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: 17N7Z

Calculation Name: 1AM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AM2

Chain ID: A

ChEMBL ID:

UniProt ID: P72065

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793325.151431
FMO2-HF: Nuclear repulsion 1726397.609292
FMO2-HF: Total energy -66927.542139
FMO2-MP2: Total energy -67127.825336


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(A:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-9.411-24.88525.8812.338-12.743-0.025
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : 0.026
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].
3A2ILE0-0.012-0.0062.61710.357-0.598-0.03011.498-0.513-0.002
4A3THR00.0780.0415.6030.3840.3840.0000.0000.0000.000
5A4GLY0-0.022-0.0209.0970.1460.1460.0000.0000.0000.000
6A5ASP-1-0.972-0.99911.110-0.317-0.3170.0000.0000.0000.000
7A6ALA0-0.0110.0119.3010.0440.0440.0000.0000.0000.000
8A7LEU00.016-0.00411.3580.1120.1120.0000.0000.0000.000
9A8VAL0-0.008-0.0129.693-0.002-0.0020.0000.0000.0000.000
10A9ALA0-0.004-0.00612.325-0.033-0.0330.0000.0000.0000.000
11A10LEU0-0.030-0.00914.9560.1110.1110.0000.0000.0000.000
12A11PRO00.020-0.01017.386-0.031-0.0310.0000.0000.0000.000
13A12GLU-1-0.938-0.97720.7060.2140.2140.0000.0000.0000.000
14A13GLY0-0.051-0.01222.199-0.019-0.0190.0000.0000.0000.000
15A14GLU-1-0.900-0.93120.4920.1320.1320.0000.0000.0000.000
16A15SER0-0.054-0.04016.3770.0120.0120.0000.0000.0000.000
17A16VAL00.0170.01314.159-0.025-0.0250.0000.0000.0000.000
18A17ARG10.8460.89913.6180.0310.0310.0000.0000.0000.000
19A18ILE00.0250.0176.5950.0580.0580.0000.0000.0000.000
20A19ALA0-0.049-0.02210.9220.0650.0650.0000.0000.0000.000
21A20ASP-1-0.852-0.89712.8140.0740.0740.0000.0000.0000.000
22A21ILE00.0020.01510.8990.0180.0180.0000.0000.0000.000
23A22VAL0-0.0110.00113.7210.0090.0090.0000.0000.0000.000
24A23PRO00.002-0.00515.565-0.036-0.0360.0000.0000.0000.000
25A24GLY0-0.028-0.01317.5220.0030.0030.0000.0000.0000.000
26A25ALA00.0120.02013.217-0.011-0.0110.0000.0000.0000.000
27A26ARG10.9300.96715.247-0.194-0.1940.0000.0000.0000.000
28A27PRO00.0500.03412.3340.0600.0600.0000.0000.0000.000
29A28ASN0-0.050-0.02710.247-0.055-0.0550.0000.0000.0000.000
30A29SER0-0.058-0.03910.9310.0400.0400.0000.0000.0000.000
31A30ASP-1-0.802-0.89710.2251.0361.0360.0000.0000.0000.000
32A31ASN0-0.091-0.05810.936-0.194-0.1940.0000.0000.0000.000
33A32ALA00.0230.01312.1490.1150.1150.0000.0000.0000.000
34A33ILE0-0.043-0.01211.377-0.089-0.0890.0000.0000.0000.000
35A34ASP-1-0.786-0.90015.1320.5300.5300.0000.0000.0000.000
36A35LEU0-0.026-0.00213.901-0.071-0.0710.0000.0000.0000.000
37A36LYS10.8180.91015.746-0.418-0.4180.0000.0000.0000.000
38A37VAL00.014-0.00611.557-0.032-0.0320.0000.0000.0000.000
39A38LEU0-0.0120.00715.005-0.004-0.0040.0000.0000.0000.000
40A39ASP-1-0.780-0.90213.0000.5790.5790.0000.0000.0000.000
41A40ARG10.8220.88112.825-0.488-0.4880.0000.0000.0000.000
42A41HIS10.8010.88013.849-0.335-0.3350.0000.0000.0000.000
43A42GLY00.0290.02916.474-0.053-0.0530.0000.0000.0000.000
44A43ASN0-0.021-0.00117.781-0.064-0.0640.0000.0000.0000.000
45A44PRO0-0.0080.00017.3300.0590.0590.0000.0000.0000.000
46A45VAL0-0.015-0.00413.683-0.012-0.0120.0000.0000.0000.000
47A46LEU0-0.0080.00415.376-0.031-0.0310.0000.0000.0000.000
48A47ALA00.0150.00010.9710.1460.1460.0000.0000.0000.000
49A48ASP-1-0.766-0.90111.5461.0551.0550.0000.0000.0000.000
50A49ARG10.8110.8989.027-1.062-1.0620.0000.0000.0000.000
51A50LEU00.0220.0248.4540.2570.2570.0000.0000.0000.000
52A51PHE0-0.022-0.0214.418-0.351-0.276-0.001-0.009-0.0640.000
53A52HIS00.0520.0446.852-0.022-0.0220.0000.0000.0000.000
54A53SER0-0.009-0.0244.769-0.094-0.025-0.001-0.003-0.0650.000
55A54GLY00.0410.0347.187-0.163-0.1630.0000.0000.0000.000
56A55GLU-1-0.961-1.0069.493-0.450-0.4500.0000.0000.0000.000
57A56HIS0-0.042-0.0178.062-0.159-0.1590.0000.0000.0000.000
58A57PRO00.001-0.00210.3580.0490.0490.0000.0000.0000.000
59A58VAL0-0.0320.0048.810-0.374-0.3740.0000.0000.0000.000
60A59TYR00.0320.01410.6860.2250.2250.0000.0000.0000.000
61A60ALA0-0.032-0.02011.308-0.123-0.1230.0000.0000.0000.000
62A61VAL00.0070.01210.7740.0910.0910.0000.0000.0000.000
63A62ARG10.8910.93613.6060.5240.5240.0000.0000.0000.000
64A63THR00.0030.00416.842-0.014-0.0140.0000.0000.0000.000
65A64VAL0-0.042-0.01518.4830.0160.0160.0000.0000.0000.000
66A65GLU-1-0.772-0.87521.098-0.172-0.1720.0000.0000.0000.000
67A66GLY0-0.016-0.00721.1450.0200.0200.0000.0000.0000.000
68A67LEU0-0.018-0.00516.331-0.014-0.0140.0000.0000.0000.000
69A68ARG10.9660.96214.6330.3360.3360.0000.0000.0000.000
70A69VAL00.0260.0298.7720.0780.0780.0000.0000.0000.000
71A70THR0-0.015-0.00610.667-0.022-0.0220.0000.0000.0000.000
72A71GLY00.0810.0346.7230.0700.0700.0000.0000.0000.000
73A72THR00.0220.0005.320-0.098-0.051-0.001-0.015-0.0310.000
74A73ALA00.0440.0227.039-0.423-0.4230.0000.0000.0000.000
75A74ASN00.0460.0334.1580.4940.647-0.001-0.032-0.1200.000
76A75HIS0-0.0050.0132.052-8.450-11.3729.211-2.690-3.600-0.026
77A76PRO0-0.001-0.0072.6221.3622.0750.430-0.305-0.8370.000
78A77LEU00.0100.0105.0640.3100.364-0.001-0.002-0.0500.000
79A78LEU0-0.0080.0087.7660.0530.0530.0000.0000.0000.000
80A79CYS0-0.052-0.01910.805-0.055-0.0550.0000.0000.0000.000
81A80LEU0-0.018-0.00913.8470.0660.0660.0000.0000.0000.000
82A81VAL0-0.031-0.02715.863-0.037-0.0370.0000.0000.0000.000
83A82ASP-1-0.916-0.95218.714-0.070-0.0700.0000.0000.0000.000
84A83VAL00.012-0.00219.908-0.021-0.0210.0000.0000.0000.000
85A84ALA0-0.021-0.01922.8560.0180.0180.0000.0000.0000.000
86A85GLY00.0140.00826.2090.0130.0130.0000.0000.0000.000
87A86VAL0-0.0040.00223.8260.0100.0100.0000.0000.0000.000
88A87PRO0-0.033-0.00722.400-0.014-0.0140.0000.0000.0000.000
89A88THR00.004-0.00718.2840.0330.0330.0000.0000.0000.000
90A89LEU0-0.024-0.00115.474-0.045-0.0450.0000.0000.0000.000
91A90LEU0-0.006-0.01413.8360.0540.0540.0000.0000.0000.000
92A91TRP00.0100.0087.482-0.053-0.0530.0000.0000.0000.000
93A92LYS10.8060.8909.7380.6090.6090.0000.0000.0000.000
94A93LEU00.0000.0056.104-0.118-0.1180.0000.0000.0000.000
95A94ILE0-0.009-0.0097.1090.5070.5070.0000.0000.0000.000
96A95ASP-1-0.885-0.9549.269-1.095-1.0950.0000.0000.0000.000
97A96GLU-1-0.978-0.98911.393-0.448-0.4480.0000.0000.0000.000
98A97ILE0-0.098-0.02110.2170.1900.1900.0000.0000.0000.000
99A98LYS10.8760.92313.9870.4420.4420.0000.0000.0000.000
100A99PRO00.009-0.00817.5630.0160.0160.0000.0000.0000.000
101A100GLY0-0.067-0.04219.8640.0210.0210.0000.0000.0000.000
102A101ASP-1-0.743-0.84016.228-0.425-0.4250.0000.0000.0000.000
103A102TYR00.0250.00417.5860.0090.0090.0000.0000.0000.000
104A103ALA00.0790.04613.056-0.006-0.0060.0000.0000.0000.000
105A104VAL0-0.034-0.02813.5400.0470.0470.0000.0000.0000.000
106A105ILE0-0.037-0.01713.566-0.021-0.0210.0000.0000.0000.000
107A106GLN00.0450.03414.9060.0050.0050.0000.0000.0000.000
108A107ARG10.8890.90616.612-0.024-0.0240.0000.0000.0000.000
109A108SER0-0.011-0.01518.956-0.012-0.0120.0000.0000.0000.000
110A109ALA0-0.073-0.01716.0200.0180.0180.0000.0000.0000.000
111A110PHE0-0.036-0.01117.382-0.026-0.0260.0000.0000.0000.000
112A111SER00.0080.01421.1480.0140.0140.0000.0000.0000.000
113A130THR00.009-0.01224.233-0.001-0.0010.0000.0000.0000.000
114A131VAL0-0.040-0.02825.5600.0140.0140.0000.0000.0000.000
115A132GLY00.0040.00727.213-0.005-0.0050.0000.0000.0000.000
116A133VAL00.0170.03322.906-0.014-0.0140.0000.0000.0000.000
117A134PRO00.008-0.00622.1740.0030.0030.0000.0000.0000.000
118A135GLY0-0.012-0.01124.3970.0000.0000.0000.0000.0000.000
119A136LEU00.0390.03126.2400.0040.0040.0000.0000.0000.000
120A137VAL00.0300.00827.8450.0070.0070.0000.0000.0000.000
121A138ARG10.9991.00027.5100.0910.0910.0000.0000.0000.000
122A139PHE00.0100.02128.2310.0030.0030.0000.0000.0000.000
123A140LEU0-0.009-0.00530.3070.0070.0070.0000.0000.0000.000
124A141GLU-1-0.916-0.97832.456-0.029-0.0290.0000.0000.0000.000
125A142ALA0-0.048-0.01933.0450.0020.0020.0000.0000.0000.000
126A143HIS00.0030.00530.3000.0090.0090.0000.0000.0000.000
127A144HIS10.9360.99332.7130.0030.0030.0000.0000.0000.000
128A145ARG10.7650.86334.010-0.027-0.0270.0000.0000.0000.000
129A146ASP-1-0.745-0.85630.4900.0270.0270.0000.0000.0000.000
130A147PRO0-0.088-0.06832.6190.0020.0020.0000.0000.0000.000
131A148ASP-1-0.830-0.91126.5470.0960.0960.0000.0000.0000.000
132A149ALA0-0.040-0.02228.2040.0020.0020.0000.0000.0000.000
133A150LYS10.8090.88929.251-0.080-0.0800.0000.0000.0000.000
134A151ALA00.0070.00326.6830.0030.0030.0000.0000.0000.000
135A152ILE00.0410.02224.0190.0080.0080.0000.0000.0000.000
136A153ALA0-0.016-0.01724.613-0.001-0.0010.0000.0000.0000.000
137A154ASP-1-0.868-0.90826.0880.0870.0870.0000.0000.0000.000
138A155GLU-1-0.809-0.91018.3060.2060.2060.0000.0000.0000.000
139A156LEU0-0.052-0.03820.467-0.002-0.0020.0000.0000.0000.000
140A157THR0-0.016-0.03022.518-0.020-0.0200.0000.0000.0000.000
141A158ASP-1-0.824-0.86821.1710.1470.1470.0000.0000.0000.000
142A159GLY00.0210.00823.209-0.014-0.0140.0000.0000.0000.000
143A160ARG10.8390.89820.490-0.220-0.2200.0000.0000.0000.000
144A161PHE0-0.0410.00215.9460.0030.0030.0000.0000.0000.000
145A162TYR0-0.100-0.07918.8080.0020.0020.0000.0000.0000.000
146A163TYR00.006-0.01718.373-0.013-0.0130.0000.0000.0000.000
147A164ALA00.0030.01217.3060.0080.0080.0000.0000.0000.000
148A165LYS10.8240.92118.0800.1840.1840.0000.0000.0000.000
149A166VAL00.0310.02215.1620.0040.0040.0000.0000.0000.000
150A167ALA0-0.0030.00218.1840.0300.0300.0000.0000.0000.000
151A168SER0-0.030-0.03918.4920.0110.0110.0000.0000.0000.000
152A169VAL00.0780.05313.289-0.007-0.0070.0000.0000.0000.000
153A170THR0-0.035-0.01515.9290.0660.0660.0000.0000.0000.000
154A171ASP-1-0.865-0.92715.665-0.791-0.7910.0000.0000.0000.000
155A172ALA0-0.039-0.03013.9200.0840.0840.0000.0000.0000.000
156A173GLY00.0150.02315.8150.0470.0470.0000.0000.0000.000
157A174VAL0-0.026-0.01413.365-0.122-0.1220.0000.0000.0000.000
158A175GLN0-0.009-0.01411.8120.1010.1010.0000.0000.0000.000
159A176PRO00.0040.02110.968-0.125-0.1250.0000.0000.0000.000
160A177VAL0-0.056-0.0225.512-0.115-0.1150.0000.0000.0000.000
161A178TYR00.030-0.0116.2060.1250.1250.0000.0000.0000.000
162A179SER00.014-0.0142.441-4.301-2.2352.160-2.009-2.216-0.001
163A180LEU00.0150.0204.211-1.029-0.9630.000-0.056-0.0100.000
164A181ARG10.7930.9125.357-0.086-0.0860.0000.0000.0000.000
165A182VAL0-0.041-0.0267.630-0.543-0.5430.0000.0000.0000.000
166A183ASP-1-0.857-0.92410.4301.1621.1620.0000.0000.0000.000
167A184THR0-0.070-0.05712.753-0.235-0.2350.0000.0000.0000.000
168A185ALA0-0.029-0.00612.6230.1360.1360.0000.0000.0000.000
169A186ASP-1-0.801-0.88212.3960.7020.7020.0000.0000.0000.000
170A187HIS0-0.0100.0047.8010.4090.4090.0000.0000.0000.000
171A188ALA00.0390.0187.4130.7060.7060.0000.0000.0000.000
172A189PHE00.004-0.0044.492-0.549-0.466-0.001-0.008-0.0750.000
173A190ILE0-0.0260.0018.934-0.188-0.1880.0000.0000.0000.000
174A191THR00.0180.0217.025-0.017-0.0170.0000.0000.0000.000
175A192ASN00.0170.00510.282-0.100-0.1000.0000.0000.0000.000
176A193GLY00.0220.01213.390-0.051-0.0510.0000.0000.0000.000
177A194PHE0-0.029-0.02010.1620.0160.0160.0000.0000.0000.000
178A195VAL00.0190.0209.8230.1030.1030.0000.0000.0000.000
179A196SER00.014-0.0124.758-0.682-0.673-0.001-0.001-0.0070.000
180A197HIS00.0250.0113.978-1.447-1.0880.001-0.164-0.1960.001
181A198ASN00.0120.0051.968-7.589-12.88014.116-3.866-4.9590.003