FMO DATABASE

FMODB ID: G5RR1

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	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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1009598.214031
FMO2-HF: Nuclear repulsion	960819.994883
FMO2-HF: Total energy	-48778.219149
FMO2-MP2: Total energy	-48920.36405

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.
2.103	2.79	0.001	-0.122	-0.566	0

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 : 0.271 / q_NPA : 0.208

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].
3	A	5	PRO	0	0.025	-0.008	4.803	-0.251	0.019	-0.001	-0.041	-0.228
4	A	6	PRO	0	-0.006	0.008	7.181	0.418	0.418	0.000	0.000	0.000
5	A	7	GLY	0	0.045	0.013	9.237	0.040	0.040	0.000	0.000	0.000
6	A	8	ASP	-1	-0.868	-0.917	12.281	-0.373	-0.373	0.000	0.000	0.000
7	A	9	ILE	0	-0.005	0.018	15.837	0.034	0.034	0.000	0.000	0.000
8	A	10	GLN	0	-0.029	-0.018	18.098	0.008	0.008	0.000	0.000	0.000
9	A	11	THR	0	0.026	0.006	21.851	-0.004	-0.004	0.000	0.000	0.000
10	A	12	GLN	0	-0.018	0.023	24.239	0.008	0.008	0.000	0.000	0.000
11	A	13	PRO	0	0.157	0.062	27.959	0.003	0.003	0.000	0.000	0.000
12	A	14	GLY	0	0.016	0.027	26.373	-0.008	-0.008	0.000	0.000	0.000
13	A	15	THR	0	-0.032	-0.035	25.998	-0.012	-0.012	0.000	0.000	0.000
14	A	16	LYS	1	0.826	0.902	28.051	0.075	0.075	0.000	0.000	0.000
15	A	17	ILE	0	-0.006	0.001	29.822	0.003	0.003	0.000	0.000	0.000
16	A	18	VAL	0	0.002	0.004	31.853	-0.001	-0.001	0.000	0.000	0.000
17	A	19	PHE	0	0.003	0.004	32.067	0.001	0.001	0.000	0.000	0.000
18	A	20	ASN	0	0.025	0.021	37.384	-0.001	-0.001	0.000	0.000	0.000
19	A	21	ALA	0	0.021	0.038	41.111	0.000	0.000	0.000	0.000	0.000
20	A	22	PRO	0	0.017	-0.003	43.835	0.000	0.000	0.000	0.000	0.000
21	A	23	TYR	0	-0.041	-0.064	39.987	-0.001	-0.001	0.000	0.000	0.000
22	A	24	ASP	-1	-0.897	-0.943	43.572	-0.035	-0.035	0.000	0.000	0.000
23	A	25	ASP	-1	-0.863	-0.934	43.923	-0.031	-0.031	0.000	0.000	0.000
24	A	26	LYS	1	0.761	0.877	36.933	0.040	0.040	0.000	0.000	0.000
25	A	27	HIS	0	-0.001	0.009	38.780	0.001	0.001	0.000	0.000	0.000
26	A	28	THR	0	-0.035	-0.046	34.020	-0.004	-0.004	0.000	0.000	0.000
27	A	29	TYR	0	0.001	0.010	33.109	0.001	0.001	0.000	0.000	0.000
28	A	30	HIS	0	0.031	0.003	30.792	-0.001	-0.001	0.000	0.000	0.000
29	A	31	ILE	0	-0.031	-0.008	25.536	-0.004	-0.004	0.000	0.000	0.000
30	A	32	LYS	1	0.872	0.937	25.591	0.060	0.060	0.000	0.000	0.000
31	A	33	VAL	0	-0.005	-0.006	19.727	-0.012	-0.012	0.000	0.000	0.000
32	A	34	ILE	0	0.016	-0.001	20.910	0.015	0.015	0.000	0.000	0.000
33	A	35	ASN	0	0.054	0.034	13.756	-0.062	-0.062	0.000	0.000	0.000
34	A	36	SER	0	-0.034	-0.026	17.517	0.024	0.024	0.000	0.000	0.000
35	A	37	SER	0	-0.041	-0.012	12.791	0.012	0.012	0.000	0.000	0.000
36	A	38	ALA	0	0.019	0.000	12.693	0.029	0.029	0.000	0.000	0.000
37	A	39	ARG	1	0.969	0.983	7.115	-0.410	-0.410	0.000	0.000	0.000
38	A	40	ARG	1	0.890	0.928	10.832	-0.148	-0.148	0.000	0.000	0.000
39	A	41	ILE	0	-0.036	0.000	9.957	-0.044	-0.044	0.000	0.000	0.000
40	A	42	GLY	0	0.028	0.015	11.526	0.065	0.065	0.000	0.000	0.000
41	A	43	TYR	0	-0.004	-0.022	13.196	-0.063	-0.063	0.000	0.000	0.000
42	A	44	GLY	0	0.024	0.009	15.698	0.030	0.030	0.000	0.000	0.000
43	A	45	ILE	0	-0.031	-0.017	17.881	-0.020	-0.020	0.000	0.000	0.000
44	A	46	LYS	1	0.843	0.906	17.605	0.212	0.212	0.000	0.000	0.000
45	A	47	THR	0	0.025	0.009	22.912	-0.004	-0.004	0.000	0.000	0.000
46	A	48	THR	0	-0.025	-0.006	26.377	-0.004	-0.004	0.000	0.000	0.000
47	A	49	ASN	0	0.045	0.022	28.388	0.007	0.007	0.000	0.000	0.000
48	A	50	MET	0	0.008	0.010	28.148	0.001	0.001	0.000	0.000	0.000
49	A	51	LYS	1	0.925	0.967	30.833	0.054	0.054	0.000	0.000	0.000
50	A	52	ARG	1	0.866	0.944	34.443	0.064	0.064	0.000	0.000	0.000
51	A	53	LEU	0	-0.014	-0.019	30.639	0.000	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.028	0.020	29.776	-0.002	-0.002	0.000	0.000	0.000
53	A	55	VAL	0	-0.086	-0.053	25.275	-0.002	-0.002	0.000	0.000	0.000
54	A	56	ASP	-1	-0.907	-0.915	26.943	-0.052	-0.052	0.000	0.000	0.000
55	A	57	PRO	0	0.061	0.017	23.586	0.002	0.002	0.000	0.000	0.000
56	A	58	PRO	0	0.009	0.002	23.256	-0.009	-0.009	0.000	0.000	0.000
57	A	59	CYS	0	-0.042	-0.042	18.467	-0.015	-0.015	0.000	0.000	0.000
58	A	60	GLY	0	0.000	0.010	18.205	0.020	0.020	0.000	0.000	0.000
59	A	61	VAL	0	-0.034	-0.022	13.975	-0.022	-0.022	0.000	0.000	0.000
60	A	62	LEU	0	-0.014	-0.003	15.279	0.010	0.010	0.000	0.000	0.000
61	A	63	ASP	-1	-0.764	-0.851	14.925	0.059	0.059	0.000	0.000	0.000
62	A	64	PRO	0	0.019	0.003	13.718	-0.027	-0.027	0.000	0.000	0.000
63	A	65	LYS	1	0.944	0.963	16.163	0.004	0.004	0.000	0.000	0.000
64	A	66	GLU	-1	-0.834	-0.852	18.848	-0.010	-0.010	0.000	0.000	0.000
65	A	67	ALA	0	-0.028	-0.038	19.993	-0.019	-0.019	0.000	0.000	0.000
66	A	68	VAL	0	0.032	0.024	21.299	0.010	0.010	0.000	0.000	0.000
67	A	69	LEU	0	-0.038	-0.026	23.769	-0.008	-0.008	0.000	0.000	0.000
68	A	70	LEU	0	-0.041	-0.017	22.800	0.002	0.002	0.000	0.000	0.000
69	A	71	ALA	0	0.044	0.018	27.138	0.001	0.001	0.000	0.000	0.000
70	A	72	VAL	0	-0.020	-0.026	28.055	-0.004	-0.004	0.000	0.000	0.000
71	A	73	SER	0	-0.017	0.002	30.661	0.004	0.004	0.000	0.000	0.000
72	A	74	CYS	0	-0.015	-0.016	33.263	-0.005	-0.005	0.000	0.000	0.000
73	A	75	ASP	-1	-0.841	-0.905	35.885	-0.039	-0.039	0.000	0.000	0.000
74	A	76	ALA	0	0.050	0.058	38.563	-0.002	-0.002	0.000	0.000	0.000
75	A	77	PHE	0	-0.100	-0.071	39.462	-0.002	-0.002	0.000	0.000	0.000
76	A	78	ALA	0	0.037	0.029	42.418	0.001	0.001	0.000	0.000	0.000
77	A	79	PHE	0	0.039	0.000	40.792	-0.001	-0.001	0.000	0.000	0.000
78	A	80	GLY	0	-0.043	-0.030	43.506	-0.001	-0.001	0.000	0.000	0.000
79	A	81	GLN	0	-0.076	-0.043	45.417	0.001	0.001	0.000	0.000	0.000
80	A	82	GLU	-1	-0.825	-0.881	40.371	-0.050	-0.050	0.000	0.000	0.000
81	A	83	ASP	-1	-0.892	-0.927	37.831	-0.060	-0.060	0.000	0.000	0.000
82	A	84	THR	0	-0.015	-0.033	36.990	-0.001	-0.001	0.000	0.000	0.000
83	A	85	ASN	0	-0.014	-0.004	36.239	-0.002	-0.002	0.000	0.000	0.000
84	A	86	ASN	0	-0.039	-0.026	32.254	-0.010	-0.010	0.000	0.000	0.000
85	A	87	ASP	-1	-0.747	-0.839	30.902	-0.083	-0.083	0.000	0.000	0.000
86	A	88	ARG	1	0.917	0.956	24.414	0.145	0.145	0.000	0.000	0.000
87	A	89	ILE	0	0.042	0.035	24.186	0.002	0.002	0.000	0.000	0.000
88	A	90	THR	0	-0.086	-0.063	19.403	-0.004	-0.004	0.000	0.000	0.000
89	A	91	VAL	0	0.016	0.014	17.906	0.007	0.007	0.000	0.000	0.000
90	A	92	GLU	-1	-0.779	-0.876	14.794	-0.276	-0.276	0.000	0.000	0.000
91	A	93	TRP	0	0.006	-0.020	12.186	0.050	0.050	0.000	0.000	0.000
92	A	94	THR	0	-0.004	-0.015	7.152	-0.127	-0.127	0.000	0.000	0.000
93	A	95	ASN	0	-0.032	-0.021	5.555	0.528	0.528	0.000	0.000	0.000
94	A	96	THR	0	-0.017	-0.002	7.044	-0.112	-0.112	0.000	0.000	0.000
95	A	97	PRO	0	-0.026	-0.017	5.699	0.117	0.117	0.000	0.000	0.000
96	A	98	ASP	-1	-0.893	-0.966	6.084	1.462	1.462	0.000	0.000	0.000
97	A	99	GLY	0	-0.026	0.003	8.055	-0.103	-0.103	0.000	0.000	0.000
98	A	100	ALA	0	0.010	0.027	10.734	-0.051	-0.051	0.000	0.000	0.000
99	A	101	ALA	0	0.009	-0.007	12.451	0.013	0.013	0.000	0.000	0.000
100	A	102	LYS	1	0.806	0.873	14.781	-0.023	-0.023	0.000	0.000	0.000
101	A	103	GLN	0	0.000	-0.020	16.281	-0.001	-0.001	0.000	0.000	0.000
102	A	104	PHE	0	-0.021	-0.007	14.266	0.005	0.005	0.000	0.000	0.000
103	A	105	ARG	1	0.980	1.002	13.794	0.041	0.041	0.000	0.000	0.000
104	A	106	ARG	1	1.011	0.991	13.723	0.065	0.065	0.000	0.000	0.000
105	A	107	GLU	-1	-0.853	-0.920	11.679	-0.108	-0.108	0.000	0.000	0.000
106	A	108	TRP	0	-0.009	-0.009	9.271	-0.030	-0.030	0.000	0.000	0.000
107	A	109	PHE	0	-0.081	-0.050	8.586	-0.112	-0.112	0.000	0.000	0.000
108	A	110	GLN	0	-0.101	-0.046	10.903	0.000	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.030	0.021	8.776	0.036	0.036	0.000	0.000	0.000
110	A	112	ASP	-1	-0.914	-0.943	5.534	0.262	0.262	0.000	0.000	0.000
111	A	113	GLY	0	-0.008	-0.017	3.697	-0.536	-0.291	0.002	-0.045	-0.202
112	A	114	MET	0	-0.035	0.003	3.932	0.441	0.613	0.000	-0.036	-0.136
113	A	115	VAL	0	0.040	0.039	6.800	0.060	0.060	0.000	0.000	0.000
114	A	116	ARG	1	0.765	0.876	10.067	0.506	0.506	0.000	0.000	0.000
115	A	117	ARG	1	0.901	0.918	12.633	0.326	0.326	0.000	0.000	0.000
116	A	118	LYS	1	0.853	0.926	16.320	0.168	0.168	0.000	0.000	0.000
117	A	119	ASN	0	-0.045	-0.018	19.656	0.015	0.015	0.000	0.000	0.000
118	A	120	LEU	0	0.003	-0.001	22.948	-0.001	-0.001	0.000	0.000	0.000
119	A	121	PRO	0	0.007	-0.010	26.067	0.004	0.004	0.000	0.000	0.000
120	A	122	ILE	0	-0.004	0.008	28.997	0.001	0.001	0.000	0.000	0.000
121	A	123	GLU	-1	-0.832	-0.891	31.933	-0.075	-0.075	0.000	0.000	0.000
122	A	124	TYR	0	-0.006	-0.035	34.797	0.003	0.003	0.000	0.000	0.000
123	A	125	ASN	0	-0.043	-0.030	38.520	0.001	0.001	0.000	0.000	0.000
124	A	126	PRO	0	0.021	0.032	41.493	0.004	0.004	0.000	0.000	0.000

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