Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6N49Z

Calculation Name: 1AD0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AD0

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptHSide
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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2288285.296455
FMO2-HF: Nuclear repulsion 2204420.548495
FMO2-HF: Total energy -83864.747961
FMO2-MP2: Total energy -84108.709738


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


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


Summations of interaction energy for fragment #1(B:1: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.
-90.168-90.57714.214-7.601-6.2050.062
Interaction energy analysis for fragmet #1(B:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.872 / q_NPA : -0.925
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   
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].
3B3GLN0-0.033-0.0261.711-28.409-30.03114.146-6.924-5.6010.066
4B4LEU0-0.035-0.0244.942-5.569-5.515-0.001-0.005-0.0470.000
5B5LEU00.0270.0178.5410.7250.7250.0000.0000.0000.000
6B6GLU-1-0.771-0.88211.05321.08521.0850.0000.0000.0000.000
7B7SER0-0.040-0.02014.675-0.168-0.1680.0000.0000.0000.000
8B8GLY00.0300.00217.682-0.298-0.2980.0000.0000.0000.000
9B9GLY0-0.0050.00920.734-0.670-0.6700.0000.0000.0000.000
10B10GLY00.0370.00722.5750.1550.1550.0000.0000.0000.000
11B11LEU0-0.048-0.01025.662-0.045-0.0450.0000.0000.0000.000
12B12VAL0-0.032-0.01328.552-0.050-0.0500.0000.0000.0000.000
13B13GLN00.0540.03231.258-0.170-0.1700.0000.0000.0000.000
14B14PRO00.004-0.02334.4440.1320.1320.0000.0000.0000.000
15B15GLY0-0.015-0.00235.202-0.228-0.2280.0000.0000.0000.000
16B16GLY0-0.036-0.00634.008-0.108-0.1080.0000.0000.0000.000
17B17SER0-0.024-0.04830.9280.0220.0220.0000.0000.0000.000
18B18LEU0-0.015-0.00324.815-0.002-0.0020.0000.0000.0000.000
19B19ARG10.8800.96322.945-12.589-12.5890.0000.0000.0000.000
20B20LEU00.0060.02219.7470.2710.2710.0000.0000.0000.000
21B21SER0-0.064-0.04118.016-0.134-0.1340.0000.0000.0000.000
22B22CYS0-0.055-0.02412.9710.1670.1670.0000.0000.0000.000
23B23ALA00.0150.03212.603-0.659-0.6590.0000.0000.0000.000
24B24THR0-0.038-0.0379.2741.6641.6640.0000.0000.0000.000
25B25SER00.0290.0036.7840.4090.4090.0000.0000.0000.000
26B26GLY00.0710.0393.4622.3672.6810.021-0.200-0.1360.000
27B27PHE0-0.034-0.0263.216-2.098-1.2530.048-0.472-0.421-0.004
28B28THR00.0010.0086.035-0.156-0.1560.0000.0000.0000.000
29B29PHE00.0820.0519.733-1.285-1.2850.0000.0000.0000.000
30B30THR0-0.059-0.04811.737-0.618-0.6180.0000.0000.0000.000
31B31ASP-1-0.845-0.93212.21216.03016.0300.0000.0000.0000.000
32B32TYR0-0.0060.0069.7830.0620.0620.0000.0000.0000.000
33B33TYR00.0090.03513.958-0.532-0.5320.0000.0000.0000.000
34B34MET0-0.0240.00111.9710.9880.9880.0000.0000.0000.000
35B35ASN00.032-0.00115.819-1.770-1.7700.0000.0000.0000.000
36B36TRP00.0330.01616.6751.0321.0320.0000.0000.0000.000
37B37VAL0-0.0010.00617.962-0.828-0.8280.0000.0000.0000.000
38B38ARG10.8020.89319.087-10.765-10.7650.0000.0000.0000.000
39B39GLN00.0450.02520.2410.3930.3930.0000.0000.0000.000
40B40ALA00.0720.04822.6960.0430.0430.0000.0000.0000.000
41B41PRO00.0560.01625.2130.0550.0550.0000.0000.0000.000
42B42GLY0-0.023-0.01725.614-0.352-0.3520.0000.0000.0000.000
43B43LYS10.8350.93026.690-11.132-11.1320.0000.0000.0000.000
44B44GLY00.0450.01824.9520.3990.3990.0000.0000.0000.000
45B45LEU0-0.0030.00218.9800.1600.1600.0000.0000.0000.000
46B46GLU-1-0.801-0.86022.78210.72410.7240.0000.0000.0000.000
47B47TRP0-0.040-0.02220.5550.1100.1100.0000.0000.0000.000
48B48LEU0-0.010-0.00922.159-0.500-0.5000.0000.0000.0000.000
49B49GLY00.0600.00022.264-0.629-0.6290.0000.0000.0000.000
50B50PHE0-0.064-0.03020.1930.7210.7210.0000.0000.0000.000
51B51ILE0-0.0200.00619.364-0.644-0.6440.0000.0000.0000.000
52B52GLY00.0360.00419.3990.7320.7320.0000.0000.0000.000
53B52ASN00.0030.00116.574-0.399-0.3990.0000.0000.0000.000
54B52LYS10.8640.95418.488-12.495-12.4950.0000.0000.0000.000
55B52ALA00.0190.00420.583-0.150-0.1500.0000.0000.0000.000
56B53ASN00.002-0.01422.315-0.509-0.5090.0000.0000.0000.000
57B54GLY0-0.033-0.00723.724-0.187-0.1870.0000.0000.0000.000
58B55TYR0-0.031-0.01519.9660.0450.0450.0000.0000.0000.000
59B56THR00.0910.03023.431-0.206-0.2060.0000.0000.0000.000
60B57THR0-0.038-0.01823.9520.4200.4200.0000.0000.0000.000
61B58GLU-1-0.884-0.91125.14710.02910.0290.0000.0000.0000.000
62B59TYR00.0140.00625.3380.5030.5030.0000.0000.0000.000
63B60SER00.0390.02927.100-0.299-0.2990.0000.0000.0000.000
64B61ALA00.020-0.01828.749-0.097-0.0970.0000.0000.0000.000
65B62SER0-0.029-0.02429.139-0.169-0.1690.0000.0000.0000.000
66B63VAL00.0230.01126.663-0.044-0.0440.0000.0000.0000.000
67B64LYS10.9350.98330.157-9.517-9.5170.0000.0000.0000.000
68B65GLY00.0030.00831.634-0.276-0.2760.0000.0000.0000.000
69B66ARG10.7640.86131.063-9.800-9.8000.0000.0000.0000.000
70B67PHE00.013-0.01325.6670.1880.1880.0000.0000.0000.000
71B68THR0-0.036-0.01826.915-0.250-0.2500.0000.0000.0000.000
72B69ILE0-0.0030.01220.9180.3690.3690.0000.0000.0000.000
73B70SER0-0.012-0.01922.217-0.399-0.3990.0000.0000.0000.000
74B71ARG10.8000.89115.142-15.281-15.2810.0000.0000.0000.000
75B72ASP-1-0.777-0.85218.93213.11713.1170.0000.0000.0000.000
76B73LYS10.9630.96816.612-13.606-13.6060.0000.0000.0000.000
77B74SER0-0.091-0.06716.4250.6070.6070.0000.0000.0000.000
78B75LYS10.9240.94916.608-13.612-13.6120.0000.0000.0000.000
79B76SER00.0030.01712.0411.0121.0120.0000.0000.0000.000
80B77THR00.0000.00513.5541.4261.4260.0000.0000.0000.000
81B78LEU0-0.038-0.01215.434-1.097-1.0970.0000.0000.0000.000
82B79TYR00.006-0.02817.3900.2770.2770.0000.0000.0000.000
83B80LEU00.0140.01320.443-0.278-0.2780.0000.0000.0000.000
84B81GLN0-0.013-0.01222.5510.2480.2480.0000.0000.0000.000
85B82MET0-0.0150.00324.539-0.123-0.1230.0000.0000.0000.000
86B82ASN00.0690.04427.947-0.030-0.0300.0000.0000.0000.000
87B82THR00.0270.00731.7300.0810.0810.0000.0000.0000.000
88B82LEU0-0.0130.00828.255-0.025-0.0250.0000.0000.0000.000
89B83GLN00.005-0.00532.172-0.448-0.4480.0000.0000.0000.000
90B84ALA00.0810.03732.0690.3260.3260.0000.0000.0000.000
91B85GLU-1-0.878-0.94131.9029.2319.2310.0000.0000.0000.000
92B86ASP-1-0.772-0.83328.45510.45210.4520.0000.0000.0000.000
93B87SER0-0.0060.01527.1640.5100.5100.0000.0000.0000.000
94B88ALA0-0.034-0.02723.861-0.133-0.1330.0000.0000.0000.000
95B89ILE00.0080.02418.305-0.006-0.0060.0000.0000.0000.000
96B90TYR0-0.035-0.04719.475-0.218-0.2180.0000.0000.0000.000
97B91TYR00.012-0.01014.6290.6840.6840.0000.0000.0000.000
98B93THR0-0.011-0.04212.2951.0571.0570.0000.0000.0000.000
99B94ARG10.8030.8657.839-25.734-25.7340.0000.0000.0000.000
100B95ASP-1-0.781-0.90112.49615.70115.7010.0000.0000.0000.000
101B96ARG10.9160.96911.501-18.811-18.8110.0000.0000.0000.000
102B97GLY0-0.018-0.02513.645-0.089-0.0890.0000.0000.0000.000
103B98LEU0-0.043-0.01716.9720.0740.0740.0000.0000.0000.000
104B99ARG10.8660.92920.279-11.667-11.6670.0000.0000.0000.000
105B100PHE0-0.022-0.00316.797-0.302-0.3020.0000.0000.0000.000
106B100TYR00.0180.00512.586-0.522-0.5220.0000.0000.0000.000
107B100PHE0-0.007-0.00914.5700.2090.2090.0000.0000.0000.000
108B101ASP-1-0.764-0.85910.08624.28924.2890.0000.0000.0000.000
109B102TYR00.0090.0124.8480.7700.7700.0000.0000.0000.000
110B103TRP0-0.008-0.0098.949-3.215-3.2150.0000.0000.0000.000
111B104GLY00.0800.0618.8403.0303.0300.0000.0000.0000.000
112B105GLN0-0.042-0.03410.1430.7950.7950.0000.0000.0000.000
113B106GLY0-0.010-0.00212.491-1.521-1.5210.0000.0000.0000.000
114B107THR0-0.048-0.02615.623-0.128-0.1280.0000.0000.0000.000
115B108LEU0-0.017-0.01318.468-0.427-0.4270.0000.0000.0000.000
116B109VAL0-0.0060.00621.970-0.191-0.1910.0000.0000.0000.000
117B110THR0-0.037-0.02524.966-0.147-0.1470.0000.0000.0000.000
118B111VAL00.0120.01528.432-0.130-0.1300.0000.0000.0000.000
119B112SER0-0.016-0.01831.488-0.302-0.3020.0000.0000.0000.000
120B113SER00.0510.02134.4600.1100.1100.0000.0000.0000.000
121B114ALA0-0.052-0.00335.626-0.169-0.1690.0000.0000.0000.000
122B115SER00.022-0.00535.6460.0960.0960.0000.0000.0000.000
123B116THR0-0.030-0.01730.8370.0340.0340.0000.0000.0000.000
124B117LYS10.8420.93333.007-8.718-8.7180.0000.0000.0000.000
125B118GLY00.0580.03131.4330.2820.2820.0000.0000.0000.000
126B119PRO0-0.037-0.00729.357-0.274-0.2740.0000.0000.0000.000
127B120SER0-0.038-0.01232.693-0.167-0.1670.0000.0000.0000.000
128B121VAL0-0.004-0.01230.3520.1110.1110.0000.0000.0000.000
129B122PHE00.000-0.00533.484-0.209-0.2090.0000.0000.0000.000
130B123PRO00.0070.00934.7040.2790.2790.0000.0000.0000.000
131B124LEU0-0.038-0.01033.414-0.226-0.2260.0000.0000.0000.000
132B125ALA00.0290.00335.8720.2260.2260.0000.0000.0000.000
133B126PRO00.0290.02438.222-0.153-0.1530.0000.0000.0000.000
134B127CYS0-0.011-0.01441.117-0.046-0.0460.0000.0000.0000.000
135B128SER0-0.025-0.01344.380-0.128-0.1280.0000.0000.0000.000
136B129ARG10.8830.93040.872-7.651-7.6510.0000.0000.0000.000
137B130SER00.001-0.00342.3410.0210.0210.0000.0000.0000.000
138B131THR00.006-0.01843.4290.1280.1280.0000.0000.0000.000
139B132SER0-0.0380.00144.752-0.001-0.0010.0000.0000.0000.000
140B133GLU-1-0.849-0.90340.6317.6447.6440.0000.0000.0000.000
141B134SER00.0170.00738.4400.0660.0660.0000.0000.0000.000
142B135THR0-0.078-0.03133.7460.3220.3220.0000.0000.0000.000
143B136ALA00.0500.03235.606-0.209-0.2090.0000.0000.0000.000
144B137ALA0-0.007-0.00733.5880.3340.3340.0000.0000.0000.000
145B138LEU0-0.0110.00432.404-0.277-0.2770.0000.0000.0000.000
146B139GLY00.059-0.00531.0930.2810.2810.0000.0000.0000.000
147B140CYS0-0.087-0.01626.9370.1270.1270.0000.0000.0000.000
148B141LEU00.0220.01831.3430.1960.1960.0000.0000.0000.000
149B142VAL0-0.016-0.00628.179-0.202-0.2020.0000.0000.0000.000
150B143LYS10.9170.92131.523-8.322-8.3220.0000.0000.0000.000
151B144ASP-1-0.806-0.89034.4118.3908.3900.0000.0000.0000.000
152B145TYR0-0.009-0.01927.526-0.143-0.1430.0000.0000.0000.000
153B146PHE00.0270.03731.1720.0200.0200.0000.0000.0000.000
154B147PRO00.0140.00627.513-0.157-0.1570.0000.0000.0000.000
155B148GLU-1-0.783-0.87325.27012.35512.3550.0000.0000.0000.000
156B149PRO0-0.005-0.01521.149-0.031-0.0310.0000.0000.0000.000
157B150VAL0-0.006-0.02124.076-0.148-0.1480.0000.0000.0000.000
158B151THR0-0.045-0.01518.8660.7440.7440.0000.0000.0000.000
159B152VAL0-0.001-0.01221.772-0.610-0.6100.0000.0000.0000.000
160B153SER0-0.0040.00620.2430.7140.7140.0000.0000.0000.000
161B154TRP0-0.0020.01122.210-0.869-0.8690.0000.0000.0000.000
162B155ASN0-0.033-0.03523.5480.2160.2160.0000.0000.0000.000
163B156SER00.002-0.01722.0340.1060.1060.0000.0000.0000.000
164B157GLY00.0220.02519.0540.6700.6700.0000.0000.0000.000
165B158ALA0-0.026-0.00219.6190.4870.4870.0000.0000.0000.000
166B159LEU0-0.081-0.02921.957-0.148-0.1480.0000.0000.0000.000
167B160THR00.0440.00518.127-0.003-0.0030.0000.0000.0000.000
168B161SER0-0.002-0.00121.3530.0030.0030.0000.0000.0000.000
169B162GLY00.0590.02123.330-0.426-0.4260.0000.0000.0000.000
170B163VAL0-0.062-0.02822.807-0.483-0.4830.0000.0000.0000.000
171B164HIS00.0160.01623.9380.5330.5330.0000.0000.0000.000
172B165THR0-0.0010.00023.352-0.699-0.6990.0000.0000.0000.000
173B166PHE0-0.0110.00224.9570.3030.3030.0000.0000.0000.000
174B167PRO00.0110.00926.4270.2040.2040.0000.0000.0000.000
175B168ALA00.0100.00527.386-0.445-0.4450.0000.0000.0000.000
176B169VAL0-0.0110.00529.499-0.048-0.0480.0000.0000.0000.000
177B170LEU0-0.031-0.01733.0250.0110.0110.0000.0000.0000.000
178B171GLN0-0.015-0.01834.753-0.362-0.3620.0000.0000.0000.000
179B172SER00.0220.00737.9810.0690.0690.0000.0000.0000.000
180B173SER00.001-0.00339.704-0.067-0.0670.0000.0000.0000.000
181B173GLY00.0020.00137.524-0.017-0.0170.0000.0000.0000.000
182B174LEU0-0.049-0.00935.0120.2610.2610.0000.0000.0000.000
183B175TYR00.0340.00830.258-0.174-0.1740.0000.0000.0000.000
184B176SER0-0.013-0.01832.576-0.216-0.2160.0000.0000.0000.000
185B177LEU0-0.0220.01126.1560.0000.0000.0000.0000.0000.000
186B178SER00.0420.01330.643-0.166-0.1660.0000.0000.0000.000
187B179SER0-0.015-0.00925.6020.2710.2710.0000.0000.0000.000
188B180VAL00.0330.00528.330-0.357-0.3570.0000.0000.0000.000
189B181VAL00.0100.00526.8790.5280.5280.0000.0000.0000.000
190B182THR0-0.0120.01028.890-0.410-0.4100.0000.0000.0000.000
191B183VAL0-0.026-0.01929.7020.4080.4080.0000.0000.0000.000
192B184PRO00.0540.03131.947-0.266-0.2660.0000.0000.0000.000
193B185SER00.0810.00534.8680.1110.1110.0000.0000.0000.000
194B186SER0-0.052-0.02137.298-0.075-0.0750.0000.0000.0000.000
195B187SER0-0.033-0.02734.2530.1080.1080.0000.0000.0000.000
196B188LEU0-0.0170.01435.8180.0940.0940.0000.0000.0000.000
197B189GLY00.0510.03538.092-0.278-0.2780.0000.0000.0000.000
198B190THR0-0.059-0.01336.989-0.185-0.1850.0000.0000.0000.000
199B191LYS10.9530.98528.593-10.912-10.9120.0000.0000.0000.000
200B192THR0-0.022-0.01931.320-0.190-0.1900.0000.0000.0000.000
201B193TYR00.0400.01729.6070.5180.5180.0000.0000.0000.000
202B194THR00.009-0.00728.669-0.501-0.5010.0000.0000.0000.000
203B196ASN0-0.010-0.02823.317-0.015-0.0150.0000.0000.0000.000
204B197VAL00.0270.00824.0380.5380.5380.0000.0000.0000.000
205B198ASP-1-0.850-0.91521.77314.00014.0000.0000.0000.0000.000
206B199HIS00.0520.04823.9990.1820.1820.0000.0000.0000.000
207B200LYS10.9300.93318.511-16.072-16.0720.0000.0000.0000.000
208B201PRO0-0.0130.00824.048-0.270-0.2700.0000.0000.0000.000
209B202SER0-0.011-0.03026.646-0.405-0.4050.0000.0000.0000.000
210B203ASN0-0.069-0.02926.847-0.032-0.0320.0000.0000.0000.000
211B204THR00.0120.01327.799-0.399-0.3990.0000.0000.0000.000
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