FMO DATABASE

FMODB ID: ZVJ8N

Calculation Name: 3C12-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C12

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P9B5

Base Structure: X-ray

Registration Date: 2023-09-24

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-972719.360006
FMO2-HF: Nuclear repulsion	925097.888319
FMO2-HF: Total energy	-47621.471688
FMO2-MP2: Total energy	-47762.954742

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:50:ASP)

Summations of interaction energy for fragment #1(A:50:ASP)

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.
-69.99	-61.973	15.15	-9.371	-13.798	0.099

Interaction energy analysis for fragmet #1(A:50:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.788 / q_NPA : -0.910

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	52	VAL	0	-0.130	-0.067	2.085	-21.572	-19.349	12.932	-6.611	-8.544	0.055
4	A	53	LEU	0	0.057	0.027	2.455	-21.105	-15.832	2.204	-2.591	-4.887	0.043
5	A	54	LYS	1	0.907	0.974	3.910	-50.412	-49.891	0.014	-0.169	-0.367	0.001
6	A	55	GLY	0	0.058	0.051	6.143	-5.181	-5.181	0.000	0.000	0.000	0.000
7	A	56	ALA	0	0.004	-0.019	8.114	-1.669	-1.669	0.000	0.000	0.000	0.000
8	A	57	ALA	0	-0.056	-0.034	10.146	-2.265	-2.265	0.000	0.000	0.000	0.000
9	A	58	LEU	0	-0.002	-0.001	11.069	-1.474	-1.474	0.000	0.000	0.000	0.000
10	A	59	VAL	0	-0.006	0.002	13.106	-1.248	-1.248	0.000	0.000	0.000	0.000
11	A	60	GLY	0	-0.014	0.009	15.561	-0.229	-0.229	0.000	0.000	0.000	0.000
12	A	61	HIS	0	-0.024	0.001	17.118	-1.244	-1.244	0.000	0.000	0.000	0.000
13	A	62	ASN	0	-0.052	-0.055	19.250	0.039	0.039	0.000	0.000	0.000	0.000
14	A	63	VAL	0	-0.027	-0.014	15.698	0.696	0.696	0.000	0.000	0.000	0.000
15	A	64	LEU	0	0.005	0.013	18.973	-0.843	-0.843	0.000	0.000	0.000	0.000
16	A	65	VAL	0	0.030	0.018	17.370	0.916	0.916	0.000	0.000	0.000	0.000
17	A	66	PRO	0	-0.009	-0.004	19.592	-0.943	-0.943	0.000	0.000	0.000	0.000
18	A	67	SER	0	-0.027	-0.023	22.326	0.371	0.371	0.000	0.000	0.000	0.000
19	A	68	ALA	0	0.007	0.015	24.830	-0.360	-0.360	0.000	0.000	0.000	0.000
20	A	69	GLN	0	0.021	-0.001	27.376	-0.218	-0.218	0.000	0.000	0.000	0.000
21	A	70	VAL	0	0.019	0.028	27.410	0.540	0.540	0.000	0.000	0.000	0.000
22	A	71	ALA	0	0.007	-0.005	27.789	-0.194	-0.194	0.000	0.000	0.000	0.000
23	A	72	ILE	0	-0.040	0.005	29.652	0.087	0.087	0.000	0.000	0.000	0.000
24	A	73	ASP	-1	-0.746	-0.878	31.129	9.867	9.867	0.000	0.000	0.000	0.000
25	A	74	ALA	0	0.008	-0.027	32.756	-0.216	-0.216	0.000	0.000	0.000	0.000
26	A	75	THR	0	-0.037	-0.003	33.417	-0.389	-0.389	0.000	0.000	0.000	0.000
27	A	76	GLY	0	-0.129	-0.087	34.496	-0.234	-0.234	0.000	0.000	0.000	0.000
28	A	77	SER	0	0.057	-0.011	32.986	0.037	0.037	0.000	0.000	0.000	0.000
29	A	78	ALA	0	0.008	0.025	29.997	0.335	0.335	0.000	0.000	0.000	0.000
30	A	79	LYS	1	0.930	0.969	26.825	-11.976	-11.976	0.000	0.000	0.000	0.000
31	A	80	GLY	0	0.054	0.007	27.022	0.482	0.482	0.000	0.000	0.000	0.000
32	A	81	VAL	0	-0.046	-0.016	25.501	-0.433	-0.433	0.000	0.000	0.000	0.000
33	A	82	VAL	0	0.015	-0.005	27.596	0.285	0.285	0.000	0.000	0.000	0.000
34	A	83	ALA	0	-0.002	0.001	27.146	-0.131	-0.131	0.000	0.000	0.000	0.000
35	A	84	ALA	0	0.011	0.024	29.210	-0.091	-0.091	0.000	0.000	0.000	0.000
36	A	85	THR	0	0.006	-0.010	31.639	0.021	0.021	0.000	0.000	0.000	0.000
37	A	86	SER	0	-0.023	-0.020	33.793	-0.185	-0.185	0.000	0.000	0.000	0.000
38	A	87	ALA	0	0.055	0.043	37.144	0.139	0.139	0.000	0.000	0.000	0.000
39	A	88	GLY	0	-0.024	-0.013	39.487	-0.134	-0.134	0.000	0.000	0.000	0.000
40	A	89	PHE	0	-0.050	-0.020	39.756	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	90	VAL	0	-0.008	-0.002	34.619	0.036	0.036	0.000	0.000	0.000	0.000
42	A	91	ASN	0	0.046	0.025	37.960	0.006	0.006	0.000	0.000	0.000	0.000
43	A	92	PHE	0	0.002	-0.015	32.173	0.184	0.184	0.000	0.000	0.000	0.000
44	A	93	GLU	-1	-0.930	-0.966	36.795	7.912	7.912	0.000	0.000	0.000	0.000
45	A	94	ILE	0	0.009	-0.003	34.924	0.280	0.280	0.000	0.000	0.000	0.000
46	A	95	THR	0	0.012	0.004	36.322	-0.194	-0.194	0.000	0.000	0.000	0.000
47	A	96	ASP	-1	-0.791	-0.909	36.375	8.292	8.292	0.000	0.000	0.000	0.000
48	A	97	ALA	0	-0.025	-0.020	36.020	0.086	0.086	0.000	0.000	0.000	0.000
49	A	98	ASN	0	-0.042	-0.026	37.086	0.162	0.162	0.000	0.000	0.000	0.000
50	A	99	GLY	0	0.010	0.013	38.764	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	100	THR	0	-0.091	-0.040	39.716	-0.195	-0.195	0.000	0.000	0.000	0.000
52	A	101	PHE	0	-0.008	-0.004	40.960	0.198	0.198	0.000	0.000	0.000	0.000
53	A	102	VAL	0	0.001	0.020	39.062	-0.117	-0.117	0.000	0.000	0.000	0.000
54	A	103	LYS	1	0.890	0.939	39.953	-7.927	-7.927	0.000	0.000	0.000	0.000
55	A	104	GLN	0	0.006	0.003	40.146	0.135	0.135	0.000	0.000	0.000	0.000
56	A	105	LEU	0	-0.056	-0.018	36.272	-0.144	-0.144	0.000	0.000	0.000	0.000
57	A	106	SER	0	0.001	-0.018	39.786	0.007	0.007	0.000	0.000	0.000	0.000
58	A	107	VAL	0	-0.041	-0.009	36.242	-0.078	-0.078	0.000	0.000	0.000	0.000
59	A	108	PRO	0	-0.008	0.002	38.935	0.027	0.027	0.000	0.000	0.000	0.000
60	A	109	ALA	0	0.041	0.009	36.608	0.217	0.217	0.000	0.000	0.000	0.000
61	A	110	SER	0	-0.015	-0.011	36.987	-0.089	-0.089	0.000	0.000	0.000	0.000
62	A	111	ALA	0	0.013	-0.015	37.038	-0.226	-0.226	0.000	0.000	0.000	0.000
63	A	112	ALA	0	-0.029	0.009	33.391	0.157	0.157	0.000	0.000	0.000	0.000
64	A	113	GLY	0	0.019	0.003	30.515	0.029	0.029	0.000	0.000	0.000	0.000
65	A	114	GLU	-1	-0.879	-0.932	25.404	12.257	12.257	0.000	0.000	0.000	0.000
66	A	115	VAL	0	0.010	0.005	29.688	-0.341	-0.341	0.000	0.000	0.000	0.000
67	A	116	SER	0	0.007	-0.003	29.646	0.244	0.244	0.000	0.000	0.000	0.000
68	A	117	PHE	0	-0.019	0.009	29.168	-0.359	-0.359	0.000	0.000	0.000	0.000
69	A	118	ALA	0	0.000	-0.026	32.021	0.330	0.330	0.000	0.000	0.000	0.000
70	A	119	TRP	0	-0.015	0.001	33.804	-0.170	-0.170	0.000	0.000	0.000	0.000
71	A	120	ASP	-1	-0.808	-0.885	35.003	8.296	8.296	0.000	0.000	0.000	0.000
72	A	121	GLY	0	-0.004	-0.012	36.871	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	122	THR	0	-0.028	-0.050	37.492	-0.164	-0.164	0.000	0.000	0.000	0.000
74	A	123	ASP	-1	-0.765	-0.891	40.897	7.312	7.312	0.000	0.000	0.000	0.000
75	A	124	ALA	0	-0.052	-0.046	42.989	-0.071	-0.071	0.000	0.000	0.000	0.000
76	A	125	ASN	0	-0.085	-0.035	45.425	-0.226	-0.226	0.000	0.000	0.000	0.000
77	A	126	GLY	0	-0.018	0.005	45.764	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	127	ASN	0	-0.002	0.000	45.424	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	128	ARG	1	0.846	1.003	35.787	-8.386	-8.386	0.000	0.000	0.000	0.000
80	A	129	MET	0	-0.007	0.004	38.699	-0.160	-0.160	0.000	0.000	0.000	0.000
81	A	130	ALA	0	-0.011	-0.007	38.545	0.086	0.086	0.000	0.000	0.000	0.000
82	A	131	ALA	0	0.021	0.020	33.701	0.156	0.156	0.000	0.000	0.000	0.000
83	A	132	GLY	0	-0.020	-0.017	32.096	-0.113	-0.113	0.000	0.000	0.000	0.000
84	A	133	LYS	1	0.846	0.930	25.408	-12.245	-12.245	0.000	0.000	0.000	0.000
85	A	134	TYR	0	-0.001	-0.008	31.138	-0.381	-0.381	0.000	0.000	0.000	0.000
86	A	135	GLY	0	0.002	0.022	31.582	0.434	0.434	0.000	0.000	0.000	0.000
87	A	136	ILE	0	-0.019	-0.009	30.232	-0.287	-0.287	0.000	0.000	0.000	0.000
88	A	137	THR	0	-0.012	0.000	32.025	0.361	0.361	0.000	0.000	0.000	0.000
89	A	138	ALA	0	0.015	0.015	32.720	-0.227	-0.227	0.000	0.000	0.000	0.000
90	A	139	THR	0	-0.026	-0.024	34.669	0.106	0.106	0.000	0.000	0.000	0.000
91	A	140	GLN	0	0.050	0.030	35.489	0.120	0.120	0.000	0.000	0.000	0.000
92	A	141	THR	0	-0.023	-0.015	37.814	-0.161	-0.161	0.000	0.000	0.000	0.000
93	A	142	ASP	-1	-0.828	-0.907	40.272	7.621	7.621	0.000	0.000	0.000	0.000
94	A	143	THR	0	-0.018	-0.020	41.767	-0.156	-0.156	0.000	0.000	0.000	0.000
95	A	144	ALA	0	0.009	-0.009	44.929	-0.029	-0.029	0.000	0.000	0.000	0.000
96	A	145	GLY	0	-0.050	-0.012	45.249	-0.154	-0.154	0.000	0.000	0.000	0.000
97	A	146	ALA	0	-0.020	0.006	42.217	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	147	LYS	1	0.941	0.961	40.998	-7.238	-7.238	0.000	0.000	0.000	0.000
99	A	148	SER	0	-0.019	-0.007	36.155	0.126	0.126	0.000	0.000	0.000	0.000
100	A	149	LYS	1	0.979	0.999	32.562	-9.693	-9.693	0.000	0.000	0.000	0.000
101	A	150	LEU	0	-0.020	0.003	31.132	0.146	0.146	0.000	0.000	0.000	0.000
102	A	151	ALA	0	-0.013	-0.005	26.358	-0.036	-0.036	0.000	0.000	0.000	0.000
103	A	152	THR	0	0.022	-0.003	27.985	-0.129	-0.129	0.000	0.000	0.000	0.000
104	A	153	TYR	0	-0.034	-0.014	21.728	0.334	0.334	0.000	0.000	0.000	0.000
105	A	154	VAL	0	-0.013	-0.011	24.013	-0.496	-0.496	0.000	0.000	0.000	0.000
106	A	155	ASP	-1	-0.868	-0.919	22.907	14.032	14.032	0.000	0.000	0.000	0.000
107	A	156	ALA	0	-0.001	-0.007	21.525	-0.547	-0.547	0.000	0.000	0.000	0.000
108	A	157	PRO	0	-0.007	0.016	20.860	0.694	0.694	0.000	0.000	0.000	0.000
109	A	158	VAL	0	-0.003	-0.026	14.763	0.059	0.059	0.000	0.000	0.000	0.000
110	A	159	ASP	-1	-0.945	-0.962	18.146	14.945	14.945	0.000	0.000	0.000	0.000
111	A	160	SER	0	0.005	-0.013	16.357	-0.241	-0.241	0.000	0.000	0.000	0.000
112	A	161	VAL	0	-0.031	-0.015	9.842	0.470	0.470	0.000	0.000	0.000	0.000
113	A	162	THR	0	-0.030	-0.005	12.608	-0.792	-0.792	0.000	0.000	0.000	0.000
114	A	163	ILE	0	-0.013	-0.011	7.221	1.933	1.933	0.000	0.000	0.000	0.000
115	A	164	GLY	0	0.023	0.022	10.278	-1.783	-1.783	0.000	0.000	0.000	0.000
116	A	165	SER	0	-0.027	-0.026	10.835	2.124	2.124	0.000	0.000	0.000	0.000
117	A	166	ASP	-1	-0.910	-0.940	11.412	22.501	22.501	0.000	0.000	0.000	0.000
118	A	167	GLY	0	0.021	0.023	8.029	0.666	0.666	0.000	0.000	0.000	0.000
119	A	168	LEU	0	-0.040	-0.025	6.566	-2.362	-2.362	0.000	0.000	0.000	0.000
120	A	169	TYR	0	-0.064	-0.051	8.780	-1.686	-1.686	0.000	0.000	0.000	0.000
121	A	170	LEU	0	0.009	-0.006	11.161	0.184	0.184	0.000	0.000	0.000	0.000
122	A	171	ASN	0	0.003	0.005	14.214	-0.391	-0.391	0.000	0.000	0.000	0.000
123	A	172	LEU	0	0.028	0.004	17.131	-0.254	-0.254	0.000	0.000	0.000	0.000
124	A	173	THR	0	0.069	0.023	19.936	-0.621	-0.621	0.000	0.000	0.000	0.000
125	A	174	GLY	0	-0.001	0.012	23.298	-0.251	-0.251	0.000	0.000	0.000	0.000
126	A	175	LEU	0	-0.010	-0.016	22.472	-0.309	-0.309	0.000	0.000	0.000	0.000
127	A	176	GLY	0	-0.019	-0.019	22.077	-0.342	-0.342	0.000	0.000	0.000	0.000
128	A	177	THR	0	0.022	0.012	16.785	0.708	0.708	0.000	0.000	0.000	0.000
129	A	178	SER	0	0.007	-0.003	15.476	-1.037	-1.037	0.000	0.000	0.000	0.000
130	A	179	PRO	0	-0.002	0.033	12.536	0.910	0.910	0.000	0.000	0.000	0.000
131	A	180	LEU	0	0.009	0.012	7.756	-1.438	-1.438	0.000	0.000	0.000	0.000
132	A	181	ALA	0	0.017	-0.014	10.025	2.199	2.199	0.000	0.000	0.000	0.000
133	A	182	ASN	0	-0.016	-0.001	11.930	-0.276	-0.276	0.000	0.000	0.000	0.000
134	A	183	VAL	0	-0.058	-0.030	13.503	-1.372	-1.372	0.000	0.000	0.000	0.000
135	A	184	LEU	0	-0.007	0.004	15.222	0.412	0.412	0.000	0.000	0.000	0.000
136	A	185	ARG	1	0.830	0.864	16.173	-13.648	-13.648	0.000	0.000	0.000	0.000
137	A	186	VAL	0	0.019	0.018	15.177	-0.225	-0.225	0.000	0.000	0.000	0.000
138	A	187	SER	0	0.009	0.033	17.913	-0.556	-0.556	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:50:ASP)