FMO DATABASE

FMODB ID: 6YZYZ

Calculation Name: 1ALY-A-Xray372

Preferred Name: CD40 ligand

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ALY

Chain ID: A

ChEMBL ID: CHEMBL3580491

UniProt ID: P29965

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1274492.021641
FMO2-HF: Nuclear repulsion	1219151.770334
FMO2-HF: Total energy	-55340.251307
FMO2-MP2: Total energy	-55502.512806

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:116:GLY)

Summations of interaction energy for fragment #1(A:116: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.
18.967	-36.188	73.697	-11.143	-7.401	-0.085

Interaction energy analysis for fragmet #1(A:116:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.059

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	118	GLN	0	0.071	0.041	1.594	10.026	-17.442	30.797	0.214	-3.544	-0.048
4	A	119	ASN	0	-0.001	0.003	1.624	8.031	-19.785	42.901	-11.329	-3.757	-0.037
5	A	120	PRO	0	-0.013	-0.004	4.134	0.487	0.616	-0.001	-0.028	-0.100	0.000
6	A	121	GLN	0	0.067	0.041	7.389	0.205	0.205	0.000	0.000	0.000	0.000
7	A	122	ILE	0	-0.074	-0.014	9.542	0.083	0.083	0.000	0.000	0.000	0.000
8	A	123	ALA	0	0.021	-0.002	10.900	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	124	ALA	0	0.011	0.006	11.411	0.077	0.077	0.000	0.000	0.000	0.000
10	A	125	HIS	0	0.016	0.043	13.618	-0.061	-0.061	0.000	0.000	0.000	0.000
11	A	126	VAL	0	0.053	0.040	14.778	0.058	0.058	0.000	0.000	0.000	0.000
12	A	127	ILE	0	-0.007	-0.008	17.086	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	128	SER	0	-0.043	-0.064	20.064	0.012	0.012	0.000	0.000	0.000	0.000
14	A	129	GLU	-1	-0.942	-0.982	23.471	0.203	0.203	0.000	0.000	0.000	0.000
15	A	130	ALA	0	0.040	0.037	25.576	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	131	SER	0	0.023	0.020	28.950	0.012	0.012	0.000	0.000	0.000	0.000
17	A	132	SER	0	0.006	0.003	30.570	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	133	LYS	1	0.939	0.974	32.484	-0.100	-0.100	0.000	0.000	0.000	0.000
19	A	134	THR	0	0.046	-0.009	34.390	0.000	0.000	0.000	0.000	0.000	0.000
20	A	135	THR	0	-0.059	0.004	31.600	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	136	SER	0	0.024	0.021	33.220	0.004	0.004	0.000	0.000	0.000	0.000
22	A	137	VAL	0	-0.027	-0.013	27.963	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	138	LEU	0	-0.010	-0.015	26.806	0.007	0.007	0.000	0.000	0.000	0.000
24	A	139	GLN	0	-0.001	0.000	25.384	0.019	0.019	0.000	0.000	0.000	0.000
25	A	140	TRP	0	0.071	0.015	20.516	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	141	ALA	0	0.011	0.004	19.588	0.012	0.012	0.000	0.000	0.000	0.000
27	A	142	GLU	-1	-0.869	-0.940	13.769	0.445	0.445	0.000	0.000	0.000	0.000
28	A	143	LYS	1	0.890	0.948	15.841	-0.155	-0.155	0.000	0.000	0.000	0.000
29	A	144	GLY	0	0.021	-0.001	16.798	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	145	TYR	0	-0.012	-0.007	14.688	0.043	0.043	0.000	0.000	0.000	0.000
31	A	146	TYR	0	-0.029	-0.006	11.125	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	147	THR	0	-0.035	-0.019	9.020	0.008	0.008	0.000	0.000	0.000	0.000
33	A	148	MET	0	0.027	0.007	9.264	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	149	SER	0	-0.063	-0.043	6.960	0.249	0.249	0.000	0.000	0.000	0.000
35	A	150	ASN	0	0.036	0.017	6.076	0.026	0.026	0.000	0.000	0.000	0.000
36	A	151	ASN	0	0.052	0.017	8.264	-0.125	-0.125	0.000	0.000	0.000	0.000
37	A	152	LEU	0	0.003	-0.002	11.459	-0.065	-0.065	0.000	0.000	0.000	0.000
38	A	153	VAL	0	-0.047	-0.024	11.961	-0.075	-0.075	0.000	0.000	0.000	0.000
39	A	154	THR	0	0.021	-0.012	13.098	0.060	0.060	0.000	0.000	0.000	0.000
40	A	155	LEU	0	0.024	0.019	15.567	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	156	GLU	-1	-0.863	-0.899	17.867	0.274	0.274	0.000	0.000	0.000	0.000
42	A	157	ASN	0	0.027	0.008	20.946	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	158	GLY	0	-0.029	0.016	23.839	0.003	0.003	0.000	0.000	0.000	0.000
44	A	159	LYS	1	0.786	0.904	21.629	-0.203	-0.203	0.000	0.000	0.000	0.000
45	A	160	GLN	0	-0.027	-0.024	22.463	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	161	LEU	0	0.009	0.017	16.590	0.025	0.025	0.000	0.000	0.000	0.000
47	A	162	THR	0	-0.007	-0.028	18.847	-0.038	-0.038	0.000	0.000	0.000	0.000
48	A	163	VAL	0	0.025	0.010	17.159	0.029	0.029	0.000	0.000	0.000	0.000
49	A	164	LYS	1	0.848	0.933	15.590	-0.255	-0.255	0.000	0.000	0.000	0.000
50	A	165	ARG	1	0.950	0.979	15.963	0.006	0.006	0.000	0.000	0.000	0.000
51	A	166	GLN	0	-0.017	0.003	19.080	0.003	0.003	0.000	0.000	0.000	0.000
52	A	167	GLY	0	0.002	-0.012	21.050	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	168	LEU	0	0.031	0.027	22.409	0.011	0.011	0.000	0.000	0.000	0.000
54	A	169	TYR	0	-0.007	-0.010	16.562	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	170	TYR	0	0.036	0.019	19.809	0.009	0.009	0.000	0.000	0.000	0.000
56	A	171	ILE	0	-0.043	-0.015	19.837	0.006	0.006	0.000	0.000	0.000	0.000
57	A	172	TYR	0	-0.028	-0.043	17.441	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	173	ALA	0	0.021	0.000	22.142	0.016	0.016	0.000	0.000	0.000	0.000
59	A	174	GLN	0	-0.046	-0.007	24.376	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	175	VAL	0	0.045	0.006	26.058	0.012	0.012	0.000	0.000	0.000	0.000
61	A	176	THR	0	-0.012	0.007	28.717	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	177	PHE	0	0.034	0.017	30.871	0.007	0.007	0.000	0.000	0.000	0.000
63	A	178	CYS	0	-0.062	-0.055	33.982	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	179	SER	0	0.045	0.001	37.019	0.003	0.003	0.000	0.000	0.000	0.000
65	A	180	ASN	0	-0.055	0.002	40.194	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	181	ARG	1	0.814	0.928	42.945	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	182	GLU	-1	-0.816	-0.920	46.015	0.016	0.016	0.000	0.000	0.000	0.000
68	A	183	ALA	0	-0.042	-0.001	45.371	0.001	0.001	0.000	0.000	0.000	0.000
69	A	184	SER	0	0.002	-0.005	42.528	0.002	0.002	0.000	0.000	0.000	0.000
70	A	185	SER	0	-0.042	-0.024	44.782	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	186	GLN	0	-0.004	-0.005	41.430	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	187	ALA	0	0.014	0.022	45.463	0.000	0.000	0.000	0.000	0.000	0.000
73	A	188	PRO	0	-0.086	-0.042	41.091	0.000	0.000	0.000	0.000	0.000	0.000
74	A	189	PHE	0	0.039	0.030	32.985	0.002	0.002	0.000	0.000	0.000	0.000
75	A	190	ILE	0	0.015	-0.013	35.578	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	191	ALA	0	0.001	0.019	30.769	0.005	0.005	0.000	0.000	0.000	0.000
77	A	192	SER	0	-0.032	-0.025	31.814	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	193	LEU	0	-0.021	0.009	24.635	0.007	0.007	0.000	0.000	0.000	0.000
79	A	194	CYS	0	0.003	-0.017	28.112	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	195	LEU	0	-0.011	-0.006	26.022	0.005	0.005	0.000	0.000	0.000	0.000
81	A	196	LYS	1	1.020	1.021	25.960	-0.098	-0.098	0.000	0.000	0.000	0.000
82	A	197	SER	0	0.035	-0.011	26.914	0.004	0.004	0.000	0.000	0.000	0.000
83	A	198	PRO	0	-0.052	-0.047	26.333	0.000	0.000	0.000	0.000	0.000	0.000
84	A	199	GLY	0	0.037	0.023	29.111	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	200	ARG	1	0.851	0.949	29.504	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	201	PHE	0	0.048	-0.001	33.049	0.004	0.004	0.000	0.000	0.000	0.000
87	A	202	GLU	-1	-0.894	-0.904	31.246	0.061	0.061	0.000	0.000	0.000	0.000
88	A	203	ARG	1	0.902	0.943	30.442	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	204	ILE	0	0.019	0.021	31.651	0.004	0.004	0.000	0.000	0.000	0.000
90	A	205	LEU	0	-0.065	-0.018	26.821	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	206	LEU	0	0.030	0.013	27.929	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	207	ARG	1	0.930	0.960	31.529	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	208	ALA	0	-0.001	0.013	32.918	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	209	ALA	0	-0.010	-0.007	34.560	0.005	0.005	0.000	0.000	0.000	0.000
95	A	210	ASN	0	0.001	0.006	35.409	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	211	THR	0	0.022	0.006	38.652	0.004	0.004	0.000	0.000	0.000	0.000
97	A	212	HIS	0	0.100	0.081	39.820	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	213	SER	0	-0.034	-0.029	42.934	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	214	SER	0	0.009	0.010	46.580	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	215	ALA	0	0.090	0.036	49.393	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	216	LYS	1	0.900	0.938	45.972	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	217	PRO	0	0.060	-0.003	45.196	0.002	0.002	0.000	0.000	0.000	0.000
103	A	219	GLY	0	0.015	0.032	40.441	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	220	GLN	0	0.018	0.011	32.965	0.007	0.007	0.000	0.000	0.000	0.000
105	A	221	GLN	0	-0.003	0.004	35.548	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	222	SER	0	0.033	0.010	30.397	0.006	0.006	0.000	0.000	0.000	0.000
107	A	223	ILE	0	-0.038	-0.002	30.135	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	224	HIS	0	0.039	0.021	23.659	0.010	0.010	0.000	0.000	0.000	0.000
109	A	225	LEU	0	-0.010	-0.004	27.318	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	226	GLY	0	0.022	-0.013	25.668	0.001	0.001	0.000	0.000	0.000	0.000
111	A	227	GLY	0	-0.011	0.002	25.283	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	228	VAL	0	-0.003	0.005	23.906	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	229	PHE	0	0.027	0.009	24.503	0.007	0.007	0.000	0.000	0.000	0.000
114	A	230	GLU	-1	-0.870	-0.942	24.242	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	231	LEU	0	-0.070	-0.027	20.881	0.013	0.013	0.000	0.000	0.000	0.000
116	A	232	GLN	0	0.105	0.041	23.766	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	233	PRO	0	-0.020	-0.013	21.790	0.008	0.008	0.000	0.000	0.000	0.000
118	A	234	GLY	0	0.004	-0.009	21.259	0.001	0.001	0.000	0.000	0.000	0.000
119	A	235	ALA	0	-0.085	-0.015	21.209	0.009	0.009	0.000	0.000	0.000	0.000
120	A	236	SER	0	-0.018	-0.019	22.666	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	237	VAL	0	0.007	-0.001	21.697	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	238	PHE	0	0.031	0.008	23.397	0.016	0.016	0.000	0.000	0.000	0.000
123	A	239	VAL	0	0.027	0.019	25.051	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	240	ASN	0	0.055	0.022	27.697	0.012	0.012	0.000	0.000	0.000	0.000
125	A	241	VAL	0	-0.022	-0.025	31.111	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	242	THR	0	0.024	-0.013	33.584	0.002	0.002	0.000	0.000	0.000	0.000
127	A	243	ASP	-1	-0.858	-0.909	36.270	0.037	0.037	0.000	0.000	0.000	0.000
128	A	244	PRO	0	0.033	-0.005	32.893	0.001	0.001	0.000	0.000	0.000	0.000
129	A	245	SER	0	0.014	0.007	33.894	0.004	0.004	0.000	0.000	0.000	0.000
130	A	246	GLN	0	0.002	0.015	35.916	0.002	0.002	0.000	0.000	0.000	0.000
131	A	247	VAL	0	-0.064	-0.012	29.829	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	248	SER	0	0.018	-0.020	30.896	0.005	0.005	0.000	0.000	0.000	0.000
133	A	249	HIS	0	0.022	0.056	27.387	0.006	0.006	0.000	0.000	0.000	0.000
134	A	250	GLY	0	-0.070	0.001	25.525	0.009	0.009	0.000	0.000	0.000	0.000
135	A	251	THR	0	0.014	-0.027	23.309	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	252	GLY	0	0.047	0.009	22.578	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	253	PHE	0	-0.034	0.002	23.626	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	254	THR	0	0.044	0.002	25.155	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	255	SER	0	-0.067	-0.044	20.293	0.012	0.012	0.000	0.000	0.000	0.000
140	A	256	PHE	0	-0.010	-0.008	20.171	-0.014	-0.014	0.000	0.000	0.000	0.000
141	A	257	GLY	0	0.036	0.015	17.667	0.024	0.024	0.000	0.000	0.000	0.000
142	A	258	LEU	0	-0.015	-0.013	15.484	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	259	LEU	0	0.022	0.014	15.228	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	260	LYS	1	0.896	0.951	15.126	0.105	0.105	0.000	0.000	0.000	0.000
145	A	261	LEU	0	-0.015	0.001	16.635	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:116:GLY)