FMO DATABASE

FMODB ID: 397NL

Calculation Name: 3CYP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CYP

Chain ID: B

ChEMBL ID:

UniProt ID: P56427

Base Structure: X-ray

Registration Date: 2023-06-22

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1209201.505953
FMO2-HF: Nuclear repulsion	1155712.590299
FMO2-HF: Total energy	-53488.915653
FMO2-MP2: Total energy	-53645.464127

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(B:119:GLY)

Summations of interaction energy for fragment #1(B:119: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.
-2.258	0.529	2.683	-2.26	-3.212	-0.005

Interaction energy analysis for fragmet #1(B:119:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.013

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	B	121	ASP	-1	-0.830	-0.868	3.864	-4.885	-3.396	-0.005	-0.731	-0.753	0.003
4	B	122	PRO	0	-0.054	-0.027	6.197	0.613	0.613	0.000	0.000	0.000	0.000
5	B	123	PHE	0	0.058	-0.016	9.571	0.002	0.002	0.000	0.000	0.000	0.000
6	B	124	THR	0	0.043	0.011	12.307	0.136	0.136	0.000	0.000	0.000	0.000
7	B	125	PHE	0	-0.041	-0.033	14.590	0.024	0.024	0.000	0.000	0.000	0.000
8	B	126	GLU	-1	-0.857	-0.922	17.898	-0.543	-0.543	0.000	0.000	0.000	0.000
9	B	127	ASN	0	-0.010	-0.006	20.227	0.052	0.052	0.000	0.000	0.000	0.000
10	B	128	ALA	0	0.076	0.048	22.817	-0.009	-0.009	0.000	0.000	0.000	0.000
11	B	129	THR	0	-0.019	-0.011	23.786	0.004	0.004	0.000	0.000	0.000	0.000
12	B	130	SER	0	-0.081	-0.039	23.519	0.008	0.008	0.000	0.000	0.000	0.000
13	B	131	ASP	-1	-0.707	-0.836	22.308	-0.316	-0.316	0.000	0.000	0.000	0.000
14	B	132	ALA	0	-0.022	-0.010	22.592	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	133	ILE	0	0.012	-0.002	17.532	-0.016	-0.016	0.000	0.000	0.000	0.000
16	B	134	ASN	0	0.018	0.019	17.064	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	135	GLN	0	0.058	0.014	18.906	-0.010	-0.010	0.000	0.000	0.000	0.000
18	B	136	ASP	-1	-0.864	-0.930	15.232	-0.640	-0.640	0.000	0.000	0.000	0.000
19	B	137	MET	0	0.016	0.033	12.074	-0.184	-0.184	0.000	0.000	0.000	0.000
20	B	138	MET	0	-0.059	-0.029	14.737	-0.052	-0.052	0.000	0.000	0.000	0.000
21	B	139	LEU	0	0.007	0.004	15.274	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	140	TYR	0	-0.020	-0.039	5.801	0.029	0.029	0.000	0.000	0.000	0.000
23	B	141	ILE	0	-0.010	-0.019	11.426	-0.097	-0.097	0.000	0.000	0.000	0.000
24	B	142	GLU	-1	-0.818	-0.886	13.576	-0.440	-0.440	0.000	0.000	0.000	0.000
25	B	143	ARG	1	0.812	0.891	6.174	1.768	1.768	0.000	0.000	0.000	0.000
26	B	144	ILE	0	0.016	0.000	7.200	0.112	0.112	0.000	0.000	0.000	0.000
27	B	145	ALA	0	-0.001	-0.008	10.600	0.159	0.159	0.000	0.000	0.000	0.000
28	B	146	LYS	1	0.862	0.923	13.652	0.573	0.573	0.000	0.000	0.000	0.000
29	B	147	ILE	0	-0.017	0.008	7.059	0.096	0.096	0.000	0.000	0.000	0.000
30	B	148	ILE	0	0.023	-0.003	11.150	0.152	0.152	0.000	0.000	0.000	0.000
31	B	149	GLN	0	-0.111	-0.071	13.012	0.120	0.120	0.000	0.000	0.000	0.000
32	B	150	LYS	1	0.817	0.912	11.745	0.314	0.314	0.000	0.000	0.000	0.000
33	B	151	LEU	0	-0.015	0.012	10.375	0.080	0.080	0.000	0.000	0.000	0.000
34	B	152	PRO	0	-0.006	-0.004	14.474	-0.019	-0.019	0.000	0.000	0.000	0.000
35	B	153	LYS	1	0.970	0.969	17.787	0.033	0.033	0.000	0.000	0.000	0.000
36	B	154	ARG	1	0.788	0.870	20.102	-0.107	-0.107	0.000	0.000	0.000	0.000
37	B	155	VAL	0	-0.024	0.004	13.827	0.009	0.009	0.000	0.000	0.000	0.000
38	B	156	HIS	0	-0.029	0.001	17.301	-0.023	-0.023	0.000	0.000	0.000	0.000
39	B	157	ILE	0	-0.015	-0.012	12.771	0.013	0.013	0.000	0.000	0.000	0.000
40	B	158	ASN	0	-0.044	-0.018	15.086	0.019	0.019	0.000	0.000	0.000	0.000
41	B	159	VAL	0	0.027	0.018	14.958	-0.035	-0.035	0.000	0.000	0.000	0.000
42	B	160	ARG	1	0.874	0.936	14.978	0.258	0.258	0.000	0.000	0.000	0.000
43	B	161	GLY	0	0.034	0.022	15.716	-0.079	-0.079	0.000	0.000	0.000	0.000
44	B	162	PHE	0	-0.008	-0.009	14.792	0.065	0.065	0.000	0.000	0.000	0.000
45	B	163	THR	0	-0.054	-0.056	19.320	-0.027	-0.027	0.000	0.000	0.000	0.000
46	B	164	ASP	-1	-0.736	-0.828	21.034	-0.256	-0.256	0.000	0.000	0.000	0.000
47	B	165	ASP	-1	-0.820	-0.915	22.838	-0.158	-0.158	0.000	0.000	0.000	0.000
48	B	166	THR	0	-0.052	-0.036	25.338	0.021	0.021	0.000	0.000	0.000	0.000
49	B	167	PRO	0	-0.026	-0.012	27.836	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	168	LEU	0	-0.015	-0.008	27.376	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	169	VAL	0	0.038	0.012	31.337	0.011	0.011	0.000	0.000	0.000	0.000
52	B	170	LYS	1	0.928	0.968	31.657	0.166	0.166	0.000	0.000	0.000	0.000
53	B	171	THR	0	-0.004	-0.009	28.876	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	172	ARG	1	0.827	0.898	27.344	0.246	0.246	0.000	0.000	0.000	0.000
55	B	173	PHE	0	-0.075	-0.024	26.908	0.002	0.002	0.000	0.000	0.000	0.000
56	B	174	LYS	1	0.909	0.924	31.294	0.142	0.142	0.000	0.000	0.000	0.000
57	B	175	SER	0	0.025	0.007	30.309	0.006	0.006	0.000	0.000	0.000	0.000
58	B	176	HIS	0	0.066	0.016	25.456	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	177	TYR	0	0.053	0.032	25.023	-0.021	-0.021	0.000	0.000	0.000	0.000
60	B	178	GLU	-1	-0.810	-0.869	25.972	-0.162	-0.162	0.000	0.000	0.000	0.000
61	B	179	LEU	0	0.004	0.021	23.678	-0.010	-0.010	0.000	0.000	0.000	0.000
62	B	180	ALA	0	-0.003	0.003	21.650	-0.027	-0.027	0.000	0.000	0.000	0.000
63	B	181	ALA	0	0.004	0.000	21.512	-0.026	-0.026	0.000	0.000	0.000	0.000
64	B	182	ASN	0	-0.064	-0.040	23.364	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	183	ARG	1	0.760	0.879	19.253	0.374	0.374	0.000	0.000	0.000	0.000
66	B	184	ALA	0	0.044	0.023	18.519	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	185	TYR	0	-0.012	-0.005	19.576	-0.012	-0.012	0.000	0.000	0.000	0.000
68	B	186	ARG	1	0.857	0.920	21.302	0.341	0.341	0.000	0.000	0.000	0.000
69	B	187	VAL	0	0.050	0.022	14.898	0.003	0.003	0.000	0.000	0.000	0.000
70	B	188	MET	0	0.005	0.014	17.824	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	189	LYS	1	0.921	0.960	19.278	0.263	0.263	0.000	0.000	0.000	0.000
72	B	190	VAL	0	0.005	0.015	17.745	0.020	0.020	0.000	0.000	0.000	0.000
73	B	191	LEU	0	0.002	-0.003	13.429	0.000	0.000	0.000	0.000	0.000	0.000
74	B	192	ILE	0	-0.022	-0.008	17.444	0.027	0.027	0.000	0.000	0.000	0.000
75	B	193	GLN	0	-0.065	-0.028	20.664	0.035	0.035	0.000	0.000	0.000	0.000
76	B	194	TYR	0	-0.038	-0.032	17.739	0.024	0.024	0.000	0.000	0.000	0.000
77	B	195	GLY	0	0.032	0.029	18.836	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	196	VAL	0	-0.042	-0.007	15.699	0.030	0.030	0.000	0.000	0.000	0.000
79	B	197	ASN	0	0.015	-0.001	18.797	0.012	0.012	0.000	0.000	0.000	0.000
80	B	198	PRO	0	0.048	0.003	21.044	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	199	ASN	0	-0.002	0.014	22.978	0.003	0.003	0.000	0.000	0.000	0.000
82	B	200	GLN	0	-0.056	-0.033	17.825	0.009	0.009	0.000	0.000	0.000	0.000
83	B	201	LEU	0	-0.006	-0.001	16.463	-0.024	-0.024	0.000	0.000	0.000	0.000
84	B	202	SER	0	0.013	0.010	19.170	0.032	0.032	0.000	0.000	0.000	0.000
85	B	203	PHE	0	0.019	-0.002	18.952	-0.037	-0.037	0.000	0.000	0.000	0.000
86	B	204	SER	0	-0.034	-0.016	19.496	0.045	0.045	0.000	0.000	0.000	0.000
87	B	205	SER	0	-0.036	-0.028	20.134	-0.042	-0.042	0.000	0.000	0.000	0.000
88	B	206	TYR	0	0.053	0.028	18.841	0.035	0.035	0.000	0.000	0.000	0.000
89	B	207	GLY	0	0.008	0.016	21.996	0.019	0.019	0.000	0.000	0.000	0.000
90	B	208	SER	0	0.008	0.012	21.873	-0.021	-0.021	0.000	0.000	0.000	0.000
91	B	209	THR	0	-0.049	-0.031	22.700	0.013	0.013	0.000	0.000	0.000	0.000
92	B	210	ASN	0	-0.037	-0.030	18.153	-0.004	-0.004	0.000	0.000	0.000	0.000
93	B	211	PRO	0	0.000	0.015	17.627	-0.041	-0.041	0.000	0.000	0.000	0.000
94	B	212	ILE	0	0.012	0.010	11.906	0.028	0.028	0.000	0.000	0.000	0.000
95	B	213	ALA	0	-0.015	-0.006	15.656	0.043	0.043	0.000	0.000	0.000	0.000
96	B	214	PRO	0	0.031	0.032	18.353	-0.017	-0.017	0.000	0.000	0.000	0.000
97	B	215	ASN	0	0.002	-0.007	21.704	-0.044	-0.044	0.000	0.000	0.000	0.000
98	B	216	ASP	-1	-0.816	-0.912	23.208	-0.120	-0.120	0.000	0.000	0.000	0.000
99	B	217	SER	0	-0.027	-0.036	21.484	0.001	0.001	0.000	0.000	0.000	0.000
100	B	218	LEU	0	0.007	0.009	21.931	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	219	GLU	-1	-0.752	-0.871	17.891	-0.261	-0.261	0.000	0.000	0.000	0.000
102	B	220	ASN	0	-0.043	0.002	17.401	-0.083	-0.083	0.000	0.000	0.000	0.000
103	B	221	ARG	1	0.903	0.939	18.444	0.161	0.161	0.000	0.000	0.000	0.000
104	B	222	MET	0	-0.048	-0.026	17.493	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	223	LYS	1	0.870	0.927	13.369	0.299	0.299	0.000	0.000	0.000	0.000
106	B	224	ASN	0	-0.011	-0.017	14.957	-0.074	-0.074	0.000	0.000	0.000	0.000
107	B	225	ASN	0	-0.019	-0.017	17.607	0.020	0.020	0.000	0.000	0.000	0.000
108	B	226	ARG	1	0.791	0.893	13.030	0.397	0.397	0.000	0.000	0.000	0.000
109	B	227	VAL	0	-0.033	-0.023	14.280	0.115	0.115	0.000	0.000	0.000	0.000
110	B	228	GLU	-1	-0.822	-0.894	10.923	-0.669	-0.669	0.000	0.000	0.000	0.000
111	B	229	ILE	0	-0.003	-0.009	9.300	0.116	0.116	0.000	0.000	0.000	0.000
112	B	230	PHE	0	0.014	0.016	10.020	0.051	0.051	0.000	0.000	0.000	0.000
113	B	231	PHE	0	0.035	0.003	8.036	0.013	0.013	0.000	0.000	0.000	0.000
114	B	232	SER	0	-0.011	0.002	13.350	0.050	0.050	0.000	0.000	0.000	0.000
115	B	233	THR	0	0.013	-0.014	14.362	-0.020	-0.020	0.000	0.000	0.000	0.000
116	B	234	ASP	-1	-0.765	-0.834	17.509	0.162	0.162	0.000	0.000	0.000	0.000
117	B	235	ALA	0	0.086	0.025	17.477	0.022	0.022	0.000	0.000	0.000	0.000
118	B	236	ASN	0	-0.039	-0.022	17.476	0.058	0.058	0.000	0.000	0.000	0.000
119	B	237	ASP	-1	-0.757	-0.878	16.703	0.150	0.150	0.000	0.000	0.000	0.000
120	B	238	LEU	0	-0.001	0.010	12.523	0.009	0.009	0.000	0.000	0.000	0.000
121	B	239	SER	0	0.011	-0.004	12.390	0.116	0.116	0.000	0.000	0.000	0.000
122	B	240	LYS	1	0.825	0.910	13.028	-0.118	-0.118	0.000	0.000	0.000	0.000
123	B	241	ILE	0	0.007	0.003	8.860	0.004	0.004	0.000	0.000	0.000	0.000
124	B	242	HIS	0	-0.035	-0.016	7.925	-0.140	-0.140	0.000	0.000	0.000	0.000
125	B	243	SER	0	0.001	0.002	7.986	0.258	0.258	0.000	0.000	0.000	0.000
126	B	244	ILE	0	-0.017	0.000	8.855	0.046	0.046	0.000	0.000	0.000	0.000
127	B	245	LEU	0	-0.003	-0.017	4.245	-0.275	-0.216	-0.001	-0.010	-0.048	0.000
128	B	246	ASP	-1	-0.843	-0.896	4.212	2.823	2.970	-0.001	-0.035	-0.112	0.000
129	B	247	ASN	0	-0.013	-0.032	6.112	-0.057	-0.057	0.000	0.000	0.000	0.000
130	B	248	GLU	-1	-0.863	-0.902	5.870	-0.769	-0.769	0.000	0.000	0.000	0.000
131	B	249	PHE	0	-0.050	-0.025	2.125	-2.817	-1.906	2.691	-1.450	-2.152	-0.008
132	B	250	ASN	0	-0.039	-0.006	4.215	0.419	0.600	-0.001	-0.034	-0.147	0.000
133	B	251	PRO	0	-0.028	-0.003	6.562	-0.228	-0.228	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:119:GLY)