FMO DATABASE

FMODB ID: 7GRVK

Calculation Name: 5CIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CIV

Chain ID: A

ChEMBL ID:

UniProt ID: D0EVD3

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptAll
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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1885575.495839
FMO2-HF: Nuclear repulsion	1816536.562866
FMO2-HF: Total energy	-69038.932973
FMO2-MP2: Total energy	-69244.349156

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:16:GLU)

Summations of interaction energy for fragment #1(A:16: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.
-106.658	-106.573	12.382	-6.703	-5.763	0.077

Interaction energy analysis for fragmet #1(A:16:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.953

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	18	THR	0	0.005	0.004	3.887	1.563	3.589	-0.014	-1.061	-0.951	0.004
4	A	19	SER	0	0.003	0.001	6.569	-1.356	-1.356	0.000	0.000	0.000	0.000
5	A	20	LYS	1	0.889	0.930	8.225	-17.007	-17.007	0.000	0.000	0.000	0.000
6	A	21	GLU	-1	-0.908	-0.932	10.334	16.832	16.832	0.000	0.000	0.000	0.000
7	A	22	GLU	-1	-0.842	-0.931	6.721	26.152	26.152	0.000	0.000	0.000	0.000
8	A	23	LEU	0	0.018	0.028	5.842	-0.411	-0.411	0.000	0.000	0.000	0.000
9	A	24	LYS	1	0.833	0.893	8.225	-16.557	-16.557	0.000	0.000	0.000	0.000
10	A	25	LYS	1	0.846	0.930	11.416	-18.601	-18.601	0.000	0.000	0.000	0.000
11	A	26	THR	0	-0.026	-0.021	7.102	-1.087	-1.087	0.000	0.000	0.000	0.000
12	A	27	ILE	0	-0.044	-0.014	9.186	-0.736	-0.736	0.000	0.000	0.000	0.000
13	A	28	HIS	1	0.871	0.913	11.273	-14.800	-14.800	0.000	0.000	0.000	0.000
14	A	29	ALA	0	0.001	0.006	13.028	-0.893	-0.893	0.000	0.000	0.000	0.000
15	A	30	ALA	0	-0.029	-0.021	11.746	-0.716	-0.716	0.000	0.000	0.000	0.000
16	A	31	TYR	0	0.012	0.010	13.857	-0.590	-0.590	0.000	0.000	0.000	0.000
17	A	32	LEU	0	-0.003	0.000	16.573	-0.651	-0.651	0.000	0.000	0.000	0.000
18	A	33	LEU	0	-0.057	-0.029	15.522	-0.581	-0.581	0.000	0.000	0.000	0.000
19	A	34	LEU	0	-0.056	-0.019	17.511	-0.310	-0.310	0.000	0.000	0.000	0.000
20	A	35	ASP	-1	-0.809	-0.895	19.281	10.433	10.433	0.000	0.000	0.000	0.000
21	A	36	GLY	0	0.067	0.032	22.000	-0.454	-0.454	0.000	0.000	0.000	0.000
22	A	37	GLU	-1	-0.863	-0.903	21.710	10.910	10.910	0.000	0.000	0.000	0.000
23	A	38	PHE	0	0.011	-0.011	22.290	-0.242	-0.242	0.000	0.000	0.000	0.000
24	A	39	GLU	-1	-0.823	-0.879	26.828	8.950	8.950	0.000	0.000	0.000	0.000
25	A	40	GLY	0	-0.037	-0.019	29.173	0.040	0.040	0.000	0.000	0.000	0.000
26	A	41	ILE	0	-0.122	-0.049	27.505	-0.083	-0.083	0.000	0.000	0.000	0.000
27	A	42	ASP	-1	-0.770	-0.864	31.644	7.731	7.731	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.744	-0.845	33.411	8.572	8.572	0.000	0.000	0.000	0.000
29	A	44	SER	0	-0.077	-0.060	34.711	0.067	0.067	0.000	0.000	0.000	0.000
30	A	45	GLN	0	-0.009	-0.013	33.361	0.036	0.036	0.000	0.000	0.000	0.000
31	A	46	LYS	1	0.828	0.910	31.121	-8.470	-8.470	0.000	0.000	0.000	0.000
32	A	47	ASP	-1	-0.820	-0.899	30.665	9.046	9.046	0.000	0.000	0.000	0.000
33	A	48	ASN	0	0.012	0.010	32.954	-0.092	-0.092	0.000	0.000	0.000	0.000
34	A	49	ARG	1	0.806	0.865	28.678	-9.372	-9.372	0.000	0.000	0.000	0.000
35	A	50	VAL	0	-0.008	0.001	29.764	-0.248	-0.248	0.000	0.000	0.000	0.000
36	A	51	PRO	0	0.049	0.024	30.586	0.275	0.275	0.000	0.000	0.000	0.000
37	A	52	GLU	-1	-0.894	-0.958	28.546	9.350	9.350	0.000	0.000	0.000	0.000
38	A	53	VAL	0	-0.072	-0.049	24.690	0.531	0.531	0.000	0.000	0.000	0.000
39	A	54	ASP	-1	-0.762	-0.856	23.102	12.130	12.130	0.000	0.000	0.000	0.000
40	A	55	ARG	1	0.775	0.878	22.813	-11.500	-11.500	0.000	0.000	0.000	0.000
41	A	56	THR	0	0.038	0.043	26.310	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	57	PRO	0	0.020	-0.006	26.417	0.451	0.451	0.000	0.000	0.000	0.000
43	A	58	ALA	0	0.077	0.041	26.051	0.319	0.319	0.000	0.000	0.000	0.000
44	A	59	GLU	-1	-0.757	-0.841	25.572	10.648	10.648	0.000	0.000	0.000	0.000
45	A	60	ILE	0	-0.079	-0.042	21.299	0.607	0.607	0.000	0.000	0.000	0.000
46	A	61	ILE	0	0.027	0.027	21.224	0.666	0.666	0.000	0.000	0.000	0.000
47	A	62	ALA	0	0.040	0.017	22.187	0.397	0.397	0.000	0.000	0.000	0.000
48	A	63	TYR	0	-0.051	-0.024	16.625	0.456	0.456	0.000	0.000	0.000	0.000
49	A	64	GLN	0	-0.040	-0.028	16.760	1.280	1.280	0.000	0.000	0.000	0.000
50	A	65	LEU	0	-0.018	0.007	19.055	0.434	0.434	0.000	0.000	0.000	0.000
51	A	66	GLY	0	0.054	0.027	21.798	0.024	0.024	0.000	0.000	0.000	0.000
52	A	67	TRP	0	-0.012	-0.016	16.485	0.241	0.241	0.000	0.000	0.000	0.000
53	A	68	LEU	0	-0.031	-0.004	15.244	0.434	0.434	0.000	0.000	0.000	0.000
54	A	69	HIS	0	0.015	-0.008	18.005	0.347	0.347	0.000	0.000	0.000	0.000
55	A	70	LEU	0	-0.065	-0.014	19.997	-0.178	-0.178	0.000	0.000	0.000	0.000
56	A	71	VAL	0	-0.031	-0.012	13.824	0.104	0.104	0.000	0.000	0.000	0.000
57	A	72	MET	0	-0.004	0.003	17.303	0.190	0.190	0.000	0.000	0.000	0.000
58	A	73	GLY	0	-0.040	-0.018	18.658	-0.425	-0.425	0.000	0.000	0.000	0.000
59	A	74	TRP	0	-0.002	-0.015	15.011	0.092	0.092	0.000	0.000	0.000	0.000
60	A	75	ASP	-1	-0.686	-0.820	16.797	17.397	17.397	0.000	0.000	0.000	0.000
61	A	76	ARG	1	0.954	0.988	18.776	-13.055	-13.055	0.000	0.000	0.000	0.000
62	A	77	ASP	-1	-0.845	-0.913	22.043	11.421	11.421	0.000	0.000	0.000	0.000
63	A	78	GLU	-1	-0.778	-0.892	19.289	16.203	16.203	0.000	0.000	0.000	0.000
64	A	79	LEU	0	-0.026	-0.007	19.165	-0.418	-0.418	0.000	0.000	0.000	0.000
65	A	80	ALA	0	-0.045	-0.007	23.174	-0.461	-0.461	0.000	0.000	0.000	0.000
66	A	81	GLY	0	-0.007	0.006	25.928	-0.491	-0.491	0.000	0.000	0.000	0.000
67	A	82	LYS	1	0.774	0.872	26.602	-11.622	-11.622	0.000	0.000	0.000	0.000
68	A	83	PRO	0	-0.020	-0.026	25.598	0.521	0.521	0.000	0.000	0.000	0.000
69	A	84	VAL	0	0.038	0.038	20.444	-0.235	-0.235	0.000	0.000	0.000	0.000
70	A	85	ILE	0	-0.058	-0.028	23.781	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	86	MET	0	-0.045	0.017	16.275	-0.114	-0.114	0.000	0.000	0.000	0.000
72	A	87	PRO	0	-0.042	-0.026	19.595	-0.249	-0.249	0.000	0.000	0.000	0.000
73	A	88	ALA	0	0.093	0.029	21.025	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	89	PRO	0	0.032	0.012	24.542	-0.147	-0.147	0.000	0.000	0.000	0.000
75	A	90	GLY	0	0.001	-0.003	27.843	-0.140	-0.140	0.000	0.000	0.000	0.000
76	A	91	TYR	0	-0.036	-0.016	25.776	-0.264	-0.264	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.974	0.981	24.387	-11.017	-11.017	0.000	0.000	0.000	0.000
78	A	93	TRP	0	0.111	0.033	16.241	-0.121	-0.121	0.000	0.000	0.000	0.000
79	A	94	ASN	0	-0.032	-0.018	21.935	0.536	0.536	0.000	0.000	0.000	0.000
80	A	95	GLN	0	0.022	0.021	24.745	-0.282	-0.282	0.000	0.000	0.000	0.000
81	A	96	LEU	0	0.011	0.017	19.084	-0.325	-0.325	0.000	0.000	0.000	0.000
82	A	97	GLY	0	0.013	0.015	23.342	-0.108	-0.108	0.000	0.000	0.000	0.000
83	A	98	GLY	0	0.019	0.005	25.643	-0.311	-0.311	0.000	0.000	0.000	0.000
84	A	99	LEU	0	0.017	0.023	21.539	-0.238	-0.238	0.000	0.000	0.000	0.000
85	A	100	TYR	0	0.018	0.014	18.630	-0.085	-0.085	0.000	0.000	0.000	0.000
86	A	101	GLN	0	0.029	0.011	24.563	-0.425	-0.425	0.000	0.000	0.000	0.000
87	A	102	SER	0	-0.069	-0.045	26.633	-0.281	-0.281	0.000	0.000	0.000	0.000
88	A	103	PHE	0	0.015	-0.002	20.294	-0.161	-0.161	0.000	0.000	0.000	0.000
89	A	104	TYR	0	-0.020	-0.026	23.105	-0.085	-0.085	0.000	0.000	0.000	0.000
90	A	105	ALA	0	0.005	-0.001	28.108	-0.250	-0.250	0.000	0.000	0.000	0.000
91	A	106	ALA	0	-0.045	-0.015	28.138	-0.270	-0.270	0.000	0.000	0.000	0.000
92	A	107	TYR	0	0.000	-0.005	25.111	0.160	0.160	0.000	0.000	0.000	0.000
93	A	108	ALA	0	-0.001	0.005	30.298	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	109	ASP	-1	-0.894	-0.943	32.617	8.431	8.431	0.000	0.000	0.000	0.000
95	A	110	LEU	0	-0.027	0.003	29.640	-0.113	-0.113	0.000	0.000	0.000	0.000
96	A	111	SER	0	-0.004	-0.035	32.545	0.145	0.145	0.000	0.000	0.000	0.000
97	A	112	LEU	0	0.024	0.003	27.899	0.303	0.303	0.000	0.000	0.000	0.000
98	A	113	THR	0	-0.022	-0.036	29.077	0.353	0.353	0.000	0.000	0.000	0.000
99	A	114	GLU	-1	-0.868	-0.908	30.191	8.570	8.570	0.000	0.000	0.000	0.000
100	A	115	LEU	0	-0.015	-0.006	26.839	0.316	0.316	0.000	0.000	0.000	0.000
101	A	116	ARG	1	0.790	0.847	25.284	-9.608	-9.608	0.000	0.000	0.000	0.000
102	A	117	ARG	1	0.809	0.901	25.353	-8.471	-8.471	0.000	0.000	0.000	0.000
103	A	118	LEU	0	0.059	0.031	25.904	0.233	0.233	0.000	0.000	0.000	0.000
104	A	119	PHE	0	-0.001	0.001	18.016	0.512	0.512	0.000	0.000	0.000	0.000
105	A	120	ARG	1	0.854	0.900	21.488	-9.558	-9.558	0.000	0.000	0.000	0.000
106	A	121	ASP	-1	-0.818	-0.886	22.195	10.593	10.593	0.000	0.000	0.000	0.000
107	A	122	THR	0	-0.022	-0.023	19.978	0.180	0.180	0.000	0.000	0.000	0.000
108	A	123	GLU	-1	-0.797	-0.891	16.098	15.263	15.263	0.000	0.000	0.000	0.000
109	A	124	ARG	1	0.811	0.880	18.135	-11.881	-11.881	0.000	0.000	0.000	0.000
110	A	125	GLN	0	0.046	0.014	20.026	0.437	0.437	0.000	0.000	0.000	0.000
111	A	126	TRP	0	-0.019	-0.010	12.156	0.295	0.295	0.000	0.000	0.000	0.000
112	A	127	LEU	0	-0.037	-0.028	14.199	0.794	0.794	0.000	0.000	0.000	0.000
113	A	128	ASP	-1	-0.804	-0.877	16.460	12.833	12.833	0.000	0.000	0.000	0.000
114	A	129	TRP	0	-0.041	-0.031	13.487	0.431	0.431	0.000	0.000	0.000	0.000
115	A	130	ILE	0	0.028	0.010	11.515	0.489	0.489	0.000	0.000	0.000	0.000
116	A	131	ASP	-1	-0.827	-0.900	14.237	15.870	15.870	0.000	0.000	0.000	0.000
117	A	132	THR	0	-0.103	-0.061	16.609	-0.219	-0.219	0.000	0.000	0.000	0.000
118	A	133	LEU	0	-0.020	0.019	12.655	0.051	0.051	0.000	0.000	0.000	0.000
119	A	134	SER	0	0.000	-0.028	14.857	0.164	0.164	0.000	0.000	0.000	0.000
120	A	135	GLU	-1	-0.776	-0.932	10.808	23.051	23.051	0.000	0.000	0.000	0.000
121	A	136	GLU	-1	-0.919	-0.953	10.472	22.165	22.165	0.000	0.000	0.000	0.000
122	A	137	ASP	-1	-0.783	-0.842	12.116	20.058	20.058	0.000	0.000	0.000	0.000
123	A	138	LEU	0	-0.034	-0.013	8.145	1.490	1.490	0.000	0.000	0.000	0.000
124	A	139	PHE	0	-0.043	-0.030	4.469	3.616	3.733	-0.001	-0.005	-0.111	0.000
125	A	140	THR	0	-0.038	-0.016	7.756	3.021	3.021	0.000	0.000	0.000	0.000
126	A	141	GLN	0	-0.021	-0.031	9.197	-1.216	-1.216	0.000	0.000	0.000	0.000
127	A	142	SER	0	-0.041	-0.057	11.052	-0.797	-0.797	0.000	0.000	0.000	0.000
128	A	143	VAL	0	-0.033	0.002	13.287	-1.655	-1.655	0.000	0.000	0.000	0.000
129	A	144	ARG	1	0.760	0.868	15.039	-19.260	-19.260	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.949	0.957	16.526	-14.547	-14.547	0.000	0.000	0.000	0.000
131	A	146	TRP	0	-0.040	-0.052	12.617	1.070	1.070	0.000	0.000	0.000	0.000
132	A	147	THR	0	-0.017	-0.004	11.821	-0.198	-0.198	0.000	0.000	0.000	0.000
133	A	148	GLY	0	-0.040	-0.019	12.689	1.717	1.717	0.000	0.000	0.000	0.000
134	A	149	ASP	-1	-0.812	-0.887	13.266	20.565	20.565	0.000	0.000	0.000	0.000
135	A	150	LYS	1	0.897	0.954	10.441	-21.988	-21.988	0.000	0.000	0.000	0.000
136	A	151	PRO	0	0.085	0.030	7.691	1.887	1.887	0.000	0.000	0.000	0.000
137	A	152	ASN	0	-0.041	-0.036	1.752	-35.782	-38.479	12.398	-5.555	-4.146	0.073
138	A	153	TRP	0	-0.044	-0.011	4.430	3.338	3.499	-0.001	-0.021	-0.138	0.000
139	A	154	PRO	0	0.109	0.077	5.284	-4.159	-4.159	0.000	0.000	0.000	0.000
140	A	155	MET	0	0.026	0.015	7.637	1.348	1.348	0.000	0.000	0.000	0.000
141	A	156	ALA	0	0.038	0.018	5.047	-1.144	-1.144	0.000	0.000	0.000	0.000
142	A	157	ARG	1	0.845	0.937	3.805	-52.361	-52.031	0.001	-0.053	-0.278	0.000
143	A	158	TRP	0	-0.017	-0.017	5.907	-3.334	-3.334	0.000	0.000	0.000	0.000
144	A	159	ILE	0	0.051	0.035	8.455	-1.895	-1.895	0.000	0.000	0.000	0.000
145	A	160	HIS	0	0.042	0.043	4.983	-3.242	-3.094	-0.001	-0.008	-0.139	0.000
146	A	161	ILE	0	-0.068	-0.044	7.105	-2.085	-2.085	0.000	0.000	0.000	0.000
147	A	162	ASN	0	-0.037	-0.024	9.352	-2.856	-2.856	0.000	0.000	0.000	0.000
148	A	163	SER	0	0.036	0.004	10.538	-1.278	-1.278	0.000	0.000	0.000	0.000
149	A	164	ALA	0	0.015	0.021	7.309	-0.818	-0.818	0.000	0.000	0.000	0.000
150	A	165	ALA	0	-0.044	-0.008	7.856	-0.806	-0.806	0.000	0.000	0.000	0.000
151	A	166	PRO	0	0.007	0.026	9.523	-1.340	-1.340	0.000	0.000	0.000	0.000
152	A	167	PHE	0	0.086	0.025	12.930	-1.020	-1.020	0.000	0.000	0.000	0.000
153	A	168	LYS	1	1.002	0.998	9.269	-21.879	-21.879	0.000	0.000	0.000	0.000
154	A	169	THR	0	-0.062	-0.042	12.726	-0.753	-0.753	0.000	0.000	0.000	0.000
155	A	170	PHE	0	0.001	-0.020	15.148	-0.868	-0.868	0.000	0.000	0.000	0.000
156	A	171	ARG	1	0.917	0.969	17.109	-13.614	-13.614	0.000	0.000	0.000	0.000
157	A	172	ALA	0	-0.012	-0.005	17.860	-0.665	-0.665	0.000	0.000	0.000	0.000
158	A	173	LYS	1	0.796	0.903	19.080	-13.933	-13.933	0.000	0.000	0.000	0.000
159	A	174	ILE	0	0.084	0.045	21.592	-0.488	-0.488	0.000	0.000	0.000	0.000
160	A	175	ARG	1	0.871	0.930	21.026	-11.807	-11.807	0.000	0.000	0.000	0.000
161	A	176	LYS	1	0.846	0.928	23.697	-11.680	-11.680	0.000	0.000	0.000	0.000
162	A	177	TRP	0	0.000	-0.017	25.521	-0.315	-0.315	0.000	0.000	0.000	0.000
163	A	178	LYS	1	0.890	0.924	25.761	-10.499	-10.499	0.000	0.000	0.000	0.000
164	A	179	LYS	1	0.830	0.919	28.241	-9.548	-9.548	0.000	0.000	0.000	0.000
165	A	180	HIS	1	0.837	0.915	28.727	-9.636	-9.636	0.000	0.000	0.000	0.000
166	A	181	GLN	0	0.045	0.049	31.355	-0.410	-0.410	0.000	0.000	0.000	0.000
167	A	182	ARG	1	0.858	0.921	33.817	-7.891	-7.891	0.000	0.000	0.000	0.000
168	A	183	GLN	0	0.054	0.051	32.419	0.035	0.035	0.000	0.000	0.000	0.000
169	A	184	ALA	0	0.081	0.044	32.703	0.445	0.445	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLU)