FMO DATABASE

FMODB ID: YZQM2

Calculation Name: 1GME-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GME

Chain ID: A

ChEMBL ID:

UniProt ID: Q41560

Base Structure: X-ray

Registration Date: 2023-06-21

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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204706.84367
FMO2-HF: Nuclear repulsion	1147105.494018
FMO2-HF: Total energy	-57601.349652
FMO2-MP2: Total energy	-57772.839964

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-2.471	-0.935	-0.014	-0.642	-0.879	0.002

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.003

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	4	VAL	0	0.021	0.019	3.801	-0.465	0.905	-0.017	-0.568	-0.784	0.002
4	A	5	ARG	1	0.975	0.981	6.294	-1.986	-1.986	0.000	0.000	0.000	0.000
5	A	6	ARG	1	0.902	0.944	9.161	-0.721	-0.721	0.000	0.000	0.000	0.000
6	A	7	SER	0	0.026	0.017	10.326	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	8	ASN	0	-0.011	-0.006	11.154	0.183	0.183	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.015	-0.008	12.365	-0.053	-0.053	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.013	0.002	15.309	0.042	0.042	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.737	-0.867	16.583	0.286	0.286	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.015	-0.004	17.979	0.007	0.007	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.015	-0.016	20.323	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.021	0.004	15.042	0.032	0.032	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.843	-0.940	15.087	0.429	0.429	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.072	-0.026	11.910	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	TRP	0	-0.062	-0.040	14.492	-0.092	-0.092	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.017	0.001	17.872	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.850	-0.919	17.217	0.073	0.073	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.019	0.003	16.609	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.004	-0.007	16.493	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.893	-0.932	14.112	0.128	0.128	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.050	0.021	11.611	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.066	-0.040	11.929	-0.099	-0.099	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.904	0.940	13.210	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.010	-0.009	9.348	-0.056	-0.056	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.025	-0.013	7.458	-0.166	-0.166	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.007	0.016	9.255	-0.247	-0.247	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.046	-0.034	9.709	-0.098	-0.098	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.042	-0.022	4.946	-0.206	-0.206	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.006	0.013	6.193	-0.429	-0.429	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.050	-0.007	8.699	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.002	-0.017	5.122	-0.132	-0.132	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.026	-0.004	3.828	-0.126	-0.017	0.003	-0.045	-0.067	0.000
34	A	35	GLY	0	0.034	0.014	4.251	0.675	0.732	0.000	-0.029	-0.028	0.000
35	A	36	SER	0	-0.002	-0.008	7.611	0.033	0.033	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.837	-0.914	10.267	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.003	-0.005	12.984	0.087	0.087	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.020	0.012	15.000	0.055	0.055	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.026	0.005	16.579	0.044	0.044	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.005	-0.026	14.091	0.033	0.033	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.046	-0.002	18.443	0.035	0.035	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.015	-0.014	21.115	0.017	0.017	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.015	0.011	22.268	0.018	0.018	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.934	0.979	22.669	0.163	0.163	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.015	-0.026	22.727	0.009	0.009	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.917	-0.925	23.889	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	48	TRP	0	-0.017	-0.022	21.570	0.004	0.004	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.920	0.969	26.408	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.760	-0.862	29.050	0.092	0.092	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.077	-0.040	30.965	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.029	-0.043	34.323	0.006	0.006	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.827	-0.905	36.556	0.044	0.044	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.009	0.014	33.997	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	HIS	0	-0.012	-0.007	28.552	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.048	-0.038	30.600	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	PHE	0	0.029	0.012	23.783	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.891	0.935	27.767	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.028	0.008	26.045	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.900	-0.924	27.296	-0.066	-0.066	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.067	-0.041	25.906	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.042	0.006	29.416	0.007	0.007	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.017	-0.020	31.992	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.046	-0.009	29.390	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.947	0.980	32.782	0.054	0.054	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.964	0.949	33.169	0.008	0.008	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.877	-0.916	33.112	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.831	-0.910	30.446	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.044	-0.018	27.747	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.803	0.888	25.221	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.003	-0.004	26.393	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.826	-0.892	25.405	0.040	0.040	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.019	-0.007	25.674	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.844	-0.905	20.461	0.153	0.153	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.933	-0.986	20.901	0.275	0.275	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.027	0.036	24.324	0.011	0.011	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.053	-0.043	22.852	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.001	0.003	19.437	0.006	0.006	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.000	0.025	22.562	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.004	-0.010	20.818	0.002	0.002	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.005	0.000	22.078	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.033	-0.017	22.001	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.056	0.023	23.488	0.010	0.010	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.868	-0.938	24.416	-0.140	-0.140	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.829	0.951	26.710	0.111	0.111	0.000	0.000	0.000	0.000
85	A	86	THR	0	-0.072	-0.052	29.606	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.932	0.961	30.332	0.107	0.107	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.689	-0.812	33.397	-0.087	-0.087	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.888	0.961	36.532	0.048	0.048	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.927	-0.984	39.081	-0.069	-0.069	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.899	-0.946	40.752	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.932	0.962	37.155	0.083	0.083	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.056	-0.042	41.292	0.003	0.003	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.839	-0.898	41.077	-0.080	-0.080	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.838	0.922	40.917	0.084	0.084	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.007	-0.013	33.078	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	97	HIS	0	0.018	0.013	37.795	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.872	0.906	34.015	0.126	0.126	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.010	0.008	31.200	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.833	-0.888	30.255	-0.144	-0.144	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.820	0.870	29.058	0.087	0.087	0.000	0.000	0.000	0.000
101	A	102	SER	0	0.014	0.008	25.630	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	SER	0	-0.012	-0.004	25.471	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.019	0.009	23.382	0.001	0.001	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.818	0.902	21.046	0.133	0.133	0.000	0.000	0.000	0.000
105	A	106	PHE	0	-0.029	-0.017	19.329	-0.030	-0.030	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.008	-0.008	16.851	0.024	0.024	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.842	0.937	17.497	0.059	0.059	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.869	0.917	16.645	-0.101	-0.101	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.018	-0.004	18.155	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.896	0.937	16.211	-0.352	-0.352	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.045	-0.024	20.968	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.021	-0.016	24.362	0.019	0.019	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.889	-0.946	26.243	0.114	0.114	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.862	-0.928	27.497	0.179	0.179	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.004	0.005	29.020	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.873	0.941	30.825	-0.069	-0.069	0.000	0.000	0.000	0.000
117	A	118	VAL	0	0.020	-0.003	30.566	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.866	-0.926	33.158	0.069	0.069	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.849	-0.953	35.957	0.057	0.057	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.027	0.005	30.711	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.780	0.906	34.028	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.041	0.004	32.244	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.016	0.006	33.935	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.049	-0.028	32.449	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.926	-0.967	35.367	-0.014	-0.014	0.000	0.000	0.000	0.000
126	A	127	ASN	0	0.000	0.004	36.451	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	128	GLY	0	-0.020	-0.008	34.099	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	129	VAL	0	0.026	0.019	31.607	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.008	0.000	27.984	0.006	0.006	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.008	-0.004	30.740	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.015	0.004	28.485	0.002	0.002	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.026	-0.014	30.712	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	VAL	0	0.030	-0.004	28.836	0.001	0.001	0.000	0.000	0.000	0.000
134	A	135	PRO	0	-0.014	-0.006	32.170	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.805	0.918	31.394	-0.068	-0.068	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.001	0.009	34.567	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.937	-0.969	36.991	0.065	0.065	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.021	-0.001	36.279	0.004	0.004	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.902	0.946	39.625	-0.062	-0.062	0.000	0.000	0.000	0.000
140	A	141	LYS	1	0.994	0.996	37.693	-0.053	-0.053	0.000	0.000	0.000	0.000
141	A	142	PRO	0	-0.008	-0.015	37.562	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.851	-0.901	40.125	0.061	0.061	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.020	0.012	38.643	0.005	0.005	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.783	0.892	39.967	-0.074	-0.074	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.028	0.011	40.492	0.001	0.001	0.000	0.000	0.000	0.000
146	A	147	ILE	0	-0.003	-0.005	39.873	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	148	GLN	0	-0.015	-0.006	43.049	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	149	ILE	0	-0.006	-0.007	41.366	0.003	0.003	0.000	0.000	0.000	0.000
149	A	150	SER	0	0.003	0.018	44.673	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	151	GLY	0	0.020	0.008	45.829	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)