FMO DATABASE

FMODB ID: X1N9Z

Calculation Name: 3NG8-A-Xray17

Preferred Name:

Target Type:

Ligand Name: calcium ion

ligand 3-letter code: CA

PDB ID: 3NG8

Chain ID: A

ChEMBL ID:

UniProt ID: Q16849

Base Structure: X-ray

Registration Date: 2018-06-01

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	148
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-686480.971848
FMO2-HF: Nuclear repulsion	649659.44164
FMO2-HF: Total energy	-36821.530208
FMO2-MP2: Total energy	-36929.123391

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:470:GLU)

Summations of interaction energy for fragment #1(A:470:GLU)

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.
-84.204	-136.543	119.755	-50.639	-16.774	0.145

Interaction energy analysis for fragmet #1(A:470:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.802 / q_NPA : -0.834

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	472	GLY	0	0.064	0.044	3.803	1.701	3.860	-0.022	-1.083	-1.054	0.002
4	A	473	TYR	0	-0.036	-0.041	6.073	-2.187	-2.187	0.000	0.000	0.000	0.000
5	A	474	ILE	0	0.041	0.027	9.241	0.298	0.298	0.000	0.000	0.000	0.000
6	A	475	VAL	0	-0.045	-0.015	12.836	-0.550	-0.550	0.000	0.000	0.000	0.000
7	A	476	THR	0	0.042	0.011	15.206	-0.677	-0.677	0.000	0.000	0.000	0.000
8	A	477	ASP	-1	-0.777	-0.883	18.807	12.789	12.789	0.000	0.000	0.000	0.000
9	A	478	GLN	0	0.040	0.011	21.204	-0.458	-0.458	0.000	0.000	0.000	0.000
10	A	479	LYS	1	0.932	0.993	20.358	-12.665	-12.665	0.000	0.000	0.000	0.000
11	A	480	PRO	0	-0.042	-0.034	20.912	-0.490	-0.490	0.000	0.000	0.000	0.000
12	A	481	LEU	0	0.047	0.027	16.777	-0.447	-0.447	0.000	0.000	0.000	0.000
13	A	482	SER	0	0.009	0.006	20.066	0.178	0.178	0.000	0.000	0.000	0.000
14	A	483	LEU	0	0.065	0.013	17.714	0.459	0.459	0.000	0.000	0.000	0.000
15	A	484	ALA	0	0.024	0.010	19.984	0.421	0.421	0.000	0.000	0.000	0.000
16	A	485	ALA	0	0.037	0.020	21.862	0.076	0.076	0.000	0.000	0.000	0.000
17	A	486	GLY	0	0.026	0.007	17.766	0.333	0.333	0.000	0.000	0.000	0.000
18	A	487	VAL	0	0.006	-0.012	17.175	0.654	0.654	0.000	0.000	0.000	0.000
19	A	488	LYS	1	0.975	1.005	18.743	-11.880	-11.880	0.000	0.000	0.000	0.000
20	A	489	LEU	0	-0.004	-0.001	16.982	0.034	0.034	0.000	0.000	0.000	0.000
21	A	490	LEU	0	-0.010	-0.007	12.940	0.340	0.340	0.000	0.000	0.000	0.000
22	A	491	GLU	-1	-0.770	-0.827	16.788	14.191	14.191	0.000	0.000	0.000	0.000
23	A	492	ILE	0	0.019	0.021	20.187	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	493	LEU	0	-0.024	-0.006	13.223	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	494	ALA	0	-0.027	-0.021	17.520	0.298	0.298	0.000	0.000	0.000	0.000
26	A	495	GLU	-1	-0.694	-0.799	18.309	12.296	12.296	0.000	0.000	0.000	0.000
27	A	496	HIS	0	-0.009	0.021	18.251	-0.734	-0.734	0.000	0.000	0.000	0.000
28	A	497	VAL	0	-0.031	-0.014	15.557	-0.086	-0.086	0.000	0.000	0.000	0.000
29	A	498	HIS	0	-0.015	0.013	18.728	0.263	0.263	0.000	0.000	0.000	0.000
30	A	499	MET	0	-0.046	-0.008	13.536	0.680	0.680	0.000	0.000	0.000	0.000
31	A	500	SER	0	0.044	0.037	18.928	-0.451	-0.451	0.000	0.000	0.000	0.000
32	A	501	SER	0	0.042	-0.025	17.339	1.068	1.068	0.000	0.000	0.000	0.000
33	A	502	GLY	0	0.033	0.020	16.856	0.712	0.712	0.000	0.000	0.000	0.000
34	A	503	SER	0	-0.055	-0.036	14.288	0.085	0.085	0.000	0.000	0.000	0.000
35	A	504	PHE	0	0.006	0.020	11.257	2.112	2.112	0.000	0.000	0.000	0.000
36	A	505	ILE	0	-0.014	-0.007	9.239	-1.723	-1.723	0.000	0.000	0.000	0.000
37	A	506	ASN	0	-0.032	-0.034	7.880	4.082	4.082	0.000	0.000	0.000	0.000
38	A	507	ILE	0	0.056	0.044	10.115	1.221	1.221	0.000	0.000	0.000	0.000
39	A	508	ALA	0	0.002	0.010	11.921	-1.038	-1.038	0.000	0.000	0.000	0.000
40	A	509	VAL	0	-0.031	0.000	13.012	0.911	0.911	0.000	0.000	0.000	0.000
41	A	510	VAL	0	0.016	0.011	11.833	-0.617	-0.617	0.000	0.000	0.000	0.000
42	A	511	GLY	0	0.020	0.014	14.975	0.363	0.363	0.000	0.000	0.000	0.000
43	A	512	PRO	0	0.019	0.009	16.517	-0.392	-0.392	0.000	0.000	0.000	0.000
44	A	513	ALA	0	0.009	0.015	12.605	0.101	0.101	0.000	0.000	0.000	0.000
45	A	514	LEU	0	0.015	0.022	12.630	-0.582	-0.582	0.000	0.000	0.000	0.000
46	A	515	THR	0	-0.021	0.009	8.189	1.532	1.532	0.000	0.000	0.000	0.000
47	A	516	PHE	0	0.034	0.009	8.226	-1.623	-1.623	0.000	0.000	0.000	0.000
48	A	517	ARG	1	0.844	0.909	3.377	-40.068	-38.596	0.025	-0.818	-0.679	0.005
49	A	518	ILE	0	0.011	0.002	7.405	-2.876	-2.876	0.000	0.000	0.000	0.000
50	A	519	ARG	1	0.906	0.979	9.003	-16.461	-16.461	0.000	0.000	0.000	0.000
51	A	520	HIS	0	0.039	0.000	11.799	0.906	0.906	0.000	0.000	0.000	0.000
52	A	521	ASN	0	-0.006	-0.015	12.708	-1.772	-1.772	0.000	0.000	0.000	0.000
53	A	522	GLU	-1	-0.885	-0.946	16.002	15.598	15.598	0.000	0.000	0.000	0.000
54	A	523	GLN	0	0.016	0.023	16.781	0.026	0.026	0.000	0.000	0.000	0.000
55	A	524	ASN	0	-0.091	-0.037	14.244	0.458	0.458	0.000	0.000	0.000	0.000
56	A	525	LEU	0	0.037	0.025	12.503	1.189	1.189	0.000	0.000	0.000	0.000
57	A	526	SER	0	-0.016	-0.003	7.210	2.515	2.515	0.000	0.000	0.000	0.000
58	A	527	LEU	0	0.014	-0.014	2.979	-4.705	-3.678	0.228	-0.453	-0.802	0.002
59	A	528	ALA	0	0.039	0.044	6.428	-3.227	-3.227	0.000	0.000	0.000	0.000
60	A	529	ASP	-1	-0.852	-0.925	7.855	24.111	24.111	0.000	0.000	0.000	0.000
61	A	530	VAL	0	-0.009	-0.010	9.197	-2.351	-2.351	0.000	0.000	0.000	0.000
62	A	531	THR	0	-0.023	-0.033	7.763	-1.968	-1.968	0.000	0.000	0.000	0.000
63	A	532	GLN	0	0.038	0.022	10.719	-1.069	-1.069	0.000	0.000	0.000	0.000
64	A	533	GLN	0	0.063	0.036	13.295	-3.142	-3.142	0.000	0.000	0.000	0.000
65	A	534	ALA	0	0.012	0.004	13.463	-1.346	-1.346	0.000	0.000	0.000	0.000
66	A	535	GLY	0	-0.012	-0.004	14.776	-1.012	-1.012	0.000	0.000	0.000	0.000
67	A	536	LEU	0	-0.058	-0.032	16.434	-1.139	-1.139	0.000	0.000	0.000	0.000
68	A	537	VAL	0	-0.020	0.024	18.548	-1.042	-1.042	0.000	0.000	0.000	0.000
69	A	538	LYS	1	0.976	0.996	18.957	-14.514	-14.514	0.000	0.000	0.000	0.000
70	A	539	SER	0	0.015	0.004	20.371	-0.461	-0.461	0.000	0.000	0.000	0.000
71	A	540	GLU	-1	-0.788	-0.843	23.032	12.239	12.239	0.000	0.000	0.000	0.000
72	A	541	LEU	0	-0.019	-0.016	17.398	-0.234	-0.234	0.000	0.000	0.000	0.000
73	A	542	GLU	-1	-0.668	-0.778	21.816	13.088	13.088	0.000	0.000	0.000	0.000
74	A	543	ALA	0	-0.027	-0.008	24.018	-0.434	-0.434	0.000	0.000	0.000	0.000
75	A	544	GLN	0	-0.012	0.008	24.877	-0.345	-0.345	0.000	0.000	0.000	0.000
76	A	545	THR	0	-0.048	-0.031	22.048	-0.121	-0.121	0.000	0.000	0.000	0.000
77	A	546	GLY	0	0.035	0.030	25.266	-0.185	-0.185	0.000	0.000	0.000	0.000
78	A	547	LEU	0	-0.067	0.002	20.427	-0.039	-0.039	0.000	0.000	0.000	0.000
79	A	548	GLN	0	0.004	0.012	22.745	-0.404	-0.404	0.000	0.000	0.000	0.000
80	A	549	ILE	0	-0.042	-0.045	16.624	0.576	0.576	0.000	0.000	0.000	0.000
81	A	550	LEU	0	-0.043	-0.021	18.212	-0.259	-0.259	0.000	0.000	0.000	0.000
82	A	551	GLN	0	-0.014	-0.025	13.709	1.330	1.330	0.000	0.000	0.000	0.000
83	A	552	THR	0	0.001	0.018	11.843	-0.352	-0.352	0.000	0.000	0.000	0.000
84	A	553	GLY	0	0.030	0.022	8.793	-0.636	-0.636	0.000	0.000	0.000	0.000
85	A	554	VAL	0	0.044	0.022	2.582	-3.594	-2.124	0.726	-0.681	-1.515	0.003
86	A	555	GLY	0	0.022	0.023	4.118	-1.560	-1.085	-0.001	-0.084	-0.390	0.000
87	A	556	GLN	0	0.055	0.039	2.238	4.603	8.295	5.483	-4.753	-4.422	-0.041
88	A	0	NME	0	-0.005	0.012	3.587	-4.164	-4.025	0.015	-0.020	-0.133	0.000
89	A	2	HOH	0	-0.105	-0.105	26.878	-0.137	-0.137	0.000	0.000	0.000	0.000
90	A	9	HOH	0	0.013	0.006	21.876	0.168	0.168	0.000	0.000	0.000	0.000
91	A	12	HOH	0	-0.083	-0.070	23.816	-0.163	-0.163	0.000	0.000	0.000	0.000
92	A	14	HOH	0	0.039	0.020	4.903	-2.250	-2.250	0.000	0.000	0.000	0.000
93	A	17	HOH	0	-0.019	-0.016	18.297	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	21	HOH	0	-0.048	-0.032	20.384	-0.138	-0.138	0.000	0.000	0.000	0.000
95	A	23	HOH	0	-0.045	-0.034	22.021	-0.211	-0.211	0.000	0.000	0.000	0.000
96	A	24	HOH	0	-0.040	-0.024	21.026	-0.025	-0.025	0.000	0.000	0.000	0.000
97	A	25	HOH	0	-0.030	-0.019	23.065	-0.238	-0.238	0.000	0.000	0.000	0.000
98	A	26	HOH	0	-0.036	-0.024	3.795	-4.023	-3.826	0.001	-0.095	-0.102	0.001
99	A	31	HOH	0	-0.004	-0.009	18.799	0.015	0.015	0.000	0.000	0.000	0.000
100	A	32	HOH	0	0.022	0.015	23.891	0.162	0.162	0.000	0.000	0.000	0.000
101	A	42	HOH	0	-0.012	-0.004	11.859	0.238	0.238	0.000	0.000	0.000	0.000
102	A	44	HOH	0	-0.022	-0.019	14.854	-0.526	-0.526	0.000	0.000	0.000	0.000
103	A	45	HOH	0	-0.068	-0.056	9.176	0.536	0.536	0.000	0.000	0.000	0.000
104	A	49	HOH	0	-0.008	0.003	23.282	0.100	0.100	0.000	0.000	0.000	0.000
105	A	51	HOH	0	-0.027	-0.019	22.606	-0.045	-0.045	0.000	0.000	0.000	0.000
106	A	52	HOH	0	0.002	-0.004	21.919	0.026	0.026	0.000	0.000	0.000	0.000
107	A	56	HOH	0	-0.047	-0.027	6.465	-0.800	-0.800	0.000	0.000	0.000	0.000
108	A	57	HOH	0	-0.039	-0.027	26.553	-0.174	-0.174	0.000	0.000	0.000	0.000
109	A	59	HOH	0	-0.011	0.012	22.233	-0.120	-0.120	0.000	0.000	0.000	0.000
110	A	63	HOH	0	0.024	0.014	10.664	-0.481	-0.481	0.000	0.000	0.000	0.000
111	A	64	HOH	0	-0.022	-0.020	13.034	-0.219	-0.219	0.000	0.000	0.000	0.000
112	A	68	HOH	0	-0.019	-0.025	1.886	-10.589	-16.298	12.713	-4.780	-2.223	0.034
113	A	70	HOH	0	-0.044	-0.039	22.727	-0.110	-0.110	0.000	0.000	0.000	0.000
114	A	78	HOH	0	0.000	0.008	20.768	-0.220	-0.220	0.000	0.000	0.000	0.000
115	A	82	HOH	0	-0.028	-0.025	26.524	-0.180	-0.180	0.000	0.000	0.000	0.000
116	A	83	HOH	0	-0.028	-0.020	24.179	-0.202	-0.202	0.000	0.000	0.000	0.000
117	A	90	HOH	0	-0.029	-0.020	25.116	0.111	0.111	0.000	0.000	0.000	0.000
118	A	91	HOH	0	-0.044	-0.034	9.391	0.814	0.814	0.000	0.000	0.000	0.000
119	A	95	HOH	0	0.000	0.015	24.886	-0.109	-0.109	0.000	0.000	0.000	0.000
120	A	96	HOH	0	0.003	0.001	4.295	-4.243	-4.169	-0.001	-0.031	-0.042	0.000
121	A	107	HOH	0	-0.032	-0.019	19.585	0.027	0.027	0.000	0.000	0.000	0.000
122	A	116	HOH	0	-0.018	-0.018	9.113	-0.179	-0.179	0.000	0.000	0.000	0.000
123	A	117	HOH	0	-0.026	-0.037	2.807	-5.496	-4.553	0.226	-0.582	-0.587	0.001
124	A	118	HOH	0	-0.085	-0.094	1.302	-9.539	-63.408	87.033	-31.724	-1.440	0.086
125	A	124	HOH	0	-0.050	-0.027	24.455	0.032	0.032	0.000	0.000	0.000	0.000
126	A	125	HOH	0	-0.027	-0.024	20.833	0.231	0.231	0.000	0.000	0.000	0.000
127	A	127	HOH	0	0.007	0.007	17.807	-0.291	-0.291	0.000	0.000	0.000	0.000
128	A	128	HOH	0	-0.028	-0.021	18.367	0.157	0.157	0.000	0.000	0.000	0.000
129	A	132	HOH	0	-0.003	0.001	4.036	-5.960	-5.794	0.000	-0.084	-0.082	0.000
130	A	133	HOH	0	-0.182	-0.137	21.467	-0.138	-0.138	0.000	0.000	0.000	0.000
131	A	165	HOH	0	-0.036	-0.025	18.299	0.318	0.318	0.000	0.000	0.000	0.000
132	A	169	HOH	0	0.009	-0.001	1.698	-23.021	-28.840	13.132	-4.743	-2.569	0.055
133	A	175	HOH	0	-0.030	-0.040	22.355	-0.081	-0.081	0.000	0.000	0.000	0.000
134	A	176	HOH	0	-0.022	-0.033	26.171	-0.025	-0.025	0.000	0.000	0.000	0.000
135	A	177	HOH	0	-0.042	-0.031	25.557	-0.134	-0.134	0.000	0.000	0.000	0.000
136	A	178	HOH	0	-0.100	-0.094	24.355	-0.176	-0.176	0.000	0.000	0.000	0.000
137	A	179	HOH	0	-0.051	-0.049	24.921	0.096	0.096	0.000	0.000	0.000	0.000
138	A	180	HOH	0	-0.023	-0.022	6.723	-0.395	-0.395	0.000	0.000	0.000	0.000
139	A	196	HOH	0	0.022	0.010	23.849	0.160	0.160	0.000	0.000	0.000	0.000
140	A	199	HOH	0	-0.033	-0.017	26.368	-0.053	-0.053	0.000	0.000	0.000	0.000
141	A	207	HOH	0	0.027	0.025	24.392	-0.021	-0.021	0.000	0.000	0.000	0.000
142	A	210	HOH	0	-0.035	-0.026	22.652	-0.160	-0.160	0.000	0.000	0.000	0.000
143	A	214	HOH	0	0.003	-0.009	2.742	-4.272	-3.028	0.197	-0.708	-0.734	-0.003
144	A	259	HOH	0	-0.007	-0.014	24.405	0.051	0.051	0.000	0.000	0.000	0.000
145	A	264	HOH	0	0.020	0.018	19.100	0.301	0.301	0.000	0.000	0.000	0.000
146	A	302	HOH	0	-0.029	-0.022	16.327	0.119	0.119	0.000	0.000	0.000	0.000
147	A	305	HOH	0	-0.035	-0.027	19.761	-0.245	-0.245	0.000	0.000	0.000	0.000
148	B	72	HOH	0	-0.026	-0.015	19.064	-0.113	-0.113	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:470:GLU)