FMO DATABASE

FMODB ID: K3V93

Calculation Name: 3C1D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C1D

Chain ID: A

ChEMBL ID:

UniProt ID: P66000

Base Structure: X-ray

Registration Date: 2023-03-14

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1275907.452035
FMO2-HF: Nuclear repulsion	1217956.453084
FMO2-HF: Total energy	-57950.998951
FMO2-MP2: Total energy	-58122.303005

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:8:GLY)

Summations of interaction energy for fragment #1(A:8:GLY)

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.
1.173	4.711	2.141	-2.402	-3.277	0.01

Interaction energy analysis for fragmet #1(A:8:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.100 / q_NPA : 0.047

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	10	ALA	0	-0.004	-0.006	3.822	0.170	1.516	-0.002	-0.676	-0.668	0.002
4	A	11	TYR	0	0.045	0.030	2.272	0.235	0.824	1.974	-0.964	-1.600	0.004
5	A	12	ALA	0	0.045	0.024	3.770	1.676	1.966	0.000	-0.093	-0.196	0.000
6	A	13	ARG	1	0.950	0.980	5.413	3.335	3.335	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.014	-0.009	7.506	0.559	0.559	0.000	0.000	0.000	0.000
8	A	15	LEU	0	0.035	0.025	7.412	0.370	0.370	0.000	0.000	0.000	0.000
9	A	16	ASP	-1	-0.851	-0.912	9.236	-0.624	-0.624	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.892	0.945	11.489	1.042	1.042	0.000	0.000	0.000	0.000
11	A	18	ALA	0	0.007	0.007	12.383	0.147	0.147	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.045	0.018	12.637	0.126	0.126	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.850	0.916	14.537	0.841	0.841	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.072	-0.025	16.573	0.071	0.071	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.020	-0.029	16.236	0.051	0.051	0.000	0.000	0.000	0.000
16	A	23	ALA	0	-0.014	0.003	19.055	0.041	0.041	0.000	0.000	0.000	0.000
17	A	24	VAL	0	-0.051	-0.004	20.704	0.035	0.035	0.000	0.000	0.000	0.000
18	A	25	ARG	1	0.924	0.952	23.226	0.229	0.229	0.000	0.000	0.000	0.000
19	A	26	ASP	-1	-0.840	-0.907	23.309	-0.188	-0.188	0.000	0.000	0.000	0.000
20	A	27	HIS	0	-0.028	-0.005	21.332	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	28	SER	0	0.020	0.000	22.680	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.730	-0.868	17.831	-0.210	-0.210	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.021	-0.015	19.330	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.871	-0.922	21.271	-0.214	-0.214	0.000	0.000	0.000	0.000
25	A	32	LEU	0	0.003	0.012	14.905	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	33	ARG	1	0.806	0.876	15.308	0.186	0.186	0.000	0.000	0.000	0.000
27	A	34	ARG	1	0.889	0.940	17.768	0.169	0.169	0.000	0.000	0.000	0.000
28	A	35	LYS	1	0.848	0.918	19.371	0.313	0.313	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.030	-0.017	12.319	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	37	ALA	0	-0.035	-0.013	15.396	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.022	0.010	17.515	0.025	0.025	0.000	0.000	0.000	0.000
32	A	39	PRO	0	-0.019	-0.007	18.419	-0.080	-0.080	0.000	0.000	0.000	0.000
33	A	51	ALA	0	-0.009	-0.004	7.693	-0.155	-0.155	0.000	0.000	0.000	0.000
34	A	52	THR	0	-0.036	-0.027	6.795	0.415	0.415	0.000	0.000	0.000	0.000
35	A	53	ALA	0	0.045	0.001	9.069	-0.143	-0.143	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.882	-0.946	7.379	1.149	1.149	0.000	0.000	0.000	0.000
37	A	55	ASP	-1	-0.849	-0.921	4.098	-2.573	-2.420	-0.001	-0.056	-0.095	0.000
38	A	56	TYR	0	0.005	-0.017	6.428	-0.161	-0.161	0.000	0.000	0.000	0.000
39	A	57	GLU	-1	-0.800	-0.880	9.855	-0.206	-0.206	0.000	0.000	0.000	0.000
40	A	58	ARG	1	0.951	0.984	2.736	-6.116	-4.956	0.170	-0.613	-0.718	0.004
41	A	59	VAL	0	-0.027	-0.012	7.247	0.002	0.002	0.000	0.000	0.000	0.000
42	A	60	ILE	0	-0.015	-0.001	9.489	0.084	0.084	0.000	0.000	0.000	0.000
43	A	61	ALA	0	0.034	0.012	11.478	0.039	0.039	0.000	0.000	0.000	0.000
44	A	62	TRP	0	0.029	0.020	9.876	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	63	CYS	0	-0.056	-0.046	12.020	0.018	0.018	0.000	0.000	0.000	0.000
46	A	64	HIS	0	-0.041	-0.032	14.707	0.036	0.036	0.000	0.000	0.000	0.000
47	A	65	GLU	-1	-0.965	-0.965	14.081	0.095	0.095	0.000	0.000	0.000	0.000
48	A	66	HIS	1	0.834	0.914	13.193	0.145	0.145	0.000	0.000	0.000	0.000
49	A	67	GLY	0	0.054	0.048	17.105	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	68	TYR	0	-0.007	-0.017	16.529	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	69	LEU	0	-0.046	-0.017	16.594	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	70	ASP	-1	-0.753	-0.875	19.833	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	71	ASP	-1	-0.818	-0.921	22.872	-0.151	-0.151	0.000	0.000	0.000	0.000
54	A	72	SER	0	-0.068	-0.031	24.980	0.007	0.007	0.000	0.000	0.000	0.000
55	A	73	ARG	1	0.914	0.953	22.235	0.158	0.158	0.000	0.000	0.000	0.000
56	A	74	PHE	0	-0.038	-0.023	25.781	0.002	0.002	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.006	-0.017	27.822	0.002	0.002	0.000	0.000	0.000	0.000
58	A	76	ALA	0	0.062	0.042	30.599	0.004	0.004	0.000	0.000	0.000	0.000
59	A	77	ARG	1	0.872	0.930	27.692	0.124	0.124	0.000	0.000	0.000	0.000
60	A	78	PHE	0	-0.038	-0.016	31.338	0.000	0.000	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.040	0.014	33.285	0.002	0.002	0.000	0.000	0.000	0.000
62	A	80	ALA	0	0.062	0.037	36.134	0.002	0.002	0.000	0.000	0.000	0.000
63	A	81	SER	0	-0.090	-0.046	35.417	0.003	0.003	0.000	0.000	0.000	0.000
64	A	82	ARG	1	0.785	0.857	35.772	0.096	0.096	0.000	0.000	0.000	0.000
65	A	83	SER	0	0.026	0.021	38.689	0.004	0.004	0.000	0.000	0.000	0.000
66	A	84	ARG	1	0.972	0.988	37.101	0.081	0.081	0.000	0.000	0.000	0.000
67	A	85	LYS	1	0.865	0.937	37.147	0.102	0.102	0.000	0.000	0.000	0.000
68	A	86	GLY	0	0.016	0.022	42.840	0.000	0.000	0.000	0.000	0.000	0.000
69	A	87	TYR	0	-0.077	-0.027	41.054	0.000	0.000	0.000	0.000	0.000	0.000
70	A	88	GLY	0	0.077	0.033	42.983	0.001	0.001	0.000	0.000	0.000	0.000
71	A	89	PRO	0	0.057	0.016	40.818	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	90	ALA	0	-0.003	0.008	40.064	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	91	ARG	1	0.904	0.952	40.129	0.073	0.073	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.010	0.009	36.246	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	93	ARG	1	0.871	0.909	35.570	0.040	0.040	0.000	0.000	0.000	0.000
76	A	94	GLN	0	-0.012	0.008	34.837	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	95	GLU	-1	-0.814	-0.891	34.073	-0.100	-0.100	0.000	0.000	0.000	0.000
78	A	96	LEU	0	0.003	-0.009	30.962	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	97	ASN	0	0.024	0.021	29.987	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	98	GLN	0	-0.007	-0.002	29.582	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.795	0.884	27.415	0.144	0.144	0.000	0.000	0.000	0.000
82	A	100	GLY	0	-0.006	0.009	25.411	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	101	ILE	0	-0.007	0.017	25.430	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	102	SER	0	0.066	0.037	27.002	0.005	0.005	0.000	0.000	0.000	0.000
85	A	103	ARG	1	1.019	0.984	28.642	0.038	0.038	0.000	0.000	0.000	0.000
86	A	104	GLU	-1	-0.912	-0.958	29.482	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	105	ALA	0	0.016	0.013	28.345	0.003	0.003	0.000	0.000	0.000	0.000
88	A	106	THR	0	-0.015	-0.012	30.524	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	107	GLU	-1	-0.850	-0.924	33.215	-0.042	-0.042	0.000	0.000	0.000	0.000
90	A	108	LYS	1	0.891	0.953	31.437	0.028	0.028	0.000	0.000	0.000	0.000
91	A	109	ALA	0	0.025	0.011	32.963	0.001	0.001	0.000	0.000	0.000	0.000
92	A	110	MET	0	-0.051	-0.032	35.007	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.902	0.953	38.233	0.025	0.025	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.866	-0.930	35.127	-0.030	-0.030	0.000	0.000	0.000	0.000
95	A	113	ALA	0	-0.078	-0.023	38.275	0.000	0.000	0.000	0.000	0.000	0.000
96	A	114	ASP	-1	-0.932	-0.959	39.813	-0.028	-0.028	0.000	0.000	0.000	0.000
97	A	115	ILE	0	-0.031	-0.013	40.458	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.830	-0.912	44.408	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	117	TRP	0	0.002	-0.036	40.715	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	118	ALA	0	0.059	0.035	47.483	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	119	ALA	0	0.016	0.019	50.749	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	120	LEU	0	-0.047	-0.024	45.056	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	121	ALA	0	-0.004	-0.006	49.193	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.910	0.959	50.596	0.032	0.032	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.878	-0.938	50.916	-0.048	-0.048	0.000	0.000	0.000	0.000
106	A	124	GLN	0	-0.014	-0.018	48.042	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	125	ALA	0	-0.027	-0.014	51.477	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	126	THR	0	0.013	0.007	54.738	0.000	0.000	0.000	0.000	0.000	0.000
109	A	127	ARG	1	0.870	0.960	48.195	0.052	0.052	0.000	0.000	0.000	0.000
110	A	128	LYS	1	0.853	0.947	52.642	0.051	0.051	0.000	0.000	0.000	0.000
111	A	129	TYR	0	-0.056	-0.055	54.818	0.000	0.000	0.000	0.000	0.000	0.000
112	A	130	GLY	0	0.041	0.039	58.733	0.001	0.001	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.870	-0.942	59.915	-0.034	-0.034	0.000	0.000	0.000	0.000
114	A	132	PRO	0	0.016	-0.015	62.073	0.000	0.000	0.000	0.000	0.000	0.000
115	A	133	LEU	0	-0.026	0.002	57.913	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	134	PRO	0	0.018	0.021	61.095	0.001	0.001	0.000	0.000	0.000	0.000
117	A	135	THR	0	-0.009	-0.015	63.140	0.000	0.000	0.000	0.000	0.000	0.000
118	A	136	VAL	0	0.015	0.034	65.601	0.001	0.001	0.000	0.000	0.000	0.000
119	A	137	PHE	0	0.054	0.015	64.287	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	138	SER	0	0.017	-0.006	63.749	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	139	GLU	-1	-0.894	-0.960	62.362	-0.034	-0.034	0.000	0.000	0.000	0.000
122	A	140	LYS	1	0.967	1.001	60.548	0.026	0.026	0.000	0.000	0.000	0.000
123	A	141	VAL	0	0.048	0.028	58.933	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	142	LYS	1	0.916	0.959	57.578	0.037	0.037	0.000	0.000	0.000	0.000
125	A	143	ILE	0	0.017	0.010	55.977	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	144	GLN	0	0.034	0.005	54.600	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	145	ARG	1	0.963	0.999	51.420	0.047	0.047	0.000	0.000	0.000	0.000
128	A	146	PHE	0	-0.058	-0.040	50.185	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	147	LEU	0	0.030	0.024	49.853	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.038	0.014	48.568	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	149	TYR	0	-0.055	-0.029	47.286	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	150	ARG	1	0.815	0.914	45.367	0.058	0.058	0.000	0.000	0.000	0.000
133	A	151	GLY	0	0.013	0.007	43.626	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	152	TYR	0	-0.012	-0.002	44.645	0.000	0.000	0.000	0.000	0.000	0.000
135	A	153	LEU	0	-0.016	-0.008	44.586	0.000	0.000	0.000	0.000	0.000	0.000
136	A	154	MET	0	0.032	0.009	48.460	0.000	0.000	0.000	0.000	0.000	0.000
137	A	155	GLU	-1	-0.885	-0.950	50.312	-0.029	-0.029	0.000	0.000	0.000	0.000
138	A	156	ASP	-1	-0.819	-0.911	47.391	-0.039	-0.039	0.000	0.000	0.000	0.000
139	A	157	ILE	0	-0.068	-0.052	50.809	0.000	0.000	0.000	0.000	0.000	0.000
140	A	158	GLN	0	-0.065	-0.036	53.663	0.000	0.000	0.000	0.000	0.000	0.000
141	A	159	ASP	-1	-0.852	-0.922	55.799	-0.023	-0.023	0.000	0.000	0.000	0.000
142	A	160	ILE	0	-0.101	-0.033	54.220	0.000	0.000	0.000	0.000	0.000	0.000
143	A	161	TRP	0	-0.029	-0.027	57.156	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLY)