FMO DATABASE

FMODB ID: 5298Z

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	OptH
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	-1204282.269949
FMO2-HF: Nuclear repulsion	1146682.144769
FMO2-HF: Total energy	-57600.12518
FMO2-MP2: Total energy	-57771.65495

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.
-3.913	-2.381	-0.012	-0.654	-0.867	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 : 0.008 / q_NPA : -0.002

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	0.016	0.019	3.801	-2.761	-1.424	-0.015	-0.574	-0.748	0.002
4	A	5	ARG	1	0.982	0.985	6.294	-0.461	-0.461	0.000	0.000	0.000	0.000
5	A	6	ARG	1	0.887	0.931	8.948	-0.120	-0.120	0.000	0.000	0.000	0.000
6	A	7	SER	0	0.009	0.007	10.364	-0.125	-0.125	0.000	0.000	0.000	0.000
7	A	8	ASN	0	0.044	0.030	11.008	0.096	0.096	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.015	-0.005	12.397	0.026	0.026	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.009	0.001	15.350	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.794	-0.917	16.628	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.049	-0.014	17.868	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.001	-0.008	20.068	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.017	0.004	14.527	0.016	0.016	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.839	-0.940	14.541	0.003	0.003	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.068	-0.017	11.937	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	TRP	0	-0.036	-0.027	14.054	-0.056	-0.056	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.004	0.009	17.464	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.859	-0.924	16.920	-0.140	-0.140	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.016	0.006	16.592	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.001	-0.013	16.616	-0.057	-0.057	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.904	-0.931	14.040	-0.242	-0.242	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.039	-0.002	11.560	-0.059	-0.059	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.072	-0.040	12.198	-0.126	-0.126	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.920	0.942	13.473	0.168	0.168	0.000	0.000	0.000	0.000
25	A	26	SER	0	0.005	0.002	9.680	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.041	-0.013	7.397	-0.181	-0.181	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.023	0.011	9.461	-0.163	-0.163	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.053	-0.041	9.827	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.030	-0.014	5.092	-0.120	-0.120	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.003	0.016	6.449	-0.390	-0.390	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.054	-0.010	8.728	0.001	0.001	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.003	-0.017	5.182	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.027	-0.004	3.771	-0.250	-0.118	0.003	-0.049	-0.086	0.000
34	A	35	GLY	0	0.037	0.014	4.217	0.683	0.746	0.000	-0.031	-0.033	0.000
35	A	36	SER	0	-0.004	-0.008	7.557	-0.085	-0.085	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.883	-0.940	10.243	-0.378	-0.378	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.024	-0.013	12.858	0.115	0.115	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.032	0.016	14.985	0.065	0.065	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.026	0.005	16.555	0.050	0.050	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.005	-0.024	13.750	0.041	0.041	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.068	-0.020	18.438	0.035	0.035	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.023	-0.008	21.103	0.032	0.032	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.014	0.011	22.273	0.024	0.024	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.944	0.978	22.280	0.248	0.248	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.021	-0.028	22.760	0.012	0.012	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.922	-0.923	23.901	-0.169	-0.169	0.000	0.000	0.000	0.000
47	A	48	TRP	0	0.014	-0.016	21.435	0.003	0.003	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.920	0.970	26.433	0.077	0.077	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.850	-0.933	28.938	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.065	-0.014	30.998	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.058	-0.063	34.359	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.824	-0.927	36.533	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.003	0.005	34.045	0.004	0.004	0.000	0.000	0.000	0.000
54	A	55	HIS	0	-0.010	0.016	28.656	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.046	-0.037	30.609	0.002	0.002	0.000	0.000	0.000	0.000
56	A	57	PHE	0	0.026	0.011	23.783	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.913	0.958	27.776	0.100	0.100	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.027	0.010	26.070	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.895	-0.921	27.306	-0.135	-0.135	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.061	-0.037	26.102	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.036	0.006	29.351	0.012	0.012	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.015	-0.030	31.985	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.018	0.011	29.414	0.002	0.002	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.942	0.984	32.780	0.075	0.075	0.000	0.000	0.000	0.000
65	A	66	LYS	1	1.005	0.985	33.173	0.046	0.046	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.923	-0.953	33.121	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.852	-0.947	30.315	-0.089	-0.089	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.047	-0.017	27.698	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.930	0.965	26.551	0.060	0.060	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.002	-0.004	26.411	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.940	-0.966	24.740	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.009	-0.008	25.728	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.898	-0.951	20.631	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.938	-0.992	20.976	0.094	0.094	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.028	0.038	24.118	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.018	-0.014	22.345	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.007	0.005	19.598	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.002	0.024	22.604	0.003	0.003	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.001	-0.013	20.678	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.000	0.005	22.095	0.009	0.009	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.027	-0.018	21.996	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.036	0.012	23.499	0.015	0.015	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.959	-0.997	24.415	-0.154	-0.154	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.907	0.988	26.706	0.150	0.150	0.000	0.000	0.000	0.000
85	A	86	THR	0	-0.049	-0.023	29.618	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.913	0.953	30.779	0.100	0.100	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.784	-0.883	33.414	-0.100	-0.100	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.843	0.943	36.538	0.061	0.061	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.904	-0.974	39.099	-0.085	-0.085	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.882	-0.939	40.764	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.908	0.965	37.184	0.076	0.076	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.044	-0.047	41.329	0.001	0.001	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.828	-0.883	41.095	-0.078	-0.078	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.880	0.940	40.912	0.085	0.085	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.008	-0.011	32.972	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.021	-0.015	37.764	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.869	0.900	33.918	0.143	0.143	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.019	0.016	30.934	0.005	0.005	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.841	-0.893	30.198	-0.168	-0.168	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.839	0.896	29.001	0.109	0.109	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.019	-0.001	26.007	0.013	0.013	0.000	0.000	0.000	0.000
102	A	103	SER	0	0.011	0.004	25.466	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.013	0.005	23.383	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.944	0.980	20.475	0.140	0.140	0.000	0.000	0.000	0.000
105	A	106	PHE	0	-0.041	-0.024	19.327	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.017	0.003	16.849	0.033	0.033	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.881	0.951	17.421	0.232	0.232	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.936	0.972	15.996	0.106	0.106	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.027	-0.008	18.185	-0.036	-0.036	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.930	0.969	15.653	0.027	0.027	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.024	-0.012	20.959	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.032	-0.022	24.087	0.009	0.009	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.916	-0.961	25.919	0.004	0.004	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.902	-0.956	27.275	0.038	0.038	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.002	0.008	28.828	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.956	0.991	30.774	0.000	0.000	0.000	0.000	0.000	0.000
117	A	118	VAL	0	0.018	-0.004	30.625	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.914	-0.953	33.198	0.001	0.001	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.949	-0.998	36.033	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.064	-0.015	30.835	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.903	0.959	34.062	0.028	0.028	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.034	0.001	32.275	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.024	0.002	33.958	0.004	0.004	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.034	-0.022	32.422	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.920	-0.963	35.378	-0.058	-0.058	0.000	0.000	0.000	0.000
126	A	127	ASN	0	-0.018	-0.008	36.457	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	128	GLY	0	-0.022	-0.009	34.098	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	129	VAL	0	0.033	0.027	31.641	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.025	-0.008	27.869	0.009	0.009	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.014	-0.027	30.755	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.008	0.005	28.388	0.007	0.007	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.037	-0.024	30.739	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	134	VAL	0	0.039	0.003	28.899	0.004	0.004	0.000	0.000	0.000	0.000
134	A	135	PRO	0	-0.009	-0.010	32.206	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.883	0.983	31.691	0.038	0.038	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.035	0.028	34.507	0.001	0.001	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.937	-0.968	36.725	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.010	-0.003	35.928	0.004	0.004	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.907	0.946	39.182	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	141	LYS	1	0.973	0.988	37.347	0.031	0.031	0.000	0.000	0.000	0.000
141	A	142	PRO	0	-0.015	-0.029	36.419	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.940	-0.941	39.444	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.002	0.001	38.153	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.917	0.961	39.313	0.001	0.001	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.030	0.014	39.914	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	147	ILE	0	-0.005	-0.003	39.128	0.002	0.002	0.000	0.000	0.000	0.000
147	A	148	GLN	0	-0.022	-0.012	42.566	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	149	ILE	0	-0.003	-0.005	41.164	0.002	0.002	0.000	0.000	0.000	0.000
149	A	150	SER	0	-0.029	0.005	44.348	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	151	GLY	0	0.049	0.019	45.590	-0.002	-0.002	0.000	0.000	0.000	0.000

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