0	-0.009	0.005	6.050	0.196	0.196	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.882	-0.958	5.991	1.565	1.565	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.009	-0.001	8.736	-0.118	-0.118	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.046	-0.002	11.214	-0.063	-0.063	0.000	0.000	0.000	0.000
99	A	101	ALA	0	0.022	0.003	12.845	0.025	0.025	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.789	0.858	15.038	-0.057	-0.057	0.000	0.000	0.000	0.000
101	A	103	GLN	0	0.000	-0.009	16.534	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.015	-0.003	14.134	0.002	0.002	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.877	0.922	14.212	0.140	0.140	0.000	0.000	0.000	0.000
104	A	106	ARG	1	0.999	0.989	13.861	0.131	0.131	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.758	-0.871	11.828	-0.232	-0.232	0.000	0.000	0.000	0.000
106	A	108	TRP	0	0.000	0.002	9.266	-0.061	-0.061	0.000	0.000	0.000	0.000
107	A	109	PHE	0	-0.077	-0.043	9.008	-0.160	-0.160	0.000	0.000	0.000	0.000
108	A	110	GLN	0	-0.077	-0.035	11.156	0.034	0.034	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.027	0.025	9.377	0.063	0.063	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.930	-0.960	5.907	-0.348	-0.348	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.009	-0.001	3.341	-0.651	-0.345	0.014	-0.071	-0.249	0.000
112	A	114	MET	0	-0.036	-0.004	3.739	0.667	0.904	0.002	-0.059	-0.179	0.000
113	A	115	VAL	0	0.014	0.031	6.539	0.111	0.111	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.764	0.863	9.871	0.554	0.554	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.911	0.926	12.447	0.458	0.458	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.848	0.919	16.194	0.191	0.191	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.018	0.000	19.699	0.009	0.009	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.000	0.001	23.123	0.004	0.004	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.003	-0.012	26.350	0.004	0.004	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.003	0.012	29.368	0.003	0.003	0.000	0.000	0.000	0.000
121	A	123	GLU	-1	-0.815	-0.884	32.386	-0.093	-0.093	0.000	0.000	0.000	0.000
122	A	124	TYR	0	-0.008	-0.043	34.956	0.005	0.005	0.000	0.000	0.000	0.000
123	A	125	ASN	0	-0.020	-0.003	38.529	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	PRO	0	-0.002	0.001	41.421	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)